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LICENSE
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LICENSE
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CeCILL FREE SOFTWARE LICENSE AGREEMENT
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Version 2.1 dated 2013-06-21
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Notice
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This Agreement is a Free Software license agreement that is the result
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of discussions between its authors in order to ensure compliance with
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the two main principles guiding its drafting:
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* firstly, compliance with the principles governing the distribution
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of Free Software: access to source code, broad rights granted to users,
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* secondly, the election of a governing law, French law, with which it
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is conformant, both as regards the law of torts and intellectual
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property law, and the protection that it offers to both authors and
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holders of the economic rights over software.
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The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
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license are:
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Commissariat à l'énergie atomique et aux énergies alternatives - CEA, a
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public scientific, technical and industrial research establishment,
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having its principal place of business at 25 rue Leblanc, immeuble Le
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Ponant D, 75015 Paris, France.
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Centre National de la Recherche Scientifique - CNRS, a public scientific
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and technological establishment, having its principal place of business
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at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
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Institut National de Recherche en Informatique et en Automatique -
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Inria, a public scientific and technological establishment, having its
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principal place of business at Domaine de Voluceau, Rocquencourt, BP
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105, 78153 Le Chesnay cedex, France.
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Preamble
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The purpose of this Free Software license agreement is to grant users
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the right to modify and redistribute the software governed by this
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license within the framework of an open source distribution model.
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The exercising of this right is conditional upon certain obligations for
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users so as to preserve this status for all subsequent redistributions.
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In consideration of access to the source code and the rights to copy,
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modify and redistribute granted by the license, users are provided only
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with a limited warranty and the software's author, the holder of the
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economic rights, and the successive licensors only have limited liability.
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In this respect, the risks associated with loading, using, modifying
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and/or developing or reproducing the software by the user are brought to
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the user's attention, given its Free Software status, which may make it
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complicated to use, with the result that its use is reserved for
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developers and experienced professionals having in-depth computer
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knowledge. Users are therefore encouraged to load and test the
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suitability of the software as regards their requirements in conditions
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enabling the security of their systems and/or data to be ensured and,
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more generally, to use and operate it in the same conditions of
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security. This Agreement may be freely reproduced and published,
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provided it is not altered, and that no provisions are either added or
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removed herefrom.
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This Agreement may apply to any or all software for which the holder of
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the economic rights decides to submit the use thereof to its provisions.
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Frequently asked questions can be found on the official website of the
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CeCILL licenses family (http://www.cecill.info/index.en.html) for any
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necessary clarification.
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Article 1 - DEFINITIONS
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For the purpose of this Agreement, when the following expressions
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commence with a capital letter, they shall have the following meaning:
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Agreement: means this license agreement, and its possible subsequent
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versions and annexes.
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Software: means the software in its Object Code and/or Source Code form
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and, where applicable, its documentation, "as is" when the Licensee
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accepts the Agreement.
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Initial Software: means the Software in its Source Code and possibly its
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Object Code form and, where applicable, its documentation, "as is" when
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it is first distributed under the terms and conditions of the Agreement.
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Modified Software: means the Software modified by at least one
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Contribution.
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Source Code: means all the Software's instructions and program lines to
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which access is required so as to modify the Software.
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Object Code: means the binary files originating from the compilation of
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the Source Code.
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Holder: means the holder(s) of the economic rights over the Initial
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||||||
Software.
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Licensee: means the Software user(s) having accepted the Agreement.
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Contributor: means a Licensee having made at least one Contribution.
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Licensor: means the Holder, or any other individual or legal entity, who
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distributes the Software under the Agreement.
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Contribution: means any or all modifications, corrections, translations,
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adaptations and/or new functions integrated into the Software by any or
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all Contributors, as well as any or all Internal Modules.
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Module: means a set of sources files including their documentation that
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enables supplementary functions or services in addition to those offered
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by the Software.
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External Module: means any or all Modules, not derived from the
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Software, so that this Module and the Software run in separate address
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spaces, with one calling the other when they are run.
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Internal Module: means any or all Module, connected to the Software so
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that they both execute in the same address space.
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GNU GPL: means the GNU General Public License version 2 or any
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subsequent version, as published by the Free Software Foundation Inc.
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GNU Affero GPL: means the GNU Affero General Public License version 3 or
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any subsequent version, as published by the Free Software Foundation Inc.
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EUPL: means the European Union Public License version 1.1 or any
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subsequent version, as published by the European Commission.
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Parties: mean both the Licensee and the Licensor.
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These expressions may be used both in singular and plural form.
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Article 2 - PURPOSE
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The purpose of the Agreement is the grant by the Licensor to the
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Licensee of a non-exclusive, transferable and worldwide license for the
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Software as set forth in Article 5 <#scope> hereinafter for the whole
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term of the protection granted by the rights over said Software.
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Article 3 - ACCEPTANCE
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3.1 The Licensee shall be deemed as having accepted the terms and
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conditions of this Agreement upon the occurrence of the first of the
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following events:
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* (i) loading the Software by any or all means, notably, by
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downloading from a remote server, or by loading from a physical medium;
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* (ii) the first time the Licensee exercises any of the rights granted
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hereunder.
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3.2 One copy of the Agreement, containing a notice relating to the
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characteristics of the Software, to the limited warranty, and to the
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fact that its use is restricted to experienced users has been provided
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to the Licensee prior to its acceptance as set forth in Article 3.1
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<#accepting> hereinabove, and the Licensee hereby acknowledges that it
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has read and understood it.
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Article 4 - EFFECTIVE DATE AND TERM
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4.1 EFFECTIVE DATE
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The Agreement shall become effective on the date when it is accepted by
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the Licensee as set forth in Article 3.1 <#accepting>.
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4.2 TERM
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The Agreement shall remain in force for the entire legal term of
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protection of the economic rights over the Software.
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Article 5 - SCOPE OF RIGHTS GRANTED
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The Licensor hereby grants to the Licensee, who accepts, the following
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rights over the Software for any or all use, and for the term of the
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Agreement, on the basis of the terms and conditions set forth hereinafter.
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Besides, if the Licensor owns or comes to own one or more patents
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protecting all or part of the functions of the Software or of its
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components, the Licensor undertakes not to enforce the rights granted by
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these patents against successive Licensees using, exploiting or
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modifying the Software. If these patents are transferred, the Licensor
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undertakes to have the transferees subscribe to the obligations set
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forth in this paragraph.
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5.1 RIGHT OF USE
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The Licensee is authorized to use the Software, without any limitation
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as to its fields of application, with it being hereinafter specified
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that this comprises:
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1. permanent or temporary reproduction of all or part of the Software
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||||||
by any or all means and in any or all form.
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2. loading, displaying, running, or storing the Software on any or all
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medium.
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3. entitlement to observe, study or test its operation so as to
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determine the ideas and principles behind any or all constituent
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elements of said Software. This shall apply when the Licensee
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carries out any or all loading, displaying, running, transmission or
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storage operation as regards the Software, that it is entitled to
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carry out hereunder.
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5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
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The right to make Contributions includes the right to translate, adapt,
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arrange, or make any or all modifications to the Software, and the right
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to reproduce the resulting software.
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The Licensee is authorized to make any or all Contributions to the
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Software provided that it includes an explicit notice that it is the
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author of said Contribution and indicates the date of the creation thereof.
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5.3 RIGHT OF DISTRIBUTION
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In particular, the right of distribution includes the right to publish,
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transmit and communicate the Software to the general public on any or
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all medium, and by any or all means, and the right to market, either in
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consideration of a fee, or free of charge, one or more copies of the
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Software by any means.
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The Licensee is further authorized to distribute copies of the modified
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or unmodified Software to third parties according to the terms and
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conditions set forth hereinafter.
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5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
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The Licensee is authorized to distribute true copies of the Software in
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Source Code or Object Code form, provided that said distribution
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complies with all the provisions of the Agreement and is accompanied by:
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||||||
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||||||
1. a copy of the Agreement,
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||||||
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||||||
2. a notice relating to the limitation of both the Licensor's warranty
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|
||||||
and liability as set forth in Articles 8 and 9,
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||||||
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||||||
and that, in the event that only the Object Code of the Software is
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redistributed, the Licensee allows effective access to the full Source
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Code of the Software for a period of at least three years from the
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||||||
distribution of the Software, it being understood that the additional
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||||||
acquisition cost of the Source Code shall not exceed the cost of the
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||||||
data transfer.
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5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
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When the Licensee makes a Contribution to the Software, the terms and
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conditions for the distribution of the resulting Modified Software
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become subject to all the provisions of this Agreement.
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The Licensee is authorized to distribute the Modified Software, in
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source code or object code form, provided that said distribution
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|
||||||
complies with all the provisions of the Agreement and is accompanied by:
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|
||||||
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|
||||||
1. a copy of the Agreement,
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||||||
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|
||||||
2. a notice relating to the limitation of both the Licensor's warranty
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|
||||||
and liability as set forth in Articles 8 and 9,
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||||||
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|
||||||
and, in the event that only the object code of the Modified Software is
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redistributed,
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||||||
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3. a note stating the conditions of effective access to the full source
|
|
||||||
code of the Modified Software for a period of at least three years
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|
||||||
from the distribution of the Modified Software, it being understood
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|
||||||
that the additional acquisition cost of the source code shall not
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||||||
exceed the cost of the data transfer.
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5.3.3 DISTRIBUTION OF EXTERNAL MODULES
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When the Licensee has developed an External Module, the terms and
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conditions of this Agreement do not apply to said External Module, that
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may be distributed under a separate license agreement.
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5.3.4 COMPATIBILITY WITH OTHER LICENSES
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The Licensee can include a code that is subject to the provisions of one
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|
||||||
of the versions of the GNU GPL, GNU Affero GPL and/or EUPL in the
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|
||||||
Modified or unmodified Software, and distribute that entire code under
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|
||||||
the terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
|
|
||||||
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|
||||||
The Licensee can include the Modified or unmodified Software in a code
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|
||||||
that is subject to the provisions of one of the versions of the GNU GPL,
|
|
||||||
GNU Affero GPL and/or EUPL and distribute that entire code under the
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|
||||||
terms of the same version of the GNU GPL, GNU Affero GPL and/or EUPL.
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Article 6 - INTELLECTUAL PROPERTY
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6.1 OVER THE INITIAL SOFTWARE
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|
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The Holder owns the economic rights over the Initial Software. Any or
|
|
||||||
all use of the Initial Software is subject to compliance with the terms
|
|
||||||
and conditions under which the Holder has elected to distribute its work
|
|
||||||
and no one shall be entitled to modify the terms and conditions for the
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|
||||||
distribution of said Initial Software.
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||||||
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|
||||||
The Holder undertakes that the Initial Software will remain ruled at
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|
||||||
least by this Agreement, for the duration set forth in Article 4.2 <#term>.
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||||||
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6.2 OVER THE CONTRIBUTIONS
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||||||
The Licensee who develops a Contribution is the owner of the
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|
||||||
intellectual property rights over this Contribution as defined by
|
|
||||||
applicable law.
|
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||||||
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||||||
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6.3 OVER THE EXTERNAL MODULES
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||||||
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|
||||||
The Licensee who develops an External Module is the owner of the
|
|
||||||
intellectual property rights over this External Module as defined by
|
|
||||||
applicable law and is free to choose the type of agreement that shall
|
|
||||||
govern its distribution.
|
|
||||||
|
|
||||||
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||||||
6.4 JOINT PROVISIONS
|
|
||||||
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|
||||||
The Licensee expressly undertakes:
|
|
||||||
|
|
||||||
1. not to remove, or modify, in any manner, the intellectual property
|
|
||||||
notices attached to the Software;
|
|
||||||
|
|
||||||
2. to reproduce said notices, in an identical manner, in the copies of
|
|
||||||
the Software modified or not.
|
|
||||||
|
|
||||||
The Licensee undertakes not to directly or indirectly infringe the
|
|
||||||
intellectual property rights on the Software of the Holder and/or
|
|
||||||
Contributors, and to take, where applicable, vis-à-vis its staff, any
|
|
||||||
and all measures required to ensure respect of said intellectual
|
|
||||||
property rights of the Holder and/or Contributors.
|
|
||||||
|
|
||||||
|
|
||||||
Article 7 - RELATED SERVICES
|
|
||||||
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|
||||||
7.1 Under no circumstances shall the Agreement oblige the Licensor to
|
|
||||||
provide technical assistance or maintenance services for the Software.
|
|
||||||
|
|
||||||
However, the Licensor is entitled to offer this type of services. The
|
|
||||||
terms and conditions of such technical assistance, and/or such
|
|
||||||
maintenance, shall be set forth in a separate instrument. Only the
|
|
||||||
Licensor offering said maintenance and/or technical assistance services
|
|
||||||
shall incur liability therefor.
|
|
||||||
|
|
||||||
7.2 Similarly, any Licensor is entitled to offer to its licensees, under
|
|
||||||
its sole responsibility, a warranty, that shall only be binding upon
|
|
||||||
itself, for the redistribution of the Software and/or the Modified
|
|
||||||
Software, under terms and conditions that it is free to decide. Said
|
|
||||||
warranty, and the financial terms and conditions of its application,
|
|
||||||
shall be subject of a separate instrument executed between the Licensor
|
|
||||||
and the Licensee.
|
|
||||||
|
|
||||||
|
|
||||||
Article 8 - LIABILITY
|
|
||||||
|
|
||||||
8.1 Subject to the provisions of Article 8.2, the Licensee shall be
|
|
||||||
entitled to claim compensation for any direct loss it may have suffered
|
|
||||||
from the Software as a result of a fault on the part of the relevant
|
|
||||||
Licensor, subject to providing evidence thereof.
|
|
||||||
|
|
||||||
8.2 The Licensor's liability is limited to the commitments made under
|
|
||||||
this Agreement and shall not be incurred as a result of in particular:
|
|
||||||
(i) loss due the Licensee's total or partial failure to fulfill its
|
|
||||||
obligations, (ii) direct or consequential loss that is suffered by the
|
|
||||||
Licensee due to the use or performance of the Software, and (iii) more
|
|
||||||
generally, any consequential loss. In particular the Parties expressly
|
|
||||||
agree that any or all pecuniary or business loss (i.e. loss of data,
|
|
||||||
loss of profits, operating loss, loss of customers or orders,
|
|
||||||
opportunity cost, any disturbance to business activities) or any or all
|
|
||||||
legal proceedings instituted against the Licensee by a third party,
|
|
||||||
shall constitute consequential loss and shall not provide entitlement to
|
|
||||||
any or all compensation from the Licensor.
|
|
||||||
|
|
||||||
|
|
||||||
Article 9 - WARRANTY
|
|
||||||
|
|
||||||
9.1 The Licensee acknowledges that the scientific and technical
|
|
||||||
state-of-the-art when the Software was distributed did not enable all
|
|
||||||
possible uses to be tested and verified, nor for the presence of
|
|
||||||
possible defects to be detected. In this respect, the Licensee's
|
|
||||||
attention has been drawn to the risks associated with loading, using,
|
|
||||||
modifying and/or developing and reproducing the Software which are
|
|
||||||
reserved for experienced users.
|
|
||||||
|
|
||||||
The Licensee shall be responsible for verifying, by any or all means,
|
|
||||||
the suitability of the product for its requirements, its good working
|
|
||||||
order, and for ensuring that it shall not cause damage to either persons
|
|
||||||
or properties.
|
|
||||||
|
|
||||||
9.2 The Licensor hereby represents, in good faith, that it is entitled
|
|
||||||
to grant all the rights over the Software (including in particular the
|
|
||||||
rights set forth in Article 5 <#scope>).
|
|
||||||
|
|
||||||
9.3 The Licensee acknowledges that the Software is supplied "as is" by
|
|
||||||
the Licensor without any other express or tacit warranty, other than
|
|
||||||
that provided for in Article 9.2 <#good-faith> and, in particular,
|
|
||||||
without any warranty as to its commercial value, its secured, safe,
|
|
||||||
innovative or relevant nature.
|
|
||||||
|
|
||||||
Specifically, the Licensor does not warrant that the Software is free
|
|
||||||
from any error, that it will operate without interruption, that it will
|
|
||||||
be compatible with the Licensee's own equipment and software
|
|
||||||
configuration, nor that it will meet the Licensee's requirements.
|
|
||||||
|
|
||||||
9.4 The Licensor does not either expressly or tacitly warrant that the
|
|
||||||
Software does not infringe any third party intellectual property right
|
|
||||||
relating to a patent, software or any other property right. Therefore,
|
|
||||||
the Licensor disclaims any and all liability towards the Licensee
|
|
||||||
arising out of any or all proceedings for infringement that may be
|
|
||||||
instituted in respect of the use, modification and redistribution of the
|
|
||||||
Software. Nevertheless, should such proceedings be instituted against
|
|
||||||
the Licensee, the Licensor shall provide it with technical and legal
|
|
||||||
expertise for its defense. Such technical and legal expertise shall be
|
|
||||||
decided on a case-by-case basis between the relevant Licensor and the
|
|
||||||
Licensee pursuant to a memorandum of understanding. The Licensor
|
|
||||||
disclaims any and all liability as regards the Licensee's use of the
|
|
||||||
name of the Software. No warranty is given as regards the existence of
|
|
||||||
prior rights over the name of the Software or as regards the existence
|
|
||||||
of a trademark.
|
|
||||||
|
|
||||||
|
|
||||||
Article 10 - TERMINATION
|
|
||||||
|
|
||||||
10.1 In the event of a breach by the Licensee of its obligations
|
|
||||||
hereunder, the Licensor may automatically terminate this Agreement
|
|
||||||
thirty (30) days after notice has been sent to the Licensee and has
|
|
||||||
remained ineffective.
|
|
||||||
|
|
||||||
10.2 A Licensee whose Agreement is terminated shall no longer be
|
|
||||||
authorized to use, modify or distribute the Software. However, any
|
|
||||||
licenses that it may have granted prior to termination of the Agreement
|
|
||||||
shall remain valid subject to their having been granted in compliance
|
|
||||||
with the terms and conditions hereof.
|
|
||||||
|
|
||||||
|
|
||||||
Article 11 - MISCELLANEOUS
|
|
||||||
|
|
||||||
|
|
||||||
11.1 EXCUSABLE EVENTS
|
|
||||||
|
|
||||||
Neither Party shall be liable for any or all delay, or failure to
|
|
||||||
perform the Agreement, that may be attributable to an event of force
|
|
||||||
majeure, an act of God or an outside cause, such as defective
|
|
||||||
functioning or interruptions of the electricity or telecommunications
|
|
||||||
networks, network paralysis following a virus attack, intervention by
|
|
||||||
government authorities, natural disasters, water damage, earthquakes,
|
|
||||||
fire, explosions, strikes and labor unrest, war, etc.
|
|
||||||
|
|
||||||
11.2 Any failure by either Party, on one or more occasions, to invoke
|
|
||||||
one or more of the provisions hereof, shall under no circumstances be
|
|
||||||
interpreted as being a waiver by the interested Party of its right to
|
|
||||||
invoke said provision(s) subsequently.
|
|
||||||
|
|
||||||
11.3 The Agreement cancels and replaces any or all previous agreements,
|
|
||||||
whether written or oral, between the Parties and having the same
|
|
||||||
purpose, and constitutes the entirety of the agreement between said
|
|
||||||
Parties concerning said purpose. No supplement or modification to the
|
|
||||||
terms and conditions hereof shall be effective as between the Parties
|
|
||||||
unless it is made in writing and signed by their duly authorized
|
|
||||||
representatives.
|
|
||||||
|
|
||||||
11.4 In the event that one or more of the provisions hereof were to
|
|
||||||
conflict with a current or future applicable act or legislative text,
|
|
||||||
said act or legislative text shall prevail, and the Parties shall make
|
|
||||||
the necessary amendments so as to comply with said act or legislative
|
|
||||||
text. All other provisions shall remain effective. Similarly, invalidity
|
|
||||||
of a provision of the Agreement, for any reason whatsoever, shall not
|
|
||||||
cause the Agreement as a whole to be invalid.
|
|
||||||
|
|
||||||
|
|
||||||
11.5 LANGUAGE
|
|
||||||
|
|
||||||
The Agreement is drafted in both French and English and both versions
|
|
||||||
are deemed authentic.
|
|
||||||
|
|
||||||
|
|
||||||
Article 12 - NEW VERSIONS OF THE AGREEMENT
|
|
||||||
|
|
||||||
12.1 Any person is authorized to duplicate and distribute copies of this
|
|
||||||
Agreement.
|
|
||||||
|
|
||||||
12.2 So as to ensure coherence, the wording of this Agreement is
|
|
||||||
protected and may only be modified by the authors of the License, who
|
|
||||||
reserve the right to periodically publish updates or new versions of the
|
|
||||||
Agreement, each with a separate number. These subsequent versions may
|
|
||||||
address new issues encountered by Free Software.
|
|
||||||
|
|
||||||
12.3 Any Software distributed under a given version of the Agreement may
|
|
||||||
only be subsequently distributed under the same version of the Agreement
|
|
||||||
or a subsequent version, subject to the provisions of Article 5.3.4
|
|
||||||
<#compatibility>.
|
|
||||||
|
|
||||||
|
|
||||||
Article 13 - GOVERNING LAW AND JURISDICTION
|
|
||||||
|
|
||||||
13.1 The Agreement is governed by French law. The Parties agree to
|
|
||||||
endeavor to seek an amicable solution to any disagreements or disputes
|
|
||||||
that may arise during the performance of the Agreement.
|
|
||||||
|
|
||||||
13.2 Failing an amicable solution within two (2) months as from their
|
|
||||||
occurrence, and unless emergency proceedings are necessary, the
|
|
||||||
disagreements or disputes shall be referred to the Paris Courts having
|
|
||||||
jurisdiction, by the more diligent Party.
|
|
||||||
@ -7,109 +7,107 @@ Created on 13 fevr. 2014
|
|||||||
from distutils import log
|
from distutils import log
|
||||||
import os
|
import os
|
||||||
|
|
||||||
|
from Cython.Distutils import build_ext as ori_build_ext # @UnresolvedImport
|
||||||
|
|
||||||
|
from Cython.Compiler import Options as cython_options # @UnresolvedImport
|
||||||
|
|
||||||
from distutils.errors import DistutilsSetupError
|
from distutils.errors import DistutilsSetupError
|
||||||
|
|
||||||
try:
|
class build_ext(ori_build_ext):
|
||||||
from Cython.Distutils import build_ext as ori_build_ext # @UnresolvedImport
|
|
||||||
from Cython.Compiler import Options as cython_options # @UnresolvedImport
|
|
||||||
class build_ext(ori_build_ext):
|
|
||||||
|
|
||||||
|
|
||||||
def modifyDocScripts(self):
|
|
||||||
build_dir_file=open("doc/sphinx/build_dir.txt","w")
|
|
||||||
print(self.build_lib,file=build_dir_file)
|
|
||||||
build_dir_file.close()
|
|
||||||
|
|
||||||
def initialize_options(self):
|
|
||||||
ori_build_ext.initialize_options(self) # @UndefinedVariable
|
|
||||||
self.littlebigman = None
|
|
||||||
self.built_files = None
|
|
||||||
|
|
||||||
|
|
||||||
def finalize_options(self):
|
|
||||||
ori_build_ext.finalize_options(self) # @UndefinedVariable
|
|
||||||
|
|
||||||
self.set_undefined_options('littlebigman',
|
|
||||||
('littlebigman', 'littlebigman'))
|
|
||||||
|
|
||||||
self.set_undefined_options('build_files',
|
|
||||||
('files', 'built_files'))
|
|
||||||
|
|
||||||
self.cython_c_in_temp = 1
|
|
||||||
|
|
||||||
if self.littlebigman =='-DLITTLE_END':
|
|
||||||
if self.define is None:
|
|
||||||
self.define=[('LITTLE_END',None)]
|
|
||||||
else:
|
|
||||||
self.define.append('LITTLE_END',None)
|
|
||||||
|
|
||||||
def substitute_sources(self,exe_name,sources):
|
|
||||||
"""
|
|
||||||
Substitutes source file name starting by an @ by the actual
|
|
||||||
name of the built file (see --> build_files)
|
|
||||||
"""
|
|
||||||
sources = list(sources)
|
|
||||||
for i in range(len(sources)):
|
|
||||||
message = "%s :-> %s" % (exe_name,sources[i])
|
|
||||||
if sources[i][0]=='@':
|
|
||||||
try:
|
|
||||||
filename = self.built_files[sources[i][1:]]
|
|
||||||
except KeyError:
|
|
||||||
tmpfilename = os.path.join(self.build_temp,sources[i][1:])
|
|
||||||
if os.path.isfile (tmpfilename):
|
|
||||||
filename = tmpfilename
|
|
||||||
else:
|
|
||||||
raise DistutilsSetupError(
|
|
||||||
'The %s filename declared in the source '
|
|
||||||
'files of the program %s have not been '
|
|
||||||
'built by the installation process' % (sources[i],
|
|
||||||
exe_name))
|
|
||||||
sources[i]=filename
|
|
||||||
log.info("%s changed to %s",message,filename)
|
|
||||||
else:
|
|
||||||
log.info("%s ok",message)
|
|
||||||
|
|
||||||
return sources
|
|
||||||
|
|
||||||
def build_extensions(self):
|
|
||||||
# First, sanity-check the 'extensions' list
|
|
||||||
|
|
||||||
for ext in self.extensions:
|
|
||||||
ext.sources = self.substitute_sources(ext.name,ext.sources)
|
|
||||||
|
|
||||||
self.check_extensions_list(self.extensions)
|
|
||||||
|
|
||||||
for ext in self.extensions:
|
|
||||||
log.info("%s :-> %s",ext.name,ext.sources)
|
|
||||||
ext.sources = self.cython_sources(ext.sources, ext)
|
|
||||||
self.build_extension(ext)
|
|
||||||
|
|
||||||
|
|
||||||
def run(self):
|
|
||||||
self.modifyDocScripts()
|
|
||||||
|
|
||||||
for cmd_name in self.get_sub_commands():
|
|
||||||
self.run_command(cmd_name)
|
|
||||||
|
|
||||||
cython_options.annotate = True
|
|
||||||
ori_build_ext.run(self) # @UndefinedVariable
|
|
||||||
|
|
||||||
|
|
||||||
def has_files(self):
|
|
||||||
return self.distribution.has_files()
|
|
||||||
|
|
||||||
def has_executables(self):
|
|
||||||
return self.distribution.has_executables()
|
|
||||||
|
|
||||||
sub_commands = [('build_files',has_files),
|
|
||||||
('build_cexe', has_executables)
|
|
||||||
] + \
|
|
||||||
ori_build_ext.sub_commands
|
|
||||||
|
|
||||||
except ImportError:
|
|
||||||
from distutils.command import build_ext # @UnusedImport
|
def modifyDocScripts(self):
|
||||||
|
build_dir_file=open("doc/sphinx/build_dir.txt","w")
|
||||||
|
print(self.build_lib,file=build_dir_file)
|
||||||
|
build_dir_file.close()
|
||||||
|
|
||||||
|
def initialize_options(self):
|
||||||
|
ori_build_ext.initialize_options(self) # @UndefinedVariable
|
||||||
|
self.littlebigman = None
|
||||||
|
self.built_files = None
|
||||||
|
|
||||||
|
|
||||||
|
def finalize_options(self):
|
||||||
|
ori_build_ext.finalize_options(self) # @UndefinedVariable
|
||||||
|
|
||||||
|
self.set_undefined_options('littlebigman',
|
||||||
|
('littlebigman', 'littlebigman'))
|
||||||
|
|
||||||
|
self.set_undefined_options('build_files',
|
||||||
|
('files', 'built_files'))
|
||||||
|
|
||||||
|
self.cython_c_in_temp = 1
|
||||||
|
|
||||||
|
if self.littlebigman =='-DLITTLE_END':
|
||||||
|
if self.define is None:
|
||||||
|
self.define=[('LITTLE_END',None)]
|
||||||
|
else:
|
||||||
|
self.define.append('LITTLE_END',None)
|
||||||
|
|
||||||
|
def substitute_sources(self,exe_name,sources):
|
||||||
|
"""
|
||||||
|
Substitutes source file name starting by an @ by the actual
|
||||||
|
name of the built file (see --> build_files)
|
||||||
|
"""
|
||||||
|
sources = list(sources)
|
||||||
|
for i in range(len(sources)):
|
||||||
|
message = "%s :-> %s" % (exe_name,sources[i])
|
||||||
|
if sources[i][0]=='@':
|
||||||
|
try:
|
||||||
|
filename = self.built_files[sources[i][1:]]
|
||||||
|
except KeyError:
|
||||||
|
tmpfilename = os.path.join(self.build_temp,sources[i][1:])
|
||||||
|
if os.path.isfile (tmpfilename):
|
||||||
|
filename = tmpfilename
|
||||||
|
else:
|
||||||
|
raise DistutilsSetupError(
|
||||||
|
'The %s filename declared in the source '
|
||||||
|
'files of the program %s have not been '
|
||||||
|
'built by the installation process' % (sources[i],
|
||||||
|
exe_name))
|
||||||
|
sources[i]=filename
|
||||||
|
log.info("%s changed to %s",message,filename)
|
||||||
|
else:
|
||||||
|
log.info("%s ok",message)
|
||||||
|
|
||||||
|
return sources
|
||||||
|
|
||||||
|
def build_extensions(self):
|
||||||
|
# First, sanity-check the 'extensions' list
|
||||||
|
|
||||||
|
for ext in self.extensions:
|
||||||
|
ext.sources = self.substitute_sources(ext.name,ext.sources)
|
||||||
|
|
||||||
|
self.check_extensions_list(self.extensions)
|
||||||
|
|
||||||
|
for ext in self.extensions:
|
||||||
|
log.info("%s :-> %s",ext.name,ext.sources)
|
||||||
|
ext.sources = self.cython_sources(ext.sources, ext)
|
||||||
|
self.build_extension(ext)
|
||||||
|
|
||||||
|
|
||||||
|
def run(self):
|
||||||
|
self.modifyDocScripts()
|
||||||
|
|
||||||
|
for cmd_name in self.get_sub_commands():
|
||||||
|
self.run_command(cmd_name)
|
||||||
|
|
||||||
|
cython_options.annotate = True
|
||||||
|
ori_build_ext.run(self) # @UndefinedVariable
|
||||||
|
|
||||||
|
|
||||||
|
def has_files(self):
|
||||||
|
return self.distribution.has_files()
|
||||||
|
|
||||||
|
def has_executables(self):
|
||||||
|
return self.distribution.has_executables()
|
||||||
|
|
||||||
|
sub_commands = [('build_files',has_files),
|
||||||
|
('build_cexe', has_executables)
|
||||||
|
] + \
|
||||||
|
ori_build_ext.sub_commands
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,36 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 22 janv. 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import sys
|
|
||||||
from urllib import request
|
|
||||||
import os.path
|
|
||||||
|
|
||||||
from obidistutils.serenity.util import get_serenity_dir
|
|
||||||
from obidistutils.serenity.rerun import rerun_with_anothe_python
|
|
||||||
from obidistutils.serenity.checkpython import is_a_virtualenv_python
|
|
||||||
|
|
||||||
getpipurl="https://bootstrap.pypa.io/get-pip.py"
|
|
||||||
|
|
||||||
def bootstrap():
|
|
||||||
|
|
||||||
getpipfile=os.path.join(get_serenity_dir(),"get-pip.py")
|
|
||||||
|
|
||||||
with request.urlopen(getpipurl) as getpip:
|
|
||||||
with open(getpipfile,"wb") as out:
|
|
||||||
for l in getpip:
|
|
||||||
out.write(l)
|
|
||||||
|
|
||||||
python = sys.executable
|
|
||||||
|
|
||||||
if is_a_virtualenv_python():
|
|
||||||
command= "%s %s" % (python,getpipfile)
|
|
||||||
else:
|
|
||||||
command= "%s %s --user" % (python,getpipfile)
|
|
||||||
|
|
||||||
os.system(command)
|
|
||||||
|
|
||||||
rerun_with_anothe_python(python)
|
|
||||||
|
|
||||||
@ -7,13 +7,8 @@ Created on 2 oct. 2014
|
|||||||
import re
|
import re
|
||||||
import os
|
import os
|
||||||
|
|
||||||
try:
|
import pip # @UnresolvedImport
|
||||||
import pip # @UnresolvedImport
|
from pip.utils import get_installed_distributions # @UnresolvedImport
|
||||||
from pip.utils import get_installed_distributions # @UnresolvedImport
|
|
||||||
except ImportError:
|
|
||||||
from .bootstrappip import bootstrap
|
|
||||||
bootstrap()
|
|
||||||
|
|
||||||
from distutils.version import StrictVersion # @UnusedImport
|
from distutils.version import StrictVersion # @UnusedImport
|
||||||
from distutils.errors import DistutilsError
|
from distutils.errors import DistutilsError
|
||||||
from distutils import log
|
from distutils import log
|
||||||
|
|||||||
@ -59,7 +59,7 @@ def serenity_virtualenv(envname,package,version,minversion='3.4',maxversion=None
|
|||||||
clear=True,
|
clear=True,
|
||||||
symlinks=False,
|
symlinks=False,
|
||||||
with_pip=True)
|
with_pip=True)
|
||||||
|
|
||||||
# check the newly created virtualenv
|
# check the newly created virtualenv
|
||||||
return serenity_virtualenv(envname,package,version)
|
return serenity_virtualenv(envname,package,version)
|
||||||
|
|
||||||
|
|||||||
@ -1,50 +0,0 @@
|
|||||||
#!/usr/local/bin/python3.4
|
|
||||||
'''
|
|
||||||
obi -- shortdesc
|
|
||||||
|
|
||||||
obi is a description
|
|
||||||
|
|
||||||
It defines classes_and_methods
|
|
||||||
|
|
||||||
@author: user_name
|
|
||||||
|
|
||||||
@copyright: 2014 organization_name. All rights reserved.
|
|
||||||
|
|
||||||
@license: license
|
|
||||||
|
|
||||||
@contact: user_email
|
|
||||||
@deffield updated: Updated
|
|
||||||
'''
|
|
||||||
|
|
||||||
|
|
||||||
default_config = { 'software' : "The OBITools",
|
|
||||||
'log' : False,
|
|
||||||
'loglevel' : 'INFO',
|
|
||||||
'progress' : True,
|
|
||||||
'defaultdms' : None
|
|
||||||
}
|
|
||||||
|
|
||||||
root_config_name='obi'
|
|
||||||
|
|
||||||
from obitools3.apps.config import getConfiguration # @UnresolvedImport
|
|
||||||
from obitools3.version import version
|
|
||||||
|
|
||||||
__all__ = []
|
|
||||||
__version__ = version
|
|
||||||
__date__ = '2014-09-28'
|
|
||||||
__updated__ = '2014-09-28'
|
|
||||||
|
|
||||||
DEBUG = 1
|
|
||||||
TESTRUN = 0
|
|
||||||
PROFILE = 0
|
|
||||||
|
|
||||||
|
|
||||||
if __name__ =="__main__":
|
|
||||||
|
|
||||||
config = getConfiguration(root_config_name,
|
|
||||||
default_config)
|
|
||||||
|
|
||||||
config[root_config_name]['module'].run(config)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,3 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
cpdef buildArgumentParser(str configname, str softname)
|
|
||||||
@ -1,61 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
'''
|
|
||||||
Created on 27 mars 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import argparse
|
|
||||||
import sys
|
|
||||||
|
|
||||||
|
|
||||||
from .command import getCommandsList
|
|
||||||
|
|
||||||
class ObiParser(argparse.ArgumentParser):
|
|
||||||
def error(self, message):
|
|
||||||
sys.stderr.write('error: %s\n' % message)
|
|
||||||
self.print_help()
|
|
||||||
sys.exit(2)
|
|
||||||
|
|
||||||
cpdef buildArgumentParser(str configname,
|
|
||||||
str softname):
|
|
||||||
parser = ObiParser()
|
|
||||||
|
|
||||||
parser.add_argument('--version', dest='%s:version' % configname,
|
|
||||||
action='store_true',
|
|
||||||
default=False,
|
|
||||||
help='Print the version of %s' % softname)
|
|
||||||
|
|
||||||
parser.add_argument('--log', dest='%s:log' % configname,
|
|
||||||
action='store',
|
|
||||||
type=str,
|
|
||||||
default=None,
|
|
||||||
help='Create a logfile')
|
|
||||||
|
|
||||||
parser.add_argument('--no-progress', dest='%s:progress' % configname,
|
|
||||||
action='store_false',
|
|
||||||
default=None,
|
|
||||||
help='Do not print the progress bar during analyzes')
|
|
||||||
|
|
||||||
subparsers = parser.add_subparsers(title='subcommands',
|
|
||||||
description='valid subcommands',
|
|
||||||
help='additional help')
|
|
||||||
|
|
||||||
commands = getCommandsList()
|
|
||||||
|
|
||||||
for c in commands:
|
|
||||||
module = commands[c]
|
|
||||||
|
|
||||||
if hasattr(module, "run"):
|
|
||||||
if hasattr(module, "__title__"):
|
|
||||||
sub = subparsers.add_parser(c,help=module.__title__)
|
|
||||||
else:
|
|
||||||
sub = subparsers.add_parser(c)
|
|
||||||
|
|
||||||
if hasattr(module, "addOptions"):
|
|
||||||
module.addOptions(sub)
|
|
||||||
|
|
||||||
sub.set_defaults(**{'%s:module' % configname : module})
|
|
||||||
|
|
||||||
return parser
|
|
||||||
@ -1,3 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
cdef object loadCommand(str name,loader)
|
|
||||||
@ -1,44 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
'''
|
|
||||||
Created on 27 mars 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import pkgutil
|
|
||||||
|
|
||||||
from obitools3 import commands
|
|
||||||
|
|
||||||
cdef object loadCommand(str name,loader):
|
|
||||||
'''
|
|
||||||
Load a command module from its name and an ImpLoader
|
|
||||||
|
|
||||||
This function is for internal use
|
|
||||||
|
|
||||||
@param name: name of the module
|
|
||||||
@type name: str
|
|
||||||
@param loader: the module loader
|
|
||||||
@type loader: ImpLoader
|
|
||||||
|
|
||||||
@return the loaded module
|
|
||||||
@rtype: module
|
|
||||||
'''
|
|
||||||
|
|
||||||
module = loader.find_module(name).load_module(name)
|
|
||||||
return module
|
|
||||||
|
|
||||||
def getCommandsList():
|
|
||||||
'''
|
|
||||||
Returns the list of sub-commands available to the main `obi` command
|
|
||||||
|
|
||||||
@return: a dict instance with key corresponding to each command and
|
|
||||||
value corresponding to the module
|
|
||||||
|
|
||||||
@rtype: dict
|
|
||||||
'''
|
|
||||||
|
|
||||||
cdef dict cmds = dict((x[1],loadCommand(x[1],x[0]))
|
|
||||||
for x in pkgutil.iter_modules(commands.__path__)
|
|
||||||
if not x[2])
|
|
||||||
return cmds
|
|
||||||
@ -1,10 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
cpdef str setRootConfigName(str rootname)
|
|
||||||
cpdef str getRootConfigName()
|
|
||||||
|
|
||||||
cdef dict buildDefaultConfiguration(str root_config_name,
|
|
||||||
dict config)
|
|
||||||
|
|
||||||
cpdef dict getConfiguration(str root_config_name=?,
|
|
||||||
dict config=?)
|
|
||||||
@ -1,103 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
'''
|
|
||||||
Created on 27 mars 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import sys
|
|
||||||
|
|
||||||
from .command import getCommandsList
|
|
||||||
from .logging cimport getLogger
|
|
||||||
from .arguments cimport buildArgumentParser
|
|
||||||
|
|
||||||
from ..version import version
|
|
||||||
from _curses import version
|
|
||||||
|
|
||||||
cdef dict __default_config__ = {}
|
|
||||||
|
|
||||||
|
|
||||||
cpdef str setRootConfigName(str rootname):
|
|
||||||
global __default_config__
|
|
||||||
if '__root_config__' in __default_config__:
|
|
||||||
if __default_config__["__root_config__"] in __default_config__:
|
|
||||||
__default_config__[rootname]=__default_config__[__default_config__["__root_config__"]]
|
|
||||||
del __default_config__[__default_config__["__root_config__"]]
|
|
||||||
__default_config__['__root_config__']=rootname
|
|
||||||
return rootname
|
|
||||||
|
|
||||||
cpdef str getRootConfigName():
|
|
||||||
global __default_config__
|
|
||||||
return __default_config__.get('__root_config__',None)
|
|
||||||
|
|
||||||
cdef dict buildDefaultConfiguration(str root_config_name,
|
|
||||||
dict config):
|
|
||||||
global __default_config__
|
|
||||||
|
|
||||||
__default_config__.clear()
|
|
||||||
setRootConfigName(root_config_name)
|
|
||||||
|
|
||||||
__default_config__[root_config_name]=config
|
|
||||||
|
|
||||||
config['version']=version
|
|
||||||
|
|
||||||
commands = getCommandsList()
|
|
||||||
|
|
||||||
for c in commands:
|
|
||||||
module = commands[c]
|
|
||||||
|
|
||||||
assert hasattr(module, "run")
|
|
||||||
|
|
||||||
if hasattr(module, 'default_config'):
|
|
||||||
__default_config__[c]=module.default_config
|
|
||||||
else:
|
|
||||||
__default_config__[c]={}
|
|
||||||
|
|
||||||
return __default_config__
|
|
||||||
|
|
||||||
|
|
||||||
cpdef dict getConfiguration(str root_config_name="__default__",
|
|
||||||
dict config={}):
|
|
||||||
global __default_config__
|
|
||||||
|
|
||||||
if '__done__' in __default_config__:
|
|
||||||
return __default_config__
|
|
||||||
|
|
||||||
if root_config_name=="__default__":
|
|
||||||
raise RuntimeError("No root_config_name specified")
|
|
||||||
|
|
||||||
if not config:
|
|
||||||
raise RuntimeError("Base configuration is empty")
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
config = buildDefaultConfiguration(root_config_name,
|
|
||||||
config)
|
|
||||||
|
|
||||||
parser = buildArgumentParser(root_config_name,
|
|
||||||
config[root_config_name]['software'])
|
|
||||||
|
|
||||||
options = vars(parser.parse_args())
|
|
||||||
|
|
||||||
if options['%s:version' % root_config_name]:
|
|
||||||
print("%s - Version %s" % (config[root_config_name]['software'],
|
|
||||||
config[root_config_name]['version']))
|
|
||||||
sys.exit(0)
|
|
||||||
|
|
||||||
for k in options:
|
|
||||||
section,key = k.split(':')
|
|
||||||
s = config[section]
|
|
||||||
if options[k] is not None:
|
|
||||||
s[key]=options[k]
|
|
||||||
|
|
||||||
if not 'module' in config[root_config_name]:
|
|
||||||
print('\nError: No command specified',file=sys.stderr)
|
|
||||||
parser.print_help()
|
|
||||||
sys.exit(2)
|
|
||||||
|
|
||||||
getLogger(config)
|
|
||||||
|
|
||||||
config['__done__']=True
|
|
||||||
|
|
||||||
return config
|
|
||||||
@ -1,3 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
cpdef getLogger(dict config)
|
|
||||||
@ -1,46 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
'''
|
|
||||||
Created on 27 mars 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import logging
|
|
||||||
import sys
|
|
||||||
|
|
||||||
cpdef getLogger(dict config):
|
|
||||||
'''
|
|
||||||
Returns the logger as defined by the command line option
|
|
||||||
or by the config file
|
|
||||||
:param config:
|
|
||||||
'''
|
|
||||||
|
|
||||||
root = config["__root_config__"]
|
|
||||||
|
|
||||||
level = config[root]['loglevel']
|
|
||||||
logfile= config[root]['log']
|
|
||||||
|
|
||||||
rootlogger = logging.getLogger()
|
|
||||||
logFormatter = logging.Formatter("%(asctime)s [%(levelname)-5.5s] %(message)s")
|
|
||||||
|
|
||||||
stderrHandler = logging.StreamHandler(sys.stderr)
|
|
||||||
stderrHandler.setFormatter(logFormatter)
|
|
||||||
|
|
||||||
rootlogger.addHandler(stderrHandler)
|
|
||||||
|
|
||||||
if logfile:
|
|
||||||
fileHandler = logging.FileHandler(logfile)
|
|
||||||
fileHandler.setFormatter(logFormatter)
|
|
||||||
rootlogger.addHandler(fileHandler)
|
|
||||||
|
|
||||||
try:
|
|
||||||
loglevel = getattr(logging, level)
|
|
||||||
except:
|
|
||||||
loglevel = logging.INFO
|
|
||||||
|
|
||||||
rootlogger.setLevel(loglevel)
|
|
||||||
|
|
||||||
config[root]['logger']=rootlogger
|
|
||||||
|
|
||||||
return rootlogger
|
|
||||||
@ -1,65 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
from ..utils cimport str2bytes
|
|
||||||
|
|
||||||
cdef extern from "stdio.h":
|
|
||||||
struct FILE
|
|
||||||
int fprintf(FILE *stream, char *format, ...)
|
|
||||||
FILE* stderr
|
|
||||||
ctypedef unsigned int off_t "unsigned long long"
|
|
||||||
|
|
||||||
cdef extern from "unistd.h":
|
|
||||||
int fsync(int fd);
|
|
||||||
|
|
||||||
cdef extern from "time.h":
|
|
||||||
struct tm :
|
|
||||||
int tm_yday
|
|
||||||
int tm_hour
|
|
||||||
int tm_min
|
|
||||||
int tm_sec
|
|
||||||
|
|
||||||
enum: CLOCKS_PER_SEC
|
|
||||||
|
|
||||||
ctypedef int time_t
|
|
||||||
ctypedef int clock_t
|
|
||||||
ctypedef int suseconds_t
|
|
||||||
|
|
||||||
struct timeval:
|
|
||||||
time_t tv_sec # seconds */
|
|
||||||
suseconds_t tv_usec # microseconds */
|
|
||||||
|
|
||||||
|
|
||||||
struct timezone :
|
|
||||||
int tz_minuteswest; # minutes west of Greenwich
|
|
||||||
int tz_dsttime; # type of DST correction
|
|
||||||
|
|
||||||
|
|
||||||
int gettimeofday(timeval *tv, timezone *tz)
|
|
||||||
|
|
||||||
|
|
||||||
tm *gmtime_r(time_t *clock, tm *result)
|
|
||||||
time_t time(time_t *tloc)
|
|
||||||
clock_t clock()
|
|
||||||
|
|
||||||
cdef class ProgressBar:
|
|
||||||
cdef off_t maxi
|
|
||||||
cdef clock_t starttime
|
|
||||||
cdef clock_t lasttime
|
|
||||||
cdef clock_t tickcount
|
|
||||||
cdef int freq
|
|
||||||
cdef int cycle
|
|
||||||
cdef int arrow
|
|
||||||
cdef int lastlog
|
|
||||||
cdef bint ontty
|
|
||||||
cdef int fd
|
|
||||||
|
|
||||||
cdef bytes head
|
|
||||||
cdef char *chead
|
|
||||||
|
|
||||||
cdef object logger
|
|
||||||
|
|
||||||
cdef char *wheel
|
|
||||||
cdef char *spaces
|
|
||||||
cdef char* diese
|
|
||||||
|
|
||||||
cdef clock_t clock(self)
|
|
||||||
@ -1,138 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
'''
|
|
||||||
Created on 27 mars 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import sys
|
|
||||||
from ..utils cimport bytes2str
|
|
||||||
|
|
||||||
cdef class ProgressBar:
|
|
||||||
cdef clock_t clock(self):
|
|
||||||
cdef clock_t t
|
|
||||||
cdef timeval tp
|
|
||||||
cdef clock_t s
|
|
||||||
|
|
||||||
<void> gettimeofday(&tp,NULL)
|
|
||||||
s = <clock_t> (<double> tp.tv_usec * 1.e-6 * <double> CLOCKS_PER_SEC)
|
|
||||||
t = tp.tv_sec * CLOCKS_PER_SEC + s
|
|
||||||
|
|
||||||
return t
|
|
||||||
|
|
||||||
def __init__(self,
|
|
||||||
off_t maxi,
|
|
||||||
dict config,
|
|
||||||
str head="",
|
|
||||||
double seconde=0.1):
|
|
||||||
self.starttime = self.clock()
|
|
||||||
self.lasttime = self.starttime
|
|
||||||
self.tickcount = <clock_t> (seconde * CLOCKS_PER_SEC)
|
|
||||||
self.freq = 1
|
|
||||||
self.cycle = 0
|
|
||||||
self.arrow = 0
|
|
||||||
self.lastlog = 0
|
|
||||||
|
|
||||||
self.ontty = sys.stderr.isatty()
|
|
||||||
|
|
||||||
if (maxi<=0):
|
|
||||||
maxi=1
|
|
||||||
|
|
||||||
self.maxi = maxi
|
|
||||||
self.head = str2bytes(head)
|
|
||||||
self.chead= self.head
|
|
||||||
|
|
||||||
|
|
||||||
self.logger=config[config["__root_config__"]]["logger"]
|
|
||||||
self.wheel = '|/-\\'
|
|
||||||
self.spaces=' ' \
|
|
||||||
' ' \
|
|
||||||
' ' \
|
|
||||||
' ' \
|
|
||||||
' '
|
|
||||||
self.diese ='##########' \
|
|
||||||
'##########' \
|
|
||||||
'##########' \
|
|
||||||
'##########' \
|
|
||||||
'##########'
|
|
||||||
|
|
||||||
def __call__(self,object pos):
|
|
||||||
cdef off_t ipos
|
|
||||||
cdef clock_t elapsed
|
|
||||||
cdef clock_t newtime
|
|
||||||
cdef clock_t delta
|
|
||||||
cdef clock_t more
|
|
||||||
cdef double percent
|
|
||||||
cdef tm remain
|
|
||||||
cdef int days,hour,minu,sec
|
|
||||||
cdef off_t fraction
|
|
||||||
cdef int twentyth
|
|
||||||
|
|
||||||
self.cycle+=1
|
|
||||||
|
|
||||||
if self.cycle % self.freq == 0:
|
|
||||||
self.cycle=1
|
|
||||||
newtime = self.clock()
|
|
||||||
delta = newtime - self.lasttime
|
|
||||||
self.lasttime = newtime
|
|
||||||
elapsed = newtime - self.starttime
|
|
||||||
# print(" ",delta,elapsed,elapsed/CLOCKS_PER_SEC,self.tickcount)
|
|
||||||
|
|
||||||
if delta < self.tickcount / 5 :
|
|
||||||
self.freq*=2
|
|
||||||
elif delta > self.tickcount * 5 and self.freq>1:
|
|
||||||
self.freq/=2
|
|
||||||
|
|
||||||
|
|
||||||
if callable(pos):
|
|
||||||
ipos=pos()
|
|
||||||
else:
|
|
||||||
ipos=pos
|
|
||||||
|
|
||||||
if ipos==0:
|
|
||||||
ipos=1
|
|
||||||
|
|
||||||
percent = <double>ipos/<double>self.maxi
|
|
||||||
more = <time_t>((<double>elapsed / percent * (1. - percent))/CLOCKS_PER_SEC)
|
|
||||||
<void>gmtime_r(&more, &remain)
|
|
||||||
days = remain.tm_yday
|
|
||||||
hour = remain.tm_hour
|
|
||||||
minu = remain.tm_min
|
|
||||||
sec = remain.tm_sec
|
|
||||||
|
|
||||||
if self.ontty:
|
|
||||||
fraction=<int>(percent * 50.)
|
|
||||||
self.arrow=(self.arrow+1) % 4
|
|
||||||
self.diese[fraction]=0
|
|
||||||
self.spaces[50 - fraction]=0
|
|
||||||
|
|
||||||
if days:
|
|
||||||
<void>fprintf(stderr,b'\r%s %5.1f %% |%s%c%s] remain : %d days %02d:%02d:%02d',
|
|
||||||
self.chead,
|
|
||||||
percent*100,
|
|
||||||
self.diese,self.wheel[self.arrow],self.spaces,
|
|
||||||
days,hour,minu,sec)
|
|
||||||
else:
|
|
||||||
<void>fprintf(stderr,b'\r%s %5.1f %% |%s%c%s] remain : %02d:%02d:%02d',
|
|
||||||
self.chead,
|
|
||||||
percent*100.,
|
|
||||||
self.diese,self.wheel[self.arrow],self.spaces,
|
|
||||||
hour,minu,sec)
|
|
||||||
self.diese[fraction]=b'#'
|
|
||||||
self.spaces[50 - fraction]=b' '
|
|
||||||
|
|
||||||
twentyth = int(percent * 20)
|
|
||||||
if twentyth != self.lastlog:
|
|
||||||
|
|
||||||
if self.ontty:
|
|
||||||
<void>fprintf(stderr,b'\n')
|
|
||||||
|
|
||||||
self.logger.info('%s %5.1f %% remain : %02d:%02d:%02d' % (
|
|
||||||
bytes2str(self.head),
|
|
||||||
percent*100.,
|
|
||||||
hour,minu,sec))
|
|
||||||
self.lastlog=twentyth
|
|
||||||
else:
|
|
||||||
self.cycle+=1
|
|
||||||
|
|
||||||
@ -1,44 +0,0 @@
|
|||||||
'''
|
|
||||||
Created on 8 mars 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
from obitools3.apps.progress import ProgressBar # @UnresolvedImport
|
|
||||||
import time
|
|
||||||
|
|
||||||
__title__="Counts sequences in a sequence set"
|
|
||||||
|
|
||||||
|
|
||||||
default_config = { 'countmode' : None
|
|
||||||
}
|
|
||||||
|
|
||||||
def addOptions(parser):
|
|
||||||
parser.add_argument(dest='obi:input', metavar='obi:input',
|
|
||||||
nargs='?',
|
|
||||||
default=None,
|
|
||||||
help='input data set' )
|
|
||||||
|
|
||||||
group=parser.add_argument_group('Obicount specific options')
|
|
||||||
group.add_argument('-s','--sequence',
|
|
||||||
action="store_true", dest="count:sequence",
|
|
||||||
default=False,
|
|
||||||
help="Prints only the number of sequence records."
|
|
||||||
)
|
|
||||||
|
|
||||||
group.add_argument('-a','--all',
|
|
||||||
action="store_true", dest="count:all",
|
|
||||||
default=False,
|
|
||||||
help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False)."
|
|
||||||
)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def run(config):
|
|
||||||
# The code of my command
|
|
||||||
pb = ProgressBar(1000,config,seconde=1)
|
|
||||||
|
|
||||||
for i in range(1,1001):
|
|
||||||
pb(i)
|
|
||||||
time.sleep(0.01)
|
|
||||||
|
|
||||||
@ -1,136 +0,0 @@
|
|||||||
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
|
|
||||||
from obitools3.files.universalopener cimport uopen
|
|
||||||
from obitools3.parsers.fasta import fastaIterator
|
|
||||||
from obitools3.parsers.fastq import fastqIterator
|
|
||||||
from obitools3.obidms._obidms import OBIDMS
|
|
||||||
|
|
||||||
|
|
||||||
import time
|
|
||||||
|
|
||||||
__title__="Counts sequences in a sequence set"
|
|
||||||
|
|
||||||
|
|
||||||
default_config = { 'destview' : None,
|
|
||||||
'skip' : 0,
|
|
||||||
'only' : None,
|
|
||||||
'skiperror' : False,
|
|
||||||
'seqinformat' : None,
|
|
||||||
'moltype' : 'nuc',
|
|
||||||
'filename' : None
|
|
||||||
}
|
|
||||||
|
|
||||||
def addOptions(parser):
|
|
||||||
parser.add_argument(dest='import:filename',
|
|
||||||
metavar='<FILENAME>',
|
|
||||||
nargs='?',
|
|
||||||
default=None,
|
|
||||||
help='sequence file name to be imported' )
|
|
||||||
|
|
||||||
group=parser.add_argument_group('obi import specific options')
|
|
||||||
|
|
||||||
group.add_argument('--default-dms','-d',
|
|
||||||
action="store", dest="obi:defaultdms",
|
|
||||||
metavar='<DMS NAME>',
|
|
||||||
default=None,
|
|
||||||
type=str,
|
|
||||||
help="Name of the default DMS for reading and writing data")
|
|
||||||
|
|
||||||
|
|
||||||
group.add_argument('--destination-view','-v',
|
|
||||||
action="store", dest="import:destview",
|
|
||||||
metavar='<VIEW NAME>',
|
|
||||||
default=None,
|
|
||||||
type=str,
|
|
||||||
required=True,
|
|
||||||
help="Name of the default DMS for reading and writing data")
|
|
||||||
|
|
||||||
group=parser.add_argument_group('obi import specific options')
|
|
||||||
|
|
||||||
group.add_argument('--skip',
|
|
||||||
action="store", dest="import:skip",
|
|
||||||
metavar='<N>',
|
|
||||||
default=None,
|
|
||||||
type=int,
|
|
||||||
help="skip the N first sequences")
|
|
||||||
|
|
||||||
group.add_argument('--only',
|
|
||||||
action="store", dest="import:only",
|
|
||||||
metavar='<N>',
|
|
||||||
default=None,
|
|
||||||
type=int,
|
|
||||||
help="treat only N sequences")
|
|
||||||
|
|
||||||
group.add_argument('--skip-on-error',
|
|
||||||
action="store_true", dest="import:skiperror",
|
|
||||||
default=None,
|
|
||||||
help="Skip sequence entries with parse error")
|
|
||||||
|
|
||||||
group.add_argument('--fasta',
|
|
||||||
action="store_const", dest="import:seqinformat",
|
|
||||||
default=None,
|
|
||||||
const='fasta',
|
|
||||||
help="Input file is in fasta nucleic format (including obitools fasta extentions)")
|
|
||||||
|
|
||||||
group.add_argument('--fastq',
|
|
||||||
action="store_const", dest="import:seqinformat",
|
|
||||||
default=None,
|
|
||||||
const='fastq',
|
|
||||||
help="Input file is in sanger fastq nucleic format (standard fastq)")
|
|
||||||
|
|
||||||
group.add_argument('--nuc',
|
|
||||||
action="store_const", dest="import:moltype",
|
|
||||||
default=None,
|
|
||||||
const='nuc',
|
|
||||||
help="Input file contains nucleic sequences")
|
|
||||||
|
|
||||||
group.add_argument('--prot',
|
|
||||||
action="store_const", dest="import:moltype",
|
|
||||||
default=None,
|
|
||||||
const='pep',
|
|
||||||
help="Input file contains protein sequences")
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def run(config):
|
|
||||||
pb = ProgressBar(35000000,config,seconde=5)
|
|
||||||
|
|
||||||
inputs = uopen(config['import']['filename'])
|
|
||||||
|
|
||||||
if config['import']['seqinformat']=='fasta':
|
|
||||||
iseq = fastaIterator(inputs)
|
|
||||||
view_type="NUC_SEQS_VIEW"
|
|
||||||
elif config['import']['seqinformat']=='fastq':
|
|
||||||
iseq = fastqIterator(inputs)
|
|
||||||
view_type="NUC_SEQS_VIEW"
|
|
||||||
else:
|
|
||||||
raise RuntimeError('No file format specified')
|
|
||||||
|
|
||||||
# Temporary way to handle NA values
|
|
||||||
#NA_list = ["nan"]
|
|
||||||
|
|
||||||
# Create DMS
|
|
||||||
d = OBIDMS(config['obi']['defaultdms'])
|
|
||||||
|
|
||||||
# Create view
|
|
||||||
view = d.new_view(config['import']['destview'], view_type=view_type)
|
|
||||||
|
|
||||||
i = 0
|
|
||||||
for seq in iseq:
|
|
||||||
pb(i)
|
|
||||||
view[i].set_id(seq['id'])
|
|
||||||
view[i].set_definition(seq['definition'])
|
|
||||||
view[i].set_sequence(seq['sequence'])
|
|
||||||
for tag in seq['tags'] :
|
|
||||||
#print(tag, seq['tags'][tag])
|
|
||||||
#if seq['tags'][tag] not in NA_list :
|
|
||||||
view[i][tag] = seq['tags'][tag]
|
|
||||||
i+=1
|
|
||||||
|
|
||||||
#print(view)
|
|
||||||
print(view.__repr__())
|
|
||||||
|
|
||||||
view.save_and_close()
|
|
||||||
d.close()
|
|
||||||
|
|
||||||
print("Done.")
|
|
||||||
|
|
||||||
@ -1,6 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
|
|
||||||
cdef class LineBuffer:
|
|
||||||
cdef object fileobj
|
|
||||||
cdef int size
|
|
||||||
@ -1,23 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
'''
|
|
||||||
Created on 30 mars 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
cdef class LineBuffer:
|
|
||||||
|
|
||||||
def __init__(self,object fileobj,int size=100000000):
|
|
||||||
self.fileobj=fileobj
|
|
||||||
self.size=size
|
|
||||||
|
|
||||||
def __iter__(self):
|
|
||||||
cdef list buff = self.fileobj.readlines(self.size)
|
|
||||||
cdef str l
|
|
||||||
|
|
||||||
while buff:
|
|
||||||
for l in buff:
|
|
||||||
yield l
|
|
||||||
buff = self.fileobj.readlines(self.size)
|
|
||||||
|
|
||||||
@ -1,17 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
cdef class MagicKeyFile:
|
|
||||||
cdef object stream
|
|
||||||
cdef str stream_mode
|
|
||||||
cdef object binary
|
|
||||||
cdef bytes key
|
|
||||||
cdef int keylength
|
|
||||||
cdef int pos
|
|
||||||
|
|
||||||
cpdef bytes read(self,int size=?)
|
|
||||||
cpdef int tell(self)
|
|
||||||
|
|
||||||
|
|
||||||
cdef class CompressedFile:
|
|
||||||
cdef object accessor
|
|
||||||
|
|
||||||
@ -1,114 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
'''
|
|
||||||
Created on 28 mars 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import zipfile
|
|
||||||
import bz2
|
|
||||||
import gzip
|
|
||||||
|
|
||||||
import io
|
|
||||||
|
|
||||||
cdef class MagicKeyFile:
|
|
||||||
def __init__(self,stream,length=2):
|
|
||||||
|
|
||||||
binary=stream
|
|
||||||
self.stream = stream
|
|
||||||
self.stream_mode = None
|
|
||||||
if hasattr(stream, "mode"):
|
|
||||||
self.stream_mode = stream.mode
|
|
||||||
if (not 'b' in stream.mode and
|
|
||||||
hasattr(stream, "buffer") and
|
|
||||||
'b' in stream.buffer.mode):
|
|
||||||
binary=stream.buffer
|
|
||||||
|
|
||||||
if (self.stream_mode is None and
|
|
||||||
not (hasattr(stream, 'headers') and
|
|
||||||
hasattr(stream.headers, "keys") and
|
|
||||||
'Content-type' in stream.headers)):
|
|
||||||
raise TypeError("stream does not present the good interface")
|
|
||||||
|
|
||||||
self.binary=binary
|
|
||||||
self.key=binary.read(length)
|
|
||||||
self.keylength=length
|
|
||||||
self.pos=0
|
|
||||||
|
|
||||||
cpdef bytes read(self,int size=-1):
|
|
||||||
cdef bytes r
|
|
||||||
|
|
||||||
if self.pos < self.keylength:
|
|
||||||
if size > (self.keylength - self.pos):
|
|
||||||
size = size - self.keylength + self.pos
|
|
||||||
r = self.key[self.pos:] + self.binary.read(size)
|
|
||||||
self.pos=self.keylength + 1
|
|
||||||
elif size >=0 :
|
|
||||||
r = self.key[self.pos:(self.pos+size)]
|
|
||||||
self.pos+=size
|
|
||||||
else:
|
|
||||||
r = self.key[self.pos:] + self.binary.read(size)
|
|
||||||
self.pos=self.keylength + 1
|
|
||||||
else:
|
|
||||||
r = self.binary.read(size)
|
|
||||||
|
|
||||||
return r
|
|
||||||
|
|
||||||
cpdef int tell(self):
|
|
||||||
cdef int p
|
|
||||||
|
|
||||||
if self.pos < self.keylength:
|
|
||||||
p = self.pos
|
|
||||||
else:
|
|
||||||
p = self.tell()
|
|
||||||
|
|
||||||
return p
|
|
||||||
|
|
||||||
def __getattr__(self,name):
|
|
||||||
return getattr(self.binary, name)
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
cdef class CompressedFile:
|
|
||||||
|
|
||||||
|
|
||||||
def __init__(self,stream):
|
|
||||||
cdef int keylength
|
|
||||||
cdef MagicKeyFile magic
|
|
||||||
cdef str compressor
|
|
||||||
cdef bytes k
|
|
||||||
cdef object c
|
|
||||||
|
|
||||||
cdef dict compress = { 'zip' : (b'\x50\x4b\x03\x04',zipfile.ZipFile),
|
|
||||||
'bz2' : (b'\x42\x5a\x68',bz2.BZ2File),
|
|
||||||
'gz' : (b'\x1f\x8b\x08',gzip.open)
|
|
||||||
}
|
|
||||||
|
|
||||||
keylength = max([len(x[0]) for x in compress.values()])
|
|
||||||
magic=MagicKeyFile(stream,keylength)
|
|
||||||
|
|
||||||
self.accessor = None
|
|
||||||
|
|
||||||
for compressor in compress:
|
|
||||||
k,c = compress[compressor]
|
|
||||||
if magic.key.startswith(k):
|
|
||||||
self.accessor = c(magic)
|
|
||||||
|
|
||||||
if self.accessor is None:
|
|
||||||
self.accessor = magic
|
|
||||||
|
|
||||||
if ((hasattr(stream, 'headers') and
|
|
||||||
hasattr(stream.headers, "keys") and
|
|
||||||
'Content-type' in stream.headers and
|
|
||||||
stream.headers['Content-type'].startswith('text/')) or
|
|
||||||
'b' not in magic.stream_mode):
|
|
||||||
self.accessor = io.TextIOWrapper(self.accessor)
|
|
||||||
|
|
||||||
|
|
||||||
def __getattr__(self,name):
|
|
||||||
return getattr(self.accessor, name)
|
|
||||||
|
|
||||||
def __iter__(self):
|
|
||||||
for x in self.accessor:
|
|
||||||
yield x
|
|
||||||
@ -1,5 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
from .uncompress cimport CompressedFile
|
|
||||||
|
|
||||||
cpdef CompressedFile uopen(str name, mode=?)
|
|
||||||
@ -1,23 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
'''
|
|
||||||
Created on 25 mars 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
from urllib.request import urlopen
|
|
||||||
|
|
||||||
|
|
||||||
cpdef CompressedFile uopen(str name, mode='r'):
|
|
||||||
cdef CompressedFile c
|
|
||||||
|
|
||||||
try:
|
|
||||||
f = urlopen(name)
|
|
||||||
except:
|
|
||||||
f = open(name,mode)
|
|
||||||
|
|
||||||
c = CompressedFile(f)
|
|
||||||
|
|
||||||
return c
|
|
||||||
|
|
||||||
@ -1,28 +1,7 @@
|
|||||||
../../../src/bloom.h
|
|
||||||
../../../src/bloom.c
|
|
||||||
../../../src/char_str_indexer.h
|
|
||||||
../../../src/char_str_indexer.c
|
|
||||||
../../../src/crc64.h
|
|
||||||
../../../src/crc64.c
|
|
||||||
../../../src/dna_seq_indexer.h
|
|
||||||
../../../src/dna_seq_indexer.c
|
|
||||||
../../../src/encode.h
|
|
||||||
../../../src/encode.c
|
|
||||||
../../../src/murmurhash2.h
|
|
||||||
../../../src/murmurhash2.c
|
|
||||||
../../../src/obiavl.h
|
|
||||||
../../../src/obiavl.c
|
|
||||||
../../../src/obiblob_indexer.h
|
|
||||||
../../../src/obiblob_indexer.c
|
|
||||||
../../../src/obiblob.h
|
|
||||||
../../../src/obiblob.c
|
|
||||||
../../../src/obidebug.h
|
|
||||||
../../../src/obidms_taxonomy.h
|
|
||||||
../../../src/obidms_taxonomy.c
|
|
||||||
../../../src/obidms.h
|
../../../src/obidms.h
|
||||||
../../../src/obidms.c
|
../../../src/obidms.c
|
||||||
../../../src/obidmscolumn_idx.h
|
../../../src/obiview.h
|
||||||
../../../src/obidmscolumn_idx.c
|
../../../src/obiview.c
|
||||||
../../../src/obidmscolumn.h
|
../../../src/obidmscolumn.h
|
||||||
../../../src/obidmscolumn.c
|
../../../src/obidmscolumn.c
|
||||||
../../../src/obidmscolumndir.h
|
../../../src/obidmscolumndir.h
|
||||||
@ -33,19 +12,13 @@
|
|||||||
../../../src/obilittlebigman.c
|
../../../src/obilittlebigman.c
|
||||||
../../../src/obitypes.h
|
../../../src/obitypes.h
|
||||||
../../../src/obitypes.c
|
../../../src/obitypes.c
|
||||||
../../../src/obiview.h
|
../../../src/private_at_functions.h
|
||||||
../../../src/obiview.c
|
../../../src/private_at_functions.c
|
||||||
../../../src/utils.h
|
../../../src/obiavl.h
|
||||||
../../../src/utils.c
|
../../../src/obiavl.c
|
||||||
../../../src/obidmscolumn_bool.c
|
../../../src/encode.h
|
||||||
../../../src/obidmscolumn_bool.h
|
../../../src/encode.c
|
||||||
../../../src/obidmscolumn_char.c
|
../../../src/obidmscolumn_idx.h
|
||||||
../../../src/obidmscolumn_char.h
|
../../../src/obidmscolumn_idx.c
|
||||||
../../../src/obidmscolumn_float.c
|
../../../src/obidms_taxonomy.c
|
||||||
../../../src/obidmscolumn_float.h
|
../../../src/obidms_taxonomy.h
|
||||||
../../../src/obidmscolumn_int.c
|
|
||||||
../../../src/obidmscolumn_int.h
|
|
||||||
../../../src/obidmscolumn_seq.c
|
|
||||||
../../../src/obidmscolumn_seq.h
|
|
||||||
../../../src/obidmscolumn_str.c
|
|
||||||
../../../src/obidmscolumn_str.h
|
|
||||||
|
|||||||
@ -56,7 +56,7 @@ cdef class OBIView:
|
|||||||
index_t nb_lines=*,
|
index_t nb_lines=*,
|
||||||
index_t nb_elements_per_line=*,
|
index_t nb_elements_per_line=*,
|
||||||
list elements_names=*,
|
list elements_names=*,
|
||||||
str indexer_name=*,
|
str avl_name=*,
|
||||||
str comments=*,
|
str comments=*,
|
||||||
bint create=*
|
bint create=*
|
||||||
)
|
)
|
||||||
@ -69,7 +69,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
|
|||||||
|
|
||||||
cdef OBIDMS_column ids
|
cdef OBIDMS_column ids
|
||||||
cdef OBIDMS_column sequences
|
cdef OBIDMS_column sequences
|
||||||
cdef OBIDMS_column definitions
|
cdef OBIDMS_column descriptions
|
||||||
|
|
||||||
cpdef delete_column(self, str column_name)
|
cpdef delete_column(self, str column_name)
|
||||||
|
|
||||||
|
|||||||
@ -5,11 +5,10 @@ from obitools3.utils cimport bytes2str, str2bytes
|
|||||||
from .capi.obidms cimport obi_dms, \
|
from .capi.obidms cimport obi_dms, \
|
||||||
obi_close_dms
|
obi_close_dms
|
||||||
|
|
||||||
from .capi.obidmscolumn cimport obi_close_column, \
|
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
|
||||||
|
obi_column_format_date, \
|
||||||
OBIDMS_column_p, \
|
OBIDMS_column_p, \
|
||||||
OBIDMS_column_header_p
|
OBIDMS_column_header_p
|
||||||
|
|
||||||
from .capi.obiutils cimport obi_format_date
|
|
||||||
|
|
||||||
from .capi.obitypes cimport const_char_p, \
|
from .capi.obitypes cimport const_char_p, \
|
||||||
OBIType_t, \
|
OBIType_t, \
|
||||||
@ -58,8 +57,8 @@ from .capi.obiview cimport Obiview_p, \
|
|||||||
obi_new_view_cloned_from_name, \
|
obi_new_view_cloned_from_name, \
|
||||||
obi_new_view_nuc_seqs_cloned_from_name, \
|
obi_new_view_nuc_seqs_cloned_from_name, \
|
||||||
obi_open_view, \
|
obi_open_view, \
|
||||||
obi_read_view_infos, \
|
obi_read_views, \
|
||||||
obi_close_view_infos, \
|
obi_unmap_read_views, \
|
||||||
obi_view_delete_column, \
|
obi_view_delete_column, \
|
||||||
obi_view_add_column, \
|
obi_view_add_column, \
|
||||||
obi_view_get_column, \
|
obi_view_get_column, \
|
||||||
@ -70,7 +69,7 @@ from .capi.obiview cimport Obiview_p, \
|
|||||||
VIEW_TYPE_NUC_SEQS, \
|
VIEW_TYPE_NUC_SEQS, \
|
||||||
NUC_SEQUENCE_COLUMN, \
|
NUC_SEQUENCE_COLUMN, \
|
||||||
ID_COLUMN, \
|
ID_COLUMN, \
|
||||||
DEFINITION_COLUMN
|
DESCRIPTION_COLUMN
|
||||||
|
|
||||||
from libc.stdlib cimport malloc
|
from libc.stdlib cimport malloc
|
||||||
from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
|
from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
|
||||||
@ -132,7 +131,7 @@ cdef class OBIDMS_column :
|
|||||||
return (self.pointer)[0].header.lines_used
|
return (self.pointer)[0].header.lines_used
|
||||||
|
|
||||||
cpdef str get_creation_date(self):
|
cpdef str get_creation_date(self):
|
||||||
return bytes2str(obi_format_date((self.pointer)[0].header.creation_date))
|
return bytes2str(obi_column_format_date((self.pointer)[0].header.creation_date))
|
||||||
|
|
||||||
cpdef str get_comments(self):
|
cpdef str get_comments(self):
|
||||||
return bytes2str((self.pointer)[0].header.comments)
|
return bytes2str((self.pointer)[0].header.comments)
|
||||||
@ -145,7 +144,7 @@ cdef class OBIDMS_column :
|
|||||||
return to_print
|
return to_print
|
||||||
|
|
||||||
cpdef close(self):
|
cpdef close(self):
|
||||||
if obi_close_column((self.pointer)[0]) < 0 :
|
if obi_truncate_and_close_column((self.pointer)[0]) < 0 :
|
||||||
raise Exception("Problem closing a column")
|
raise Exception("Problem closing a column")
|
||||||
|
|
||||||
|
|
||||||
@ -353,7 +352,7 @@ cdef class OBIView :
|
|||||||
index_t nb_lines=0,
|
index_t nb_lines=0,
|
||||||
index_t nb_elements_per_line=1, # TODO 1?
|
index_t nb_elements_per_line=1, # TODO 1?
|
||||||
list elements_names=None,
|
list elements_names=None,
|
||||||
str indexer_name="",
|
str avl_name="default_AVL_tree",
|
||||||
str comments="",
|
str comments="",
|
||||||
bint create=True # TODO
|
bint create=True # TODO
|
||||||
) :
|
) :
|
||||||
@ -389,7 +388,7 @@ cdef class OBIView :
|
|||||||
|
|
||||||
if (obi_view_add_column(self.pointer, column_name_b, version_number, # should return pointer on column?
|
if (obi_view_add_column(self.pointer, column_name_b, version_number, # should return pointer on column?
|
||||||
data_type, nb_lines, nb_elements_per_line,
|
data_type, nb_lines, nb_elements_per_line,
|
||||||
elements_names_b, str2bytes(indexer_name),
|
elements_names_b, str2bytes(avl_name),
|
||||||
str2bytes(comments), create) < 0) :
|
str2bytes(comments), create) < 0) :
|
||||||
raise Exception("Problem adding a column in a view")
|
raise Exception("Problem adding a column in a view")
|
||||||
|
|
||||||
@ -530,7 +529,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
|
|||||||
|
|
||||||
self.ids = self.columns[bytes2str(ID_COLUMN)]
|
self.ids = self.columns[bytes2str(ID_COLUMN)]
|
||||||
self.sequences = self.columns[bytes2str(NUC_SEQUENCE_COLUMN)]
|
self.sequences = self.columns[bytes2str(NUC_SEQUENCE_COLUMN)]
|
||||||
self.definitions = self.columns[bytes2str(DEFINITION_COLUMN)]
|
self.descriptions = self.columns[bytes2str(DESCRIPTION_COLUMN)]
|
||||||
|
|
||||||
|
|
||||||
cpdef delete_column(self, str column_name) :
|
cpdef delete_column(self, str column_name) :
|
||||||
@ -543,7 +542,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
|
|||||||
cdef OBIDMS_column_header_p header
|
cdef OBIDMS_column_header_p header
|
||||||
cdef str column_n
|
cdef str column_n
|
||||||
|
|
||||||
if ((column_name == bytes2str(ID_COLUMN)) or (column_name == bytes2str(NUC_SEQUENCE_COLUMN)) or (column_name == bytes2str(DEFINITION_COLUMN))) :
|
if ((column_name == bytes2str(ID_COLUMN)) or (column_name == bytes2str(NUC_SEQUENCE_COLUMN)) or (column_name == bytes2str(DESCRIPTION_COLUMN))) :
|
||||||
raise Exception("Can't delete an obligatory column from a NUC_SEQS view")
|
raise Exception("Can't delete an obligatory column from a NUC_SEQS view")
|
||||||
|
|
||||||
view = self.pointer
|
view = self.pointer
|
||||||
@ -704,7 +703,7 @@ cdef class OBIDMS :
|
|||||||
cdef bytes name_b
|
cdef bytes name_b
|
||||||
|
|
||||||
views = {}
|
views = {}
|
||||||
all_views_p = obi_read_view_infos(self.pointer)
|
all_views_p = obi_read_views(self.pointer)
|
||||||
if all_views_p == NULL :
|
if all_views_p == NULL :
|
||||||
raise Exception("No views to read")
|
raise Exception("No views to read")
|
||||||
nb_views = <int> (all_views_p.header).view_count
|
nb_views = <int> (all_views_p.header).view_count
|
||||||
@ -718,7 +717,7 @@ cdef class OBIDMS :
|
|||||||
views[view_name]["line_count"] = <int> view_p.line_count
|
views[view_name]["line_count"] = <int> view_p.line_count
|
||||||
views[view_name]["view_number"] = <int> view_p.view_number
|
views[view_name]["view_number"] = <int> view_p.view_number
|
||||||
views[view_name]["created_from"] = bytes2str(view_p.created_from)
|
views[view_name]["created_from"] = bytes2str(view_p.created_from)
|
||||||
views[view_name]["creation_date"] = bytes2str(obi_format_date(view_p.creation_date)) # TODO move this function in utils or somethings
|
views[view_name]["creation_date"] = bytes2str(obi_column_format_date(view_p.creation_date)) # TODO move this function in utils or somethings
|
||||||
if (view_p.all_lines) :
|
if (view_p.all_lines) :
|
||||||
views[view_name]["line_selection"] = None
|
views[view_name]["line_selection"] = None
|
||||||
else :
|
else :
|
||||||
@ -732,7 +731,7 @@ cdef class OBIDMS :
|
|||||||
views[view_name]["column_references"][column_name] = {}
|
views[view_name]["column_references"][column_name] = {}
|
||||||
views[view_name]["column_references"][column_name]["version"] = column_refs[j].version
|
views[view_name]["column_references"][column_name]["version"] = column_refs[j].version
|
||||||
|
|
||||||
obi_close_view_infos(all_views_p);
|
obi_unmap_read_views(all_views_p);
|
||||||
|
|
||||||
return views
|
return views
|
||||||
|
|
||||||
|
|||||||
@ -1,51 +1,20 @@
|
|||||||
../../../src/bloom.h
|
../../../src/obidmscolumn_bool.c
|
||||||
../../../src/bloom.c
|
../../../src/obidmscolumn_bool.h
|
||||||
../../../src/char_str_indexer.h
|
../../../src/obiview.h
|
||||||
../../../src/char_str_indexer.c
|
../../../src/obiview.c
|
||||||
../../../src/crc64.h
|
|
||||||
../../../src/crc64.c
|
|
||||||
../../../src/dna_seq_indexer.h
|
|
||||||
../../../src/dna_seq_indexer.c
|
|
||||||
../../../src/encode.h
|
|
||||||
../../../src/encode.c
|
|
||||||
../../../src/murmurhash2.h
|
|
||||||
../../../src/murmurhash2.c
|
|
||||||
../../../src/obiavl.h
|
|
||||||
../../../src/obiavl.c
|
|
||||||
../../../src/obiblob_indexer.h
|
|
||||||
../../../src/obiblob_indexer.c
|
|
||||||
../../../src/obiblob.h
|
|
||||||
../../../src/obiblob.c
|
|
||||||
../../../src/obidebug.h
|
|
||||||
../../../src/obidms_taxonomy.h
|
|
||||||
../../../src/obidms_taxonomy.c
|
|
||||||
../../../src/obidms.h
|
|
||||||
../../../src/obidms.c
|
|
||||||
../../../src/obidmscolumn_idx.h
|
|
||||||
../../../src/obidmscolumn_idx.c
|
|
||||||
../../../src/obidmscolumn.h
|
../../../src/obidmscolumn.h
|
||||||
../../../src/obidmscolumn.c
|
../../../src/obidmscolumn.c
|
||||||
../../../src/obidmscolumndir.h
|
../../../src/obidmscolumndir.h
|
||||||
../../../src/obidmscolumndir.c
|
../../../src/obidmscolumndir.c
|
||||||
|
../../../src/obidms.h
|
||||||
|
../../../src/obidms.c
|
||||||
../../../src/obierrno.h
|
../../../src/obierrno.h
|
||||||
../../../src/obierrno.c
|
../../../src/obierrno.c
|
||||||
../../../src/obilittlebigman.h
|
../../../src/obilittlebigman.h
|
||||||
../../../src/obilittlebigman.c
|
../../../src/obilittlebigman.c
|
||||||
../../../src/obitypes.h
|
../../../src/obitypes.h
|
||||||
../../../src/obitypes.c
|
../../../src/obitypes.c
|
||||||
../../../src/obiview.h
|
../../../src/private_at_functions.h
|
||||||
../../../src/obiview.c
|
../../../src/private_at_functions.c
|
||||||
../../../src/utils.h
|
../../../src/obiavl.h
|
||||||
../../../src/utils.c
|
../../../src/obiavl.c
|
||||||
../../../src/obidmscolumn_bool.c
|
|
||||||
../../../src/obidmscolumn_bool.h
|
|
||||||
../../../src/obidmscolumn_char.c
|
|
||||||
../../../src/obidmscolumn_char.h
|
|
||||||
../../../src/obidmscolumn_float.c
|
|
||||||
../../../src/obidmscolumn_float.h
|
|
||||||
../../../src/obidmscolumn_int.c
|
|
||||||
../../../src/obidmscolumn_int.h
|
|
||||||
../../../src/obidmscolumn_seq.c
|
|
||||||
../../../src/obidmscolumn_seq.h
|
|
||||||
../../../src/obidmscolumn_str.c
|
|
||||||
../../../src/obidmscolumn_str.h
|
|
||||||
|
|||||||
@ -1,6 +1,7 @@
|
|||||||
#cython: language_level=3
|
#cython: language_level=3
|
||||||
|
|
||||||
from .capi.obiview cimport obi_column_get_obibool_with_elt_name_in_view, \
|
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
|
||||||
|
obi_column_get_obibool_with_elt_name_in_view, \
|
||||||
obi_column_get_obibool_with_elt_idx_in_view, \
|
obi_column_get_obibool_with_elt_idx_in_view, \
|
||||||
obi_column_set_obibool_with_elt_name_in_view, \
|
obi_column_set_obibool_with_elt_name_in_view, \
|
||||||
obi_column_set_obibool_with_elt_idx_in_view
|
obi_column_set_obibool_with_elt_idx_in_view
|
||||||
|
|||||||
@ -1,51 +1,20 @@
|
|||||||
../../../src/bloom.h
|
../../../src/obidmscolumn_char.c
|
||||||
../../../src/bloom.c
|
../../../src/obidmscolumn_char.h
|
||||||
../../../src/char_str_indexer.h
|
../../../src/obiview.h
|
||||||
../../../src/char_str_indexer.c
|
../../../src/obiview.c
|
||||||
../../../src/crc64.h
|
|
||||||
../../../src/crc64.c
|
|
||||||
../../../src/dna_seq_indexer.h
|
|
||||||
../../../src/dna_seq_indexer.c
|
|
||||||
../../../src/encode.h
|
|
||||||
../../../src/encode.c
|
|
||||||
../../../src/murmurhash2.h
|
|
||||||
../../../src/murmurhash2.c
|
|
||||||
../../../src/obiavl.h
|
|
||||||
../../../src/obiavl.c
|
|
||||||
../../../src/obiblob_indexer.h
|
|
||||||
../../../src/obiblob_indexer.c
|
|
||||||
../../../src/obiblob.h
|
|
||||||
../../../src/obiblob.c
|
|
||||||
../../../src/obidebug.h
|
|
||||||
../../../src/obidms_taxonomy.h
|
|
||||||
../../../src/obidms_taxonomy.c
|
|
||||||
../../../src/obidms.h
|
|
||||||
../../../src/obidms.c
|
|
||||||
../../../src/obidmscolumn_idx.h
|
|
||||||
../../../src/obidmscolumn_idx.c
|
|
||||||
../../../src/obidmscolumn.h
|
../../../src/obidmscolumn.h
|
||||||
../../../src/obidmscolumn.c
|
../../../src/obidmscolumn.c
|
||||||
../../../src/obidmscolumndir.h
|
../../../src/obidmscolumndir.h
|
||||||
../../../src/obidmscolumndir.c
|
../../../src/obidmscolumndir.c
|
||||||
|
../../../src/obidms.h
|
||||||
|
../../../src/obidms.c
|
||||||
../../../src/obierrno.h
|
../../../src/obierrno.h
|
||||||
../../../src/obierrno.c
|
../../../src/obierrno.c
|
||||||
../../../src/obilittlebigman.h
|
../../../src/obilittlebigman.h
|
||||||
../../../src/obilittlebigman.c
|
../../../src/obilittlebigman.c
|
||||||
../../../src/obitypes.h
|
../../../src/obitypes.h
|
||||||
../../../src/obitypes.c
|
../../../src/obitypes.c
|
||||||
../../../src/obiview.h
|
../../../src/private_at_functions.h
|
||||||
../../../src/obiview.c
|
../../../src/private_at_functions.c
|
||||||
../../../src/utils.h
|
../../../src/obiavl.h
|
||||||
../../../src/utils.c
|
../../../src/obiavl.c
|
||||||
../../../src/obidmscolumn_bool.c
|
|
||||||
../../../src/obidmscolumn_bool.h
|
|
||||||
../../../src/obidmscolumn_char.c
|
|
||||||
../../../src/obidmscolumn_char.h
|
|
||||||
../../../src/obidmscolumn_float.c
|
|
||||||
../../../src/obidmscolumn_float.h
|
|
||||||
../../../src/obidmscolumn_int.c
|
|
||||||
../../../src/obidmscolumn_int.h
|
|
||||||
../../../src/obidmscolumn_seq.c
|
|
||||||
../../../src/obidmscolumn_seq.h
|
|
||||||
../../../src/obidmscolumn_str.c
|
|
||||||
../../../src/obidmscolumn_str.h
|
|
||||||
|
|||||||
@ -1,6 +1,7 @@
|
|||||||
#cython: language_level=3
|
#cython: language_level=3
|
||||||
|
|
||||||
from .capi.obiview cimport obi_column_get_obichar_with_elt_name_in_view, \
|
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
|
||||||
|
obi_column_get_obichar_with_elt_name_in_view, \
|
||||||
obi_column_get_obichar_with_elt_idx_in_view, \
|
obi_column_get_obichar_with_elt_idx_in_view, \
|
||||||
obi_column_set_obichar_with_elt_name_in_view, \
|
obi_column_set_obichar_with_elt_name_in_view, \
|
||||||
obi_column_set_obichar_with_elt_idx_in_view
|
obi_column_set_obichar_with_elt_idx_in_view
|
||||||
|
|||||||
@ -1,51 +1,20 @@
|
|||||||
../../../src/bloom.h
|
../../../src/obidmscolumn_float.c
|
||||||
../../../src/bloom.c
|
../../../src/obidmscolumn_float.h
|
||||||
../../../src/char_str_indexer.h
|
../../../src/obiview.h
|
||||||
../../../src/char_str_indexer.c
|
../../../src/obiview.c
|
||||||
../../../src/crc64.h
|
|
||||||
../../../src/crc64.c
|
|
||||||
../../../src/dna_seq_indexer.h
|
|
||||||
../../../src/dna_seq_indexer.c
|
|
||||||
../../../src/encode.h
|
|
||||||
../../../src/encode.c
|
|
||||||
../../../src/murmurhash2.h
|
|
||||||
../../../src/murmurhash2.c
|
|
||||||
../../../src/obiavl.h
|
|
||||||
../../../src/obiavl.c
|
|
||||||
../../../src/obiblob_indexer.h
|
|
||||||
../../../src/obiblob_indexer.c
|
|
||||||
../../../src/obiblob.h
|
|
||||||
../../../src/obiblob.c
|
|
||||||
../../../src/obidebug.h
|
|
||||||
../../../src/obidms_taxonomy.h
|
|
||||||
../../../src/obidms_taxonomy.c
|
|
||||||
../../../src/obidms.h
|
|
||||||
../../../src/obidms.c
|
|
||||||
../../../src/obidmscolumn_idx.h
|
|
||||||
../../../src/obidmscolumn_idx.c
|
|
||||||
../../../src/obidmscolumn.h
|
../../../src/obidmscolumn.h
|
||||||
../../../src/obidmscolumn.c
|
../../../src/obidmscolumn.c
|
||||||
../../../src/obidmscolumndir.h
|
../../../src/obidmscolumndir.h
|
||||||
../../../src/obidmscolumndir.c
|
../../../src/obidmscolumndir.c
|
||||||
|
../../../src/obidms.h
|
||||||
|
../../../src/obidms.c
|
||||||
../../../src/obierrno.h
|
../../../src/obierrno.h
|
||||||
../../../src/obierrno.c
|
../../../src/obierrno.c
|
||||||
../../../src/obilittlebigman.h
|
../../../src/obilittlebigman.h
|
||||||
../../../src/obilittlebigman.c
|
../../../src/obilittlebigman.c
|
||||||
../../../src/obitypes.h
|
../../../src/obitypes.h
|
||||||
../../../src/obitypes.c
|
../../../src/obitypes.c
|
||||||
../../../src/obiview.h
|
../../../src/private_at_functions.h
|
||||||
../../../src/obiview.c
|
../../../src/private_at_functions.c
|
||||||
../../../src/utils.h
|
../../../src/obiavl.h
|
||||||
../../../src/utils.c
|
../../../src/obiavl.c
|
||||||
../../../src/obidmscolumn_bool.c
|
|
||||||
../../../src/obidmscolumn_bool.h
|
|
||||||
../../../src/obidmscolumn_char.c
|
|
||||||
../../../src/obidmscolumn_char.h
|
|
||||||
../../../src/obidmscolumn_float.c
|
|
||||||
../../../src/obidmscolumn_float.h
|
|
||||||
../../../src/obidmscolumn_int.c
|
|
||||||
../../../src/obidmscolumn_int.h
|
|
||||||
../../../src/obidmscolumn_seq.c
|
|
||||||
../../../src/obidmscolumn_seq.h
|
|
||||||
../../../src/obidmscolumn_str.c
|
|
||||||
../../../src/obidmscolumn_str.h
|
|
||||||
|
|||||||
@ -1,6 +1,7 @@
|
|||||||
#cython: language_level=3
|
#cython: language_level=3
|
||||||
|
|
||||||
from .capi.obiview cimport obi_column_get_obifloat_with_elt_name_in_view, \
|
from .capi.obidmscolumn cimport obi_truncate_and_close_column,\
|
||||||
|
obi_column_get_obifloat_with_elt_name_in_view, \
|
||||||
obi_column_get_obifloat_with_elt_idx_in_view, \
|
obi_column_get_obifloat_with_elt_idx_in_view, \
|
||||||
obi_column_set_obifloat_with_elt_name_in_view, \
|
obi_column_set_obifloat_with_elt_name_in_view, \
|
||||||
obi_column_set_obifloat_with_elt_idx_in_view
|
obi_column_set_obifloat_with_elt_idx_in_view
|
||||||
|
|||||||
@ -1,51 +1,20 @@
|
|||||||
../../../src/bloom.h
|
../../../src/obidmscolumn_int.c
|
||||||
../../../src/bloom.c
|
../../../src/obidmscolumn_int.h
|
||||||
../../../src/char_str_indexer.h
|
../../../src/obiview.h
|
||||||
../../../src/char_str_indexer.c
|
../../../src/obiview.c
|
||||||
../../../src/crc64.h
|
|
||||||
../../../src/crc64.c
|
|
||||||
../../../src/dna_seq_indexer.h
|
|
||||||
../../../src/dna_seq_indexer.c
|
|
||||||
../../../src/encode.h
|
|
||||||
../../../src/encode.c
|
|
||||||
../../../src/murmurhash2.h
|
|
||||||
../../../src/murmurhash2.c
|
|
||||||
../../../src/obiavl.h
|
|
||||||
../../../src/obiavl.c
|
|
||||||
../../../src/obiblob_indexer.h
|
|
||||||
../../../src/obiblob_indexer.c
|
|
||||||
../../../src/obiblob.h
|
|
||||||
../../../src/obiblob.c
|
|
||||||
../../../src/obidebug.h
|
|
||||||
../../../src/obidms_taxonomy.h
|
|
||||||
../../../src/obidms_taxonomy.c
|
|
||||||
../../../src/obidms.h
|
|
||||||
../../../src/obidms.c
|
|
||||||
../../../src/obidmscolumn_idx.h
|
|
||||||
../../../src/obidmscolumn_idx.c
|
|
||||||
../../../src/obidmscolumn.h
|
../../../src/obidmscolumn.h
|
||||||
../../../src/obidmscolumn.c
|
../../../src/obidmscolumn.c
|
||||||
../../../src/obidmscolumndir.h
|
../../../src/obidmscolumndir.h
|
||||||
../../../src/obidmscolumndir.c
|
../../../src/obidmscolumndir.c
|
||||||
|
../../../src/obidms.h
|
||||||
|
../../../src/obidms.c
|
||||||
../../../src/obierrno.h
|
../../../src/obierrno.h
|
||||||
../../../src/obierrno.c
|
../../../src/obierrno.c
|
||||||
../../../src/obilittlebigman.h
|
../../../src/obilittlebigman.h
|
||||||
../../../src/obilittlebigman.c
|
../../../src/obilittlebigman.c
|
||||||
../../../src/obitypes.h
|
../../../src/obitypes.h
|
||||||
../../../src/obitypes.c
|
../../../src/obitypes.c
|
||||||
../../../src/obiview.h
|
../../../src/private_at_functions.h
|
||||||
../../../src/obiview.c
|
../../../src/private_at_functions.c
|
||||||
../../../src/utils.h
|
../../../src/obiavl.h
|
||||||
../../../src/utils.c
|
../../../src/obiavl.c
|
||||||
../../../src/obidmscolumn_bool.c
|
|
||||||
../../../src/obidmscolumn_bool.h
|
|
||||||
../../../src/obidmscolumn_char.c
|
|
||||||
../../../src/obidmscolumn_char.h
|
|
||||||
../../../src/obidmscolumn_float.c
|
|
||||||
../../../src/obidmscolumn_float.h
|
|
||||||
../../../src/obidmscolumn_int.c
|
|
||||||
../../../src/obidmscolumn_int.h
|
|
||||||
../../../src/obidmscolumn_seq.c
|
|
||||||
../../../src/obidmscolumn_seq.h
|
|
||||||
../../../src/obidmscolumn_str.c
|
|
||||||
../../../src/obidmscolumn_str.h
|
|
||||||
|
|||||||
@ -1,6 +1,7 @@
|
|||||||
#cython: language_level=3
|
#cython: language_level=3
|
||||||
|
|
||||||
from .capi.obiview cimport obi_column_get_obiint_with_elt_name_in_view, \
|
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
|
||||||
|
obi_column_get_obiint_with_elt_name_in_view, \
|
||||||
obi_column_get_obiint_with_elt_idx_in_view, \
|
obi_column_get_obiint_with_elt_idx_in_view, \
|
||||||
obi_column_set_obiint_with_elt_name_in_view, \
|
obi_column_set_obiint_with_elt_name_in_view, \
|
||||||
obi_column_set_obiint_with_elt_idx_in_view
|
obi_column_set_obiint_with_elt_idx_in_view
|
||||||
|
|||||||
@ -1,51 +1,20 @@
|
|||||||
../../../src/bloom.h
|
../../../src/obidmscolumn_seq.c
|
||||||
../../../src/bloom.c
|
../../../src/obidmscolumn_seq.h
|
||||||
../../../src/char_str_indexer.h
|
../../../src/obiview.h
|
||||||
../../../src/char_str_indexer.c
|
../../../src/obiview.c
|
||||||
../../../src/crc64.h
|
|
||||||
../../../src/crc64.c
|
|
||||||
../../../src/dna_seq_indexer.h
|
|
||||||
../../../src/dna_seq_indexer.c
|
|
||||||
../../../src/encode.h
|
|
||||||
../../../src/encode.c
|
|
||||||
../../../src/murmurhash2.h
|
|
||||||
../../../src/murmurhash2.c
|
|
||||||
../../../src/obiavl.h
|
|
||||||
../../../src/obiavl.c
|
|
||||||
../../../src/obiblob_indexer.h
|
|
||||||
../../../src/obiblob_indexer.c
|
|
||||||
../../../src/obiblob.h
|
|
||||||
../../../src/obiblob.c
|
|
||||||
../../../src/obidebug.h
|
|
||||||
../../../src/obidms_taxonomy.h
|
|
||||||
../../../src/obidms_taxonomy.c
|
|
||||||
../../../src/obidms.h
|
|
||||||
../../../src/obidms.c
|
|
||||||
../../../src/obidmscolumn_idx.h
|
|
||||||
../../../src/obidmscolumn_idx.c
|
|
||||||
../../../src/obidmscolumn.h
|
../../../src/obidmscolumn.h
|
||||||
../../../src/obidmscolumn.c
|
../../../src/obidmscolumn.c
|
||||||
../../../src/obidmscolumndir.h
|
../../../src/obidmscolumndir.h
|
||||||
../../../src/obidmscolumndir.c
|
../../../src/obidmscolumndir.c
|
||||||
|
../../../src/obidms.h
|
||||||
|
../../../src/obidms.c
|
||||||
../../../src/obierrno.h
|
../../../src/obierrno.h
|
||||||
../../../src/obierrno.c
|
../../../src/obierrno.c
|
||||||
../../../src/obilittlebigman.h
|
../../../src/obilittlebigman.h
|
||||||
../../../src/obilittlebigman.c
|
../../../src/obilittlebigman.c
|
||||||
../../../src/obitypes.h
|
../../../src/obitypes.h
|
||||||
../../../src/obitypes.c
|
../../../src/obitypes.c
|
||||||
../../../src/obiview.h
|
../../../src/private_at_functions.h
|
||||||
../../../src/obiview.c
|
../../../src/private_at_functions.c
|
||||||
../../../src/utils.h
|
../../../src/obiavl.h
|
||||||
../../../src/utils.c
|
../../../src/obiavl.c
|
||||||
../../../src/obidmscolumn_bool.c
|
|
||||||
../../../src/obidmscolumn_bool.h
|
|
||||||
../../../src/obidmscolumn_char.c
|
|
||||||
../../../src/obidmscolumn_char.h
|
|
||||||
../../../src/obidmscolumn_float.c
|
|
||||||
../../../src/obidmscolumn_float.h
|
|
||||||
../../../src/obidmscolumn_int.c
|
|
||||||
../../../src/obidmscolumn_int.h
|
|
||||||
../../../src/obidmscolumn_seq.c
|
|
||||||
../../../src/obidmscolumn_seq.h
|
|
||||||
../../../src/obidmscolumn_str.c
|
|
||||||
../../../src/obidmscolumn_str.h
|
|
||||||
|
|||||||
@ -1,6 +1,7 @@
|
|||||||
#cython: language_level=3
|
#cython: language_level=3
|
||||||
|
|
||||||
from .capi.obiview cimport obi_column_get_obiseq_with_elt_name_in_view, \
|
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
|
||||||
|
obi_column_get_obiseq_with_elt_name_in_view, \
|
||||||
obi_column_get_obiseq_with_elt_idx_in_view, \
|
obi_column_get_obiseq_with_elt_idx_in_view, \
|
||||||
obi_column_set_obiseq_with_elt_name_in_view, \
|
obi_column_set_obiseq_with_elt_name_in_view, \
|
||||||
obi_column_set_obiseq_with_elt_idx_in_view
|
obi_column_set_obiseq_with_elt_idx_in_view
|
||||||
@ -9,23 +10,19 @@ from .capi.obitypes cimport OBISeq_NA, const_char_p
|
|||||||
|
|
||||||
from obitools3.utils cimport str2bytes, bytes2str
|
from obitools3.utils cimport str2bytes, bytes2str
|
||||||
|
|
||||||
from libc.stdlib cimport free
|
|
||||||
from libc.string cimport strcmp
|
|
||||||
|
|
||||||
|
|
||||||
cdef class OBIDMS_column_seq(OBIDMS_column):
|
cdef class OBIDMS_column_seq(OBIDMS_column):
|
||||||
|
|
||||||
cpdef object get_line(self, index_t line_nb):
|
cpdef object get_line(self, index_t line_nb):
|
||||||
cdef char* value
|
cdef bytes value
|
||||||
cdef object result
|
cdef object result
|
||||||
value = obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
|
value = <bytes> obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
|
||||||
if obi_errno > 0 :
|
if obi_errno > 0 :
|
||||||
raise IndexError(line_nb)
|
raise IndexError(line_nb)
|
||||||
if strcmp(value, OBISeq_NA) == 0 :
|
if value == OBISeq_NA : # TODO
|
||||||
result = None
|
result = None
|
||||||
else :
|
else :
|
||||||
result = bytes2str(value)
|
result = bytes2str(value)
|
||||||
free(value)
|
|
||||||
return result
|
return result
|
||||||
|
|
||||||
cpdef set_line(self, index_t line_nb, object value):
|
cpdef set_line(self, index_t line_nb, object value):
|
||||||
@ -41,35 +38,33 @@ cdef class OBIDMS_column_seq(OBIDMS_column):
|
|||||||
cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
|
cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
|
||||||
|
|
||||||
cpdef object get_item(self, index_t line_nb, str element_name):
|
cpdef object get_item(self, index_t line_nb, str element_name):
|
||||||
cdef char* value
|
cdef bytes value
|
||||||
cdef object result
|
cdef object result
|
||||||
value = obi_column_get_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
|
value = <bytes> obi_column_get_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||||
if obi_errno > 0 :
|
if obi_errno > 0 :
|
||||||
raise IndexError(line_nb, element_name)
|
raise IndexError(line_nb, element_name)
|
||||||
if strcmp(value, OBISeq_NA) == 0 :
|
if value == OBISeq_NA :
|
||||||
result = None
|
result = None
|
||||||
else :
|
else :
|
||||||
result = bytes2str(value)
|
result = bytes2str(value)
|
||||||
free(value)
|
|
||||||
return result
|
return result
|
||||||
|
|
||||||
cpdef object get_line(self, index_t line_nb) :
|
cpdef object get_line(self, index_t line_nb) :
|
||||||
cdef char* value
|
cdef bytes value
|
||||||
cdef object value_in_result
|
cdef object value_in_result
|
||||||
cdef dict result
|
cdef dict result
|
||||||
cdef index_t i
|
cdef index_t i
|
||||||
cdef bint all_NA
|
cdef bint all_NA
|
||||||
result = {}
|
result = {}
|
||||||
all_NA = True
|
all_NA = True
|
||||||
for i in range(self.nb_elements_per_line) :
|
for i in range(self.nb_elements_per_line) :
|
||||||
value = obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
|
value = <bytes> obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
|
||||||
if obi_errno > 0 :
|
if obi_errno > 0 :
|
||||||
raise IndexError(line_nb)
|
raise IndexError(line_nb)
|
||||||
if strcmp(value, OBISeq_NA) == 0 :
|
if value == OBISeq_NA :
|
||||||
value_in_result = None
|
value_in_result = None
|
||||||
else :
|
else :
|
||||||
value_in_result = bytes2str(value)
|
value_in_result = bytes2str(value)
|
||||||
free(value)
|
|
||||||
result[self.elements_names[i]] = value_in_result
|
result[self.elements_names[i]] = value_in_result
|
||||||
if all_NA and (value_in_result is not None) :
|
if all_NA and (value_in_result is not None) :
|
||||||
all_NA = False
|
all_NA = False
|
||||||
|
|||||||
@ -1,51 +1,20 @@
|
|||||||
../../../src/bloom.h
|
../../../src/obidmscolumn_str.c
|
||||||
../../../src/bloom.c
|
../../../src/obidmscolumn_str.h
|
||||||
../../../src/char_str_indexer.h
|
../../../src/obiview.h
|
||||||
../../../src/char_str_indexer.c
|
../../../src/obiview.c
|
||||||
../../../src/crc64.h
|
|
||||||
../../../src/crc64.c
|
|
||||||
../../../src/dna_seq_indexer.h
|
|
||||||
../../../src/dna_seq_indexer.c
|
|
||||||
../../../src/encode.h
|
|
||||||
../../../src/encode.c
|
|
||||||
../../../src/murmurhash2.h
|
|
||||||
../../../src/murmurhash2.c
|
|
||||||
../../../src/obiavl.h
|
|
||||||
../../../src/obiavl.c
|
|
||||||
../../../src/obiblob_indexer.h
|
|
||||||
../../../src/obiblob_indexer.c
|
|
||||||
../../../src/obiblob.h
|
|
||||||
../../../src/obiblob.c
|
|
||||||
../../../src/obidebug.h
|
|
||||||
../../../src/obidms_taxonomy.h
|
|
||||||
../../../src/obidms_taxonomy.c
|
|
||||||
../../../src/obidms.h
|
|
||||||
../../../src/obidms.c
|
|
||||||
../../../src/obidmscolumn_idx.h
|
|
||||||
../../../src/obidmscolumn_idx.c
|
|
||||||
../../../src/obidmscolumn.h
|
../../../src/obidmscolumn.h
|
||||||
../../../src/obidmscolumn.c
|
../../../src/obidmscolumn.c
|
||||||
../../../src/obidmscolumndir.h
|
../../../src/obidmscolumndir.h
|
||||||
../../../src/obidmscolumndir.c
|
../../../src/obidmscolumndir.c
|
||||||
|
../../../src/obidms.h
|
||||||
|
../../../src/obidms.c
|
||||||
../../../src/obierrno.h
|
../../../src/obierrno.h
|
||||||
../../../src/obierrno.c
|
../../../src/obierrno.c
|
||||||
../../../src/obilittlebigman.h
|
../../../src/obilittlebigman.h
|
||||||
../../../src/obilittlebigman.c
|
../../../src/obilittlebigman.c
|
||||||
../../../src/obitypes.h
|
../../../src/obitypes.h
|
||||||
../../../src/obitypes.c
|
../../../src/obitypes.c
|
||||||
../../../src/obiview.h
|
../../../src/private_at_functions.h
|
||||||
../../../src/obiview.c
|
../../../src/private_at_functions.c
|
||||||
../../../src/utils.h
|
../../../src/obiavl.h
|
||||||
../../../src/utils.c
|
../../../src/obiavl.c
|
||||||
../../../src/obidmscolumn_bool.c
|
|
||||||
../../../src/obidmscolumn_bool.h
|
|
||||||
../../../src/obidmscolumn_char.c
|
|
||||||
../../../src/obidmscolumn_char.h
|
|
||||||
../../../src/obidmscolumn_float.c
|
|
||||||
../../../src/obidmscolumn_float.h
|
|
||||||
../../../src/obidmscolumn_int.c
|
|
||||||
../../../src/obidmscolumn_int.h
|
|
||||||
../../../src/obidmscolumn_seq.c
|
|
||||||
../../../src/obidmscolumn_seq.h
|
|
||||||
../../../src/obidmscolumn_str.c
|
|
||||||
../../../src/obidmscolumn_str.h
|
|
||||||
|
|||||||
@ -1,6 +1,7 @@
|
|||||||
#cython: language_level=3
|
#cython: language_level=3
|
||||||
|
|
||||||
from .capi.obiview cimport obi_column_get_obistr_with_elt_name_in_view, \
|
from .capi.obidmscolumn cimport obi_truncate_and_close_column, \
|
||||||
|
obi_column_get_obistr_with_elt_name_in_view, \
|
||||||
obi_column_get_obistr_with_elt_idx_in_view, \
|
obi_column_get_obistr_with_elt_idx_in_view, \
|
||||||
obi_column_set_obistr_with_elt_name_in_view, \
|
obi_column_set_obistr_with_elt_name_in_view, \
|
||||||
obi_column_set_obistr_with_elt_idx_in_view
|
obi_column_set_obistr_with_elt_idx_in_view
|
||||||
@ -9,22 +10,19 @@ from .capi.obitypes cimport OBIStr_NA, const_char_p
|
|||||||
|
|
||||||
from obitools3.utils cimport str2bytes, bytes2str
|
from obitools3.utils cimport str2bytes, bytes2str
|
||||||
|
|
||||||
from libc.string cimport strcmp
|
|
||||||
|
|
||||||
|
|
||||||
cdef class OBIDMS_column_str(OBIDMS_column):
|
cdef class OBIDMS_column_str(OBIDMS_column):
|
||||||
|
|
||||||
cpdef object get_line(self, index_t line_nb):
|
cpdef object get_line(self, index_t line_nb):
|
||||||
cdef const_char_p value
|
cdef bytes value
|
||||||
cdef object result
|
cdef object result
|
||||||
value = obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
|
value = <bytes> obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
|
||||||
if obi_errno > 0 :
|
if obi_errno > 0 :
|
||||||
raise IndexError(line_nb)
|
raise IndexError(line_nb)
|
||||||
if strcmp(value, OBIStr_NA) == 0 :
|
if value == OBIStr_NA : # TODO
|
||||||
result = None
|
result = None
|
||||||
else :
|
else :
|
||||||
result = bytes2str(value)
|
result = bytes2str(value)
|
||||||
# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
|
|
||||||
return result
|
return result
|
||||||
|
|
||||||
cpdef set_line(self, index_t line_nb, object value):
|
cpdef set_line(self, index_t line_nb, object value):
|
||||||
@ -40,35 +38,33 @@ cdef class OBIDMS_column_str(OBIDMS_column):
|
|||||||
cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
|
cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
|
||||||
|
|
||||||
cpdef object get_item(self, index_t line_nb, str element_name):
|
cpdef object get_item(self, index_t line_nb, str element_name):
|
||||||
cdef const_char_p value
|
cdef bytes value
|
||||||
cdef object result
|
cdef object result
|
||||||
value = obi_column_get_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
|
value = <bytes> obi_column_get_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||||
if obi_errno > 0 :
|
if obi_errno > 0 :
|
||||||
raise IndexError(line_nb, element_name)
|
raise IndexError(line_nb, element_name)
|
||||||
if strcmp(value, OBIStr_NA) == 0 :
|
if value == OBIStr_NA :
|
||||||
result = None
|
result = None
|
||||||
else :
|
else :
|
||||||
result = bytes2str(value)
|
result = bytes2str(value)
|
||||||
# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
|
|
||||||
return result
|
return result
|
||||||
|
|
||||||
cpdef object get_line(self, index_t line_nb) :
|
cpdef object get_line(self, index_t line_nb) :
|
||||||
cdef const_char_p value
|
cdef bytes value
|
||||||
cdef object value_in_result
|
cdef object value_in_result
|
||||||
cdef dict result
|
cdef dict result
|
||||||
cdef index_t i
|
cdef index_t i
|
||||||
cdef bint all_NA
|
cdef bint all_NA
|
||||||
result = {}
|
result = {}
|
||||||
all_NA = True
|
all_NA = True
|
||||||
for i in range(self.nb_elements_per_line) :
|
for i in range(self.nb_elements_per_line) :
|
||||||
value = obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
|
value = <bytes> obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
|
||||||
if obi_errno > 0 :
|
if obi_errno > 0 :
|
||||||
raise IndexError(line_nb)
|
raise IndexError(line_nb)
|
||||||
if strcmp(value, OBIStr_NA) == 0 :
|
if value == OBIStr_NA :
|
||||||
value_in_result = None
|
value_in_result = None
|
||||||
else :
|
else :
|
||||||
value_in_result = bytes2str(value)
|
value_in_result = bytes2str(value)
|
||||||
# NOTE: value is not freed because the pointer points to a mmapped region in an AVL data file. (TODO discuss)
|
|
||||||
result[self.elements_names[i]] = value_in_result
|
result[self.elements_names[i]] = value_in_result
|
||||||
if all_NA and (value_in_result is not None) :
|
if all_NA and (value_in_result is not None) :
|
||||||
all_NA = False
|
all_NA = False
|
||||||
|
|||||||
@ -1,28 +1,7 @@
|
|||||||
../../../src/bloom.h
|
|
||||||
../../../src/bloom.c
|
|
||||||
../../../src/char_str_indexer.h
|
|
||||||
../../../src/char_str_indexer.c
|
|
||||||
../../../src/crc64.h
|
|
||||||
../../../src/crc64.c
|
|
||||||
../../../src/dna_seq_indexer.h
|
|
||||||
../../../src/dna_seq_indexer.c
|
|
||||||
../../../src/encode.h
|
|
||||||
../../../src/encode.c
|
|
||||||
../../../src/murmurhash2.h
|
|
||||||
../../../src/murmurhash2.c
|
|
||||||
../../../src/obiavl.h
|
|
||||||
../../../src/obiavl.c
|
|
||||||
../../../src/obiblob_indexer.h
|
|
||||||
../../../src/obiblob_indexer.c
|
|
||||||
../../../src/obiblob.h
|
|
||||||
../../../src/obiblob.c
|
|
||||||
../../../src/obidebug.h
|
|
||||||
../../../src/obidms_taxonomy.h
|
|
||||||
../../../src/obidms_taxonomy.c
|
|
||||||
../../../src/obidms.h
|
../../../src/obidms.h
|
||||||
../../../src/obidms.c
|
../../../src/obidms.c
|
||||||
../../../src/obidmscolumn_idx.h
|
../../../src/obiview.h
|
||||||
../../../src/obidmscolumn_idx.c
|
../../../src/obiview.c
|
||||||
../../../src/obidmscolumn.h
|
../../../src/obidmscolumn.h
|
||||||
../../../src/obidmscolumn.c
|
../../../src/obidmscolumn.c
|
||||||
../../../src/obidmscolumndir.h
|
../../../src/obidmscolumndir.h
|
||||||
@ -33,19 +12,11 @@
|
|||||||
../../../src/obilittlebigman.c
|
../../../src/obilittlebigman.c
|
||||||
../../../src/obitypes.h
|
../../../src/obitypes.h
|
||||||
../../../src/obitypes.c
|
../../../src/obitypes.c
|
||||||
../../../src/obiview.h
|
../../../src/private_at_functions.h
|
||||||
../../../src/obiview.c
|
../../../src/private_at_functions.c
|
||||||
../../../src/utils.h
|
../../../src/obiavl.h
|
||||||
../../../src/utils.c
|
../../../src/obiavl.c
|
||||||
../../../src/obidmscolumn_bool.c
|
../../../src/encode.h
|
||||||
../../../src/obidmscolumn_bool.h
|
../../../src/encode.c
|
||||||
../../../src/obidmscolumn_char.c
|
../../../src/obidmscolumn_idx.h
|
||||||
../../../src/obidmscolumn_char.h
|
../../../src/obidmscolumn_idx.c
|
||||||
../../../src/obidmscolumn_float.c
|
|
||||||
../../../src/obidmscolumn_float.h
|
|
||||||
../../../src/obidmscolumn_int.c
|
|
||||||
../../../src/obidmscolumn_int.h
|
|
||||||
../../../src/obidmscolumn_seq.c
|
|
||||||
../../../src/obidmscolumn_seq.h
|
|
||||||
../../../src/obidmscolumn_str.c
|
|
||||||
../../../src/obidmscolumn_str.h
|
|
||||||
|
|||||||
@ -5,13 +5,13 @@ from ._obidms cimport OBIView_line
|
|||||||
|
|
||||||
cdef class OBI_Seq(dict) :
|
cdef class OBI_Seq(dict) :
|
||||||
cdef str id
|
cdef str id
|
||||||
cdef str definition
|
cdef str description
|
||||||
cdef str sequence
|
cdef str sequence
|
||||||
|
|
||||||
cpdef set_id(self, str id)
|
cpdef set_id(self, str id)
|
||||||
cpdef get_id(self)
|
cpdef get_id(self)
|
||||||
cpdef set_definition(self, str definition)
|
cpdef set_description(self, str description)
|
||||||
cpdef get_definition(self)
|
cpdef get_description(self)
|
||||||
cpdef get_sequence(self)
|
cpdef get_sequence(self)
|
||||||
|
|
||||||
|
|
||||||
@ -21,10 +21,14 @@ cdef class OBI_Nuc_Seq(OBI_Seq) :
|
|||||||
|
|
||||||
|
|
||||||
cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
|
cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
|
||||||
|
cdef str id
|
||||||
|
cdef str description
|
||||||
|
cdef str sequence
|
||||||
|
|
||||||
cpdef set_id(self, str id)
|
cpdef set_id(self, str id)
|
||||||
cpdef get_id(self)
|
cpdef get_id(self)
|
||||||
cpdef set_definition(self, str definition)
|
cpdef set_description(self, str description)
|
||||||
cpdef get_definition(self)
|
cpdef get_description(self)
|
||||||
cpdef set_sequence(self, str sequence)
|
cpdef set_sequence(self, str sequence)
|
||||||
cpdef get_sequence(self)
|
cpdef get_sequence(self)
|
||||||
# cpdef str reverse_complement(self)
|
# cpdef str reverse_complement(self)
|
||||||
|
|||||||
@ -4,15 +4,15 @@ from obitools3.utils cimport bytes2str, str2bytes
|
|||||||
|
|
||||||
from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
|
from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
|
||||||
ID_COLUMN, \
|
ID_COLUMN, \
|
||||||
DEFINITION_COLUMN
|
DESCRIPTION_COLUMN
|
||||||
|
|
||||||
cdef class OBI_Seq(dict) :
|
cdef class OBI_Seq(dict) :
|
||||||
|
|
||||||
def __init__(self, str id, str seq, str definition=None) :
|
def __init__(self, str id, str seq, str description=None) :
|
||||||
self.set_id(id)
|
self.set_id(id)
|
||||||
self.set_sequence(seq)
|
self.set_sequence(seq)
|
||||||
if definition is not None :
|
if description is not None :
|
||||||
self.set_definition(definition)
|
self.set_description(description)
|
||||||
|
|
||||||
cpdef set_id(self, str id) :
|
cpdef set_id(self, str id) :
|
||||||
self.id = id
|
self.id = id
|
||||||
@ -21,12 +21,12 @@ cdef class OBI_Seq(dict) :
|
|||||||
cpdef get_id(self) :
|
cpdef get_id(self) :
|
||||||
return self.id
|
return self.id
|
||||||
|
|
||||||
cpdef set_definition(self, str definition) :
|
cpdef set_description(self, str description) :
|
||||||
self.definition = definition
|
self.description = description
|
||||||
self[bytes2str(DEFINITION_COLUMN)] = definition
|
self[bytes2str(DESCRIPTION_COLUMN)] = description
|
||||||
|
|
||||||
cpdef get_definition(self) :
|
cpdef get_description(self) :
|
||||||
return self.definition
|
return self.description
|
||||||
|
|
||||||
cpdef get_sequence(self) :
|
cpdef get_sequence(self) :
|
||||||
return self.sequence
|
return self.sequence
|
||||||
@ -48,25 +48,28 @@ cdef class OBI_Nuc_Seq(OBI_Seq) :
|
|||||||
cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
|
cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
|
||||||
|
|
||||||
cpdef set_id(self, str id) :
|
cpdef set_id(self, str id) :
|
||||||
|
self.id = id
|
||||||
self[bytes2str(ID_COLUMN)] = id
|
self[bytes2str(ID_COLUMN)] = id
|
||||||
|
|
||||||
cpdef get_id(self) :
|
cpdef get_id(self) :
|
||||||
return self[bytes2str(ID_COLUMN)]
|
return self.id
|
||||||
|
|
||||||
cpdef set_definition(self, str definition) :
|
cpdef set_description(self, str description) :
|
||||||
self[bytes2str(DEFINITION_COLUMN)] = definition
|
self.description = description
|
||||||
|
self[bytes2str(DESCRIPTION_COLUMN)] = description
|
||||||
|
|
||||||
cpdef get_definition(self) :
|
cpdef get_description(self) :
|
||||||
return self[bytes2str(DEFINITION_COLUMN)]
|
return self.description
|
||||||
|
|
||||||
cpdef set_sequence(self, str sequence) :
|
cpdef set_sequence(self, str sequence) :
|
||||||
|
self.sequence = sequence
|
||||||
self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
|
self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
|
||||||
|
|
||||||
cpdef get_sequence(self) :
|
cpdef get_sequence(self) :
|
||||||
return self[bytes2str(NUC_SEQUENCE_COLUMN)]
|
return self.sequence
|
||||||
|
|
||||||
# def __str__(self) :
|
def __str__(self) :
|
||||||
# return self[bytes2str(NUC_SEQUENCE_COLUMN)] # or not
|
return self.sequence # or not
|
||||||
|
|
||||||
# cpdef str reverse_complement(self) : TODO in C ?
|
# cpdef str reverse_complement(self) : TODO in C ?
|
||||||
# pass
|
# pass
|
||||||
|
|||||||
@ -1,28 +1,7 @@
|
|||||||
../../../src/bloom.h
|
|
||||||
../../../src/bloom.c
|
|
||||||
../../../src/char_str_indexer.h
|
|
||||||
../../../src/char_str_indexer.c
|
|
||||||
../../../src/crc64.h
|
|
||||||
../../../src/crc64.c
|
|
||||||
../../../src/dna_seq_indexer.h
|
|
||||||
../../../src/dna_seq_indexer.c
|
|
||||||
../../../src/encode.h
|
|
||||||
../../../src/encode.c
|
|
||||||
../../../src/murmurhash2.h
|
|
||||||
../../../src/murmurhash2.c
|
|
||||||
../../../src/obiavl.h
|
|
||||||
../../../src/obiavl.c
|
|
||||||
../../../src/obiblob_indexer.h
|
|
||||||
../../../src/obiblob_indexer.c
|
|
||||||
../../../src/obiblob.h
|
|
||||||
../../../src/obiblob.c
|
|
||||||
../../../src/obidebug.h
|
|
||||||
../../../src/obidms_taxonomy.h
|
|
||||||
../../../src/obidms_taxonomy.c
|
|
||||||
../../../src/obidms.h
|
../../../src/obidms.h
|
||||||
../../../src/obidms.c
|
../../../src/obidms.c
|
||||||
../../../src/obidmscolumn_idx.h
|
../../../src/obiview.h
|
||||||
../../../src/obidmscolumn_idx.c
|
../../../src/obiview.c
|
||||||
../../../src/obidmscolumn.h
|
../../../src/obidmscolumn.h
|
||||||
../../../src/obidmscolumn.c
|
../../../src/obidmscolumn.c
|
||||||
../../../src/obidmscolumndir.h
|
../../../src/obidmscolumndir.h
|
||||||
@ -33,19 +12,13 @@
|
|||||||
../../../src/obilittlebigman.c
|
../../../src/obilittlebigman.c
|
||||||
../../../src/obitypes.h
|
../../../src/obitypes.h
|
||||||
../../../src/obitypes.c
|
../../../src/obitypes.c
|
||||||
../../../src/obiview.h
|
../../../src/private_at_functions.h
|
||||||
../../../src/obiview.c
|
../../../src/private_at_functions.c
|
||||||
../../../src/utils.h
|
../../../src/obiavl.h
|
||||||
../../../src/utils.c
|
../../../src/obiavl.c
|
||||||
../../../src/obidmscolumn_bool.c
|
../../../src/encode.h
|
||||||
../../../src/obidmscolumn_bool.h
|
../../../src/encode.c
|
||||||
../../../src/obidmscolumn_char.c
|
../../../src/obidmscolumn_idx.h
|
||||||
../../../src/obidmscolumn_char.h
|
../../../src/obidmscolumn_idx.c
|
||||||
../../../src/obidmscolumn_float.c
|
../../../src/obidms_taxonomy.c
|
||||||
../../../src/obidmscolumn_float.h
|
../../../src/obidms_taxonomy.h
|
||||||
../../../src/obidmscolumn_int.c
|
|
||||||
../../../src/obidmscolumn_int.h
|
|
||||||
../../../src/obidmscolumn_seq.c
|
|
||||||
../../../src/obidmscolumn_seq.h
|
|
||||||
../../../src/obidmscolumn_str.c
|
|
||||||
../../../src/obidmscolumn_str.h
|
|
||||||
|
|||||||
@ -27,7 +27,7 @@ cdef extern from "obidmscolumn.h" nogil:
|
|||||||
obiversion_t version
|
obiversion_t version
|
||||||
obiversion_t cloned_from
|
obiversion_t cloned_from
|
||||||
const_char_p name
|
const_char_p name
|
||||||
const_char_p indexer_name
|
const_char_p avl_name
|
||||||
const_char_p comments
|
const_char_p comments
|
||||||
|
|
||||||
ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
|
ctypedef OBIDMS_column_header_t* OBIDMS_column_header_p
|
||||||
@ -45,7 +45,7 @@ cdef extern from "obidmscolumn.h" nogil:
|
|||||||
index_t nb_lines,
|
index_t nb_lines,
|
||||||
index_t nb_elements_per_line,
|
index_t nb_elements_per_line,
|
||||||
const_char_p elements_names,
|
const_char_p elements_names,
|
||||||
const_char_p indexer_name,
|
const_char_p avl_name,
|
||||||
const_char_p comments)
|
const_char_p comments)
|
||||||
|
|
||||||
OBIDMS_column_p obi_open_column(OBIDMS_p dms,
|
OBIDMS_column_p obi_open_column(OBIDMS_p dms,
|
||||||
@ -60,7 +60,7 @@ cdef extern from "obidmscolumn.h" nogil:
|
|||||||
obiversion_t version_number,
|
obiversion_t version_number,
|
||||||
bint clone_data)
|
bint clone_data)
|
||||||
|
|
||||||
int obi_close_column(OBIDMS_column_p column)
|
int obi_truncate_and_close_column(OBIDMS_column_p column)
|
||||||
|
|
||||||
obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms,
|
obiversion_t obi_column_get_latest_version_from_name(OBIDMS_p dms,
|
||||||
const_char_p column_name)
|
const_char_p column_name)
|
||||||
@ -69,12 +69,37 @@ cdef extern from "obidmscolumn.h" nogil:
|
|||||||
const_char_p column_name,
|
const_char_p column_name,
|
||||||
obiversion_t version_number)
|
obiversion_t version_number)
|
||||||
|
|
||||||
int obi_close_header(OBIDMS_column_header_p header)
|
int obi_unmap_header(OBIDMS_column_header_p header)
|
||||||
|
|
||||||
|
char* obi_column_format_date(time_t date)
|
||||||
|
|
||||||
int obi_select(OBIDMS_column_p line_selection_column, index_t line_to_grep)
|
int obi_select(OBIDMS_column_p line_selection_column, index_t line_to_grep)
|
||||||
|
|
||||||
|
|
||||||
|
from ..capi.obiview cimport Obiview_p # TODO
|
||||||
|
|
||||||
cdef extern from "obidmscolumn_int.h" nogil:
|
cdef extern from "obidmscolumn_int.h" nogil:
|
||||||
|
int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
const_char_p element_name,
|
||||||
|
obiint_t value)
|
||||||
|
|
||||||
|
int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
index_t element_idx,
|
||||||
|
obiint_t value)
|
||||||
|
|
||||||
|
obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
const_char_p element_name)
|
||||||
|
|
||||||
|
obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
index_t element_idx)
|
||||||
|
|
||||||
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column,
|
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
@ -96,6 +121,28 @@ cdef extern from "obidmscolumn_int.h" nogil:
|
|||||||
|
|
||||||
cdef extern from "obidmscolumn_bool.h" nogil:
|
cdef extern from "obidmscolumn_bool.h" nogil:
|
||||||
|
|
||||||
|
int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
const_char_p element_name,
|
||||||
|
obibool_t value)
|
||||||
|
|
||||||
|
int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
index_t element_idx,
|
||||||
|
obibool_t value)
|
||||||
|
|
||||||
|
obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
const_char_p element_name)
|
||||||
|
|
||||||
|
obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
index_t element_idx)
|
||||||
|
|
||||||
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column,
|
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
const_char_p element_name,
|
const_char_p element_name,
|
||||||
@ -116,6 +163,28 @@ cdef extern from "obidmscolumn_bool.h" nogil:
|
|||||||
|
|
||||||
cdef extern from "obidmscolumn_char.h" nogil:
|
cdef extern from "obidmscolumn_char.h" nogil:
|
||||||
|
|
||||||
|
int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
const_char_p element_name,
|
||||||
|
obichar_t value)
|
||||||
|
|
||||||
|
int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
index_t element_idx,
|
||||||
|
obichar_t value)
|
||||||
|
|
||||||
|
obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
const_char_p element_name)
|
||||||
|
|
||||||
|
obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
index_t element_idx)
|
||||||
|
|
||||||
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column,
|
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
const_char_p element_name,
|
const_char_p element_name,
|
||||||
@ -136,39 +205,83 @@ cdef extern from "obidmscolumn_char.h" nogil:
|
|||||||
|
|
||||||
cdef extern from "obidmscolumn_float.h" nogil:
|
cdef extern from "obidmscolumn_float.h" nogil:
|
||||||
|
|
||||||
|
int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
const_char_p element_name,
|
||||||
|
obifloat_t value)
|
||||||
|
|
||||||
|
int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
index_t element_idx,
|
||||||
|
obifloat_t value)
|
||||||
|
|
||||||
|
obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
const_char_p element_name)
|
||||||
|
|
||||||
|
obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
index_t element_idx)
|
||||||
|
|
||||||
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column,
|
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
const_char_p element_name,
|
const_char_p element_name,
|
||||||
obifloat_t value)
|
obifloat_t value)
|
||||||
|
|
||||||
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column,
|
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
index_t element_idx,
|
index_t element_idx,
|
||||||
obifloat_t value)
|
obifloat_t value)
|
||||||
|
|
||||||
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column,
|
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
const_char_p element_name)
|
const_char_p element_name)
|
||||||
|
|
||||||
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column,
|
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
index_t element_idx)
|
index_t element_idx)
|
||||||
|
|
||||||
cdef extern from "obidmscolumn_str.h" nogil:
|
cdef extern from "obidmscolumn_str.h" nogil:
|
||||||
|
|
||||||
|
int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
const_char_p element_name,
|
||||||
|
char* value)
|
||||||
|
|
||||||
|
int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
index_t element_idx,
|
||||||
|
char* value)
|
||||||
|
|
||||||
|
const_char_p obi_column_get_obistr_with_elt_name_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
const_char_p element_name)
|
||||||
|
|
||||||
|
const_char_p obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
index_t element_idx)
|
||||||
|
|
||||||
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column,
|
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
const_char_p element_name,
|
const_char_p element_name,
|
||||||
const_char_p value)
|
char* value)
|
||||||
|
|
||||||
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column,
|
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
index_t element_idx,
|
index_t element_idx,
|
||||||
const_char_p value)
|
char* value)
|
||||||
|
|
||||||
const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column,
|
const_char_p obi_column_get_obistr_with_elt_name(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
const_char_p element_name)
|
char* element_name)
|
||||||
|
|
||||||
const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column,
|
const_char_p obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
@ -176,21 +289,43 @@ cdef extern from "obidmscolumn_str.h" nogil:
|
|||||||
|
|
||||||
cdef extern from "obidmscolumn_seq.h" nogil:
|
cdef extern from "obidmscolumn_seq.h" nogil:
|
||||||
|
|
||||||
|
int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
const_char_p element_name,
|
||||||
|
char* value)
|
||||||
|
|
||||||
|
int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
index_t element_idx,
|
||||||
|
char* value)
|
||||||
|
|
||||||
|
const_char_p obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
const_char_p element_name)
|
||||||
|
|
||||||
|
const_char_p obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view,
|
||||||
|
OBIDMS_column_p column,
|
||||||
|
index_t line_nb,
|
||||||
|
index_t element_idx)
|
||||||
|
|
||||||
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column,
|
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
const_char_p element_name,
|
const_char_p element_name,
|
||||||
const_char_p value)
|
char* value)
|
||||||
|
|
||||||
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column,
|
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
index_t element_idx,
|
index_t element_idx,
|
||||||
const_char_p value)
|
char* value)
|
||||||
|
|
||||||
char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column,
|
const_char_p obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
const_char_p element_name)
|
char* element_name)
|
||||||
|
|
||||||
char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column,
|
const_char_p obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column,
|
||||||
index_t line_nb,
|
index_t line_nb,
|
||||||
index_t element_idx)
|
index_t element_idx)
|
||||||
|
|
||||||
|
|||||||
@ -8,11 +8,15 @@ from posix.types cimport time_t
|
|||||||
cdef extern from *:
|
cdef extern from *:
|
||||||
ctypedef char* const_char_p "const char*"
|
ctypedef char* const_char_p "const char*"
|
||||||
|
|
||||||
|
|
||||||
cdef extern from "encode.h" nogil:
|
cdef extern from "encode.h" nogil:
|
||||||
bint only_ATGC(const_char_p seq)
|
bint only_ATGC(const_char_p seq)
|
||||||
|
|
||||||
|
|
||||||
|
cdef extern from "obidmscolumn.h" nogil:
|
||||||
|
|
||||||
|
ctypedef int32_t obiversion_t
|
||||||
|
|
||||||
|
|
||||||
cdef extern from "obitypes.h" nogil:
|
cdef extern from "obitypes.h" nogil:
|
||||||
|
|
||||||
enum OBIType:
|
enum OBIType:
|
||||||
@ -33,12 +37,10 @@ cdef extern from "obitypes.h" nogil:
|
|||||||
|
|
||||||
ctypedef OBIBool obibool_t
|
ctypedef OBIBool obibool_t
|
||||||
ctypedef int32_t obiint_t
|
ctypedef int32_t obiint_t
|
||||||
ctypedef double obifloat_t
|
ctypedef double obifloat_t
|
||||||
ctypedef char obichar_t
|
ctypedef char obichar_t
|
||||||
ctypedef int64_t index_t
|
ctypedef int64_t index_t
|
||||||
|
|
||||||
ctypedef int32_t obiversion_t
|
|
||||||
|
|
||||||
extern obiint_t OBIInt_NA
|
extern obiint_t OBIInt_NA
|
||||||
extern index_t OBIIdx_NA
|
extern index_t OBIIdx_NA
|
||||||
extern obifloat_t OBIFloat_NA
|
extern obifloat_t OBIFloat_NA
|
||||||
|
|||||||
@ -1,12 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
|
|
||||||
from posix.types cimport time_t
|
|
||||||
|
|
||||||
from ..capi.obitypes cimport const_char_p
|
|
||||||
|
|
||||||
|
|
||||||
cdef extern from "utils.h" nogil:
|
|
||||||
|
|
||||||
const_char_p obi_format_date(time_t date)
|
|
||||||
|
|
||||||
@ -3,10 +3,6 @@
|
|||||||
from .obitypes cimport const_char_p, \
|
from .obitypes cimport const_char_p, \
|
||||||
OBIType_t, \
|
OBIType_t, \
|
||||||
obiversion_t, \
|
obiversion_t, \
|
||||||
obiint_t, \
|
|
||||||
obibool_t, \
|
|
||||||
obichar_t, \
|
|
||||||
obifloat_t, \
|
|
||||||
index_t, \
|
index_t, \
|
||||||
time_t
|
time_t
|
||||||
from ..capi.obidms cimport OBIDMS_p
|
from ..capi.obidms cimport OBIDMS_p
|
||||||
@ -18,23 +14,7 @@ cdef extern from "obiview.h" nogil:
|
|||||||
extern const_char_p VIEW_TYPE_NUC_SEQS
|
extern const_char_p VIEW_TYPE_NUC_SEQS
|
||||||
extern const_char_p NUC_SEQUENCE_COLUMN
|
extern const_char_p NUC_SEQUENCE_COLUMN
|
||||||
extern const_char_p ID_COLUMN
|
extern const_char_p ID_COLUMN
|
||||||
extern const_char_p DEFINITION_COLUMN
|
extern const_char_p DESCRIPTION_COLUMN
|
||||||
|
|
||||||
struct Obiview_t :
|
|
||||||
OBIDMS_p dms
|
|
||||||
const_char_p name
|
|
||||||
const_char_p created_from
|
|
||||||
const_char_p view_type
|
|
||||||
bint read_only
|
|
||||||
OBIDMS_column_p line_selection
|
|
||||||
OBIDMS_column_p new_line_selection
|
|
||||||
index_t line_count
|
|
||||||
int column_count
|
|
||||||
OBIDMS_column_p columns
|
|
||||||
const_char_p comments
|
|
||||||
|
|
||||||
ctypedef Obiview_t* Obiview_p
|
|
||||||
|
|
||||||
|
|
||||||
struct Column_reference_t :
|
struct Column_reference_t :
|
||||||
const_char_p column_name
|
const_char_p column_name
|
||||||
@ -43,17 +23,32 @@ cdef extern from "obiview.h" nogil:
|
|||||||
ctypedef Column_reference_t* Column_reference_p
|
ctypedef Column_reference_t* Column_reference_p
|
||||||
|
|
||||||
|
|
||||||
struct Obiview_infos_t :
|
struct Obiview_t :
|
||||||
int view_number
|
OBIDMS_p dms
|
||||||
time_t creation_date
|
|
||||||
const_char_p name
|
const_char_p name
|
||||||
const_char_p created_from
|
OBIDMS_column_p line_selection
|
||||||
const_char_p view_type
|
OBIDMS_column_p new_line_selection
|
||||||
bint all_lines
|
OBIDMS_column_p columns
|
||||||
Column_reference_t line_selection
|
bint read_only
|
||||||
|
Column_reference_t line_selection_reference
|
||||||
index_t line_count
|
index_t line_count
|
||||||
int column_count
|
int column_count
|
||||||
|
const_char_p comments
|
||||||
|
|
||||||
|
ctypedef Obiview_t* Obiview_p
|
||||||
|
|
||||||
|
|
||||||
|
struct Obiview_infos_t :
|
||||||
|
int view_number
|
||||||
|
int column_count
|
||||||
|
index_t line_count
|
||||||
|
const_char_p name
|
||||||
|
const_char_p created_from
|
||||||
|
time_t creation_date
|
||||||
|
bint all_lines
|
||||||
|
Column_reference_t line_selection
|
||||||
Column_reference_p column_references
|
Column_reference_p column_references
|
||||||
|
const_char_p view_type
|
||||||
const_char_p comments
|
const_char_p comments
|
||||||
|
|
||||||
ctypedef Obiview_infos_t* Obiview_infos_p
|
ctypedef Obiview_infos_t* Obiview_infos_p
|
||||||
@ -84,6 +79,10 @@ cdef extern from "obiview.h" nogil:
|
|||||||
|
|
||||||
Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
|
Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
|
||||||
|
|
||||||
|
Obiviews_infos_all_p obi_read_views(OBIDMS_p dms)
|
||||||
|
|
||||||
|
int obi_unmap_read_views(Obiviews_infos_all_p views)
|
||||||
|
|
||||||
int obi_view_add_column(Obiview_p view,
|
int obi_view_add_column(Obiview_p view,
|
||||||
const_char_p column_name,
|
const_char_p column_name,
|
||||||
obiversion_t version_number,
|
obiversion_t version_number,
|
||||||
@ -91,7 +90,7 @@ cdef extern from "obiview.h" nogil:
|
|||||||
index_t nb_lines,
|
index_t nb_lines,
|
||||||
index_t nb_elements_per_line,
|
index_t nb_elements_per_line,
|
||||||
const_char_p elements_names,
|
const_char_p elements_names,
|
||||||
const_char_p indexer_name,
|
const_char_p avl_name,
|
||||||
const_char_p comments,
|
const_char_p comments,
|
||||||
bint create)
|
bint create)
|
||||||
|
|
||||||
@ -100,6 +99,8 @@ cdef extern from "obiview.h" nogil:
|
|||||||
int obi_select_line(Obiview_p view, index_t line_nb)
|
int obi_select_line(Obiview_p view, index_t line_nb)
|
||||||
|
|
||||||
int obi_select_lines(Obiview_p view, index_t* line_nbs)
|
int obi_select_lines(Obiview_p view, index_t* line_nbs)
|
||||||
|
|
||||||
|
OBIDMS_column_p obi_view_clone_column(Obiview_p view, const_char_p column_name)
|
||||||
|
|
||||||
OBIDMS_column_p obi_view_get_column(Obiview_p view, const_char_p column_name)
|
OBIDMS_column_p obi_view_get_column(Obiview_p view, const_char_p column_name)
|
||||||
|
|
||||||
@ -110,140 +111,4 @@ cdef extern from "obiview.h" nogil:
|
|||||||
int obi_close_view(Obiview_p view)
|
int obi_close_view(Obiview_p view)
|
||||||
|
|
||||||
int obi_save_and_close_view(Obiview_p view)
|
int obi_save_and_close_view(Obiview_p view)
|
||||||
|
|
||||||
Obiviews_infos_all_p obi_read_view_infos(OBIDMS_p dms)
|
|
||||||
|
|
||||||
int obi_close_view_infos(Obiviews_infos_all_p views)
|
|
||||||
|
|
||||||
int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
const_char_p element_name,
|
|
||||||
obiint_t value)
|
|
||||||
|
|
||||||
int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
index_t element_idx,
|
|
||||||
obiint_t value)
|
|
||||||
|
|
||||||
obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
const_char_p element_name)
|
|
||||||
|
|
||||||
obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
index_t element_idx)
|
|
||||||
|
|
||||||
int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
const_char_p element_name,
|
|
||||||
obibool_t value)
|
|
||||||
|
|
||||||
int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
index_t element_idx,
|
|
||||||
obibool_t value)
|
|
||||||
|
|
||||||
obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
const_char_p element_name)
|
|
||||||
|
|
||||||
obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
index_t element_idx)
|
|
||||||
|
|
||||||
int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
const_char_p element_name,
|
|
||||||
obichar_t value)
|
|
||||||
|
|
||||||
int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
index_t element_idx,
|
|
||||||
obichar_t value)
|
|
||||||
|
|
||||||
obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
const_char_p element_name)
|
|
||||||
|
|
||||||
obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
index_t element_idx)
|
|
||||||
|
|
||||||
int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
const_char_p element_name,
|
|
||||||
obifloat_t value)
|
|
||||||
|
|
||||||
int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
index_t element_idx,
|
|
||||||
obifloat_t value)
|
|
||||||
|
|
||||||
obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
const_char_p element_name)
|
|
||||||
|
|
||||||
obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
index_t element_idx)
|
|
||||||
|
|
||||||
int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
const_char_p element_name,
|
|
||||||
const_char_p value)
|
|
||||||
|
|
||||||
int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
index_t element_idx,
|
|
||||||
const_char_p value)
|
|
||||||
|
|
||||||
const_char_p obi_column_get_obistr_with_elt_name_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
const_char_p element_name)
|
|
||||||
|
|
||||||
const_char_p obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
index_t element_idx)
|
|
||||||
|
|
||||||
int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
const_char_p element_name,
|
|
||||||
const_char_p value)
|
|
||||||
|
|
||||||
int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
index_t element_idx,
|
|
||||||
const_char_p value)
|
|
||||||
|
|
||||||
char* obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
const_char_p element_name)
|
|
||||||
|
|
||||||
char* obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view,
|
|
||||||
OBIDMS_column_p column,
|
|
||||||
index_t line_nb,
|
|
||||||
index_t element_idx)
|
|
||||||
|
|
||||||
|
|||||||
@ -1,51 +0,0 @@
|
|||||||
import sys
|
|
||||||
import argparse
|
|
||||||
|
|
||||||
from obitools3.obidms._obidms import OBIDMS
|
|
||||||
|
|
||||||
if __name__ == '__main__':
|
|
||||||
|
|
||||||
parser = argparse.ArgumentParser(description='Pseudo obigrep.')
|
|
||||||
|
|
||||||
parser.add_argument('-V', '--view', dest='view', type=str,
|
|
||||||
help='Name of the view that should be considered')
|
|
||||||
|
|
||||||
parser.add_argument('-N', '--new_view', dest='new_view', type=str,
|
|
||||||
help='Name of the new view that should be created')
|
|
||||||
|
|
||||||
# parser.add_argument('-k', '--key', dest='key', type=str,
|
|
||||||
# help='Name of the key that should be considered')
|
|
||||||
#
|
|
||||||
# parser.add_argument('-c', '--comp', dest='comparison', type=int,
|
|
||||||
# help='Comparison to be made: -1:< ; 0:== ; 1:>')
|
|
||||||
#
|
|
||||||
# parser.add_argument('-v', '--value', dest='value', type=object,
|
|
||||||
# help='Value to be compared')
|
|
||||||
|
|
||||||
args = parser.parse_args()
|
|
||||||
|
|
||||||
d = OBIDMS('tdms')
|
|
||||||
|
|
||||||
#condition = 1
|
|
||||||
line_selec = []
|
|
||||||
|
|
||||||
v = d.open_view(args.view)
|
|
||||||
|
|
||||||
i = 0
|
|
||||||
for l in v :
|
|
||||||
if l['score'] > 350 :
|
|
||||||
line_selec.append(i)
|
|
||||||
i+=1
|
|
||||||
|
|
||||||
new_v = d.new_view(args.new_view, view_to_clone=v, line_selection=line_selec, view_type="NUC_SEQS_VIEW", comments="obigrep "+args.view+" to "+args.new_view) #args.key+" "+str(args.comparison)+" "+str(args.value)+" "+)
|
|
||||||
|
|
||||||
print("\n")
|
|
||||||
print(new_v.__repr__())
|
|
||||||
|
|
||||||
v.save_and_close()
|
|
||||||
new_v.save_and_close()
|
|
||||||
|
|
||||||
d.close()
|
|
||||||
|
|
||||||
print("\nDone.")
|
|
||||||
|
|
||||||
@ -1,43 +0,0 @@
|
|||||||
import sys
|
|
||||||
import argparse
|
|
||||||
|
|
||||||
from obitools3.obidms._obidms import OBIDMS
|
|
||||||
|
|
||||||
if __name__ == '__main__':
|
|
||||||
|
|
||||||
parser = argparse.ArgumentParser(description='Pseudo obihead.')
|
|
||||||
|
|
||||||
parser.add_argument('-V', '--view', dest='view', type=str,
|
|
||||||
help='Name of the view that should be considered')
|
|
||||||
|
|
||||||
parser.add_argument('-N', '--new_view', dest='new_view', type=str,
|
|
||||||
help='Name of the new view that should be created')
|
|
||||||
|
|
||||||
parser.add_argument('-n', '--nb', dest='nb_lines', type=int,
|
|
||||||
help='Number of lines that should be taken')
|
|
||||||
|
|
||||||
|
|
||||||
args = parser.parse_args()
|
|
||||||
|
|
||||||
d = OBIDMS('tdms')
|
|
||||||
|
|
||||||
#condition = 1
|
|
||||||
line_selec = []
|
|
||||||
|
|
||||||
v = d.open_view(args.view)
|
|
||||||
|
|
||||||
for i in range(0, args.nb_lines) :
|
|
||||||
line_selec.append(i)
|
|
||||||
|
|
||||||
new_v = d.new_view(args.new_view, view_to_clone=v, line_selection=line_selec, view_type="NUC_SEQS_VIEW", comments="obihead "+str(args.nb_lines)+", "+args.view+" to "+args.new_view) #args.key+" "+str(args.comparison)+" "+str(args.value)+" "+)
|
|
||||||
|
|
||||||
print("\n")
|
|
||||||
print(new_v.__repr__())
|
|
||||||
|
|
||||||
v.save_and_close()
|
|
||||||
new_v.save_and_close()
|
|
||||||
|
|
||||||
d.close()
|
|
||||||
|
|
||||||
print("\nDone.")
|
|
||||||
|
|
||||||
@ -1,199 +0,0 @@
|
|||||||
import sys
|
|
||||||
import argparse
|
|
||||||
import time
|
|
||||||
|
|
||||||
from obitools3.obidms._obidms import OBIDMS
|
|
||||||
|
|
||||||
|
|
||||||
def bufferedRead(fileobj,size=209715200): ## 200 MB
|
|
||||||
buffer = fileobj.readlines(size)
|
|
||||||
while buffer:
|
|
||||||
for l in buffer:
|
|
||||||
yield l
|
|
||||||
buffer = fileobj.readlines(size)
|
|
||||||
|
|
||||||
|
|
||||||
if __name__ == '__main__':
|
|
||||||
|
|
||||||
parser = argparse.ArgumentParser(description='Convert a fasta file in an OBIDMS.')
|
|
||||||
|
|
||||||
parser.add_argument('-i', '--input', dest='input_file', type=str,
|
|
||||||
help='Name of the file containing the sequences')
|
|
||||||
|
|
||||||
args = parser.parse_args()
|
|
||||||
|
|
||||||
d = OBIDMS('tdms')
|
|
||||||
|
|
||||||
view = d.new_view('uniq view', view_type="NUC_SEQS_VIEW")
|
|
||||||
|
|
||||||
# for i in range(35000000) :
|
|
||||||
# if (not (i%500000)) :
|
|
||||||
# print(str(time.time())+'\t'+str(i))
|
|
||||||
# id = "@HWI-D00405:142:C71BAANXX:4:1101:1234:2234_CONS_SUB_SUB_"+str(i)
|
|
||||||
# view[i].set_id(id)
|
|
||||||
# if id != view[i]["ID"] :
|
|
||||||
# print("nope", id, view[i]["ID"])
|
|
||||||
|
|
||||||
input_file = open(args.input_file, 'r')
|
|
||||||
input_file_buffered = bufferedRead(input_file)
|
|
||||||
|
|
||||||
#
|
|
||||||
# if args.input_file[-1:] == "a" :
|
|
||||||
#
|
|
||||||
# i = 0
|
|
||||||
# next = False
|
|
||||||
# first = True
|
|
||||||
#
|
|
||||||
# for line in input_file :
|
|
||||||
#
|
|
||||||
# if line[0] == ">" :
|
|
||||||
#
|
|
||||||
# if not first :
|
|
||||||
# # save seq
|
|
||||||
# #print(i, id, seq)
|
|
||||||
# view[i].set_sequence(seq)
|
|
||||||
# i+=1
|
|
||||||
#
|
|
||||||
# first = False
|
|
||||||
#
|
|
||||||
# #id = line.split(" ", 1)[0][1:]
|
|
||||||
# #rest = (line[:-1].split(" ", 1)[1]).split(";")
|
|
||||||
# #view[i].set_id(id)
|
|
||||||
#
|
|
||||||
# # description = ""
|
|
||||||
# # for j in range(len(rest)) :
|
|
||||||
# # if "=" in rest[j] :
|
|
||||||
# # rest[j] = rest[j].strip()
|
|
||||||
# # rest[j] = rest[j].split("=", 1)
|
|
||||||
# # column_name = rest[j][0]
|
|
||||||
# # v = rest[j][1]
|
|
||||||
# # if ((not v.isalpha()) and (v.isalnum())) :
|
|
||||||
# # conv_v = int(v)
|
|
||||||
# # elif (v == "True") or (v == "False") :
|
|
||||||
# # conv_v = bool(v)
|
|
||||||
# # else :
|
|
||||||
# # f = True
|
|
||||||
# # for letter in v :
|
|
||||||
# # if ((not letter.isalnum()) or (letter != ".")) :
|
|
||||||
# # f = False
|
|
||||||
# # if f :
|
|
||||||
# # conv_v = float(v)
|
|
||||||
# # else :
|
|
||||||
# # conv_v = v
|
|
||||||
# # view[i][column_name] = conv_v
|
|
||||||
# # else :
|
|
||||||
# # description+=rest[j]
|
|
||||||
# #
|
|
||||||
# # if description != "" :
|
|
||||||
# # description = description.strip()
|
|
||||||
# # view[i].set_description(description)
|
|
||||||
#
|
|
||||||
# #print(id)
|
|
||||||
# #print(rest)
|
|
||||||
# #print(description)
|
|
||||||
#
|
|
||||||
# next = True
|
|
||||||
#
|
|
||||||
# elif next == True :
|
|
||||||
#
|
|
||||||
# # if not (i % 1E5) :
|
|
||||||
# # print(i)
|
|
||||||
#
|
|
||||||
# seq = line[:-1]
|
|
||||||
# next = False
|
|
||||||
#
|
|
||||||
# elif not next :
|
|
||||||
#
|
|
||||||
# seq += line[:-1]
|
|
||||||
#
|
|
||||||
#
|
|
||||||
# elif args.input_file[-1:] == "q" :
|
|
||||||
#
|
|
||||||
# i = 0
|
|
||||||
# l = 0
|
|
||||||
# next = False
|
|
||||||
#
|
|
||||||
l=0
|
|
||||||
i=0
|
|
||||||
# while (True):
|
|
||||||
# l+=1
|
|
||||||
# line = input_file.readline()
|
|
||||||
# if line=="":
|
|
||||||
# break
|
|
||||||
for line in input_file_buffered :
|
|
||||||
#
|
|
||||||
#if i > 1E7 :
|
|
||||||
# # print('hmm?')
|
|
||||||
#
|
|
||||||
# if i == 6000000 :
|
|
||||||
# break
|
|
||||||
#
|
|
||||||
if l%4 == 0 :
|
|
||||||
#
|
|
||||||
if (not (i%500000)) :
|
|
||||||
print(str(time.time())+'\t'+str(i))
|
|
||||||
# #
|
|
||||||
# # #print("header", line)
|
|
||||||
# #
|
|
||||||
id = line.split(" ", 1)[0][1:]
|
|
||||||
# print(id)
|
|
||||||
# # #rest = (line[:-1].split(" ", 1)[1]).split(";")
|
|
||||||
view[i].set_id(id)
|
|
||||||
# print(view[i]["ID"])
|
|
||||||
#
|
|
||||||
# i+=1
|
|
||||||
|
|
||||||
# l+=1
|
|
||||||
#
|
|
||||||
# # description = ""
|
|
||||||
# # for j in range(len(rest)) :
|
|
||||||
# # if "=" in rest[j] :
|
|
||||||
# # rest[j] = rest[j].strip()
|
|
||||||
# # rest[j] = rest[j].split("=", 1)
|
|
||||||
# # column_name = rest[j][0]
|
|
||||||
# # #print("COLUMN", column_name)
|
|
||||||
# # v = rest[j][1]
|
|
||||||
# # if (v == "") and (column_name in view) and (view[column_name].get_data_type() == "OBI_SEQ") :
|
|
||||||
# # #print(">>>>>>YUP")
|
|
||||||
# # conv_v = "aa"
|
|
||||||
# # else :
|
|
||||||
# # if ((not v.isalpha()) and (v.isalnum())) :
|
|
||||||
# # conv_v = int(v)
|
|
||||||
# # elif (v == "True") or (v == "False") :
|
|
||||||
# # conv_v = bool(v)
|
|
||||||
# # else :
|
|
||||||
# # f = True
|
|
||||||
# # for letter in v :
|
|
||||||
# # if ((not letter.isalnum()) or (letter != ".")) :
|
|
||||||
# # f = False
|
|
||||||
# # if f :
|
|
||||||
# # conv_v = float(v)
|
|
||||||
# # else :
|
|
||||||
# # conv_v = v
|
|
||||||
# # view[i][column_name] = conv_v
|
|
||||||
# # else :
|
|
||||||
# # description+=rest[j]
|
|
||||||
# #
|
|
||||||
# # if description != "" :
|
|
||||||
# # description = description.strip()
|
|
||||||
# # view[i].set_description(description)
|
|
||||||
#
|
|
||||||
elif l%4 == 1 :
|
|
||||||
# #
|
|
||||||
seq = line[:-1]
|
|
||||||
# #print("seq", seq)
|
|
||||||
view[i].set_sequence(seq)
|
|
||||||
i+=1
|
|
||||||
#
|
|
||||||
l+=1
|
|
||||||
#
|
|
||||||
#
|
|
||||||
input_file.close()
|
|
||||||
|
|
||||||
#print(view)
|
|
||||||
print(view.__repr__())
|
|
||||||
|
|
||||||
view.save_and_close()
|
|
||||||
d.close()
|
|
||||||
|
|
||||||
print("Done.")
|
|
||||||
@ -1,8 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
from .header cimport parseHeader
|
|
||||||
from ..files.universalopener cimport uopen
|
|
||||||
from ..files.linebuffer cimport LineBuffer
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,46 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
'''
|
|
||||||
Created on 30 mars 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
def fastaIterator(lineiterator, int buffersize=100000000):
|
|
||||||
cdef LineBuffer lb
|
|
||||||
cdef str ident
|
|
||||||
cdef str definition
|
|
||||||
cdef dict tags
|
|
||||||
cdef list s
|
|
||||||
|
|
||||||
if isinstance(lineiterator,(str,bytes)):
|
|
||||||
lineiterator=uopen(lineiterator)
|
|
||||||
|
|
||||||
if isinstance(lineiterator, LineBuffer):
|
|
||||||
lb=lineiterator
|
|
||||||
else:
|
|
||||||
lb=LineBuffer(lineiterator,buffersize)
|
|
||||||
|
|
||||||
i = iter(lb)
|
|
||||||
line = next(i)
|
|
||||||
|
|
||||||
while True:
|
|
||||||
ident,tags,definition = parseHeader(line)
|
|
||||||
s = []
|
|
||||||
line = next(i)
|
|
||||||
while line[0]!='>':
|
|
||||||
s.append(line[0:-1])
|
|
||||||
line = next(i)
|
|
||||||
sequence = "".join(s)
|
|
||||||
quality = None
|
|
||||||
|
|
||||||
yield { "id" : ident,
|
|
||||||
"definition" : definition,
|
|
||||||
"sequence" : sequence,
|
|
||||||
"quality" : quality,
|
|
||||||
"tags" : tags,
|
|
||||||
"annotation" : {}
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,8 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
from .header cimport parseHeader
|
|
||||||
from ..files.universalopener cimport uopen
|
|
||||||
from ..files.linebuffer cimport LineBuffer
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,41 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
'''
|
|
||||||
Created on 30 mars 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def fastqIterator(lineiterator, int buffersize=100000000):
|
|
||||||
cdef LineBuffer lb
|
|
||||||
cdef str ident
|
|
||||||
cdef str definition
|
|
||||||
cdef dict tags
|
|
||||||
|
|
||||||
if isinstance(lineiterator,(str,bytes)):
|
|
||||||
lineiterator=uopen(lineiterator)
|
|
||||||
|
|
||||||
if isinstance(lineiterator, LineBuffer):
|
|
||||||
lb=lineiterator
|
|
||||||
else:
|
|
||||||
lb=LineBuffer(lineiterator,buffersize)
|
|
||||||
|
|
||||||
i = iter(lb)
|
|
||||||
for line in i:
|
|
||||||
ident,tags,definition = parseHeader(line)
|
|
||||||
sequence = next(i)[0:-1]
|
|
||||||
next(i)
|
|
||||||
quality = next(i)[0:-1]
|
|
||||||
|
|
||||||
yield { "id" : ident,
|
|
||||||
"definition" : definition,
|
|
||||||
"sequence" : sequence,
|
|
||||||
"quality" : quality,
|
|
||||||
"tags" : tags,
|
|
||||||
"annotation" : {}
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,5 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
cdef object __etag__(str x)
|
|
||||||
|
|
||||||
cpdef tuple parseHeader(str header)
|
|
||||||
@ -1,78 +0,0 @@
|
|||||||
#cython: language_level=3
|
|
||||||
|
|
||||||
'''
|
|
||||||
Created on 25 mars 2016
|
|
||||||
|
|
||||||
@author: coissac
|
|
||||||
'''
|
|
||||||
|
|
||||||
import re
|
|
||||||
|
|
||||||
__ret__ = re.compile('''(([^ ]+)=('[^']*'|"[^"]*"|[^;]+); *)+?''')
|
|
||||||
__re_int__ = re.compile("^[+-]?[0-9]+$")
|
|
||||||
__re_float__ = re.compile("^[+-]?[0-9]+(\.[0-9]*)?([eE][+-]?[0-9]+)?$")
|
|
||||||
__re_str__ = re.compile("""^"[^"]*"|'[^']*'$""")
|
|
||||||
__re_dict__ = re.compile("""^\{\ *
|
|
||||||
(
|
|
||||||
("[^"]*"|'[^']*')
|
|
||||||
\ *:\ *
|
|
||||||
([^,}]+|
|
|
||||||
"[^"]*"|
|
|
||||||
'[^']*'
|
|
||||||
)
|
|
||||||
)?
|
|
||||||
(\ *,\ *
|
|
||||||
("[^"]*"|'[^']*')
|
|
||||||
\ *:\ *
|
|
||||||
([^,}]+|
|
|
||||||
"[^"]*"|
|
|
||||||
'[^']*'
|
|
||||||
)
|
|
||||||
)*\ *\}$""", re.VERBOSE)
|
|
||||||
|
|
||||||
|
|
||||||
cdef object __etag__(str x):
|
|
||||||
if __re_int__.match(x):
|
|
||||||
v=int(x)
|
|
||||||
elif __re_float__.match(x):
|
|
||||||
v=float(x)
|
|
||||||
elif __re_str__.match(x):
|
|
||||||
v=x[1:-1]
|
|
||||||
elif x=='False':
|
|
||||||
v=False
|
|
||||||
elif x=='True':
|
|
||||||
v=True
|
|
||||||
elif __re_dict__.match(x):
|
|
||||||
v=eval(x)
|
|
||||||
else:
|
|
||||||
v=x
|
|
||||||
return v
|
|
||||||
|
|
||||||
cpdef tuple parseHeader(str header):
|
|
||||||
cdef list m
|
|
||||||
cdef dict tags
|
|
||||||
cdef str definition
|
|
||||||
cdef str ident
|
|
||||||
cdef str second
|
|
||||||
|
|
||||||
m=header[1:-1].split(maxsplit=1)
|
|
||||||
|
|
||||||
ident=m[0]
|
|
||||||
|
|
||||||
if len(m)==1:
|
|
||||||
tags={}
|
|
||||||
definition=''
|
|
||||||
else:
|
|
||||||
second=m[1]
|
|
||||||
m = __ret__.findall(second)
|
|
||||||
|
|
||||||
if m:
|
|
||||||
tags = dict([(a[1],__etag__(a[2])) for a in m])
|
|
||||||
definition = second.split(m[-1][0],1)[1].strip()
|
|
||||||
else:
|
|
||||||
tags = {}
|
|
||||||
definition = second.strip()
|
|
||||||
|
|
||||||
return ident,tags,definition
|
|
||||||
|
|
||||||
|
|
||||||
@ -1,6 +1,5 @@
|
|||||||
#cython: language_level=3
|
#cython: language_level=3
|
||||||
|
|
||||||
|
|
||||||
cdef bytes str2bytes(str string)
|
cdef bytes str2bytes(str string)
|
||||||
|
|
||||||
cdef str bytes2str(bytes string)
|
cdef str bytes2str(bytes string)
|
||||||
@ -1,28 +1,7 @@
|
|||||||
#cython: language_level=3
|
#cython: language_level=3
|
||||||
|
|
||||||
import sys
|
|
||||||
import io
|
|
||||||
|
|
||||||
cdef bytes str2bytes(str string):
|
cdef bytes str2bytes(str string):
|
||||||
"""
|
|
||||||
Short cut to convert ascii encoded python string (str) to bytes
|
|
||||||
which can be easily converted to C-strings.
|
|
||||||
|
|
||||||
@param string: the python string to be converted.
|
|
||||||
@type string: str
|
|
||||||
@return a transcoded string
|
|
||||||
@rtype: bytes
|
|
||||||
"""
|
|
||||||
return string.encode('ascii')
|
return string.encode('ascii')
|
||||||
|
|
||||||
cdef str bytes2str(bytes string):
|
cdef str bytes2str(bytes string):
|
||||||
"""
|
return string.decode('ascii')
|
||||||
Short cut to convert bytes (C-strings) to ascii encoded python string (str).
|
|
||||||
|
|
||||||
@param string: the binary (C-string) string to be converted.
|
|
||||||
@type string: bytes
|
|
||||||
@return an ascii transcoded string
|
|
||||||
@rtype: str
|
|
||||||
"""
|
|
||||||
return string.decode('ascii')
|
|
||||||
|
|
||||||
@ -1,5 +1,5 @@
|
|||||||
--extra-index-url https://pypi.python.org/simple/
|
--extra-index-url https://pypi.python.org/simple/
|
||||||
Cython==0.23.5
|
Cython>=0.21
|
||||||
Sphinx>=1.2.0
|
Sphinx>=1.2.0
|
||||||
ipython>=3.0.0
|
ipython>=3.0.0
|
||||||
breathe>=4.0.0
|
breathe>=4.0.0
|
||||||
|
|||||||
248
src/bloom.c
248
src/bloom.c
@ -1,248 +0,0 @@
|
|||||||
/*
|
|
||||||
* Copyright (c) 2012-2015, Jyri J. Virkki
|
|
||||||
* All rights reserved.
|
|
||||||
*
|
|
||||||
* This file is under BSD license. See LICENSE file.
|
|
||||||
*/
|
|
||||||
|
|
||||||
/*
|
|
||||||
* Refer to bloom.h for documentation on the public interfaces.
|
|
||||||
*/
|
|
||||||
|
|
||||||
#include <assert.h>
|
|
||||||
#include <fcntl.h>
|
|
||||||
#include <math.h>
|
|
||||||
#include <stdint.h>
|
|
||||||
#include <stdio.h>
|
|
||||||
#include <stdlib.h>
|
|
||||||
#include <string.h>
|
|
||||||
#include <sys/stat.h>
|
|
||||||
#include <sys/types.h>
|
|
||||||
#include <unistd.h>
|
|
||||||
|
|
||||||
#include "bloom.h"
|
|
||||||
#include "murmurhash2.h"
|
|
||||||
|
|
||||||
#define MAKESTRING(n) STRING(n)
|
|
||||||
#define STRING(n) #n
|
|
||||||
|
|
||||||
//#ifdef __linux__ // TODO commented because triggers error on luke21
|
|
||||||
//unsigned detect_bucket_size(unsigned fallback_size);
|
|
||||||
//#endif
|
|
||||||
|
|
||||||
|
|
||||||
static int test_bit_set_bit(unsigned char * buf, unsigned int x, int set_bit)
|
|
||||||
{
|
|
||||||
register uint32_t * word_buf = (uint32_t *)buf;
|
|
||||||
register unsigned int offset = x >> 5;
|
|
||||||
register uint32_t word = word_buf[offset];
|
|
||||||
register unsigned int mask = 1 << (x % 32);
|
|
||||||
|
|
||||||
if (word & mask) {
|
|
||||||
return 1;
|
|
||||||
} else {
|
|
||||||
if (set_bit) {
|
|
||||||
word_buf[offset] = word | mask;
|
|
||||||
}
|
|
||||||
return 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
static int bloom_check_add(struct bloom * bloom,
|
|
||||||
const void * buffer, int len, int add)
|
|
||||||
{
|
|
||||||
if (bloom->ready == 0) {
|
|
||||||
(void)printf("bloom at %p not initialized!\n", (void *)bloom);
|
|
||||||
return -1;
|
|
||||||
}
|
|
||||||
|
|
||||||
int hits = 0;
|
|
||||||
register unsigned int a = murmurhash2(buffer, len, 0x9747b28c);
|
|
||||||
register unsigned int b = murmurhash2(buffer, len, a);
|
|
||||||
register unsigned int x;
|
|
||||||
register int i; // TODO why was it unsigned?
|
|
||||||
|
|
||||||
unsigned bucket_index = (a % bloom->buckets);
|
|
||||||
|
|
||||||
unsigned char * bucket_ptr =
|
|
||||||
(bloom->bf + (bucket_index << bloom->bucket_bytes_exponent));
|
|
||||||
|
|
||||||
for (i = 0; i < bloom->hashes; i++) {
|
|
||||||
x = (a + i*b) & bloom->bucket_bits_fast_mod_operand;
|
|
||||||
if (test_bit_set_bit(bucket_ptr, x, add)) {
|
|
||||||
hits++;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
if (hits == bloom->hashes) {
|
|
||||||
return 1; // 1 == element already in (or collision)
|
|
||||||
}
|
|
||||||
|
|
||||||
return 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
static void setup_buckets(struct bloom * bloom, unsigned int cache_size)
|
|
||||||
{
|
|
||||||
// If caller passed a non-zero cache_size, use it as given, otherwise
|
|
||||||
// either compute it or use built-in default
|
|
||||||
|
|
||||||
if (cache_size == 0) {
|
|
||||||
//#ifdef __linux__ // TODO commented because triggers error on luke21
|
|
||||||
// cache_size = detect_bucket_size(BLOOM_BUCKET_SIZE_FALLBACK);
|
|
||||||
//#else
|
|
||||||
cache_size = BLOOM_BUCKET_SIZE_FALLBACK;
|
|
||||||
//#endif
|
|
||||||
}
|
|
||||||
|
|
||||||
bloom->buckets = (bloom->bytes / cache_size);
|
|
||||||
bloom->bucket_bytes = cache_size;
|
|
||||||
|
|
||||||
// make sure bloom buffer bytes and bucket_bytes are even
|
|
||||||
int not_even_by = (bloom->bytes % bloom->bucket_bytes);
|
|
||||||
|
|
||||||
if (not_even_by) {
|
|
||||||
// adjust bytes
|
|
||||||
bloom->bytes += (bloom->bucket_bytes - not_even_by);
|
|
||||||
assert((bloom->bytes % bloom->bucket_bytes) == 0); // Should get even
|
|
||||||
|
|
||||||
// adjust bits
|
|
||||||
bloom->bits = bloom->bytes * 8;
|
|
||||||
|
|
||||||
// adjust bits per element
|
|
||||||
bloom->bpe = bloom->bits*1. / bloom->entries;
|
|
||||||
|
|
||||||
// adjust buckets
|
|
||||||
bloom->buckets++;
|
|
||||||
}
|
|
||||||
|
|
||||||
bloom->bucket_bytes_exponent = __builtin_ctz(cache_size);
|
|
||||||
bloom->bucket_bits_fast_mod_operand = (cache_size * 8 - 1);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int bloom_filter_size(int entries, double error)
|
|
||||||
{
|
|
||||||
int bytes;
|
|
||||||
double num;
|
|
||||||
double denom;
|
|
||||||
double bpe;
|
|
||||||
int bits;
|
|
||||||
unsigned bucket_bytes;
|
|
||||||
int not_even_by;
|
|
||||||
|
|
||||||
num = log(error);
|
|
||||||
denom = 0.480453013918201; // ln(2)^2
|
|
||||||
bpe = -(num / denom);
|
|
||||||
bits = (int)(((double)entries) * bpe);
|
|
||||||
|
|
||||||
if (bits % 8) {
|
|
||||||
bytes = (bits / 8) + 1;
|
|
||||||
}
|
|
||||||
else {
|
|
||||||
bytes = bits / 8;
|
|
||||||
}
|
|
||||||
|
|
||||||
bucket_bytes = BLOOM_BUCKET_SIZE_FALLBACK;
|
|
||||||
not_even_by = bytes % bucket_bytes;
|
|
||||||
if (not_even_by) {
|
|
||||||
// adjust bytes
|
|
||||||
bytes += (bucket_bytes - not_even_by);
|
|
||||||
}
|
|
||||||
|
|
||||||
return bytes;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int bloom_init_size(struct bloom * bloom, int entries, double error,
|
|
||||||
unsigned int cache_size)
|
|
||||||
{
|
|
||||||
bloom->ready = 0;
|
|
||||||
|
|
||||||
if (entries < 1 || error == 0) {
|
|
||||||
return 1;
|
|
||||||
}
|
|
||||||
|
|
||||||
bloom->entries = entries;
|
|
||||||
bloom->error = error;
|
|
||||||
|
|
||||||
double num = log(bloom->error);
|
|
||||||
double denom = 0.480453013918201; // ln(2)^2
|
|
||||||
bloom->bpe = -(num / denom);
|
|
||||||
|
|
||||||
double dentries = (double)entries;
|
|
||||||
bloom->bits = (int)(dentries * bloom->bpe);
|
|
||||||
|
|
||||||
if (bloom->bits % 8) {
|
|
||||||
bloom->bytes = (bloom->bits / 8) + 1;
|
|
||||||
} else {
|
|
||||||
bloom->bytes = bloom->bits / 8;
|
|
||||||
}
|
|
||||||
|
|
||||||
bloom->hashes = (int)ceil(0.693147180559945 * bloom->bpe); // ln(2)
|
|
||||||
|
|
||||||
setup_buckets(bloom, cache_size);
|
|
||||||
|
|
||||||
// celine.mercier@metabarcoding.org :
|
|
||||||
// Replaced the calloc with a memset, as the memory for the bloom filter is mapped in our data structure
|
|
||||||
memset(bloom->bf, 0, bloom->bytes);
|
|
||||||
//bloom->bf = (unsigned char *)calloc(bloom->bytes, sizeof(unsigned char));
|
|
||||||
//if (bloom->bf == NULL) {
|
|
||||||
// return 1;
|
|
||||||
//}
|
|
||||||
|
|
||||||
bloom->ready = 1;
|
|
||||||
return 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int bloom_init(struct bloom * bloom, int entries) //, double error)
|
|
||||||
{
|
|
||||||
return bloom_init_size(bloom, entries, BLOOM_FILTER_ERROR_RATE, 0);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int bloom_check(struct bloom * bloom, const void * buffer, int len)
|
|
||||||
{
|
|
||||||
return bloom_check_add(bloom, buffer, len, 0);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int bloom_add(struct bloom * bloom, const void * buffer, int len)
|
|
||||||
{
|
|
||||||
return bloom_check_add(bloom, buffer, len, 1);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
void bloom_print(struct bloom * bloom)
|
|
||||||
{
|
|
||||||
(void)printf("bloom at %p\n", (void *)bloom);
|
|
||||||
(void)printf(" ->entries = %d\n", bloom->entries);
|
|
||||||
(void)printf(" ->error = %f\n", bloom->error);
|
|
||||||
(void)printf(" ->bits = %d\n", bloom->bits);
|
|
||||||
(void)printf(" ->bits per elem = %f\n", bloom->bpe);
|
|
||||||
(void)printf(" ->bytes = %d\n", bloom->bytes);
|
|
||||||
(void)printf(" ->buckets = %u\n", bloom->buckets);
|
|
||||||
(void)printf(" ->bucket_bytes = %u\n", bloom->bucket_bytes);
|
|
||||||
(void)printf(" ->bucket_bytes_exponent = %u\n",
|
|
||||||
bloom->bucket_bytes_exponent);
|
|
||||||
(void)printf(" ->bucket_bits_fast_mod_operand = 0%o\n",
|
|
||||||
bloom->bucket_bits_fast_mod_operand);
|
|
||||||
(void)printf(" ->hash functions = %d\n", bloom->hashes);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
void bloom_free(struct bloom * bloom)
|
|
||||||
{
|
|
||||||
if (bloom->ready) {
|
|
||||||
free(bloom->bf);
|
|
||||||
}
|
|
||||||
bloom->ready = 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
const char * bloom_version()
|
|
||||||
{
|
|
||||||
return MAKESTRING(BLOOM_VERSION);
|
|
||||||
}
|
|
||||||
210
src/bloom.h
210
src/bloom.h
@ -1,210 +0,0 @@
|
|||||||
/*
|
|
||||||
* Copyright (c) 2012-2015, Jyri J. Virkki
|
|
||||||
* All rights reserved.
|
|
||||||
*
|
|
||||||
* This file is under BSD license. See LICENSE file.
|
|
||||||
*/
|
|
||||||
|
|
||||||
#ifndef _BLOOM_H
|
|
||||||
#define _BLOOM_H
|
|
||||||
|
|
||||||
|
|
||||||
/** ***************************************************************************
|
|
||||||
* Added by celine.mercier@metabarcoding.org
|
|
||||||
*
|
|
||||||
* Bloom filter error rate wanted.
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
#define BLOOM_FILTER_ERROR_RATE (0.001)
|
|
||||||
|
|
||||||
|
|
||||||
/** ***************************************************************************
|
|
||||||
* On Linux, the code attempts to compute a bucket size based on CPU cache
|
|
||||||
* size info, if available. If that fails for any reason, this fallback size
|
|
||||||
* is used instead.
|
|
||||||
*
|
|
||||||
* On non-Linux systems, this is the bucket size always used unless the
|
|
||||||
* caller overrides it (see bloom_init_size()).
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
#define BLOOM_BUCKET_SIZE_FALLBACK (32 * 1024)
|
|
||||||
|
|
||||||
|
|
||||||
/** ***************************************************************************
|
|
||||||
* It was found that using multiplier x0.5 for CPU L1 cache size is
|
|
||||||
* more effective in terms of CPU usage and, surprisingly, collisions
|
|
||||||
* number.
|
|
||||||
*
|
|
||||||
* Feel free to tune this constant the way it will work for you.
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
#define BLOOM_L1_CACHE_SIZE_DIV 1
|
|
||||||
|
|
||||||
|
|
||||||
/** ***************************************************************************
|
|
||||||
* Structure to keep track of one bloom filter. Caller needs to
|
|
||||||
* allocate this and pass it to the functions below. First call for
|
|
||||||
* every struct must be to bloom_init().
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
struct bloom
|
|
||||||
{
|
|
||||||
// These fields are part of the public interface of this structure.
|
|
||||||
// Client code may read these values if desired. Client code MUST NOT
|
|
||||||
// modify any of these.
|
|
||||||
int entries;
|
|
||||||
double error;
|
|
||||||
int bits;
|
|
||||||
int bytes;
|
|
||||||
int hashes;
|
|
||||||
|
|
||||||
// Fields below are private to the implementation. These may go away or
|
|
||||||
// change incompatibly at any moment. Client code MUST NOT access or rely
|
|
||||||
// on these.
|
|
||||||
unsigned buckets;
|
|
||||||
unsigned bucket_bytes;
|
|
||||||
|
|
||||||
// x86 CPU divide by/multiply by operation optimization helpers
|
|
||||||
unsigned bucket_bytes_exponent;
|
|
||||||
unsigned bucket_bits_fast_mod_operand;
|
|
||||||
|
|
||||||
double bpe;
|
|
||||||
int ready;
|
|
||||||
|
|
||||||
unsigned char bf[];
|
|
||||||
};
|
|
||||||
|
|
||||||
typedef struct bloom bloom_t;
|
|
||||||
|
|
||||||
|
|
||||||
/** ***************************************************************************
|
|
||||||
* Added by celine.mercier@metabarcoding.org
|
|
||||||
*
|
|
||||||
* This function computes the size needed by the bloom filter
|
|
||||||
* depending on the number of entries and the error rate.
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
int bloom_filter_size(int entries, double error);
|
|
||||||
|
|
||||||
|
|
||||||
/** ***************************************************************************
|
|
||||||
* Initialize the bloom filter for use.
|
|
||||||
*
|
|
||||||
* The filter is initialized with a bit field and number of hash functions
|
|
||||||
* according to the computations from the wikipedia entry:
|
|
||||||
* http://en.wikipedia.org/wiki/Bloom_filter
|
|
||||||
*
|
|
||||||
* Optimal number of bits is:
|
|
||||||
* bits = (entries * ln(error)) / ln(2)^2
|
|
||||||
*
|
|
||||||
* Optimal number of hash functions is:
|
|
||||||
* hashes = bpe * ln(2)
|
|
||||||
*
|
|
||||||
* Parameters:
|
|
||||||
* -----------
|
|
||||||
* bloom - Pointer to an allocated struct bloom (see above).
|
|
||||||
* entries - The expected number of entries which will be inserted.
|
|
||||||
* error - Probability of collision (as long as entries are not
|
|
||||||
* exceeded).
|
|
||||||
*
|
|
||||||
* Return:
|
|
||||||
* -------
|
|
||||||
* 0 - on success
|
|
||||||
* 1 - on failure
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
int bloom_init(struct bloom * bloom, int entries); //, double error);
|
|
||||||
|
|
||||||
|
|
||||||
/** ***************************************************************************
|
|
||||||
* Initialize the bloom filter for use.
|
|
||||||
*
|
|
||||||
* See comments above for general information.
|
|
||||||
*
|
|
||||||
* This is the same as bloom_init() but allows the caller to pass in a
|
|
||||||
* cache_size to override the internal value (which is either computed
|
|
||||||
* or the default of BLOOM_BUCKET_SIZE_FALLBACK). Mostly useful for
|
|
||||||
* experimenting.
|
|
||||||
*
|
|
||||||
* See misc/bucketsize for a script which can help identify a good value
|
|
||||||
* for cache_size.
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
int bloom_init_size(struct bloom * bloom, int entries, double error,
|
|
||||||
unsigned int cache_size);
|
|
||||||
|
|
||||||
|
|
||||||
/** ***************************************************************************
|
|
||||||
* Check if the given element is in the bloom filter. Remember this may
|
|
||||||
* return false positive if a collision occured.
|
|
||||||
*
|
|
||||||
* Parameters:
|
|
||||||
* -----------
|
|
||||||
* bloom - Pointer to an allocated struct bloom (see above).
|
|
||||||
* buffer - Pointer to buffer containing element to check.
|
|
||||||
* len - Size of 'buffer'.
|
|
||||||
*
|
|
||||||
* Return:
|
|
||||||
* -------
|
|
||||||
* 0 - element is not present
|
|
||||||
* 1 - element is present (or false positive due to collision)
|
|
||||||
* -1 - bloom not initialized
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
int bloom_check(struct bloom * bloom, const void * buffer, int len);
|
|
||||||
|
|
||||||
|
|
||||||
/** ***************************************************************************
|
|
||||||
* Add the given element to the bloom filter.
|
|
||||||
* The return code indicates if the element (or a collision) was already in,
|
|
||||||
* so for the common check+add use case, no need to call check separately.
|
|
||||||
*
|
|
||||||
* Parameters:
|
|
||||||
* -----------
|
|
||||||
* bloom - Pointer to an allocated struct bloom (see above).
|
|
||||||
* buffer - Pointer to buffer containing element to add.
|
|
||||||
* len - Size of 'buffer'.
|
|
||||||
*
|
|
||||||
* Return:
|
|
||||||
* -------
|
|
||||||
* 0 - element was not present and was added
|
|
||||||
* 1 - element (or a collision) had already been added previously
|
|
||||||
* -1 - bloom not initialized
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
int bloom_add(struct bloom * bloom, const void * buffer, int len);
|
|
||||||
|
|
||||||
|
|
||||||
/** ***************************************************************************
|
|
||||||
* Print (to stdout) info about this bloom filter. Debugging aid.
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
void bloom_print(struct bloom * bloom);
|
|
||||||
|
|
||||||
|
|
||||||
/** ***************************************************************************
|
|
||||||
* Deallocate internal storage.
|
|
||||||
*
|
|
||||||
* Upon return, the bloom struct is no longer usable. You may call bloom_init
|
|
||||||
* again on the same struct to reinitialize it again.
|
|
||||||
*
|
|
||||||
* Parameters:
|
|
||||||
* -----------
|
|
||||||
* bloom - Pointer to an allocated struct bloom (see above).
|
|
||||||
*
|
|
||||||
* Return: none
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
void bloom_free(struct bloom * bloom);
|
|
||||||
|
|
||||||
|
|
||||||
/** ***************************************************************************
|
|
||||||
* Returns version string compiled into library.
|
|
||||||
*
|
|
||||||
* Return: version string
|
|
||||||
*
|
|
||||||
*/
|
|
||||||
const char * bloom_version();
|
|
||||||
|
|
||||||
|
|
||||||
#endif
|
|
||||||
@ -1,80 +0,0 @@
|
|||||||
/****************************************************************************
|
|
||||||
* Character string indexing functions *
|
|
||||||
****************************************************************************/
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @file char_str_indexer.c
|
|
||||||
* @author Celine Mercier
|
|
||||||
* @date April 12th 2016
|
|
||||||
* @brief Functions handling the indexing and retrieval of character strings.
|
|
||||||
*/
|
|
||||||
|
|
||||||
|
|
||||||
#include <stdlib.h>
|
|
||||||
#include <stdio.h>
|
|
||||||
#include <math.h>
|
|
||||||
|
|
||||||
#include "obiblob.h"
|
|
||||||
#include "obiblob_indexer.h"
|
|
||||||
#include "obidebug.h"
|
|
||||||
#include "obitypes.h"
|
|
||||||
|
|
||||||
|
|
||||||
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
|
||||||
|
|
||||||
|
|
||||||
Obi_blob_p obi_str_to_blob(const char* value)
|
|
||||||
{
|
|
||||||
Obi_blob_p value_b;
|
|
||||||
int32_t length;
|
|
||||||
|
|
||||||
// Compute the number of bytes on which the value will be encoded
|
|
||||||
length = strlen(value) + 1; // +1 to store \0 at the end (makes retrieving faster)
|
|
||||||
|
|
||||||
value_b = obi_blob((byte_t*)value, ELEMENT_SIZE_STR, length, length);
|
|
||||||
if (value_b == NULL)
|
|
||||||
{
|
|
||||||
obidebug(1, "\nError encoding a character string in a blob");
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
return value_b;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
char* obi_blob_to_str(Obi_blob_p value_b)
|
|
||||||
{
|
|
||||||
return value_b->value;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
index_t obi_index_char_str(Obi_indexer_p indexer, const char* value)
|
|
||||||
{
|
|
||||||
Obi_blob_p value_b;
|
|
||||||
index_t idx;
|
|
||||||
|
|
||||||
// Encode value
|
|
||||||
value_b = obi_str_to_blob(value);
|
|
||||||
if (value_b == NULL)
|
|
||||||
return -1;
|
|
||||||
|
|
||||||
// Add in the indexer
|
|
||||||
idx = obi_indexer_add(indexer, value_b);
|
|
||||||
|
|
||||||
free(value_b);
|
|
||||||
|
|
||||||
return idx;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
char* obi_retrieve_char_str(Obi_indexer_p indexer, index_t idx)
|
|
||||||
{
|
|
||||||
Obi_blob_p value_b;
|
|
||||||
|
|
||||||
// Get encoded value
|
|
||||||
value_b = obi_indexer_get(indexer, idx);
|
|
||||||
|
|
||||||
// Return decoded character string
|
|
||||||
return obi_blob_to_str(value_b);
|
|
||||||
}
|
|
||||||
|
|
||||||
@ -1,87 +0,0 @@
|
|||||||
/****************************************************************************
|
|
||||||
* DNA sequence indexer header file *
|
|
||||||
****************************************************************************/
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @file dna_seq_indexer.h
|
|
||||||
* @author Celine Mercier
|
|
||||||
* @date April 12th 2016
|
|
||||||
* @brief Header file for the functions handling the indexing of DNA sequences.
|
|
||||||
*/
|
|
||||||
|
|
||||||
|
|
||||||
#ifndef CHAR_STR_INDEXER_H_
|
|
||||||
#define CHAR_STR_INDEXER_H_
|
|
||||||
|
|
||||||
|
|
||||||
#include <stdlib.h>
|
|
||||||
#include <stdio.h>
|
|
||||||
|
|
||||||
#include "obitypes.h"
|
|
||||||
#include "obiblob.h"
|
|
||||||
#include "obiblob_indexer.h"
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Converts a character string to a blob.
|
|
||||||
*
|
|
||||||
* @warning The blob must be freed by the caller.
|
|
||||||
*
|
|
||||||
* @param value The character string to convert.
|
|
||||||
*
|
|
||||||
* @returns A pointer to the blob created.
|
|
||||||
* @retval NULL if an error occurred.
|
|
||||||
*
|
|
||||||
* @since October 2015
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
Obi_blob_p obi_str_to_blob(char* value);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Converts a blob to a character string.
|
|
||||||
*
|
|
||||||
* @warning The character string returned is mapped.
|
|
||||||
*
|
|
||||||
* @param value_b The blob to convert.
|
|
||||||
*
|
|
||||||
* @returns A pointer on the character string contained in the blob.
|
|
||||||
*
|
|
||||||
* @since October 2015
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
const char* obi_blob_to_str(Obi_blob_p value_b);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Stores a character string in an indexer and returns the index.
|
|
||||||
*
|
|
||||||
* @param indexer The indexer structure.
|
|
||||||
* @param value The character string to index.
|
|
||||||
*
|
|
||||||
* @returns The index referring to the stored character string in the indexer.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
index_t obi_index_char_str(Obi_indexer_p indexer, const char* value);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Retrieves a character string from an indexer.
|
|
||||||
*
|
|
||||||
* @warning The character string returned is mapped.
|
|
||||||
*
|
|
||||||
* @param indexer The indexer structure.
|
|
||||||
* @param idx The index referring to the character string to retrieve in the indexer.
|
|
||||||
*
|
|
||||||
* @returns A pointer on the character string.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
char* obi_retrieve_char_str(Obi_indexer_p indexer, index_t idx);
|
|
||||||
|
|
||||||
|
|
||||||
#endif /* CHAR_STR_INDEXER_H_ */
|
|
||||||
|
|
||||||
198
src/crc64.c
198
src/crc64.c
@ -1,198 +0,0 @@
|
|||||||
/* Redis uses the CRC64 variant with "Jones" coefficients and init value of 0.
|
|
||||||
*
|
|
||||||
* Specification of this CRC64 variant follows:
|
|
||||||
* Name: crc-64-jones
|
|
||||||
* Width: 64 bites
|
|
||||||
* Poly: 0xad93d23594c935a9
|
|
||||||
* Reflected In: True
|
|
||||||
* Xor_In: 0xffffffffffffffff
|
|
||||||
* Reflected_Out: True
|
|
||||||
* Xor_Out: 0x0
|
|
||||||
* Check("123456789"): 0xe9c6d914c4b8d9ca
|
|
||||||
*
|
|
||||||
* Copyright (c) 2012, Salvatore Sanfilippo <antirez at gmail dot com>
|
|
||||||
* All rights reserved.
|
|
||||||
*
|
|
||||||
* Redistribution and use in source and binary forms, with or without
|
|
||||||
* modification, are permitted provided that the following conditions are met:
|
|
||||||
*
|
|
||||||
* * Redistributions of source code must retain the above copyright notice,
|
|
||||||
* this list of conditions and the following disclaimer.
|
|
||||||
* * Redistributions in binary form must reproduce the above copyright
|
|
||||||
* notice, this list of conditions and the following disclaimer in the
|
|
||||||
* documentation and/or other materials provided with the distribution.
|
|
||||||
* * Neither the name of Redis nor the names of its contributors may be used
|
|
||||||
* to endorse or promote products derived from this software without
|
|
||||||
* specific prior written permission.
|
|
||||||
*
|
|
||||||
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
|
||||||
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
|
||||||
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
|
|
||||||
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
|
|
||||||
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
|
|
||||||
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
|
|
||||||
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
|
|
||||||
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
|
|
||||||
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
|
|
||||||
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
|
|
||||||
* POSSIBILITY OF SUCH DAMAGE. */
|
|
||||||
|
|
||||||
#include <stdint.h>
|
|
||||||
|
|
||||||
static const uint64_t crc64_tab[256] = {
|
|
||||||
UINT64_C(0x0000000000000000), UINT64_C(0x7ad870c830358979),
|
|
||||||
UINT64_C(0xf5b0e190606b12f2), UINT64_C(0x8f689158505e9b8b),
|
|
||||||
UINT64_C(0xc038e5739841b68f), UINT64_C(0xbae095bba8743ff6),
|
|
||||||
UINT64_C(0x358804e3f82aa47d), UINT64_C(0x4f50742bc81f2d04),
|
|
||||||
UINT64_C(0xab28ecb46814fe75), UINT64_C(0xd1f09c7c5821770c),
|
|
||||||
UINT64_C(0x5e980d24087fec87), UINT64_C(0x24407dec384a65fe),
|
|
||||||
UINT64_C(0x6b1009c7f05548fa), UINT64_C(0x11c8790fc060c183),
|
|
||||||
UINT64_C(0x9ea0e857903e5a08), UINT64_C(0xe478989fa00bd371),
|
|
||||||
UINT64_C(0x7d08ff3b88be6f81), UINT64_C(0x07d08ff3b88be6f8),
|
|
||||||
UINT64_C(0x88b81eabe8d57d73), UINT64_C(0xf2606e63d8e0f40a),
|
|
||||||
UINT64_C(0xbd301a4810ffd90e), UINT64_C(0xc7e86a8020ca5077),
|
|
||||||
UINT64_C(0x4880fbd87094cbfc), UINT64_C(0x32588b1040a14285),
|
|
||||||
UINT64_C(0xd620138fe0aa91f4), UINT64_C(0xacf86347d09f188d),
|
|
||||||
UINT64_C(0x2390f21f80c18306), UINT64_C(0x594882d7b0f40a7f),
|
|
||||||
UINT64_C(0x1618f6fc78eb277b), UINT64_C(0x6cc0863448deae02),
|
|
||||||
UINT64_C(0xe3a8176c18803589), UINT64_C(0x997067a428b5bcf0),
|
|
||||||
UINT64_C(0xfa11fe77117cdf02), UINT64_C(0x80c98ebf2149567b),
|
|
||||||
UINT64_C(0x0fa11fe77117cdf0), UINT64_C(0x75796f2f41224489),
|
|
||||||
UINT64_C(0x3a291b04893d698d), UINT64_C(0x40f16bccb908e0f4),
|
|
||||||
UINT64_C(0xcf99fa94e9567b7f), UINT64_C(0xb5418a5cd963f206),
|
|
||||||
UINT64_C(0x513912c379682177), UINT64_C(0x2be1620b495da80e),
|
|
||||||
UINT64_C(0xa489f35319033385), UINT64_C(0xde51839b2936bafc),
|
|
||||||
UINT64_C(0x9101f7b0e12997f8), UINT64_C(0xebd98778d11c1e81),
|
|
||||||
UINT64_C(0x64b116208142850a), UINT64_C(0x1e6966e8b1770c73),
|
|
||||||
UINT64_C(0x8719014c99c2b083), UINT64_C(0xfdc17184a9f739fa),
|
|
||||||
UINT64_C(0x72a9e0dcf9a9a271), UINT64_C(0x08719014c99c2b08),
|
|
||||||
UINT64_C(0x4721e43f0183060c), UINT64_C(0x3df994f731b68f75),
|
|
||||||
UINT64_C(0xb29105af61e814fe), UINT64_C(0xc849756751dd9d87),
|
|
||||||
UINT64_C(0x2c31edf8f1d64ef6), UINT64_C(0x56e99d30c1e3c78f),
|
|
||||||
UINT64_C(0xd9810c6891bd5c04), UINT64_C(0xa3597ca0a188d57d),
|
|
||||||
UINT64_C(0xec09088b6997f879), UINT64_C(0x96d1784359a27100),
|
|
||||||
UINT64_C(0x19b9e91b09fcea8b), UINT64_C(0x636199d339c963f2),
|
|
||||||
UINT64_C(0xdf7adabd7a6e2d6f), UINT64_C(0xa5a2aa754a5ba416),
|
|
||||||
UINT64_C(0x2aca3b2d1a053f9d), UINT64_C(0x50124be52a30b6e4),
|
|
||||||
UINT64_C(0x1f423fcee22f9be0), UINT64_C(0x659a4f06d21a1299),
|
|
||||||
UINT64_C(0xeaf2de5e82448912), UINT64_C(0x902aae96b271006b),
|
|
||||||
UINT64_C(0x74523609127ad31a), UINT64_C(0x0e8a46c1224f5a63),
|
|
||||||
UINT64_C(0x81e2d7997211c1e8), UINT64_C(0xfb3aa75142244891),
|
|
||||||
UINT64_C(0xb46ad37a8a3b6595), UINT64_C(0xceb2a3b2ba0eecec),
|
|
||||||
UINT64_C(0x41da32eaea507767), UINT64_C(0x3b024222da65fe1e),
|
|
||||||
UINT64_C(0xa2722586f2d042ee), UINT64_C(0xd8aa554ec2e5cb97),
|
|
||||||
UINT64_C(0x57c2c41692bb501c), UINT64_C(0x2d1ab4dea28ed965),
|
|
||||||
UINT64_C(0x624ac0f56a91f461), UINT64_C(0x1892b03d5aa47d18),
|
|
||||||
UINT64_C(0x97fa21650afae693), UINT64_C(0xed2251ad3acf6fea),
|
|
||||||
UINT64_C(0x095ac9329ac4bc9b), UINT64_C(0x7382b9faaaf135e2),
|
|
||||||
UINT64_C(0xfcea28a2faafae69), UINT64_C(0x8632586aca9a2710),
|
|
||||||
UINT64_C(0xc9622c4102850a14), UINT64_C(0xb3ba5c8932b0836d),
|
|
||||||
UINT64_C(0x3cd2cdd162ee18e6), UINT64_C(0x460abd1952db919f),
|
|
||||||
UINT64_C(0x256b24ca6b12f26d), UINT64_C(0x5fb354025b277b14),
|
|
||||||
UINT64_C(0xd0dbc55a0b79e09f), UINT64_C(0xaa03b5923b4c69e6),
|
|
||||||
UINT64_C(0xe553c1b9f35344e2), UINT64_C(0x9f8bb171c366cd9b),
|
|
||||||
UINT64_C(0x10e3202993385610), UINT64_C(0x6a3b50e1a30ddf69),
|
|
||||||
UINT64_C(0x8e43c87e03060c18), UINT64_C(0xf49bb8b633338561),
|
|
||||||
UINT64_C(0x7bf329ee636d1eea), UINT64_C(0x012b592653589793),
|
|
||||||
UINT64_C(0x4e7b2d0d9b47ba97), UINT64_C(0x34a35dc5ab7233ee),
|
|
||||||
UINT64_C(0xbbcbcc9dfb2ca865), UINT64_C(0xc113bc55cb19211c),
|
|
||||||
UINT64_C(0x5863dbf1e3ac9dec), UINT64_C(0x22bbab39d3991495),
|
|
||||||
UINT64_C(0xadd33a6183c78f1e), UINT64_C(0xd70b4aa9b3f20667),
|
|
||||||
UINT64_C(0x985b3e827bed2b63), UINT64_C(0xe2834e4a4bd8a21a),
|
|
||||||
UINT64_C(0x6debdf121b863991), UINT64_C(0x1733afda2bb3b0e8),
|
|
||||||
UINT64_C(0xf34b37458bb86399), UINT64_C(0x8993478dbb8deae0),
|
|
||||||
UINT64_C(0x06fbd6d5ebd3716b), UINT64_C(0x7c23a61ddbe6f812),
|
|
||||||
UINT64_C(0x3373d23613f9d516), UINT64_C(0x49aba2fe23cc5c6f),
|
|
||||||
UINT64_C(0xc6c333a67392c7e4), UINT64_C(0xbc1b436e43a74e9d),
|
|
||||||
UINT64_C(0x95ac9329ac4bc9b5), UINT64_C(0xef74e3e19c7e40cc),
|
|
||||||
UINT64_C(0x601c72b9cc20db47), UINT64_C(0x1ac40271fc15523e),
|
|
||||||
UINT64_C(0x5594765a340a7f3a), UINT64_C(0x2f4c0692043ff643),
|
|
||||||
UINT64_C(0xa02497ca54616dc8), UINT64_C(0xdafce7026454e4b1),
|
|
||||||
UINT64_C(0x3e847f9dc45f37c0), UINT64_C(0x445c0f55f46abeb9),
|
|
||||||
UINT64_C(0xcb349e0da4342532), UINT64_C(0xb1eceec59401ac4b),
|
|
||||||
UINT64_C(0xfebc9aee5c1e814f), UINT64_C(0x8464ea266c2b0836),
|
|
||||||
UINT64_C(0x0b0c7b7e3c7593bd), UINT64_C(0x71d40bb60c401ac4),
|
|
||||||
UINT64_C(0xe8a46c1224f5a634), UINT64_C(0x927c1cda14c02f4d),
|
|
||||||
UINT64_C(0x1d148d82449eb4c6), UINT64_C(0x67ccfd4a74ab3dbf),
|
|
||||||
UINT64_C(0x289c8961bcb410bb), UINT64_C(0x5244f9a98c8199c2),
|
|
||||||
UINT64_C(0xdd2c68f1dcdf0249), UINT64_C(0xa7f41839ecea8b30),
|
|
||||||
UINT64_C(0x438c80a64ce15841), UINT64_C(0x3954f06e7cd4d138),
|
|
||||||
UINT64_C(0xb63c61362c8a4ab3), UINT64_C(0xcce411fe1cbfc3ca),
|
|
||||||
UINT64_C(0x83b465d5d4a0eece), UINT64_C(0xf96c151de49567b7),
|
|
||||||
UINT64_C(0x76048445b4cbfc3c), UINT64_C(0x0cdcf48d84fe7545),
|
|
||||||
UINT64_C(0x6fbd6d5ebd3716b7), UINT64_C(0x15651d968d029fce),
|
|
||||||
UINT64_C(0x9a0d8ccedd5c0445), UINT64_C(0xe0d5fc06ed698d3c),
|
|
||||||
UINT64_C(0xaf85882d2576a038), UINT64_C(0xd55df8e515432941),
|
|
||||||
UINT64_C(0x5a3569bd451db2ca), UINT64_C(0x20ed197575283bb3),
|
|
||||||
UINT64_C(0xc49581ead523e8c2), UINT64_C(0xbe4df122e51661bb),
|
|
||||||
UINT64_C(0x3125607ab548fa30), UINT64_C(0x4bfd10b2857d7349),
|
|
||||||
UINT64_C(0x04ad64994d625e4d), UINT64_C(0x7e7514517d57d734),
|
|
||||||
UINT64_C(0xf11d85092d094cbf), UINT64_C(0x8bc5f5c11d3cc5c6),
|
|
||||||
UINT64_C(0x12b5926535897936), UINT64_C(0x686de2ad05bcf04f),
|
|
||||||
UINT64_C(0xe70573f555e26bc4), UINT64_C(0x9ddd033d65d7e2bd),
|
|
||||||
UINT64_C(0xd28d7716adc8cfb9), UINT64_C(0xa85507de9dfd46c0),
|
|
||||||
UINT64_C(0x273d9686cda3dd4b), UINT64_C(0x5de5e64efd965432),
|
|
||||||
UINT64_C(0xb99d7ed15d9d8743), UINT64_C(0xc3450e196da80e3a),
|
|
||||||
UINT64_C(0x4c2d9f413df695b1), UINT64_C(0x36f5ef890dc31cc8),
|
|
||||||
UINT64_C(0x79a59ba2c5dc31cc), UINT64_C(0x037deb6af5e9b8b5),
|
|
||||||
UINT64_C(0x8c157a32a5b7233e), UINT64_C(0xf6cd0afa9582aa47),
|
|
||||||
UINT64_C(0x4ad64994d625e4da), UINT64_C(0x300e395ce6106da3),
|
|
||||||
UINT64_C(0xbf66a804b64ef628), UINT64_C(0xc5bed8cc867b7f51),
|
|
||||||
UINT64_C(0x8aeeace74e645255), UINT64_C(0xf036dc2f7e51db2c),
|
|
||||||
UINT64_C(0x7f5e4d772e0f40a7), UINT64_C(0x05863dbf1e3ac9de),
|
|
||||||
UINT64_C(0xe1fea520be311aaf), UINT64_C(0x9b26d5e88e0493d6),
|
|
||||||
UINT64_C(0x144e44b0de5a085d), UINT64_C(0x6e963478ee6f8124),
|
|
||||||
UINT64_C(0x21c640532670ac20), UINT64_C(0x5b1e309b16452559),
|
|
||||||
UINT64_C(0xd476a1c3461bbed2), UINT64_C(0xaeaed10b762e37ab),
|
|
||||||
UINT64_C(0x37deb6af5e9b8b5b), UINT64_C(0x4d06c6676eae0222),
|
|
||||||
UINT64_C(0xc26e573f3ef099a9), UINT64_C(0xb8b627f70ec510d0),
|
|
||||||
UINT64_C(0xf7e653dcc6da3dd4), UINT64_C(0x8d3e2314f6efb4ad),
|
|
||||||
UINT64_C(0x0256b24ca6b12f26), UINT64_C(0x788ec2849684a65f),
|
|
||||||
UINT64_C(0x9cf65a1b368f752e), UINT64_C(0xe62e2ad306bafc57),
|
|
||||||
UINT64_C(0x6946bb8b56e467dc), UINT64_C(0x139ecb4366d1eea5),
|
|
||||||
UINT64_C(0x5ccebf68aecec3a1), UINT64_C(0x2616cfa09efb4ad8),
|
|
||||||
UINT64_C(0xa97e5ef8cea5d153), UINT64_C(0xd3a62e30fe90582a),
|
|
||||||
UINT64_C(0xb0c7b7e3c7593bd8), UINT64_C(0xca1fc72bf76cb2a1),
|
|
||||||
UINT64_C(0x45775673a732292a), UINT64_C(0x3faf26bb9707a053),
|
|
||||||
UINT64_C(0x70ff52905f188d57), UINT64_C(0x0a2722586f2d042e),
|
|
||||||
UINT64_C(0x854fb3003f739fa5), UINT64_C(0xff97c3c80f4616dc),
|
|
||||||
UINT64_C(0x1bef5b57af4dc5ad), UINT64_C(0x61372b9f9f784cd4),
|
|
||||||
UINT64_C(0xee5fbac7cf26d75f), UINT64_C(0x9487ca0fff135e26),
|
|
||||||
UINT64_C(0xdbd7be24370c7322), UINT64_C(0xa10fceec0739fa5b),
|
|
||||||
UINT64_C(0x2e675fb4576761d0), UINT64_C(0x54bf2f7c6752e8a9),
|
|
||||||
UINT64_C(0xcdcf48d84fe75459), UINT64_C(0xb71738107fd2dd20),
|
|
||||||
UINT64_C(0x387fa9482f8c46ab), UINT64_C(0x42a7d9801fb9cfd2),
|
|
||||||
UINT64_C(0x0df7adabd7a6e2d6), UINT64_C(0x772fdd63e7936baf),
|
|
||||||
UINT64_C(0xf8474c3bb7cdf024), UINT64_C(0x829f3cf387f8795d),
|
|
||||||
UINT64_C(0x66e7a46c27f3aa2c), UINT64_C(0x1c3fd4a417c62355),
|
|
||||||
UINT64_C(0x935745fc4798b8de), UINT64_C(0xe98f353477ad31a7),
|
|
||||||
UINT64_C(0xa6df411fbfb21ca3), UINT64_C(0xdc0731d78f8795da),
|
|
||||||
UINT64_C(0x536fa08fdfd90e51), UINT64_C(0x29b7d047efec8728),
|
|
||||||
};
|
|
||||||
|
|
||||||
|
|
||||||
uint64_t crc64(const char* s, uint64_t l)
|
|
||||||
{
|
|
||||||
uint64_t j;
|
|
||||||
uint64_t crc = 0;
|
|
||||||
|
|
||||||
for (j = 0; j < l; j++)
|
|
||||||
{
|
|
||||||
uint8_t byte = s[j];
|
|
||||||
crc = crc64_tab[(uint8_t)crc ^ byte] ^ (crc >> 8);
|
|
||||||
}
|
|
||||||
return crc;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
/* Test main */
|
|
||||||
//#ifdef TEST_MAIN
|
|
||||||
//#include <stdio.h>
|
|
||||||
//int main(void) {
|
|
||||||
// printf("e9c6d914c4b8d9ca == %016llx\n",
|
|
||||||
// (unsigned long long) crc64(0,(unsigned char*)"123456789",9));
|
|
||||||
// return 0;
|
|
||||||
//}
|
|
||||||
//#endif
|
|
||||||
|
|
||||||
|
|
||||||
14
src/crc64.h
14
src/crc64.h
@ -1,14 +0,0 @@
|
|||||||
/**
|
|
||||||
* @file crc64.h
|
|
||||||
* @date March 24th 2016
|
|
||||||
* @brief Header file for CRC64 function.
|
|
||||||
*/
|
|
||||||
|
|
||||||
#include <stdint.h>
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Generates and returns a 64-bit Cyclic Redundancy Check from a
|
|
||||||
* character string s of length l.
|
|
||||||
*/
|
|
||||||
uint64_t crc64(const char* s, uint64_t l);
|
|
||||||
@ -1,102 +0,0 @@
|
|||||||
/****************************************************************************
|
|
||||||
* DNA sequence indexing functions *
|
|
||||||
****************************************************************************/
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @file dna_seq_indexer.c
|
|
||||||
* @author Celine Mercier
|
|
||||||
* @date April 12th 2016
|
|
||||||
* @brief Functions handling the indexing and retrieval of DNA sequences.
|
|
||||||
*/
|
|
||||||
|
|
||||||
|
|
||||||
#include <stdlib.h>
|
|
||||||
#include <stdio.h>
|
|
||||||
#include <math.h>
|
|
||||||
|
|
||||||
#include "obiblob.h"
|
|
||||||
#include "obiblob_indexer.h"
|
|
||||||
#include "obidebug.h"
|
|
||||||
#include "obitypes.h"
|
|
||||||
|
|
||||||
|
|
||||||
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
|
||||||
|
|
||||||
|
|
||||||
Obi_blob_p obi_seq_to_blob(const char* seq)
|
|
||||||
{
|
|
||||||
Obi_blob_p value_b;
|
|
||||||
int32_t length_encoded_seq; // length of the encoded sequence in bytes
|
|
||||||
int32_t seq_length;
|
|
||||||
byte_t* encoded_seq;
|
|
||||||
|
|
||||||
seq_length = strlen(seq);
|
|
||||||
|
|
||||||
// Check if just ATGC and encode accordingly
|
|
||||||
if (only_ATGC(seq))
|
|
||||||
{
|
|
||||||
// Compute the length (in bytes) of the encoded sequence
|
|
||||||
length_encoded_seq = ceil((double) seq_length / (double) 4.0);
|
|
||||||
// Encode
|
|
||||||
encoded_seq = encode_seq_on_2_bits(seq, seq_length);
|
|
||||||
if (encoded_seq == NULL)
|
|
||||||
return NULL;
|
|
||||||
value_b = obi_blob(encoded_seq, ELEMENT_SIZE_SEQ_2, length_encoded_seq, seq_length);
|
|
||||||
}
|
|
||||||
else
|
|
||||||
{
|
|
||||||
// Compute the length (in bytes) of the encoded sequence
|
|
||||||
length_encoded_seq = ceil((double) seq_length / (double) 2.0);
|
|
||||||
// Encode
|
|
||||||
encoded_seq = encode_seq_on_4_bits(seq, seq_length);
|
|
||||||
if (encoded_seq == NULL)
|
|
||||||
return NULL;
|
|
||||||
value_b = obi_blob(encoded_seq, ELEMENT_SIZE_SEQ_4, length_encoded_seq, seq_length);
|
|
||||||
}
|
|
||||||
|
|
||||||
free(encoded_seq);
|
|
||||||
|
|
||||||
return value_b;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
char* obi_blob_to_seq(Obi_blob_p value_b)
|
|
||||||
{
|
|
||||||
// Decode
|
|
||||||
if (value_b->element_size == 2)
|
|
||||||
return decode_seq_on_2_bits(value_b->value, value_b->length_decoded_value);
|
|
||||||
else
|
|
||||||
return decode_seq_on_4_bits(value_b->value, value_b->length_decoded_value);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
index_t obi_index_dna_seq(Obi_indexer_p indexer, const char* value)
|
|
||||||
{
|
|
||||||
Obi_blob_p value_b;
|
|
||||||
index_t idx;
|
|
||||||
|
|
||||||
// Encode value
|
|
||||||
value_b = obi_seq_to_blob(value);
|
|
||||||
if (value_b == NULL)
|
|
||||||
return -1;
|
|
||||||
|
|
||||||
// Add in the indexer
|
|
||||||
idx = obi_indexer_add(indexer, value_b);
|
|
||||||
|
|
||||||
free(value_b);
|
|
||||||
|
|
||||||
return idx;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
char* obi_retrieve_dna_seq(Obi_indexer_p indexer, index_t idx)
|
|
||||||
{
|
|
||||||
Obi_blob_p value_b;
|
|
||||||
|
|
||||||
// Get encoded value
|
|
||||||
value_b = obi_indexer_get(indexer, idx);
|
|
||||||
|
|
||||||
// Return decoded sequence
|
|
||||||
return obi_blob_to_seq(value_b);
|
|
||||||
}
|
|
||||||
|
|
||||||
@ -1,87 +0,0 @@
|
|||||||
/****************************************************************************
|
|
||||||
* DNA sequence indexer header file *
|
|
||||||
****************************************************************************/
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @file dna_seq_indexer.h
|
|
||||||
* @author Celine Mercier
|
|
||||||
* @date April 12th 2016
|
|
||||||
* @brief Header file for the functions handling the indexing of DNA sequences.
|
|
||||||
*/
|
|
||||||
|
|
||||||
|
|
||||||
#ifndef DNA_SEQ_INDEXER_H_
|
|
||||||
#define DNA_SEQ_INDEXER_H_
|
|
||||||
|
|
||||||
|
|
||||||
#include <stdlib.h>
|
|
||||||
#include <stdio.h>
|
|
||||||
|
|
||||||
#include "obidms.h"
|
|
||||||
#include "obitypes.h"
|
|
||||||
#include "obiblob.h"
|
|
||||||
#include "obiblob_indexer.h"
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Converts a DNA sequence to a blob.
|
|
||||||
*
|
|
||||||
* @warning The blob must be freed by the caller.
|
|
||||||
*
|
|
||||||
* @param value The DNA sequence to convert.
|
|
||||||
*
|
|
||||||
* @returns A pointer to the blob created.
|
|
||||||
* @retval NULL if an error occurred.
|
|
||||||
*
|
|
||||||
* @since November 2015
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
Obi_blob_p obi_seq_to_blob(const char* seq);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Converts a blob to a DNA sequence.
|
|
||||||
*
|
|
||||||
* @param value_b The blob to convert.
|
|
||||||
*
|
|
||||||
* @returns A pointer to the DNA sequence contained in the blob.
|
|
||||||
* @retval NULL if an error occurred.
|
|
||||||
*
|
|
||||||
* @since November 2015
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
char* obi_blob_to_seq(Obi_blob_p value_b);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Stores a DNA sequence in an indexer and returns the index.
|
|
||||||
*
|
|
||||||
* @param indexer The indexer structure.
|
|
||||||
* @param value The DNA sequence to index.
|
|
||||||
*
|
|
||||||
* @returns The index referring to the stored DNA sequence in the indexer.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
index_t obi_index_dna_seq(Obi_indexer_p indexer, const char* value);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Retrieves a DNA sequence from an indexer.
|
|
||||||
*
|
|
||||||
* @warning The DNA sequence returned must be freed by the caller.
|
|
||||||
*
|
|
||||||
* @param indexer The indexer structure.
|
|
||||||
* @param idx The index referring to the DNA sequence to retrieve in the indexer.
|
|
||||||
*
|
|
||||||
* @returns A pointer on the DNA sequence.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
char* obi_retrieve_dna_seq(Obi_indexer_p indexer, index_t idx);
|
|
||||||
|
|
||||||
|
|
||||||
#endif /* DNA_SEQ_INDEXER_H_ */
|
|
||||||
|
|
||||||
46
src/encode.c
46
src/encode.c
@ -28,9 +28,9 @@
|
|||||||
|
|
||||||
|
|
||||||
|
|
||||||
bool only_ATGC(const char* seq)
|
bool only_ATGC(char* seq)
|
||||||
{
|
{
|
||||||
const char* c = seq;
|
char* c = seq;
|
||||||
|
|
||||||
while (*c)
|
while (*c)
|
||||||
{
|
{
|
||||||
@ -54,7 +54,7 @@ bool only_ATGC(const char* seq)
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
byte_t* encode_seq_on_2_bits(const char* seq, int32_t length)
|
byte_t* encode_seq_on_2_bits(char* seq, int32_t length)
|
||||||
{
|
{
|
||||||
byte_t* seq_b;
|
byte_t* seq_b;
|
||||||
uint8_t modulo;
|
uint8_t modulo;
|
||||||
@ -63,13 +63,10 @@ byte_t* encode_seq_on_2_bits(const char* seq, int32_t length)
|
|||||||
|
|
||||||
length_b = ceil((double) length / (double) 4.0);
|
length_b = ceil((double) length / (double) 4.0);
|
||||||
|
|
||||||
seq_b = (byte_t*) calloc(length_b, sizeof(byte_t));
|
seq_b = (byte_t*) malloc(length_b * sizeof(byte_t));
|
||||||
if (seq_b == NULL)
|
|
||||||
{
|
// Initialize all the bits to 0
|
||||||
obi_set_errno(OBI_MALLOC_ERROR);
|
memset(seq_b, 0, length_b);
|
||||||
obidebug(1, "\nError allocating memory for an encoded DNA sequence");
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
for (i=0; i<length; i++)
|
for (i=0; i<length; i++)
|
||||||
{
|
{
|
||||||
@ -96,7 +93,6 @@ byte_t* encode_seq_on_2_bits(const char* seq, int32_t length)
|
|||||||
seq_b[i/4] |= NUC_T_2b;
|
seq_b[i/4] |= NUC_T_2b;
|
||||||
break;
|
break;
|
||||||
default:
|
default:
|
||||||
obi_set_errno(OBI_ENCODE_ERROR);
|
|
||||||
obidebug(1, "\nInvalid nucleotide base when encoding (not [atgcATGC])");
|
obidebug(1, "\nInvalid nucleotide base when encoding (not [atgcATGC])");
|
||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
@ -120,12 +116,6 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq)
|
|||||||
uint8_t nuc;
|
uint8_t nuc;
|
||||||
|
|
||||||
seq = (char*) malloc((length_seq+1) * sizeof(char));
|
seq = (char*) malloc((length_seq+1) * sizeof(char));
|
||||||
if (seq == NULL)
|
|
||||||
{
|
|
||||||
obi_set_errno(OBI_MALLOC_ERROR);
|
|
||||||
obidebug(1, "\nError allocating memory for a decoded DNA sequence");
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
for (i=0; i<length_seq; i++)
|
for (i=0; i<length_seq; i++)
|
||||||
{
|
{
|
||||||
@ -148,7 +138,6 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq)
|
|||||||
seq[i] = 't';
|
seq[i] = 't';
|
||||||
break;
|
break;
|
||||||
default:
|
default:
|
||||||
obi_set_errno(OBI_DECODE_ERROR);
|
|
||||||
obidebug(1, "\nInvalid nucleotide base when decoding");
|
obidebug(1, "\nInvalid nucleotide base when decoding");
|
||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
@ -160,7 +149,7 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq)
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
byte_t* encode_seq_on_4_bits(const char* seq, int32_t length)
|
byte_t* encode_seq_on_4_bits(char* seq, int32_t length)
|
||||||
{
|
{
|
||||||
byte_t* seq_b;
|
byte_t* seq_b;
|
||||||
uint8_t modulo;
|
uint8_t modulo;
|
||||||
@ -169,13 +158,10 @@ byte_t* encode_seq_on_4_bits(const char* seq, int32_t length)
|
|||||||
|
|
||||||
length_b = ceil((double) length / (double) 2.0);
|
length_b = ceil((double) length / (double) 2.0);
|
||||||
|
|
||||||
seq_b = (byte_t*) calloc(length_b, sizeof(byte_t));
|
seq_b = (byte_t*) malloc(length_b * sizeof(byte_t));
|
||||||
if (seq_b == NULL)
|
|
||||||
{
|
// Initialize all the bits to 0
|
||||||
obi_set_errno(OBI_MALLOC_ERROR);
|
memset(seq_b, 0, length_b);
|
||||||
obidebug(1, "\nError allocating memory for an encoded DNA sequence");
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
for (i=0; i<length; i++)
|
for (i=0; i<length; i++)
|
||||||
{
|
{
|
||||||
@ -246,7 +232,6 @@ byte_t* encode_seq_on_4_bits(const char* seq, int32_t length)
|
|||||||
seq_b[i/2] |= NUC_N_4b;
|
seq_b[i/2] |= NUC_N_4b;
|
||||||
break;
|
break;
|
||||||
default:
|
default:
|
||||||
obi_set_errno(OBI_ENCODE_ERROR);
|
|
||||||
obidebug(1, "\nInvalid nucleotide base when encoding (not IUPAC)");
|
obidebug(1, "\nInvalid nucleotide base when encoding (not IUPAC)");
|
||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
@ -270,12 +255,6 @@ char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq)
|
|||||||
uint8_t nuc;
|
uint8_t nuc;
|
||||||
|
|
||||||
seq = (char*) malloc((length_seq+1) * sizeof(char));
|
seq = (char*) malloc((length_seq+1) * sizeof(char));
|
||||||
if (seq == NULL)
|
|
||||||
{
|
|
||||||
obi_set_errno(OBI_MALLOC_ERROR);
|
|
||||||
obidebug(1, "\nError allocating memory for a decoded DNA sequence");
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
for (i=0; i<length_seq; i++)
|
for (i=0; i<length_seq; i++)
|
||||||
{
|
{
|
||||||
@ -331,7 +310,6 @@ char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq)
|
|||||||
seq[i] = 'n';
|
seq[i] = 'n';
|
||||||
break;
|
break;
|
||||||
default:
|
default:
|
||||||
obi_set_errno(OBI_DECODE_ERROR);
|
|
||||||
obidebug(1, "\nInvalid nucleotide base when decoding");
|
obidebug(1, "\nInvalid nucleotide base when decoding");
|
||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
|
|||||||
23
src/encode.h
23
src/encode.h
@ -10,10 +10,6 @@
|
|||||||
*/
|
*/
|
||||||
|
|
||||||
|
|
||||||
#ifndef ENCODE_H_
|
|
||||||
#define ENCODE_H_
|
|
||||||
|
|
||||||
|
|
||||||
#include <stdlib.h>
|
#include <stdlib.h>
|
||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
#include <stdint.h>
|
#include <stdint.h>
|
||||||
@ -22,10 +18,8 @@
|
|||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
|
|
||||||
|
|
||||||
#define NUC_MASK_2B 0x3 /**< Binary: 11 to use when decoding 2 bits sequences
|
#define NUC_MASK_2B 0x3 /**< Binary: 11 to use when decoding 2 bits sequences */
|
||||||
*/
|
#define NUC_MASK_4B 0xF /**< Binary: 1111 to use when decoding 4 bits sequences */
|
||||||
#define NUC_MASK_4B 0xF /**< Binary: 1111 to use when decoding 4 bits sequences
|
|
||||||
*/
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
@ -75,7 +69,7 @@ enum
|
|||||||
* @since November 2015
|
* @since November 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
bool only_ATGC(const char* seq);
|
bool only_ATGC(char* seq);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
@ -96,7 +90,7 @@ bool only_ATGC(const char* seq);
|
|||||||
* @since November 2015
|
* @since November 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
byte_t* encode_seq_on_2_bits(const char* seq, int32_t length);
|
byte_t* encode_seq_on_2_bits(char* seq, int32_t length);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
@ -107,7 +101,7 @@ byte_t* encode_seq_on_2_bits(const char* seq, int32_t length);
|
|||||||
* 10 -> t
|
* 10 -> t
|
||||||
* 11 -> g
|
* 11 -> g
|
||||||
*
|
*
|
||||||
* @param seq_b The sequence to decode.
|
* @param seq The sequence to decode.
|
||||||
* @param length_seq The initial length of the sequence before it was encoded.
|
* @param length_seq The initial length of the sequence before it was encoded.
|
||||||
*
|
*
|
||||||
* @returns The decoded sequence ended with '\0'.
|
* @returns The decoded sequence ended with '\0'.
|
||||||
@ -147,7 +141,7 @@ char* decode_seq_on_2_bits(byte_t* seq_b, int32_t length_seq);
|
|||||||
* @since November 2015
|
* @since November 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
byte_t* encode_seq_on_4_bits(const char* seq, int32_t length);
|
byte_t* encode_seq_on_4_bits(char* seq, int32_t length);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
@ -169,7 +163,7 @@ byte_t* encode_seq_on_4_bits(const char* seq, int32_t length);
|
|||||||
* V or v : 1110
|
* V or v : 1110
|
||||||
* N or n : 1111
|
* N or n : 1111
|
||||||
*
|
*
|
||||||
* @param seq_b The sequence to decode.
|
* @param seq The sequence to decode.
|
||||||
* @param length_seq The initial length of the sequence before it was encoded.
|
* @param length_seq The initial length of the sequence before it was encoded.
|
||||||
*
|
*
|
||||||
* @returns The decoded sequence ended with '\0'.
|
* @returns The decoded sequence ended with '\0'.
|
||||||
@ -185,6 +179,3 @@ char* decode_seq_on_4_bits(byte_t* seq_b, int32_t length_seq);
|
|||||||
// little endian
|
// little endian
|
||||||
void print_bits(void* ptr, int32_t length);
|
void print_bits(void* ptr, int32_t length);
|
||||||
|
|
||||||
|
|
||||||
#endif /* ENCODE_H_ */
|
|
||||||
|
|
||||||
|
|||||||
@ -1,64 +0,0 @@
|
|||||||
//-----------------------------------------------------------------------------
|
|
||||||
// MurmurHash2, by Austin Appleby
|
|
||||||
|
|
||||||
// Note - This code makes a few assumptions about how your machine behaves -
|
|
||||||
|
|
||||||
// 1. We can read a 4-byte value from any address without crashing
|
|
||||||
// 2. sizeof(int) == 4
|
|
||||||
|
|
||||||
// And it has a few limitations -
|
|
||||||
|
|
||||||
// 1. It will not work incrementally.
|
|
||||||
// 2. It will not produce the same results on little-endian and big-endian
|
|
||||||
// machines. ->TODO
|
|
||||||
|
|
||||||
unsigned int murmurhash2(const void * key, int len, const unsigned int seed)
|
|
||||||
{
|
|
||||||
// 'm' and 'r' are mixing constants generated offline.
|
|
||||||
// They're not really 'magic', they just happen to work well.
|
|
||||||
|
|
||||||
const unsigned int m = 0x5bd1e995;
|
|
||||||
const int r = 24;
|
|
||||||
|
|
||||||
// Initialize the hash to a 'random' value
|
|
||||||
|
|
||||||
unsigned int h = seed ^ len;
|
|
||||||
|
|
||||||
// Mix 4 bytes at a time into the hash
|
|
||||||
|
|
||||||
const unsigned char * data = (const unsigned char *)key;
|
|
||||||
|
|
||||||
while(len >= 4)
|
|
||||||
{
|
|
||||||
unsigned int k = *(unsigned int *)data;
|
|
||||||
|
|
||||||
k *= m;
|
|
||||||
k ^= k >> r;
|
|
||||||
k *= m;
|
|
||||||
|
|
||||||
h *= m;
|
|
||||||
h ^= k;
|
|
||||||
|
|
||||||
data += 4;
|
|
||||||
len -= 4;
|
|
||||||
}
|
|
||||||
|
|
||||||
// Handle the last few bytes of the input array
|
|
||||||
|
|
||||||
switch(len)
|
|
||||||
{
|
|
||||||
case 3: h ^= data[2] << 16;
|
|
||||||
case 2: h ^= data[1] << 8;
|
|
||||||
case 1: h ^= data[0];
|
|
||||||
h *= m;
|
|
||||||
};
|
|
||||||
|
|
||||||
// Do a few final mixes of the hash to ensure the last few
|
|
||||||
// bytes are well-incorporated.
|
|
||||||
|
|
||||||
h ^= h >> 13;
|
|
||||||
h *= m;
|
|
||||||
h ^= h >> 15;
|
|
||||||
|
|
||||||
return h;
|
|
||||||
}
|
|
||||||
@ -1,11 +0,0 @@
|
|||||||
|
|
||||||
#ifndef _BLOOM_MURMURHASH2
|
|
||||||
#define _BLOOM_MURMURHASH2
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Generates and returns a hash code from a byte array.
|
|
||||||
*/
|
|
||||||
unsigned int murmurhash2(const void * key, int len, const unsigned int seed);
|
|
||||||
|
|
||||||
#endif
|
|
||||||
1380
src/obiavl.c
1380
src/obiavl.c
File diff suppressed because it is too large
Load Diff
336
src/obiavl.h
336
src/obiavl.h
@ -6,7 +6,7 @@
|
|||||||
* @file obiavl.h
|
* @file obiavl.h
|
||||||
* @author Celine Mercier
|
* @author Celine Mercier
|
||||||
* @date December 3rd 2015
|
* @date December 3rd 2015
|
||||||
* @brief Header file for handling AVL trees for storing and retrieving blobs.
|
* @brief Header file for handling AVL trees for storing and retrieving byte arrays (i.e. coding for character strings).
|
||||||
*/
|
*/
|
||||||
|
|
||||||
|
|
||||||
@ -23,49 +23,35 @@
|
|||||||
#include <stdbool.h>
|
#include <stdbool.h>
|
||||||
|
|
||||||
#include "obidms.h"
|
#include "obidms.h"
|
||||||
#include "obiblob.h"
|
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
#include "bloom.h"
|
|
||||||
#include "utils.h"
|
|
||||||
#include "encode.h"
|
|
||||||
|
|
||||||
|
|
||||||
#define MAX_NB_OF_AVLS_IN_GROUP (100) /**< The maximum number of AVL trees in a group. // TODO discuss
|
|
||||||
*/
|
|
||||||
#define MAX_NODE_COUNT_PER_AVL (10000000) /**< The maximum number of nodes in an AVL tree.
|
|
||||||
* Only used to decide when to create a new AVL in a group, and to initialize the bloom filter // TODO discuss.
|
|
||||||
*/
|
|
||||||
#define MAX_DATA_SIZE_PER_AVL (1073741824) /**< The maximum size of the data referred to by an AVL tree in a group.
|
|
||||||
* Only used to decide when to create a new AVL in a group.
|
|
||||||
* Should not be greater than int32_t max (2,147,483,647), as indexes will have to be stored on 32 bits.
|
|
||||||
* Here 1073741824 B = 1 GB
|
|
||||||
*/
|
|
||||||
#define AVL_MAX_DEPTH (1024) /**< The maximum depth of an AVL tree. Used to save paths through the tree.
|
|
||||||
*/
|
|
||||||
#define AVL_MAX_NAME (1024) /**< The maximum length of an AVL tree name.
|
#define AVL_MAX_NAME (1024) /**< The maximum length of an AVL tree name.
|
||||||
*/
|
*/
|
||||||
#define AVL_GROWTH_FACTOR (2) /**< The growth factor when an AVL tree is enlarged.
|
#define AVL_GROWTH_FACTOR (2) /**< The growth factor when an AVL tree is enlarged.
|
||||||
*/
|
*/
|
||||||
|
#define AVL_MAX_DEPTH (1000) /**< The maximum depth of an AVL tree.
|
||||||
|
*/
|
||||||
#define LEFT_CHILD(node) (avl->tree)+(node->left_child) /**< Pointer to the left child of a node in an AVL tree.
|
#define LEFT_CHILD(node) (avl->tree)+(node->left_child) /**< Pointer to the left child of a node in an AVL tree.
|
||||||
*/
|
*/
|
||||||
#define RIGHT_CHILD(node) (avl->tree)+(node->right_child) /**< Pointer to the right child of a node in an AVL tree.
|
#define RIGHT_CHILD(node) (avl->tree)+(node->right_child) /**< Pointer to the right child of a node in an AVL tree.
|
||||||
*/
|
*/
|
||||||
|
#define BYTE_ARRAY_HEADER_SIZE (9) /**< The size of the header of a byte array.
|
||||||
|
*/
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief AVL tree node structure.
|
* @brief AVL tree node structure.
|
||||||
*/
|
*/
|
||||||
typedef struct AVL_node {
|
typedef struct AVL_node {
|
||||||
index_t left_child; /**< Index of left less child node.
|
index_t left_child; /**< Index of left less child node.
|
||||||
*/
|
*/
|
||||||
index_t right_child; /**< Index of right greater child node.
|
index_t right_child; /**< Index of right greater child node.
|
||||||
*/
|
*/
|
||||||
int8_t balance_factor; /**< Balance factor of the node.
|
int8_t balance_factor; /**< Balance factor of the node.
|
||||||
*/
|
*/
|
||||||
index_t value; /**< Index of the value associated with the node in the data array.
|
index_t value; /**< Index of the value associated with the node in the data array.
|
||||||
*/
|
*/
|
||||||
uint64_t crc64; /**< Cyclic Redundancy Check code on 64 bits associated with the value.
|
|
||||||
*/
|
|
||||||
} AVL_node_t, *AVL_node_p;
|
} AVL_node_t, *AVL_node_p;
|
||||||
|
|
||||||
|
|
||||||
@ -94,10 +80,8 @@ typedef struct OBIDMS_avl_data_header {
|
|||||||
typedef struct OBIDMS_avl_data {
|
typedef struct OBIDMS_avl_data {
|
||||||
OBIDMS_avl_data_header_p header; /**< A pointer to the header of the AVL tree data.
|
OBIDMS_avl_data_header_p header; /**< A pointer to the header of the AVL tree data.
|
||||||
*/
|
*/
|
||||||
byte_t* data; /**< A pointer to the beginning of the data.
|
byte_t* data; /**< A pointer to the beginning of the data.
|
||||||
*/
|
*/
|
||||||
int data_fd; /**< File descriptor of the file containing the data.
|
|
||||||
*/
|
|
||||||
} OBIDMS_avl_data_t, *OBIDMS_avl_data_p;
|
} OBIDMS_avl_data_t, *OBIDMS_avl_data_p;
|
||||||
|
|
||||||
|
|
||||||
@ -119,9 +103,6 @@ typedef struct OBIDMS_avl_header {
|
|||||||
*/
|
*/
|
||||||
time_t creation_date; /**< Date of creation of the file.
|
time_t creation_date; /**< Date of creation of the file.
|
||||||
*/
|
*/
|
||||||
bloom_t bloom_filter; /**< Bloom filter associated with the AVL tree, enabling to know if a value
|
|
||||||
* might already be stored in the data referred to by the tree.
|
|
||||||
*/
|
|
||||||
} OBIDMS_avl_header_t, *OBIDMS_avl_header_p;
|
} OBIDMS_avl_header_t, *OBIDMS_avl_header_p;
|
||||||
|
|
||||||
|
|
||||||
@ -129,59 +110,46 @@ typedef struct OBIDMS_avl_header {
|
|||||||
* @brief OBIDMS AVL tree structure.
|
* @brief OBIDMS AVL tree structure.
|
||||||
*/
|
*/
|
||||||
typedef struct OBIDMS_avl {
|
typedef struct OBIDMS_avl {
|
||||||
OBIDMS_p dms; /**< A pointer to the OBIDMS structure to which the AVL tree belongs.
|
OBIDMS_p dms; /**< A pointer to the OBIDMS structure to which the AVL tree belongs.
|
||||||
*/
|
*/
|
||||||
OBIDMS_avl_header_p header; /**< A pointer to the header of the AVL tree.
|
OBIDMS_avl_header_p header; /**< A pointer to the header of the AVL tree.
|
||||||
*/
|
*/
|
||||||
struct AVL_node* tree; /**< A pointer to the root of the AVL tree.
|
struct AVL_node* tree; /**< A pointer to the root of the AVL tree.
|
||||||
*/
|
*/
|
||||||
index_t path_idx[AVL_MAX_DEPTH]; /**< The path taken to a node from the root as an array of node indices.
|
index_t path_idx[AVL_MAX_DEPTH]; /**< The path taken to a node from the root as an array of node indices.
|
||||||
*/
|
*/
|
||||||
int8_t path_dir[AVL_MAX_DEPTH]; /**< The path taken to a node from the root as an array of directions
|
int8_t path_dir[AVL_MAX_DEPTH]; /**< The path taken to a node from the root as an array of directions
|
||||||
* (0 for left, -1 for right).
|
* (0 for left, -1 for right).
|
||||||
*/
|
*/
|
||||||
OBIDMS_avl_data_p data; /**< A pointer to the structure containing the data
|
OBIDMS_avl_data_p data; /**< A pointer to the structure containing the data
|
||||||
* that the AVL tree references.
|
* that the AVL tree references.
|
||||||
*/
|
*/
|
||||||
DIR* directory; /**< A directory entry usable to
|
DIR* directory; /**< A directory entry usable to
|
||||||
* refer and scan the AVL tree directory.
|
* refer and scan the AVL tree directory.
|
||||||
*/
|
*/
|
||||||
int dir_fd; /**< The file descriptor of the directory entry
|
int dir_fd; /**< The file descriptor of the directory entry
|
||||||
* usable to refer and scan the AVL tree directory.
|
* usable to refer and scan the AVL tree directory.
|
||||||
*/
|
*/
|
||||||
int avl_fd; /**< The file descriptor of the file containing the AVL tree.
|
int avl_fd; /**< The file descriptor of the file
|
||||||
*/
|
* to refer and scan the AVL tree.
|
||||||
|
*/
|
||||||
|
int data_fd; /**< The file descriptor of the file
|
||||||
|
* to refer and scan the data referred to by the AVL tree.
|
||||||
|
*/
|
||||||
|
size_t counter; /**< Indicates by how many threads/programs (TODO) the AVL tree is used.
|
||||||
|
*/
|
||||||
} OBIDMS_avl_t, *OBIDMS_avl_p;
|
} OBIDMS_avl_t, *OBIDMS_avl_p;
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief OBIDMS AVL tree group structure.
|
* @brief Checks if an AVL tree already exists or not.
|
||||||
*/
|
|
||||||
typedef struct OBIDMS_avl_group {
|
|
||||||
OBIDMS_avl_p sub_avls[MAX_NB_OF_AVLS_IN_GROUP]; /**< Array containing the pointers to the AVL trees of the group.
|
|
||||||
*/
|
|
||||||
int current_avl_idx; /**< Index in the sub_avls array of the AVL tree currently being filled.
|
|
||||||
*/
|
|
||||||
char name[AVL_MAX_NAME+1]; /**< Base name of the AVL group. The AVL trees in it have names of the form basename_idx.
|
|
||||||
*/
|
|
||||||
OBIDMS_p dms; /**< Pointer to the OBIDMS structure to which the AVL group belongs.
|
|
||||||
*/
|
|
||||||
bool writable; /**< Indicates whether the AVL group is read-only or not.
|
|
||||||
*/
|
|
||||||
size_t counter; /**< Indicates by how many threads/programs (TODO) the AVL group is used.
|
|
||||||
*/
|
|
||||||
} OBIDMS_avl_group_t, *OBIDMS_avl_group_p;
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Checks if an AVL tree or AVL tree group already exists or not.
|
|
||||||
*
|
*
|
||||||
* @param dms The OBIDMS to which the AVL tree or AVL tree group belongs.
|
* @param dms The OBIDMS to which the AVL tree belongs.
|
||||||
* @param avl_name The name of the AVL treeor the base name of the AVL tree group.
|
* @param avl_name The name of the AVL tree.
|
||||||
*
|
*
|
||||||
* @returns A value indicating whether the AVL tree or AVL tree group exists or not.
|
* @returns A value indicating whether the AVL tree exists or not.
|
||||||
* @retval 1 if the AVL tree or AVL tree group exists.
|
* @retval 1 if the AVL tree exists.
|
||||||
* @retval 0 if the AVL tree or AVL tree group does not exist.
|
* @retval 0 if the AVL tree does not exist.
|
||||||
* @retval -1 if an error occurred.
|
* @retval -1 if an error occurred.
|
||||||
*
|
*
|
||||||
* @since December 2015
|
* @since December 2015
|
||||||
@ -191,41 +159,15 @@ int obi_avl_exists(OBIDMS_p dms, const char* avl_name);
|
|||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Creates an AVL tree. Fails if it already exists.
|
* @brief Opens an AVL tree and creates it if it does not already exist.
|
||||||
*
|
*
|
||||||
* Note: An AVL tree is made of two files (referred to by two structures).
|
* Note: An AVL tree is made of two files (referred to by two structures).
|
||||||
* One file contains the tree referring to the data, and the other
|
* One file contains the indices referring to the data, and the other
|
||||||
* file contains the data itself. The AVL tree as a whole is referred
|
|
||||||
* to via the OBIDMS_avl structure. An AVL tree is stored in a directory
|
|
||||||
* with the same name, or with the base name of the AVL group if it is
|
|
||||||
* part of an AVL group.
|
|
||||||
*
|
|
||||||
* @param dms The OBIDMS to which the AVL tree belongs.
|
|
||||||
* @param avl_name The name of the AVL tree.
|
|
||||||
* @param avl_idx The index of the AVL tree if it is part of an AVL group,
|
|
||||||
* or -1 if it is not part of an AVL group.
|
|
||||||
*
|
|
||||||
* @returns A pointer to the newly created AVL tree structure.
|
|
||||||
* @retval NULL if an error occurred.
|
|
||||||
*
|
|
||||||
* @since December 2015
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name, int avl_idx);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Opens an AVL tree in read-only mode. Fails if it does not already exist.
|
|
||||||
*
|
|
||||||
* Note: An AVL tree is made of two files (referred to by two structures).
|
|
||||||
* One file contains the tree referring to the data, and the other
|
|
||||||
* file contains the data itself. The AVL tree as a whole is referred
|
* file contains the data itself. The AVL tree as a whole is referred
|
||||||
* to via the OBIDMS_avl structure.
|
* to via the OBIDMS_avl structure.
|
||||||
*
|
*
|
||||||
* @param dms The OBIDMS to which the AVL tree belongs.
|
* @param dms The OBIDMS to which the AVL tree belongs.
|
||||||
* @param avl_name The name of the AVL tree.
|
* @param avl_name The name of the AVL tree.
|
||||||
* @param avl_idx The index of the AVL tree if it is part of an AVL group,
|
|
||||||
* or -1 if it is not part of an AVL group.
|
|
||||||
*
|
*
|
||||||
* @returns A pointer to the AVL tree structure.
|
* @returns A pointer to the AVL tree structure.
|
||||||
* @retval NULL if an error occurred.
|
* @retval NULL if an error occurred.
|
||||||
@ -233,66 +175,57 @@ OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name, int avl_idx);
|
|||||||
* @since December 2015
|
* @since December 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx);
|
OBIDMS_avl_p obi_avl(OBIDMS_p dms, const char* avl_name);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Opens an AVL tree group and creates it if it does not already exist.
|
* @brief Creates an AVL tree. Fails if it already exists.
|
||||||
*
|
*
|
||||||
* Note: An AVL tree group is composed of multiple AVL trees that all have the
|
* Note: An AVL tree is made of two files (referred to by two structures).
|
||||||
* same base name, and an index differentiating them.
|
* One file contains the indices referring to the data, and the other
|
||||||
|
* file contains the data itself. The AVL tree as a whole is referred
|
||||||
|
* to via the OBIDMS_avl structure.
|
||||||
*
|
*
|
||||||
* @param dms The OBIDMS to which the AVL tree belongs.
|
* @param dms The OBIDMS to which the AVL tree belongs.
|
||||||
* @param avl_name The base name of the AVL tree group.
|
* @param avl_name The name of the AVL tree.
|
||||||
*
|
*
|
||||||
* @returns A pointer to the AVL tree group structure.
|
* @returns A pointer to the newly created AVL tree structure.
|
||||||
* @retval NULL if an error occurred.
|
* @retval NULL if an error occurred.
|
||||||
*
|
*
|
||||||
* @since April 2016
|
* @since December 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
OBIDMS_avl_group_p obi_avl_group(OBIDMS_p dms, const char* avl_name);
|
OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Creates an AVL tree group.
|
* @brief Opens an AVL tree. Fails if it does not already exist.
|
||||||
*
|
*
|
||||||
* Note: An AVL tree group is composed of multiple AVL trees that all have the
|
* Note: An AVL tree is made of two files (referred to by two structures).
|
||||||
* same base name, and an index differentiating them.
|
* One file contains the indices referring to the data, and the other
|
||||||
|
* file contains the data itself. The AVL tree as a whole is referred
|
||||||
|
* to via the OBIDMS_avl structure.
|
||||||
*
|
*
|
||||||
* @param dms The OBIDMS to which the AVL tree belongs.
|
* @param dms The OBIDMS to which the AVL tree belongs.
|
||||||
* @param avl_name The base name of the AVL tree group.
|
* @param avl_name The name of the AVL tree.
|
||||||
*
|
*
|
||||||
* @returns A pointer to the AVL tree group structure.
|
* @returns A pointer to the AVL tree structure.
|
||||||
* @retval NULL if an error occurred.
|
* @retval NULL if an error occurred.
|
||||||
*
|
*
|
||||||
* @since April 2016
|
* @since December 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name);
|
OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name);
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Opens an AVL tree group in read-only mode.
|
|
||||||
*
|
|
||||||
* Note: An AVL tree group is composed of multiple AVL trees that all have the
|
|
||||||
* same base name, and an index differentiating them.
|
|
||||||
*
|
|
||||||
* @param dms The OBIDMS to which the AVL tree belongs.
|
|
||||||
* @param avl_name The base name of the AVL tree group.
|
|
||||||
*
|
|
||||||
* @returns A pointer to the AVL tree group structure.
|
|
||||||
* @retval NULL if an error occurred.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
OBIDMS_avl_group_p obi_open_avl_group(OBIDMS_p dms, const char* avl_name);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Closes an AVL tree.
|
* @brief Closes an AVL tree.
|
||||||
*
|
*
|
||||||
|
* Note: An AVL tree is made of two files (referred to by two structures).
|
||||||
|
* One file contains the indices referring to the data, and the other
|
||||||
|
* file contains the data itself. The AVL tree as a whole is referred
|
||||||
|
* to via the OBIDMS_avl structure.
|
||||||
|
*
|
||||||
* @param avl A pointer to the AVL tree structure to close and free.
|
* @param avl A pointer to the AVL tree structure to close and free.
|
||||||
*
|
*
|
||||||
* @retval 0 if the operation was successfully completed.
|
* @retval 0 if the operation was successfully completed.
|
||||||
@ -305,61 +238,29 @@ int obi_close_avl(OBIDMS_avl_p avl);
|
|||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Closes an AVL tree group.
|
* @brief Adds a value (byte array) in an AVL tree, checking if it is already in it.
|
||||||
*
|
*
|
||||||
* @param avl_group A pointer to the AVL tree group structure to close and free.
|
* @warning The byte array to add must already be encoded and contain its header.
|
||||||
*
|
|
||||||
* @retval 0 if the operation was successfully completed.
|
|
||||||
* @retval -1 if an error occurred.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
int obi_close_avl_group(OBIDMS_avl_group_p avl_group);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Recovers a value (blob) in an AVL tree.
|
|
||||||
*
|
|
||||||
* @warning The blob recovered must be decoded to get the original value.
|
|
||||||
* @warning The blob recovered is mapped in memory.
|
|
||||||
*
|
*
|
||||||
* @param avl A pointer to the AVL tree.
|
* @param avl A pointer to the AVL tree.
|
||||||
* @param index The index of the value in the data array.
|
* @param value The byte array to add in the AVL tree.
|
||||||
*
|
*
|
||||||
* @returns A pointer to the blob recovered.
|
* @returns The index of the value, whether it was added or already in the AVL tree.
|
||||||
*
|
|
||||||
* @since December 2015
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
Obi_blob_p obi_avl_get(OBIDMS_avl_p avl, index_t index);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Adds a value (blob) in an AVL tree.
|
|
||||||
*
|
|
||||||
* @warning The value given must be already be encoded into a blob structure (Obi_blob_t).
|
|
||||||
* @warning If the value is already in the AVL tree, an error will be triggered. // TODO to discuss
|
|
||||||
*
|
|
||||||
* @param avl A pointer to the AVL tree.
|
|
||||||
* @param value The blob to add in the AVL tree.
|
|
||||||
*
|
|
||||||
* @returns The index of the value newly added in the AVL tree.
|
|
||||||
* @retval -1 if an error occurred.
|
* @retval -1 if an error occurred.
|
||||||
*
|
*
|
||||||
* @since December 2015
|
* @since December 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
index_t obi_avl_add(OBIDMS_avl_p avl, Obi_blob_p value);
|
index_t obi_avl_add(OBIDMS_avl_p avl, byte_t* value);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Finds a value (blob) in an AVL tree.
|
* @brief Finds a value (byte array) in an AVL tree, checking first if it is already in it.
|
||||||
*
|
*
|
||||||
* @warning The value given must be already be encoded into a blob structure (Obi_blob_t).
|
* @warning The byte array to add must already be encoded and contain its header.
|
||||||
*
|
*
|
||||||
* @param avl A pointer to the AVL tree.
|
* @param avl A pointer to the AVL tree.
|
||||||
* @param value The blob to add in the AVL tree.
|
* @param value The byte array to add in the AVL tree.
|
||||||
*
|
*
|
||||||
* @returns The data index of the value.
|
* @returns The data index of the value.
|
||||||
* @retval -1 if the value is not in the tree.
|
* @retval -1 if the value is not in the tree.
|
||||||
@ -367,47 +268,82 @@ index_t obi_avl_add(OBIDMS_avl_p avl, Obi_blob_p value);
|
|||||||
* @since December 2015
|
* @since December 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
index_t obi_avl_find(OBIDMS_avl_p avl, Obi_blob_p value);
|
index_t obi_avl_find(OBIDMS_avl_p avl, byte_t* value);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Recovers a value (blob) in an AVL tree.
|
* @brief Recovers a value (byte array) in an AVL tree.
|
||||||
*
|
*
|
||||||
* @warning The blob recovered must be decoded to get the original value.
|
* @warning The byte array recovered is encoded and contains its header.
|
||||||
* @warning The blob recovered is mapped in memory.
|
|
||||||
*
|
*
|
||||||
* @param avl_group A pointer to the AVL tree.
|
* @param avl A pointer to the AVL tree.
|
||||||
* @param index The index of the value in the form of a 64-bit integer
|
* @param index The index of the value in the data array.
|
||||||
* with the 32 left-most bits coding for the index of the tree of
|
|
||||||
* the group in which the value is stored, and the 32 right-most bits
|
|
||||||
* coding for the index at which the value is stored in that AVL tree.
|
|
||||||
*
|
*
|
||||||
* @returns A pointer to the blob recovered.
|
* @returns A pointer to the byte array recovered.
|
||||||
*
|
*
|
||||||
* @since April 2016
|
* @since December 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
Obi_blob_p obi_avl_group_get(OBIDMS_avl_group_p avl_group, index_t idx);
|
byte_t* obi_avl_get(OBIDMS_avl_p avl, index_t index);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Adds a value (blob) in an AVL tree group, checking if it is already in it.
|
* @brief Converts a character string to a byte array with a header.
|
||||||
*
|
*
|
||||||
* @warning The value given must be already be encoded into a blob structure (Obi_blob_t).
|
* @warning The byte array must be freed by the caller.
|
||||||
*
|
*
|
||||||
* @param avl_group A pointer to the AVL tree group.
|
* @param value The character string to convert.
|
||||||
* @param value The blob to add in the AVL tree group.
|
|
||||||
*
|
*
|
||||||
* @returns The index of the value newly added in the AVL tree group, in the form of a
|
* @returns A pointer to the byte array created.
|
||||||
* 64-bit integer with the 32 left-most bits coding for the index of the tree
|
* @retval NULL if an error occurred.
|
||||||
* of the group in which the value is stored, and the 32 right-most bits
|
|
||||||
* coding for the index at which the value is stored in that AVL tree.
|
|
||||||
* @retval -1 if an error occurred.
|
|
||||||
*
|
*
|
||||||
* @since April 2016
|
* @since October 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_blob_p value);
|
byte_t* obi_str_to_obibytes(char* value);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Converts a byte array to a character string.
|
||||||
|
*
|
||||||
|
* @param value_b The byte array to convert.
|
||||||
|
*
|
||||||
|
* @returns A pointer to the character string contained in the byte array.
|
||||||
|
*
|
||||||
|
* @since October 2015
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
const char* obi_obibytes_to_str(byte_t* value_b);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Converts a DNA sequence to a byte array with a header.
|
||||||
|
*
|
||||||
|
* @warning The byte array must be freed by the caller.
|
||||||
|
*
|
||||||
|
* @param value The DNA sequence to convert.
|
||||||
|
*
|
||||||
|
* @returns A pointer to the byte array created.
|
||||||
|
* @retval NULL if an error occurred.
|
||||||
|
*
|
||||||
|
* @since November 2015
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
byte_t* obi_seq_to_obibytes(char* seq);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Converts a byte array to a DNA sequence.
|
||||||
|
*
|
||||||
|
* @param value_b The byte array to convert.
|
||||||
|
*
|
||||||
|
* @returns A pointer to the DNA sequence contained in the byte array.
|
||||||
|
* @retval NULL if an error occurred.
|
||||||
|
*
|
||||||
|
* @since November 2015
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
const char* obi_obibytes_to_seq(byte_t* value_b);
|
||||||
|
|
||||||
|
|
||||||
#endif /* OBIAVL_H_ */
|
#endif /* OBIAVL_H_ */
|
||||||
|
|||||||
@ -1,91 +0,0 @@
|
|||||||
/****************************************************************************
|
|
||||||
* Obiblob functions *
|
|
||||||
****************************************************************************/
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @file obiblob.c
|
|
||||||
* @author Celine Mercier
|
|
||||||
* @date April 11th 2016
|
|
||||||
* @brief Functions handling Obiblob structures.
|
|
||||||
*/
|
|
||||||
|
|
||||||
|
|
||||||
#include <stdlib.h>
|
|
||||||
#include <stdio.h>
|
|
||||||
#include <stdint.h>
|
|
||||||
#include <math.h>
|
|
||||||
|
|
||||||
#include "obiblob.h"
|
|
||||||
#include "obierrno.h"
|
|
||||||
#include "obitypes.h" // For byte_t type
|
|
||||||
#include "obidebug.h"
|
|
||||||
|
|
||||||
|
|
||||||
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
|
||||||
|
|
||||||
|
|
||||||
// TODO: endianness problem?
|
|
||||||
|
|
||||||
|
|
||||||
Obi_blob_p obi_blob(byte_t* encoded_value, uint8_t element_size, int32_t length_encoded_value, int32_t length_decoded_value)
|
|
||||||
{
|
|
||||||
Obi_blob_p blob;
|
|
||||||
|
|
||||||
// Allocate the memory for the blob structure
|
|
||||||
blob = (Obi_blob_p) malloc(sizeof(Obi_blob_t) + length_encoded_value);
|
|
||||||
if (blob == NULL)
|
|
||||||
{
|
|
||||||
obi_set_errno(OBI_MALLOC_ERROR);
|
|
||||||
obidebug(1, "\nError allocating memory for a blob");
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
// Store the number of bits on which each element is encoded
|
|
||||||
blob->element_size = element_size;
|
|
||||||
|
|
||||||
// Store the length (in bytes) of the encoded value
|
|
||||||
blob->length_encoded_value = length_encoded_value;
|
|
||||||
|
|
||||||
// Store the initial length (in bytes) of the decoded value
|
|
||||||
blob->length_decoded_value = length_decoded_value;
|
|
||||||
|
|
||||||
// Store the encoded value
|
|
||||||
memcpy(blob->value, encoded_value, length_encoded_value);
|
|
||||||
|
|
||||||
return blob;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int obi_blob_compare(Obi_blob_p value_1, Obi_blob_p value_2)
|
|
||||||
{
|
|
||||||
int comp;
|
|
||||||
int32_t b;
|
|
||||||
|
|
||||||
if (value_1->element_size != value_2->element_size)
|
|
||||||
return (value_1->element_size - value_2->element_size);
|
|
||||||
|
|
||||||
if (value_1->length_encoded_value != value_2->length_encoded_value)
|
|
||||||
return (value_1->length_encoded_value - value_2->length_encoded_value);
|
|
||||||
|
|
||||||
if (value_1->element_size != ELEMENT_SIZE_STR) // because if so, length_decoded_value == length_encoded_value
|
|
||||||
{
|
|
||||||
if (value_1->length_decoded_value != value_2->length_decoded_value)
|
|
||||||
return (value_1->length_decoded_value - value_2->length_decoded_value);
|
|
||||||
}
|
|
||||||
|
|
||||||
b = 0;
|
|
||||||
comp = 0;
|
|
||||||
while (!comp && (b < value_1->length_encoded_value))
|
|
||||||
{
|
|
||||||
comp = *((value_1->value)+b) - *((value_2->value)+b);
|
|
||||||
b++;
|
|
||||||
}
|
|
||||||
return comp;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int obi_blob_sizeof(Obi_blob_p value)
|
|
||||||
{
|
|
||||||
return (sizeof(Obi_blob_t) + (value->length_encoded_value));
|
|
||||||
}
|
|
||||||
|
|
||||||
@ -1,98 +0,0 @@
|
|||||||
/****************************************************************************
|
|
||||||
* Obiblob header file *
|
|
||||||
****************************************************************************/
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @file obiblob.h
|
|
||||||
* @author Celine Mercier
|
|
||||||
* @date November 18th 2015
|
|
||||||
* @brief Header file for handling Obi_blob structures.
|
|
||||||
*/
|
|
||||||
|
|
||||||
|
|
||||||
#ifndef OBIBLOB_H_
|
|
||||||
#define OBIBLOB_H_
|
|
||||||
|
|
||||||
|
|
||||||
#include <stdlib.h>
|
|
||||||
#include <stdio.h>
|
|
||||||
#include <stdint.h>
|
|
||||||
|
|
||||||
#include "obitypes.h"
|
|
||||||
|
|
||||||
|
|
||||||
#define ELEMENT_SIZE_STR (8) /**< The size of an element from a value of type character string.
|
|
||||||
*/
|
|
||||||
#define ELEMENT_SIZE_SEQ_2 (2) /**< The size of an element from a value of type DNA sequence encoded on 2 bits.
|
|
||||||
*/
|
|
||||||
#define ELEMENT_SIZE_SEQ_4 (4) /**< The size of an element from a value of type DNA sequence encoded on 4 bits.
|
|
||||||
*/
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Blob structure, for handling encoded values.
|
|
||||||
*/
|
|
||||||
typedef struct Obi_blob {
|
|
||||||
uint8_t element_size; /**< Size in bits of one element from the encoded value.
|
|
||||||
*/
|
|
||||||
int32_t length_encoded_value; /**< Length in bytes of the encoded value.
|
|
||||||
*/
|
|
||||||
int32_t length_decoded_value; /**< Length in bytes of the decoded value.
|
|
||||||
*/
|
|
||||||
byte_t value[]; /**< Encoded value.
|
|
||||||
*/
|
|
||||||
} Obi_blob_t, *Obi_blob_p;
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Function building a blob structure.
|
|
||||||
*
|
|
||||||
* @param encoded_value A pointer to the encoded value that will be stored in the blob.
|
|
||||||
* @param element_size The size in bits of one element from the encoded value.
|
|
||||||
* @param length_encoded_value The length in bytes of the encoded value.
|
|
||||||
* @param length_decoded_value The length in bytes of the decoded value.
|
|
||||||
*
|
|
||||||
* @returns A pointer to the created blob structure.
|
|
||||||
* @retval NULL if an error occurred.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
Obi_blob_p obi_blob(byte_t* encoded_value, uint8_t element_size, int32_t length_encoded_value, int32_t length_decoded_value);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Function comparing two blobs.
|
|
||||||
*
|
|
||||||
* The encoding is compared first, then the length of the
|
|
||||||
* values, then the values themselves.
|
|
||||||
*
|
|
||||||
* @param value_1 A pointer to the first blob structure.
|
|
||||||
* @param value_2 A pointer to the second blob structure.
|
|
||||||
*
|
|
||||||
* @returns A value < 0 if value_1 < value_2,
|
|
||||||
* a value > 0 if value_1 > value_2,
|
|
||||||
* and 0 if value_1 == value_2.
|
|
||||||
*
|
|
||||||
* @since October 2015
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
int obi_blob_compare(Obi_blob_p value_1, Obi_blob_p value_2);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Function calculating the size in bytes of a blob.
|
|
||||||
*
|
|
||||||
* @param value A pointer to the blob structure.
|
|
||||||
*
|
|
||||||
* @returns The size of the blob in bytes.
|
|
||||||
*
|
|
||||||
* @since October 2015
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
int obi_blob_sizeof(Obi_blob_p value);
|
|
||||||
|
|
||||||
|
|
||||||
#endif /* OBIBLOB_H_ */
|
|
||||||
|
|
||||||
@ -1,57 +0,0 @@
|
|||||||
/****************************************************************************
|
|
||||||
* Obiblob functions *
|
|
||||||
****************************************************************************/
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @file obiblob_indexer.c
|
|
||||||
* @author Celine Mercier
|
|
||||||
* @date April 12th 2016
|
|
||||||
* @brief Functions handling the indexing and retrieval of blob structures.
|
|
||||||
*/
|
|
||||||
|
|
||||||
|
|
||||||
#include <stdlib.h>
|
|
||||||
#include <stdio.h>
|
|
||||||
|
|
||||||
#include "obiblob_indexer.h"
|
|
||||||
#include "obidms.h"
|
|
||||||
#include "obierrno.h"
|
|
||||||
#include "obidebug.h"
|
|
||||||
|
|
||||||
|
|
||||||
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
|
||||||
|
|
||||||
|
|
||||||
//inline int obi_indexer_exists(OBIDMS_p dms, const char* name);
|
|
||||||
|
|
||||||
//inline Obi_indexer_p obi_indexer(OBIDMS_p dms, const char* name);
|
|
||||||
|
|
||||||
//inline Obi_indexer_p obi_create_indexer(OBIDMS_p dms, const char* name);
|
|
||||||
|
|
||||||
//inline Obi_indexer_p obi_open_indexer(OBIDMS_p dms, const char* name);
|
|
||||||
|
|
||||||
//inline int obi_close_indexer(Obi_indexer_p indexer);
|
|
||||||
|
|
||||||
//inline index_t obi_indexer_add(Obi_indexer_p indexer, Obi_blob_p value);
|
|
||||||
|
|
||||||
//inline Obi_blob_p obi_indexer_get(Obi_indexer_p indexer, index_t idx);
|
|
||||||
|
|
||||||
|
|
||||||
char* obi_build_indexer_name(const char* column_name, obiversion_t column_version)
|
|
||||||
{
|
|
||||||
char* indexer_name;
|
|
||||||
|
|
||||||
indexer_name = (char*) malloc(INDEXER_MAX_NAME * sizeof(char));
|
|
||||||
if (indexer_name == NULL)
|
|
||||||
{
|
|
||||||
obi_set_errno(OBI_MALLOC_ERROR);
|
|
||||||
obidebug(1, "\nError allocating the memory for an indexer name");
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
strcpy(indexer_name, column_name);
|
|
||||||
sprintf(indexer_name+strlen(column_name), "_%d_indexer", column_version);
|
|
||||||
|
|
||||||
return indexer_name;
|
|
||||||
}
|
|
||||||
|
|
||||||
@ -1,159 +0,0 @@
|
|||||||
/****************************************************************************
|
|
||||||
* Blob indexer header file *
|
|
||||||
****************************************************************************/
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @file obiblob_indexer.h
|
|
||||||
* @author Celine Mercier
|
|
||||||
* @date April 12th 2016
|
|
||||||
* @brief Header file for the functions handling the indexing of values.
|
|
||||||
*/
|
|
||||||
|
|
||||||
|
|
||||||
#ifndef OBIBLOB_INDEXER_H_
|
|
||||||
#define OBIBLOB_INDEXER_H_
|
|
||||||
|
|
||||||
|
|
||||||
#include <stdlib.h>
|
|
||||||
#include <stdio.h>
|
|
||||||
|
|
||||||
#include "obidms.h"
|
|
||||||
#include "obiavl.h"
|
|
||||||
#include "obitypes.h"
|
|
||||||
#include "obiblob.h"
|
|
||||||
|
|
||||||
|
|
||||||
#define INDEXER_MAX_NAME AVL_MAX_NAME /**< Macro to refer to the maximum size of the name of an indexer structure.
|
|
||||||
*/
|
|
||||||
|
|
||||||
|
|
||||||
typedef struct OBIDMS_avl_group Obi_indexer; /**< Typedef to refer to the used indexer structure.
|
|
||||||
*/
|
|
||||||
typedef OBIDMS_avl_group_p Obi_indexer_p; /**< Typedef to refer to the pointer of the used indexer structure.
|
|
||||||
*/
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Checks if an indexer already exists or not.
|
|
||||||
*
|
|
||||||
* @param dms The OBIDMS to which the indexer belongs.
|
|
||||||
* @param name The name of the indexer.
|
|
||||||
*
|
|
||||||
* @returns A value indicating whether the indexer exists or not.
|
|
||||||
* @retval 1 if the indexer exists.
|
|
||||||
* @retval 0 if the indexer does not exist.
|
|
||||||
* @retval -1 if an error occurred.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
#define obi_indexer_exists obi_avl_exists
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Opens an indexer and creates it if it does not already exist.
|
|
||||||
*
|
|
||||||
* @param dms The OBIDMS to which the indexer belongs.
|
|
||||||
* @param name The name of the indexer.
|
|
||||||
*
|
|
||||||
* @returns A pointer to the indexer structure.
|
|
||||||
* @retval NULL if an error occurred.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
#define obi_indexer obi_avl_group
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Creates an indexer.
|
|
||||||
*
|
|
||||||
* @param dms The OBIDMS to which the indexer belongs.
|
|
||||||
* @param name The name of the indexer.
|
|
||||||
*
|
|
||||||
* @returns A pointer to the AVL tree group structure.
|
|
||||||
* @retval NULL if an error occurred.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
#define obi_create_indexer obi_create_avl_group
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Opens an indexer.
|
|
||||||
*
|
|
||||||
* @param dms The OBIDMS to which the indexer belongs.
|
|
||||||
* @param name The name of the indexer.
|
|
||||||
*
|
|
||||||
* @returns A pointer to the indexer structure.
|
|
||||||
* @retval NULL if an error occurred.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
#define obi_open_indexer obi_open_avl_group
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Closes an indexer.
|
|
||||||
*
|
|
||||||
* @param indexer A pointer to the indexer structure to close and free.
|
|
||||||
*
|
|
||||||
* @retval 0 if the operation was successfully completed.
|
|
||||||
* @retval -1 if an error occurred.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
#define obi_close_indexer obi_close_avl_group
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Indexes a blob in an indexer and returns the index referring to the blob.
|
|
||||||
*
|
|
||||||
* @param indexer A pointer to the indexer.
|
|
||||||
* @param value The blob to index.
|
|
||||||
*
|
|
||||||
* @returns The index of the blob newly added in the indexer.
|
|
||||||
* @retval -1 if an error occurred.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
#define obi_indexer_add obi_avl_group_add
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Recovers a blob from an indexer.
|
|
||||||
*
|
|
||||||
* @param indexer A pointer to the indexer.
|
|
||||||
* @param index The index of the blob in the indexer.
|
|
||||||
*
|
|
||||||
* @returns A pointer to the blob recovered.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
#define obi_indexer_get obi_avl_group_get
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Builds an indexer name in the form columnname_columnversion_indexer.
|
|
||||||
*
|
|
||||||
* @warning The returned pointer has to be freed by the caller.
|
|
||||||
*
|
|
||||||
* @param column_name The name of the column associated with the indexer.
|
|
||||||
* @param column_version The version of the column associated with the indexer.
|
|
||||||
*
|
|
||||||
* @returns A pointer on the indexer name built.
|
|
||||||
* @retval NULL if an error occurred.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
char* obi_build_indexer_name(const char* column_name, obiversion_t column_version);
|
|
||||||
|
|
||||||
|
|
||||||
#endif /* OBIBLOB_INDEXER_H_ */
|
|
||||||
|
|
||||||
225
src/obidms.c
225
src/obidms.c
@ -23,8 +23,7 @@
|
|||||||
#include "obierrno.h"
|
#include "obierrno.h"
|
||||||
#include "obidebug.h"
|
#include "obidebug.h"
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
#include "obiblob_indexer.h"
|
#include "private_at_functions.h"
|
||||||
#include "utils.h"
|
|
||||||
#include "obilittlebigman.h"
|
#include "obilittlebigman.h"
|
||||||
|
|
||||||
|
|
||||||
@ -106,8 +105,7 @@ static char* build_directory_name(const char* dms_name)
|
|||||||
char* directory_name;
|
char* directory_name;
|
||||||
|
|
||||||
// Build the database directory name
|
// Build the database directory name
|
||||||
directory_name = (char*) malloc((strlen(dms_name) + 8)*sizeof(char));
|
if (asprintf(&directory_name, "%s.obidms", dms_name) < 0)
|
||||||
if (sprintf(directory_name, "%s.obidms", dms_name) < 0)
|
|
||||||
{
|
{
|
||||||
obi_set_errno(OBIDMS_MEMORY_ERROR);
|
obi_set_errno(OBIDMS_MEMORY_ERROR);
|
||||||
obidebug(1, "\nProblem building an OBIDMS directory name");
|
obidebug(1, "\nProblem building an OBIDMS directory name");
|
||||||
@ -132,8 +130,7 @@ static char* build_infos_file_name(const char* dms_name)
|
|||||||
char* file_name;
|
char* file_name;
|
||||||
|
|
||||||
// Build file name
|
// Build file name
|
||||||
file_name = (char*) malloc((strlen(dms_name) + 7)*sizeof(char));
|
if (asprintf(&file_name, "%s_infos", dms_name) < 0)
|
||||||
if (sprintf(file_name, "%s_infos", dms_name) < 0)
|
|
||||||
{
|
{
|
||||||
obi_set_errno(OBIDMS_MEMORY_ERROR);
|
obi_set_errno(OBIDMS_MEMORY_ERROR);
|
||||||
obidebug(1, "\nProblem building an informations file name");
|
obidebug(1, "\nProblem building an informations file name");
|
||||||
@ -250,7 +247,7 @@ OBIDMS_p obi_create_dms(const char* dms_name)
|
|||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
|
|
||||||
// Get file descriptor of DMS directory to create the indexer directory
|
// Get file descriptor of DMS directory to create the AVL trees directory
|
||||||
dms_dir = opendir(directory_name);
|
dms_dir = opendir(directory_name);
|
||||||
if (dms_dir == NULL)
|
if (dms_dir == NULL)
|
||||||
{
|
{
|
||||||
@ -270,11 +267,11 @@ OBIDMS_p obi_create_dms(const char* dms_name)
|
|||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
|
|
||||||
// Create the indexer directory
|
// Create the AVL trees directory
|
||||||
if (mkdirat(dms_file_descriptor, INDEXER_DIR_NAME, 00777) < 0)
|
if (mkdirat(dms_file_descriptor, AVL_TREES_DIR_NAME, 00777) < 0)
|
||||||
{
|
{
|
||||||
obi_set_errno(OBI_INDEXER_ERROR);
|
obi_set_errno(OBI_AVL_ERROR);
|
||||||
obidebug(1, "\nProblem creating an indexer directory");
|
obidebug(1, "\nProblem creating an AVL trees directory");
|
||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -393,24 +390,24 @@ OBIDMS_p obi_open_dms(const char* dms_name)
|
|||||||
|
|
||||||
dms->little_endian = little_endian_dms;
|
dms->little_endian = little_endian_dms;
|
||||||
|
|
||||||
// Open the indexer directory
|
// Open the AVL trees directory
|
||||||
dms->indexer_directory = opendir_in_dms(dms, INDEXER_DIR_NAME);
|
dms->avl_directory = private_opendirat(dms->dir_fd, AVL_TREES_DIR_NAME);
|
||||||
if (dms->indexer_directory == NULL)
|
if (dms->avl_directory == NULL)
|
||||||
{
|
{
|
||||||
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
|
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
|
||||||
obidebug(1, "\nError opening the indexer directory");
|
obidebug(1, "\nError opening the AVL trees directory");
|
||||||
closedir(dms->directory);
|
closedir(dms->directory);
|
||||||
free(dms);
|
free(dms);
|
||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
|
|
||||||
// Store the indexer directory's file descriptor
|
// Store the AVL trees directory's file descriptor
|
||||||
dms->indexer_dir_fd = dirfd(dms->indexer_directory);
|
dms->avl_dir_fd = dirfd(dms->avl_directory);
|
||||||
if (dms->indexer_dir_fd < 0)
|
if (dms->avl_dir_fd < 0)
|
||||||
{
|
{
|
||||||
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
|
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
|
||||||
obidebug(1, "\nError getting the file descriptor of the indexer directory");
|
obidebug(1, "\nError getting the file descriptor of the AVL trees directory");
|
||||||
closedir(dms->indexer_directory);
|
closedir(dms->avl_directory);
|
||||||
closedir(dms->directory);
|
closedir(dms->directory);
|
||||||
free(dms);
|
free(dms);
|
||||||
return NULL;
|
return NULL;
|
||||||
@ -418,11 +415,13 @@ OBIDMS_p obi_open_dms(const char* dms_name)
|
|||||||
|
|
||||||
// Initialize the list of opened columns
|
// Initialize the list of opened columns
|
||||||
dms->opened_columns = (Opened_columns_list_p) malloc(sizeof(Opened_columns_list_t));
|
dms->opened_columns = (Opened_columns_list_p) malloc(sizeof(Opened_columns_list_t));
|
||||||
|
(dms->opened_columns)->columns = (OBIDMS_column_p*) malloc(MAX_NB_OPENED_COLUMNS*sizeof(OBIDMS_column_p));
|
||||||
(dms->opened_columns)->nb_opened_columns = 0;
|
(dms->opened_columns)->nb_opened_columns = 0;
|
||||||
|
|
||||||
// Initialize the list of opened indexers
|
// Initialize the list of opened AVL trees
|
||||||
dms->opened_indexers = (Opened_indexers_list_p) malloc(sizeof(Opened_indexers_list_t));
|
dms->opened_avls = (Opened_avls_list_p) malloc(sizeof(Opened_avls_list_t));
|
||||||
(dms->opened_indexers)->nb_opened_indexers = 0;
|
(dms->opened_avls)->avls = (OBIDMS_avl_p*) malloc(MAX_NB_OPENED_AVL_TREES*sizeof(OBIDMS_avl_p));
|
||||||
|
(dms->opened_avls)->nb_opened_avls = 0;
|
||||||
|
|
||||||
return dms;
|
return dms;
|
||||||
}
|
}
|
||||||
@ -455,7 +454,7 @@ int obi_close_dms(OBIDMS_p dms)
|
|||||||
while ((dms->opened_columns)->nb_opened_columns > 0)
|
while ((dms->opened_columns)->nb_opened_columns > 0)
|
||||||
obi_close_column(*((dms->opened_columns)->columns));
|
obi_close_column(*((dms->opened_columns)->columns));
|
||||||
|
|
||||||
// Close dms and indexer directories
|
// Close dms and AVL trees directories
|
||||||
if (closedir(dms->directory) < 0)
|
if (closedir(dms->directory) < 0)
|
||||||
{
|
{
|
||||||
obi_set_errno(OBIDMS_MEMORY_ERROR);
|
obi_set_errno(OBIDMS_MEMORY_ERROR);
|
||||||
@ -463,10 +462,10 @@ int obi_close_dms(OBIDMS_p dms)
|
|||||||
free(dms);
|
free(dms);
|
||||||
return -1;
|
return -1;
|
||||||
}
|
}
|
||||||
if (closedir(dms->indexer_directory) < 0)
|
if (closedir(dms->avl_directory) < 0)
|
||||||
{
|
{
|
||||||
obi_set_errno(OBI_INDEXER_ERROR);
|
obi_set_errno(OBI_AVL_ERROR);
|
||||||
obidebug(1, "\nError closing an indexer directory");
|
obidebug(1, "\nError closing an AVL trees directory");
|
||||||
free(dms);
|
free(dms);
|
||||||
return -1;
|
return -1;
|
||||||
}
|
}
|
||||||
@ -476,175 +475,3 @@ int obi_close_dms(OBIDMS_p dms)
|
|||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
int obi_dms_is_column_name_in_list(OBIDMS_p dms, const char* column_name)
|
|
||||||
{
|
|
||||||
int i;
|
|
||||||
Opened_columns_list_p columns_list;
|
|
||||||
|
|
||||||
columns_list = dms->opened_columns;
|
|
||||||
|
|
||||||
for (i=0; i < (columns_list->nb_opened_columns); i++)
|
|
||||||
{
|
|
||||||
if (!strcmp(((*((columns_list->columns)+i))->header)->name, column_name))
|
|
||||||
{ // Found it
|
|
||||||
return 1;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
return 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
OBIDMS_column_p obi_dms_get_column_from_list(OBIDMS_p dms, const char* column_name, obiversion_t version)
|
|
||||||
{
|
|
||||||
int i;
|
|
||||||
|
|
||||||
for (i=0; i < ((dms->opened_columns)->nb_opened_columns); i++)
|
|
||||||
{
|
|
||||||
if (!strcmp(((*(((dms->opened_columns)->columns)+i))->header)->name, column_name)
|
|
||||||
&& (((*(((dms->opened_columns)->columns)+i))->header)->version == version))
|
|
||||||
{ // Found the column already opened, return it
|
|
||||||
return *(((dms->opened_columns)->columns)+i);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
// Didn't find the column
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
void obi_dms_list_column(OBIDMS_p dms, OBIDMS_column_p column) // TODO add check if column already in list?
|
|
||||||
{
|
|
||||||
*(((dms->opened_columns)->columns)+((dms->opened_columns)->nb_opened_columns)) = column;
|
|
||||||
((dms->opened_columns)->nb_opened_columns)++;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int obi_dms_unlist_column(OBIDMS_p dms, OBIDMS_column_p column)
|
|
||||||
{
|
|
||||||
int i;
|
|
||||||
Opened_columns_list_p columns_list;
|
|
||||||
|
|
||||||
columns_list = dms->opened_columns;
|
|
||||||
|
|
||||||
for (i=0; i < columns_list->nb_opened_columns; i++)
|
|
||||||
{
|
|
||||||
if (!strcmp(((*((columns_list->columns)+i))->header)->name, (column->header)->name)
|
|
||||||
&& (((*((columns_list->columns)+i))->header)->version == (column->header)->version))
|
|
||||||
{ // Found the column. Rearrange list
|
|
||||||
(columns_list->nb_opened_columns)--;
|
|
||||||
(columns_list->columns)[i] = (columns_list->columns)[columns_list->nb_opened_columns];
|
|
||||||
return 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
obidebug(1, "\nCould not find the column to delete from list of open columns");
|
|
||||||
return -1;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
Obi_indexer_p obi_dms_get_indexer_from_list(OBIDMS_p dms, const char* indexer_name)
|
|
||||||
{
|
|
||||||
int i;
|
|
||||||
Opened_indexers_list_p indexers_list;
|
|
||||||
|
|
||||||
indexers_list = dms->opened_indexers;
|
|
||||||
|
|
||||||
for (i=0; i < (indexers_list->nb_opened_indexers); i++)
|
|
||||||
{
|
|
||||||
if (!strcmp(((indexers_list->indexers)[i])->name, indexer_name)) // TODO get_name function indexer
|
|
||||||
{ // Found the indexer already opened, return it
|
|
||||||
return (indexers_list->indexers)[i];
|
|
||||||
}
|
|
||||||
}
|
|
||||||
// Didn't find the indexer
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
void obi_dms_list_indexer(OBIDMS_p dms, Obi_indexer_p indexer)
|
|
||||||
{
|
|
||||||
*(((dms->opened_indexers)->indexers)+((dms->opened_indexers)->nb_opened_indexers)) = indexer;
|
|
||||||
((dms->opened_indexers)->nb_opened_indexers)++;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int obi_dms_unlist_indexer(OBIDMS_p dms, Obi_indexer_p indexer)
|
|
||||||
{
|
|
||||||
int i;
|
|
||||||
Opened_indexers_list_p indexers_list;
|
|
||||||
|
|
||||||
indexers_list = dms->opened_indexers;
|
|
||||||
|
|
||||||
for (i=0; i < indexers_list->nb_opened_indexers; i++)
|
|
||||||
{
|
|
||||||
if (!strcmp(((indexers_list->indexers)[i])->name, indexer->name)) // TODO get_name function indexer
|
|
||||||
{ // Found the indexer. Rearrange list
|
|
||||||
(indexers_list->nb_opened_indexers)--;
|
|
||||||
(indexers_list->indexers)[i] = (indexers_list->indexers)[indexers_list->nb_opened_indexers];
|
|
||||||
return 0;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
obidebug(1, "\nCould not find the indexer to delete from list of open indexers");
|
|
||||||
return -1;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
char* obi_dms_get_dms_path(OBIDMS_p dms)
|
|
||||||
{
|
|
||||||
char* full_path;
|
|
||||||
|
|
||||||
full_path = (char*) malloc((MAX_PATH_LEN)*sizeof(char));
|
|
||||||
if (full_path == NULL)
|
|
||||||
{
|
|
||||||
obi_set_errno(OBI_MALLOC_ERROR);
|
|
||||||
obidebug(1, "\nError allocating memory for the char* path to a file or directory");
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
if (getcwd(full_path, MAX_PATH_LEN) == NULL) // TODO store when opening
|
|
||||||
{
|
|
||||||
obi_set_errno(OBI_UTILS_ERROR);
|
|
||||||
obidebug(1, "\nError getting the path to a file or directory");
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
strcat(full_path, "/");
|
|
||||||
strcat(full_path, dms->directory_name);
|
|
||||||
|
|
||||||
return full_path;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
char* obi_dms_get_full_path(OBIDMS_p dms, const char* path_name)
|
|
||||||
{
|
|
||||||
char* full_path;
|
|
||||||
|
|
||||||
full_path = obi_dms_get_dms_path(dms);
|
|
||||||
strcat(full_path, "/");
|
|
||||||
strcat(full_path, path_name);
|
|
||||||
|
|
||||||
return full_path;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
DIR* opendir_in_dms(OBIDMS_p dms, const char* path_name)
|
|
||||||
{
|
|
||||||
char* full_path;
|
|
||||||
DIR* directory;
|
|
||||||
|
|
||||||
full_path = obi_dms_get_full_path(dms, path_name);
|
|
||||||
if (full_path == NULL)
|
|
||||||
return NULL;
|
|
||||||
|
|
||||||
directory = opendir(full_path);
|
|
||||||
if (directory == NULL)
|
|
||||||
{
|
|
||||||
obi_set_errno(OBI_UTILS_ERROR);
|
|
||||||
obidebug(1, "\nError opening a directory");
|
|
||||||
}
|
|
||||||
|
|
||||||
free(full_path);
|
|
||||||
|
|
||||||
return directory;
|
|
||||||
}
|
|
||||||
|
|||||||
205
src/obidms.h
205
src/obidms.h
@ -23,52 +23,34 @@
|
|||||||
#include <stdbool.h>
|
#include <stdbool.h>
|
||||||
|
|
||||||
#include "obierrno.h"
|
#include "obierrno.h"
|
||||||
#include "obitypes.h"
|
|
||||||
|
|
||||||
|
|
||||||
#define OBIDMS_MAX_NAME (2048) /**< The maximum length of an OBIDMS name.
|
#define OBIDMS_MAX_NAME (2048) /**< The maximum length of an OBIDMS name.
|
||||||
*/
|
*/
|
||||||
#define INDEXER_DIR_NAME "OBIBLOB_INDEXERS" /**< The name of the Obiblob indexer directory.
|
#define AVL_TREES_DIR_NAME "AVL_trees" /**< The name of the AVL trees directory.
|
||||||
*/
|
*/
|
||||||
#define TAXONOMY_DIR_NAME "TAXONOMY" /**< The name of the taxonomy directory.
|
#define TAXONOMY_DIR_NAME "TAXONOMY" /**< The name of the taxonomy directory.
|
||||||
*/
|
*/
|
||||||
#define MAX_NB_OPENED_COLUMNS (100) /**< The maximum number of columns open at the same time.
|
#define MAX_NB_OPENED_COLUMNS (100) /**< The maximum number of columns open at the same time.
|
||||||
*/
|
*/
|
||||||
#define MAX_NB_OPENED_INDEXERS (1000) /**< The maximum number of indexers open at the same time.
|
#define MAX_NB_OPENED_AVL_TREES (100) /**< The maximum number of AVL trees open at the same time.
|
||||||
*/
|
*/
|
||||||
#define MAX_PATH_LEN 4096 /**< Maximum length for the character string defining a
|
|
||||||
* file or directory path.
|
|
||||||
*/
|
|
||||||
|
|
||||||
|
|
||||||
struct OBIDMS_column; /**< Declarations to avoid circular dependencies. */
|
struct OBIDMS_column; // TODO
|
||||||
typedef struct OBIDMS_column* OBIDMS_column_p; /**< Declarations to avoid circular dependencies. */
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Structure listing the columns opened in a DMS, identified by their name and version number.
|
|
||||||
*/
|
|
||||||
typedef struct Opened_columns_list {
|
typedef struct Opened_columns_list {
|
||||||
int nb_opened_columns; /**< Number of opened columns.
|
size_t nb_opened_columns;
|
||||||
*/
|
struct OBIDMS_column** columns; // TODO allocate array size here
|
||||||
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS]; /**< Array of pointers on the opened columns.
|
|
||||||
*/
|
|
||||||
} Opened_columns_list_t, *Opened_columns_list_p;
|
} Opened_columns_list_t, *Opened_columns_list_p;
|
||||||
|
|
||||||
|
|
||||||
// TODO Need to find a way to not refer to AVLs specifically
|
struct OBIDMS_avl; // TODO
|
||||||
struct OBIDMS_avl_group; /**< Declarations to avoid circular dependencies. */
|
|
||||||
typedef struct OBIDMS_avl_group* OBIDMS_avl_group_p; /**< Declarations to avoid circular dependencies. */
|
|
||||||
typedef OBIDMS_avl_group_p Obi_indexer_p; /**< Declarations to avoid circular dependencies. */
|
|
||||||
|
|
||||||
/**
|
typedef struct Opened_avls_list {
|
||||||
* @brief Structure listing the indexers opened in a DMS, identified by their name.
|
size_t nb_opened_avls;
|
||||||
*/
|
struct OBIDMS_avl** avls;
|
||||||
typedef struct Opened_indexers_list {
|
} Opened_avls_list_t, *Opened_avls_list_p;
|
||||||
int nb_opened_indexers; /**< Number of opened indexers.
|
|
||||||
*/
|
|
||||||
Obi_indexer_p indexers[MAX_NB_OPENED_INDEXERS]; /**< Array of pointers on the opened indexers.
|
|
||||||
*/
|
|
||||||
} Opened_indexers_list_t, *Opened_indexers_list_p;
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
@ -87,17 +69,17 @@ typedef struct OBIDMS {
|
|||||||
int dir_fd; /**< The file descriptor of the directory entry
|
int dir_fd; /**< The file descriptor of the directory entry
|
||||||
* usable to refer and scan the database directory.
|
* usable to refer and scan the database directory.
|
||||||
*/
|
*/
|
||||||
DIR* indexer_directory; /**< A directory entry usable to
|
DIR* avl_directory; /**< A directory entry usable to
|
||||||
* refer and scan the indexer directory.
|
* refer and scan the AVL trees directory.
|
||||||
*/
|
*/
|
||||||
int indexer_dir_fd; /**< The file descriptor of the directory entry
|
int avl_dir_fd; /**< The file descriptor of the directory entry
|
||||||
* usable to refer and scan the indexer directory.
|
* usable to refer and scan the AVL trees directory.
|
||||||
*/
|
*/
|
||||||
bool little_endian; /**< Endianness of the database.
|
bool little_endian; /**< Endianness of the database.
|
||||||
*/
|
*/
|
||||||
Opened_columns_list_p opened_columns; /**< List of opened columns.
|
Opened_columns_list_p opened_columns; /**< List of opened columns.
|
||||||
*/
|
*/
|
||||||
Opened_indexers_list_p opened_indexers; /**< List of opened indexers.
|
Opened_avls_list_p opened_avls; /**< List of opened AVL trees.
|
||||||
*/
|
*/
|
||||||
} OBIDMS_t, *OBIDMS_p;
|
} OBIDMS_t, *OBIDMS_p;
|
||||||
|
|
||||||
@ -107,7 +89,7 @@ typedef struct OBIDMS {
|
|||||||
*
|
*
|
||||||
* @param dms_name A pointer to a C string containing the name of the database.
|
* @param dms_name A pointer to a C string containing the name of the database.
|
||||||
*
|
*
|
||||||
* @returns An integer value indicating the status of the database.
|
* @returns An integer value indicating the status of the database
|
||||||
* @retval 1 if the database exists.
|
* @retval 1 if the database exists.
|
||||||
* @retval 0 if the database does not exist.
|
* @retval 0 if the database does not exist.
|
||||||
* @retval -1 if an error occurred.
|
* @retval -1 if an error occurred.
|
||||||
@ -125,7 +107,7 @@ int obi_dms_exists(const char* dms_name);
|
|||||||
* if a directory with this name does not already exist
|
* if a directory with this name does not already exist
|
||||||
* before creating the new database.
|
* before creating the new database.
|
||||||
*
|
*
|
||||||
* A directory to store Obiblob indexers is also created.
|
* A directory to store AVL trees is also created.
|
||||||
*
|
*
|
||||||
* @param dms_name A pointer to a C string containing the name of the database.
|
* @param dms_name A pointer to a C string containing the name of the database.
|
||||||
* The actual directory name used to store the DMS will be
|
* The actual directory name used to store the DMS will be
|
||||||
@ -192,141 +174,4 @@ OBIDMS_p obi_dms(const char* dms_name);
|
|||||||
int obi_close_dms(OBIDMS_p dms);
|
int obi_close_dms(OBIDMS_p dms);
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Checks if a column with a given name is in the list of opened columns.
|
|
||||||
*
|
|
||||||
* @warning: Checking only the name means that the column can be of any version.
|
|
||||||
*
|
|
||||||
* @param dms The OBIDMS.
|
|
||||||
* @param column_name The column name that should be looked for.
|
|
||||||
*
|
|
||||||
* @returns An integer value indicating whether there is at least one column with that name
|
|
||||||
* in the list of opened columns.
|
|
||||||
* @retval 0 if there is at least one column with that name in the list of opened columns.
|
|
||||||
* @retval 1 if there is no column with that name in the list of opened columns.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
int obi_dms_is_column_name_in_list(OBIDMS_p dms, const char* column_name);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Returns a column identified by its name and its version number from the list of opened columns.
|
|
||||||
*
|
|
||||||
* @param dms The OBIDMS.
|
|
||||||
* @param column_name The column name that should be looked for.
|
|
||||||
* @param version The version number of the column that should be looked for.
|
|
||||||
*
|
|
||||||
* @returns A pointer on the column if it was found in the list of opened columns.
|
|
||||||
* @retval NULL if the column was not found in the list of opened columns.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
OBIDMS_column_p obi_dms_get_column_from_list(OBIDMS_p dms, const char* column_name, obiversion_t version);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Adds a column identified by its name and its version number in the list of opened columns.
|
|
||||||
*
|
|
||||||
* @param dms The OBIDMS.
|
|
||||||
* @param column A pointer on the column that should be added in the list of opened columns.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
void obi_dms_list_column(OBIDMS_p dms, OBIDMS_column_p column);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Removes a column identified by its name and its version number from the list of opened columns.
|
|
||||||
*
|
|
||||||
* @param dms The OBIDMS.
|
|
||||||
* @param column A pointer on the column that should be removed from the list of opened columns.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
int obi_dms_unlist_column(OBIDMS_p dms, OBIDMS_column_p column);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Returns an indexer identified by its name from the list of opened indexers.
|
|
||||||
*
|
|
||||||
* @param dms The OBIDMS.
|
|
||||||
* @param indexer_name The indexer name that should be looked for.
|
|
||||||
*
|
|
||||||
* @returns A pointer on the indexer if it was found in the list of opened indexers.
|
|
||||||
* @retval NULL if the indexer was not found in the list of opened indexers.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
Obi_indexer_p obi_dms_get_indexer_from_list(OBIDMS_p dms, const char* indexer_name);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Adds an indexer identified by its name in the list of opened indexers.
|
|
||||||
*
|
|
||||||
* @param dms The OBIDMS.
|
|
||||||
* @param indexer A pointer on the indexer that should be added in the list of opened indexers.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
void obi_dms_list_indexer(OBIDMS_p dms, Obi_indexer_p indexer);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Removes an indexer identified by its name from the list of opened indexers.
|
|
||||||
*
|
|
||||||
* @param dms The OBIDMS.
|
|
||||||
* @param column A pointer on the indexer that should be removed from the list of opened indexers.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
int obi_dms_unlist_indexer(OBIDMS_p dms, Obi_indexer_p indexer);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* Function meant to disappear soon
|
|
||||||
*/
|
|
||||||
char* obi_dms_get_path(OBIDMS_p dms);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Gets the full path of a file or a directory from its
|
|
||||||
* path relative to the DMS.
|
|
||||||
*
|
|
||||||
* @warning The returned pointer has to be freed by the caller.
|
|
||||||
*
|
|
||||||
* @param dms The DMS to which path_name is relative.
|
|
||||||
* @param path_name The path name for the file or directory, relative to the DMS.
|
|
||||||
*
|
|
||||||
* @returns A pointer to the full path.
|
|
||||||
* @retval NULL if an error occurred.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
char* obi_dms_get_full_path(OBIDMS_p dms, const char* path_name);
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Opens a directory relative to the DMS.
|
|
||||||
*
|
|
||||||
* @param dms The DMS to which path_name is relative.
|
|
||||||
* @param path_name The path name for the directory to be opened, relative to the DMS.
|
|
||||||
*
|
|
||||||
* @returns The directory stream of the opened directory.
|
|
||||||
* @retval NULL if an error occurred.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
DIR* opendir_in_dms(OBIDMS_p dms, const char* path_name);
|
|
||||||
|
|
||||||
|
|
||||||
#endif /* OBIDMS_H_ */
|
#endif /* OBIDMS_H_ */
|
||||||
|
|||||||
@ -20,7 +20,7 @@
|
|||||||
#include "obidms.h"
|
#include "obidms.h"
|
||||||
#include "obidebug.h"
|
#include "obidebug.h"
|
||||||
#include "obierrno.h"
|
#include "obierrno.h"
|
||||||
#include "utils.h"
|
#include "private_at_functions.h"
|
||||||
|
|
||||||
|
|
||||||
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
||||||
@ -379,9 +379,8 @@ OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, boo
|
|||||||
|
|
||||||
buffer_size = 2048; // TODO
|
buffer_size = 2048; // TODO
|
||||||
|
|
||||||
main_taxonomy_dir_path = obi_dms_get_full_path(dms, TAXONOMY_DIR_NAME);
|
main_taxonomy_dir_path = get_full_path(dms->dir_fd, TAXONOMY_DIR_NAME);
|
||||||
taxonomy_path = (char*) malloc((strlen(main_taxonomy_dir_path) + strlen(taxonomy_name) + strlen(taxonomy_name) + 3)*sizeof(char));
|
if (asprintf(&taxonomy_path, "%s/%s/%s", main_taxonomy_dir_path, taxonomy_name, taxonomy_name) < 0)
|
||||||
if (sprintf(taxonomy_path, "%s/%s/%s", main_taxonomy_dir_path, taxonomy_name, taxonomy_name) < 0)
|
|
||||||
{
|
{
|
||||||
free(main_taxonomy_dir_path);
|
free(main_taxonomy_dir_path);
|
||||||
obi_close_taxonomy(tax);
|
obi_close_taxonomy(tax);
|
||||||
|
|||||||
@ -29,8 +29,7 @@
|
|||||||
#include "obierrno.h"
|
#include "obierrno.h"
|
||||||
#include "obidebug.h"
|
#include "obidebug.h"
|
||||||
#include "obilittlebigman.h"
|
#include "obilittlebigman.h"
|
||||||
#include "obiblob_indexer.h"
|
#include "obiavl.h"
|
||||||
#include "utils.h"
|
|
||||||
|
|
||||||
|
|
||||||
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
||||||
@ -157,19 +156,9 @@ static index_t get_line_count_per_page(OBIType_t data_type, index_t nb_elements_
|
|||||||
static char* build_column_file_name(const char* column_name, obiversion_t version_number)
|
static char* build_column_file_name(const char* column_name, obiversion_t version_number)
|
||||||
{
|
{
|
||||||
char* file_name;
|
char* file_name;
|
||||||
int version_number_length;
|
|
||||||
|
|
||||||
// Build the file name
|
// Build the file name
|
||||||
version_number_length = (version_number == 0 ? 1 : (int)(log10(version_number)+1));
|
if (asprintf(&file_name,"%s@%d.odc", column_name, version_number) < 0)
|
||||||
file_name = (char*) malloc((strlen(column_name) + version_number_length + 6)*sizeof(char));
|
|
||||||
if (file_name == NULL)
|
|
||||||
{
|
|
||||||
obi_set_errno(OBI_MALLOC_ERROR);
|
|
||||||
obidebug(1, "\nError allocating the memory for a column file name");
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
if (sprintf(file_name,"%s@%d.odc", column_name, version_number) < 0)
|
|
||||||
{
|
{
|
||||||
obi_set_errno(OBICOL_MEMORY_ERROR);
|
obi_set_errno(OBICOL_MEMORY_ERROR);
|
||||||
obidebug(1, "\nError building a column file name");
|
obidebug(1, "\nError building a column file name");
|
||||||
@ -185,15 +174,7 @@ static char* build_version_file_name(const char* column_name)
|
|||||||
char* file_name;
|
char* file_name;
|
||||||
|
|
||||||
// Build the file name
|
// Build the file name
|
||||||
file_name = (char*) malloc((strlen(column_name) + 5)*sizeof(char));
|
if (asprintf(&file_name,"%s.odv", column_name) < 0)
|
||||||
if (file_name == NULL)
|
|
||||||
{
|
|
||||||
obi_set_errno(OBI_MALLOC_ERROR);
|
|
||||||
obidebug(1, "\nError allocating the memory for a version file name");
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
if (sprintf(file_name,"%s.odv", column_name) < 0)
|
|
||||||
{
|
{
|
||||||
obi_set_errno(OBICOL_MEMORY_ERROR);
|
obi_set_errno(OBICOL_MEMORY_ERROR);
|
||||||
obidebug(1, "\nError building a version file name");
|
obidebug(1, "\nError building a version file name");
|
||||||
@ -533,13 +514,14 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
|||||||
index_t nb_lines,
|
index_t nb_lines,
|
||||||
index_t nb_elements_per_line,
|
index_t nb_elements_per_line,
|
||||||
const char* elements_names,
|
const char* elements_names,
|
||||||
const char* indexer_name,
|
const char* avl_name,
|
||||||
const char* comments
|
const char* comments
|
||||||
)
|
)
|
||||||
{
|
{
|
||||||
OBIDMS_column_p new_column;
|
OBIDMS_column_p new_column;
|
||||||
OBIDMS_column_directory_p column_directory;
|
OBIDMS_column_directory_p column_directory;
|
||||||
OBIDMS_column_header_p header;
|
OBIDMS_column_header_p header;
|
||||||
|
OBIDMS_avl_p avl;
|
||||||
size_t file_size;
|
size_t file_size;
|
||||||
obiversion_t version_number;
|
obiversion_t version_number;
|
||||||
char* column_file_name;
|
char* column_file_name;
|
||||||
@ -549,7 +531,6 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
|||||||
index_t minimum_line_count;
|
index_t minimum_line_count;
|
||||||
OBIType_t returned_data_type;
|
OBIType_t returned_data_type;
|
||||||
OBIType_t stored_data_type;
|
OBIType_t stored_data_type;
|
||||||
char* final_indexer_name;
|
|
||||||
|
|
||||||
new_column = NULL;
|
new_column = NULL;
|
||||||
|
|
||||||
@ -569,39 +550,12 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
|||||||
obidebug(1, "\nCan't create column because of invalid data type");
|
obidebug(1, "\nCan't create column because of invalid data type");
|
||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
|
if (((data_type == OBI_STR) || (data_type == OBI_SEQ)) && (avl_name == NULL))
|
||||||
// Get the column directory structure associated to the column
|
|
||||||
column_directory = obi_column_directory(dms, column_name);
|
|
||||||
if (column_directory == NULL)
|
|
||||||
{
|
{
|
||||||
obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
|
obidebug(1, "\nCan't create column because of empty avl name");
|
||||||
obidebug(1, "\nError opening a column directory structure");
|
|
||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
|
|
||||||
// Get the latest version number
|
|
||||||
version_number = obi_get_new_version_number(column_directory, true);
|
|
||||||
if (version_number < 0)
|
|
||||||
{
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
|
|
||||||
// Build the indexer name if needed
|
|
||||||
if ((data_type == OBI_STR) || (data_type == OBI_SEQ))
|
|
||||||
{
|
|
||||||
if (strcmp(indexer_name, "") == 0)
|
|
||||||
{
|
|
||||||
final_indexer_name = obi_build_indexer_name(column_name, version_number);
|
|
||||||
if (final_indexer_name == NULL)
|
|
||||||
return NULL;
|
|
||||||
}
|
|
||||||
else
|
|
||||||
{
|
|
||||||
final_indexer_name = (char*) malloc((strlen(indexer_name)+1)*sizeof(char));
|
|
||||||
strcpy(final_indexer_name, indexer_name);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
returned_data_type = data_type;
|
returned_data_type = data_type;
|
||||||
if ((data_type == OBI_STR) || (data_type == OBI_SEQ))
|
if ((data_type == OBI_STR) || (data_type == OBI_SEQ))
|
||||||
// stored data is indices referring to data stored elsewhere
|
// stored data is indices referring to data stored elsewhere
|
||||||
@ -648,11 +602,27 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
|||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// Get the column directory structure associated to the column
|
||||||
|
column_directory = obi_column_directory(dms, column_name);
|
||||||
|
if (column_directory == NULL)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOLDIR_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError opening a column directory structure");
|
||||||
|
return NULL;
|
||||||
|
}
|
||||||
|
|
||||||
// Calculate the size needed
|
// Calculate the size needed
|
||||||
header_size = obi_get_platform_header_size();
|
header_size = obi_get_platform_header_size();
|
||||||
data_size = obi_array_sizeof(stored_data_type, nb_lines, nb_elements_per_line);
|
data_size = obi_array_sizeof(stored_data_type, nb_lines, nb_elements_per_line);
|
||||||
file_size = header_size + data_size;
|
file_size = header_size + data_size;
|
||||||
|
|
||||||
|
// Get the latest version number
|
||||||
|
version_number = obi_get_new_version_number(column_directory, true);
|
||||||
|
if (version_number < 0)
|
||||||
|
{
|
||||||
|
return NULL;
|
||||||
|
}
|
||||||
|
|
||||||
// Get the column file name
|
// Get the column file name
|
||||||
column_file_name = build_column_file_name(column_name, version_number);
|
column_file_name = build_column_file_name(column_name, version_number);
|
||||||
if (column_file_name == NULL)
|
if (column_file_name == NULL)
|
||||||
@ -750,19 +720,20 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
|||||||
if (comments != NULL)
|
if (comments != NULL)
|
||||||
strncpy(header->comments, comments, COMMENTS_MAX_LENGTH);
|
strncpy(header->comments, comments, COMMENTS_MAX_LENGTH);
|
||||||
|
|
||||||
// If the data type is OBI_STR or OBI_SEQ, the associated obi_indexer is opened or created
|
// If the data type is OBI_STR or OBI_SEQ, the associated obi_avl is opened or created
|
||||||
if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ))
|
if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ))
|
||||||
{
|
{
|
||||||
new_column->indexer = obi_indexer(dms, final_indexer_name);
|
avl = obi_avl(dms, avl_name);
|
||||||
if (new_column->indexer == NULL)
|
if (avl == NULL)
|
||||||
{
|
{
|
||||||
obidebug(1, "\nError opening or creating the indexer associated with a column");
|
obidebug(1, "\nError opening or creating the aVL tree associated with a column");
|
||||||
munmap(new_column->header, header_size);
|
munmap(new_column->header, header_size);
|
||||||
close(column_file_descriptor);
|
close(column_file_descriptor);
|
||||||
free(new_column);
|
free(new_column);
|
||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
strncpy(header->indexer_name, final_indexer_name, INDEXER_MAX_NAME);
|
new_column->avl = avl;
|
||||||
|
strncpy(header->avl_name, avl_name, AVL_MAX_NAME);
|
||||||
}
|
}
|
||||||
|
|
||||||
// Fill the data with NA values
|
// Fill the data with NA values
|
||||||
@ -771,9 +742,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
|||||||
close(column_file_descriptor);
|
close(column_file_descriptor);
|
||||||
|
|
||||||
// Add in the list of opened columns
|
// Add in the list of opened columns
|
||||||
obi_dms_list_column(dms, new_column);
|
*(((dms->opened_columns)->columns)+((dms->opened_columns)->nb_opened_columns)) = new_column;
|
||||||
|
((dms->opened_columns)->nb_opened_columns)++;
|
||||||
// Set counter to 1 // TODO Discuss counters
|
|
||||||
new_column->counter = 1;
|
new_column->counter = 1;
|
||||||
|
|
||||||
return new_column;
|
return new_column;
|
||||||
@ -786,9 +756,11 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
|
|||||||
{
|
{
|
||||||
OBIDMS_column_p column;
|
OBIDMS_column_p column;
|
||||||
OBIDMS_column_directory_p column_directory;
|
OBIDMS_column_directory_p column_directory;
|
||||||
|
OBIDMS_avl_p avl;
|
||||||
char* column_file_name;
|
char* column_file_name;
|
||||||
int column_file_descriptor;
|
int column_file_descriptor;
|
||||||
size_t header_size;
|
size_t header_size;
|
||||||
|
size_t i;
|
||||||
|
|
||||||
column = NULL;
|
column = NULL;
|
||||||
|
|
||||||
@ -796,7 +768,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
|
|||||||
column_directory = obi_open_column_directory(dms, column_name);
|
column_directory = obi_open_column_directory(dms, column_name);
|
||||||
if (column_directory == NULL)
|
if (column_directory == NULL)
|
||||||
{
|
{
|
||||||
obidebug(1, "\nError opening a column directory structure");
|
//obidebug(1, "\nError opening a column directory structure");
|
||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -812,12 +784,14 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
|
|||||||
}
|
}
|
||||||
|
|
||||||
// Check if the column is already in the list of opened columns
|
// Check if the column is already in the list of opened columns
|
||||||
column = obi_dms_get_column_from_list(dms, column_name, version_number);
|
for (i=0; i < ((dms->opened_columns)->nb_opened_columns); i++)
|
||||||
// If it's found, increment its counter and return it
|
|
||||||
if (column != NULL)
|
|
||||||
{
|
{
|
||||||
(column->counter)++;
|
if (!strcmp(((*(((dms->opened_columns)->columns)+i))->header)->name, column_name)
|
||||||
return column;
|
&& (((*(((dms->opened_columns)->columns)+i))->header)->version == version_number))
|
||||||
|
{ // Found the column already opened, increase its counter and return the column
|
||||||
|
((*(((dms->opened_columns)->columns)+i))->counter)++;
|
||||||
|
return *(((dms->opened_columns)->columns)+i);
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
// Get the column file name
|
// Get the column file name
|
||||||
@ -832,7 +806,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
|
|||||||
if (column_file_descriptor < 0)
|
if (column_file_descriptor < 0)
|
||||||
{
|
{
|
||||||
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
obidebug(1, "\nError opening column file");
|
//obidebug(1, "\nError opening column file");
|
||||||
free(column_file_name);
|
free(column_file_name);
|
||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
@ -865,7 +839,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
|
|||||||
column->header = mmap(NULL,
|
column->header = mmap(NULL,
|
||||||
header_size,
|
header_size,
|
||||||
PROT_READ,
|
PROT_READ,
|
||||||
MAP_SHARED,
|
MAP_PRIVATE,
|
||||||
column_file_descriptor,
|
column_file_descriptor,
|
||||||
0
|
0
|
||||||
);
|
);
|
||||||
@ -883,7 +857,7 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
|
|||||||
column->data = mmap(NULL,
|
column->data = mmap(NULL,
|
||||||
(column->header)->data_size,
|
(column->header)->data_size,
|
||||||
PROT_READ,
|
PROT_READ,
|
||||||
MAP_SHARED,
|
MAP_PRIVATE,
|
||||||
column_file_descriptor,
|
column_file_descriptor,
|
||||||
header_size
|
header_size
|
||||||
);
|
);
|
||||||
@ -900,26 +874,26 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
|
|||||||
|
|
||||||
column->writable = false;
|
column->writable = false;
|
||||||
|
|
||||||
// If the data type is OBI_STR or OBI_SEQ, the associated indexer is opened
|
// If the data type is OBI_STR or OBI_SEQ, the associated AVL tree is opened
|
||||||
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
|
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
|
||||||
{
|
{
|
||||||
column->indexer = obi_open_indexer(dms, (column->header)->indexer_name);
|
avl = obi_avl(dms, (column->header)->avl_name);
|
||||||
if (column->indexer == NULL)
|
if (avl == NULL)
|
||||||
{
|
{
|
||||||
obidebug(1, "\nError opening the indexer associated with a column");
|
obidebug(1, "\nError opening the AVL tree associated with a column");
|
||||||
munmap(column->header, header_size);
|
munmap(column->header, header_size);
|
||||||
close(column_file_descriptor);
|
close(column_file_descriptor);
|
||||||
free(column);
|
free(column);
|
||||||
return NULL;
|
return NULL;
|
||||||
}
|
}
|
||||||
|
column->avl = avl;
|
||||||
}
|
}
|
||||||
|
|
||||||
close(column_file_descriptor);
|
close(column_file_descriptor);
|
||||||
|
|
||||||
// Add in the list of opened columns
|
// Add in the list of opened columns and set column counter to 1
|
||||||
obi_dms_list_column(dms, column);
|
*(((dms->opened_columns)->columns)+((dms->opened_columns)->nb_opened_columns)) = column;
|
||||||
|
((dms->opened_columns)->nb_opened_columns)++;
|
||||||
// Set counter to 1
|
|
||||||
column->counter = 1;
|
column->counter = 1;
|
||||||
|
|
||||||
return column;
|
return column;
|
||||||
@ -965,7 +939,7 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
|||||||
nb_lines,
|
nb_lines,
|
||||||
nb_elements_per_line,
|
nb_elements_per_line,
|
||||||
(column_to_clone->header)->elements_names,
|
(column_to_clone->header)->elements_names,
|
||||||
(column_to_clone->header)->indexer_name,
|
(column_to_clone->header)->avl_name,
|
||||||
(column_to_clone->header)->comments
|
(column_to_clone->header)->comments
|
||||||
);
|
);
|
||||||
|
|
||||||
@ -988,13 +962,18 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
|||||||
}
|
}
|
||||||
else if (clone_data && (line_selection != NULL))
|
else if (clone_data && (line_selection != NULL))
|
||||||
{
|
{
|
||||||
|
obidebug(1, "\nCloning data from line selection\n");
|
||||||
line_size = obi_sizeof((new_column->header)->stored_data_type) * (new_column->header)->nb_elements_per_line;
|
line_size = obi_sizeof((new_column->header)->stored_data_type) * (new_column->header)->nb_elements_per_line;
|
||||||
|
fprintf(stderr, "\nline size = %ld\n", line_size);
|
||||||
for (i=0; i<((line_selection->header)->lines_used); i++)
|
for (i=0; i<((line_selection->header)->lines_used); i++)
|
||||||
{
|
{
|
||||||
index = *(((index_t*) (line_selection->data)) + i);
|
index = *(((index_t*) (line_selection->data)) + i);
|
||||||
|
fprintf(stderr, "\nindex = %lld, i = %lld\n", index, i);
|
||||||
memcpy((new_column->data)+(i*line_size), (column_to_clone->data)+(index*line_size), line_size);
|
memcpy((new_column->data)+(i*line_size), (column_to_clone->data)+(index*line_size), line_size);
|
||||||
|
fprintf(stderr, "\nmemcpied\n");
|
||||||
}
|
}
|
||||||
(new_column->header)->lines_used = (line_selection->header)->lines_used;
|
(new_column->header)->lines_used = (line_selection->header)->lines_used;
|
||||||
|
obidebug(1, "\nCloned data from line selection\n");
|
||||||
}
|
}
|
||||||
|
|
||||||
// Close column_to_clone
|
// Close column_to_clone
|
||||||
@ -1010,35 +989,50 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
|||||||
|
|
||||||
int obi_close_column(OBIDMS_column_p column)
|
int obi_close_column(OBIDMS_column_p column)
|
||||||
{
|
{
|
||||||
bool close_dir;
|
size_t i;
|
||||||
int ret_val = 0;
|
bool close_dir;
|
||||||
|
Opened_columns_list_p columns_list;
|
||||||
|
|
||||||
// Truncate the column to the number of lines used if it's not read-only
|
columns_list = (column->dms)->opened_columns;
|
||||||
if (column->writable)
|
|
||||||
ret_val = obi_truncate_column(column);
|
|
||||||
|
|
||||||
(column->counter)--;
|
(column->counter)--;
|
||||||
|
|
||||||
if (column->counter == 0)
|
if (column->counter == 0)
|
||||||
{
|
{
|
||||||
// Delete from the list of opened columns
|
// Delete from the list of opened columns
|
||||||
if (obi_dms_unlist_column(column->dms, column) < 0)
|
for (i=0; i < (columns_list)->nb_opened_columns; i++)
|
||||||
ret_val = -1;
|
{
|
||||||
|
if (!strcmp(((*((columns_list->columns)+i))->header)->name, (column->header)->name)
|
||||||
|
&& (((*((columns_list->columns)+i))->header)->version == (column->header)->version))
|
||||||
|
{ // Found the column. Rearrange list
|
||||||
|
(columns_list->nb_opened_columns)--;
|
||||||
|
(columns_list->columns)[i] = (columns_list->columns)[columns_list->nb_opened_columns];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
// Close column directory if it was the last column opened from that directory
|
// Close column directory if it was the last column opened from that directory
|
||||||
close_dir = obi_dms_is_column_name_in_list(column->dms, (column->header)->name);
|
close_dir = 1;
|
||||||
|
for (i=0; i < (columns_list->nb_opened_columns); i++)
|
||||||
|
{
|
||||||
|
if (!strcmp(((*((columns_list->columns)+i))->header)->name, (column->header)->name))
|
||||||
|
{ // Not the last column from that directory
|
||||||
|
close_dir = 0;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
// If the data type is OBI_STR or OBI_SEQ, the associated indexer is closed
|
// If the data type is OBI_STR or OBI_SEQ, the associated AVL tree is closed
|
||||||
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
|
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
|
||||||
if (obi_close_indexer(column->indexer) < 0)
|
{
|
||||||
ret_val = -1;
|
if (obi_close_avl(column->avl) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
// Munmap data
|
// Munmap data
|
||||||
if (munmap(column->data, (column->header)->data_size) < 0)
|
if (munmap(column->data, (column->header)->data_size) < 0)
|
||||||
{
|
{
|
||||||
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
obidebug(1, "\nError munmapping column data");
|
obidebug(1, "\nError munmapping column data");
|
||||||
ret_val = -1;
|
return -1;
|
||||||
}
|
}
|
||||||
|
|
||||||
// Munmap header
|
// Munmap header
|
||||||
@ -1046,22 +1040,20 @@ int obi_close_column(OBIDMS_column_p column)
|
|||||||
{
|
{
|
||||||
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
obidebug(1, "\nError munmapping a column header");
|
obidebug(1, "\nError munmapping a column header");
|
||||||
ret_val = -1;
|
return -1;
|
||||||
}
|
}
|
||||||
|
|
||||||
// Close column directory
|
|
||||||
if (close_dir)
|
|
||||||
if (obi_close_column_directory(column->column_directory) < 0)
|
|
||||||
ret_val = -1;
|
|
||||||
|
|
||||||
free(column);
|
free(column);
|
||||||
|
|
||||||
|
if (close_dir)
|
||||||
|
obi_close_column_directory(column->column_directory);
|
||||||
}
|
}
|
||||||
|
|
||||||
return ret_val;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
int obi_truncate_column(OBIDMS_column_p column) // TODO is it necessary to unmap/remap?
|
int obi_truncate_column_to_lines_used(OBIDMS_column_p column) // TODO is it necessary to unmap/remap?
|
||||||
{
|
{
|
||||||
size_t file_size;
|
size_t file_size;
|
||||||
size_t data_size;
|
size_t data_size;
|
||||||
@ -1236,6 +1228,20 @@ int obi_enlarge_column(OBIDMS_column_p column)
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int obi_truncate_and_close_column(OBIDMS_column_p column)
|
||||||
|
{
|
||||||
|
if (column->writable) // TODO discuss
|
||||||
|
{
|
||||||
|
if (obi_truncate_column_to_lines_used(column) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
if (obi_close_column(column) < 0)
|
||||||
|
return -1;
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
void obi_ini_to_NA_values(OBIDMS_column_p column,
|
void obi_ini_to_NA_values(OBIDMS_column_p column,
|
||||||
index_t first_line_nb,
|
index_t first_line_nb,
|
||||||
index_t nb_lines)
|
index_t nb_lines)
|
||||||
@ -1274,18 +1280,8 @@ void obi_ini_to_NA_values(OBIDMS_column_p column,
|
|||||||
}
|
}
|
||||||
break;
|
break;
|
||||||
|
|
||||||
case OBI_STR: for (i=start;i<end;i++)
|
case OBI_STR: // fallthrough
|
||||||
{
|
case OBI_SEQ: // fallthrough
|
||||||
*(((index_t*) (column->data)) + i) = OBIIdx_NA;
|
|
||||||
}
|
|
||||||
break;
|
|
||||||
|
|
||||||
case OBI_SEQ: for (i=start;i<end;i++)
|
|
||||||
{
|
|
||||||
*(((index_t*) (column->data)) + i) = OBIIdx_NA;
|
|
||||||
}
|
|
||||||
break;
|
|
||||||
|
|
||||||
case OBI_IDX: for (i=start;i<end;i++)
|
case OBI_IDX: for (i=start;i<end;i++)
|
||||||
{
|
{
|
||||||
*(((index_t*) (column->data)) + i) = OBIIdx_NA;
|
*(((index_t*) (column->data)) + i) = OBIIdx_NA;
|
||||||
@ -1352,12 +1348,12 @@ OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char*
|
|||||||
|
|
||||||
// Fill the header structure
|
// Fill the header structure
|
||||||
header = mmap(NULL,
|
header = mmap(NULL,
|
||||||
header_size,
|
header_size,
|
||||||
PROT_READ,
|
PROT_READ,
|
||||||
MAP_SHARED,
|
MAP_SHARED,
|
||||||
column_file_descriptor,
|
column_file_descriptor,
|
||||||
0
|
0
|
||||||
);
|
);
|
||||||
|
|
||||||
if (header == MAP_FAILED)
|
if (header == MAP_FAILED)
|
||||||
{
|
{
|
||||||
@ -1373,7 +1369,7 @@ OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char*
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
int obi_close_header(OBIDMS_column_header_p header)
|
int obi_unmap_header(OBIDMS_column_header_p header)
|
||||||
{
|
{
|
||||||
if (munmap(header, header->header_size) < 0)
|
if (munmap(header, header->header_size) < 0)
|
||||||
{
|
{
|
||||||
@ -1401,7 +1397,7 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
|
|||||||
|
|
||||||
element_index = 0;
|
element_index = 0;
|
||||||
|
|
||||||
name = strtok(elements_names, ";"); // TODO not thread safe, see strtok_r maybe
|
name = strtok (elements_names, ";"); // TODO not thread safe, see strtok_r maybe
|
||||||
if (strcmp(element_name, name) == 0)
|
if (strcmp(element_name, name) == 0)
|
||||||
{
|
{
|
||||||
free(elements_names);
|
free(elements_names);
|
||||||
@ -1411,7 +1407,7 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
|
|||||||
|
|
||||||
while (name != NULL)
|
while (name != NULL)
|
||||||
{
|
{
|
||||||
name = strtok(NULL, ";"); // TODO not thread safe, see strtok_r maybe
|
name = strtok (NULL, ";"); // TODO not thread safe, see strtok_r maybe
|
||||||
if (strcmp(element_name, name) == 0)
|
if (strcmp(element_name, name) == 0)
|
||||||
{
|
{
|
||||||
free(elements_names);
|
free(elements_names);
|
||||||
@ -1426,48 +1422,28 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb)
|
char* obi_column_format_date(time_t date)
|
||||||
{
|
{
|
||||||
// Check if the column is read-only
|
char* formatted_time;
|
||||||
if (!(column->writable))
|
struct tm* tmp;
|
||||||
|
|
||||||
|
formatted_time = (char*) malloc(FORMATTED_TIME_LENGTH*sizeof(char));
|
||||||
|
|
||||||
|
tmp = localtime(&date);
|
||||||
|
if (tmp == NULL)
|
||||||
{
|
{
|
||||||
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
obidebug(1, "\nError trying to set a value in a read-only column");
|
obidebug(1, "\nError formatting a date");
|
||||||
return -1;
|
return NULL;
|
||||||
}
|
}
|
||||||
|
|
||||||
// Check that the line number is not greater than the maximum allowed
|
if (strftime(formatted_time, FORMATTED_TIME_LENGTH, "%c", tmp) == 0)
|
||||||
if (line_nb >= MAXIMUM_LINE_COUNT)
|
|
||||||
{
|
{
|
||||||
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
|
obidebug(1, "\nError formatting a date");
|
||||||
return -1;
|
return NULL;
|
||||||
}
|
}
|
||||||
|
|
||||||
// Check if the file needs to be enlarged
|
return formatted_time;
|
||||||
while ((line_nb+1) > (column->header)->line_count)
|
|
||||||
{
|
|
||||||
// Enlarge the file
|
|
||||||
if (obi_enlarge_column(column) < 0)
|
|
||||||
return -1;
|
|
||||||
}
|
|
||||||
|
|
||||||
// Update lines used
|
|
||||||
if ((line_nb+1) > (column->header)->lines_used)
|
|
||||||
(column->header)->lines_used = line_nb+1;
|
|
||||||
|
|
||||||
return 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb)
|
|
||||||
{
|
|
||||||
if ((line_nb+1) > ((column->header)->line_count))
|
|
||||||
{
|
|
||||||
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
|
||||||
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
|
|
||||||
return -1;
|
|
||||||
}
|
|
||||||
return 0;
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -25,18 +25,25 @@
|
|||||||
#include "obierrno.h"
|
#include "obierrno.h"
|
||||||
#include "obilittlebigman.h"
|
#include "obilittlebigman.h"
|
||||||
#include "obidmscolumndir.h"
|
#include "obidmscolumndir.h"
|
||||||
#include "obiblob_indexer.h"
|
#include "obiavl.h"
|
||||||
|
|
||||||
|
|
||||||
|
#define ONE_IF_ZERO(x) (((x)==0)?1:(x)) /**< If x is equal to 0, x takes the value 1.
|
||||||
|
*/
|
||||||
#define ELEMENTS_NAMES_MAX (2048) /**< The maximum length of the list of elements names.
|
#define ELEMENTS_NAMES_MAX (2048) /**< The maximum length of the list of elements names.
|
||||||
*/
|
*/
|
||||||
#define COLUMN_GROWTH_FACTOR (2) /**< The growth factor when a column is enlarged.
|
#define COLUMN_GROWTH_FACTOR (2) /**< The growth factor when a column is enlarged.
|
||||||
*/
|
*/
|
||||||
#define MAXIMUM_LINE_COUNT (1000000000) /**< The maximum line count for the data of a column. //TODO
|
#define MAXIMUM_LINE_COUNT (1000000000) /**< The maximum line count for the data of a column. //TODO
|
||||||
*/
|
*/
|
||||||
|
#define FORMATTED_TIME_LENGTH (1024) /**< The length allocated for the character string containing a formatted date.
|
||||||
|
*/
|
||||||
#define COMMENTS_MAX_LENGTH (2048) /**< The maximum length for comments.
|
#define COMMENTS_MAX_LENGTH (2048) /**< The maximum length for comments.
|
||||||
*/
|
*/
|
||||||
|
|
||||||
|
typedef int32_t obiversion_t; /**< Used to store the column version number
|
||||||
|
*/
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief OBIDMS column header structure.
|
* @brief OBIDMS column header structure.
|
||||||
@ -71,7 +78,7 @@ typedef struct OBIDMS_column_header {
|
|||||||
*/
|
*/
|
||||||
char name[OBIDMS_COLUMN_MAX_NAME+1]; /**< The column name as a NULL terminated string.
|
char name[OBIDMS_COLUMN_MAX_NAME+1]; /**< The column name as a NULL terminated string.
|
||||||
*/
|
*/
|
||||||
char indexer_name[INDEXER_MAX_NAME+1]; /**< If there is one, the indexer name as a NULL terminated string.
|
char avl_name[AVL_MAX_NAME+1]; /**< If there is one, the AVL tree name as a NULL terminated string.
|
||||||
*/
|
*/
|
||||||
char comments[COMMENTS_MAX_LENGTH+1]; /**< Comments stored as a classical zero end C string.
|
char comments[COMMENTS_MAX_LENGTH+1]; /**< Comments stored as a classical zero end C string.
|
||||||
*/
|
*/
|
||||||
@ -91,7 +98,7 @@ typedef struct OBIDMS_column {
|
|||||||
*/
|
*/
|
||||||
OBIDMS_column_header_p header; /**< A pointer to the header of the column.
|
OBIDMS_column_header_p header; /**< A pointer to the header of the column.
|
||||||
*/
|
*/
|
||||||
Obi_indexer_p indexer; /**< A pointer to the blob indexer associated with the column if there is one.
|
OBIDMS_avl_p avl; /**< A pointer to the AVL tree associated with the column if there is one.
|
||||||
*/
|
*/
|
||||||
void* data; /**< A `void` pointer to the beginning of the data.
|
void* data; /**< A `void` pointer to the beginning of the data.
|
||||||
*
|
*
|
||||||
@ -157,7 +164,7 @@ size_t obi_get_platform_header_size();
|
|||||||
* @brief Creates a column.
|
* @brief Creates a column.
|
||||||
*
|
*
|
||||||
* The minimum data size allocated is one memory page, and the data is initialized to the NA value of the OBIType.
|
* The minimum data size allocated is one memory page, and the data is initialized to the NA value of the OBIType.
|
||||||
* If there is an indexer associated with the column, it is opened or created if it does not already exist.
|
* If there is an AVL tree associated with the column, it is opened or created if it does not already exist.
|
||||||
*
|
*
|
||||||
* @warning If there is one element per line, elements_names should be equal to column_name. // TODO change this condition?
|
* @warning If there is one element per line, elements_names should be equal to column_name. // TODO change this condition?
|
||||||
*
|
*
|
||||||
@ -167,7 +174,7 @@ size_t obi_get_platform_header_size();
|
|||||||
* @param nb_lines The number of lines to be stored.
|
* @param nb_lines The number of lines to be stored.
|
||||||
* @param nb_elements_per_line The number of elements per line. // TODO talk about default values
|
* @param nb_elements_per_line The number of elements per line. // TODO talk about default values
|
||||||
* @param elements_names The names of the elements with ';' as separator.
|
* @param elements_names The names of the elements with ';' as separator.
|
||||||
* @param indexer_name The name of the indexer if there is one associated with the column.
|
* @param avl_name The name of the AVL tree if there is one associated with the column.
|
||||||
* @param comments Optional comments associated with the column.
|
* @param comments Optional comments associated with the column.
|
||||||
*
|
*
|
||||||
* @returns A pointer on the newly created column structure.
|
* @returns A pointer on the newly created column structure.
|
||||||
@ -182,7 +189,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
|||||||
index_t nb_lines,
|
index_t nb_lines,
|
||||||
index_t nb_elements_per_line,
|
index_t nb_elements_per_line,
|
||||||
const char* elements_names,
|
const char* elements_names,
|
||||||
const char* indexer_name,
|
const char* avl_name,
|
||||||
const char* comments
|
const char* comments
|
||||||
);
|
);
|
||||||
|
|
||||||
@ -221,7 +228,7 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms, OBIDMS_column_p line_selection, c
|
|||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Truncates a column to the number of lines used if it is not read-only and closes it.
|
* @brief Closes a column.
|
||||||
*
|
*
|
||||||
* @param column A pointer on an OBIDMS column.
|
* @param column A pointer on an OBIDMS column.
|
||||||
*
|
*
|
||||||
@ -246,7 +253,7 @@ int obi_close_column(OBIDMS_column_p column);
|
|||||||
* @since August 2015
|
* @since August 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
int obi_truncate_column(OBIDMS_column_p column);
|
int obi_truncate_column_to_lines_used(OBIDMS_column_p column);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
@ -263,6 +270,21 @@ int obi_truncate_column(OBIDMS_column_p column);
|
|||||||
int obi_enlarge_column(OBIDMS_column_p column);
|
int obi_enlarge_column(OBIDMS_column_p column);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Truncates a column file to the number of lines used rounded to the nearest
|
||||||
|
* greater multiple of the page size and closes it.
|
||||||
|
*
|
||||||
|
* @param column A pointer on an OBIDMS column.
|
||||||
|
*
|
||||||
|
* @retval 0 if the operation was successfully completed.
|
||||||
|
* @retval -1 if an error occurred.
|
||||||
|
*
|
||||||
|
* @since August 2015
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
int obi_truncate_and_close_column(OBIDMS_column_p column);
|
||||||
|
|
||||||
|
|
||||||
/*
|
/*
|
||||||
* @brief Sets the data in a column to the NA value of the data OBIType.
|
* @brief Sets the data in a column to the NA value of the data OBIType.
|
||||||
*
|
*
|
||||||
@ -306,7 +328,7 @@ OBIDMS_column_header_p obi_column_get_header_from_name(OBIDMS_p dms, const char*
|
|||||||
* @since October 2015
|
* @since October 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
int obi_close_header(OBIDMS_column_header_p header);
|
int obi_unmap_header(OBIDMS_column_header_p header);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
@ -325,33 +347,22 @@ index_t obi_column_get_element_index_from_name(OBIDMS_column_p column, const cha
|
|||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Prepares a column to set a value.
|
* @brief Formats a date in a way that is easy to read.
|
||||||
*
|
*
|
||||||
* @param column A pointer on an OBIDMS column.
|
* @warning The pointer returned must be freed by the caller.
|
||||||
* @param line_nb The number of the line at which the value will be set.
|
|
||||||
*
|
*
|
||||||
* @retval 0 if the operation was successfully completed.
|
* @param date A date.
|
||||||
* @retval -1 if an error occurred.
|
|
||||||
*
|
*
|
||||||
* @since April 2016
|
* @returns The date formatted in a way that is easy to read.
|
||||||
|
*
|
||||||
|
* @since October 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb);
|
char* obi_column_format_date(time_t date);
|
||||||
|
|
||||||
|
|
||||||
/**
|
int obi_select(OBIDMS_column_p lines_column, index_t line_to_grep);
|
||||||
* @brief Prepares a column to recover a value.
|
|
||||||
*
|
|
||||||
* @param column A pointer on an OBIDMS column.
|
|
||||||
* @param line_nb The number of the line at which the value will be recovered.
|
|
||||||
*
|
|
||||||
* @retval 0 if the operation was successfully completed.
|
|
||||||
* @retval -1 if an error occurred.
|
|
||||||
*
|
|
||||||
* @since April 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb);
|
|
||||||
|
|
||||||
|
|
||||||
#endif /* OBIDMSCOLUMN_H_ */
|
#endif /* OBIDMSCOLUMN_H_ */
|
||||||
|
|||||||
@ -14,7 +14,13 @@
|
|||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
|
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
|
#include "obiview.h"
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
|
#include "obierrno.h"
|
||||||
|
#include "obidebug.h"
|
||||||
|
|
||||||
|
|
||||||
|
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
||||||
|
|
||||||
|
|
||||||
/**********************************************************************
|
/**********************************************************************
|
||||||
@ -26,8 +32,25 @@
|
|||||||
|
|
||||||
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value)
|
int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value)
|
||||||
{
|
{
|
||||||
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
|
// Check that the line number is not greater than the maximum allowed
|
||||||
return -1;
|
if (line_nb >= MAXIMUM_LINE_COUNT)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Check if the file needs to be enlarged
|
||||||
|
while ((line_nb+1) > (column->header)->line_count)
|
||||||
|
{
|
||||||
|
// Enlarge the file
|
||||||
|
if (obi_enlarge_column(column) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Update lines used
|
||||||
|
if ((line_nb+1) > (column->header)->lines_used)
|
||||||
|
(column->header)->lines_used = line_nb+1;
|
||||||
|
|
||||||
// Set the value
|
// Set the value
|
||||||
*(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
|
*(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
|
||||||
@ -36,31 +59,111 @@ int obi_column_set_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value)
|
||||||
|
{
|
||||||
|
// Check that the view is not read-only
|
||||||
|
if (view->read_only)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBIVIEW_ERROR);
|
||||||
|
obidebug(1, "\nError trying to set a value in a column in a read-only view");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
if ((view->line_selection != NULL) || (!(column->writable)))
|
||||||
|
{
|
||||||
|
// Get the right line number
|
||||||
|
if (column->writable)
|
||||||
|
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
|
||||||
|
|
||||||
|
column = obi_view_clone_column(view, (column->header)->name);
|
||||||
|
if (column == NULL)
|
||||||
|
{
|
||||||
|
obidebug(1, "\nError trying to clone a column to modify it");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if ((line_nb+1) > view->line_count)
|
||||||
|
{
|
||||||
|
if (obi_view_update_lines(view, (line_nb+1)) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value) < 0)
|
||||||
|
return -1;
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
obibool_t obi_column_get_obibool_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||||
{
|
{
|
||||||
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
|
if ((line_nb+1) > ((column->header)->line_count))
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
|
||||||
return OBIBool_NA;
|
return OBIBool_NA;
|
||||||
|
}
|
||||||
|
|
||||||
return *(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
return *(((obibool_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||||
|
{
|
||||||
|
if ((line_nb+1) > (view->line_count))
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
|
||||||
|
return OBIBool_NA;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (view->line_selection)
|
||||||
|
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
|
||||||
|
|
||||||
|
return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value)
|
int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value)
|
||||||
{
|
{
|
||||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
index_t element_idx;
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
if (element_idx == OBIIdx_NA)
|
if (element_idx == OBIIdx_NA)
|
||||||
return -1;
|
return -1;
|
||||||
|
obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
return obi_column_set_obibool_with_elt_idx(column, line_nb, element_idx, value);
|
|
||||||
|
int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return -1;
|
||||||
|
obi_column_set_obibool_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
|
||||||
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||||
{
|
{
|
||||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
index_t element_idx;
|
||||||
|
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
if (element_idx == OBIIdx_NA)
|
if (element_idx == OBIIdx_NA)
|
||||||
return OBIBool_NA;
|
return OBIBool_NA;
|
||||||
|
|
||||||
return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
|
return obi_column_get_obibool_with_elt_idx(column, line_nb, element_idx);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return OBIBool_NA;
|
||||||
|
return obi_column_get_obibool_with_elt_idx_in_view(view, column, line_nb, element_idx);
|
||||||
|
}
|
||||||
|
|||||||
@ -19,6 +19,7 @@
|
|||||||
|
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
|
#include "obiview.h"
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
@ -95,5 +96,79 @@ int obi_column_set_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb
|
|||||||
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
obibool_t obi_column_get_obibool_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL, using the index of the element in the line.
|
||||||
|
*
|
||||||
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be set.
|
||||||
|
* @param element_idx The index of the element that should be set in the line.
|
||||||
|
* @param value The value that should be set.
|
||||||
|
*
|
||||||
|
* @returns An integer value indicating the success of the operation.
|
||||||
|
* @retval 0 on success.
|
||||||
|
* @retval -1 if an error occurred.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
int obi_column_set_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obibool_t value);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column().
|
||||||
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
|
* @param element_idx The index of the element that should be recovered in the line.
|
||||||
|
*
|
||||||
|
* @returns The recovered value.
|
||||||
|
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
obibool_t obi_column_get_obibool_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Sets a value in an OBIDMS column containing data with the type OBI_BOOL,
|
||||||
|
* using the name of the element in the line.
|
||||||
|
*
|
||||||
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be set.
|
||||||
|
* @param element_name The name of the element that should be set in the line.
|
||||||
|
* @param value The value that should be set.
|
||||||
|
*
|
||||||
|
* @returns An integer value indicating the success of the operation.
|
||||||
|
* @retval 0 on success.
|
||||||
|
* @retval -1 if an error occurred.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
int obi_column_set_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obibool_t value);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_BOOL,
|
||||||
|
* using the name of the element in the line.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
|
* @param element_name The name of the element that should be recovered in the line.
|
||||||
|
*
|
||||||
|
* @returns The recovered value.
|
||||||
|
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
obibool_t obi_column_get_obibool_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||||
|
|
||||||
|
|
||||||
#endif /* OBIDMSCOLUMN_BOOL_H_ */
|
#endif /* OBIDMSCOLUMN_BOOL_H_ */
|
||||||
|
|
||||||
|
|||||||
@ -14,7 +14,13 @@
|
|||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
|
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
|
#include "obiview.h"
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
|
#include "obierrno.h"
|
||||||
|
#include "obidebug.h"
|
||||||
|
|
||||||
|
|
||||||
|
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
||||||
|
|
||||||
|
|
||||||
/**********************************************************************
|
/**********************************************************************
|
||||||
@ -26,8 +32,25 @@
|
|||||||
|
|
||||||
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value)
|
int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value)
|
||||||
{
|
{
|
||||||
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
|
// Check that the line number is not greater than the maximum allowed
|
||||||
return -1;
|
if (line_nb >= MAXIMUM_LINE_COUNT)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Check if the file needs to be enlarged
|
||||||
|
while ((line_nb+1) > (column->header)->line_count)
|
||||||
|
{
|
||||||
|
// Enlarge the file
|
||||||
|
if (obi_enlarge_column(column) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Update lines used
|
||||||
|
if ((line_nb+1) > (column->header)->lines_used)
|
||||||
|
(column->header)->lines_used = line_nb+1;
|
||||||
|
|
||||||
// Set the value
|
// Set the value
|
||||||
*(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
|
*(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
|
||||||
@ -36,30 +59,111 @@ int obi_column_set_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value)
|
||||||
|
{
|
||||||
|
// Check that the view is not read-only
|
||||||
|
if (view->read_only)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBIVIEW_ERROR);
|
||||||
|
obidebug(1, "\nError trying to set a value in a column in a read-only view");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
if ((view->line_selection != NULL) || (!(column->writable)))
|
||||||
|
{
|
||||||
|
// Get the right line number
|
||||||
|
if (column->writable)
|
||||||
|
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
|
||||||
|
|
||||||
|
column = obi_view_clone_column(view, (column->header)->name);
|
||||||
|
if (column == NULL)
|
||||||
|
{
|
||||||
|
obidebug(1, "\nError trying to clone a column to modify it");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if ((line_nb+1) > view->line_count)
|
||||||
|
{
|
||||||
|
if (obi_view_update_lines(view, (line_nb+1)) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value) < 0)
|
||||||
|
return -1;
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
obichar_t obi_column_get_obichar_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||||
{
|
{
|
||||||
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
|
if ((line_nb+1) > ((column->header)->line_count))
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
|
||||||
return OBIChar_NA;
|
return OBIChar_NA;
|
||||||
|
}
|
||||||
|
|
||||||
return *(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
return *(((obichar_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||||
|
{
|
||||||
|
if ((line_nb+1) > (view->line_count))
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
|
||||||
|
return OBIChar_NA;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (view->line_selection)
|
||||||
|
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
|
||||||
|
|
||||||
|
return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value)
|
int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value)
|
||||||
{
|
{
|
||||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
index_t element_idx;
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
if (element_idx == OBIIdx_NA)
|
if (element_idx == OBIIdx_NA)
|
||||||
return -1;
|
return -1;
|
||||||
|
obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
return obi_column_set_obichar_with_elt_idx(column, line_nb, element_idx, value);
|
|
||||||
|
int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return -1;
|
||||||
|
obi_column_set_obichar_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
|
||||||
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||||
{
|
{
|
||||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
index_t element_idx;
|
||||||
|
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
if (element_idx == OBIIdx_NA)
|
if (element_idx == OBIIdx_NA)
|
||||||
return OBIChar_NA;
|
return OBIChar_NA;
|
||||||
|
|
||||||
return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
|
return obi_column_get_obichar_with_elt_idx(column, line_nb, element_idx);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return OBIChar_NA;
|
||||||
|
return obi_column_get_obichar_with_elt_idx_in_view(view, column, line_nb, element_idx);
|
||||||
|
}
|
||||||
|
|||||||
@ -19,6 +19,7 @@
|
|||||||
|
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
|
#include "obiview.h"
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
@ -95,5 +96,79 @@ int obi_column_set_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb
|
|||||||
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
obichar_t obi_column_get_obichar_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR, using the index of the element in the line.
|
||||||
|
*
|
||||||
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be set.
|
||||||
|
* @param element_idx The index of the element that should be set in the line.
|
||||||
|
* @param value The value that should be set.
|
||||||
|
*
|
||||||
|
* @returns An integer value indicating the success of the operation.
|
||||||
|
* @retval 0 on success.
|
||||||
|
* @retval -1 if an error occurred.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
int obi_column_set_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obichar_t value);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column().
|
||||||
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
|
* @param element_idx The index of the element that should be recovered in the line.
|
||||||
|
*
|
||||||
|
* @returns The recovered value.
|
||||||
|
* @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
obichar_t obi_column_get_obichar_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Sets a value in an OBIDMS column containing data with the type OBI_CHAR,
|
||||||
|
* using the name of the element in the line.
|
||||||
|
*
|
||||||
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be set.
|
||||||
|
* @param element_name The name of the element that should be set in the line.
|
||||||
|
* @param value The value that should be set.
|
||||||
|
*
|
||||||
|
* @returns An integer value indicating the success of the operation.
|
||||||
|
* @retval 0 on success.
|
||||||
|
* @retval -1 if an error occurred.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
int obi_column_set_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obichar_t value);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_CHAR,
|
||||||
|
* using the name of the element in the line.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
|
* @param element_name The name of the element that should be recovered in the line.
|
||||||
|
*
|
||||||
|
* @returns The recovered value.
|
||||||
|
* @retval OBIChar_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
obichar_t obi_column_get_obichar_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||||
|
|
||||||
|
|
||||||
#endif /* OBIDMSCOLUMN_CHAR_H_ */
|
#endif /* OBIDMSCOLUMN_CHAR_H_ */
|
||||||
|
|
||||||
|
|||||||
@ -14,7 +14,13 @@
|
|||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
|
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
|
#include "obiview.h"
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
|
#include "obierrno.h"
|
||||||
|
#include "obidebug.h"
|
||||||
|
|
||||||
|
|
||||||
|
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
||||||
|
|
||||||
|
|
||||||
/**********************************************************************
|
/**********************************************************************
|
||||||
@ -25,8 +31,25 @@
|
|||||||
|
|
||||||
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value)
|
int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value)
|
||||||
{
|
{
|
||||||
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
|
// Check that the line number is not greater than the maximum allowed
|
||||||
return -1;
|
if (line_nb >= MAXIMUM_LINE_COUNT)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Check if the file needs to be enlarged
|
||||||
|
while ((line_nb+1) > (column->header)->line_count)
|
||||||
|
{
|
||||||
|
// Enlarge the file
|
||||||
|
if (obi_enlarge_column(column) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Update lines used
|
||||||
|
if ((line_nb+1) > (column->header)->lines_used)
|
||||||
|
(column->header)->lines_used = line_nb+1;
|
||||||
|
|
||||||
// Set the value
|
// Set the value
|
||||||
*(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
|
*(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
|
||||||
@ -35,31 +58,111 @@ int obi_column_set_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value)
|
||||||
|
{
|
||||||
|
// Check that the view is not read-only
|
||||||
|
if (view->read_only)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBIVIEW_ERROR);
|
||||||
|
obidebug(1, "\nError trying to set a value in a column in a read-only view");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
if ((view->line_selection != NULL) || (!(column->writable)))
|
||||||
|
{
|
||||||
|
// Get the right line number
|
||||||
|
if (column->writable)
|
||||||
|
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
|
||||||
|
|
||||||
|
column = obi_view_clone_column(view, (column->header)->name);
|
||||||
|
if (column == NULL)
|
||||||
|
{
|
||||||
|
obidebug(1, "\nError trying to clone a column to modify it");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if ((line_nb+1) > view->line_count)
|
||||||
|
{
|
||||||
|
if (obi_view_update_lines(view, (line_nb+1)) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value) < 0)
|
||||||
|
return -1;
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
obifloat_t obi_column_get_obifloat_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||||
{
|
{
|
||||||
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
|
if ((line_nb+1) > ((column->header)->line_count))
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
|
||||||
return OBIFloat_NA;
|
return OBIFloat_NA;
|
||||||
|
}
|
||||||
|
|
||||||
return *(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
return *(((obifloat_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||||
|
{
|
||||||
|
if ((line_nb+1) > (view->line_count))
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
|
||||||
|
return OBIFloat_NA;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (view->line_selection)
|
||||||
|
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
|
||||||
|
|
||||||
|
return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value)
|
int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value)
|
||||||
{
|
{
|
||||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
index_t element_idx;
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
if (element_idx == OBIIdx_NA)
|
if (element_idx == OBIIdx_NA)
|
||||||
return -1;
|
return -1;
|
||||||
|
obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
return obi_column_set_obifloat_with_elt_idx(column, line_nb, element_idx, value);
|
|
||||||
|
int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return -1;
|
||||||
|
obi_column_set_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
|
||||||
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||||
{
|
{
|
||||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
index_t element_idx;
|
||||||
|
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
if (element_idx == OBIIdx_NA)
|
if (element_idx == OBIIdx_NA)
|
||||||
return OBIFloat_NA;
|
return OBIFloat_NA;
|
||||||
|
|
||||||
return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
|
return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return OBIFloat_NA;
|
||||||
|
return obi_column_get_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx);
|
||||||
|
}
|
||||||
|
|||||||
@ -19,6 +19,7 @@
|
|||||||
|
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
|
#include "obiview.h"
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
@ -95,5 +96,79 @@ int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_n
|
|||||||
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT, using the index of the element in the line.
|
||||||
|
*
|
||||||
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be set.
|
||||||
|
* @param element_idx The index of the element that should be set in the line.
|
||||||
|
* @param value The value that should be set.
|
||||||
|
*
|
||||||
|
* @returns An integer value indicating the success of the operation.
|
||||||
|
* @retval 0 on success.
|
||||||
|
* @retval -1 if an error occurred.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
int obi_column_set_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obifloat_t value);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column().
|
||||||
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
|
* @param element_idx The index of the element that should be recovered in the line.
|
||||||
|
*
|
||||||
|
* @returns The recovered value.
|
||||||
|
* @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
obifloat_t obi_column_get_obifloat_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Sets a value in an OBIDMS column containing data with the type OBI_FLOAT,
|
||||||
|
* using the name of the element in the line.
|
||||||
|
*
|
||||||
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be set.
|
||||||
|
* @param element_name The name of the element that should be set in the line.
|
||||||
|
* @param value The value that should be set.
|
||||||
|
*
|
||||||
|
* @returns An integer value indicating the success of the operation.
|
||||||
|
* @retval 0 on success.
|
||||||
|
* @retval -1 if an error occurred.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
int obi_column_set_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obifloat_t value);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_FLOAT,
|
||||||
|
* using the name of the element in the line.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
|
* @param element_name The name of the element that should be recovered in the line.
|
||||||
|
*
|
||||||
|
* @returns The recovered value.
|
||||||
|
* @retval OBIFloat_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||||
|
|
||||||
|
|
||||||
#endif /* OBIDMSCOLUMN_FLOAT_H_ */
|
#endif /* OBIDMSCOLUMN_FLOAT_H_ */
|
||||||
|
|
||||||
|
|||||||
@ -15,6 +15,11 @@
|
|||||||
|
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
|
#include "obierrno.h"
|
||||||
|
#include "obidebug.h"
|
||||||
|
|
||||||
|
|
||||||
|
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
||||||
|
|
||||||
|
|
||||||
/**********************************************************************
|
/**********************************************************************
|
||||||
@ -26,8 +31,25 @@
|
|||||||
|
|
||||||
int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value)
|
int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value)
|
||||||
{
|
{
|
||||||
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
|
// Check that the line number is not greater than the maximum allowed
|
||||||
return -1;
|
if (line_nb >= MAXIMUM_LINE_COUNT)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Check if the file needs to be enlarged
|
||||||
|
while ((line_nb+1) > (column->header)->line_count)
|
||||||
|
{
|
||||||
|
// Enlarge the file
|
||||||
|
if (obi_enlarge_column(column) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Update lines used
|
||||||
|
if ((line_nb+1) > (column->header)->lines_used)
|
||||||
|
(column->header)->lines_used = line_nb+1;
|
||||||
|
|
||||||
// Set the value
|
// Set the value
|
||||||
*(((index_t*) (column->data)) + line_nb) = value;
|
*(((index_t*) (column->data)) + line_nb) = value;
|
||||||
@ -38,8 +60,12 @@ int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value)
|
|||||||
|
|
||||||
index_t obi_column_get_index(OBIDMS_column_p column, index_t line_nb)
|
index_t obi_column_get_index(OBIDMS_column_p column, index_t line_nb)
|
||||||
{
|
{
|
||||||
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
|
if ((line_nb+1) > ((column->header)->line_count))
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
|
||||||
return OBIIdx_NA;
|
return OBIIdx_NA;
|
||||||
|
}
|
||||||
|
|
||||||
return *(((index_t*) (column->data)) + line_nb);
|
return *(((index_t*) (column->data)) + line_nb);
|
||||||
}
|
}
|
||||||
|
|||||||
@ -7,9 +7,6 @@
|
|||||||
* @author Celine Mercier
|
* @author Celine Mercier
|
||||||
* @date February 14th 2016
|
* @date February 14th 2016
|
||||||
* @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_IDX.
|
* @brief Header file for the functions handling OBIColumns containing data with the OBIType OBI_IDX.
|
||||||
*
|
|
||||||
* Note: OBI_IDX columns contain indices referring to data stored elsewhere
|
|
||||||
* (for example lines in other columns) and contain only one element (index) per line.
|
|
||||||
*/
|
*/
|
||||||
|
|
||||||
|
|
||||||
@ -24,43 +21,8 @@
|
|||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Sets a value in an OBIDMS column containing data with the type OBI_IDX.
|
|
||||||
*
|
|
||||||
* Note: OBI_IDX columns contain indices referring to data stored elsewhere
|
|
||||||
* (for example lines in other columns) and contain only one element (index) per line.
|
|
||||||
*
|
|
||||||
* @warning Pointers returned by obi_open_column() don't allow writing.
|
|
||||||
*
|
|
||||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
|
||||||
* @param line_nb The number of the line where the value should be set.
|
|
||||||
* @param value The value that should be set.
|
|
||||||
*
|
|
||||||
* @returns An integer value indicating the success of the operation.
|
|
||||||
* @retval 0 on success.
|
|
||||||
* @retval -1 if an error occurred.
|
|
||||||
*
|
|
||||||
* @since February 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value);
|
int obi_column_set_index(OBIDMS_column_p column, index_t line_nb, index_t value);
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_IDX.
|
|
||||||
*
|
|
||||||
* Note: OBI_IDX columns contain indices referring to data stored elsewhere
|
|
||||||
* (for example lines in other columns) and contain only one element (index) per line.
|
|
||||||
*
|
|
||||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
|
||||||
* @param line_nb The number of the line where the value should be recovered.
|
|
||||||
*
|
|
||||||
* @returns The recovered value.
|
|
||||||
* @retval OBIIdx_NA the NA value of the type if an error occurred and obi_errno is set.
|
|
||||||
*
|
|
||||||
* @since February 2016
|
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
|
||||||
*/
|
|
||||||
index_t obi_column_get_index(OBIDMS_column_p column, index_t line_nb);
|
index_t obi_column_get_index(OBIDMS_column_p column, index_t line_nb);
|
||||||
|
|
||||||
|
|
||||||
|
|||||||
@ -14,7 +14,13 @@
|
|||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
|
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
|
#include "obiview.h"
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
|
#include "obierrno.h"
|
||||||
|
#include "obidebug.h"
|
||||||
|
|
||||||
|
|
||||||
|
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
||||||
|
|
||||||
|
|
||||||
/**********************************************************************
|
/**********************************************************************
|
||||||
@ -23,10 +29,28 @@
|
|||||||
*
|
*
|
||||||
**********************************************************************/
|
**********************************************************************/
|
||||||
|
|
||||||
|
|
||||||
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value)
|
int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value)
|
||||||
{
|
{
|
||||||
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
|
// Check that the line number is not greater than the maximum allowed
|
||||||
return -1;
|
if (line_nb >= MAXIMUM_LINE_COUNT)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Check if the file needs to be enlarged
|
||||||
|
while ((line_nb+1) > (column->header)->line_count)
|
||||||
|
{
|
||||||
|
// Enlarge the file
|
||||||
|
if (obi_enlarge_column(column) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Update lines used
|
||||||
|
if ((line_nb+1) > (column->header)->lines_used)
|
||||||
|
(column->header)->lines_used = line_nb+1;
|
||||||
|
|
||||||
// Set the value
|
// Set the value
|
||||||
*(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
|
*(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = value;
|
||||||
@ -35,31 +59,112 @@ int obi_column_set_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
|
|||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value)
|
||||||
|
{
|
||||||
|
// Check that the view is not read-only
|
||||||
|
if (view->read_only)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBIVIEW_ERROR);
|
||||||
|
obidebug(1, "\nError trying to set a value in a column in a read-only view");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
if ((view->line_selection != NULL) || (!(column->writable)))
|
||||||
|
{
|
||||||
|
// Get the right line number
|
||||||
|
if (column->writable)
|
||||||
|
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
|
||||||
|
|
||||||
|
column = obi_view_clone_column(view, (column->header)->name);
|
||||||
|
if (column == NULL)
|
||||||
|
{
|
||||||
|
obidebug(1, "\nError trying to clone a column to modify it");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if ((line_nb+1) > view->line_count)
|
||||||
|
{
|
||||||
|
if (obi_view_update_lines(view, (line_nb+1)) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value) < 0)
|
||||||
|
return -1;
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
obiint_t obi_column_get_obiint_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||||
{
|
{
|
||||||
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
|
if ((line_nb+1) > ((column->header)->line_count))
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
|
||||||
return OBIInt_NA;
|
return OBIInt_NA;
|
||||||
|
}
|
||||||
|
|
||||||
return *(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
return *(((obiint_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||||
|
{
|
||||||
|
if ((line_nb+1) > (view->line_count))
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
|
||||||
|
return OBIInt_NA;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (view->line_selection)
|
||||||
|
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
|
||||||
|
|
||||||
|
return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value)
|
int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value)
|
||||||
{
|
{
|
||||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
index_t element_idx;
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
if (element_idx == OBIIdx_NA)
|
if (element_idx == OBIIdx_NA)
|
||||||
return -1;
|
return -1;
|
||||||
|
obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
return obi_column_set_obiint_with_elt_idx(column, line_nb, element_idx, value);
|
|
||||||
|
int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return -1;
|
||||||
|
obi_column_set_obiint_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
|
||||||
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||||
{
|
{
|
||||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
index_t element_idx;
|
||||||
|
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
if (element_idx == OBIIdx_NA)
|
if (element_idx == OBIIdx_NA)
|
||||||
return OBIInt_NA;
|
return OBIInt_NA;
|
||||||
|
|
||||||
return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
|
return obi_column_get_obiint_with_elt_idx(column, line_nb, element_idx);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return OBIInt_NA;
|
||||||
|
return obi_column_get_obiint_with_elt_idx_in_view(view, column, line_nb, element_idx);
|
||||||
|
}
|
||||||
|
|
||||||
|
|||||||
@ -19,6 +19,7 @@
|
|||||||
|
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
|
#include "obiview.h"
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
@ -95,5 +96,79 @@ int obi_column_set_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb,
|
|||||||
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
obiint_t obi_column_get_obiint_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Sets a value in an OBIDMS column containing data with the type OBI_INT, using the index of the element in the line.
|
||||||
|
*
|
||||||
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be set.
|
||||||
|
* @param element_idx The index of the element that should be set in the line.
|
||||||
|
* @param value The value that should be set.
|
||||||
|
*
|
||||||
|
* @returns An integer value indicating the success of the operation.
|
||||||
|
* @retval 0 on success.
|
||||||
|
* @retval -1 if an error occurred.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
int obi_column_set_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, obiint_t value);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column().
|
||||||
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
|
* @param element_idx The index of the element that should be recovered in the line.
|
||||||
|
*
|
||||||
|
* @returns The recovered value.
|
||||||
|
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
obiint_t obi_column_get_obiint_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Sets a value in an OBIDMS column containing data with the type OBI_INT,
|
||||||
|
* using the name of the element in the line.
|
||||||
|
*
|
||||||
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be set.
|
||||||
|
* @param element_name The name of the element that should be set in the line.
|
||||||
|
* @param value The value that should be set.
|
||||||
|
*
|
||||||
|
* @returns An integer value indicating the success of the operation.
|
||||||
|
* @retval 0 on success.
|
||||||
|
* @retval -1 if an error occurred.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, obiint_t value);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Recovers a value in an OBIDMS column containing data with the type OBI_INT,
|
||||||
|
* using the name of the element in the line.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
|
* @param element_name The name of the element that should be recovered in the line.
|
||||||
|
*
|
||||||
|
* @returns The recovered value.
|
||||||
|
* @retval OBIBool_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
obiint_t obi_column_get_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||||
|
|
||||||
|
|
||||||
#endif /* OBIDMSCOLUMN_INT_H_ */
|
#endif /* OBIDMSCOLUMN_INT_H_ */
|
||||||
|
|
||||||
|
|||||||
@ -14,8 +14,14 @@
|
|||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
|
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
|
#include "obiview.h"
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
#include "dna_seq_indexer.h"
|
#include "obierrno.h"
|
||||||
|
#include "obidebug.h"
|
||||||
|
#include "obiavl.h"
|
||||||
|
|
||||||
|
|
||||||
|
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
||||||
|
|
||||||
|
|
||||||
/**********************************************************************
|
/**********************************************************************
|
||||||
@ -24,31 +30,99 @@
|
|||||||
*
|
*
|
||||||
**********************************************************************/
|
**********************************************************************/
|
||||||
|
|
||||||
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value)
|
|
||||||
|
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
|
||||||
{
|
{
|
||||||
|
byte_t* value_b;
|
||||||
index_t idx;
|
index_t idx;
|
||||||
|
|
||||||
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
|
// Check that the line number is not greater than the maximum allowed
|
||||||
|
if (line_nb >= MAXIMUM_LINE_COUNT)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Check if the file needs to be enlarged
|
||||||
|
while ((line_nb+1) > (column->header)->line_count)
|
||||||
|
{
|
||||||
|
// Enlarge the file
|
||||||
|
if (obi_enlarge_column(column) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Update lines used
|
||||||
|
if ((line_nb+1) > (column->header)->lines_used)
|
||||||
|
(column->header)->lines_used = line_nb+1;
|
||||||
|
|
||||||
|
// Encode the value on a byte array with a header
|
||||||
|
value_b = obi_seq_to_obibytes(value);
|
||||||
|
if (value_b == NULL)
|
||||||
return -1;
|
return -1;
|
||||||
|
|
||||||
// Add the value in the indexer
|
// Add in the AVL tree
|
||||||
idx = obi_index_dna_seq(column->indexer, value);
|
idx = obi_avl_add(column->avl, value_b);
|
||||||
if (idx == -1)
|
if (idx == -1)
|
||||||
return -1;
|
return -1;
|
||||||
|
|
||||||
// Add the value's index in the column
|
// Add the value's index in the column
|
||||||
*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
|
*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
|
||||||
|
|
||||||
|
free(value_b);
|
||||||
|
|
||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
|
||||||
|
{
|
||||||
|
// Check that the view is not read-only
|
||||||
|
if (view->read_only)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBIVIEW_ERROR);
|
||||||
|
obidebug(1, "\nError trying to set a value in a column in a read-only view");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
if ((view->line_selection != NULL) || (!(column->writable)))
|
||||||
|
{
|
||||||
|
// Get the right line number
|
||||||
|
if (column->writable)
|
||||||
|
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
|
||||||
|
|
||||||
|
column = obi_view_clone_column(view, (column->header)->name);
|
||||||
|
if (column == NULL)
|
||||||
|
{
|
||||||
|
obidebug(1, "\nError trying to clone a column to modify it");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if ((line_nb+1) > view->line_count)
|
||||||
|
{
|
||||||
|
if (obi_view_update_lines(view, (line_nb+1)) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value) < 0)
|
||||||
|
return -1;
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||||
{
|
{
|
||||||
index_t idx;
|
index_t idx;
|
||||||
|
byte_t* value_b;
|
||||||
|
|
||||||
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
|
if ((line_nb+1) > ((column->header)->line_count))
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
|
||||||
return OBISeq_NA;
|
return OBISeq_NA;
|
||||||
|
}
|
||||||
|
|
||||||
idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
||||||
|
|
||||||
@ -56,26 +130,67 @@ char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb
|
|||||||
if (idx == OBIIdx_NA)
|
if (idx == OBIIdx_NA)
|
||||||
return OBISeq_NA;
|
return OBISeq_NA;
|
||||||
|
|
||||||
return obi_retrieve_dna_seq(column->indexer, idx);
|
value_b = obi_avl_get(column->avl, idx);
|
||||||
|
return obi_obibytes_to_seq(value_b);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value)
|
const char* obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||||
{
|
{
|
||||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
if ((line_nb+1) > (view->line_count))
|
||||||
if (element_idx == OBIIdx_NA)
|
{
|
||||||
return -1;
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
|
||||||
return obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value);
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
|
||||||
{
|
|
||||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
|
||||||
if (element_idx == OBIIdx_NA)
|
|
||||||
return OBISeq_NA;
|
return OBISeq_NA;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (view->line_selection)
|
||||||
|
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
|
||||||
|
|
||||||
return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx);
|
return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return -1;
|
||||||
|
obi_column_set_obiseq_with_elt_idx(column, line_nb, element_idx, value);
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return -1;
|
||||||
|
obi_column_set_obiseq_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
const char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return OBISeq_NA;
|
||||||
|
return obi_column_get_obiseq_with_elt_idx(column, line_nb, element_idx);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
const char* obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return OBISeq_NA;
|
||||||
|
return obi_column_get_obiseq_with_elt_idx_in_view(view, column, line_nb, element_idx);
|
||||||
|
}
|
||||||
|
|
||||||
|
|||||||
@ -19,11 +19,12 @@
|
|||||||
|
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
|
#include "obiview.h"
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||||
* to DNA sequences handled by an indexer, and using the index of the element in the column's line.
|
* to DNA sequences in an AVL tree, using the index of the element in the line.
|
||||||
*
|
*
|
||||||
* @warning Pointers returned by obi_open_column() don't allow writing.
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
*
|
*
|
||||||
@ -39,29 +40,29 @@
|
|||||||
* @since November 2015
|
* @since November 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value);
|
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||||
* to DNA sequences handled by an indexer, and using the index of the element in the column's line.
|
* to DNA sequences in an AVL tree, using the index of the element in the line.
|
||||||
*
|
*
|
||||||
* @param column A pointer as returned by obi_create_column().
|
* @param column A pointer as returned by obi_create_column().
|
||||||
* @param line_nb The number of the line where the value should be recovered.
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
* @param element_idx The index of the element that should be recovered in the line.
|
* @param element_idx The index of the element that should be recovered in the line.
|
||||||
*
|
*
|
||||||
* @returns The recovered value.
|
* @returns The recovered value.
|
||||||
* @retval OBISeq_NA the NA value of the type if an error occurred and obi_errno is set.
|
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
|
||||||
*
|
*
|
||||||
* @since November 2015
|
* @since November 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
const char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||||
* to DNA sequences handled by an indexer, using the name of the element in the line.
|
* to DNA sequences in an AVL tree, using the name of the element in the line.
|
||||||
*
|
*
|
||||||
* @warning Pointers returned by obi_open_column() don't allow writing.
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
*
|
*
|
||||||
@ -77,24 +78,100 @@ char* obi_column_get_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb
|
|||||||
* @since November 2015
|
* @since November 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value);
|
int obi_column_set_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||||
* to DNA sequences handled by an indexer, using the name of the element in the line.
|
* to DNA sequences in an AVL tree, using the name of the element in the line.
|
||||||
*
|
*
|
||||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
* @param line_nb The number of the line where the value should be recovered.
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
* @param element_name The name of the element that should be recovered in the line.
|
* @param element_name The name of the element that should be recovered in the line.
|
||||||
*
|
*
|
||||||
* @returns The recovered value.
|
* @returns The recovered value.
|
||||||
* @retval OBISeq_NA the NA value of the type if an error occurred and obi_errno is set.
|
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
|
||||||
*
|
*
|
||||||
* @since November 2015
|
* @since November 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
const char* obi_column_get_obiseq_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||||
|
* to DNA sequences in an AVL tree, using the index of the element in the line.
|
||||||
|
*
|
||||||
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be set.
|
||||||
|
* @param element_idx The index of the element that should be set in the line.
|
||||||
|
* @param value The value that should be set.
|
||||||
|
*
|
||||||
|
* @returns An integer value indicating the success of the operation.
|
||||||
|
* @retval 0 on success.
|
||||||
|
* @retval -1 if an error occurred.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
int obi_column_set_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||||
|
* to DNA sequences in an AVL tree, using the index of the element in the line.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column().
|
||||||
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
|
* @param element_idx The index of the element that should be recovered in the line.
|
||||||
|
*
|
||||||
|
* @returns The recovered value.
|
||||||
|
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
const char* obi_column_get_obiseq_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||||
|
* to DNA sequences in an AVL tree, using the name of the element in the line.
|
||||||
|
*
|
||||||
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be set.
|
||||||
|
* @param element_name The name of the element that should be set in the line.
|
||||||
|
* @param value The value that should be set.
|
||||||
|
*
|
||||||
|
* @returns An integer value indicating the success of the operation.
|
||||||
|
* @retval 0 on success.
|
||||||
|
* @retval -1 if an error occurred.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
int obi_column_set_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||||
|
* to DNA sequences in an AVL tree, using the name of the element in the line.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
|
* @param element_name The name of the element that should be recovered in the line.
|
||||||
|
*
|
||||||
|
* @returns The recovered value.
|
||||||
|
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
const char* obi_column_get_obiseq_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||||
|
|
||||||
|
|
||||||
#endif /* OBIDMSCOLUMN_SEQ_H_ */
|
#endif /* OBIDMSCOLUMN_SEQ_H_ */
|
||||||
|
|||||||
@ -12,10 +12,17 @@
|
|||||||
|
|
||||||
#include <stdlib.h>
|
#include <stdlib.h>
|
||||||
#include <stdio.h>
|
#include <stdio.h>
|
||||||
|
#include <sys/mman.h>
|
||||||
|
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
|
#include "obiview.h"
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
#include "char_str_indexer.h"
|
#include "obierrno.h"
|
||||||
|
#include "obidebug.h"
|
||||||
|
#include "obiavl.h"
|
||||||
|
|
||||||
|
|
||||||
|
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
||||||
|
|
||||||
|
|
||||||
/**********************************************************************
|
/**********************************************************************
|
||||||
@ -24,21 +31,107 @@
|
|||||||
*
|
*
|
||||||
**********************************************************************/
|
**********************************************************************/
|
||||||
|
|
||||||
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value)
|
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
|
||||||
{
|
{
|
||||||
|
byte_t* value_b;
|
||||||
index_t idx;
|
index_t idx;
|
||||||
|
|
||||||
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
|
// Check that the line number is not greater than the maximum allowed
|
||||||
|
if (line_nb >= MAXIMUM_LINE_COUNT)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to set a value at a line number greater than the maximum allowed");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Check if the file needs to be enlarged
|
||||||
|
while ((line_nb+1) > (column->header)->line_count)
|
||||||
|
{
|
||||||
|
// Enlarge the file
|
||||||
|
if (obi_enlarge_column(column) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Update lines used
|
||||||
|
if ((line_nb+1) > (column->header)->lines_used)
|
||||||
|
(column->header)->lines_used = line_nb+1;
|
||||||
|
|
||||||
|
// Encode the value on a byte array with a header
|
||||||
|
value_b = obi_str_to_obibytes(value);
|
||||||
|
if (value_b == NULL)
|
||||||
return -1;
|
return -1;
|
||||||
|
|
||||||
// Add the value in the indexer
|
if (!(line_nb%100000))
|
||||||
idx = obi_index_char_str(column->indexer, value);
|
{
|
||||||
|
//fprintf(stderr, "\nbleeeh");
|
||||||
|
// Unmap and remap the AVL
|
||||||
|
if (munmap((column->avl)->tree, ((((column->avl)->header)->nb_items_max) * sizeof(AVL_node_t))) < 0)
|
||||||
|
return -1;
|
||||||
|
if (munmap(((column->avl)->data)->data, (((column->avl)->data)->header)->data_size_max) < 0)
|
||||||
|
return -1;
|
||||||
|
(column->avl)->tree = mmap(NULL,
|
||||||
|
(((column->avl)->header)->nb_items_max) * sizeof(AVL_node_t), // TODO store avl_size_max
|
||||||
|
PROT_READ | PROT_WRITE,
|
||||||
|
MAP_SHARED,
|
||||||
|
(column->avl)->avl_fd,
|
||||||
|
((column->avl)->header)->header_size
|
||||||
|
);
|
||||||
|
((column->avl)->data)->data = mmap(NULL,
|
||||||
|
(((column->avl)->data)->header)->data_size_max,
|
||||||
|
PROT_READ | PROT_WRITE,
|
||||||
|
MAP_SHARED,
|
||||||
|
(column->avl)->data_fd,
|
||||||
|
(((column->avl)->data)->header)->header_size
|
||||||
|
);
|
||||||
|
}
|
||||||
|
|
||||||
|
// Add in the AVL tree
|
||||||
|
idx = obi_avl_add(column->avl, value_b);
|
||||||
if (idx == -1)
|
if (idx == -1)
|
||||||
return -1;
|
return -1;
|
||||||
|
|
||||||
// Add the value's index in the column
|
// Add the value's index in the column
|
||||||
*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
|
*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
|
||||||
|
|
||||||
|
free(value_b);
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value)
|
||||||
|
{
|
||||||
|
// Check that the view is not read-only
|
||||||
|
if (view->read_only)
|
||||||
|
{
|
||||||
|
obi_set_errno(OBIVIEW_ERROR);
|
||||||
|
obidebug(1, "\nError trying to set a value in a column in a read-only view");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
if ((view->line_selection != NULL) || (!(column->writable)))
|
||||||
|
{
|
||||||
|
// Get the right line number
|
||||||
|
if (column->writable)
|
||||||
|
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
|
||||||
|
|
||||||
|
column = obi_view_clone_column(view, (column->header)->name);
|
||||||
|
if (column == NULL)
|
||||||
|
{
|
||||||
|
obidebug(1, "\nError trying to clone a column to modify it");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if ((line_nb+1) > view->line_count)
|
||||||
|
{
|
||||||
|
if (obi_view_update_lines(view, (line_nb+1)) < 0)
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value) < 0)
|
||||||
|
return -1;
|
||||||
|
|
||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -46,9 +139,14 @@ int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb,
|
|||||||
const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||||
{
|
{
|
||||||
index_t idx;
|
index_t idx;
|
||||||
|
byte_t* value_b;
|
||||||
|
|
||||||
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
|
if ((line_nb+1) > ((column->header)->line_count))
|
||||||
return OBISeq_NA;
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to get a value that is beyond the current number of lines used in the column");
|
||||||
|
return OBIStr_NA;
|
||||||
|
}
|
||||||
|
|
||||||
idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
||||||
|
|
||||||
@ -56,26 +154,67 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
|
|||||||
if (idx == OBIIdx_NA)
|
if (idx == OBIIdx_NA)
|
||||||
return OBIStr_NA;
|
return OBIStr_NA;
|
||||||
|
|
||||||
return obi_retrieve_char_str(column->indexer, idx);
|
value_b = obi_avl_get(column->avl, idx);
|
||||||
|
return obi_obibytes_to_str(value_b);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value)
|
const char* obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||||
{
|
{
|
||||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
if ((line_nb+1) > (view->line_count))
|
||||||
|
{
|
||||||
|
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||||
|
obidebug(1, "\nError trying to get a value that is beyond the current line count of the view");
|
||||||
|
return OBIStr_NA;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (view->line_selection)
|
||||||
|
line_nb = *(((index_t*) ((view->line_selection)->data)) + line_nb);
|
||||||
|
|
||||||
|
return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
if (element_idx == OBIIdx_NA)
|
if (element_idx == OBIIdx_NA)
|
||||||
return -1;
|
return -1;
|
||||||
|
obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
return obi_column_set_obistr_with_elt_idx(column, line_nb, element_idx, value);
|
|
||||||
|
int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return -1;
|
||||||
|
obi_column_set_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx, value);
|
||||||
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||||
{
|
{
|
||||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
index_t element_idx;
|
||||||
|
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
if (element_idx == OBIIdx_NA)
|
if (element_idx == OBIIdx_NA)
|
||||||
return OBIStr_NA;
|
return OBIStr_NA;
|
||||||
|
|
||||||
return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
|
return obi_column_get_obistr_with_elt_idx(column, line_nb, element_idx);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
const char* obi_column_get_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name)
|
||||||
|
{
|
||||||
|
index_t element_idx;
|
||||||
|
|
||||||
|
element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||||
|
if (element_idx == OBIIdx_NA)
|
||||||
|
return OBIStr_NA;
|
||||||
|
return obi_column_get_obistr_with_elt_idx_in_view(view, column, line_nb, element_idx);
|
||||||
|
}
|
||||||
|
|
||||||
|
|||||||
@ -19,11 +19,12 @@
|
|||||||
|
|
||||||
#include "obidmscolumn.h"
|
#include "obidmscolumn.h"
|
||||||
#include "obitypes.h"
|
#include "obitypes.h"
|
||||||
|
#include "obiview.h"
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||||
* to character strings handled by an indexer, using the index of the element in the line.
|
* to character strings in an AVL tree, using the index of the element in the line.
|
||||||
*
|
*
|
||||||
* @warning Pointers returned by obi_open_column() don't allow writing.
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
*
|
*
|
||||||
@ -39,19 +40,19 @@
|
|||||||
* @since October 2015
|
* @since October 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value);
|
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||||
* to character strings handled by an indexer, using the index of the element in the line.
|
* to character strings in an AVL tree, using the index of the element in the line.
|
||||||
*
|
*
|
||||||
* @param column A pointer as returned by obi_create_column().
|
* @param column A pointer as returned by obi_create_column().
|
||||||
* @param line_nb The number of the line where the value should be recovered.
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
* @param element_idx The index of the element that should be recovered in the line.
|
* @param element_idx The index of the element that should be recovered in the line.
|
||||||
*
|
*
|
||||||
* @returns The recovered value.
|
* @returns The recovered value.
|
||||||
* @retval OBIStr_NA the NA value of the type if an error occurred and obi_errno is set.
|
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
|
||||||
*
|
*
|
||||||
* @since October 2015
|
* @since October 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
@ -61,7 +62,7 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
|
|||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||||
* to character strings handled by an indexer, using the name of the element in the line.
|
* to character strings in an AVL tree, using the name of the element in the line.
|
||||||
*
|
*
|
||||||
* @warning Pointers returned by obi_open_column() don't allow writing.
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
*
|
*
|
||||||
@ -77,19 +78,19 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
|
|||||||
* @since October 2015
|
* @since October 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
*/
|
*/
|
||||||
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value);
|
int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||||
* to character strings handled by an indexer, using the name of the element in the line.
|
* to character strings in an AVL tree, using the name of the element in the line.
|
||||||
*
|
*
|
||||||
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
* @param line_nb The number of the line where the value should be recovered.
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
* @param element_name The name of the element that should be recovered in the line.
|
* @param element_name The name of the element that should be recovered in the line.
|
||||||
*
|
*
|
||||||
* @returns The recovered value.
|
* @returns The recovered value.
|
||||||
* @retval OBIStr_NA the NA value of the type if an error occurred and obi_errno is set.
|
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
|
||||||
*
|
*
|
||||||
* @since October 2015
|
* @since October 2015
|
||||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
@ -97,5 +98,81 @@ int obi_column_set_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb,
|
|||||||
const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
const char* obi_column_get_obistr_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||||
|
* to character strings in an AVL tree, using the index of the element in the line.
|
||||||
|
*
|
||||||
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be set.
|
||||||
|
* @param element_idx The index of the element that should be set in the line.
|
||||||
|
* @param value The value that should be set.
|
||||||
|
*
|
||||||
|
* @returns An integer value indicating the success of the operation.
|
||||||
|
* @retval 0 on success.
|
||||||
|
* @retval -1 if an error occurred.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
int obi_column_set_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, char* value);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||||
|
* to character strings in an AVL tree, using the index of the element in the line.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column().
|
||||||
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
|
* @param element_idx The index of the element that should be recovered in the line.
|
||||||
|
*
|
||||||
|
* @returns The recovered value.
|
||||||
|
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
const char* obi_column_get_obistr_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||||
|
* to character strings in an AVL tree, using the name of the element in the line.
|
||||||
|
*
|
||||||
|
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be set.
|
||||||
|
* @param element_name The name of the element that should be set in the line.
|
||||||
|
* @param value The value that should be set.
|
||||||
|
*
|
||||||
|
* @returns An integer value indicating the success of the operation.
|
||||||
|
* @retval 0 on success.
|
||||||
|
* @retval -1 if an error occurred.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, char* value);
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||||
|
* to character strings in an AVL tree, using the name of the element in the line.
|
||||||
|
*
|
||||||
|
* @param column A pointer as returned by obi_create_column() or obi_clone_column().
|
||||||
|
* @param line_nb The number of the line where the value should be recovered.
|
||||||
|
* @param element_name The name of the element that should be recovered in the line.
|
||||||
|
*
|
||||||
|
* @returns The recovered value.
|
||||||
|
* @retval '\0' the NA value of the type if an error occurred and obi_errno is set.
|
||||||
|
*
|
||||||
|
* @since February 2016
|
||||||
|
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||||
|
*/
|
||||||
|
const char* obi_column_get_obistr_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||||
|
|
||||||
|
|
||||||
#endif /* OBIDMSCOLUMN_STR_H_ */
|
#endif /* OBIDMSCOLUMN_STR_H_ */
|
||||||
|
|
||||||
|
|||||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user