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@ -1,506 +0,0 @@
|
||||
|
||||
CeCILL FREE SOFTWARE LICENSE AGREEMENT
|
||||
|
||||
|
||||
Notice
|
||||
|
||||
This Agreement is a Free Software license agreement that is the result
|
||||
of discussions between its authors in order to ensure compliance with
|
||||
the two main principles guiding its drafting:
|
||||
|
||||
* firstly, compliance with the principles governing the distribution
|
||||
of Free Software: access to source code, broad rights granted to
|
||||
users,
|
||||
* secondly, the election of a governing law, French law, with which
|
||||
it is conformant, both as regards the law of torts and
|
||||
intellectual property law, and the protection that it offers to
|
||||
both authors and holders of the economic rights over software.
|
||||
|
||||
The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
|
||||
license are:
|
||||
|
||||
Commissariat <20> l'Energie Atomique - CEA, a public scientific, technical
|
||||
and industrial research establishment, having its principal place of
|
||||
business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
|
||||
|
||||
Centre National de la Recherche Scientifique - CNRS, a public scientific
|
||||
and technological establishment, having its principal place of business
|
||||
at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
|
||||
|
||||
Institut National de Recherche en Informatique et en Automatique -
|
||||
INRIA, a public scientific and technological establishment, having its
|
||||
principal place of business at Domaine de Voluceau, Rocquencourt, BP
|
||||
105, 78153 Le Chesnay cedex, France.
|
||||
|
||||
|
||||
Preamble
|
||||
|
||||
The purpose of this Free Software license agreement is to grant users
|
||||
the right to modify and redistribute the software governed by this
|
||||
license within the framework of an open source distribution model.
|
||||
|
||||
The exercising of these rights is conditional upon certain obligations
|
||||
for users so as to preserve this status for all subsequent redistributions.
|
||||
|
||||
In consideration of access to the source code and the rights to copy,
|
||||
modify and redistribute granted by the license, users are provided only
|
||||
with a limited warranty and the software's author, the holder of the
|
||||
economic rights, and the successive licensors only have limited liability.
|
||||
|
||||
In this respect, the risks associated with loading, using, modifying
|
||||
and/or developing or reproducing the software by the user are brought to
|
||||
the user's attention, given its Free Software status, which may make it
|
||||
complicated to use, with the result that its use is reserved for
|
||||
developers and experienced professionals having in-depth computer
|
||||
knowledge. Users are therefore encouraged to load and test the
|
||||
suitability of the software as regards their requirements in conditions
|
||||
enabling the security of their systems and/or data to be ensured and,
|
||||
more generally, to use and operate it in the same conditions of
|
||||
security. This Agreement may be freely reproduced and published,
|
||||
provided it is not altered, and that no provisions are either added or
|
||||
removed herefrom.
|
||||
|
||||
This Agreement may apply to any or all software for which the holder of
|
||||
the economic rights decides to submit the use thereof to its provisions.
|
||||
|
||||
|
||||
Article 1 - DEFINITIONS
|
||||
|
||||
For the purpose of this Agreement, when the following expressions
|
||||
commence with a capital letter, they shall have the following meaning:
|
||||
|
||||
Agreement: means this license agreement, and its possible subsequent
|
||||
versions and annexes.
|
||||
|
||||
Software: means the software in its Object Code and/or Source Code form
|
||||
and, where applicable, its documentation, "as is" when the Licensee
|
||||
accepts the Agreement.
|
||||
|
||||
Initial Software: means the Software in its Source Code and possibly its
|
||||
Object Code form and, where applicable, its documentation, "as is" when
|
||||
it is first distributed under the terms and conditions of the Agreement.
|
||||
|
||||
Modified Software: means the Software modified by at least one
|
||||
Contribution.
|
||||
|
||||
Source Code: means all the Software's instructions and program lines to
|
||||
which access is required so as to modify the Software.
|
||||
|
||||
Object Code: means the binary files originating from the compilation of
|
||||
the Source Code.
|
||||
|
||||
Holder: means the holder(s) of the economic rights over the Initial
|
||||
Software.
|
||||
|
||||
Licensee: means the Software user(s) having accepted the Agreement.
|
||||
|
||||
Contributor: means a Licensee having made at least one Contribution.
|
||||
|
||||
Licensor: means the Holder, or any other individual or legal entity, who
|
||||
distributes the Software under the Agreement.
|
||||
|
||||
Contribution: means any or all modifications, corrections, translations,
|
||||
adaptations and/or new functions integrated into the Software by any or
|
||||
all Contributors, as well as any or all Internal Modules.
|
||||
|
||||
Module: means a set of sources files including their documentation that
|
||||
enables supplementary functions or services in addition to those offered
|
||||
by the Software.
|
||||
|
||||
External Module: means any or all Modules, not derived from the
|
||||
Software, so that this Module and the Software run in separate address
|
||||
spaces, with one calling the other when they are run.
|
||||
|
||||
Internal Module: means any or all Module, connected to the Software so
|
||||
that they both execute in the same address space.
|
||||
|
||||
GNU GPL: means the GNU General Public License version 2 or any
|
||||
subsequent version, as published by the Free Software Foundation Inc.
|
||||
|
||||
Parties: mean both the Licensee and the Licensor.
|
||||
|
||||
These expressions may be used both in singular and plural form.
|
||||
|
||||
|
||||
Article 2 - PURPOSE
|
||||
|
||||
The purpose of the Agreement is the grant by the Licensor to the
|
||||
Licensee of a non-exclusive, transferable and worldwide license for the
|
||||
Software as set forth in Article 5 hereinafter for the whole term of the
|
||||
protection granted by the rights over said Software.
|
||||
|
||||
|
||||
Article 3 - ACCEPTANCE
|
||||
|
||||
3.1 The Licensee shall be deemed as having accepted the terms and
|
||||
conditions of this Agreement upon the occurrence of the first of the
|
||||
following events:
|
||||
|
||||
* (i) loading the Software by any or all means, notably, by
|
||||
downloading from a remote server, or by loading from a physical
|
||||
medium;
|
||||
* (ii) the first time the Licensee exercises any of the rights
|
||||
granted hereunder.
|
||||
|
||||
3.2 One copy of the Agreement, containing a notice relating to the
|
||||
characteristics of the Software, to the limited warranty, and to the
|
||||
fact that its use is restricted to experienced users has been provided
|
||||
to the Licensee prior to its acceptance as set forth in Article 3.1
|
||||
hereinabove, and the Licensee hereby acknowledges that it has read and
|
||||
understood it.
|
||||
|
||||
|
||||
Article 4 - EFFECTIVE DATE AND TERM
|
||||
|
||||
|
||||
4.1 EFFECTIVE DATE
|
||||
|
||||
The Agreement shall become effective on the date when it is accepted by
|
||||
the Licensee as set forth in Article 3.1.
|
||||
|
||||
|
||||
4.2 TERM
|
||||
|
||||
The Agreement shall remain in force for the entire legal term of
|
||||
protection of the economic rights over the Software.
|
||||
|
||||
|
||||
Article 5 - SCOPE OF RIGHTS GRANTED
|
||||
|
||||
The Licensor hereby grants to the Licensee, who accepts, the following
|
||||
rights over the Software for any or all use, and for the term of the
|
||||
Agreement, on the basis of the terms and conditions set forth hereinafter.
|
||||
|
||||
Besides, if the Licensor owns or comes to own one or more patents
|
||||
protecting all or part of the functions of the Software or of its
|
||||
components, the Licensor undertakes not to enforce the rights granted by
|
||||
these patents against successive Licensees using, exploiting or
|
||||
modifying the Software. If these patents are transferred, the Licensor
|
||||
undertakes to have the transferees subscribe to the obligations set
|
||||
forth in this paragraph.
|
||||
|
||||
|
||||
5.1 RIGHT OF USE
|
||||
|
||||
The Licensee is authorized to use the Software, without any limitation
|
||||
as to its fields of application, with it being hereinafter specified
|
||||
that this comprises:
|
||||
|
||||
1. permanent or temporary reproduction of all or part of the Software
|
||||
by any or all means and in any or all form.
|
||||
|
||||
2. loading, displaying, running, or storing the Software on any or
|
||||
all medium.
|
||||
|
||||
3. entitlement to observe, study or test its operation so as to
|
||||
determine the ideas and principles behind any or all constituent
|
||||
elements of said Software. This shall apply when the Licensee
|
||||
carries out any or all loading, displaying, running, transmission
|
||||
or storage operation as regards the Software, that it is entitled
|
||||
to carry out hereunder.
|
||||
|
||||
|
||||
5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
|
||||
|
||||
The right to make Contributions includes the right to translate, adapt,
|
||||
arrange, or make any or all modifications to the Software, and the right
|
||||
to reproduce the resulting software.
|
||||
|
||||
The Licensee is authorized to make any or all Contributions to the
|
||||
Software provided that it includes an explicit notice that it is the
|
||||
author of said Contribution and indicates the date of the creation thereof.
|
||||
|
||||
|
||||
5.3 RIGHT OF DISTRIBUTION
|
||||
|
||||
In particular, the right of distribution includes the right to publish,
|
||||
transmit and communicate the Software to the general public on any or
|
||||
all medium, and by any or all means, and the right to market, either in
|
||||
consideration of a fee, or free of charge, one or more copies of the
|
||||
Software by any means.
|
||||
|
||||
The Licensee is further authorized to distribute copies of the modified
|
||||
or unmodified Software to third parties according to the terms and
|
||||
conditions set forth hereinafter.
|
||||
|
||||
|
||||
5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
|
||||
|
||||
The Licensee is authorized to distribute true copies of the Software in
|
||||
Source Code or Object Code form, provided that said distribution
|
||||
complies with all the provisions of the Agreement and is accompanied by:
|
||||
|
||||
1. a copy of the Agreement,
|
||||
|
||||
2. a notice relating to the limitation of both the Licensor's
|
||||
warranty and liability as set forth in Articles 8 and 9,
|
||||
|
||||
and that, in the event that only the Object Code of the Software is
|
||||
redistributed, the Licensee allows future Licensees unhindered access to
|
||||
the full Source Code of the Software by indicating how to access it, it
|
||||
being understood that the additional cost of acquiring the Source Code
|
||||
shall not exceed the cost of transferring the data.
|
||||
|
||||
|
||||
5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
|
||||
|
||||
When the Licensee makes a Contribution to the Software, the terms and
|
||||
conditions for the distribution of the resulting Modified Software
|
||||
become subject to all the provisions of this Agreement.
|
||||
|
||||
The Licensee is authorized to distribute the Modified Software, in
|
||||
source code or object code form, provided that said distribution
|
||||
complies with all the provisions of the Agreement and is accompanied by:
|
||||
|
||||
1. a copy of the Agreement,
|
||||
|
||||
2. a notice relating to the limitation of both the Licensor's
|
||||
warranty and liability as set forth in Articles 8 and 9,
|
||||
|
||||
and that, in the event that only the object code of the Modified
|
||||
Software is redistributed, the Licensee allows future Licensees
|
||||
unhindered access to the full source code of the Modified Software by
|
||||
indicating how to access it, it being understood that the additional
|
||||
cost of acquiring the source code shall not exceed the cost of
|
||||
transferring the data.
|
||||
|
||||
|
||||
5.3.3 DISTRIBUTION OF EXTERNAL MODULES
|
||||
|
||||
When the Licensee has developed an External Module, the terms and
|
||||
conditions of this Agreement do not apply to said External Module, that
|
||||
may be distributed under a separate license agreement.
|
||||
|
||||
|
||||
5.3.4 COMPATIBILITY WITH THE GNU GPL
|
||||
|
||||
The Licensee can include a code that is subject to the provisions of one
|
||||
of the versions of the GNU GPL in the Modified or unmodified Software,
|
||||
and distribute that entire code under the terms of the same version of
|
||||
the GNU GPL.
|
||||
|
||||
The Licensee can include the Modified or unmodified Software in a code
|
||||
that is subject to the provisions of one of the versions of the GNU GPL,
|
||||
and distribute that entire code under the terms of the same version of
|
||||
the GNU GPL.
|
||||
|
||||
|
||||
Article 6 - INTELLECTUAL PROPERTY
|
||||
|
||||
|
||||
6.1 OVER THE INITIAL SOFTWARE
|
||||
|
||||
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
|
||||
distribution of said Initial Software.
|
||||
|
||||
The Holder undertakes that the Initial Software will remain ruled at
|
||||
least by this Agreement, for the duration set forth in Article 4.2.
|
||||
|
||||
|
||||
6.2 OVER THE CONTRIBUTIONS
|
||||
|
||||
The Licensee who develops a Contribution is the owner of the
|
||||
intellectual property rights over this Contribution as defined by
|
||||
applicable law.
|
||||
|
||||
|
||||
6.3 OVER THE EXTERNAL MODULES
|
||||
|
||||
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.
|
||||
|
||||
|
||||
6.4 JOINT PROVISIONS
|
||||
|
||||
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 of the Holder and/or Contributors on the
|
||||
Software and to take, where applicable, vis-<2D>-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
|
||||
|
||||
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).
|
||||
|
||||
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 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
|
||||
assistance for its defense. Such technical and legal assistance 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.
|
||||
|
||||
|
||||
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.
|
||||
|
||||
|
||||
Version 2.0 dated 2006-09-05.
|
||||
@ -1,512 +0,0 @@
|
||||
|
||||
CONTRAT DE LICENCE DE LOGICIEL LIBRE CeCILL
|
||||
|
||||
|
||||
Avertissement
|
||||
|
||||
Ce contrat est une licence de logiciel libre issue d'une concertation
|
||||
entre ses auteurs afin que le respect de deux grands principes pr<70>side <20>
|
||||
sa r<>daction:
|
||||
|
||||
* d'une part, le respect des principes de diffusion des logiciels
|
||||
libres: acc<63>s au code source, droits <20>tendus conf<6E>r<EFBFBD>s aux
|
||||
utilisateurs,
|
||||
* d'autre part, la d<>signation d'un droit applicable, le droit
|
||||
fran<61>ais, auquel elle est conforme, tant au regard du droit de la
|
||||
responsabilit<69> civile que du droit de la propri<72>t<EFBFBD> intellectuelle
|
||||
et de la protection qu'il offre aux auteurs et titulaires des
|
||||
droits patrimoniaux sur un logiciel.
|
||||
|
||||
Les auteurs de la licence CeCILL (pour Ce[a] C[nrs] I[nria] L[ogiciel]
|
||||
L[ibre]) sont:
|
||||
|
||||
Commissariat <20> l'Energie Atomique - CEA, <20>tablissement public de
|
||||
recherche <20> caract<63>re scientifique, technique et industriel, dont le
|
||||
si<EFBFBD>ge est situ<74> 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris.
|
||||
|
||||
Centre National de la Recherche Scientifique - CNRS, <20>tablissement
|
||||
public <20> caract<63>re scientifique et technologique, dont le si<73>ge est
|
||||
situ<EFBFBD> 3 rue Michel-Ange, 75794 Paris cedex 16.
|
||||
|
||||
Institut National de Recherche en Informatique et en Automatique -
|
||||
INRIA, <20>tablissement public <20> caract<63>re scientifique et technologique,
|
||||
dont le si<73>ge est situ<74> Domaine de Voluceau, Rocquencourt, BP 105, 78153
|
||||
Le Chesnay cedex.
|
||||
|
||||
|
||||
Pr<50>ambule
|
||||
|
||||
Ce contrat est une licence de logiciel libre dont l'objectif est de
|
||||
conf<EFBFBD>rer aux utilisateurs la libert<72> de modification et de
|
||||
redistribution du logiciel r<>gi par cette licence dans le cadre d'un
|
||||
mod<EFBFBD>le de diffusion en logiciel libre.
|
||||
|
||||
L'exercice de ces libert<72>s est assorti de certains devoirs <20> la charge
|
||||
des utilisateurs afin de pr<70>server ce statut au cours des
|
||||
redistributions ult<6C>rieures.
|
||||
|
||||
L'accessibilit<69> au code source et les droits de copie, de modification
|
||||
et de redistribution qui en d<>coulent ont pour contrepartie de n'offrir
|
||||
aux utilisateurs qu'une garantie limit<69>e et de ne faire peser sur
|
||||
l'auteur du logiciel, le titulaire des droits patrimoniaux et les
|
||||
conc<EFBFBD>dants successifs qu'une responsabilit<69> restreinte.
|
||||
|
||||
A cet <20>gard l'attention de l'utilisateur est attir<69>e sur les risques
|
||||
associ<EFBFBD>s au chargement, <20> l'utilisation, <20> la modification et/ou au
|
||||
d<EFBFBD>veloppement et <20> la reproduction du logiciel par l'utilisateur <20>tant
|
||||
donn<EFBFBD> sa sp<73>cificit<69> de logiciel libre, qui peut le rendre complexe <20>
|
||||
manipuler et qui le r<>serve donc <20> des d<>veloppeurs ou des
|
||||
professionnels avertis poss<73>dant des connaissances informatiques
|
||||
approfondies. Les utilisateurs sont donc invit<69>s <20> charger et tester
|
||||
l'ad<61>quation du logiciel <20> leurs besoins dans des conditions permettant
|
||||
d'assurer la s<>curit<69> de leurs syst<73>mes et/ou de leurs donn<6E>es et, plus
|
||||
g<EFBFBD>n<EFBFBD>ralement, <20> l'utiliser et l'exploiter dans les m<>mes conditions de
|
||||
s<EFBFBD>curit<EFBFBD>. Ce contrat peut <20>tre reproduit et diffus<75> librement, sous
|
||||
r<EFBFBD>serve de le conserver en l'<27>tat, sans ajout ni suppression de clauses.
|
||||
|
||||
Ce contrat est susceptible de s'appliquer <20> tout logiciel dont le
|
||||
titulaire des droits patrimoniaux d<>cide de soumettre l'exploitation aux
|
||||
dispositions qu'il contient.
|
||||
|
||||
|
||||
Article 1 - DEFINITIONS
|
||||
|
||||
Dans ce contrat, les termes suivants, lorsqu'ils seront <20>crits avec une
|
||||
lettre capitale, auront la signification suivante:
|
||||
|
||||
Contrat: d<>signe le pr<70>sent contrat de licence, ses <20>ventuelles versions
|
||||
post<EFBFBD>rieures et annexes.
|
||||
|
||||
Logiciel: d<>signe le logiciel sous sa forme de Code Objet et/ou de Code
|
||||
Source et le cas <20>ch<63>ant sa documentation, dans leur <20>tat au moment de
|
||||
l'acceptation du Contrat par le Licenci<63>.
|
||||
|
||||
Logiciel Initial: d<>signe le Logiciel sous sa forme de Code Source et
|
||||
<EFBFBD>ventuellement de Code Objet et le cas <20>ch<63>ant sa documentation, dans
|
||||
leur <20>tat au moment de leur premi<6D>re diffusion sous les termes du Contrat.
|
||||
|
||||
Logiciel Modifi<66>: d<>signe le Logiciel modifi<66> par au moins une
|
||||
Contribution.
|
||||
|
||||
Code Source: d<>signe l'ensemble des instructions et des lignes de
|
||||
programme du Logiciel et auquel l'acc<63>s est n<>cessaire en vue de
|
||||
modifier le Logiciel.
|
||||
|
||||
Code Objet: d<>signe les fichiers binaires issus de la compilation du
|
||||
Code Source.
|
||||
|
||||
Titulaire: d<>signe le ou les d<>tenteurs des droits patrimoniaux d'auteur
|
||||
sur le Logiciel Initial.
|
||||
|
||||
Licenci<EFBFBD>: d<>signe le ou les utilisateurs du Logiciel ayant accept<70> le
|
||||
Contrat.
|
||||
|
||||
Contributeur: d<>signe le Licenci<63> auteur d'au moins une Contribution.
|
||||
|
||||
Conc<EFBFBD>dant: d<>signe le Titulaire ou toute personne physique ou morale
|
||||
distribuant le Logiciel sous le Contrat.
|
||||
|
||||
Contribution: d<>signe l'ensemble des modifications, corrections,
|
||||
traductions, adaptations et/ou nouvelles fonctionnalit<69>s int<6E>gr<67>es dans
|
||||
le Logiciel par tout Contributeur, ainsi que tout Module Interne.
|
||||
|
||||
Module: d<>signe un ensemble de fichiers sources y compris leur
|
||||
documentation qui permet de r<>aliser des fonctionnalit<69>s ou services
|
||||
suppl<EFBFBD>mentaires <20> ceux fournis par le Logiciel.
|
||||
|
||||
Module Externe: d<>signe tout Module, non d<>riv<69> du Logiciel, tel que ce
|
||||
Module et le Logiciel s'ex<65>cutent dans des espaces d'adressage
|
||||
diff<EFBFBD>rents, l'un appelant l'autre au moment de leur ex<65>cution.
|
||||
|
||||
Module Interne: d<>signe tout Module li<6C> au Logiciel de telle sorte
|
||||
qu'ils s'ex<65>cutent dans le m<>me espace d'adressage.
|
||||
|
||||
GNU GPL: d<>signe la GNU General Public License dans sa version 2 ou
|
||||
toute version ult<6C>rieure, telle que publi<6C>e par Free Software Foundation
|
||||
Inc.
|
||||
|
||||
Parties: d<>signe collectivement le Licenci<63> et le Conc<6E>dant.
|
||||
|
||||
Ces termes s'entendent au singulier comme au pluriel.
|
||||
|
||||
|
||||
Article 2 - OBJET
|
||||
|
||||
Le Contrat a pour objet la concession par le Conc<6E>dant au Licenci<63> d'une
|
||||
licence non exclusive, cessible et mondiale du Logiciel telle que
|
||||
d<EFBFBD>finie ci-apr<70>s <20> l'article 5 pour toute la dur<75>e de protection des droits
|
||||
portant sur ce Logiciel.
|
||||
|
||||
|
||||
Article 3 - ACCEPTATION
|
||||
|
||||
3.1 L'acceptation par le Licenci<63> des termes du Contrat est r<>put<75>e
|
||||
acquise du fait du premier des faits suivants:
|
||||
|
||||
* (i) le chargement du Logiciel par tout moyen notamment par
|
||||
t<>l<EFBFBD>chargement <20> partir d'un serveur distant ou par chargement <20>
|
||||
partir d'un support physique;
|
||||
* (ii) le premier exercice par le Licenci<63> de l'un quelconque des
|
||||
droits conc<6E>d<EFBFBD>s par le Contrat.
|
||||
|
||||
3.2 Un exemplaire du Contrat, contenant notamment un avertissement
|
||||
relatif aux sp<73>cificit<69>s du Logiciel, <20> la restriction de garantie et <20>
|
||||
la limitation <20> un usage par des utilisateurs exp<78>riment<6E>s a <20>t<EFBFBD> mis <20>
|
||||
disposition du Licenci<63> pr<70>alablement <20> son acceptation telle que
|
||||
d<EFBFBD>finie <20> l'article 3.1 ci dessus et le Licenci<63> reconna<6E>t en avoir pris
|
||||
connaissance.
|
||||
|
||||
|
||||
Article 4 - ENTREE EN VIGUEUR ET DUREE
|
||||
|
||||
|
||||
4.1 ENTREE EN VIGUEUR
|
||||
|
||||
Le Contrat entre en vigueur <20> la date de son acceptation par le Licenci<63>
|
||||
telle que d<>finie en 3.1.
|
||||
|
||||
|
||||
4.2 DUREE
|
||||
|
||||
Le Contrat produira ses effets pendant toute la dur<75>e l<>gale de
|
||||
protection des droits patrimoniaux portant sur le Logiciel.
|
||||
|
||||
|
||||
Article 5 - ETENDUE DES DROITS CONCEDES
|
||||
|
||||
Le Conc<6E>dant conc<6E>de au Licenci<63>, qui accepte, les droits suivants sur
|
||||
le Logiciel pour toutes destinations et pour la dur<75>e du Contrat dans
|
||||
les conditions ci-apr<70>s d<>taill<6C>es.
|
||||
|
||||
Par ailleurs, si le Conc<6E>dant d<>tient ou venait <20> d<>tenir un ou
|
||||
plusieurs brevets d'invention prot<6F>geant tout ou partie des
|
||||
fonctionnalit<EFBFBD>s du Logiciel ou de ses composants, il s'engage <20> ne pas
|
||||
opposer les <20>ventuels droits conf<6E>r<EFBFBD>s par ces brevets aux Licenci<63>s
|
||||
successifs qui utiliseraient, exploiteraient ou modifieraient le
|
||||
Logiciel. En cas de cession de ces brevets, le Conc<6E>dant s'engage <20>
|
||||
faire reprendre les obligations du pr<70>sent alin<69>a aux cessionnaires.
|
||||
|
||||
|
||||
5.1 DROIT D'UTILISATION
|
||||
|
||||
Le Licenci<63> est autoris<69> <20> utiliser le Logiciel, sans restriction quant
|
||||
aux domaines d'application, <20>tant ci-apr<70>s pr<70>cis<69> que cela comporte:
|
||||
|
||||
1. la reproduction permanente ou provisoire du Logiciel en tout ou
|
||||
partie par tout moyen et sous toute forme.
|
||||
|
||||
2. le chargement, l'affichage, l'ex<65>cution, ou le stockage du
|
||||
Logiciel sur tout support.
|
||||
|
||||
3. la possibilit<69> d'en observer, d'en <20>tudier, ou d'en tester le
|
||||
fonctionnement afin de d<>terminer les id<69>es et principes qui sont
|
||||
<20> la base de n'importe quel <20>l<EFBFBD>ment de ce Logiciel; et ceci,
|
||||
lorsque le Licenci<63> effectue toute op<6F>ration de chargement,
|
||||
d'affichage, d'ex<65>cution, de transmission ou de stockage du
|
||||
Logiciel qu'il est en droit d'effectuer en vertu du Contrat.
|
||||
|
||||
|
||||
5.2 DROIT D'APPORTER DES CONTRIBUTIONS
|
||||
|
||||
Le droit d'apporter des Contributions comporte le droit de traduire,
|
||||
d'adapter, d'arranger ou d'apporter toute autre modification au Logiciel
|
||||
et le droit de reproduire le logiciel en r<>sultant.
|
||||
|
||||
Le Licenci<63> est autoris<69> <20> apporter toute Contribution au Logiciel sous
|
||||
r<EFBFBD>serve de mentionner, de fa<66>on explicite, son nom en tant qu'auteur de
|
||||
cette Contribution et la date de cr<63>ation de celle-ci.
|
||||
|
||||
|
||||
5.3 DROIT DE DISTRIBUTION
|
||||
|
||||
Le droit de distribution comporte notamment le droit de diffuser, de
|
||||
transmettre et de communiquer le Logiciel au public sur tout support et
|
||||
par tout moyen ainsi que le droit de mettre sur le march<63> <20> titre
|
||||
on<EFBFBD>reux ou gratuit, un ou des exemplaires du Logiciel par tout proc<6F>d<EFBFBD>.
|
||||
|
||||
Le Licenci<63> est autoris<69> <20> distribuer des copies du Logiciel, modifi<66> ou
|
||||
non, <20> des tiers dans les conditions ci-apr<70>s d<>taill<6C>es.
|
||||
|
||||
|
||||
5.3.1 DISTRIBUTION DU LOGICIEL SANS MODIFICATION
|
||||
|
||||
Le Licenci<63> est autoris<69> <20> distribuer des copies conformes du Logiciel,
|
||||
sous forme de Code Source ou de Code Objet, <20> condition que cette
|
||||
distribution respecte les dispositions du Contrat dans leur totalit<69> et
|
||||
soit accompagn<67>e:
|
||||
|
||||
1. d'un exemplaire du Contrat,
|
||||
|
||||
2. d'un avertissement relatif <20> la restriction de garantie et de
|
||||
responsabilit<69> du Conc<6E>dant telle que pr<70>vue aux articles 8
|
||||
et 9,
|
||||
|
||||
et que, dans le cas o<> seul le Code Objet du Logiciel est redistribu<62>,
|
||||
le Licenci<63> permette aux futurs Licenci<63>s d'acc<63>der facilement au Code
|
||||
Source complet du Logiciel en indiquant les modalit<69>s d'acc<63>s, <20>tant
|
||||
entendu que le co<63>t additionnel d'acquisition du Code Source ne devra
|
||||
pas exc<78>der le simple co<63>t de transfert des donn<6E>es.
|
||||
|
||||
|
||||
5.3.2 DISTRIBUTION DU LOGICIEL MODIFIE
|
||||
|
||||
Lorsque le Licenci<63> apporte une Contribution au Logiciel, les conditions
|
||||
de distribution du Logiciel Modifi<66> en r<>sultant sont alors soumises <20>
|
||||
l'int<6E>gralit<69> des dispositions du Contrat.
|
||||
|
||||
Le Licenci<63> est autoris<69> <20> distribuer le Logiciel Modifi<66>, sous forme de
|
||||
code source ou de code objet, <20> condition que cette distribution
|
||||
respecte les dispositions du Contrat dans leur totalit<69> et soit
|
||||
accompagn<EFBFBD>e:
|
||||
|
||||
1. d'un exemplaire du Contrat,
|
||||
|
||||
2. d'un avertissement relatif <20> la restriction de garantie et de
|
||||
responsabilit<69> du Conc<6E>dant telle que pr<70>vue aux articles 8
|
||||
et 9,
|
||||
|
||||
et que, dans le cas o<> seul le code objet du Logiciel Modifi<66> est
|
||||
redistribu<EFBFBD>, le Licenci<63> permette aux futurs Licenci<63>s d'acc<63>der
|
||||
facilement au code source complet du Logiciel Modifi<66> en indiquant les
|
||||
modalit<EFBFBD>s d'acc<63>s, <20>tant entendu que le co<63>t additionnel d'acquisition
|
||||
du code source ne devra pas exc<78>der le simple co<63>t de transfert des donn<6E>es.
|
||||
|
||||
|
||||
5.3.3 DISTRIBUTION DES MODULES EXTERNES
|
||||
|
||||
Lorsque le Licenci<63> a d<>velopp<70> un Module Externe les conditions du
|
||||
Contrat ne s'appliquent pas <20> ce Module Externe, qui peut <20>tre distribu<62>
|
||||
sous un contrat de licence diff<66>rent.
|
||||
|
||||
|
||||
5.3.4 COMPATIBILITE AVEC LA LICENCE GNU GPL
|
||||
|
||||
Le Licenci<63> peut inclure un code soumis aux dispositions d'une des
|
||||
versions de la licence GNU GPL dans le Logiciel modifi<66> ou non et
|
||||
distribuer l'ensemble sous les conditions de la m<>me version de la
|
||||
licence GNU GPL.
|
||||
|
||||
Le Licenci<63> peut inclure le Logiciel modifi<66> ou non dans un code soumis
|
||||
aux dispositions d'une des versions de la licence GNU GPL et distribuer
|
||||
l'ensemble sous les conditions de la m<>me version de la licence GNU GPL.
|
||||
|
||||
|
||||
Article 6 - PROPRIETE INTELLECTUELLE
|
||||
|
||||
|
||||
6.1 SUR LE LOGICIEL INITIAL
|
||||
|
||||
Le Titulaire est d<>tenteur des droits patrimoniaux sur le Logiciel
|
||||
Initial. Toute utilisation du Logiciel Initial est soumise au respect
|
||||
des conditions dans lesquelles le Titulaire a choisi de diffuser son
|
||||
oeuvre et nul autre n'a la facult<6C> de modifier les conditions de
|
||||
diffusion de ce Logiciel Initial.
|
||||
|
||||
Le Titulaire s'engage <20> ce que le Logiciel Initial reste au moins r<>gi
|
||||
par le Contrat et ce, pour la dur<75>e vis<69>e <20> l'article 4.2.
|
||||
|
||||
|
||||
6.2 SUR LES CONTRIBUTIONS
|
||||
|
||||
Le Licenci<63> qui a d<>velopp<70> une Contribution est titulaire sur celle-ci
|
||||
des droits de propri<72>t<EFBFBD> intellectuelle dans les conditions d<>finies par
|
||||
la l<>gislation applicable.
|
||||
|
||||
|
||||
6.3 SUR LES MODULES EXTERNES
|
||||
|
||||
Le Licenci<63> qui a d<>velopp<70> un Module Externe est titulaire sur celui-ci
|
||||
des droits de propri<72>t<EFBFBD> intellectuelle dans les conditions d<>finies par
|
||||
la l<>gislation applicable et reste libre du choix du contrat r<>gissant
|
||||
sa diffusion.
|
||||
|
||||
|
||||
6.4 DISPOSITIONS COMMUNES
|
||||
|
||||
Le Licenci<63> s'engage express<73>ment:
|
||||
|
||||
1. <20> ne pas supprimer ou modifier de quelque mani<6E>re que ce soit les
|
||||
mentions de propri<72>t<EFBFBD> intellectuelle appos<6F>es sur le Logiciel;
|
||||
|
||||
2. <20> reproduire <20> l'identique lesdites mentions de propri<72>t<EFBFBD>
|
||||
intellectuelle sur les copies du Logiciel modifi<66> ou non.
|
||||
|
||||
Le Licenci<63> s'engage <20> ne pas porter atteinte, directement ou
|
||||
indirectement, aux droits de propri<72>t<EFBFBD> intellectuelle du Titulaire et/ou
|
||||
des Contributeurs sur le Logiciel et <20> prendre, le cas <20>ch<63>ant, <20>
|
||||
l'<27>gard de son personnel toutes les mesures n<>cessaires pour assurer le
|
||||
respect des dits droits de propri<72>t<EFBFBD> intellectuelle du Titulaire et/ou
|
||||
des Contributeurs.
|
||||
|
||||
|
||||
Article 7 - SERVICES ASSOCIES
|
||||
|
||||
7.1 Le Contrat n'oblige en aucun cas le Conc<6E>dant <20> la r<>alisation de
|
||||
prestations d'assistance technique ou de maintenance du Logiciel.
|
||||
|
||||
Cependant le Conc<6E>dant reste libre de proposer ce type de services. Les
|
||||
termes et conditions d'une telle assistance technique et/ou d'une telle
|
||||
maintenance seront alors d<>termin<69>s dans un acte s<>par<61>. Ces actes de
|
||||
maintenance et/ou assistance technique n'engageront que la seule
|
||||
responsabilit<EFBFBD> du Conc<6E>dant qui les propose.
|
||||
|
||||
7.2 De m<>me, tout Conc<6E>dant est libre de proposer, sous sa seule
|
||||
responsabilit<EFBFBD>, <20> ses licenci<63>s une garantie, qui n'engagera que lui,
|
||||
lors de la redistribution du Logiciel et/ou du Logiciel Modifi<66> et ce,
|
||||
dans les conditions qu'il souhaite. Cette garantie et les modalit<69>s
|
||||
financi<EFBFBD>res de son application feront l'objet d'un acte s<>par<61> entre le
|
||||
Conc<EFBFBD>dant et le Licenci<63>.
|
||||
|
||||
|
||||
Article 8 - RESPONSABILITE
|
||||
|
||||
8.1 Sous r<>serve des dispositions de l'article 8.2, le Licenci<63> a la
|
||||
facult<EFBFBD>, sous r<>serve de prouver la faute du Conc<6E>dant concern<72>, de
|
||||
solliciter la r<>paration du pr<70>judice direct qu'il subirait du fait du
|
||||
Logiciel et dont il apportera la preuve.
|
||||
|
||||
8.2 La responsabilit<69> du Conc<6E>dant est limit<69>e aux engagements pris en
|
||||
application du Contrat et ne saurait <20>tre engag<61>e en raison notamment:
|
||||
(i) des dommages dus <20> l'inex<65>cution, totale ou partielle, de ses
|
||||
obligations par le Licenci<63>, (ii) des dommages directs ou indirects
|
||||
d<EFBFBD>coulant de l'utilisation ou des performances du Logiciel subis par le
|
||||
Licenci<EFBFBD> et (iii) plus g<>n<EFBFBD>ralement d'un quelconque dommage indirect. En
|
||||
particulier, les Parties conviennent express<73>ment que tout pr<70>judice
|
||||
financier ou commercial (par exemple perte de donn<6E>es, perte de
|
||||
b<EFBFBD>n<EFBFBD>fices, perte d'exploitation, perte de client<6E>le ou de commandes,
|
||||
manque <20> gagner, trouble commercial quelconque) ou toute action dirig<69>e
|
||||
contre le Licenci<63> par un tiers, constitue un dommage indirect et
|
||||
n'ouvre pas droit <20> r<>paration par le Conc<6E>dant.
|
||||
|
||||
|
||||
Article 9 - GARANTIE
|
||||
|
||||
9.1 Le Licenci<63> reconna<6E>t que l'<27>tat actuel des connaissances
|
||||
scientifiques et techniques au moment de la mise en circulation du
|
||||
Logiciel ne permet pas d'en tester et d'en v<>rifier toutes les
|
||||
utilisations ni de d<>tecter l'existence d'<27>ventuels d<>fauts. L'attention
|
||||
du Licenci<63> a <20>t<EFBFBD> attir<69>e sur ce point sur les risques associ<63>s au
|
||||
chargement, <20> l'utilisation, la modification et/ou au d<>veloppement et <20>
|
||||
la reproduction du Logiciel qui sont r<>serv<72>s <20> des utilisateurs avertis.
|
||||
|
||||
Il rel<65>ve de la responsabilit<69> du Licenci<63> de contr<74>ler, par tous
|
||||
moyens, l'ad<61>quation du produit <20> ses besoins, son bon fonctionnement et
|
||||
de s'assurer qu'il ne causera pas de dommages aux personnes et aux biens.
|
||||
|
||||
9.2 Le Conc<6E>dant d<>clare de bonne foi <20>tre en droit de conc<6E>der
|
||||
l'ensemble des droits attach<63>s au Logiciel (comprenant notamment les
|
||||
droits vis<69>s <20> l'article 5).
|
||||
|
||||
9.3 Le Licenci<63> reconna<6E>t que le Logiciel est fourni "en l'<27>tat" par le
|
||||
Conc<EFBFBD>dant sans autre garantie, expresse ou tacite, que celle pr<70>vue <20>
|
||||
l'article 9.2 et notamment sans aucune garantie sur sa valeur commerciale,
|
||||
son caract<63>re s<>curis<69>, innovant ou pertinent.
|
||||
|
||||
En particulier, le Conc<6E>dant ne garantit pas que le Logiciel est exempt
|
||||
d'erreur, qu'il fonctionnera sans interruption, qu'il sera compatible
|
||||
avec l'<27>quipement du Licenci<63> et sa configuration logicielle ni qu'il
|
||||
remplira les besoins du Licenci<63>.
|
||||
|
||||
9.4 Le Conc<6E>dant ne garantit pas, de mani<6E>re expresse ou tacite, que le
|
||||
Logiciel ne porte pas atteinte <20> un quelconque droit de propri<72>t<EFBFBD>
|
||||
intellectuelle d'un tiers portant sur un brevet, un logiciel ou sur tout
|
||||
autre droit de propri<72>t<EFBFBD>. Ainsi, le Conc<6E>dant exclut toute garantie au
|
||||
profit du Licenci<63> contre les actions en contrefa<66>on qui pourraient <20>tre
|
||||
diligent<EFBFBD>es au titre de l'utilisation, de la modification, et de la
|
||||
redistribution du Logiciel. N<>anmoins, si de telles actions sont
|
||||
exerc<EFBFBD>es contre le Licenci<63>, le Conc<6E>dant lui apportera son aide
|
||||
technique et juridique pour sa d<>fense. Cette aide technique et
|
||||
juridique est d<>termin<69>e au cas par cas entre le Conc<6E>dant concern<72> et
|
||||
le Licenci<63> dans le cadre d'un protocole d'accord. Le Conc<6E>dant d<>gage
|
||||
toute responsabilit<69> quant <20> l'utilisation de la d<>nomination du
|
||||
Logiciel par le Licenci<63>. Aucune garantie n'est apport<72>e quant <20>
|
||||
l'existence de droits ant<6E>rieurs sur le nom du Logiciel et sur
|
||||
l'existence d'une marque.
|
||||
|
||||
|
||||
Article 10 - RESILIATION
|
||||
|
||||
10.1 En cas de manquement par le Licenci<63> aux obligations mises <20> sa
|
||||
charge par le Contrat, le Conc<6E>dant pourra r<>silier de plein droit le
|
||||
Contrat trente (30) jours apr<70>s notification adress<73>e au Licenci<63> et
|
||||
rest<EFBFBD>e sans effet.
|
||||
|
||||
10.2 Le Licenci<63> dont le Contrat est r<>sili<6C> n'est plus autoris<69> <20>
|
||||
utiliser, modifier ou distribuer le Logiciel. Cependant, toutes les
|
||||
licences qu'il aura conc<6E>d<EFBFBD>es ant<6E>rieurement <20> la r<>siliation du Contrat
|
||||
resteront valides sous r<>serve qu'elles aient <20>t<EFBFBD> effectu<74>es en
|
||||
conformit<EFBFBD> avec le Contrat.
|
||||
|
||||
|
||||
Article 11 - DISPOSITIONS DIVERSES
|
||||
|
||||
|
||||
11.1 CAUSE EXTERIEURE
|
||||
|
||||
Aucune des Parties ne sera responsable d'un retard ou d'une d<>faillance
|
||||
d'ex<65>cution du Contrat qui serait d<> <20> un cas de force majeure, un cas
|
||||
fortuit ou une cause ext<78>rieure, telle que, notamment, le mauvais
|
||||
fonctionnement ou les interruptions du r<>seau <20>lectrique ou de
|
||||
t<EFBFBD>l<EFBFBD>communication, la paralysie du r<>seau li<6C>e <20> une attaque
|
||||
informatique, l'intervention des autorit<69>s gouvernementales, les
|
||||
catastrophes naturelles, les d<>g<EFBFBD>ts des eaux, les tremblements de terre,
|
||||
le feu, les explosions, les gr<67>ves et les conflits sociaux, l'<27>tat de
|
||||
guerre...
|
||||
|
||||
11.2 Le fait, par l'une ou l'autre des Parties, d'omettre en une ou
|
||||
plusieurs occasions de se pr<70>valoir d'une ou plusieurs dispositions du
|
||||
Contrat, ne pourra en aucun cas impliquer renonciation par la Partie
|
||||
int<EFBFBD>ress<EFBFBD>e <20> s'en pr<70>valoir ult<6C>rieurement.
|
||||
|
||||
11.3 Le Contrat annule et remplace toute convention ant<6E>rieure, <20>crite
|
||||
ou orale, entre les Parties sur le m<>me objet et constitue l'accord
|
||||
entier entre les Parties sur cet objet. Aucune addition ou modification
|
||||
aux termes du Contrat n'aura d'effet <20> l'<27>gard des Parties <20> moins
|
||||
d'<27>tre faite par <20>crit et sign<67>e par leurs repr<70>sentants d<>ment habilit<69>s.
|
||||
|
||||
11.4 Dans l'hypoth<74>se o<> une ou plusieurs des dispositions du Contrat
|
||||
s'av<61>rerait contraire <20> une loi ou <20> un texte applicable, existants ou
|
||||
futurs, cette loi ou ce texte pr<70>vaudrait, et les Parties feraient les
|
||||
amendements n<>cessaires pour se conformer <20> cette loi ou <20> ce texte.
|
||||
Toutes les autres dispositions resteront en vigueur. De m<>me, la
|
||||
nullit<EFBFBD>, pour quelque raison que ce soit, d'une des dispositions du
|
||||
Contrat ne saurait entra<72>ner la nullit<69> de l'ensemble du Contrat.
|
||||
|
||||
|
||||
11.5 LANGUE
|
||||
|
||||
Le Contrat est r<>dig<69> en langue fran<61>aise et en langue anglaise, ces
|
||||
deux versions faisant <20>galement foi.
|
||||
|
||||
|
||||
Article 12 - NOUVELLES VERSIONS DU CONTRAT
|
||||
|
||||
12.1 Toute personne est autoris<69>e <20> copier et distribuer des copies de
|
||||
ce Contrat.
|
||||
|
||||
12.2 Afin d'en pr<70>server la coh<6F>rence, le texte du Contrat est prot<6F>g<EFBFBD>
|
||||
et ne peut <20>tre modifi<66> que par les auteurs de la licence, lesquels se
|
||||
r<EFBFBD>servent le droit de publier p<>riodiquement des mises <20> jour ou de
|
||||
nouvelles versions du Contrat, qui poss<73>deront chacune un num<75>ro
|
||||
distinct. Ces versions ult<6C>rieures seront susceptibles de prendre en
|
||||
compte de nouvelles probl<62>matiques rencontr<74>es par les logiciels libres.
|
||||
|
||||
12.3 Tout Logiciel diffus<75> sous une version donn<6E>e du Contrat ne pourra
|
||||
faire l'objet d'une diffusion ult<6C>rieure que sous la m<>me version du
|
||||
Contrat ou une version post<73>rieure, sous r<>serve des dispositions de
|
||||
l'article 5.3.4.
|
||||
|
||||
|
||||
Article 13 - LOI APPLICABLE ET COMPETENCE TERRITORIALE
|
||||
|
||||
13.1 Le Contrat est r<>gi par la loi fran<61>aise. Les Parties conviennent
|
||||
de tenter de r<>gler <20> l'amiable les diff<66>rends ou litiges qui
|
||||
viendraient <20> se produire par suite ou <20> l'occasion du Contrat.
|
||||
|
||||
13.2 A d<>faut d'accord amiable dans un d<>lai de deux (2) mois <20> compter
|
||||
de leur survenance et sauf situation relevant d'une proc<6F>dure d'urgence,
|
||||
les diff<66>rends ou litiges seront port<72>s par la Partie la plus diligente
|
||||
devant les Tribunaux comp<6D>tents de Paris.
|
||||
|
||||
|
||||
Version 2.0 du 2006-09-05.
|
||||
@ -5,6 +5,7 @@ from ..utils cimport str2bytes
|
||||
cdef extern from "stdio.h":
|
||||
struct FILE
|
||||
int fprintf(FILE *stream, char *format, ...)
|
||||
int fputs(char *string, FILE *stream)
|
||||
FILE* stderr
|
||||
ctypedef unsigned int off_t "unsigned long long"
|
||||
|
||||
|
||||
@ -126,7 +126,7 @@ cdef class ProgressBar:
|
||||
if twentyth != self.lastlog:
|
||||
|
||||
if self.ontty:
|
||||
<void>fprintf(stderr,b'\n')
|
||||
<void>fputs(b'\n',stderr)
|
||||
|
||||
self.logger.info('%s %5.1f %% remain : %02d:%02d:%02d' % (
|
||||
bytes2str(self.head),
|
||||
|
||||
@ -35,7 +35,6 @@ def addOptions(parser):
|
||||
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>',
|
||||
@ -96,12 +95,14 @@ def run(config):
|
||||
|
||||
inputs = uopen(config['import']['filename'])
|
||||
|
||||
get_quality = False
|
||||
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"
|
||||
get_quality = True
|
||||
else:
|
||||
raise RuntimeError('No file format specified')
|
||||
|
||||
@ -120,13 +121,15 @@ def run(config):
|
||||
view[i].set_id(seq['id'])
|
||||
view[i].set_definition(seq['definition'])
|
||||
view[i].set_sequence(seq['sequence'])
|
||||
if get_quality :
|
||||
view[i].set_quality(seq['quality'])
|
||||
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(i)
|
||||
print(view.__repr__())
|
||||
|
||||
view.save_and_close()
|
||||
|
||||
@ -9,6 +9,7 @@ cdef class MagicKeyFile:
|
||||
cdef int pos
|
||||
|
||||
cpdef bytes read(self,int size=?)
|
||||
cpdef bytes read1(self,int size=?)
|
||||
cpdef int tell(self)
|
||||
|
||||
|
||||
|
||||
@ -54,14 +54,17 @@ cdef class MagicKeyFile:
|
||||
r = self.binary.read(size)
|
||||
|
||||
return r
|
||||
|
||||
|
||||
cpdef bytes read1(self,int size=-1):
|
||||
return self.read(size)
|
||||
|
||||
cpdef int tell(self):
|
||||
cdef int p
|
||||
|
||||
if self.pos < self.keylength:
|
||||
p = self.pos
|
||||
else:
|
||||
p = self.tell()
|
||||
p = self.binary.tell()
|
||||
|
||||
return p
|
||||
|
||||
|
||||
0
python/obitools3/format/__init__.py
Normal file
0
python/obitools3/format/__init__.py
Normal file
10
python/obitools3/format/fasta.pxd
Normal file
10
python/obitools3/format/fasta.pxd
Normal file
@ -0,0 +1,10 @@
|
||||
from ..utils cimport bytes2str
|
||||
from .header cimport HeaderFormat
|
||||
from cython.view cimport array as cvarray
|
||||
|
||||
cdef class FastaFormat:
|
||||
|
||||
cdef HeaderFormat headerFormater
|
||||
|
||||
cdef size_t sequenceBufferLength
|
||||
cdef char* sequenceBuffer
|
||||
32
python/obitools3/format/fasta.pyx
Normal file
32
python/obitools3/format/fasta.pyx
Normal file
@ -0,0 +1,32 @@
|
||||
cimport cython
|
||||
from libc.stdlib cimport malloc, free, realloc
|
||||
from libc.string cimport strncpy
|
||||
|
||||
cdef class FastaFormat:
|
||||
|
||||
def __init__(self, list tags=[], bint printNAKeys=False):
|
||||
self.headerFormater = HeaderFormat(True,
|
||||
tags,
|
||||
printNAKeys)
|
||||
|
||||
@cython.boundscheck(False)
|
||||
def __call__(self, dict data):
|
||||
cdef bytes brawseq = data['sequence']
|
||||
cdef size_t lseq = len(brawseq)
|
||||
cdef size_t k=0
|
||||
cdef list lines = []
|
||||
|
||||
for k in range(0,lseq,60):
|
||||
lines.append(brawseq[k:(k+60)])
|
||||
|
||||
brawseq = b'\n'.join(lines)
|
||||
|
||||
return "%s\n%s" % (self.headerFormater(data),bytes2str(brawseq))
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
7
python/obitools3/format/header.pxd
Normal file
7
python/obitools3/format/header.pxd
Normal file
@ -0,0 +1,7 @@
|
||||
cdef class HeaderFormat:
|
||||
|
||||
cdef str start
|
||||
cdef set tags
|
||||
cdef bint printNaKeys
|
||||
cdef size_t headerBufferLength
|
||||
|
||||
60
python/obitools3/format/header.pyx
Normal file
60
python/obitools3/format/header.pyx
Normal file
@ -0,0 +1,60 @@
|
||||
|
||||
cdef class HeaderFormat:
|
||||
|
||||
def __init__(self, bint fastaHeader=True, list tags=[], bint printNAKeys=False):
|
||||
'''
|
||||
|
||||
@param fastaHeader:
|
||||
@type fastaHeader: `bool`
|
||||
|
||||
@param tags:
|
||||
@type tags: `list` of `bytes`
|
||||
|
||||
@param printNAKeys:
|
||||
@type printNAKeys: `bool`
|
||||
'''
|
||||
|
||||
self.tags = set(tags)
|
||||
self.printNaKeys = printNAKeys
|
||||
|
||||
if fastaHeader:
|
||||
self.start=">"
|
||||
else:
|
||||
self.start="@"
|
||||
|
||||
self.headerBufferLength = 1000
|
||||
#self.headerBuffer = []
|
||||
|
||||
def __call__(self, dict data):
|
||||
cdef str header
|
||||
cdef dict tags = data['tags']
|
||||
cdef set ktags
|
||||
cdef list lines = [""]
|
||||
cdef str tagline
|
||||
|
||||
if self.tags is not None and self.tags:
|
||||
ktags = self.tags
|
||||
else:
|
||||
ktags = set(tags.keys())
|
||||
|
||||
for k in ktags:
|
||||
if k in tags:
|
||||
value = tags[k]
|
||||
if value is not None or self.printNaKeys:
|
||||
lines.append("%s=%s;" % (k,tags[k]))
|
||||
|
||||
if len(lines) > 1:
|
||||
tagline=" ".join(lines)
|
||||
else:
|
||||
tagline=""
|
||||
|
||||
if data['definition'] is not None:
|
||||
header = "%s%s%s %s" % (self.start,data['id'],
|
||||
tagline,
|
||||
data['definition'])
|
||||
else:
|
||||
header = "%s%s%s" % (self.start,data['id'],
|
||||
tagline)
|
||||
|
||||
return header
|
||||
|
||||
@ -10,6 +10,8 @@
|
||||
../../../src/encode.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obi_align.h
|
||||
../../../src/obi_align.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/obiblob_indexer.h
|
||||
@ -21,8 +23,22 @@
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.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_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obidmscolumndir.h
|
||||
@ -35,17 +51,9 @@
|
||||
../../../src/obitypes.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.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
|
||||
|
||||
@ -6,11 +6,12 @@ from .capi.obiview cimport Obiview_p
|
||||
from .capi.obitypes cimport obiversion_t, OBIType_t, index_t
|
||||
from ._obitaxo cimport OBI_Taxonomy
|
||||
|
||||
|
||||
cdef class OBIDMS_column:
|
||||
|
||||
cdef OBIDMS_column_p* pointer
|
||||
cdef OBIDMS dms
|
||||
cdef Obiview_p view
|
||||
cdef OBIView view
|
||||
cdef str data_type
|
||||
cdef str dms_name
|
||||
cdef str column_name
|
||||
@ -69,6 +70,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
|
||||
cdef OBIDMS_column ids
|
||||
cdef OBIDMS_column sequences
|
||||
cdef OBIDMS_column definitions
|
||||
cdef OBIDMS_column qualities
|
||||
|
||||
cpdef delete_column(self, str column_name)
|
||||
|
||||
@ -89,5 +91,5 @@ cdef class OBIDMS:
|
||||
cpdef OBIView open_view(self, str view_name)
|
||||
cpdef OBIView new_view(self, str view_name, object view_to_clone=*, list line_selection=*, str view_type=*, str comments=*)
|
||||
cpdef dict read_view_infos(self, str view_name)
|
||||
cpdef dict read_views(self)
|
||||
# cpdef dict read_views(self) TODO
|
||||
|
||||
|
||||
@ -17,6 +17,7 @@ from .capi.obitypes cimport const_char_p, \
|
||||
OBI_FLOAT, \
|
||||
OBI_BOOL, \
|
||||
OBI_CHAR, \
|
||||
OBI_QUAL, \
|
||||
OBI_STR, \
|
||||
OBI_SEQ, \
|
||||
name_data_type, \
|
||||
@ -43,6 +44,9 @@ from ._obidmscolumn_bool cimport OBIDMS_column_bool, \
|
||||
from ._obidmscolumn_char cimport OBIDMS_column_char, \
|
||||
OBIDMS_column_multi_elts_char
|
||||
|
||||
from ._obidmscolumn_qual cimport OBIDMS_column_qual, \
|
||||
OBIDMS_column_multi_elts_qual
|
||||
|
||||
from ._obidmscolumn_str cimport OBIDMS_column_str, \
|
||||
OBIDMS_column_multi_elts_str
|
||||
|
||||
@ -50,19 +54,19 @@ from ._obidmscolumn_seq cimport OBIDMS_column_seq, \
|
||||
OBIDMS_column_multi_elts_seq
|
||||
|
||||
from .capi.obiview cimport Obiview_p, \
|
||||
Obiviews_infos_all_p, \
|
||||
Obiview_infos_p, \
|
||||
Column_reference_p, \
|
||||
obi_new_view_nuc_seqs, \
|
||||
obi_new_view, \
|
||||
obi_new_view_cloned_from_name, \
|
||||
obi_new_view_nuc_seqs_cloned_from_name, \
|
||||
obi_view_map_file, \
|
||||
obi_view_unmap_file, \
|
||||
obi_open_view, \
|
||||
obi_read_view_infos, \
|
||||
obi_close_view_infos, \
|
||||
obi_view_delete_column, \
|
||||
obi_view_add_column, \
|
||||
obi_view_get_column, \
|
||||
obi_view_get_column, \
|
||||
obi_view_get_pointer_on_column_in_view, \
|
||||
obi_select_line, \
|
||||
obi_select_lines, \
|
||||
@ -70,7 +74,8 @@ from .capi.obiview cimport Obiview_p, \
|
||||
VIEW_TYPE_NUC_SEQS, \
|
||||
NUC_SEQUENCE_COLUMN, \
|
||||
ID_COLUMN, \
|
||||
DEFINITION_COLUMN
|
||||
DEFINITION_COLUMN, \
|
||||
QUALITY_COLUMN
|
||||
|
||||
from libc.stdlib cimport malloc
|
||||
from cpython.pycapsule cimport PyCapsule_New, PyCapsule_GetPointer
|
||||
@ -90,7 +95,7 @@ cdef class OBIDMS_column :
|
||||
# Fill structure
|
||||
self.pointer = column_pp
|
||||
self.dms = view.dms
|
||||
self.view = view.pointer
|
||||
self.view = view
|
||||
self.data_type = bytes2str(name_data_type((column_p.header).returned_data_type))
|
||||
self.column_name = bytes2str((column_p.header).name)
|
||||
self.nb_elements_per_line = (column_p.header).nb_elements_per_line
|
||||
@ -120,7 +125,7 @@ cdef class OBIDMS_column :
|
||||
yield self.get_line(line_nb)
|
||||
|
||||
cpdef update_pointer(self):
|
||||
self.pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self.view, str2bytes(self.column_name))
|
||||
self.pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self.view.pointer, str2bytes(self.column_name))
|
||||
|
||||
cpdef list get_elements_names(self):
|
||||
return self.elements_names
|
||||
@ -186,6 +191,11 @@ cdef class OBIDMS_column :
|
||||
subclass = OBIDMS_column_char
|
||||
else :
|
||||
subclass = OBIDMS_column_multi_elts_char
|
||||
elif col_type == OBI_QUAL :
|
||||
if col_one_element_per_line :
|
||||
subclass = OBIDMS_column_qual
|
||||
else :
|
||||
subclass = OBIDMS_column_multi_elts_qual
|
||||
elif col_type == OBI_STR :
|
||||
if col_one_element_per_line :
|
||||
subclass = OBIDMS_column_str
|
||||
@ -239,15 +249,15 @@ cdef class OBIDMS_column_line :
|
||||
cdef class OBIView :
|
||||
|
||||
def __init__(self, OBIDMS dms, str view_name, bint new=False, object view_to_clone=None, list line_selection=None, str comments=""):
|
||||
|
||||
cdef Obiview_p view = NULL
|
||||
cdef int i
|
||||
cdef list col_list
|
||||
cdef str col_name
|
||||
cdef OBIDMS_column column
|
||||
cdef OBIDMS_column_p column_p
|
||||
|
||||
cdef Obiview_p view = NULL
|
||||
cdef int i
|
||||
cdef list col_list
|
||||
cdef str col_name
|
||||
cdef OBIDMS_column column
|
||||
cdef OBIDMS_column_p column_p
|
||||
cdef OBIDMS_column_header_p header
|
||||
cdef index_t* line_selection_p
|
||||
cdef index_t* line_selection_p
|
||||
|
||||
self.dms = dms
|
||||
|
||||
@ -280,11 +290,11 @@ cdef class OBIView :
|
||||
raise Exception("Error creating/opening a view")
|
||||
|
||||
self.pointer = view
|
||||
self.name = bytes2str(view.name)
|
||||
self.name = bytes2str(view.infos.name)
|
||||
|
||||
# Go through columns to build list of corresponding python instances
|
||||
self.columns = {}
|
||||
for i in range(view.column_count) :
|
||||
for i in range(view.infos.column_count) :
|
||||
column_p = <OBIDMS_column_p> (view.columns)[i]
|
||||
header = (column_p).header
|
||||
col_name = bytes2str(header.name)
|
||||
@ -293,13 +303,8 @@ cdef class OBIView :
|
||||
|
||||
|
||||
def __repr__(self) :
|
||||
|
||||
cdef str s
|
||||
cdef OBIDMS_column column
|
||||
cdef OBIDMS_column_p column_p
|
||||
|
||||
s = self.name
|
||||
s = s + ", " + self.comments + ", " + str(self.pointer.line_count) + " lines\n"
|
||||
s = str(self.name) + ", " + str(self.comments) + ", " + str(self.pointer.infos.line_count) + " lines\n"
|
||||
for column_name in self.columns :
|
||||
s = s + self.columns[column_name].__repr__() + '\n'
|
||||
return s
|
||||
@ -308,7 +313,7 @@ cdef class OBIView :
|
||||
cpdef delete_column(self, str column_name) :
|
||||
|
||||
cdef int i
|
||||
cdef Obiview_p view
|
||||
cdef Obiview_p view_p
|
||||
cdef OBIDMS_column column
|
||||
cdef OBIDMS_column_p column_p
|
||||
cdef OBIDMS_column_header_p header
|
||||
@ -316,7 +321,7 @@ cdef class OBIView :
|
||||
|
||||
view = self.pointer
|
||||
|
||||
if obi_view_delete_column(view, str2bytes(column_name)) < 0 :
|
||||
if obi_view_delete_column(view_p, str2bytes(column_name)) < 0 :
|
||||
raise Exception("Problem deleting a column from a view")
|
||||
|
||||
# Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
|
||||
@ -324,7 +329,7 @@ cdef class OBIView :
|
||||
|
||||
for column_n in self.columns :
|
||||
(self.columns[column_n]).update_pointer()
|
||||
|
||||
|
||||
|
||||
cpdef add_column(self,
|
||||
str column_name,
|
||||
@ -341,7 +346,6 @@ cdef class OBIView :
|
||||
cdef bytes column_name_b
|
||||
cdef bytes elements_names_b
|
||||
cdef object subclass
|
||||
cdef OBIDMS_column_p* column_pp
|
||||
cdef OBIDMS_column_p column_p
|
||||
|
||||
column_name_b = str2bytes(column_name)
|
||||
@ -360,6 +364,8 @@ cdef class OBIView :
|
||||
data_type = OBI_BOOL
|
||||
elif type == 'OBI_CHAR' :
|
||||
data_type = OBI_CHAR
|
||||
elif type == 'OBI_QUAL' :
|
||||
data_type = OBI_QUAL
|
||||
elif type == 'OBI_STR' :
|
||||
data_type = OBI_STR
|
||||
elif type == 'OBI_SEQ' :
|
||||
@ -374,10 +380,9 @@ cdef class OBIView :
|
||||
raise Exception("Problem adding a column in a view")
|
||||
|
||||
# Get the column pointer
|
||||
column_pp = obi_view_get_pointer_on_column_in_view(self.pointer, column_name_b)
|
||||
column_p = obi_view_get_column(self.pointer, column_name_b)
|
||||
|
||||
# Open and store the subclass
|
||||
column_p = column_pp[0] # TODO ugly cython dereferencing
|
||||
subclass = OBIDMS_column.get_subclass_type(column_p)
|
||||
(self.columns)[column_name] = subclass(self, column_name)
|
||||
|
||||
@ -396,7 +401,7 @@ cdef class OBIView :
|
||||
cdef OBIView_line line # TODO Check that this works for NUC SEQ views
|
||||
|
||||
# Yield each line
|
||||
lines_used = (self.pointer).line_count
|
||||
lines_used = self.pointer.infos.line_count
|
||||
|
||||
for line_nb in range(lines_used) :
|
||||
line = self[line_nb]
|
||||
@ -480,12 +485,12 @@ cdef class OBIView_NUC_SEQS(OBIView):
|
||||
raise Exception("Error creating/opening view")
|
||||
|
||||
self.pointer = view
|
||||
self.name = bytes2str(view.name)
|
||||
self.comments = bytes2str(view.comments)
|
||||
self.name = bytes2str(view.infos.name)
|
||||
self.comments = bytes2str(view.infos.comments)
|
||||
|
||||
# Go through columns to build list of corresponding python instances
|
||||
self.columns = {}
|
||||
for i in range(view.column_count) :
|
||||
for i in range(view.infos.column_count) :
|
||||
column_p = <OBIDMS_column_p> (view.columns)[i]
|
||||
header = (column_p).header
|
||||
col_name = bytes2str(header.name)
|
||||
@ -495,31 +500,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
|
||||
self.ids = self.columns[bytes2str(ID_COLUMN)]
|
||||
self.sequences = self.columns[bytes2str(NUC_SEQUENCE_COLUMN)]
|
||||
self.definitions = self.columns[bytes2str(DEFINITION_COLUMN)]
|
||||
|
||||
|
||||
cpdef delete_column(self, str column_name) :
|
||||
|
||||
cdef int i
|
||||
cdef Obiview_p view
|
||||
cdef OBIDMS_column column
|
||||
cdef OBIDMS_column_p column_p
|
||||
cdef OBIDMS_column_header_p header
|
||||
cdef str column_n
|
||||
|
||||
if ((column_name == bytes2str(ID_COLUMN)) or (column_name == bytes2str(NUC_SEQUENCE_COLUMN)) or (column_name == bytes2str(DEFINITION_COLUMN))) :
|
||||
raise Exception("Can't delete an obligatory column from a NUC_SEQS view")
|
||||
|
||||
view = self.pointer
|
||||
|
||||
if obi_view_delete_column(view, str2bytes(column_name)) < 0 :
|
||||
raise Exception("Problem deleting a column from a view")
|
||||
|
||||
# Remove instance from the dictionary
|
||||
(self.columns).pop(column_name)
|
||||
|
||||
for column_n in self.columns :
|
||||
(self.columns[column_n]).update_pointer()
|
||||
|
||||
self.qualities = self.columns[bytes2str(QUALITY_COLUMN)]
|
||||
|
||||
def __getitem__(self, object item) :
|
||||
if type(item) == str :
|
||||
@ -527,7 +508,6 @@ cdef class OBIView_NUC_SEQS(OBIView):
|
||||
elif type(item) == int :
|
||||
return OBI_Nuc_Seq_Stored(self, item)
|
||||
|
||||
|
||||
def __setitem__(self, index_t line_idx, OBI_Nuc_Seq sequence_obj) :
|
||||
for key in sequence_obj :
|
||||
self[line_idx][key] = sequence_obj[key]
|
||||
@ -546,6 +526,7 @@ cdef class OBIView_line :
|
||||
|
||||
def __setitem__(self, str column_name, object value):
|
||||
# TODO detect multiple elements (dict type)? put somewhere else? but more risky (in get)
|
||||
# TODO OBI_QUAL ?
|
||||
cdef type value_type
|
||||
cdef str value_obitype
|
||||
if column_name not in self.view :
|
||||
@ -621,7 +602,7 @@ cdef class OBIDMS :
|
||||
view_class = OBIView_NUC_SEQS
|
||||
else :
|
||||
view_class = OBIView
|
||||
|
||||
|
||||
return view_class(self, view_name)
|
||||
|
||||
|
||||
@ -639,54 +620,84 @@ cdef class OBIDMS :
|
||||
|
||||
|
||||
cpdef dict read_view_infos(self, str view_name) :
|
||||
all_views = self.read_views()
|
||||
return all_views[view_name]
|
||||
|
||||
cdef Obiview_infos_p view_infos_p
|
||||
cdef dict view_infos_d
|
||||
cdef Column_reference_p column_refs
|
||||
cdef int i, j
|
||||
cdef str column_name
|
||||
|
||||
view_infos_p = obi_view_map_file(self.pointer, str2bytes(view_name))
|
||||
view_infos_d = {}
|
||||
view_infos_d["name"] = bytes2str(view_infos_p.name)
|
||||
view_infos_d["comments"] = bytes2str(view_infos_p.comments)
|
||||
view_infos_d["view_type"] = bytes2str(view_infos_p.view_type)
|
||||
view_infos_d["column_count"] = <int> view_infos_p.column_count
|
||||
view_infos_d["line_count"] = <int> view_infos_p.line_count
|
||||
view_infos_d["created_from"] = bytes2str(view_infos_p.created_from)
|
||||
view_infos_d["creation_date"] = bytes2str(obi_format_date(view_infos_p.creation_date))
|
||||
if (view_infos_p.all_lines) :
|
||||
view_infos_d["line_selection"] = None
|
||||
else :
|
||||
view_infos_d["line_selection"] = {}
|
||||
view_infos_d["line_selection"]["column_name"] = bytes2str((view_infos_p.line_selection).column_name)
|
||||
view_infos_d["line_selection"]["version"] = <int> (view_infos_p.line_selection).version
|
||||
view_infos_d["column_references"] = {}
|
||||
column_refs = view_infos_p.column_references
|
||||
for j in range(view_infos_d["column_count"]) :
|
||||
column_name = bytes2str((column_refs[j]).column_name)
|
||||
view_infos_d["column_references"][column_name] = {}
|
||||
view_infos_d["column_references"][column_name]["version"] = column_refs[j].version
|
||||
|
||||
obi_view_unmap_file(self.pointer, view_infos_p)
|
||||
|
||||
return view_infos_d
|
||||
|
||||
|
||||
cpdef dict read_views(self) : # TODO function that prints the dic nicely and function that prints 1 view nicely. Add column type in col ref
|
||||
|
||||
cdef Obiviews_infos_all_p all_views_p
|
||||
cdef Obiview_infos_p view_p
|
||||
cdef Column_reference_p column_refs
|
||||
cdef int nb_views
|
||||
cdef int i, j
|
||||
cdef str view_name
|
||||
cdef str column_name
|
||||
cdef dict views
|
||||
cdef bytes name_b
|
||||
|
||||
views = {}
|
||||
all_views_p = obi_read_view_infos(self.pointer)
|
||||
if all_views_p == NULL :
|
||||
raise Exception("No views to read")
|
||||
nb_views = <int> (all_views_p.header).view_count
|
||||
for i in range(nb_views) :
|
||||
view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
|
||||
view_name = bytes2str(view_p.name)
|
||||
views[view_name] = {}
|
||||
views[view_name]["comments"] = bytes2str(view_p.comments)
|
||||
views[view_name]["view_type"] = bytes2str(view_p.view_type)
|
||||
views[view_name]["column_count"] = <int> view_p.column_count
|
||||
views[view_name]["line_count"] = <int> view_p.line_count
|
||||
views[view_name]["view_number"] = <int> view_p.view_number
|
||||
views[view_name]["created_from"] = bytes2str(view_p.created_from)
|
||||
views[view_name]["creation_date"] = bytes2str(obi_format_date(view_p.creation_date))
|
||||
if (view_p.all_lines) :
|
||||
views[view_name]["line_selection"] = None
|
||||
else :
|
||||
views[view_name]["line_selection"] = {}
|
||||
views[view_name]["line_selection"]["column_name"] = bytes2str((view_p.line_selection).column_name)
|
||||
views[view_name]["line_selection"]["version"] = <int> (view_p.line_selection).version
|
||||
views[view_name]["column_references"] = {}
|
||||
column_refs = view_p.column_references
|
||||
for j in range(views[view_name]["column_count"]) :
|
||||
column_name = bytes2str((column_refs[j]).column_name)
|
||||
views[view_name]["column_references"][column_name] = {}
|
||||
views[view_name]["column_references"][column_name]["version"] = column_refs[j].version
|
||||
|
||||
obi_close_view_infos(all_views_p);
|
||||
|
||||
return views
|
||||
# cpdef dict read_views(self) : # TODO function that prints the dic nicely and function that prints 1 view nicely. Add column type in col ref
|
||||
#
|
||||
# cdef Obiviews_infos_all_p all_views_p
|
||||
# cdef Obiview_infos_p view_p
|
||||
# cdef Column_reference_p column_refs
|
||||
# cdef int nb_views
|
||||
# cdef int i, j
|
||||
# cdef str view_name
|
||||
# cdef str column_name
|
||||
# cdef dict views
|
||||
# cdef bytes name_b
|
||||
#
|
||||
# views = {}
|
||||
# all_views_p = obi_read_view_infos(self.pointer)
|
||||
# if all_views_p == NULL :
|
||||
# raise Exception("No views to read")
|
||||
# nb_views = <int> (all_views_p.header).view_count
|
||||
# for i in range(nb_views) :
|
||||
# view_p = (<Obiview_infos_p> (all_views_p.view_infos)) + i
|
||||
# view_name = bytes2str(view_p.name)
|
||||
# views[view_name] = {}
|
||||
# views[view_name]["comments"] = bytes2str(view_p.comments)
|
||||
# views[view_name]["view_type"] = bytes2str(view_p.view_type)
|
||||
# views[view_name]["column_count"] = <int> view_p.column_count
|
||||
# views[view_name]["line_count"] = <int> view_p.line_count
|
||||
# views[view_name]["view_number"] = <int> view_p.view_number
|
||||
# views[view_name]["created_from"] = bytes2str(view_p.created_from)
|
||||
# views[view_name]["creation_date"] = bytes2str(obi_format_date(view_p.creation_date))
|
||||
# if (view_p.all_lines) :
|
||||
# views[view_name]["line_selection"] = None
|
||||
# else :
|
||||
# views[view_name]["line_selection"] = {}
|
||||
# views[view_name]["line_selection"]["column_name"] = bytes2str((view_p.line_selection).column_name)
|
||||
# views[view_name]["line_selection"]["version"] = <int> (view_p.line_selection).version
|
||||
# views[view_name]["column_references"] = {}
|
||||
# column_refs = view_p.column_references
|
||||
# for j in range(views[view_name]["column_count"]) :
|
||||
# column_name = bytes2str((column_refs[j]).column_name)
|
||||
# views[view_name]["column_references"][column_name] = {}
|
||||
# views[view_name]["column_references"][column_name]["version"] = column_refs[j].version
|
||||
#
|
||||
# obi_close_view_infos(all_views_p);
|
||||
#
|
||||
# return views
|
||||
|
||||
|
||||
|
||||
|
||||
@ -10,6 +10,8 @@
|
||||
../../../src/encode.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obi_align.h
|
||||
../../../src/obi_align.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/obiblob_indexer.h
|
||||
@ -21,8 +23,22 @@
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.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_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obidmscolumndir.h
|
||||
@ -35,17 +51,9 @@
|
||||
../../../src/obitypes.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.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
|
||||
|
||||
@ -17,7 +17,7 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
|
||||
cpdef object get_line(self, index_t line_nb):
|
||||
cdef obibool_t value
|
||||
cdef object result
|
||||
value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
|
||||
value = obi_column_get_obibool_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIBool_NA :
|
||||
@ -29,7 +29,7 @@ cdef class OBIDMS_column_bool(OBIDMS_column):
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
if value is None :
|
||||
value = OBIBool_NA
|
||||
if obi_column_set_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obibool_t> value) < 0:
|
||||
if obi_column_set_obibool_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, <obibool_t> value) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
|
||||
@ -38,7 +38,7 @@ cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
|
||||
cpdef object get_item(self, index_t line_nb, str element_name):
|
||||
cdef obibool_t value
|
||||
cdef object result
|
||||
value = obi_column_get_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
value = obi_column_get_obibool_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb, element_name)
|
||||
if value == OBIBool_NA :
|
||||
@ -56,7 +56,7 @@ cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
|
||||
result = {}
|
||||
all_NA = True
|
||||
for i in range(self.nb_elements_per_line) :
|
||||
value = obi_column_get_obibool_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
|
||||
value = obi_column_get_obibool_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIBool_NA :
|
||||
@ -73,5 +73,5 @@ cdef class OBIDMS_column_multi_elts_bool(OBIDMS_column_multi_elts):
|
||||
cpdef set_item(self, index_t line_nb, str element_name, object value):
|
||||
if value is None :
|
||||
value = OBIBool_NA
|
||||
if obi_column_set_obibool_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0:
|
||||
if obi_column_set_obibool_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), <obibool_t> value) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
@ -10,6 +10,8 @@
|
||||
../../../src/encode.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obi_align.h
|
||||
../../../src/obi_align.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/obiblob_indexer.h
|
||||
@ -21,8 +23,22 @@
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.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_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obidmscolumndir.h
|
||||
@ -35,17 +51,9 @@
|
||||
../../../src/obitypes.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.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
|
||||
|
||||
@ -15,7 +15,7 @@ cdef class OBIDMS_column_char(OBIDMS_column):
|
||||
cpdef object get_line(self, index_t line_nb):
|
||||
cdef obichar_t value
|
||||
cdef object result
|
||||
value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
|
||||
value = obi_column_get_obichar_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIChar_NA :
|
||||
@ -27,7 +27,7 @@ cdef class OBIDMS_column_char(OBIDMS_column):
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
if value is None :
|
||||
value = OBIChar_NA
|
||||
if obi_column_set_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, str2bytes(value)[0]) < 0:
|
||||
if obi_column_set_obichar_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)[0]) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
|
||||
@ -36,7 +36,7 @@ cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
|
||||
cpdef object get_item(self, index_t line_nb, str element_name):
|
||||
cdef obichar_t value
|
||||
cdef object result
|
||||
value = obi_column_get_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
value = obi_column_get_obichar_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb, element_name)
|
||||
if value == OBIChar_NA :
|
||||
@ -54,7 +54,7 @@ cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
|
||||
result = {}
|
||||
all_NA = True
|
||||
for i in range(self.nb_elements_per_line) :
|
||||
value = obi_column_get_obichar_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
|
||||
value = obi_column_get_obichar_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIChar_NA :
|
||||
@ -71,6 +71,6 @@ cdef class OBIDMS_column_multi_elts_char(OBIDMS_column_multi_elts):
|
||||
cpdef set_item(self, index_t line_nb, str element_name, object value):
|
||||
if value is None :
|
||||
value = OBIChar_NA
|
||||
if obi_column_set_obichar_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
|
||||
if obi_column_set_obichar_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)[0]) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
|
||||
@ -10,6 +10,8 @@
|
||||
../../../src/encode.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obi_align.h
|
||||
../../../src/obi_align.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/obiblob_indexer.h
|
||||
@ -21,8 +23,22 @@
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.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_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obidmscolumndir.h
|
||||
@ -35,17 +51,9 @@
|
||||
../../../src/obitypes.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.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
|
||||
|
||||
@ -15,7 +15,7 @@ cdef class OBIDMS_column_float(OBIDMS_column):
|
||||
cpdef object get_line(self, index_t line_nb):
|
||||
cdef obifloat_t value
|
||||
cdef object result
|
||||
value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
|
||||
value = obi_column_get_obifloat_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIFloat_NA :
|
||||
@ -27,7 +27,7 @@ cdef class OBIDMS_column_float(OBIDMS_column):
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
if value is None :
|
||||
value = OBIFloat_NA
|
||||
if obi_column_set_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obifloat_t> value) < 0:
|
||||
if obi_column_set_obifloat_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, <obifloat_t> value) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
|
||||
@ -36,7 +36,7 @@ cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
|
||||
cpdef object get_item(self, index_t line_nb, str element_name):
|
||||
cdef obifloat_t value
|
||||
cdef object result
|
||||
value = obi_column_get_obifloat_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
value = obi_column_get_obifloat_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb, element_name)
|
||||
if value == OBIFloat_NA :
|
||||
@ -54,7 +54,7 @@ cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
|
||||
result = {}
|
||||
all_NA = True
|
||||
for i in range(self.nb_elements_per_line) :
|
||||
value = obi_column_get_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
|
||||
value = obi_column_get_obifloat_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIFloat_NA :
|
||||
@ -71,6 +71,6 @@ cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
|
||||
cpdef set_item(self, index_t line_nb, str element_name, object value):
|
||||
if value is None :
|
||||
value = OBIFloat_NA
|
||||
if obi_column_set_obifloat_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obifloat_t> value) < 0:
|
||||
if obi_column_set_obifloat_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), <obifloat_t> value) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
@ -10,6 +10,8 @@
|
||||
../../../src/encode.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obi_align.h
|
||||
../../../src/obi_align.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/obiblob_indexer.h
|
||||
@ -21,8 +23,22 @@
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.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_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obidmscolumndir.h
|
||||
@ -35,17 +51,9 @@
|
||||
../../../src/obitypes.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.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
|
||||
|
||||
@ -17,7 +17,7 @@ cdef class OBIDMS_column_int(OBIDMS_column):
|
||||
cpdef object get_line(self, index_t line_nb):
|
||||
cdef obiint_t value
|
||||
cdef object result
|
||||
value = obi_column_get_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
|
||||
value = obi_column_get_obiint_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIInt_NA :
|
||||
@ -29,7 +29,7 @@ cdef class OBIDMS_column_int(OBIDMS_column):
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
if value is None :
|
||||
value = OBIInt_NA
|
||||
if obi_column_set_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obiint_t> value) < 0:
|
||||
if obi_column_set_obiint_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, <obiint_t> value) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
|
||||
@ -38,7 +38,7 @@ cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
|
||||
cpdef object get_item(self, index_t line_nb, str element_name):
|
||||
cdef obiint_t value
|
||||
cdef object result
|
||||
value = obi_column_get_obiint_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
value = obi_column_get_obiint_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb, element_name)
|
||||
if value == OBIInt_NA :
|
||||
@ -56,7 +56,7 @@ cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
|
||||
result = {}
|
||||
all_NA = True
|
||||
for i in range(self.nb_elements_per_line) :
|
||||
value = obi_column_get_obiint_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, i)
|
||||
value = obi_column_get_obiint_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIInt_NA :
|
||||
@ -73,6 +73,6 @@ cdef class OBIDMS_column_multi_elts_int(OBIDMS_column_multi_elts):
|
||||
cpdef set_item(self, index_t line_nb, str element_name, object value):
|
||||
if value is None :
|
||||
value = OBIInt_NA
|
||||
if obi_column_set_obiint_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), <obiint_t> value) < 0:
|
||||
if obi_column_set_obiint_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), <obiint_t> value) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
|
||||
59
python/obitools3/obidms/_obidmscolumn_qual.cfiles
Normal file
59
python/obitools3/obidms/_obidmscolumn_qual.cfiles
Normal file
@ -0,0 +1,59 @@
|
||||
../../../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/obi_align.h
|
||||
../../../src/obi_align.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_bool.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
20
python/obitools3/obidms/_obidmscolumn_qual.pxd
Normal file
20
python/obitools3/obidms/_obidmscolumn_qual.pxd
Normal file
@ -0,0 +1,20 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from .capi.obitypes cimport index_t
|
||||
from ._obidms cimport OBIDMS_column , OBIDMS_column_multi_elts
|
||||
|
||||
|
||||
cdef class OBIDMS_column_qual(OBIDMS_column):
|
||||
cpdef object get_line(self, index_t line_nb)
|
||||
cpdef object get_str_line(self, index_t line_nb)
|
||||
cpdef set_line(self, index_t line_nb, object value)
|
||||
cpdef set_str_line(self, index_t line_nb, object value)
|
||||
|
||||
|
||||
cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
|
||||
cpdef object get_item(self, index_t line_nb, str element_name)
|
||||
cpdef object get_str_item(self, index_t line_nb, str element_name)
|
||||
cpdef object get_line(self, index_t line_nb)
|
||||
cpdef object get_str_line(self, index_t line_nb)
|
||||
cpdef set_item(self, index_t line_nb, str element_name, object value)
|
||||
cpdef set_str_item(self, index_t line_nb, str element_name, object value)
|
||||
184
python/obitools3/obidms/_obidmscolumn_qual.pyx
Normal file
184
python/obitools3/obidms/_obidmscolumn_qual.pyx
Normal file
@ -0,0 +1,184 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from .capi.obiview cimport obi_column_get_obiqual_char_with_elt_name_in_view, \
|
||||
obi_column_get_obiqual_char_with_elt_idx_in_view, \
|
||||
obi_column_set_obiqual_char_with_elt_name_in_view, \
|
||||
obi_column_set_obiqual_char_with_elt_idx_in_view, \
|
||||
obi_column_get_obiqual_int_with_elt_name_in_view, \
|
||||
obi_column_get_obiqual_int_with_elt_idx_in_view, \
|
||||
obi_column_set_obiqual_int_with_elt_name_in_view, \
|
||||
obi_column_set_obiqual_int_with_elt_idx_in_view
|
||||
|
||||
from .capi.obierrno cimport obi_errno
|
||||
from .capi.obitypes cimport OBIQual_char_NA, OBIQual_int_NA, const_char_p
|
||||
|
||||
from ._obidms cimport OBIView
|
||||
|
||||
from obitools3.utils cimport str2bytes, bytes2str
|
||||
|
||||
from libc.stdlib cimport free
|
||||
from libc.string cimport strcmp
|
||||
from libc.stdint cimport uint8_t
|
||||
from libc.stdlib cimport malloc
|
||||
|
||||
|
||||
cdef class OBIDMS_column_qual(OBIDMS_column):
|
||||
|
||||
cpdef object get_line(self, index_t line_nb):
|
||||
cdef const uint8_t* value
|
||||
cdef int value_length
|
||||
cdef object result
|
||||
cdef int i
|
||||
value = obi_column_get_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, &value_length)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIQual_int_NA :
|
||||
result = None
|
||||
else :
|
||||
result = []
|
||||
for i in range(value_length) :
|
||||
result.append(<int>value[i])
|
||||
return result
|
||||
|
||||
cpdef object get_str_line(self, index_t line_nb):
|
||||
cdef char* value
|
||||
cdef object result
|
||||
cdef int i
|
||||
value = obi_column_get_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIQual_char_NA :
|
||||
result = None
|
||||
else :
|
||||
result = bytes2str(value)
|
||||
free(value)
|
||||
return result
|
||||
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
cdef uint8_t* value_b
|
||||
cdef int value_length
|
||||
if value is None :
|
||||
if obi_column_set_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIQual_int_NA, 0) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
else :
|
||||
value_length = len(value)
|
||||
value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
|
||||
for i in range(value_length) :
|
||||
value_b[i] = <uint8_t>value[i]
|
||||
if obi_column_set_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b, value_length) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
free(value_b)
|
||||
|
||||
cpdef set_str_line(self, index_t line_nb, object value):
|
||||
if value is None :
|
||||
if obi_column_set_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIQual_char_NA) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
else :
|
||||
if obi_column_set_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
|
||||
cdef class OBIDMS_column_multi_elts_qual(OBIDMS_column_multi_elts):
|
||||
|
||||
cpdef object get_item(self, index_t line_nb, str element_name):
|
||||
cdef const uint8_t* value
|
||||
cdef int value_length
|
||||
cdef object result
|
||||
cdef int i
|
||||
value = obi_column_get_obiqual_int_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), &value_length)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb, element_name)
|
||||
if value == OBIQual_int_NA :
|
||||
result = None
|
||||
else :
|
||||
result = []
|
||||
for i in range(value_length) :
|
||||
result.append(<int>value[i])
|
||||
return result
|
||||
|
||||
cpdef object get_str_item(self, index_t line_nb, str element_name):
|
||||
cdef char* value
|
||||
cdef object result
|
||||
value = obi_column_get_obiqual_char_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb, element_name)
|
||||
if value == OBIQual_char_NA :
|
||||
result = None
|
||||
else :
|
||||
result = bytes2str(value)
|
||||
free(value)
|
||||
return result
|
||||
|
||||
cpdef object get_line(self, index_t line_nb) :
|
||||
cdef const uint8_t* value
|
||||
cdef int value_length
|
||||
cdef object value_in_result
|
||||
cdef dict result
|
||||
cdef index_t i
|
||||
cdef int j
|
||||
cdef bint all_NA
|
||||
result = {}
|
||||
all_NA = True
|
||||
for i in range(self.nb_elements_per_line) :
|
||||
value = obi_column_get_obiqual_int_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i, &value_length)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIQual_int_NA :
|
||||
value_in_result = None
|
||||
else :
|
||||
value_in_result = []
|
||||
for j in range(value_length) :
|
||||
value_in_result.append(<int>value[j])
|
||||
result[self.elements_names[i]] = value_in_result
|
||||
if all_NA and (value_in_result is not None) :
|
||||
all_NA = False
|
||||
if all_NA :
|
||||
result = None
|
||||
return result
|
||||
|
||||
cpdef object get_str_line(self, index_t line_nb) :
|
||||
cdef char* value
|
||||
cdef object value_in_result
|
||||
cdef dict result
|
||||
cdef index_t i
|
||||
cdef bint all_NA
|
||||
result = {}
|
||||
all_NA = True
|
||||
for i in range(self.nb_elements_per_line) :
|
||||
value = obi_column_get_obiqual_char_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if value == OBIQual_char_NA :
|
||||
value_in_result = None
|
||||
else :
|
||||
value_in_result = bytes2str(value)
|
||||
free(value)
|
||||
result[self.elements_names[i]] = value_in_result
|
||||
if all_NA and (value_in_result is not None) :
|
||||
all_NA = False
|
||||
if all_NA :
|
||||
result = None
|
||||
return result
|
||||
|
||||
cpdef set_item(self, index_t line_nb, str element_name, object value):
|
||||
cdef uint8_t* value_b
|
||||
cdef int value_length
|
||||
if value is None :
|
||||
if obi_column_set_obiqual_int_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), OBIQual_int_NA, 0) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
else :
|
||||
value_length = len(value)
|
||||
value_b = <uint8_t*> malloc(value_length * sizeof(uint8_t))
|
||||
for i in range(value_length) :
|
||||
value_b[i] = <uint8_t>value[i]
|
||||
if obi_column_set_obiqual_int_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b, value_length) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
free(value_b)
|
||||
|
||||
cpdef set_str_item(self, index_t line_nb, str element_name, object value):
|
||||
if value is None :
|
||||
if obi_column_set_obiqual_char_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), OBIQual_char_NA) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
else :
|
||||
if obi_column_set_obiqual_char_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), str2bytes(value)) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
@ -10,6 +10,8 @@
|
||||
../../../src/encode.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obi_align.h
|
||||
../../../src/obi_align.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/obiblob_indexer.h
|
||||
@ -21,8 +23,22 @@
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.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_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obidmscolumndir.h
|
||||
@ -35,17 +51,9 @@
|
||||
../../../src/obitypes.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.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
|
||||
|
||||
@ -1,12 +1,24 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from .capi.obitypes cimport index_t
|
||||
from ._obidms cimport OBIDMS_column, OBIDMS_column_multi_elts
|
||||
from ._obidms cimport OBIView, OBIDMS_column, OBIDMS_column_multi_elts
|
||||
|
||||
|
||||
cdef class OBIDMS_column_seq(OBIDMS_column):
|
||||
cpdef object get_line(self, index_t line_nb)
|
||||
cpdef set_line(self, index_t line_nb, object value)
|
||||
|
||||
# TO DISCUSS :
|
||||
# I'am not sure that this method has to be declared here
|
||||
# Alignment must be declared outside of the sequence object
|
||||
cpdef align(self,
|
||||
OBIView score_view,
|
||||
OBIDMS_column score_column,
|
||||
double threshold = *,
|
||||
bint normalize = *,
|
||||
int reference = *,
|
||||
bint similarity_mode = *)
|
||||
|
||||
|
||||
cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
|
||||
cpdef object get_item(self, index_t line_nb, str element_name)
|
||||
|
||||
@ -4,13 +4,15 @@ from .capi.obiview cimport obi_column_get_obiseq_with_elt_name_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_idx_in_view
|
||||
from .capi.obialign cimport obi_align_one_column
|
||||
from .capi.obierrno cimport obi_errno
|
||||
from .capi.obitypes cimport OBISeq_NA, const_char_p
|
||||
|
||||
from ._obidms cimport OBIView
|
||||
|
||||
from obitools3.utils cimport str2bytes, bytes2str
|
||||
|
||||
from libc.stdlib cimport free
|
||||
from libc.string cimport strcmp
|
||||
|
||||
|
||||
cdef class OBIDMS_column_seq(OBIDMS_column):
|
||||
@ -18,41 +20,67 @@ cdef class OBIDMS_column_seq(OBIDMS_column):
|
||||
cpdef object get_line(self, index_t line_nb):
|
||||
cdef char* value
|
||||
cdef object result
|
||||
value = obi_column_get_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
|
||||
value = obi_column_get_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if strcmp(value, OBISeq_NA) == 0 :
|
||||
if value == OBISeq_NA :
|
||||
result = None
|
||||
else :
|
||||
result = bytes2str(value)
|
||||
free(value)
|
||||
try:
|
||||
result = <bytes> value
|
||||
finally:
|
||||
free(value)
|
||||
return result
|
||||
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
cdef bytes value_b
|
||||
|
||||
if value is None :
|
||||
value_b = OBISeq_NA
|
||||
else :
|
||||
elif isinstance(value, bytes) :
|
||||
value_b = value
|
||||
elif isinstance(value, str) :
|
||||
value_b = str2bytes(value)
|
||||
if obi_column_set_obiseq_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, value_b) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
else:
|
||||
raise TypeError('Sequence value must be of type Bytes, Str or None')
|
||||
|
||||
if obi_column_set_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
else :
|
||||
if obi_column_set_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
# TODO choose alignment type (lcs or other) with supplementary argument
|
||||
cpdef align(self,
|
||||
OBIView score_view,
|
||||
OBIDMS_column score_column,
|
||||
double threshold = 0.0,
|
||||
bint normalize = True,
|
||||
int reference = 0, # TODO
|
||||
bint similarity_mode = True):
|
||||
if (obi_align_one_column(self.view.pointer, (self.pointer)[0], score_view.pointer, (score_column.pointer)[0], threshold, normalize, reference, similarity_mode) < 0) :
|
||||
raise Exception("An error occurred while aligning sequences")
|
||||
|
||||
|
||||
|
||||
cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
|
||||
|
||||
cpdef object get_item(self, index_t line_nb, str element_name):
|
||||
cdef char* value
|
||||
cdef object result
|
||||
value = obi_column_get_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
value = obi_column_get_obiseq_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb, element_name)
|
||||
if strcmp(value, OBISeq_NA) == 0 :
|
||||
if value == OBISeq_NA :
|
||||
result = None
|
||||
else :
|
||||
result = bytes2str(value)
|
||||
free(value)
|
||||
try:
|
||||
result = <bytes> value
|
||||
finally:
|
||||
free(value)
|
||||
return result
|
||||
|
||||
|
||||
cpdef object get_line(self, index_t line_nb) :
|
||||
cdef char* value
|
||||
cdef object value_in_result
|
||||
@ -62,14 +90,16 @@ cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
|
||||
result = {}
|
||||
all_NA = True
|
||||
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 = obi_column_get_obiseq_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if strcmp(value, OBISeq_NA) == 0 :
|
||||
if value == OBISeq_NA :
|
||||
value_in_result = None
|
||||
else :
|
||||
value_in_result = bytes2str(value)
|
||||
free(value)
|
||||
try:
|
||||
value_in_result = <bytes> value
|
||||
finally:
|
||||
free(value)
|
||||
result[self.elements_names[i]] = value_in_result
|
||||
if all_NA and (value_in_result is not None) :
|
||||
all_NA = False
|
||||
@ -79,10 +109,19 @@ cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
|
||||
|
||||
cpdef set_item(self, index_t line_nb, str element_name, object value):
|
||||
cdef bytes value_b
|
||||
|
||||
if value is None :
|
||||
value_b = OBISeq_NA
|
||||
else :
|
||||
elif isinstance(value, bytes) :
|
||||
value_b = value
|
||||
elif isinstance(value, str) :
|
||||
value_b = str2bytes(value)
|
||||
if obi_column_set_obiseq_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
|
||||
else:
|
||||
raise TypeError('Sequence value must be of type Bytes, Str or None')
|
||||
|
||||
if obi_column_set_obiseq_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
# cpdef align(self, ): # TODO
|
||||
# raise Exception("Columns with multiple sequences per line can't be aligned") # TODO discuss
|
||||
|
||||
|
||||
@ -10,6 +10,8 @@
|
||||
../../../src/encode.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obi_align.h
|
||||
../../../src/obi_align.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/obiblob_indexer.h
|
||||
@ -21,8 +23,22 @@
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.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_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obidmscolumndir.h
|
||||
@ -35,17 +51,9 @@
|
||||
../../../src/obitypes.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.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
|
||||
|
||||
@ -9,18 +9,16 @@ from .capi.obitypes cimport OBIStr_NA, const_char_p
|
||||
|
||||
from obitools3.utils cimport str2bytes, bytes2str
|
||||
|
||||
from libc.string cimport strcmp
|
||||
|
||||
|
||||
cdef class OBIDMS_column_str(OBIDMS_column):
|
||||
|
||||
cpdef object get_line(self, index_t line_nb):
|
||||
cdef const_char_p value
|
||||
cdef object result
|
||||
value = obi_column_get_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0)
|
||||
value = obi_column_get_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if strcmp(value, OBIStr_NA) == 0 :
|
||||
if value == OBIStr_NA :
|
||||
result = None
|
||||
else :
|
||||
result = bytes2str(value)
|
||||
@ -28,13 +26,12 @@ cdef class OBIDMS_column_str(OBIDMS_column):
|
||||
return result
|
||||
|
||||
cpdef set_line(self, index_t line_nb, object value):
|
||||
cdef bytes value_b
|
||||
if value is None :
|
||||
value_b = OBIStr_NA
|
||||
if obi_column_set_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBIStr_NA) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
else :
|
||||
value_b = str2bytes(value)
|
||||
if obi_column_set_obistr_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, value_b) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
if obi_column_set_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
|
||||
cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
|
||||
@ -42,10 +39,10 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
|
||||
cpdef object get_item(self, index_t line_nb, str element_name):
|
||||
cdef const_char_p value
|
||||
cdef object result
|
||||
value = obi_column_get_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
value = obi_column_get_obistr_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name))
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb, element_name)
|
||||
if strcmp(value, OBIStr_NA) == 0 :
|
||||
if value == OBIStr_NA :
|
||||
result = None
|
||||
else :
|
||||
result = bytes2str(value)
|
||||
@ -61,10 +58,10 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
|
||||
result = {}
|
||||
all_NA = True
|
||||
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 = obi_column_get_obistr_with_elt_idx_in_view(self.view.pointer, (self.pointer)[0], line_nb, i)
|
||||
if obi_errno > 0 :
|
||||
raise IndexError(line_nb)
|
||||
if strcmp(value, OBIStr_NA) == 0 :
|
||||
if value == OBIStr_NA :
|
||||
value_in_result = None
|
||||
else :
|
||||
value_in_result = bytes2str(value)
|
||||
@ -82,6 +79,6 @@ cdef class OBIDMS_column_multi_elts_str(OBIDMS_column_multi_elts):
|
||||
value_b = OBIStr_NA
|
||||
else :
|
||||
value_b = str2bytes(value)
|
||||
if obi_column_set_obistr_with_elt_name_in_view(self.view, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
|
||||
if obi_column_set_obistr_with_elt_name_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
|
||||
raise Exception("Problem setting a value in a column")
|
||||
|
||||
|
||||
@ -10,6 +10,8 @@
|
||||
../../../src/encode.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obi_align.h
|
||||
../../../src/obi_align.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/obiblob_indexer.h
|
||||
@ -21,8 +23,22 @@
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.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_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obidmscolumndir.h
|
||||
@ -35,17 +51,9 @@
|
||||
../../../src/obitypes.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.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
|
||||
|
||||
@ -4,27 +4,35 @@ from ._obidms cimport OBIView_line
|
||||
|
||||
|
||||
cdef class OBI_Seq(dict) :
|
||||
cdef str id
|
||||
cdef str definition
|
||||
cdef str sequence
|
||||
cdef object id
|
||||
cdef object definition
|
||||
cdef object sequence
|
||||
|
||||
cpdef set_id(self, str id)
|
||||
cpdef get_id(self)
|
||||
cpdef set_definition(self, str definition)
|
||||
cpdef get_definition(self)
|
||||
cpdef get_sequence(self)
|
||||
cpdef set_id(self, object id)
|
||||
cpdef object get_id(self)
|
||||
cpdef set_definition(self, object definition)
|
||||
cpdef object get_definition(self)
|
||||
cpdef object get_sequence(self)
|
||||
|
||||
|
||||
cdef class OBI_Nuc_Seq(OBI_Seq) :
|
||||
#cpdef str reverse_complement(self)
|
||||
cpdef set_sequence(self, str sequence)
|
||||
cdef object quality
|
||||
|
||||
#cpdef object reverse_complement(self)
|
||||
cpdef set_sequence(self, object sequence)
|
||||
cpdef set_quality(self, object quality)
|
||||
cpdef object get_quality(self)
|
||||
|
||||
|
||||
cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
|
||||
cpdef set_id(self, str id)
|
||||
cpdef get_id(self)
|
||||
cpdef set_definition(self, str definition)
|
||||
cpdef get_definition(self)
|
||||
cpdef set_sequence(self, str sequence)
|
||||
cpdef get_sequence(self)
|
||||
# cpdef str reverse_complement(self)
|
||||
cpdef set_id(self, object id)
|
||||
cpdef object get_id(self)
|
||||
cpdef set_definition(self, object definition)
|
||||
cpdef object get_definition(self)
|
||||
cpdef set_sequence(self, object sequence)
|
||||
cpdef object get_sequence(self)
|
||||
cpdef set_quality(self, object quality)
|
||||
cpdef object get_quality(self)
|
||||
cpdef object get_str_quality(self)
|
||||
|
||||
# cpdef object reverse_complement(self)
|
||||
|
||||
@ -4,30 +4,31 @@ from obitools3.utils cimport bytes2str, str2bytes
|
||||
|
||||
from .capi.obiview cimport NUC_SEQUENCE_COLUMN, \
|
||||
ID_COLUMN, \
|
||||
DEFINITION_COLUMN
|
||||
DEFINITION_COLUMN, \
|
||||
QUALITY_COLUMN
|
||||
|
||||
cdef class OBI_Seq(dict) :
|
||||
|
||||
def __init__(self, str id, str seq, str definition=None) :
|
||||
def __init__(self, object id, object seq, object definition=None) :
|
||||
self.set_id(id)
|
||||
self.set_sequence(seq)
|
||||
if definition is not None :
|
||||
self.set_definition(definition)
|
||||
|
||||
cpdef set_id(self, str id) :
|
||||
cpdef set_id(self, object id) :
|
||||
self.id = id
|
||||
self[bytes2str(ID_COLUMN)] = id
|
||||
|
||||
cpdef get_id(self) :
|
||||
return self.id
|
||||
|
||||
cpdef set_definition(self, str definition) :
|
||||
cpdef set_definition(self, object definition) :
|
||||
self.definition = definition
|
||||
self[bytes2str(DEFINITION_COLUMN)] = definition
|
||||
|
||||
cpdef get_definition(self) :
|
||||
return self.definition
|
||||
|
||||
|
||||
cpdef get_sequence(self) :
|
||||
return self.sequence
|
||||
|
||||
@ -37,34 +38,55 @@ cdef class OBI_Seq(dict) :
|
||||
|
||||
cdef class OBI_Nuc_Seq(OBI_Seq) :
|
||||
|
||||
cpdef set_sequence(self, str sequence) :
|
||||
cpdef set_sequence(self, object sequence) :
|
||||
self.sequence = sequence
|
||||
self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
|
||||
|
||||
cpdef set_quality(self, object quality) :
|
||||
self.quality = quality
|
||||
self[bytes2str(QUALITY_COLUMN)] = quality
|
||||
|
||||
cpdef get_quality(self) :
|
||||
return self.quality
|
||||
|
||||
# cpdef str reverse_complement(self) : TODO in C ?
|
||||
# pass
|
||||
|
||||
|
||||
cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
|
||||
|
||||
cpdef set_id(self, str id) :
|
||||
# TODO store the str version of column name macros
|
||||
|
||||
cpdef set_id(self, object id) :
|
||||
self[bytes2str(ID_COLUMN)] = id
|
||||
|
||||
cpdef get_id(self) :
|
||||
cpdef object get_id(self) :
|
||||
return self[bytes2str(ID_COLUMN)]
|
||||
|
||||
cpdef set_definition(self, str definition) :
|
||||
cpdef set_definition(self, object definition) :
|
||||
self[bytes2str(DEFINITION_COLUMN)] = definition
|
||||
|
||||
cpdef get_definition(self) :
|
||||
cpdef object get_definition(self) :
|
||||
return self[bytes2str(DEFINITION_COLUMN)]
|
||||
|
||||
cpdef set_sequence(self, str sequence) :
|
||||
cpdef set_sequence(self, object sequence) :
|
||||
self[bytes2str(NUC_SEQUENCE_COLUMN)] = sequence
|
||||
|
||||
cpdef get_sequence(self) :
|
||||
cpdef object get_sequence(self) :
|
||||
return self[bytes2str(NUC_SEQUENCE_COLUMN)]
|
||||
|
||||
cpdef set_quality(self, object quality) :
|
||||
if (type(quality) == list) or (quality is None) :
|
||||
self[bytes2str(QUALITY_COLUMN)] = quality
|
||||
else : # Quality is in str form
|
||||
(((self.view).columns)[bytes2str(QUALITY_COLUMN)]).set_str_line(self.index, quality)
|
||||
|
||||
cpdef object get_quality(self) :
|
||||
return self[bytes2str(QUALITY_COLUMN)]
|
||||
|
||||
cpdef object get_str_quality(self) :
|
||||
return ((self.view).columns)[bytes2str(QUALITY_COLUMN)].get_str_line(self.index)
|
||||
|
||||
# def __str__(self) :
|
||||
# return self[bytes2str(NUC_SEQUENCE_COLUMN)] # or not
|
||||
|
||||
|
||||
@ -10,6 +10,8 @@
|
||||
../../../src/encode.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obi_align.h
|
||||
../../../src/obi_align.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/obiblob_indexer.h
|
||||
@ -21,8 +23,22 @@
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.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_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obidmscolumndir.h
|
||||
@ -35,17 +51,9 @@
|
||||
../../../src/obitypes.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.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
|
||||
|
||||
10
python/obitools3/obidms/capi/obialign.pxd
Normal file
10
python/obitools3/obidms/capi/obialign.pxd
Normal file
@ -0,0 +1,10 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from ..capi.obiview cimport Obiview_p
|
||||
from ..capi.obidmscolumn cimport OBIDMS_column_p
|
||||
|
||||
|
||||
cdef extern from "obi_align.h" nogil:
|
||||
|
||||
int obi_align_one_column(Obiview_p seq_view, OBIDMS_column_p seq_column, Obiview_p score_view, OBIDMS_column_p score_column, double threshold, bint normalize, int reference, bint similarity_mode)
|
||||
|
||||
@ -11,6 +11,8 @@ from ..capi.obitypes cimport const_char_p, \
|
||||
index_t, \
|
||||
time_t
|
||||
|
||||
from libc.stdint cimport uint8_t
|
||||
|
||||
|
||||
cdef extern from "obidmscolumn.h" nogil:
|
||||
|
||||
@ -194,3 +196,46 @@ cdef extern from "obidmscolumn_seq.h" nogil:
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
|
||||
cdef extern from "obidmscolumn_qual.h" nogil:
|
||||
|
||||
int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
const_char_p value)
|
||||
|
||||
int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
const_char_p value)
|
||||
|
||||
int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
const uint8_t* value,
|
||||
int value_length)
|
||||
|
||||
int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
const uint8_t* value,
|
||||
int value_length)
|
||||
|
||||
char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name)
|
||||
|
||||
char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
const uint8_t* obi_column_get_obiqual_int_with_elt_name(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const_char_p element_name,
|
||||
int* value_length)
|
||||
|
||||
const uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
int* value_length)
|
||||
|
||||
|
||||
@ -1,7 +1,8 @@
|
||||
#cython: language_level=3
|
||||
|
||||
|
||||
from libc.stdint cimport int32_t, int64_t
|
||||
from libc.stdint cimport int32_t, int64_t, uint8_t
|
||||
|
||||
from posix.types cimport time_t
|
||||
|
||||
|
||||
@ -21,6 +22,7 @@ cdef extern from "obitypes.h" nogil:
|
||||
OBI_FLOAT,
|
||||
OBI_BOOL,
|
||||
OBI_CHAR,
|
||||
OBI_QUAL,
|
||||
OBI_STR,
|
||||
OBI_SEQ,
|
||||
OBI_IDX
|
||||
@ -46,5 +48,8 @@ cdef extern from "obitypes.h" nogil:
|
||||
extern obibool_t OBIBool_NA
|
||||
extern const_char_p OBISeq_NA
|
||||
extern const_char_p OBIStr_NA
|
||||
extern const_char_p OBIQual_char_NA
|
||||
extern uint8_t* OBIQual_int_NA
|
||||
|
||||
const_char_p name_data_type(int data_type)
|
||||
|
||||
|
||||
@ -12,6 +12,8 @@ from .obitypes cimport const_char_p, \
|
||||
from ..capi.obidms cimport OBIDMS_p
|
||||
from ..capi.obidmscolumn cimport OBIDMS_column_p
|
||||
|
||||
from libc.stdint cimport uint8_t
|
||||
|
||||
|
||||
cdef extern from "obiview.h" nogil:
|
||||
|
||||
@ -19,21 +21,7 @@ cdef extern from "obiview.h" nogil:
|
||||
extern const_char_p NUC_SEQUENCE_COLUMN
|
||||
extern const_char_p ID_COLUMN
|
||||
extern const_char_p DEFINITION_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
|
||||
extern const_char_p QUALITY_COLUMN
|
||||
|
||||
|
||||
struct Column_reference_t :
|
||||
@ -44,7 +32,6 @@ cdef extern from "obiview.h" nogil:
|
||||
|
||||
|
||||
struct Obiview_infos_t :
|
||||
int view_number
|
||||
time_t creation_date
|
||||
const_char_p name
|
||||
const_char_p created_from
|
||||
@ -59,19 +46,15 @@ cdef extern from "obiview.h" nogil:
|
||||
ctypedef Obiview_infos_t* Obiview_infos_p
|
||||
|
||||
|
||||
struct Obiviews_header_t :
|
||||
size_t header_size
|
||||
size_t views_size
|
||||
int view_count
|
||||
|
||||
ctypedef Obiviews_header_t* Obiviews_header_p
|
||||
struct Obiview_t :
|
||||
Obiview_infos_p infos
|
||||
OBIDMS_p dms
|
||||
bint read_only
|
||||
OBIDMS_column_p line_selection
|
||||
OBIDMS_column_p new_line_selection
|
||||
OBIDMS_column_p columns
|
||||
|
||||
|
||||
struct Obiviews_infos_all_t :
|
||||
Obiviews_header_p header
|
||||
Obiview_infos_p view_infos
|
||||
|
||||
ctypedef Obiviews_infos_all_t* Obiviews_infos_all_p
|
||||
ctypedef Obiview_t* Obiview_p
|
||||
|
||||
|
||||
Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const_char_p view_name, Obiview_p view_to_clone, index_t* line_selection, const_char_p comments)
|
||||
@ -82,6 +65,10 @@ cdef extern from "obiview.h" nogil:
|
||||
|
||||
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const_char_p view_name, const_char_p view_to_clone_name, index_t* line_selection, const_char_p comments)
|
||||
|
||||
Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name)
|
||||
|
||||
int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos)
|
||||
|
||||
Obiview_p obi_open_view(OBIDMS_p dms, const_char_p view_name)
|
||||
|
||||
int obi_view_add_column(Obiview_p view,
|
||||
@ -110,10 +97,6 @@ cdef extern from "obiview.h" nogil:
|
||||
int obi_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,
|
||||
@ -203,6 +186,54 @@ cdef extern from "obiview.h" nogil:
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
int obi_column_set_obiqual_char_with_elt_idx_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
const char* value)
|
||||
|
||||
int obi_column_set_obiqual_int_with_elt_idx_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
const uint8_t* value,
|
||||
int value_length)
|
||||
|
||||
char* obi_column_get_obiqual_char_with_elt_idx_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx)
|
||||
|
||||
const uint8_t* obi_column_get_obiqual_int_with_elt_idx_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
index_t element_idx,
|
||||
int* value_length)
|
||||
|
||||
int obi_column_set_obiqual_char_with_elt_name_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const char* element_name,
|
||||
const char* value)
|
||||
|
||||
int obi_column_set_obiqual_int_with_elt_name_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const char* element_name,
|
||||
const uint8_t* value,
|
||||
int value_length)
|
||||
|
||||
char* obi_column_get_obiqual_char_with_elt_name_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const char* element_name)
|
||||
|
||||
const uint8_t* obi_column_get_obiqual_int_with_elt_name_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
const char* element_name,
|
||||
int* value_length)
|
||||
|
||||
int obi_column_set_obistr_with_elt_name_in_view(Obiview_p view,
|
||||
OBIDMS_column_p column,
|
||||
index_t line_nb,
|
||||
|
||||
@ -36,7 +36,7 @@ if __name__ == '__main__':
|
||||
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")
|
||||
|
||||
@ -1,5 +1,6 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from ..utils cimport str2bytes
|
||||
from .header cimport parseHeader
|
||||
from ..files.universalopener cimport uopen
|
||||
from ..files.linebuffer cimport LineBuffer
|
||||
|
||||
@ -6,12 +6,15 @@ 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
|
||||
cdef bytes sequence
|
||||
cdef bytes quality
|
||||
|
||||
if isinstance(lineiterator,(str,bytes)):
|
||||
lineiterator=uopen(lineiterator)
|
||||
@ -28,10 +31,15 @@ def fastaIterator(lineiterator, int buffersize=100000000):
|
||||
ident,tags,definition = parseHeader(line)
|
||||
s = []
|
||||
line = next(i)
|
||||
while line[0]!='>':
|
||||
s.append(line[0:-1])
|
||||
line = next(i)
|
||||
sequence = "".join(s)
|
||||
|
||||
try:
|
||||
while line[0]!='>':
|
||||
s.append(str2bytes(line)[0:-1])
|
||||
line = next(i)
|
||||
except StopIteration:
|
||||
pass
|
||||
|
||||
sequence = b"".join(s)
|
||||
quality = None
|
||||
|
||||
yield { "id" : ident,
|
||||
@ -42,5 +50,6 @@ def fastaIterator(lineiterator, int buffersize=100000000):
|
||||
"annotation" : {}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@ -1,5 +1,7 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from ..utils cimport str2bytes
|
||||
|
||||
from .header cimport parseHeader
|
||||
from ..files.universalopener cimport uopen
|
||||
from ..files.linebuffer cimport LineBuffer
|
||||
|
||||
@ -6,13 +6,13 @@ 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
|
||||
cdef bytes sequence
|
||||
cdef bytes quality
|
||||
|
||||
if isinstance(lineiterator,(str,bytes)):
|
||||
lineiterator=uopen(lineiterator)
|
||||
@ -25,9 +25,9 @@ def fastqIterator(lineiterator, int buffersize=100000000):
|
||||
i = iter(lb)
|
||||
for line in i:
|
||||
ident,tags,definition = parseHeader(line)
|
||||
sequence = next(i)[0:-1]
|
||||
sequence = str2bytes(next(i)[0:-1])
|
||||
next(i)
|
||||
quality = next(i)[0:-1]
|
||||
quality = str2bytes(next(i)[0:-1])
|
||||
|
||||
yield { "id" : ident,
|
||||
"definition" : definition,
|
||||
@ -38,4 +38,3 @@ def fastqIterator(lineiterator, int buffersize=100000000):
|
||||
}
|
||||
|
||||
|
||||
|
||||
@ -30,20 +30,27 @@ __re_dict__ = re.compile("""^\{\ *
|
||||
)
|
||||
)*\ *\}$""", re.VERBOSE)
|
||||
|
||||
__re_val__ = re.compile("""(("[^"]*"|'[^']*') *: *([^,}]+|"[^"]*"|'[^']*') *[,}] *)""")
|
||||
|
||||
cdef object __etag__(str x):
|
||||
cdef list elements
|
||||
cdef tuple i
|
||||
|
||||
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=='None':
|
||||
v=None
|
||||
elif x=='False':
|
||||
v=False
|
||||
elif x=='True':
|
||||
v=True
|
||||
elif __re_dict__.match(x):
|
||||
v=eval(x)
|
||||
elements=__re_val__.findall(x)
|
||||
v=dict([(i[1][1:-1],__etag__(i[2])) for i in elements])
|
||||
else:
|
||||
v=x
|
||||
return v
|
||||
@ -56,7 +63,7 @@ cpdef tuple parseHeader(str header):
|
||||
cdef str second
|
||||
|
||||
m=header[1:-1].split(maxsplit=1)
|
||||
|
||||
|
||||
ident=m[0]
|
||||
|
||||
if len(m)==1:
|
||||
@ -75,4 +82,4 @@ cpdef tuple parseHeader(str header):
|
||||
|
||||
return ident,tags,definition
|
||||
|
||||
|
||||
|
||||
|
||||
@ -1,7 +1,5 @@
|
||||
#cython: language_level=3
|
||||
|
||||
import sys
|
||||
import io
|
||||
|
||||
cdef bytes str2bytes(str string):
|
||||
"""
|
||||
|
||||
961
src/_sse.h
Normal file
961
src/_sse.h
Normal file
@ -0,0 +1,961 @@
|
||||
#ifndef _SSE_H_
|
||||
#define _SSE_H_
|
||||
|
||||
#include <string.h>
|
||||
|
||||
#include <inttypes.h>
|
||||
#ifdef __SSE2__
|
||||
#include <xmmintrin.h>
|
||||
#else
|
||||
typedef long long __m128i __attribute__ ((__vector_size__ (16), __may_alias__));
|
||||
#endif /* __SSE2__ */
|
||||
|
||||
#ifndef MAX
|
||||
#define MAX(x,y) (((x)>(y)) ? (x):(y))
|
||||
#define MIN(x,y) (((x)<(y)) ? (x):(y))
|
||||
#endif
|
||||
|
||||
#define ALIGN __attribute__((aligned(16)))
|
||||
typedef __m128i vUInt8;
|
||||
typedef __m128i vInt8;
|
||||
|
||||
typedef __m128i vUInt16;
|
||||
typedef __m128i vInt16;
|
||||
|
||||
typedef __m128i vUInt64;
|
||||
|
||||
typedef union
|
||||
{
|
||||
__m128i i;
|
||||
int64_t s64[ 2];
|
||||
int16_t s16[ 8];
|
||||
int8_t s8 [16];
|
||||
uint8_t u8 [16];
|
||||
uint16_t u16[8 ];
|
||||
uint32_t u32[4 ];
|
||||
uint64_t u64[2 ];
|
||||
} um128;
|
||||
|
||||
typedef union
|
||||
{
|
||||
vUInt8 m;
|
||||
uint8_t c[16];
|
||||
} uchar_v;
|
||||
|
||||
typedef union
|
||||
{
|
||||
vUInt16 m;
|
||||
uint16_t c[8];
|
||||
} ushort_v;
|
||||
|
||||
typedef union
|
||||
{
|
||||
vUInt64 m;
|
||||
uint64_t c[2];
|
||||
} uint64_v;
|
||||
|
||||
|
||||
#ifdef __SSE2__
|
||||
|
||||
static inline int8_t _s2_extract_epi8(__m128i r, const int p)
|
||||
{
|
||||
#define ACTIONP(r,x) return _mm_extract_epi16(r,x) & 0xFF
|
||||
#define ACTIONI(r,x) return _mm_extract_epi16(r,x) >> 8
|
||||
switch (p) {
|
||||
case 0: ACTIONP(r,0);
|
||||
case 1: ACTIONI(r,0);
|
||||
case 2: ACTIONP(r,1);
|
||||
case 3: ACTIONI(r,1);
|
||||
case 4: ACTIONP(r,2);
|
||||
case 5: ACTIONI(r,2);
|
||||
case 6: ACTIONP(r,3);
|
||||
case 7: ACTIONI(r,3);
|
||||
case 8: ACTIONP(r,4);
|
||||
case 9: ACTIONI(r,4);
|
||||
case 10: ACTIONP(r,5);
|
||||
case 11: ACTIONI(r,5);
|
||||
case 12: ACTIONP(r,6);
|
||||
case 13: ACTIONI(r,6);
|
||||
case 14: ACTIONP(r,7);
|
||||
case 15: ACTIONI(r,7);
|
||||
}
|
||||
#undef ACTIONP
|
||||
#undef ACTIONI
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
static inline __m128i _s2_max_epi8(__m128i a, __m128i b)
|
||||
{
|
||||
__m128i mask = _mm_cmpgt_epi8( a, b );
|
||||
a = _mm_and_si128 (a,mask );
|
||||
b = _mm_andnot_si128(mask,b);
|
||||
return _mm_or_si128(a,b);
|
||||
}
|
||||
|
||||
static inline __m128i _s2_min_epi8(__m128i a, __m128i b)
|
||||
{
|
||||
__m128i mask = _mm_cmplt_epi8( a, b );
|
||||
a = _mm_and_si128 (a,mask );
|
||||
b = _mm_andnot_si128(mask,b);
|
||||
return _mm_or_si128(a,b);
|
||||
}
|
||||
|
||||
static inline __m128i _s2_insert_epi8(__m128i r, int b, const int p)
|
||||
{
|
||||
#define ACTIONP(r,x) return _mm_insert_epi16(r,(_mm_extract_epi16(r,x) & 0xFF00) | (b & 0x00FF),x)
|
||||
#define ACTIONI(r,x) return _mm_insert_epi16(r,(_mm_extract_epi16(r,x) & 0x00FF) | ((b << 8)& 0xFF00),x)
|
||||
switch (p) {
|
||||
case 0: ACTIONP(r,0);
|
||||
case 1: ACTIONI(r,0);
|
||||
case 2: ACTIONP(r,1);
|
||||
case 3: ACTIONI(r,1);
|
||||
case 4: ACTIONP(r,2);
|
||||
case 5: ACTIONI(r,2);
|
||||
case 6: ACTIONP(r,3);
|
||||
case 7: ACTIONI(r,3);
|
||||
case 8: ACTIONP(r,4);
|
||||
case 9: ACTIONI(r,4);
|
||||
case 10: ACTIONP(r,5);
|
||||
case 11: ACTIONI(r,5);
|
||||
case 12: ACTIONP(r,6);
|
||||
case 13: ACTIONI(r,6);
|
||||
case 14: ACTIONP(r,7);
|
||||
case 15: ACTIONI(r,7);
|
||||
}
|
||||
#undef ACTIONP
|
||||
#undef ACTIONI
|
||||
|
||||
return _mm_setzero_si128();
|
||||
}
|
||||
|
||||
// Fill a SSE Register with 16 time the same 8bits integer value
|
||||
#define _MM_SET1_EPI8(x) _mm_set1_epi8(x)
|
||||
#define _MM_INSERT_EPI8(r,x,i) _s2_insert_epi8((r),(x),(i))
|
||||
#define _MM_CMPEQ_EPI8(x,y) _mm_cmpeq_epi8((x),(y))
|
||||
#define _MM_CMPGT_EPI8(x,y) _mm_cmpgt_epi8((x),(y))
|
||||
#define _MM_CMPLT_EPI8(x,y) _mm_cmplt_epi8((x),(y))
|
||||
#define _MM_MAX_EPI8(x,y) _s2_max_epi8((x),(y))
|
||||
#define _MM_MIN_EPI8(x,y) _s2_min_epi8((x),(y))
|
||||
#define _MM_ADD_EPI8(x,y) _mm_add_epi8((x),(y))
|
||||
#define _MM_SUB_EPI8(x,y) _mm_sub_epi8((x),(y))
|
||||
#define _MM_EXTRACT_EPI8(r,p) _s2_extract_epi8((r),(p))
|
||||
|
||||
#define _MM_MIN_EPU8(x,y) _mm_min_epu8((x),(y))
|
||||
|
||||
// Fill a SSE Register with 8 time the same 16bits integer value
|
||||
#define _MM_SET1_EPI16(x) _mm_set1_epi16(x)
|
||||
|
||||
#define _MM_INSERT_EPI16(r,x,i) _mm_insert_epi16((r),(x),(i))
|
||||
#define _MM_CMPEQ_EPI16(x,y) _mm_cmpeq_epi16((x),(y))
|
||||
#define _MM_CMPGT_EPI16(x,y) _mm_cmpgt_epi16((x),(y))
|
||||
#define _MM_CMPGT_EPU16(x,y) _mm_cmpgt_epu16((x),(y)) // n'existe pas ??
|
||||
#define _MM_CMPLT_EPI16(x,y) _mm_cmplt_epi16((x),(y))
|
||||
#define _MM_MAX_EPI16(x,y) _mm_max_epi16((x),(y))
|
||||
#define _MM_MIN_EPI16(x,y) _mm_min_epi16((x),(y))
|
||||
#define _MM_ADD_EPI16(x,y) _mm_add_epi16((x),(y))
|
||||
#define _MM_SUB_EPI16(x,y) _mm_sub_epi16((x),(y))
|
||||
#define _MM_EXTRACT_EPI16(r,p) _mm_extract_epi16((r),(p))
|
||||
#define _MM_UNPACKLO_EPI8(a,b) _mm_unpacklo_epi8((a),(b))
|
||||
#define _MM_UNPACKHI_EPI8(a,b) _mm_unpackhi_epi8((a),(b))
|
||||
#define _MM_ADDS_EPU16(x,y) _mm_adds_epu16((x),(y))
|
||||
|
||||
// Multiplication
|
||||
#define _MM_MULLO_EPI16(x,y) _mm_mullo_epi16((x), (y))
|
||||
|
||||
#define _MM_SRLI_EPI64(r,x) _mm_srli_epi64((r),(x))
|
||||
#define _MM_SLLI_EPI64(r,x) _mm_slli_epi64((r),(x))
|
||||
|
||||
// Set a SSE Register to 0
|
||||
#define _MM_SETZERO_SI128() _mm_setzero_si128()
|
||||
|
||||
#define _MM_AND_SI128(x,y) _mm_and_si128((x),(y))
|
||||
#define _MM_ANDNOT_SI128(x,y) _mm_andnot_si128((x),(y))
|
||||
#define _MM_OR_SI128(x,y) _mm_or_si128((x),(y))
|
||||
#define _MM_XOR_SI128(x,y) _mm_xor_si128((x),(y))
|
||||
#define _MM_SLLI_SI128(r,s) _mm_slli_si128((r),(s))
|
||||
#define _MM_SRLI_SI128(r,s) _mm_srli_si128((r),(s))
|
||||
|
||||
// Load a SSE register from an unaligned address
|
||||
#define _MM_LOADU_SI128(x) _mm_loadu_si128(x)
|
||||
|
||||
// Load a SSE register from an aligned address (/!\ not defined when SSE not available)
|
||||
#define _MM_LOAD_SI128(x) _mm_load_si128(x)
|
||||
|
||||
// #define _MM_UNPACKLO_EPI8(x,y) _mm_unpacklo_epi8((x),(y))
|
||||
|
||||
#else /* __SSE2__ Not defined */
|
||||
|
||||
static inline __m128i _em_set1_epi8(int x)
|
||||
{
|
||||
um128 a;
|
||||
|
||||
x&=0xFF;
|
||||
a.s8[0]=x;
|
||||
a.s8[1]=x;
|
||||
a.u16[1]=a.u16[0];
|
||||
a.u32[1]=a.u32[0];
|
||||
a.u64[1]=a.u64[0];
|
||||
|
||||
return a.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_insert_epi8(__m128i r, int x, const int i)
|
||||
{
|
||||
um128 a;
|
||||
a.i=r;
|
||||
a.s8[i]=x & 0xFF;
|
||||
return a.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_cmpeq_epi8(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s8[z]=(x.s8[z]==y.s8[z]) ? 0xFF:0
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
R(8);
|
||||
R(9);
|
||||
R(10);
|
||||
R(11);
|
||||
R(12);
|
||||
R(13);
|
||||
R(14);
|
||||
R(15);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_cmpgt_epi8(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s8[z]=(x.s8[z]>y.s8[z]) ? 0xFF:0
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
R(8);
|
||||
R(9);
|
||||
R(10);
|
||||
R(11);
|
||||
R(12);
|
||||
R(13);
|
||||
R(14);
|
||||
R(15);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_cmplt_epi8(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s8[z]=(x.s8[z]<y.s8[z]) ? 0xFF:0
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
R(8);
|
||||
R(9);
|
||||
R(10);
|
||||
R(11);
|
||||
R(12);
|
||||
R(13);
|
||||
R(14);
|
||||
R(15);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_max_epi8(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s8[z]=MAX(x.s8[z],y.s8[z])
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
R(8);
|
||||
R(9);
|
||||
R(10);
|
||||
R(11);
|
||||
R(12);
|
||||
R(13);
|
||||
R(14);
|
||||
R(15);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_min_epi8(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s8[z]=MIN(x.s8[z],y.s8[z])
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
R(8);
|
||||
R(9);
|
||||
R(10);
|
||||
R(11);
|
||||
R(12);
|
||||
R(13);
|
||||
R(14);
|
||||
R(15);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_add_epi8(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s8[z]=x.s8[z]+y.s8[z]
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
R(8);
|
||||
R(9);
|
||||
R(10);
|
||||
R(11);
|
||||
R(12);
|
||||
R(13);
|
||||
R(14);
|
||||
R(15);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_sub_epi8(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s8[z]=x.s8[z]+y.s8[z]
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
R(8);
|
||||
R(9);
|
||||
R(10);
|
||||
R(11);
|
||||
R(12);
|
||||
R(13);
|
||||
R(14);
|
||||
R(15);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
|
||||
static inline int _em_extract_epi8(__m128i r, const int i)
|
||||
{
|
||||
um128 a;
|
||||
|
||||
a.i=r;
|
||||
|
||||
return a.s8[i] & 0xFF;
|
||||
}
|
||||
|
||||
static inline __m128i _em_min_epu8(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.u8[z]=MIN(x.u8[z],y.u8[z])
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
R(8);
|
||||
R(9);
|
||||
R(10);
|
||||
R(11);
|
||||
R(12);
|
||||
R(13);
|
||||
R(14);
|
||||
R(15);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_set1_epi16(int x)
|
||||
{
|
||||
um128 a;
|
||||
|
||||
x&=0xFFFF;
|
||||
a.s16[0]=x;
|
||||
a.s16[1]=x;
|
||||
a.u32[1]=a.u32[0];
|
||||
a.u64[1]=a.u64[0];
|
||||
|
||||
return a.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_insert_epi16(__m128i r, int x, const int i)
|
||||
{
|
||||
um128 a;
|
||||
a.i=r;
|
||||
a.s16[i]=x & 0xFFFF;
|
||||
return a.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_cmpeq_epi16(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s16[z]=(x.s16[z]==y.s16[z]) ? 0xFFFF:0
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_cmpgt_epi16(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s16[z]=(x.s16[z]>y.s16[z]) ? 0xFFFF:0
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_cmplt_epi16(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s16[z]=(x.s16[z]<y.s16[z]) ? 0xFFFF:0
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_max_epi16(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
|
||||
#define R(z) r.s16[z]=MAX(x.s16[z],y.s16[z])
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_min_epi16(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
|
||||
#define R(z) r.s16[z]=MIN(x.s16[z],y.s16[z])
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_add_epi16(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s16[z]=x.s16[z]+y.s16[z]
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_sub_epi16(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s16[z]=x.s16[z]+y.s16[z]
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline int _em_extract_epi16(__m128i r, const int i)
|
||||
{
|
||||
um128 a;
|
||||
a.i=r;
|
||||
return a.s16[i] & 0xFFFF;
|
||||
}
|
||||
|
||||
static inline __m128i _em_unpacklo_epi8(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s16[z]=(((int16_t)(y.s8[z])) << 8) | (int16_t)(x.s8[z])
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_unpackhi_epi8(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.s16[z]=(((int16_t)(y.s8[z+8])) << 8) | (int16_t)(x.s8[z+8])
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_adds_epu16(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
|
||||
#define R(z) r.u16[z]=x.u16[z]+y.u16[z]
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_srli_epi64(__m128i a, int b)
|
||||
{
|
||||
um128 x;
|
||||
|
||||
x.i=a;
|
||||
|
||||
x.s64[0]>>=b;
|
||||
x.s64[1]>>=b;
|
||||
|
||||
return x.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_slli_epi64(__m128i a, int b)
|
||||
{
|
||||
um128 x;
|
||||
|
||||
x.i=a;
|
||||
|
||||
x.s64[0]<<=b;
|
||||
x.s64[1]<<=b;
|
||||
|
||||
return x.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_setzero_si128()
|
||||
{
|
||||
um128 x;
|
||||
|
||||
x.s64[0]=x.s64[1]=0;
|
||||
|
||||
return x.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_and_si128(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
|
||||
#define R(z) r.u64[z]=x.u64[z] & y.u64[z]
|
||||
R(0);
|
||||
R(1);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_andnot_si128(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
|
||||
#define R(z) r.u64[z]=(~x.u64[z]) & y.u64[z]
|
||||
R(0);
|
||||
R(1);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_or_si128(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.u64[z]=x.u64[z] | y.u64[z]
|
||||
R(0);
|
||||
R(1);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_xor_si128(__m128i a, __m128i b)
|
||||
{
|
||||
um128 x;
|
||||
um128 y;
|
||||
um128 r;
|
||||
|
||||
x.i=a;
|
||||
y.i=b;
|
||||
|
||||
#define R(z) r.u64[z]=x.u64[z] ^ y.u64[z]
|
||||
R(0);
|
||||
R(1);
|
||||
#undef R
|
||||
|
||||
return r.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_slli_si128(__m128i a, int b)
|
||||
{
|
||||
um128 x;
|
||||
|
||||
x.i=a;
|
||||
|
||||
#define R(z) x.u8[z]=(z>=b) ? x.u8[z-b]:0
|
||||
R(15);
|
||||
R(14);
|
||||
R(13);
|
||||
R(12);
|
||||
R(11);
|
||||
R(10);
|
||||
R(9);
|
||||
R(8);
|
||||
R(7);
|
||||
R(6);
|
||||
R(5);
|
||||
R(4);
|
||||
R(3);
|
||||
R(2);
|
||||
R(1);
|
||||
R(0);
|
||||
#undef R
|
||||
|
||||
return x.i;
|
||||
}
|
||||
|
||||
static inline __m128i _em_srli_si128(__m128i a, int b)
|
||||
{
|
||||
um128 x;
|
||||
|
||||
x.i=a;
|
||||
|
||||
#define R(z) x.u8[z]=((b+z) > 15) ? 0:x.u8[z+b]
|
||||
R(0);
|
||||
R(1);
|
||||
R(2);
|
||||
R(3);
|
||||
R(4);
|
||||
R(5);
|
||||
R(6);
|
||||
R(7);
|
||||
R(8);
|
||||
R(9);
|
||||
R(10);
|
||||
R(11);
|
||||
R(12);
|
||||
R(13);
|
||||
R(14);
|
||||
R(15);
|
||||
#undef R
|
||||
|
||||
return x.i;
|
||||
}
|
||||
|
||||
inline static __m128i _em_loadu_si128(__m128i const *P)
|
||||
{
|
||||
um128 tmp;
|
||||
um128 *pp=(um128*)P;
|
||||
|
||||
tmp.u8[0]=(*pp).u8[0];
|
||||
tmp.u8[1]=(*pp).u8[1];
|
||||
tmp.u8[2]=(*pp).u8[2];
|
||||
tmp.u8[3]=(*pp).u8[3];
|
||||
tmp.u8[4]=(*pp).u8[4];
|
||||
tmp.u8[5]=(*pp).u8[5];
|
||||
tmp.u8[6]=(*pp).u8[6];
|
||||
tmp.u8[7]=(*pp).u8[7];
|
||||
tmp.u8[8]=(*pp).u8[8];
|
||||
tmp.u8[9]=(*pp).u8[9];
|
||||
tmp.u8[10]=(*pp).u8[10];
|
||||
tmp.u8[11]=(*pp).u8[11];
|
||||
tmp.u8[12]=(*pp).u8[12];
|
||||
tmp.u8[13]=(*pp).u8[13];
|
||||
tmp.u8[14]=(*pp).u8[14];
|
||||
tmp.u8[15]=(*pp).u8[15];
|
||||
return tmp.i;
|
||||
}
|
||||
|
||||
|
||||
#define _MM_SET1_EPI8(x) _em_set1_epi8(x)
|
||||
#define _MM_INSERT_EPI8(r,x,i) _em_insert_epi8((r),(x),(i))
|
||||
#define _MM_CMPEQ_EPI8(x,y) _em_cmpeq_epi8((x),(y))
|
||||
#define _MM_CMPGT_EPI8(x,y) _em_cmpgt_epi8((x),(y))
|
||||
#define _MM_CMPLT_EPI8(x,y) _em_cmplt_epi8((x),(y))
|
||||
#define _MM_MAX_EPI8(x,y) _em_max_epi8((x),(y))
|
||||
#define _MM_MIN_EPI8(x,y) _em_min_epi8((x),(y))
|
||||
#define _MM_ADD_EPI8(x,y) _em_add_epi8((x),(y))
|
||||
#define _MM_SUB_EPI8(x,y) _em_sub_epi8((x),(y))
|
||||
#define _MM_EXTRACT_EPI8(r,p) _em_extract_epi8((r),(p))
|
||||
|
||||
#define _MM_MIN_EPU8(x,y) _em_min_epu8((x),(y))
|
||||
|
||||
#define _MM_SET1_EPI16(x) _em_set1_epi16(x)
|
||||
#define _MM_INSERT_EPI16(r,x,i) _em_insert_epi16((r),(x),(i))
|
||||
#define _MM_CMPEQ_EPI16(x,y) _em_cmpeq_epi16((x),(y))
|
||||
#define _MM_CMPGT_EPI16(x,y) _em_cmpgt_epi16((x),(y))
|
||||
#define _MM_CMPLT_EPI16(x,y) _em_cmplt_epi16((x),(y))
|
||||
#define _MM_MAX_EPI16(x,y) _em_max_epi16((x),(y))
|
||||
#define _MM_MIN_EPI16(x,y) _em_min_epi16((x),(y))
|
||||
#define _MM_ADD_EPI16(x,y) _em_add_epi16((x),(y))
|
||||
#define _MM_SUB_EPI16(x,y) _em_sub_epi16((x),(y))
|
||||
#define _MM_EXTRACT_EPI16(r,p) _em_extract_epi16((r),(p))
|
||||
#define _MM_UNPACKLO_EPI8(a,b) _em_unpacklo_epi8((a),(b))
|
||||
#define _MM_UNPACKHI_EPI8(a,b) _em_unpackhi_epi8((a),(b))
|
||||
#define _MM_ADDS_EPU16(x,y) _em_adds_epu16((x),(y))
|
||||
|
||||
#define _MM_SRLI_EPI64(r,x) _em_srli_epi64((r),(x))
|
||||
#define _MM_SLLI_EPI64(r,x) _em_slli_epi64((r),(x))
|
||||
|
||||
#define _MM_SETZERO_SI128() _em_setzero_si128()
|
||||
|
||||
#define _MM_AND_SI128(x,y) _em_and_si128((x),(y))
|
||||
#define _MM_ANDNOT_SI128(x,y) _em_andnot_si128((x),(y))
|
||||
#define _MM_OR_SI128(x,y) _em_or_si128((x),(y))
|
||||
#define _MM_XOR_SI128(x,y) _em_xor_si128((x),(y))
|
||||
#define _MM_SLLI_SI128(r,s) _em_slli_si128((r),(s))
|
||||
#define _MM_SRLI_SI128(r,s) _em_srli_si128((r),(s))
|
||||
|
||||
#define _MM_LOADU_SI128(x) _em_loadu_si128(x)
|
||||
#define _MM_LOAD_SI128(x) _em_loadu_si128(x)
|
||||
|
||||
|
||||
#endif /* __SSE2__ */
|
||||
|
||||
#define _MM_NOT_SI128(x) _MM_XOR_SI128((x),(_MM_SET1_EPI8(0xFFFF)))
|
||||
|
||||
#endif
|
||||
@ -14,6 +14,7 @@
|
||||
#include <stdio.h>
|
||||
#include <math.h>
|
||||
|
||||
#include "char_str_indexer.h"
|
||||
#include "obiblob.h"
|
||||
#include "obiblob_indexer.h"
|
||||
#include "obidebug.h"
|
||||
@ -25,24 +26,16 @@
|
||||
|
||||
Obi_blob_p obi_str_to_blob(const char* value)
|
||||
{
|
||||
Obi_blob_p value_b;
|
||||
int32_t length;
|
||||
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;
|
||||
return obi_blob((byte_t*)value, ELEMENT_SIZE_STR, length, length);
|
||||
}
|
||||
|
||||
|
||||
char* obi_blob_to_str(Obi_blob_p value_b)
|
||||
const char* obi_blob_to_str(Obi_blob_p value_b)
|
||||
{
|
||||
return value_b->value;
|
||||
}
|
||||
@ -67,7 +60,7 @@ index_t obi_index_char_str(Obi_indexer_p indexer, const char* value)
|
||||
}
|
||||
|
||||
|
||||
char* obi_retrieve_char_str(Obi_indexer_p indexer, index_t idx)
|
||||
const char* obi_retrieve_char_str(Obi_indexer_p indexer, index_t idx)
|
||||
{
|
||||
Obi_blob_p value_b;
|
||||
|
||||
|
||||
@ -35,7 +35,7 @@
|
||||
* @since October 2015
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
Obi_blob_p obi_str_to_blob(char* value);
|
||||
Obi_blob_p obi_str_to_blob(const char* value);
|
||||
|
||||
|
||||
/**
|
||||
@ -80,7 +80,7 @@ index_t obi_index_char_str(Obi_indexer_p indexer, const char* value);
|
||||
* @since April 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
char* obi_retrieve_char_str(Obi_indexer_p indexer, index_t idx);
|
||||
const char* obi_retrieve_char_str(Obi_indexer_p indexer, index_t idx);
|
||||
|
||||
|
||||
#endif /* CHAR_STR_INDEXER_H_ */
|
||||
|
||||
@ -14,6 +14,7 @@
|
||||
#include <stdio.h>
|
||||
#include <math.h>
|
||||
|
||||
#include "dna_seq_indexer.h"
|
||||
#include "obiblob.h"
|
||||
#include "obiblob_indexer.h"
|
||||
#include "obidebug.h"
|
||||
|
||||
109
src/obi_align.c
Normal file
109
src/obi_align.c
Normal file
@ -0,0 +1,109 @@
|
||||
/****************************************************************************
|
||||
* Sequence alignment functions *
|
||||
****************************************************************************/
|
||||
|
||||
/**
|
||||
* @file obi_align.c
|
||||
* @author Celine Mercier
|
||||
* @date May 4th 2016
|
||||
* @brief Functions handling sequence alignments.
|
||||
*/
|
||||
|
||||
|
||||
#include <stdlib.h>
|
||||
#include <stdio.h>
|
||||
#include <stdbool.h>
|
||||
|
||||
#include "obidebug.h"
|
||||
#include "obierrno.h"
|
||||
#include "obitypes.h"
|
||||
#include "obiview.h"
|
||||
#include "sse_banded_LCS_alignment.h"
|
||||
|
||||
|
||||
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
||||
|
||||
|
||||
// TODO
|
||||
// use openMP pragmas : garder scores en memoire et ecrire a la fin? (normalement c bon avec index)
|
||||
// tout ecrire en stdint?
|
||||
// check NUC_SEQS and score type (int or float if normalize)
|
||||
// what's with multiple sequence/line columns?
|
||||
// make function that put blobs in int16
|
||||
|
||||
|
||||
int obi_align_one_column(Obiview_p seq_view, OBIDMS_column_p seq_column, Obiview_p score_view, OBIDMS_column_p score_column, double threshold, bool normalize, int reference, bool similarity_mode)
|
||||
{
|
||||
index_t i, j, k;
|
||||
index_t seq_count;
|
||||
char* seq1;
|
||||
char* seq2;
|
||||
double score;
|
||||
|
||||
k = 0;
|
||||
|
||||
if ((seq_column->header)->returned_data_type != OBI_SEQ)
|
||||
{
|
||||
obi_set_errno(OBI_ALIGN_ERROR);
|
||||
obidebug(1, "\nTrying to align a column of a different type than OBI_SEQ");
|
||||
return -1;
|
||||
}
|
||||
|
||||
if ((normalize && ((score_column->header)->returned_data_type != OBI_FLOAT)) ||
|
||||
(!normalize && ((score_column->header)->returned_data_type != OBI_INT)))
|
||||
{
|
||||
obi_set_errno(OBI_ALIGN_ERROR);
|
||||
obidebug(1, "\nTrying to store alignment scores in a column of an inappropriate type");
|
||||
return -1;
|
||||
}
|
||||
|
||||
seq_count = (seq_column->header)->lines_used;
|
||||
|
||||
for (i=0; i < (seq_count - 1); i++)
|
||||
{
|
||||
for (j=i+1; j < seq_count; j++)
|
||||
{
|
||||
//fprintf(stderr, "\ni=%lld, j=%lld, k=%lld", i, j, k);
|
||||
|
||||
seq1 = obi_column_get_obiseq_with_elt_idx_in_view(seq_view, seq_column, i, 0);
|
||||
seq2 = obi_column_get_obiseq_with_elt_idx_in_view(seq_view, seq_column, j, 0);
|
||||
|
||||
if ((seq1 == NULL) || (seq2 == NULL))
|
||||
{
|
||||
obidebug(1, "\nError retrieving sequences to align");
|
||||
return -1;
|
||||
}
|
||||
|
||||
// TODO filter
|
||||
score = generic_sse_banded_lcs_align(seq1, seq2, threshold, normalize, reference, similarity_mode);
|
||||
|
||||
if (normalize)
|
||||
{
|
||||
if (obi_column_set_obifloat_with_elt_idx_in_view(score_view, score_column, k, 0, (obifloat_t) score) < 0)
|
||||
{
|
||||
obidebug(1, "\nError writing alignment score in a column");
|
||||
return -1;
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
if (obi_column_set_obiint_with_elt_idx_in_view(score_view, score_column, k, 0, (obiint_t) score) < 0)
|
||||
{
|
||||
obidebug(1, "\nError writing alignment score in a column");
|
||||
return -1;
|
||||
}
|
||||
}
|
||||
|
||||
k++;
|
||||
}
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
int obi_align_two_columns(OBIDMS_column_p seq_column_1, OBIDMS_column_p seq_column_2, OBIDMS_column_p score_column, double threshold, bool normalize, int reference, bool similarity_mode)
|
||||
{
|
||||
// TODO
|
||||
return 0;
|
||||
}
|
||||
37
src/obi_align.h
Normal file
37
src/obi_align.h
Normal file
@ -0,0 +1,37 @@
|
||||
/****************************************************************************
|
||||
* Sequence alignment functions header file *
|
||||
****************************************************************************/
|
||||
|
||||
/**
|
||||
* @file obi_align.h
|
||||
* @author Celine Mercier
|
||||
* @date May 11th 2016
|
||||
* @brief Header file for the functions handling the alignment of DNA sequences.
|
||||
*/
|
||||
|
||||
|
||||
#ifndef OBI_ALIGN_H_
|
||||
#define OBI_ALIGN_H_
|
||||
|
||||
|
||||
#include <stdlib.h>
|
||||
#include <stdio.h>
|
||||
#include <stdbool.h>
|
||||
|
||||
#include "obidms.h"
|
||||
#include "obidmscolumn.h"
|
||||
#include "obitypes.h"
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* @brief
|
||||
*
|
||||
* TODO
|
||||
*
|
||||
*/
|
||||
int obi_align_one_column(Obiview_p seq_view, OBIDMS_column_p seq_column, Obiview_p score_view, OBIDMS_column_p score_column, double threshold, bool normalize, int reference, bool similarity_mode);
|
||||
|
||||
|
||||
#endif /* OBI_ALIGN_H_ */
|
||||
|
||||
313
src/obiavl.c
313
src/obiavl.c
@ -107,6 +107,42 @@ static char* build_avl_file_name(const char* avl_name);
|
||||
static char* build_avl_data_file_name(const char* avl_name);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Internal function building the full path of an AVL tree file.
|
||||
*
|
||||
* @warning The returned pointer has to be freed by the caller.
|
||||
*
|
||||
* @param dms A pointer to 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 if it's part of an AVL group, or -1 if not.
|
||||
*
|
||||
* @returns A pointer to the full path of the file where the AVL tree is stored.
|
||||
* @retval NULL if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
static char* get_full_path_of_avl_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Internal function building the file name for an AVL data file.
|
||||
*
|
||||
* @warning The returned pointer has to be freed by the caller.
|
||||
*
|
||||
* @param dms A pointer to 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 if it's part of an AVL group, or -1 if not.
|
||||
*
|
||||
* @returns A pointer to the full path of the file where the data referred to by the AVL tree is stored.
|
||||
* @retval NULL if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
static char* get_full_path_of_avl_data_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Internal function returning the size of an AVL tree header on this platform,
|
||||
* including the size of the bloom filter associated with the AVL tree.
|
||||
@ -253,9 +289,12 @@ int remap_an_avl(OBIDMS_avl_p avl);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Internal function (re)mapping the tree and data parts of an AVL tree structure.
|
||||
* @brief Internal function creating and adding a new AVL in an AVL group.
|
||||
*
|
||||
* @param avl A pointer to the AVL tree group structure.
|
||||
* @warning The previous AVL in the list of the group is unmapped,
|
||||
* if it's not the 1st AVL being added.
|
||||
*
|
||||
* @param avl A pointer on the AVL tree group structure.
|
||||
*
|
||||
* @retval 0 if the operation was successfully completed.
|
||||
* @retval -1 if an error occurred.
|
||||
@ -547,6 +586,102 @@ static char* build_avl_data_file_name(const char* avl_name)
|
||||
}
|
||||
|
||||
|
||||
static char* get_full_path_of_avl_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx)
|
||||
{
|
||||
char* complete_avl_name;
|
||||
char* full_path;
|
||||
char* avl_file_name;
|
||||
|
||||
if (avl_idx >= 0)
|
||||
{
|
||||
complete_avl_name = build_avl_name_with_idx(avl_name, avl_idx);
|
||||
if (complete_avl_name == NULL)
|
||||
return NULL;
|
||||
}
|
||||
else
|
||||
{
|
||||
complete_avl_name = (char*) malloc((strlen(avl_name)+1)*sizeof(char));
|
||||
if (complete_avl_name == NULL)
|
||||
{
|
||||
obi_set_errno(OBI_MALLOC_ERROR);
|
||||
obidebug(1, "\nError allocating memory for an AVL name");
|
||||
return NULL;
|
||||
}
|
||||
strcpy(complete_avl_name, avl_name);
|
||||
}
|
||||
|
||||
avl_file_name = build_avl_file_name(complete_avl_name);
|
||||
if (avl_file_name == NULL)
|
||||
{
|
||||
free(complete_avl_name);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
full_path = get_full_path_of_avl_dir(dms, avl_name);
|
||||
if (full_path == NULL)
|
||||
{
|
||||
free(complete_avl_name);
|
||||
free(avl_file_name);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
strcat(full_path, "/");
|
||||
strcat(full_path, avl_file_name);
|
||||
|
||||
free(complete_avl_name);
|
||||
|
||||
return full_path;
|
||||
}
|
||||
|
||||
|
||||
static char* get_full_path_of_avl_data_file_name(OBIDMS_p dms, const char* avl_name, int avl_idx)
|
||||
{
|
||||
char* complete_avl_name;
|
||||
char* full_path;
|
||||
char* avl_data_file_name;
|
||||
|
||||
if (avl_idx >= 0)
|
||||
{
|
||||
complete_avl_name = build_avl_name_with_idx(avl_name, avl_idx);
|
||||
if (complete_avl_name == NULL)
|
||||
return NULL;
|
||||
}
|
||||
else
|
||||
{
|
||||
complete_avl_name = (char*) malloc((strlen(avl_name)+1)*sizeof(char));
|
||||
if (complete_avl_name == NULL)
|
||||
{
|
||||
obi_set_errno(OBI_MALLOC_ERROR);
|
||||
obidebug(1, "\nError allocating memory for an AVL name");
|
||||
return NULL;
|
||||
}
|
||||
strcpy(complete_avl_name, avl_name);
|
||||
}
|
||||
|
||||
avl_data_file_name = build_avl_data_file_name(complete_avl_name);
|
||||
if (avl_data_file_name == NULL)
|
||||
{
|
||||
free(complete_avl_name);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
full_path = get_full_path_of_avl_dir(dms, avl_name);
|
||||
if (full_path == NULL)
|
||||
{
|
||||
free(complete_avl_name);
|
||||
free(avl_data_file_name);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
strcat(full_path, "/");
|
||||
strcat(full_path, avl_data_file_name);
|
||||
|
||||
free(complete_avl_name);
|
||||
|
||||
return full_path;
|
||||
}
|
||||
|
||||
|
||||
size_t get_avl_header_size()
|
||||
{
|
||||
size_t header_size;
|
||||
@ -646,7 +781,6 @@ int truncate_avl_to_size_used(OBIDMS_avl_p avl) // TODO is it necessary to unmap
|
||||
file_descriptor,
|
||||
(avl->header)->header_size
|
||||
);
|
||||
|
||||
if (avl->tree == MAP_FAILED)
|
||||
{
|
||||
obi_set_errno(OBI_AVL_ERROR);
|
||||
@ -923,23 +1057,24 @@ int remap_an_avl(OBIDMS_avl_p avl)
|
||||
int add_new_avl_in_group(OBIDMS_avl_group_p avl_group)
|
||||
{
|
||||
// Check that maximum number of AVLs in a group was not reached
|
||||
if (avl_group->current_avl_idx == (MAX_NB_OF_AVLS_IN_GROUP-1))
|
||||
if (avl_group->last_avl_idx == (MAX_NB_OF_AVLS_IN_GROUP - 1))
|
||||
{
|
||||
obi_set_errno(OBI_AVL_ERROR);
|
||||
obidebug(1, "\nError: Trying to add new AVL in AVL group but maximum number of AVLs in a group reached");
|
||||
return -1;
|
||||
}
|
||||
|
||||
// Unmap the previous AVL
|
||||
if (unmap_an_avl((avl_group->sub_avls)[avl_group->current_avl_idx]) < 0)
|
||||
return -1;
|
||||
// Unmap the previous AVL if it's not the 1st
|
||||
if (avl_group->last_avl_idx > 0)
|
||||
if (unmap_an_avl((avl_group->sub_avls)[avl_group->last_avl_idx]) < 0)
|
||||
return -1;
|
||||
|
||||
// Increment current AVL index
|
||||
(avl_group->current_avl_idx)++;
|
||||
(avl_group->last_avl_idx)++;
|
||||
|
||||
// Create the new AVL
|
||||
(avl_group->sub_avls)[avl_group->current_avl_idx] = obi_create_avl(avl_group->dms, avl_group->name, avl_group->current_avl_idx);
|
||||
if ((avl_group->sub_avls)[avl_group->current_avl_idx] == NULL)
|
||||
(avl_group->sub_avls)[avl_group->last_avl_idx] = obi_create_avl(avl_group->dms, avl_group->name, avl_group->last_avl_idx);
|
||||
if ((avl_group->sub_avls)[avl_group->last_avl_idx] == NULL)
|
||||
{
|
||||
obidebug(1, "\nError creating a new AVL tree in a group");
|
||||
return -1;
|
||||
@ -949,6 +1084,36 @@ int add_new_avl_in_group(OBIDMS_avl_group_p avl_group)
|
||||
}
|
||||
|
||||
|
||||
// TODO doc
|
||||
int add_existing_avl_in_group(OBIDMS_avl_group_p avl_group_dest, OBIDMS_avl_group_p avl_group_source, int avl_idx)
|
||||
{
|
||||
if (link(get_full_path_of_avl_file_name(avl_group_source->dms, avl_group_source->name, avl_idx), get_full_path_of_avl_file_name(avl_group_dest->dms, avl_group_dest->name, avl_idx)) < 0)
|
||||
{
|
||||
obi_set_errno(OBI_AVL_ERROR);
|
||||
obidebug(1, "\nError creating a hard link to an existing AVL tree file");
|
||||
return -1;
|
||||
}
|
||||
if (link(get_full_path_of_avl_data_file_name(avl_group_source->dms, avl_group_source->name, avl_idx), get_full_path_of_avl_data_file_name(avl_group_dest->dms, avl_group_dest->name, avl_idx)) < 0)
|
||||
{
|
||||
obi_set_errno(OBI_AVL_ERROR);
|
||||
obidebug(1, "\nError creating a hard link to an existing AVL data file");
|
||||
return -1;
|
||||
}
|
||||
|
||||
// Increment current AVL index
|
||||
(avl_group_dest->last_avl_idx)++;
|
||||
|
||||
// Open AVL for that group TODO ideally not needed, but needed for now
|
||||
avl_group_dest->sub_avls[avl_group_dest->last_avl_idx] = obi_open_avl(avl_group_source->dms, avl_group_source->name, avl_idx);
|
||||
if ((avl_group_dest->sub_avls)[avl_group_dest->last_avl_idx] == NULL)
|
||||
{
|
||||
obidebug(1, "\nError opening an AVL to add in an AVL group");
|
||||
return -1;
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
int maybe_in_avl(OBIDMS_avl_p avl, Obi_blob_p value)
|
||||
{
|
||||
return (bloom_check(&((avl->header)->bloom_filter), value, obi_blob_sizeof(value)));
|
||||
@ -1529,8 +1694,7 @@ OBIDMS_avl_p obi_create_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
|
||||
// Bloom filter
|
||||
bloom_init(&((avl->header)->bloom_filter), MAX_NODE_COUNT_PER_AVL);
|
||||
|
||||
if (avl_idx >= 0)
|
||||
free(complete_avl_name);
|
||||
free(complete_avl_name);
|
||||
|
||||
return avl;
|
||||
}
|
||||
@ -1777,8 +1941,7 @@ OBIDMS_avl_p obi_open_avl(OBIDMS_p dms, const char* avl_name, int avl_idx)
|
||||
avl->dir_fd = avl_dir_file_descriptor;
|
||||
avl->avl_fd = avl_file_descriptor;
|
||||
|
||||
if (avl_idx >= 0)
|
||||
free(complete_avl_name);
|
||||
free(complete_avl_name);
|
||||
|
||||
return avl;
|
||||
}
|
||||
@ -1806,6 +1969,7 @@ OBIDMS_avl_group_p obi_avl_group(OBIDMS_p dms, const char* avl_name)
|
||||
OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name)
|
||||
{
|
||||
OBIDMS_avl_group_p avl_group;
|
||||
char* avl_dir_name;
|
||||
|
||||
avl_group = (OBIDMS_avl_group_p) malloc(sizeof(OBIDMS_avl_group_t));
|
||||
if (avl_group == NULL)
|
||||
@ -1815,18 +1979,22 @@ OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name)
|
||||
return NULL;
|
||||
}
|
||||
|
||||
// Create 1st avl
|
||||
(avl_group->sub_avls)[0] = obi_create_avl(dms, avl_name, 0);
|
||||
if ((avl_group->sub_avls)[0] == NULL)
|
||||
{
|
||||
obidebug(1, "\nError creating the first AVL of an AVL group");
|
||||
return NULL;
|
||||
}
|
||||
|
||||
avl_group->current_avl_idx = 0;
|
||||
avl_group->last_avl_idx = -1;
|
||||
avl_group->dms = dms;
|
||||
strcpy(avl_group->name, avl_name);
|
||||
|
||||
avl_group->dms = dms;
|
||||
// Create the directory for that AVL group
|
||||
avl_dir_name = get_full_path_of_avl_dir(dms, avl_name);
|
||||
if (avl_dir_name == NULL)
|
||||
return NULL;
|
||||
|
||||
if (mkdirat(dms->indexer_dir_fd, avl_dir_name, 00777) < 0)
|
||||
{
|
||||
obi_set_errno(OBI_AVL_ERROR);
|
||||
obidebug(1, "\nError creating an AVL directory");
|
||||
free(avl_dir_name);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
// Add in the list of open indexers
|
||||
obi_dms_list_indexer(dms, avl_group);
|
||||
@ -1883,7 +2051,7 @@ OBIDMS_avl_group_p obi_open_avl_group(OBIDMS_p dms, const char* avl_name)
|
||||
if ((avl_group->sub_avls)[i] == NULL)
|
||||
return NULL;
|
||||
}
|
||||
avl_group->current_avl_idx = avl_count-1; // TODO latest. discuss
|
||||
avl_group->last_avl_idx = avl_count-1; // TODO latest. discuss
|
||||
strcpy(avl_group->name, avl_name);
|
||||
|
||||
avl_group->dms = dms;
|
||||
@ -1901,6 +2069,59 @@ OBIDMS_avl_group_p obi_open_avl_group(OBIDMS_p dms, const char* avl_name)
|
||||
}
|
||||
|
||||
|
||||
void obi_clone_avl(OBIDMS_avl_p avl, OBIDMS_avl_p new_avl)
|
||||
{
|
||||
// Clone AVL tree
|
||||
memcpy(new_avl->tree, avl->tree, (avl->header)->avl_size);
|
||||
(new_avl->header)->avl_size = (avl->header)->avl_size;
|
||||
(new_avl->header)->nb_items = (avl->header)->nb_items;
|
||||
(new_avl->header)->root_idx = (avl->header)->root_idx;
|
||||
(new_avl->header)->bloom_filter = (avl->header)->bloom_filter;
|
||||
|
||||
// Clone AVL data
|
||||
memcpy((new_avl->data)->data, (avl->data)->data, ((avl->data)->header)->data_size_used);
|
||||
((new_avl->data)->header)->data_size_used = ((avl->data)->header)->data_size_used;
|
||||
((new_avl->data)->header)->data_size_max = ((avl->data)->header)->data_size_max;
|
||||
((new_avl->data)->header)->nb_items = ((avl->data)->header)->nb_items;
|
||||
}
|
||||
|
||||
|
||||
OBIDMS_avl_group_p obi_clone_avl_group(OBIDMS_avl_group_p avl_group, const char* new_avl_name)
|
||||
{
|
||||
OBIDMS_avl_group_p new_avl_group;
|
||||
int i;
|
||||
|
||||
// Create the new AVL group
|
||||
new_avl_group = obi_create_avl_group(avl_group->dms, new_avl_name);
|
||||
|
||||
// Create hard links to all the full AVLs that won't be modified: all but the last one
|
||||
for (i=0; i<(avl_group->last_avl_idx); i++)
|
||||
{
|
||||
if (add_existing_avl_in_group(new_avl_group, avl_group, i) < 0)
|
||||
return NULL;
|
||||
}
|
||||
|
||||
// Create the last AVL to copy data in it
|
||||
if (add_new_avl_in_group(new_avl_group) < 0)
|
||||
{
|
||||
obi_close_avl_group(new_avl_group);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
// Copy the data from the last AVL to a new one that can be modified
|
||||
obi_clone_avl((avl_group->sub_avls)[avl_group->last_avl_idx], (new_avl_group->sub_avls)[new_avl_group->last_avl_idx]);
|
||||
|
||||
// Close old AVL group
|
||||
if (obi_close_avl_group(avl_group) < 0)
|
||||
{
|
||||
obi_close_avl_group(new_avl_group);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
return new_avl_group;
|
||||
}
|
||||
|
||||
|
||||
int obi_close_avl(OBIDMS_avl_p avl)
|
||||
{
|
||||
int ret_val = 0;
|
||||
@ -1909,7 +2130,7 @@ int obi_close_avl(OBIDMS_avl_p avl)
|
||||
|
||||
ret_val = truncate_avl_to_size_used(avl);
|
||||
|
||||
if (munmap(avl->tree, (((avl->header)->nb_items_max) * sizeof(AVL_node_t))) < 0)
|
||||
if (munmap(avl->tree, (avl->header)->avl_size) < 0)
|
||||
{
|
||||
obi_set_errno(OBI_AVL_ERROR);
|
||||
obidebug(1, "\nError munmapping the tree of an AVL tree file");
|
||||
@ -1946,9 +2167,17 @@ int obi_close_avl_group(OBIDMS_avl_group_p avl_group)
|
||||
ret_val = obi_dms_unlist_indexer(avl_group->dms, avl_group);
|
||||
|
||||
// Close each AVL of the group
|
||||
for (i=0; i < (avl_group->current_avl_idx); i++)
|
||||
for (i=0; i <= (avl_group->last_avl_idx); i++)
|
||||
{
|
||||
// Remap all but the last AVL (already mapped) before closing to truncate and close properly
|
||||
if (i < (avl_group->last_avl_idx))
|
||||
{
|
||||
if (remap_an_avl((avl_group->sub_avls)[i]) < 0)
|
||||
ret_val = -1;
|
||||
}
|
||||
if (obi_close_avl((avl_group->sub_avls)[i]) < 0)
|
||||
ret_val = -1;
|
||||
}
|
||||
|
||||
free(avl_group);
|
||||
}
|
||||
@ -2157,18 +2386,29 @@ index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_blob_p value)
|
||||
index_t index_with_avl;
|
||||
int i;
|
||||
|
||||
if (maybe_in_avl((avl_group->sub_avls)[avl_group->current_avl_idx], value))
|
||||
// Create 1st AVL if group is empty
|
||||
if (avl_group->last_avl_idx == -1)
|
||||
{
|
||||
index_in_avl = (int32_t) obi_avl_find((avl_group->sub_avls)[avl_group->current_avl_idx], value);
|
||||
if (add_new_avl_in_group(avl_group) < 0)
|
||||
{
|
||||
obidebug(1, "\nError creating the first AVL of an AVL group");
|
||||
return -1;
|
||||
}
|
||||
}
|
||||
|
||||
if (maybe_in_avl((avl_group->sub_avls)[avl_group->last_avl_idx], value))
|
||||
{
|
||||
index_in_avl = (int32_t) obi_avl_find((avl_group->sub_avls)[avl_group->last_avl_idx], value);
|
||||
if (index_in_avl >= 0)
|
||||
{
|
||||
index_with_avl = avl_group->current_avl_idx;
|
||||
index_with_avl = avl_group->last_avl_idx;
|
||||
index_with_avl = index_with_avl << 32;
|
||||
index_with_avl = index_with_avl + index_in_avl;
|
||||
return index_with_avl;
|
||||
}
|
||||
}
|
||||
for (i=0; i < (avl_group->current_avl_idx); i++)
|
||||
|
||||
for (i=0; i < (avl_group->last_avl_idx); i++)
|
||||
{
|
||||
if (maybe_in_avl((avl_group->sub_avls)[i], value))
|
||||
{
|
||||
@ -2192,24 +2432,23 @@ index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_blob_p value)
|
||||
// Check if the AVL group is writable
|
||||
if (!(avl_group->writable))
|
||||
{
|
||||
obi_set_errno(OBI_AVL_ERROR);
|
||||
obidebug(1, "\nTrying to add a value in an AVL group that is read-only.");
|
||||
obi_set_errno(OBI_READ_ONLY_INDEXER_ERROR);
|
||||
return -1;
|
||||
}
|
||||
|
||||
// Check if need to make new AVL
|
||||
if (((((avl_group->sub_avls)[avl_group->current_avl_idx])->header)->nb_items == MAX_NODE_COUNT_PER_AVL) || (((((avl_group->sub_avls)[avl_group->current_avl_idx])->data)->header)->data_size_used >= MAX_DATA_SIZE_PER_AVL))
|
||||
if (((((avl_group->sub_avls)[avl_group->last_avl_idx])->header)->nb_items == MAX_NODE_COUNT_PER_AVL) || (((((avl_group->sub_avls)[avl_group->last_avl_idx])->data)->header)->data_size_used >= MAX_DATA_SIZE_PER_AVL))
|
||||
{
|
||||
if (add_new_avl_in_group(avl_group) < 0)
|
||||
return -1;
|
||||
}
|
||||
|
||||
// Add in the current AVL
|
||||
bloom_add(&((((avl_group->sub_avls)[avl_group->current_avl_idx])->header)->bloom_filter), value, obi_blob_sizeof(value));
|
||||
index_in_avl = (int32_t) obi_avl_add((avl_group->sub_avls)[avl_group->current_avl_idx], value);
|
||||
bloom_add(&((((avl_group->sub_avls)[avl_group->last_avl_idx])->header)->bloom_filter), value, obi_blob_sizeof(value));
|
||||
index_in_avl = (int32_t) obi_avl_add((avl_group->sub_avls)[avl_group->last_avl_idx], value);
|
||||
|
||||
// Build the index containing the AVL index
|
||||
index_with_avl = avl_group->current_avl_idx;
|
||||
index_with_avl = avl_group->last_avl_idx;
|
||||
index_with_avl = index_with_avl << 32;
|
||||
index_with_avl = index_with_avl + index_in_avl;
|
||||
|
||||
|
||||
37
src/obiavl.h
37
src/obiavl.h
@ -73,7 +73,7 @@ typedef struct AVL_node {
|
||||
* @brief OBIDMS AVL tree data header structure.
|
||||
*/
|
||||
typedef struct OBIDMS_avl_data_header {
|
||||
int header_size; /**< Size of the header in bytes.
|
||||
size_t header_size; /**< Size of the header in bytes.
|
||||
*/
|
||||
index_t data_size_used; /**< Size of the data used in bytes.
|
||||
*/
|
||||
@ -105,7 +105,7 @@ typedef struct OBIDMS_avl_data {
|
||||
* @brief OBIDMS AVL tree header structure.
|
||||
*/
|
||||
typedef struct OBIDMS_avl_header {
|
||||
int header_size; /**< Size of the header in bytes.
|
||||
size_t header_size; /**< Size of the header in bytes.
|
||||
*/
|
||||
size_t avl_size; /**< Size of the AVL tree in bytes.
|
||||
*/
|
||||
@ -160,7 +160,7 @@ typedef struct OBIDMS_avl {
|
||||
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.
|
||||
int last_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.
|
||||
*/
|
||||
@ -290,6 +290,37 @@ OBIDMS_avl_group_p obi_create_avl_group(OBIDMS_p dms, const char* avl_name);
|
||||
OBIDMS_avl_group_p obi_open_avl_group(OBIDMS_p dms, const char* avl_name);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Clones an AVL.
|
||||
*
|
||||
* The tree and the data are both cloned into the new AVL.
|
||||
*
|
||||
* @param avl A pointer on the AVL to clone.
|
||||
* @param new_avl A pointer on the new AVL to fill.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
void obi_clone_avl(OBIDMS_avl_p avl, OBIDMS_avl_p new_avl);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Clones an AVL group.
|
||||
*
|
||||
* @warning The AVL group that has be cloned is closed by the function.
|
||||
*
|
||||
* @param avl_group A pointer on the AVL group to clone.
|
||||
* @param new_avl_name The name of the new AVL group.
|
||||
*
|
||||
* @returns A pointer on the new AVL group structure.
|
||||
* @retval NULL if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
OBIDMS_avl_group_p obi_clone_avl_group(OBIDMS_avl_group_p avl_group, const char* new_avl_name);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Closes an AVL tree.
|
||||
*
|
||||
|
||||
@ -23,6 +23,8 @@
|
||||
|
||||
#define ELEMENT_SIZE_STR (8) /**< The size of an element from a value of type character string.
|
||||
*/
|
||||
#define ELEMENT_SIZE_UINT8 (8) /**< The size of an element from a value of type uint8_t.
|
||||
*/
|
||||
#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.
|
||||
|
||||
@ -30,6 +30,8 @@ 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 Obi_indexer_p obi_clone_indexer(Obi_indexer_p indexer, 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);
|
||||
|
||||
@ -107,6 +107,24 @@ inline Obi_indexer_p obi_open_indexer(OBIDMS_p dms, const char* name)
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @brief Clones an indexer.
|
||||
*
|
||||
* @param indexer The indexer to clone.
|
||||
* @param name The name of the new indexer.
|
||||
*
|
||||
* @returns A pointer on the new indexer structure.
|
||||
* @retval NULL if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
inline Obi_indexer_p obi_clone_indexer(Obi_indexer_p indexer, const char* name)
|
||||
{
|
||||
return obi_clone_avl_group(indexer, name);
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* @brief Closes an indexer.
|
||||
*
|
||||
|
||||
43
src/obidms.c
43
src/obidms.c
@ -252,7 +252,7 @@ OBIDMS_p obi_create_dms(const char* dms_path)
|
||||
return NULL;
|
||||
}
|
||||
|
||||
// Get file descriptor of DMS directory to create the indexer directory
|
||||
// Get file descriptor of DMS directory to create other directories
|
||||
dms_dir = opendir(directory_name);
|
||||
if (dms_dir == NULL)
|
||||
{
|
||||
@ -280,6 +280,14 @@ OBIDMS_p obi_create_dms(const char* dms_path)
|
||||
return NULL;
|
||||
}
|
||||
|
||||
// Create the view directory
|
||||
if (mkdirat(dms_file_descriptor, VIEW_DIR_NAME, 00777) < 0)
|
||||
{
|
||||
obi_set_errno(OBIVIEW_ERROR);
|
||||
obidebug(1, "\nProblem creating a view directory");
|
||||
return NULL;
|
||||
}
|
||||
|
||||
// Isolate the dms name
|
||||
j = 0;
|
||||
for (i=0; i<strlen(dms_path); i++)
|
||||
@ -447,6 +455,30 @@ OBIDMS_p obi_open_dms(const char* dms_path)
|
||||
return NULL;
|
||||
}
|
||||
|
||||
// Open the view directory
|
||||
dms->view_directory = opendir_in_dms(dms, VIEW_DIR_NAME);
|
||||
if (dms->view_directory == NULL)
|
||||
{
|
||||
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
|
||||
obidebug(1, "\nError opening the view directory");
|
||||
closedir(dms->indexer_directory);
|
||||
closedir(dms->directory);
|
||||
free(dms);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
// Store the view directory's file descriptor
|
||||
dms->view_dir_fd = dirfd(dms->view_directory);
|
||||
if (dms->view_dir_fd < 0)
|
||||
{
|
||||
obi_set_errno(OBIDMS_UNKNOWN_ERROR);
|
||||
obidebug(1, "\nError getting the file descriptor of the view directory");
|
||||
closedir(dms->view_directory);
|
||||
closedir(dms->directory);
|
||||
free(dms);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
// Initialize the list of opened columns
|
||||
dms->opened_columns = (Opened_columns_list_p) malloc(sizeof(Opened_columns_list_t));
|
||||
(dms->opened_columns)->nb_opened_columns = 0;
|
||||
@ -486,7 +518,7 @@ int obi_close_dms(OBIDMS_p dms)
|
||||
while ((dms->opened_columns)->nb_opened_columns > 0)
|
||||
obi_close_column(*((dms->opened_columns)->columns));
|
||||
|
||||
// Close dms and indexer directories
|
||||
// Close dms, and view and indexer directories
|
||||
if (closedir(dms->directory) < 0)
|
||||
{
|
||||
obi_set_errno(OBIDMS_MEMORY_ERROR);
|
||||
@ -501,6 +533,13 @@ int obi_close_dms(OBIDMS_p dms)
|
||||
free(dms);
|
||||
return -1;
|
||||
}
|
||||
if (closedir(dms->view_directory) < 0)
|
||||
{
|
||||
obi_set_errno(OBIVIEW_ERROR);
|
||||
obidebug(1, "\nError closing a view directory");
|
||||
free(dms);
|
||||
return -1;
|
||||
}
|
||||
free(dms);
|
||||
}
|
||||
|
||||
|
||||
@ -30,6 +30,8 @@
|
||||
*/
|
||||
#define INDEXER_DIR_NAME "OBIBLOB_INDEXERS" /**< The name of the Obiblob indexer directory.
|
||||
*/
|
||||
#define VIEW_DIR_NAME "VIEWS" /**< The name of the view 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.
|
||||
@ -98,6 +100,12 @@ typedef struct OBIDMS {
|
||||
int indexer_dir_fd; /**< The file descriptor of the directory entry
|
||||
* usable to refer and scan the indexer directory.
|
||||
*/
|
||||
DIR* view_directory; /**< A directory entry usable to
|
||||
* refer and scan the view directory.
|
||||
*/
|
||||
int view_dir_fd; /**< The file descriptor of the directory entry
|
||||
* usable to refer and scan the view directory.
|
||||
*/
|
||||
bool little_endian; /**< Endianness of the database.
|
||||
*/
|
||||
Opened_columns_list_p opened_columns; /**< List of opened columns.
|
||||
|
||||
@ -587,7 +587,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
}
|
||||
|
||||
// Build the indexer name if needed
|
||||
if ((data_type == OBI_STR) || (data_type == OBI_SEQ))
|
||||
if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || (data_type == OBI_QUAL))
|
||||
{
|
||||
if (strcmp(indexer_name, "") == 0)
|
||||
{
|
||||
@ -603,7 +603,7 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
}
|
||||
|
||||
returned_data_type = data_type;
|
||||
if ((data_type == OBI_STR) || (data_type == OBI_SEQ))
|
||||
if ((data_type == OBI_STR) || (data_type == OBI_SEQ) || (data_type == OBI_QUAL))
|
||||
// stored data is indices referring to data stored elsewhere
|
||||
stored_data_type = OBI_IDX;
|
||||
else
|
||||
@ -750,8 +750,8 @@ OBIDMS_column_p obi_create_column(OBIDMS_p dms,
|
||||
if (comments != NULL)
|
||||
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 ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ))
|
||||
// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated obi_indexer is opened or created
|
||||
if ((returned_data_type == OBI_STR) || (returned_data_type == OBI_SEQ) || (returned_data_type == OBI_QUAL))
|
||||
{
|
||||
new_column->indexer = obi_indexer(dms, final_indexer_name);
|
||||
if (new_column->indexer == NULL)
|
||||
@ -900,8 +900,8 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
|
||||
|
||||
column->writable = false;
|
||||
|
||||
// If the data type is OBI_STR or OBI_SEQ, the associated indexer is opened
|
||||
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
|
||||
// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated indexer is opened
|
||||
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ) || ((column->header)->returned_data_type == OBI_QUAL))
|
||||
{
|
||||
column->indexer = obi_open_indexer(dms, (column->header)->indexer_name);
|
||||
if (column->indexer == NULL)
|
||||
@ -940,8 +940,6 @@ OBIDMS_column_p obi_clone_column(OBIDMS_p dms,
|
||||
size_t line_size;
|
||||
index_t i, index;
|
||||
|
||||
obidebug(1, "\nline_selection == NULL = %d\n", (line_selection == NULL));
|
||||
|
||||
column_to_clone = obi_open_column(dms, column_name, version_number);
|
||||
if (column_to_clone == NULL)
|
||||
{
|
||||
@ -1028,8 +1026,8 @@ int obi_close_column(OBIDMS_column_p column)
|
||||
// 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);
|
||||
|
||||
// If the data type is OBI_STR or OBI_SEQ, the associated indexer is closed
|
||||
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ))
|
||||
// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated indexer is closed
|
||||
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ) || ((column->header)->returned_data_type == OBI_QUAL))
|
||||
if (obi_close_indexer(column->indexer) < 0)
|
||||
ret_val = -1;
|
||||
|
||||
@ -1155,6 +1153,14 @@ int obi_enlarge_column(OBIDMS_column_p column)
|
||||
int column_file_descriptor;
|
||||
char* column_file_name;
|
||||
|
||||
// Check if the column is read-only
|
||||
if (!(column->writable))
|
||||
{
|
||||
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||
obidebug(1, "\nError trying to enlarge a read-only column");
|
||||
return -1;
|
||||
}
|
||||
|
||||
// Get the column file name
|
||||
column_file_name = build_column_file_name((column->header)->name, (column->header)->version);
|
||||
if (column_file_name == NULL)
|
||||
@ -1209,12 +1215,12 @@ int obi_enlarge_column(OBIDMS_column_p column)
|
||||
}
|
||||
|
||||
column->data = mmap(NULL,
|
||||
new_data_size,
|
||||
PROT_READ | PROT_WRITE,
|
||||
MAP_SHARED,
|
||||
column_file_descriptor,
|
||||
header_size
|
||||
);
|
||||
new_data_size,
|
||||
PROT_READ | PROT_WRITE,
|
||||
MAP_SHARED,
|
||||
column_file_descriptor,
|
||||
header_size
|
||||
);
|
||||
if (column->data == MAP_FAILED)
|
||||
{
|
||||
obi_set_errno(OBICOL_UNKNOWN_ERROR);
|
||||
@ -1274,23 +1280,29 @@ void obi_ini_to_NA_values(OBIDMS_column_p column,
|
||||
}
|
||||
break;
|
||||
|
||||
case OBI_STR: for (i=start;i<end;i++)
|
||||
{
|
||||
*(((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++)
|
||||
{
|
||||
*(((index_t*) (column->data)) + i) = OBIIdx_NA;
|
||||
}
|
||||
break;
|
||||
|
||||
case OBI_QUAL: for (i=start;i<end;i++) // case not used since OBI_QUAL is only a returned_data_type
|
||||
{
|
||||
*(((index_t*) (column->data)) + i) = OBIIdx_NA;
|
||||
}
|
||||
break;
|
||||
|
||||
case OBI_STR: for (i=start;i<end;i++) // case not used since OBI_QUAL is only a returned_data_type
|
||||
{
|
||||
*(((index_t*) (column->data)) + i) = OBIIdx_NA;
|
||||
}
|
||||
break;
|
||||
|
||||
case OBI_SEQ: for (i=start;i<end;i++) // case not used since OBI_QUAL is only a returned_data_type
|
||||
{
|
||||
*(((index_t*) (column->data)) + i) = OBIIdx_NA;
|
||||
}
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
@ -1460,12 +1472,12 @@ int obi_column_prepare_to_set_value(OBIDMS_column_p column, index_t line_nb)
|
||||
}
|
||||
|
||||
|
||||
int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb)
|
||||
int obi_column_prepare_to_get_value(OBIDMS_column_p column, index_t line_nb) // TODO problem with some columns in a view being empty or shorter and triggering an error because they've been truncated when the view was closed. Fixed with obiview.c in update_lines() for now
|
||||
{
|
||||
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");
|
||||
obidebug(1, "\nError trying to get a value that is beyond the current number of lines of the column");
|
||||
return -1;
|
||||
}
|
||||
return 0;
|
||||
|
||||
184
src/obidmscolumn_qual.c
Normal file
184
src/obidmscolumn_qual.c
Normal file
@ -0,0 +1,184 @@
|
||||
/****************************************************************************
|
||||
* OBIDMS_column_qual functions *
|
||||
****************************************************************************/
|
||||
|
||||
/**
|
||||
* @file obidsmcolumn_qual.c
|
||||
* @author Celine Mercier
|
||||
* @date May 4th 2016
|
||||
* @brief Functions handling OBIColumns containing data in the form of indices referring to sequence qualities.
|
||||
*/
|
||||
|
||||
|
||||
#include <stdlib.h>
|
||||
#include <stdio.h>
|
||||
#include <stdint.h>
|
||||
|
||||
#include "obidmscolumn_qual.h"
|
||||
#include "obidmscolumn.h"
|
||||
#include "obitypes.h"
|
||||
#include "uint8_indexer.h"
|
||||
|
||||
|
||||
/**********************************************************************
|
||||
*
|
||||
* D E F I N I T I O N O F T H E P U B L I C F U N C T I O N S
|
||||
*
|
||||
**********************************************************************/
|
||||
|
||||
int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value)
|
||||
{
|
||||
uint8_t* int_value;
|
||||
int int_value_length;
|
||||
int i;
|
||||
int ret_value;
|
||||
|
||||
// Check NA value
|
||||
if (value == OBIQual_char_NA)
|
||||
{
|
||||
ret_value = obi_column_set_obiqual_int_with_elt_idx(column, line_nb, element_idx, OBIQual_int_NA, 0);
|
||||
}
|
||||
else
|
||||
{
|
||||
int_value_length = strlen(value);
|
||||
int_value = (uint8_t*) malloc(int_value_length * sizeof(uint8_t));
|
||||
|
||||
// Convert in uint8_t array to index in that format
|
||||
for (i=0; i<int_value_length; i++)
|
||||
int_value[i] = ((uint8_t)(value[i])) - QUALITY_ASCII_BASE;
|
||||
ret_value = obi_column_set_obiqual_int_with_elt_idx(column, line_nb, element_idx, int_value, int_value_length);
|
||||
free(int_value);
|
||||
}
|
||||
|
||||
return ret_value;
|
||||
}
|
||||
|
||||
|
||||
int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const uint8_t* value, int value_length)
|
||||
{
|
||||
index_t idx;
|
||||
char* new_indexer_name;
|
||||
|
||||
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
|
||||
return -1;
|
||||
|
||||
if (value == OBIQual_int_NA)
|
||||
{
|
||||
idx = OBIIdx_NA;
|
||||
}
|
||||
else
|
||||
{
|
||||
// Add the value in the indexer
|
||||
idx = obi_index_uint8(column->indexer, value, value_length);
|
||||
if (idx == -1) // An error occurred
|
||||
{
|
||||
if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
|
||||
{
|
||||
// TODO PUT IN A COLUMN FUNCTION
|
||||
// If the error is that the indexer is read-only, clone it
|
||||
new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
|
||||
if (new_indexer_name == NULL)
|
||||
return -1;
|
||||
column->indexer = obi_clone_indexer(column->indexer, new_indexer_name); // TODO Need to lock this somehow?
|
||||
strcpy((column->header)->indexer_name, new_indexer_name);
|
||||
free(new_indexer_name);
|
||||
obi_set_errno(0);
|
||||
|
||||
// Add the value in the new indexer
|
||||
idx = obi_index_uint8(column->indexer, value, value_length);
|
||||
if (idx == -1)
|
||||
return -1;
|
||||
}
|
||||
else
|
||||
return -1;
|
||||
}
|
||||
}
|
||||
|
||||
// Add the value's index in the column
|
||||
*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx)
|
||||
{
|
||||
char* value;
|
||||
const uint8_t* int_value;
|
||||
int int_value_length;
|
||||
int i;
|
||||
|
||||
int_value = obi_column_get_obiqual_int_with_elt_idx(column, line_nb, element_idx, &int_value_length);
|
||||
|
||||
// Check NA
|
||||
if (int_value == OBIQual_int_NA)
|
||||
return OBIQual_char_NA;
|
||||
|
||||
value = (char*) malloc((int_value_length + 1) * sizeof(char));
|
||||
|
||||
// Encode int quality to char quality
|
||||
for (i=0; i<int_value_length; i++)
|
||||
value[i] = (char)(int_value[i] + QUALITY_ASCII_BASE);
|
||||
|
||||
value[i] = '\0';
|
||||
|
||||
return value;
|
||||
}
|
||||
|
||||
|
||||
const uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, int* value_length)
|
||||
{
|
||||
index_t idx;
|
||||
|
||||
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
|
||||
return OBIQual_int_NA;
|
||||
|
||||
idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
||||
|
||||
// Check NA
|
||||
if (idx == OBIIdx_NA)
|
||||
return OBIQual_int_NA;
|
||||
|
||||
return obi_retrieve_uint8(column->indexer, idx, value_length);
|
||||
}
|
||||
|
||||
|
||||
int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value)
|
||||
{
|
||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||
if (element_idx == OBIIdx_NA)
|
||||
return -1;
|
||||
|
||||
return obi_column_set_obiqual_char_with_elt_idx(column, line_nb, element_idx, value);
|
||||
}
|
||||
|
||||
|
||||
int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const uint8_t* value, int value_length)
|
||||
{
|
||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||
if (element_idx == OBIIdx_NA)
|
||||
return -1;
|
||||
|
||||
return obi_column_set_obiqual_int_with_elt_idx(column, line_nb, element_idx, value, value_length);
|
||||
}
|
||||
|
||||
|
||||
char* obi_column_get_obiqual_char_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 OBIQual_char_NA;
|
||||
|
||||
return obi_column_get_obiqual_char_with_elt_idx(column, line_nb, element_idx);
|
||||
}
|
||||
|
||||
|
||||
const uint8_t* obi_column_get_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, int* value_length)
|
||||
{
|
||||
index_t element_idx = obi_column_get_element_index_from_name(column, element_name);
|
||||
if (element_idx == OBIIdx_NA)
|
||||
return OBIQual_int_NA;
|
||||
|
||||
return obi_column_get_obiqual_int_with_elt_idx(column, line_nb, element_idx, value_length);
|
||||
}
|
||||
|
||||
204
src/obidmscolumn_qual.h
Normal file
204
src/obidmscolumn_qual.h
Normal file
@ -0,0 +1,204 @@
|
||||
/****************************************************************************
|
||||
* OBIDMS_column_qual header file *
|
||||
****************************************************************************/
|
||||
|
||||
/**
|
||||
* @file obidsmcolumn_qual.h
|
||||
* @author Celine Mercier
|
||||
* @date May 4th 2016
|
||||
* @brief Header file for the functions handling OBIColumns containing data in the form of indices referring to sequence qualities.
|
||||
*/
|
||||
|
||||
|
||||
#ifndef OBIDMSCOLUMN_QUAL_H_
|
||||
#define OBIDMSCOLUMN_QUAL_H_
|
||||
|
||||
|
||||
#include <stdlib.h>
|
||||
#include <stdio.h>
|
||||
#include <stdint.h>
|
||||
|
||||
#include "obidmscolumn.h"
|
||||
#include "obitypes.h"
|
||||
|
||||
|
||||
#define QUALITY_ASCII_BASE (33) /**< The ASCII base of sequence quality.
|
||||
* Used to convert sequence qualities from characters to integers
|
||||
* and the other way around.
|
||||
*/
|
||||
|
||||
|
||||
/**
|
||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line.
|
||||
*
|
||||
* This function is for qualities in the character string format.
|
||||
*
|
||||
* @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, in the character string format.
|
||||
*
|
||||
* @returns An integer value indicating the success of the operation.
|
||||
* @retval 0 on success.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line.
|
||||
*
|
||||
* This function is for qualities in the integer format.
|
||||
*
|
||||
* @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, in the integer array format.
|
||||
* @param value_length The length of the integer array.
|
||||
*
|
||||
* @returns An integer value indicating the success of the operation.
|
||||
* @retval 0 on success.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const uint8_t* value, int value_length);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line.
|
||||
*
|
||||
* This function returns quality scores in the character string format.
|
||||
*
|
||||
* @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, in the character string format.
|
||||
* @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
char* obi_column_get_obiqual_char_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line.
|
||||
*
|
||||
* This function returns quality scores in the integer format.
|
||||
*
|
||||
* @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.
|
||||
* @param value_length A pointer on an integer to store the length of the integer array recovered.
|
||||
*
|
||||
* @returns The recovered value, in the integer array format.
|
||||
* @retval OBIQual_int_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
const uint8_t* obi_column_get_obiqual_int_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, int* value_length);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line.
|
||||
*
|
||||
* This function is for quality scores in the character string format.
|
||||
*
|
||||
* @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, in the character string format.
|
||||
*
|
||||
* @returns An integer value indicating the success of the operation.
|
||||
* @retval 0 on success.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line.
|
||||
*
|
||||
* This function is for quality scores in the integer array format.
|
||||
*
|
||||
* @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, in the integer format.
|
||||
* @param value_length The length of the integer array.
|
||||
*
|
||||
* @returns An integer value indicating the success of the operation.
|
||||
* @retval 0 on success.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, const uint8_t* value, int value_length);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line.
|
||||
*
|
||||
* This function returns quality scores in the character string format.
|
||||
*
|
||||
* @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, in the character string format.
|
||||
* @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
char* obi_column_get_obiqual_char_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line.
|
||||
*
|
||||
* This function returns quality scores in the integer array format.
|
||||
*
|
||||
* @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.
|
||||
* @param value_length A pointer on an integer to store the length of the integer array recovered.
|
||||
*
|
||||
* @returns The recovered value, in the integer format.
|
||||
* @retval OBIQual_int_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
const uint8_t* obi_column_get_obiqual_int_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name, int* value_length);
|
||||
|
||||
|
||||
#endif /* OBIDMSCOLUMN_QUAL_H_ */
|
||||
|
||||
@ -27,14 +27,42 @@
|
||||
int obi_column_set_obiseq_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value)
|
||||
{
|
||||
index_t idx;
|
||||
char* new_indexer_name;
|
||||
|
||||
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
|
||||
return -1;
|
||||
|
||||
// Add the value in the indexer
|
||||
idx = obi_index_dna_seq(column->indexer, value);
|
||||
if (idx == -1)
|
||||
return -1;
|
||||
if (value == OBISeq_NA)
|
||||
{
|
||||
idx = OBIIdx_NA;
|
||||
}
|
||||
else
|
||||
{
|
||||
// Add the value in the indexer
|
||||
idx = obi_index_dna_seq(column->indexer, value);
|
||||
if (idx == -1) // An error occurred
|
||||
{
|
||||
if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
|
||||
{
|
||||
// TODO PUT IN A COLUMN FUNCTION
|
||||
// If the error is that the indexer is read-only, clone it
|
||||
new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
|
||||
if (new_indexer_name == NULL)
|
||||
return -1;
|
||||
column->indexer = obi_clone_indexer(column->indexer, new_indexer_name); // TODO Need to lock this somehow?
|
||||
strcpy((column->header)->indexer_name, new_indexer_name);
|
||||
free(new_indexer_name);
|
||||
obi_set_errno(0);
|
||||
|
||||
// Add the value in the new indexer
|
||||
idx = obi_index_dna_seq(column->indexer, value);
|
||||
if (idx == -1)
|
||||
return -1;
|
||||
}
|
||||
else
|
||||
return -1;
|
||||
}
|
||||
}
|
||||
|
||||
// Add the value's index in the column
|
||||
*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
|
||||
|
||||
@ -27,14 +27,42 @@
|
||||
int obi_column_set_obistr_with_elt_idx(OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value)
|
||||
{
|
||||
index_t idx;
|
||||
char* new_indexer_name;
|
||||
|
||||
if (obi_column_prepare_to_set_value(column, line_nb) < 0)
|
||||
return -1;
|
||||
|
||||
// Add the value in the indexer
|
||||
idx = obi_index_char_str(column->indexer, value);
|
||||
if (idx == -1)
|
||||
return -1;
|
||||
if (value == OBIStr_NA)
|
||||
{
|
||||
idx = OBIIdx_NA;
|
||||
}
|
||||
else
|
||||
{
|
||||
// Add the value in the indexer
|
||||
idx = obi_index_char_str(column->indexer, value);
|
||||
if (idx == -1) // An error occurred
|
||||
{
|
||||
if (obi_errno == OBI_READ_ONLY_INDEXER_ERROR)
|
||||
{
|
||||
// TODO PUT IN A COLUMN FUNCTION
|
||||
// If the error is that the indexer is read-only, clone it
|
||||
new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
|
||||
if (new_indexer_name == NULL)
|
||||
return -1;
|
||||
column->indexer = obi_clone_indexer(column->indexer, new_indexer_name); // TODO Need to lock this somehow?
|
||||
strcpy((column->header)->indexer_name, new_indexer_name);
|
||||
free(new_indexer_name);
|
||||
obi_set_errno(0);
|
||||
|
||||
// Add the value in the new indexer
|
||||
idx = obi_index_char_str(column->indexer, value);
|
||||
if (idx == -1)
|
||||
return -1;
|
||||
}
|
||||
else
|
||||
return -1;
|
||||
}
|
||||
}
|
||||
|
||||
// Add the value's index in the column
|
||||
*(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx) = idx;
|
||||
@ -48,7 +76,7 @@ const char* obi_column_get_obistr_with_elt_idx(OBIDMS_column_p column, index_t l
|
||||
index_t idx;
|
||||
|
||||
if (obi_column_prepare_to_get_value(column, line_nb) < 0)
|
||||
return OBISeq_NA;
|
||||
return OBIStr_NA;
|
||||
|
||||
idx = *(((index_t*) (column->data)) + (line_nb * ((column->header)->nb_elements_per_line)) + element_idx);
|
||||
|
||||
|
||||
@ -114,6 +114,10 @@ extern int obi_errno;
|
||||
*/
|
||||
#define OBI_INDEXER_ERROR (27) /** Error handling a blob indexer
|
||||
*/
|
||||
#define OBI_READ_ONLY_INDEXER_ERROR (28) /** Error trying to modify a read-only a blob indexer
|
||||
*/
|
||||
#define OBI_ALIGN_ERROR (29) /** Error while aligning sequences
|
||||
*/
|
||||
/**@}*/
|
||||
|
||||
#endif /* OBIERRNO_H_ */
|
||||
|
||||
@ -40,6 +40,9 @@ size_t obi_sizeof(OBIType_t type)
|
||||
case OBI_CHAR: size = sizeof(obichar_t);
|
||||
break;
|
||||
|
||||
case OBI_QUAL: size = sizeof(index_t);
|
||||
break;
|
||||
|
||||
case OBI_STR: size = sizeof(index_t);
|
||||
break;
|
||||
|
||||
@ -96,6 +99,9 @@ char* name_data_type(int data_type)
|
||||
case OBI_CHAR: name = strdup("OBI_CHAR");
|
||||
break;
|
||||
|
||||
case OBI_QUAL: name = strdup("OBI_QUAL");
|
||||
break;
|
||||
|
||||
case OBI_STR: name = strdup("OBI_STR");
|
||||
break;
|
||||
|
||||
|
||||
@ -22,8 +22,10 @@
|
||||
#define OBIIdx_NA (INT64_MIN) /**< NA value for indices */
|
||||
#define OBIFloat_NA (float_NA()) /**< NA value for the type OBI_FLOAT */
|
||||
#define OBIChar_NA (0) /**< NA value for the type OBI_CHAR */ // TODO not sure about this one as it can be impossible to distinguish from uninitialized values
|
||||
#define OBISeq_NA ("\0") /**< NA value for the type OBI_SEQ */ // TODO discuss
|
||||
#define OBIStr_NA ("\0") /**< NA value for the type OBI_STR */ // TODO discuss
|
||||
#define OBISeq_NA (NULL) /**< NA value for the type OBI_SEQ */ // TODO discuss
|
||||
#define OBIStr_NA (NULL) /**< NA value for the type OBI_STR */ // TODO discuss
|
||||
#define OBIQual_char_NA (NULL) /**< NA value for the type OBI_QUAL if the quality is in character string format */
|
||||
#define OBIQual_int_NA (NULL) /**< NA value for the type OBI_QUAL if the quality is in integer format */
|
||||
|
||||
|
||||
/**
|
||||
@ -45,6 +47,7 @@ typedef enum OBIType {
|
||||
OBI_FLOAT, /**< a floating value (C type : double) */
|
||||
OBI_BOOL, /**< a boolean true/false value, see obibool_t enum */
|
||||
OBI_CHAR, /**< a character (C type : char) */
|
||||
OBI_QUAL, /**< an index in a data structure (C type : int64_t) referring to a quality score array */
|
||||
OBI_STR, /**< an index in a data structure (C type : int64_t) referring to a character string */
|
||||
OBI_SEQ, /**< an index in a data structure (C type : int64_t) referring to a DNA sequence */
|
||||
OBI_IDX /**< an index referring to a line in another column (C type : int64_t) */
|
||||
|
||||
994
src/obiview.c
994
src/obiview.c
File diff suppressed because it is too large
Load Diff
297
src/obiview.h
297
src/obiview.h
@ -17,6 +17,7 @@
|
||||
#include <stdlib.h>
|
||||
#include <errno.h>
|
||||
#include <stdio.h>
|
||||
#include <stdint.h>
|
||||
#include <stdbool.h>
|
||||
#include <time.h>
|
||||
#include <math.h>
|
||||
@ -33,8 +34,6 @@
|
||||
*/
|
||||
#define VIEW_TYPE_MAX_LENGTH (1024) /**< The maximum length of the type name of a view.
|
||||
*/
|
||||
#define OBIVIEW_FILE_NAME "obiviews" /**< The default name of a view file.
|
||||
*/
|
||||
#define LINES_COLUMN_NAME "LINES" /**< The name of the column containing the line selections
|
||||
* in all views.
|
||||
*/
|
||||
@ -44,62 +43,17 @@
|
||||
#define NUC_SEQUENCE_COLUMN "NUC_SEQ" /**< The name of the column containing the nucleotide sequences
|
||||
* in NUC_SEQS_VIEW views.
|
||||
*/
|
||||
#define NUC_SEQUENCE_INDEXER "NUC_SEQ_INDEXER" /**< The name of the indexer containing the nucleotide sequences
|
||||
* in NUC_SEQS_VIEW views.
|
||||
*/
|
||||
#define ID_COLUMN "ID" /**< The name of the column containing the sequence identifiers
|
||||
* in NUC_SEQS_VIEW views.
|
||||
*/
|
||||
#define ID_INDEXER "ID_INDEXER" /**< The name of the indexer containing the sequence identifiers
|
||||
* in NUC_SEQS_VIEW views.
|
||||
*/
|
||||
#define DEFINITION_COLUMN "DEFINITION" /**< The name of the column containing the sequence definitions
|
||||
* in NUC_SEQS_VIEW views.
|
||||
*/
|
||||
#define DEFINITION_INDEXER "DEFINITION_INDEXER" /**< The name of the indexer containing the sequence definitions
|
||||
#define QUALITY_COLUMN "QUALITY" /**< The name of the column containing the sequence qualities
|
||||
* in NUC_SEQS_VIEW views.
|
||||
*/
|
||||
|
||||
|
||||
/**
|
||||
* @brief Structure for an opened view.
|
||||
*/
|
||||
typedef struct Obiview {
|
||||
|
||||
OBIDMS_p dms; /**< A pointer on the DMS to which the view belongs.
|
||||
*/
|
||||
char name[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view.
|
||||
*/
|
||||
char created_from[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view from which that view was cloned if the view was cloned.
|
||||
*/
|
||||
char view_type[VIEW_TYPE_MAX_LENGTH+1]; /**< Type of the view if there is one.
|
||||
* Types existing: NUC_SEQS_VIEW.
|
||||
*/
|
||||
bool read_only; /**< Whether the view is read-only or can be modified.
|
||||
*/
|
||||
OBIDMS_column_p line_selection; /**< A pointer on the column containing the line selection
|
||||
* associated with the view if there is one.
|
||||
* This line selection is read-only, and when a line from the view is read,
|
||||
* it is this line selection that is used.
|
||||
*/
|
||||
OBIDMS_column_p new_line_selection; /**< A pointer on the column containing the new line selection being built
|
||||
* to associate with the view, if there is one.
|
||||
* When a line is selected with obi_select_line() or obi_select_lines(),
|
||||
* it is recorded in this line selection.
|
||||
*/
|
||||
index_t line_count; /**< The number of lines in the view. Refers to the number of lines in each
|
||||
* column of the view if line_selection is NULL, or to the line count of
|
||||
* line_selection if it is not NULL.
|
||||
*/
|
||||
int column_count; /**< The number of columns in the view.
|
||||
*/
|
||||
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS]; /**< Array of pointers on all the columns of the view.
|
||||
*/
|
||||
char comments[OBIVIEW_COMMENTS_MAX_LENGTH+1]; /**< Comments, additional informations on the view.
|
||||
*/
|
||||
} Obiview_t, *Obiview_p;
|
||||
|
||||
|
||||
/**
|
||||
* @brief Structure referencing a column by its name and its version.
|
||||
*/
|
||||
@ -117,8 +71,6 @@ typedef struct Column_reference {
|
||||
* Once a view has been written in the view file, it can not be modified and can only be read.
|
||||
*/
|
||||
typedef struct Obiview_infos {
|
||||
int view_number; /**< Number of the view in the view file.
|
||||
*/
|
||||
time_t creation_date; /**< Time at which the view was written in the view file.
|
||||
*/
|
||||
char name[OBIVIEW_NAME_MAX_LENGTH+1]; /**< Name of the view, used to identify it.
|
||||
@ -143,7 +95,29 @@ typedef struct Obiview_infos {
|
||||
} Obiview_infos_t, *Obiview_infos_p;
|
||||
|
||||
|
||||
// TODO : Combine the common elements of the Obiview_infos and Obiview structures in one structure used by both?
|
||||
/**
|
||||
* @brief Structure for an opened view.
|
||||
*/
|
||||
typedef struct Obiview {
|
||||
Obiview_infos_p infos; /**< A pointer on the mapped view informations.
|
||||
*/
|
||||
OBIDMS_p dms; /**< A pointer on the DMS to which the view belongs.
|
||||
*/
|
||||
bool read_only; /**< Whether the view is read-only or can be modified.
|
||||
*/
|
||||
OBIDMS_column_p line_selection; /**< A pointer on the column containing the line selection
|
||||
* associated with the view if there is one.
|
||||
* This line selection is read-only, and when a line from the view is read,
|
||||
* it is this line selection that is used.
|
||||
*/
|
||||
OBIDMS_column_p new_line_selection; /**< A pointer on the column containing the new line selection being built
|
||||
* to associate with the view, if there is one.
|
||||
* When a line is selected with obi_select_line() or obi_select_lines(),
|
||||
* it is recorded in this line selection.
|
||||
*/
|
||||
OBIDMS_column_p columns[MAX_NB_OPENED_COLUMNS]; /**< Array of pointers on all the columns of the view.
|
||||
*/
|
||||
} Obiview_t, *Obiview_p;
|
||||
|
||||
|
||||
/**
|
||||
@ -224,6 +198,7 @@ Obiview_p obi_new_view_cloned_from_name(OBIDMS_p dms, const char* view_name, con
|
||||
* - NUC_SEQUENCE_COLUMN where nucleotide sequences are stored
|
||||
* - ID_COLUMN where sequence identifiers are stored
|
||||
* - DEFINITION_COLUMN where sequence definitions are stored
|
||||
* - QUALITY_COLUMN where sequence qualities are stored
|
||||
*
|
||||
* @param dms A pointer on the OBIDMS.
|
||||
* @param view_name The unique name of the view.
|
||||
@ -255,6 +230,7 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
|
||||
* - NUC_SEQUENCE_COLUMN where nucleotide sequences are stored
|
||||
* - ID_COLUMN where sequence identifiers are stored
|
||||
* - DEFINITION_COLUMN where sequence definitions are stored
|
||||
* - QUALITY_COLUMN where sequence qualities are stored
|
||||
*
|
||||
* @param dms A pointer on the OBIDMS.
|
||||
* @param view_name The unique name of the new view.
|
||||
@ -272,6 +248,37 @@ Obiview_p obi_new_view_nuc_seqs(OBIDMS_p dms, const char* view_name, Obiview_p v
|
||||
Obiview_p obi_new_view_nuc_seqs_cloned_from_name(OBIDMS_p dms, const char* view_name, const char* view_to_clone_name, index_t* line_selection, const char* comments);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Maps a view file and returns the mapped structure stored in it.
|
||||
*
|
||||
* @param dms A pointer on the OBIDMS.
|
||||
* @param view_name The unique name identifying the view.
|
||||
*
|
||||
* @returns A pointer on the mapped view infos structure.
|
||||
* @retval NULL if an error occurred.
|
||||
*
|
||||
* @since June 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
Obiview_infos_p obi_view_map_file(OBIDMS_p dms, const char* view_name);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Unmaps a view file.
|
||||
*
|
||||
* @param dms A pointer on the OBIDMS.
|
||||
* @param view_infos A pointer on the mapped view infos structure.
|
||||
*
|
||||
* @returns A value indicating the success of the operation.
|
||||
* @retval 0 if the operation was successfully completed.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since June 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_view_unmap_file(OBIDMS_p dms, Obiview_infos_p view_infos);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Opens a view identified by its name stored in the view file.
|
||||
*
|
||||
@ -812,6 +819,194 @@ int obi_column_set_obiint_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p
|
||||
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);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line,
|
||||
* in the context of a view.
|
||||
*
|
||||
* This function is for qualities in the character string format.
|
||||
*
|
||||
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||
*
|
||||
* @param view A pointer on the opened view.
|
||||
* @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, in the character string format.
|
||||
*
|
||||
* @returns An integer value indicating the success of the operation.
|
||||
* @retval 0 on success.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obiqual_char_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, const char* value);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line,
|
||||
* in the context of a view.
|
||||
*
|
||||
* This function is for qualities in the integer format.
|
||||
*
|
||||
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||
*
|
||||
* @param view A pointer on the opened view.
|
||||
* @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, in the integer array format.
|
||||
* @param value_length The length of the integer array.
|
||||
*
|
||||
* @returns An integer value indicating the success of the operation.
|
||||
* @retval 0 on success.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obiqual_int_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, const uint8_t* value, int value_length);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line,
|
||||
* in the context of a view.
|
||||
*
|
||||
* This function returns quality scores in the character string format.
|
||||
*
|
||||
* @param view A pointer on the opened view.
|
||||
* @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, in the character string format.
|
||||
* @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
char* obi_column_get_obiqual_char_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line,
|
||||
* in the context of a view.
|
||||
*
|
||||
* This function returns quality scores in the integer format.
|
||||
*
|
||||
* @param view A pointer on the opened view.
|
||||
* @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.
|
||||
* @param value_length A pointer on an integer to store the length of the integer array recovered.
|
||||
*
|
||||
* @returns The recovered value, in the integer array format.
|
||||
* @retval OBIQual_int_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
const uint8_t* obi_column_get_obiqual_int_with_elt_idx_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, index_t element_idx, int* value_length);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line,
|
||||
* in the context of a view.
|
||||
*
|
||||
* This function is for quality scores in the character string format.
|
||||
*
|
||||
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||
*
|
||||
* @param view A pointer on the opened view.
|
||||
* @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, in the character string format.
|
||||
*
|
||||
* @returns An integer value indicating the success of the operation.
|
||||
* @retval 0 on success.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obiqual_char_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, const char* value);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Sets a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line,
|
||||
* in the context of a view.
|
||||
*
|
||||
* This function is for quality scores in the integer array format.
|
||||
*
|
||||
* @warning Pointers returned by obi_open_column() don't allow writing.
|
||||
*
|
||||
* @param view A pointer on the opened view.
|
||||
* @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, in the integer format.
|
||||
* @param value_length The length of the integer array.
|
||||
*
|
||||
* @returns An integer value indicating the success of the operation.
|
||||
* @retval 0 on success.
|
||||
* @retval -1 if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
int obi_column_set_obiqual_int_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, const uint8_t* value, int value_length);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line,
|
||||
* in the context of a view.
|
||||
*
|
||||
* This function returns quality scores in the character string format.
|
||||
*
|
||||
* @param view A pointer on the opened view.
|
||||
* @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, in the character string format.
|
||||
* @retval OBIQual_char_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
char* obi_column_get_obiqual_char_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Recovers a value in an OBIDMS column containing data in the form of indices referring
|
||||
* to sequence qualities handled by an indexer, and using the index of the element in the column's line,
|
||||
* in the context of a view.
|
||||
*
|
||||
* This function returns quality scores in the integer array format.
|
||||
*
|
||||
* @param view A pointer on the opened view.
|
||||
* @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.
|
||||
* @param value_length A pointer on an integer to store the length of the integer array recovered.
|
||||
*
|
||||
* @returns The recovered value, in the integer format.
|
||||
* @retval OBIQual_int_NA the NA value of the type if an error occurred and obi_errno is set.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
const uint8_t* obi_column_get_obiqual_int_with_elt_name_in_view(Obiview_p view, OBIDMS_column_p column, index_t line_nb, const char* element_name, int* value_length);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Sets a value in an OBIDMS column containing data with the type OBI_SEQ, using the index of the element in the line,
|
||||
* in the context of a view.
|
||||
|
||||
696
src/sse_banded_LCS_alignment.c
Normal file
696
src/sse_banded_LCS_alignment.c
Normal file
@ -0,0 +1,696 @@
|
||||
/*
|
||||
* sse_banded_LCS_alignment.c
|
||||
*
|
||||
* Created on: 7 nov. 2012
|
||||
* Author: celine mercier
|
||||
*/
|
||||
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <math.h>
|
||||
#include <stdint.h>
|
||||
#include <stdbool.h>
|
||||
|
||||
#include "obierrno.h"
|
||||
#include "obidebug.h"
|
||||
#include "utils.h"
|
||||
#include "_sse.h"
|
||||
#include "sse_banded_LCS_alignment.h"
|
||||
|
||||
|
||||
#define DEBUG_LEVEL 0 // TODO has to be defined somewhere else (cython compil flag?)
|
||||
|
||||
|
||||
static void printreg(__m128i r)
|
||||
{
|
||||
int16_t a0,a1,a2,a3,a4,a5,a6,a7;
|
||||
|
||||
a0= _MM_EXTRACT_EPI16(r,0);
|
||||
a1= _MM_EXTRACT_EPI16(r,1);
|
||||
a2= _MM_EXTRACT_EPI16(r,2);
|
||||
a3= _MM_EXTRACT_EPI16(r,3);
|
||||
a4= _MM_EXTRACT_EPI16(r,4);
|
||||
a5= _MM_EXTRACT_EPI16(r,5);
|
||||
a6= _MM_EXTRACT_EPI16(r,6);
|
||||
a7= _MM_EXTRACT_EPI16(r,7);
|
||||
|
||||
fprintf(stderr, "a00 :-> %7d %7d %7d %7d "
|
||||
" %7d %7d %7d %7d "
|
||||
"\n"
|
||||
, a0,a1,a2,a3,a4,a5,a6,a7
|
||||
);
|
||||
}
|
||||
|
||||
|
||||
static inline int extract_reg(__m128i r, int p)
|
||||
{
|
||||
switch (p) {
|
||||
case 0: return(_MM_EXTRACT_EPI16(r,0));
|
||||
case 1: return(_MM_EXTRACT_EPI16(r,1));
|
||||
case 2: return(_MM_EXTRACT_EPI16(r,2));
|
||||
case 3: return(_MM_EXTRACT_EPI16(r,3));
|
||||
case 4: return(_MM_EXTRACT_EPI16(r,4));
|
||||
case 5: return(_MM_EXTRACT_EPI16(r,5));
|
||||
case 6: return(_MM_EXTRACT_EPI16(r,6));
|
||||
case 7: return(_MM_EXTRACT_EPI16(r,7));
|
||||
}
|
||||
return(0);
|
||||
}
|
||||
|
||||
|
||||
// TODO warning on length order
|
||||
void sse_banded_align_lcs_and_ali_len(int16_t* seq1, int16_t* seq2, int l1, int l2, int bandLengthLeft, int bandLengthTotal, int16_t* address, double* lcs_length, int* ali_length)
|
||||
{
|
||||
register int j;
|
||||
int k1, k2;
|
||||
int max, diff;
|
||||
int l_reg, l_loc;
|
||||
int line;
|
||||
int numberOfRegistersPerLine;
|
||||
int numberOfRegistersFor3Lines;
|
||||
|
||||
bool even_line;
|
||||
bool odd_line;
|
||||
bool even_BLL;
|
||||
bool odd_BLL;
|
||||
|
||||
um128* SSEregisters;
|
||||
um128* p_diag;
|
||||
um128* p_gap1;
|
||||
um128* p_gap2;
|
||||
um128* p_diag_j;
|
||||
um128* p_gap1_j;
|
||||
um128* p_gap2_j;
|
||||
um128 current;
|
||||
|
||||
um128* l_ali_SSEregisters;
|
||||
um128* p_l_ali_diag;
|
||||
um128* p_l_ali_gap1;
|
||||
um128* p_l_ali_gap2;
|
||||
um128* p_l_ali_diag_j;
|
||||
um128* p_l_ali_gap1_j;
|
||||
um128* p_l_ali_gap2_j;
|
||||
um128 l_ali_current;
|
||||
|
||||
um128 nucs1;
|
||||
um128 nucs2;
|
||||
um128 scores;
|
||||
|
||||
um128 boolean_reg;
|
||||
|
||||
// Initialisations
|
||||
|
||||
odd_BLL = bandLengthLeft & 1;
|
||||
even_BLL = !odd_BLL;
|
||||
|
||||
max = INT16_MAX - l1;
|
||||
|
||||
numberOfRegistersPerLine = bandLengthTotal / 8;
|
||||
numberOfRegistersFor3Lines = 3 * numberOfRegistersPerLine;
|
||||
|
||||
SSEregisters = (um128*) calloc(numberOfRegistersFor3Lines * 2, sizeof(um128));
|
||||
l_ali_SSEregisters = SSEregisters + numberOfRegistersFor3Lines;
|
||||
|
||||
// preparer registres SSE
|
||||
|
||||
for (j=0; j<numberOfRegistersFor3Lines; j++)
|
||||
l_ali_SSEregisters[j].i = _MM_LOAD_SI128(address+j*8);
|
||||
|
||||
p_diag = SSEregisters;
|
||||
p_gap1 = SSEregisters+numberOfRegistersPerLine;
|
||||
p_gap2 = SSEregisters+2*numberOfRegistersPerLine;
|
||||
|
||||
p_l_ali_diag = l_ali_SSEregisters;
|
||||
p_l_ali_gap1 = l_ali_SSEregisters+numberOfRegistersPerLine;
|
||||
p_l_ali_gap2 = l_ali_SSEregisters+2*numberOfRegistersPerLine;
|
||||
|
||||
// Loop on diagonals = 'lines' :
|
||||
for (line=2; line <= l1+l2; line++)
|
||||
{
|
||||
odd_line = line & 1;
|
||||
even_line = !odd_line;
|
||||
|
||||
// loop on the registers of a line :
|
||||
for (j=0; j < numberOfRegistersPerLine; j++)
|
||||
{
|
||||
p_diag_j = p_diag+j;
|
||||
p_gap1_j = p_gap1+j;
|
||||
p_gap2_j = p_gap2+j;
|
||||
p_l_ali_diag_j = p_l_ali_diag+j;
|
||||
p_l_ali_gap1_j = p_l_ali_gap1+j;
|
||||
p_l_ali_gap2_j = p_l_ali_gap2+j;
|
||||
|
||||
// comparing nucleotides for diagonal scores :
|
||||
|
||||
// k1 = position of the 1st nucleotide to align for seq1 and k2 = position of the 1st nucleotide to align for seq2
|
||||
if (odd_line && odd_BLL)
|
||||
k1 = (line / 2) + ((bandLengthLeft+1) / 2) - j*8;
|
||||
else
|
||||
k1 = (line / 2) + (bandLengthLeft/2) - j*8;
|
||||
|
||||
k2 = line - k1 - 1;
|
||||
|
||||
nucs1.i = _MM_LOADU_SI128(seq1+l1-k1);
|
||||
nucs2.i = _MM_LOADU_SI128(seq2+k2);
|
||||
|
||||
/* fprintf(stderr, "\nnucs, r %d, k1 = %d, k2 = %d\n", j, k1, k2);
|
||||
printreg(nucs1.i);
|
||||
printreg(nucs2.i);
|
||||
*/
|
||||
|
||||
// computing diagonal score :
|
||||
scores.i = _MM_AND_SI128(_MM_CMPEQ_EPI16(nucs1.i, nucs2.i), _MM_SET1_EPI16(1));
|
||||
current.i = _MM_ADDS_EPU16(p_diag_j->i, scores.i);
|
||||
|
||||
// Computing alignment length
|
||||
|
||||
l_ali_current.i = p_l_ali_diag_j->i;
|
||||
boolean_reg.i = _MM_CMPGT_EPI16(p_gap1_j->i, current.i);
|
||||
l_ali_current.i = _MM_OR_SI128(
|
||||
_MM_AND_SI128(p_l_ali_gap1_j->i, boolean_reg.i),
|
||||
_MM_ANDNOT_SI128(boolean_reg.i, l_ali_current.i));
|
||||
current.i = _MM_OR_SI128(
|
||||
_MM_AND_SI128(p_gap1_j->i, boolean_reg.i),
|
||||
_MM_ANDNOT_SI128(boolean_reg.i, current.i));
|
||||
boolean_reg.i = _MM_AND_SI128(
|
||||
_MM_CMPEQ_EPI16(p_gap1_j->i, current.i),
|
||||
_MM_CMPLT_EPI16(p_l_ali_gap1_j->i, l_ali_current.i));
|
||||
l_ali_current.i = _MM_OR_SI128(
|
||||
_MM_AND_SI128(p_l_ali_gap1_j->i, boolean_reg.i),
|
||||
_MM_ANDNOT_SI128(boolean_reg.i, l_ali_current.i));
|
||||
current.i = _MM_OR_SI128(
|
||||
_MM_AND_SI128(p_gap1_j->i, boolean_reg.i),
|
||||
_MM_ANDNOT_SI128(boolean_reg.i, current.i));
|
||||
boolean_reg.i = _MM_CMPGT_EPI16(p_gap2_j->i, current.i);
|
||||
l_ali_current.i = _MM_OR_SI128(
|
||||
_MM_AND_SI128(p_l_ali_gap2_j->i, boolean_reg.i),
|
||||
_MM_ANDNOT_SI128(boolean_reg.i, l_ali_current.i));
|
||||
current.i = _MM_OR_SI128(
|
||||
_MM_AND_SI128(p_gap2_j->i, boolean_reg.i),
|
||||
_MM_ANDNOT_SI128(boolean_reg.i, current.i));
|
||||
boolean_reg.i = _MM_AND_SI128(
|
||||
_MM_CMPEQ_EPI16(p_gap2_j->i, current.i),
|
||||
_MM_CMPLT_EPI16(p_l_ali_gap2_j->i, l_ali_current.i));
|
||||
l_ali_current.i = _MM_OR_SI128(
|
||||
_MM_AND_SI128(p_l_ali_gap2_j->i, boolean_reg.i),
|
||||
_MM_ANDNOT_SI128(boolean_reg.i, l_ali_current.i));
|
||||
current.i = _MM_OR_SI128(
|
||||
_MM_AND_SI128(p_gap2_j->i, boolean_reg.i),
|
||||
_MM_ANDNOT_SI128(boolean_reg.i, current.i));
|
||||
|
||||
/*
|
||||
fprintf(stderr, "\nline = %d", line);
|
||||
fprintf(stderr, "\nDiag, r %d : ", j);
|
||||
printreg((*(p_diag_j)).i);
|
||||
fprintf(stderr, "Gap1 : ");
|
||||
printreg((*(p_gap1_j)).i);
|
||||
fprintf(stderr, "Gap2 : ");
|
||||
printreg((*(p_gap2_j)).i);
|
||||
fprintf(stderr, "current : ");
|
||||
printreg(current.i);
|
||||
fprintf(stderr, "L ALI\nDiag r %d : ", j);
|
||||
printreg((*(p_l_ali_diag_j)).i);
|
||||
fprintf(stderr, "Gap1 : ");
|
||||
printreg((*(p_l_ali_gap1_j)).i);
|
||||
fprintf(stderr, "Gap2 : ");
|
||||
printreg((*(p_l_ali_gap2_j)).i);
|
||||
fprintf(stderr, "current : ");
|
||||
printreg(l_ali_current.i);
|
||||
*/
|
||||
|
||||
// diag = gap1 and gap1 = current
|
||||
p_diag_j->i = p_gap1_j->i;
|
||||
p_gap1_j->i = current.i;
|
||||
|
||||
// l_ali_diag = l_ali_gap1 and l_ali_gap1 = l_ali_current+1
|
||||
p_l_ali_diag_j->i = p_l_ali_gap1_j->i;
|
||||
p_l_ali_gap1_j->i = _MM_ADD_EPI16(l_ali_current.i, _MM_SET1_EPI16(1));
|
||||
}
|
||||
|
||||
// shifts for gap2, to do only once all the registers of a line have been computed Copier gap2 puis le charger depuis la copie?
|
||||
|
||||
for (j=0; j < numberOfRegistersPerLine; j++)
|
||||
{
|
||||
if ((odd_line && even_BLL) || (even_line && odd_BLL))
|
||||
{
|
||||
p_gap2[j].i = _MM_LOADU_SI128((p_gap1[j].s16)-1);
|
||||
p_l_ali_gap2[j].i = _MM_LOADU_SI128((p_l_ali_gap1[j].s16)-1);
|
||||
if (j == 0)
|
||||
{
|
||||
p_gap2[j].i = _MM_INSERT_EPI16(p_gap2[j].i, 0, 0);
|
||||
p_l_ali_gap2[j].i = _MM_INSERT_EPI16(p_l_ali_gap2[j].i, max, 0);
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
p_gap2[j].i = _MM_LOADU_SI128(p_gap1[j].s16+1);
|
||||
p_l_ali_gap2[j].i = _MM_LOADU_SI128(p_l_ali_gap1[j].s16+1);
|
||||
if (j == numberOfRegistersPerLine - 1)
|
||||
{
|
||||
p_gap2[j].i = _MM_INSERT_EPI16(p_gap2[j].i, 0, 7);
|
||||
p_l_ali_gap2[j].i = _MM_INSERT_EPI16(p_l_ali_gap2[j].i, max, 7);
|
||||
}
|
||||
}
|
||||
}
|
||||
// end shifts for gap2
|
||||
|
||||
}
|
||||
|
||||
/* /// Recovering LCS and alignment lengths \\\ */
|
||||
|
||||
// finding the location of the results in the registers :
|
||||
diff = l1-l2;
|
||||
if ((diff & 1) && odd_BLL)
|
||||
l_loc = (int) floor((double)(bandLengthLeft) / (double)2) - floor((double)(diff) / (double)2);
|
||||
else
|
||||
l_loc = (int) floor((double)(bandLengthLeft) / (double)2) - ceil((double)(diff) / (double)2);
|
||||
|
||||
l_reg = (int)floor((double)l_loc/(double)8.0);
|
||||
//fprintf(stderr, "\nl_reg = %d, l_loc = %d\n", l_reg, l_loc);
|
||||
l_loc = l_loc - l_reg*8;
|
||||
|
||||
// extracting the results from the registers :
|
||||
*lcs_length = extract_reg(p_gap1[l_reg].i, l_loc);
|
||||
*ali_length = extract_reg(p_l_ali_gap1[l_reg].i, l_loc) - 1;
|
||||
|
||||
// freeing the registers
|
||||
free(SSEregisters);
|
||||
}
|
||||
|
||||
|
||||
// TODO warning on length order
|
||||
double sse_banded_align_just_lcs(int16_t* seq1, int16_t* seq2, int l1, int l2, int bandLengthLeft, int bandLengthTotal)
|
||||
{
|
||||
register int j;
|
||||
int k1, k2;
|
||||
int diff;
|
||||
int l_reg, l_loc;
|
||||
int16_t l_lcs;
|
||||
int line;
|
||||
int numberOfRegistersPerLine;
|
||||
int numberOfRegistersFor3Lines;
|
||||
|
||||
bool even_line;
|
||||
bool odd_line;
|
||||
bool even_BLL;
|
||||
bool odd_BLL;
|
||||
|
||||
um128* SSEregisters;
|
||||
um128* p_diag;
|
||||
um128* p_gap1;
|
||||
um128* p_gap2;
|
||||
um128* p_diag_j;
|
||||
um128* p_gap1_j;
|
||||
um128* p_gap2_j;
|
||||
um128 current;
|
||||
|
||||
um128 nucs1;
|
||||
um128 nucs2;
|
||||
um128 scores;
|
||||
|
||||
// Initialisations
|
||||
|
||||
odd_BLL = bandLengthLeft & 1;
|
||||
even_BLL = !odd_BLL;
|
||||
|
||||
numberOfRegistersPerLine = bandLengthTotal / 8;
|
||||
numberOfRegistersFor3Lines = 3 * numberOfRegistersPerLine;
|
||||
|
||||
SSEregisters = malloc(numberOfRegistersFor3Lines * sizeof(um128));
|
||||
if (SSEregisters == NULL)
|
||||
{
|
||||
obi_set_errno(OBI_MALLOC_ERROR);
|
||||
obidebug(1, "\nError allocating memory for SSE registers for LCS alignment");
|
||||
return 0; // TODO DOUBLE_MIN?
|
||||
}
|
||||
|
||||
// preparer registres SSE
|
||||
|
||||
for (j=0; j<numberOfRegistersFor3Lines; j++)
|
||||
(*(SSEregisters+j)).i = _MM_SETZERO_SI128();
|
||||
|
||||
p_diag = SSEregisters;
|
||||
p_gap1 = SSEregisters+numberOfRegistersPerLine;
|
||||
p_gap2 = SSEregisters+2*numberOfRegistersPerLine;
|
||||
|
||||
// Loop on diagonals = 'lines' :
|
||||
for (line=2; line <= l1+l2; line++)
|
||||
{
|
||||
odd_line = line & 1;
|
||||
even_line = !odd_line;
|
||||
|
||||
// loop on the registers of a line :
|
||||
for (j=0; j < numberOfRegistersPerLine; j++)
|
||||
{
|
||||
p_diag_j = p_diag+j;
|
||||
p_gap1_j = p_gap1+j;
|
||||
p_gap2_j = p_gap2+j;
|
||||
|
||||
// comparing nucleotides for diagonal scores :
|
||||
|
||||
// k1 = position of the 1st nucleotide to align for seq1 and k2 = position of the 1st nucleotide to align for seq2
|
||||
if (odd_line && odd_BLL)
|
||||
k1 = (line / 2) + ((bandLengthLeft+1) / 2) - j*8;
|
||||
else
|
||||
k1 = (line / 2) + (bandLengthLeft/2) - j*8;
|
||||
|
||||
k2 = line - k1 - 1;
|
||||
|
||||
nucs1.i = _MM_LOADU_SI128(seq1+l1-k1);
|
||||
nucs2.i = _MM_LOADU_SI128(seq2+k2);
|
||||
|
||||
// computing diagonal score :
|
||||
scores.i = _MM_AND_SI128(_MM_CMPEQ_EPI16(nucs1.i, nucs2.i), _MM_SET1_EPI16(1));
|
||||
current.i = _MM_ADDS_EPU16((*(p_diag_j)).i, scores.i);
|
||||
|
||||
// current = max(gap1, current)
|
||||
current.i = _MM_MAX_EPI16((*(p_gap1_j)).i, current.i);
|
||||
|
||||
// current = max(gap2, current)
|
||||
current.i = _MM_MAX_EPI16((*(p_gap2_j)).i, current.i);
|
||||
|
||||
// diag = gap1 and gap1 = current
|
||||
(*(p_diag_j)).i = (*(p_gap1_j)).i;
|
||||
(*(p_gap1_j)).i = current.i;
|
||||
}
|
||||
|
||||
// shifts for gap2, to do only once all the registers of a line have been computed
|
||||
|
||||
for (j=0; j < numberOfRegistersPerLine; j++)
|
||||
{
|
||||
if ((odd_line && even_BLL) || (even_line && odd_BLL))
|
||||
{
|
||||
(*(p_gap2+j)).i = _MM_LOADU_SI128(((*(p_gap1+j)).s16)-1);
|
||||
if (j == 0)
|
||||
{
|
||||
(*(p_gap2+j)).i = _MM_INSERT_EPI16((*(p_gap2+j)).i, 0, 0);
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
(*(p_gap2+j)).i = _MM_LOADU_SI128(((*(p_gap1+j)).s16)+1);
|
||||
if (j == numberOfRegistersPerLine - 1)
|
||||
{
|
||||
(*(p_gap2+j)).i = _MM_INSERT_EPI16((*(p_gap2+j)).i, 0, 7);
|
||||
}
|
||||
}
|
||||
}
|
||||
// end shifts for gap2
|
||||
}
|
||||
|
||||
/* /// Recovering LCS and alignment lengths \\\ */
|
||||
|
||||
// finding the location of the results in the registers :
|
||||
diff = l1-l2;
|
||||
if ((diff & 1) && odd_BLL)
|
||||
l_loc = (int) floor((double)(bandLengthLeft) / (double)2) - floor((double)(diff) / (double)2);
|
||||
else
|
||||
l_loc = (int) floor((double)(bandLengthLeft) / (double)2) - ceil((double)(diff) / (double)2);
|
||||
|
||||
l_reg = (int)floor((double)l_loc/(double)8.0);
|
||||
//fprintf(stderr, "\nl_reg = %d, l_loc = %d\n", l_reg, l_loc);
|
||||
l_loc = l_loc - l_reg*8;
|
||||
|
||||
// extracting LCS from the registers :
|
||||
l_lcs = extract_reg((*(p_gap1+l_reg)).i, l_loc);
|
||||
|
||||
// freeing the registers
|
||||
free(SSEregisters);
|
||||
|
||||
return((double) l_lcs);
|
||||
}
|
||||
|
||||
|
||||
int calculateLeftBandLength(int lmax, int LCSmin)
|
||||
{
|
||||
return (lmax - LCSmin);
|
||||
}
|
||||
|
||||
|
||||
int calculateRightBandLength(int lmin, int LCSmin)
|
||||
{
|
||||
return (lmin - LCSmin);
|
||||
}
|
||||
|
||||
|
||||
int calculateSSEBandLength(int bandLengthRight, int bandLengthLeft)
|
||||
{
|
||||
int bandLengthTotal= (double)(bandLengthRight + bandLengthLeft) / 2.0 + 1.0;
|
||||
|
||||
return (bandLengthTotal & (~ (int)7)) + (( bandLengthTotal & (int)7) ? 8:0); // Calcule le multiple de 8 superieur
|
||||
}
|
||||
|
||||
|
||||
// TODO that's gonna be fun to doc
|
||||
int calculateSizeToAllocate(int maxLen, int minLen, int LCSmin)
|
||||
{
|
||||
int size;
|
||||
|
||||
size = calculateLeftBandLength(maxLen, LCSmin);
|
||||
|
||||
size *= 2;
|
||||
size = (size & (~ (int)7)) + (( size & (int)7) ? 8:0); // Closest greater 8 multiple
|
||||
size *= 3;
|
||||
size += 16;
|
||||
|
||||
return(size*sizeof(int16_t));
|
||||
}
|
||||
|
||||
|
||||
void iniSeq(int16_t* seq, int size, int16_t iniValue)
|
||||
{
|
||||
int16_t* target = seq;
|
||||
int16_t* end = target + (size_t)size;
|
||||
|
||||
for (; target < end; target++)
|
||||
*target = iniValue;
|
||||
}
|
||||
|
||||
|
||||
void putSeqInSeq(int16_t* seq, char* s, int l, bool reverse)
|
||||
{
|
||||
int16_t *target=seq;
|
||||
int16_t *end = target + (size_t)l;
|
||||
char *source=s;
|
||||
|
||||
if (reverse)
|
||||
for (source=s + (size_t)l-1; target < end; target++, source--)
|
||||
*target=*source;
|
||||
else
|
||||
for (; target < end; source++,target++)
|
||||
*target=*source;
|
||||
}
|
||||
|
||||
|
||||
void initializeAddressWithGaps(int16_t* address, int bandLengthTotal, int bandLengthLeft, int l1)
|
||||
{
|
||||
int i;
|
||||
int address_00, x_address_10, address_01, address_01_shifted;
|
||||
int numberOfRegistersPerLine;
|
||||
int bm;
|
||||
int value=INT16_MAX-l1;
|
||||
|
||||
numberOfRegistersPerLine = bandLengthTotal / 8;
|
||||
bm = bandLengthLeft%2;
|
||||
|
||||
for (i=0; i < (3*numberOfRegistersPerLine*8); i++)
|
||||
address[i] = value;
|
||||
|
||||
|
||||
// 0,0 set to 1 and 0,1 and 1,0 set to 2
|
||||
|
||||
address_00 = bandLengthLeft / 2;
|
||||
|
||||
x_address_10 = address_00 + bm - 1;
|
||||
address_01 = numberOfRegistersPerLine*8 + x_address_10;
|
||||
|
||||
address_01_shifted = numberOfRegistersPerLine*16 + address_00 - bm;
|
||||
|
||||
// fill address_00, address_01,+1, address_01_shifted,+1
|
||||
|
||||
address[address_00] = 1;
|
||||
address[address_01] = 2;
|
||||
address[address_01+1] = 2;
|
||||
address[address_01_shifted] = 2;
|
||||
address[address_01_shifted+1] = 2;
|
||||
}
|
||||
|
||||
|
||||
// TODO warning on length order
|
||||
double sse_banded_lcs_align(int16_t* seq1, int16_t* seq2, int l1, int l2, bool normalize, int reference, bool similarity_mode, int16_t* address, int LCSmin)
|
||||
{
|
||||
double id;
|
||||
int bandLengthRight, bandLengthLeft, bandLengthTotal;
|
||||
int ali_length;
|
||||
|
||||
bandLengthLeft = calculateLeftBandLength(l1, LCSmin);
|
||||
bandLengthRight = calculateRightBandLength(l2, LCSmin);
|
||||
|
||||
// fprintf(stderr, "\nBLL = %d, BLR = %d, LCSmin = %d\n", bandLengthLeft, bandLengthRight, LCSmin);
|
||||
|
||||
bandLengthTotal = calculateSSEBandLength(bandLengthRight, bandLengthLeft);
|
||||
|
||||
// fprintf(stderr, "\nBLT = %d\n", bandLengthTotal);
|
||||
|
||||
if ((reference == ALILEN) && (normalize || !similarity_mode))
|
||||
{
|
||||
initializeAddressWithGaps(address, bandLengthTotal, bandLengthLeft, l1);
|
||||
sse_banded_align_lcs_and_ali_len(seq1, seq2, l1, l2, bandLengthLeft, bandLengthTotal, address, &id, &ali_length);
|
||||
}
|
||||
else
|
||||
id = sse_banded_align_just_lcs(seq1, seq2, l1, l2, bandLengthLeft, bandLengthTotal);
|
||||
|
||||
// fprintf(stderr, "\nid before normalizations = %f", id);
|
||||
|
||||
// fprintf(stderr, "\nlcs = %f, ali = %d\n", id, ali_length);
|
||||
|
||||
if (!similarity_mode && !normalize)
|
||||
switch(reference) {
|
||||
case ALILEN: id = ali_length - id;
|
||||
break;
|
||||
case MAXLEN: id = l1 - id;
|
||||
break;
|
||||
case MINLEN: id = l2 - id;
|
||||
}
|
||||
|
||||
// fprintf(stderr, "\n2>>> %f, %d\n", id, ali_length);
|
||||
if (normalize)
|
||||
switch(reference) {
|
||||
case ALILEN: id = id / (double) ali_length;
|
||||
break;
|
||||
case MAXLEN: id = id / (double) l1;
|
||||
break;
|
||||
case MINLEN: id = id / (double) l2;
|
||||
}
|
||||
|
||||
// fprintf(stderr, "\nid = %f\n", id);
|
||||
return(id);
|
||||
}
|
||||
|
||||
|
||||
|
||||
// PUBLIC FUNCTIONS
|
||||
|
||||
|
||||
int calculateLCSmin(int l1, int l2, double threshold, bool normalize, int reference, bool similarity_mode)
|
||||
{
|
||||
int LCSmin;
|
||||
|
||||
if (threshold > 0)
|
||||
{
|
||||
if (normalize)
|
||||
{
|
||||
if (reference == MINLEN)
|
||||
LCSmin = threshold*l2;
|
||||
else // ref = maxlen or alilen
|
||||
LCSmin = threshold*l1;
|
||||
}
|
||||
else if (similarity_mode)
|
||||
LCSmin = threshold;
|
||||
else if (reference == MINLEN) // not similarity_mode
|
||||
LCSmin = l2 - threshold;
|
||||
else // not similarity_mode and ref = maxlen or alilen
|
||||
LCSmin = l1 - threshold;
|
||||
}
|
||||
else
|
||||
LCSmin = 0;
|
||||
|
||||
return(LCSmin);
|
||||
}
|
||||
|
||||
|
||||
double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, bool normalize, int reference, bool similarity_mode)
|
||||
{
|
||||
double id;
|
||||
int l1, l2;
|
||||
int lmax, lmin;
|
||||
int sizeToAllocateForBand, sizeToAllocateForSeqs;
|
||||
int maxBLL;
|
||||
int LCSmin;
|
||||
int shift;
|
||||
int16_t* address;
|
||||
int16_t* iseq1;
|
||||
int16_t* iseq2;
|
||||
|
||||
address = NULL;
|
||||
|
||||
l1 = strlen(seq1);
|
||||
l2 = strlen(seq2);
|
||||
|
||||
if (l1 > l2)
|
||||
{
|
||||
lmax = l1;
|
||||
lmin = l2;
|
||||
}
|
||||
else
|
||||
{
|
||||
lmax = l2;
|
||||
lmin = l1;
|
||||
}
|
||||
|
||||
// If the score is expressed as a normalized distance, get the corresponding identity
|
||||
if (!similarity_mode && normalize)
|
||||
threshold = 1.0 - threshold;
|
||||
|
||||
// Calculate the minimum LCS length corresponding to the threshold
|
||||
LCSmin = calculateLCSmin(lmax, lmin, threshold, normalize, reference, similarity_mode);
|
||||
|
||||
// Allocate space for matrix band if the alignment length must be computed
|
||||
if ((reference == ALILEN) && (normalize || !similarity_mode)) // cases in which alignment length must be computed
|
||||
{
|
||||
sizeToAllocateForBand = calculateSizeToAllocate(lmax, lmin, LCSmin);
|
||||
address = obi_get_memory_aligned_on_16(sizeToAllocateForBand, &shift);
|
||||
if (address == NULL)
|
||||
{
|
||||
obi_set_errno(OBI_MALLOC_ERROR);
|
||||
obidebug(1, "\nError getting a memory address aligned on 16 bytes boundary");
|
||||
return 0; // TODO DOUBLE_MIN
|
||||
}
|
||||
}
|
||||
|
||||
// Allocate space for the int16_t arrays representing the sequences
|
||||
maxBLL = calculateLeftBandLength(lmax, LCSmin);
|
||||
sizeToAllocateForSeqs = 2*maxBLL+lmax;
|
||||
iseq1 = (int16_t*) malloc(sizeToAllocateForSeqs*sizeof(int16_t));
|
||||
iseq2 = (int16_t*) malloc(sizeToAllocateForSeqs*sizeof(int16_t));
|
||||
if ((iseq1 == NULL) || (iseq2 == NULL))
|
||||
{
|
||||
obi_set_errno(OBI_MALLOC_ERROR);
|
||||
obidebug(1, "\nError allocating memory for integer arrays to use in LCS alignment");
|
||||
return 0; // TODO DOUBLE_MIN
|
||||
}
|
||||
|
||||
// Initialize the int arrays
|
||||
iniSeq(iseq1, (2*maxBLL)+lmax, 0);
|
||||
iniSeq(iseq2, (2*maxBLL)+lmax, 255);
|
||||
|
||||
// Shift addresses to where the sequences have to be put
|
||||
iseq1 = iseq1+maxBLL;
|
||||
iseq2 = iseq2+maxBLL;
|
||||
|
||||
// Put the DNA sequences in the int arrays. Longest sequence must be first argument of sse_align function
|
||||
if (l2 > l1)
|
||||
{
|
||||
putSeqInSeq(iseq1, seq2, l2, TRUE);
|
||||
putSeqInSeq(iseq2, seq1, l1, FALSE);
|
||||
// Compute alignment
|
||||
id = sse_banded_lcs_align(iseq1, iseq2, l2, l1, normalize, reference, similarity_mode, address, LCSmin);
|
||||
}
|
||||
else
|
||||
{
|
||||
putSeqInSeq(iseq1, seq1, l1, TRUE);
|
||||
putSeqInSeq(iseq2, seq2, l2, FALSE);
|
||||
// Compute alignment
|
||||
id = sse_banded_lcs_align(iseq1, iseq2, l1, l2, normalize, reference, similarity_mode, address, LCSmin);
|
||||
}
|
||||
|
||||
// Free allocated elements
|
||||
if (address != NULL)
|
||||
free(address-shift);
|
||||
free(iseq1-maxBLL);
|
||||
free(iseq2-maxBLL);
|
||||
|
||||
return(id);
|
||||
}
|
||||
|
||||
23
src/sse_banded_LCS_alignment.h
Normal file
23
src/sse_banded_LCS_alignment.h
Normal file
@ -0,0 +1,23 @@
|
||||
/*
|
||||
* sse_banded_LCS_alignment.h
|
||||
*
|
||||
* Created on: november 29, 2012
|
||||
* Author: mercier
|
||||
*/
|
||||
|
||||
#ifndef SSE_BANDED_LCS_ALIGNMENT_H_
|
||||
#define SSE_BANDED_LCS_ALIGNMENT_H_
|
||||
|
||||
|
||||
#include <stdint.h>
|
||||
#include <stdbool.h>
|
||||
|
||||
#define ALILEN (0) // TODO enum
|
||||
#define MAXLEN (1)
|
||||
#define MINLEN (2)
|
||||
|
||||
// TODO doc
|
||||
int calculateLCSmin(int l1, int l2, double threshold, bool normalize, int reference, bool lcsmode);
|
||||
double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, bool normalize, int reference, bool similarity_mode);
|
||||
|
||||
#endif
|
||||
70
src/uint8_indexer.c
Normal file
70
src/uint8_indexer.c
Normal file
@ -0,0 +1,70 @@
|
||||
/****************************************************************************
|
||||
* Uint8 indexing functions *
|
||||
****************************************************************************/
|
||||
|
||||
/**
|
||||
* @file uint8_indexer.c
|
||||
* @author Celine Mercier
|
||||
* @date May 4th 2016
|
||||
* @brief Functions handling the indexing and retrieval of uint8 arrays.
|
||||
*/
|
||||
|
||||
|
||||
#include <stdlib.h>
|
||||
#include <stdio.h>
|
||||
#include <stdint.h>
|
||||
#include <math.h>
|
||||
|
||||
#include "uint8_indexer.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_uint8_to_blob(const uint8_t* value, int value_length)
|
||||
{
|
||||
return obi_blob((byte_t*)value, ELEMENT_SIZE_UINT8, value_length, value_length);
|
||||
}
|
||||
|
||||
|
||||
const uint8_t* obi_blob_to_uint8(Obi_blob_p value_b)
|
||||
{
|
||||
return ((uint8_t*) (value_b->value));
|
||||
}
|
||||
|
||||
|
||||
index_t obi_index_uint8(Obi_indexer_p indexer, const uint8_t* value, int value_length)
|
||||
{
|
||||
Obi_blob_p value_b;
|
||||
index_t idx;
|
||||
|
||||
// Encode value
|
||||
value_b = obi_uint8_to_blob(value, value_length);
|
||||
if (value_b == NULL)
|
||||
return -1;
|
||||
|
||||
// Add in the indexer
|
||||
idx = obi_indexer_add(indexer, value_b);
|
||||
|
||||
free(value_b);
|
||||
|
||||
return idx;
|
||||
}
|
||||
|
||||
|
||||
const uint8_t* obi_retrieve_uint8(Obi_indexer_p indexer, index_t idx, int* value_length)
|
||||
{
|
||||
Obi_blob_p value_b;
|
||||
|
||||
// Get encoded value
|
||||
value_b = obi_indexer_get(indexer, idx);
|
||||
|
||||
// Return decoded sequence
|
||||
*value_length = value_b->length_decoded_value;
|
||||
return obi_blob_to_uint8(value_b);
|
||||
}
|
||||
|
||||
92
src/uint8_indexer.h
Normal file
92
src/uint8_indexer.h
Normal file
@ -0,0 +1,92 @@
|
||||
/****************************************************************************
|
||||
* uint8 indexer header file *
|
||||
****************************************************************************/
|
||||
|
||||
/**
|
||||
* @file uint8_indexer.h
|
||||
* @author Celine Mercier
|
||||
* @date May 4th 2016
|
||||
* @brief Header file for the functions handling the indexing of uint8 arrays.
|
||||
*/
|
||||
|
||||
|
||||
#ifndef UINT8_INDEXER_H_
|
||||
#define UINT8_INDEXER_H_
|
||||
|
||||
|
||||
#include <stdlib.h>
|
||||
#include <stdio.h>
|
||||
|
||||
#include "obidms.h"
|
||||
#include "obitypes.h"
|
||||
#include "obiblob.h"
|
||||
#include "obiblob_indexer.h"
|
||||
|
||||
|
||||
/**
|
||||
* @brief Converts an uint8 array to a blob.
|
||||
*
|
||||
* @warning The blob must be freed by the caller.
|
||||
*
|
||||
* @param value The uint8 array to convert.
|
||||
* @param value_length The length of the uint8 array to convert.
|
||||
*
|
||||
* @returns A pointer on the blob created.
|
||||
* @retval NULL if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
Obi_blob_p obi_uint8_to_blob(const uint8_t* value, int value_length);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Converts a blob to an uint8 array.
|
||||
*
|
||||
* @warning The array returned is mapped.
|
||||
*
|
||||
* @param value_b The blob to convert.
|
||||
*
|
||||
* @returns A pointer on the uint8 array contained in the blob.
|
||||
* @retval NULL if an error occurred.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
const uint8_t* obi_blob_to_uint8(Obi_blob_p value_b);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Stores an uint8 array in an indexer and returns the index.
|
||||
*
|
||||
* @param indexer The indexer structure.
|
||||
* @param value The uint8 array to index.
|
||||
* @param value_length The length of the uint8 array to index.
|
||||
*
|
||||
* @returns The index referring to the stored uint8 array in the indexer.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
index_t obi_index_uint8(Obi_indexer_p indexer, const uint8_t* value, int value_length);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Retrieves an uint8 array from an indexer.
|
||||
*
|
||||
* @warning The array returned is mapped.
|
||||
*
|
||||
* @param indexer The indexer structure.
|
||||
* @param idx The index referring to the uint8 array to retrieve in the indexer.
|
||||
* @param value_length A pointer on an integer to store the length of the array retrieved.
|
||||
*
|
||||
* @returns A pointer on the uint8 array.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
const uint8_t* obi_retrieve_uint8(Obi_indexer_p indexer, index_t idx, int* value_length);
|
||||
|
||||
|
||||
#endif /* UINT8_INDEXER_H_ */
|
||||
|
||||
30
src/utils.c
30
src/utils.c
@ -65,6 +65,12 @@ char* obi_format_date(time_t date)
|
||||
struct tm* tmp;
|
||||
|
||||
formatted_time = (char*) malloc(FORMATTED_TIME_LENGTH*sizeof(char));
|
||||
if (formatted_time == NULL)
|
||||
{
|
||||
obi_set_errno(OBI_MALLOC_ERROR);
|
||||
obidebug(1, "\nError allocating memory to format a date");
|
||||
return NULL;
|
||||
}
|
||||
|
||||
tmp = localtime(&date);
|
||||
if (tmp == NULL)
|
||||
@ -84,3 +90,27 @@ char* obi_format_date(time_t date)
|
||||
return formatted_time;
|
||||
}
|
||||
|
||||
|
||||
void* obi_get_memory_aligned_on_16(int size, int* shift)
|
||||
{
|
||||
void* memory;
|
||||
|
||||
*shift = 0;
|
||||
|
||||
memory = (void*) malloc(size);
|
||||
if (memory == NULL)
|
||||
{
|
||||
obi_set_errno(OBI_MALLOC_ERROR);
|
||||
obidebug(1, "\nError allocating memory");
|
||||
return NULL;
|
||||
}
|
||||
|
||||
while ((((long long unsigned int) (memory))%16) != 0)
|
||||
{
|
||||
memory++;
|
||||
(*shift)++;
|
||||
}
|
||||
|
||||
return (memory);
|
||||
}
|
||||
|
||||
|
||||
21
src/utils.h
21
src/utils.h
@ -53,4 +53,25 @@ int count_dir(char* dir_path);
|
||||
char* obi_format_date(time_t date);
|
||||
|
||||
|
||||
/**
|
||||
* @brief Allocates a chunk of memory aligned on 16 bytes boundary.
|
||||
*
|
||||
* @warning The pointer returned must be freed by the caller.
|
||||
* @warning The memory chunk pointed at by the returned pointer can be
|
||||
* smaller than the size asked for, since the address is shifted
|
||||
* to be aligned.
|
||||
*
|
||||
* @param size The size in bytes of the memory chunk to be allocated.
|
||||
* Ideally the closest multiple of 16 greater than the wanted size.
|
||||
* @param shift A pointer on an integer corresponding to the shift made to align
|
||||
* the address. Used to free the memory chunk.
|
||||
*
|
||||
* @returns The pointer on the aligned memory.
|
||||
*
|
||||
* @since May 2016
|
||||
* @author Celine Mercier (celine.mercier@metabarcoding.org)
|
||||
*/
|
||||
void* obi_get_memory_aligned_on_16(int size, int* shift);
|
||||
|
||||
|
||||
#endif /* UTILS_H_ */
|
||||
|
||||
Reference in New Issue
Block a user