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(not worth it for now as comparisons are already fast enough)

Licence_CeCILL_V2-en.txt

@@ -0,0 +1,506 @@
+
+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.

Licence_CeCILL_V2-fr.txt

@@ -0,0 +1,512 @@
+
+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.

README.md

@@ -0,0 +1,40 @@
+The `OBITools3`: A package for the management of analyses and data in DNA metabarcoding   
+---------------------------------------------
+
+
+
+DNA metabarcoding offers new perspectives for biodiversity research [1]. This approach of ecosystem studies relies heavily on the use of Next-Generation Sequencing (NGS), and consequently requires the ability to to treat large volumes of data. The `OBITools` package  satisfies this requirement thanks to a set of programs specifically designed for analyzing NGS data in a DNA metabarcoding context [2] - <http://metabarcoding.org/obitools>. Their capacity to filter and edit sequences while taking into account taxonomic annotation helps to setup tailored-made analysis pipelines for a broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.   
+
+
+
+**The `OBITools3`.** This new version of the `OBITools` looks to significantly improve the storage efficiency and the data processing speed. To this end, the `OBITools3` rely on an ad hoc database system, inside which all the data that a DNA metabarcoding experiment must consider is stored: the sequences, the metadata (describing for instance the samples), the database containing the reference sequences used for the taxonomic annotation, as well as the taxonomic databases. Besides the gain in efficiency, this new structure allows an easier access to all the data associated with an experiment.   
+
+
+
+**Column-oriented storage.** An analysis pipeline corresponds to a succession of commands, each computing one step of the analysis, and where the result of the command *n* is used by the command *n+1*. DNA metabarcoding data can easily be represented in the form of tables, and each command can be regarded as an operation transforming one or several 'input' tables into one or several 'output' tables, which can be used by the next command. Many of the basic operations in a pipeline copy without modification an important part of the input tables to the result tables, and use for their calculations only a small part of the input data. In the original `OBITools`, those tables are kept in the form of annotated sequence files in the FASTA or FASTQ format. This has two consequences: i) keeping the transitional results of the analysis pipeline means using disk space for an important volume of redundant data, ii) The coding and decoding of informations that are not actually used represent an important part of the treatment process. The new database system used by the `OBITools3` (called DMS for Data Management System) relies on column-oriented storage. The columns are immutable and can be assembled in views representing the data tables. This way, the data not modified by a command in an input table can easily be associated to the result table without duplicating any information ; and the data not used at all by a command can be associated with the result table without being read. This strategy results in a gain in disk space efficiency by limiting data redundancy, as well as a gain in execution time by limiting data reading, writing and conversion operations. Finally, as a mean to optimize data access, each column is stored in a binary file directly mapped in memory for reading and writing operations.   
+
+
+
+**Storage optimization.** DNA metabarcoding data is intrinsically very redundant. For example, the same sequence corresponding to a species will be present several thousand times across all samples. In order to limit the disk space used and make comparison operations more efficient, data in the form of character strings is stored in columns using a complex indexing structure, efficient on millions of values, coupling hash functions, Bloom filters and AVL trees. Finally, DNA sequences are compressed by encoding each nucleotide on two or four bits depending on whether the sequences contain only the four nucleotides (A, C, G, T) or use the IUPAC codes.   
+
+
+
+**Saving the data processing history.** The totality of the informations used by the `OBITools3` is stored in immutable data structures in the DMS. If a command has to modify a column used as input to produce its result, a new version of that column is created, leaving the initial version intact. This storage system enables to keep, at minimal cost, the totality of the transitional results produced by the pipeline. The storage of metadata describing all the operations that have produced a view (a result table) in the DMS makes possible the creation of an oriented hypergraph, where each node corresponds to a view and each arrow to an operation. By retracing the dependency relationships in this hypergraph, it is possible to rebuild *a posteriori* the entirety of the process that has produced a result table.   
+
+
+
+**Tools.** The `OBITools3` offer the same tools as the original `OBITools`. Eventually, new versions of `ecoPrimers` (PCR primer design) [3], `ecoPCR` (*in silico* PCR) [4], as well as `Sumatra` (sequence alignment) and `Sumaclust` (sequence alignment and clustering) [5] will be added, taking advantage of the database structure developed for the `OBITools3`.    
+
+
+
+**Implementation and disponibility.** The lower layers managing the DMS as well as all the compute-intensive functions are coded in `C99` for efficiency reasons. A `Cython` (<http://www.cython.org>) object layer allows for a simple but efficient implementation of the `OBITools3` commands in `Python 3.5`. The `OBITools3` are still in development, and the first functional versions are expected for autumn 2016.    
+
+
+
+**References.**
+
+1. Taberlet P, Coissac E, Hajibabaei M, Rieseberg LH: Environmental DNA. Mol Ecol 2012:1789–1793.
+2. Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E: OBITools: a Unix-inspired software package for DNA metabarcoding. Mol Ecol Resour 2015:n/a–n/a.
+3. Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E: ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res 2011, 39:e145.
+4. Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, Bessière J, Taberlet P, Pompanon F: An in silico approach for the evaluation of DNA barcodes. BMC Genomics 2010, 11:434.
+5. Mercier C, Boyer F, Bonin A, Coissac E (2013) SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. Available: <http://metabarcoding.org/sumatra> and <http://metabarcoding.org/sumaclust>

python/obitools3/obidms/_obidms.pxd

@@ -45,7 +45,6 @@ cdef class OBIView:
     cdef str       name
     cdef str       comments
     cdef dict      columns
-    cdef dict      columns_pp    # TODO this dict might be unnecessary
     cdef OBIDMS    dms
     
     cpdef delete_column(self, str column_name)

python/obitools3/obidms/_obidms.pyx

@@ -84,13 +84,13 @@ cdef class OBIDMS_column :
         cdef OBIDMS_column_p  column_p
         cdef OBIDMS_column_p* column_pp
         
-        column_pp = <OBIDMS_column_p*> PyCapsule_GetPointer(((view.columns_pp)[column_name]), NULL) # or use C function
+        column_pp = obi_view_get_pointer_on_column_in_view(view.pointer, str2bytes(column_name))
         column_p = column_pp[0]     # TODO ugly cython dereferencing but can't find better
         
         # Fill structure
         self.pointer = column_pp
         self.dms = view.dms
-        self.view = view.pointer    # TODO pointer or instance?
+        self.view = view.pointer
         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
@@ -118,6 +118,9 @@ cdef class OBIDMS_column :
         lines_used = (self.pointer)[0].header.lines_used
         for line_nb in range(lines_used):
             yield self.get_line(line_nb)
+
+    def __richcmp__(self, object value, int comp):
+        return self.compare(value, comp)
     
     cpdef update_pointer(self):
         self.pointer = <OBIDMS_column_p*> obi_view_get_pointer_on_column_in_view(self.view, str2bytes(self.column_name))
@@ -137,12 +140,15 @@ cdef class OBIDMS_column :
     cpdef str get_comments(self):
         return bytes2str((self.pointer)[0].header.comments)
     
-    def __repr__(self) :
+    def __str__(self) :
         cdef str to_print
         to_print = ''
         for line in self :
             to_print = to_print + str(line) + "\n"
         return to_print
+
+    def __repr__(self) :
+        return (self.column_name + ", version " + str((self.pointer)[0].header.version) + ", data type: " + self.data_type)
         
     cpdef close(self):
         if obi_close_column((self.pointer)[0]) < 0 :
@@ -237,27 +243,27 @@ 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 OBIDMS_column_p* column_pp
+        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 object col_capsule
+        cdef index_t*               line_selection_p
         
         self.dms = dms
         
+        # Create the C array for the line selection if needed
         if line_selection is not None :
             line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
             for i in range(len(line_selection)) :
-                line_selection_p[i] = line_selection[i]     # TODO type problem?
+                line_selection_p[i] = line_selection[i]
             line_selection_p[len(line_selection)] = -1
         else :
             line_selection_p = NULL
        
+        # Create the view if needed
         if new :
             if view_to_clone is not None :
                 if type(view_to_clone) == str :
@@ -266,50 +272,36 @@ cdef class OBIView :
                     view = obi_new_view(dms.pointer, str2bytes(view_name), (<OBIView> view_to_clone).pointer, line_selection_p, str2bytes(comments))
             elif view_to_clone is None :
                 view = obi_new_view(dms.pointer, str2bytes(view_name), NULL, line_selection_p, str2bytes(comments))
+        # Else, open the existing view
         elif not new :
             if view_name is not None :
                 view = obi_open_view(dms.pointer, str2bytes(view_name))
             elif view_name is None :
-                view = obi_open_view(dms.pointer, NULL)
+                view = obi_open_view(dms.pointer, NULL) # TODO discuss
         
         if view == NULL :
-            raise Exception("Error creating/opening view")
+            raise Exception("Error creating/opening a view")
 
         self.pointer = view
         self.name = bytes2str(view.name)
         
-        # go through columns to build list and open python object (TODO make separate function?)
+        # Go through columns to build list of corresponding python instances
         self.columns = {}
-        self.columns_pp = {}
-                
-        i = 0
-        while i < view.column_count :
-            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
-            column_p = <OBIDMS_column_p> (view.columns)[i]
-            header = (column_p).header
-            
-            col_name = bytes2str(header.name)
-            col_capsule = PyCapsule_New(column_pp, NULL, NULL)   # TODO discuss
-            (self.columns_pp)[col_name] = col_capsule
-            
-            subclass = OBIDMS_column.get_subclass_type(column_p)
+        for i in range(view.column_count) :
+            column_p               = <OBIDMS_column_p> (view.columns)[i]
+            header                 = (column_p).header
+            col_name               = bytes2str(header.name)         
+            subclass               = OBIDMS_column.get_subclass_type(column_p)
             self.columns[col_name] = subclass(self, col_name)
-            
-            i+=1
 
 
     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" 
-        for column_name in self.columns :   # TODO make function in OBIDMS_column class
-            column = self.columns[column_name]
-            column_p = (column.pointer)[0]
-            s = s + "\n" + column_name + ", version " + str(column_p.header.version) + ", data type: " + column.data_type
+        s = str(self.name) + ", " + str(self.comments) + ", " + str(self.pointer.line_count) + " lines\n" 
+        for column_name in self.columns :
+            s = s + self.columns[column_name].__repr__() + '\n'
         return s
         
     
@@ -319,7 +311,6 @@ cdef class OBIView :
         cdef Obiview_p view
         cdef OBIDMS_column column
         cdef OBIDMS_column_p column_p
-        cdef OBIDMS_column_p* column_pp
         cdef OBIDMS_column_header_p header
         cdef str column_n
  
@@ -330,18 +321,7 @@ cdef class OBIView :
         
         # Update the dictionaries of column pointers and column objects, and update pointers in column objects (make function?):
         (self.columns).pop(column_name)
-        (self.columns_pp).pop(column_name)
         
-        i = 0
-        while i < view.column_count :
-            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
-            column_p = <OBIDMS_column_p> (view.columns)[i]
-            header = (column_p).header
-            col_name = bytes2str(header.name)
-            col_capsule = PyCapsule_New(column_pp, NULL, NULL)
-            (self.columns_pp)[col_name] = col_capsule
-            i+=1
-
         for column_n in self.columns :
             (self.columns[column_n]).update_pointer()
 
@@ -351,12 +331,12 @@ cdef class OBIView :
                      obiversion_t version_number=-1, 
                      str type='',
                      index_t nb_lines=0, 
-                     index_t nb_elements_per_line=1,    # TODO 1?
+                     index_t nb_elements_per_line=1,
                      list elements_names=None,
                      str indexer_name="",
                      str comments="",
-                     bint create=True   # TODO
-                     ) :
+                     bint create=True
+                    ) :
         
         cdef bytes column_name_b
         cdef bytes elements_names_b
@@ -387,19 +367,14 @@ cdef class OBIView :
             else :
                 raise Exception("Invalid provided data type")
         
-        if (obi_view_add_column(self.pointer, column_name_b, version_number,     # should return pointer on column?
+        if (obi_view_add_column(self.pointer, column_name_b, version_number,     # TODO should return pointer on column?
                                 data_type, nb_lines, nb_elements_per_line, 
                                 elements_names_b, str2bytes(indexer_name), 
                                 str2bytes(comments), create) < 0) :
             raise Exception("Problem adding a column in a view")
         
-        # Store the column pointer
+        # Get the column pointer
         column_pp = obi_view_get_pointer_on_column_in_view(self.pointer, column_name_b)
-        if column_pp == NULL :
-            raise Exception("Problem getting a column in a view")
-        
-        col_capsule = PyCapsule_New(column_pp, NULL, NULL)   # TODO
-        (self.columns_pp)[column_name] = col_capsule
         
         # Open and store the subclass
         column_p = column_pp[0]     # TODO ugly cython dereferencing
@@ -416,11 +391,11 @@ cdef class OBIView :
         # iter on each line of all columns
         
         # Declarations
-        cdef index_t lines_used
-        cdef index_t line_nb
-        cdef OBIView_line line  # TODO for NUC SEQS View
+        cdef index_t      lines_used
+        cdef index_t      line_nb
+        cdef OBIView_line line          # TODO Check that this works for NUC SEQ views
         
-        # Yield each line TODO line class
+        # Yield each line
         lines_used = (self.pointer).line_count
         
         for line_nb in range(lines_used) :
@@ -431,7 +406,7 @@ cdef class OBIView :
     def __getitem__(self, object item) :
         if type(item) == str :
             return (self.columns)[item]
-        elif type(item) == int :     # TODO int?
+        elif type(item) == int :
             return OBIView_line(self, item)
 
 
@@ -444,7 +419,7 @@ cdef class OBIView :
         cdef index_t* line_selection_p
         line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
         for i in range(len(line_selection)) :
-            line_selection_p[i] = line_selection[i]     # TODO type problem?
+            line_selection_p[i] = line_selection[i]
         line_selection_p[len(line_selection)] = -1
         if obi_select_lines(self.pointer, line_selection_p) < 0 :
             raise Exception("Problem selecting a list of lines")
@@ -468,22 +443,21 @@ cdef class OBIView_NUC_SEQS(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 OBIDMS_column_p* column_pp
+        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
         
         if line_selection is not None :
             line_selection_p = <index_t*> malloc((len(line_selection) + 1) * sizeof(index_t))
             for i in range(len(line_selection)) :
-                line_selection_p[i] = line_selection[i]     # TODO type problem?
+                line_selection_p[i] = line_selection[i]
             line_selection_p[len(line_selection)] = -1
         else :
             line_selection_p = NULL
@@ -509,24 +483,14 @@ cdef class OBIView_NUC_SEQS(OBIView):
         self.name = bytes2str(view.name)
         self.comments = bytes2str(view.comments)
         
-        # go through columns to build list and open python object (TODO make separate function?)
+        # Go through columns to build list of corresponding python instances
         self.columns = {}
-        self.columns_pp = {}
-                
-        i = 0
-        while i < view.column_count :
-            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
-            column_p = <OBIDMS_column_p> (view.columns)[i]
-            header = (column_p).header
-            
-            col_name = bytes2str(header.name)
-            col_capsule = PyCapsule_New(column_pp, NULL, NULL)   # TODO discuss
-            (self.columns_pp)[col_name] = col_capsule
-            
-            subclass = OBIDMS_column.get_subclass_type(column_p)
+        for i in range(view.column_count) :
+            column_p               = <OBIDMS_column_p> (view.columns)[i]
+            header                 = (column_p).header
+            col_name               = bytes2str(header.name)         
+            subclass               = OBIDMS_column.get_subclass_type(column_p)
             self.columns[col_name] = subclass(self, col_name)
-            
-            i+=1
         
         self.ids = self.columns[bytes2str(ID_COLUMN)]
         self.sequences = self.columns[bytes2str(NUC_SEQUENCE_COLUMN)]
@@ -539,7 +503,6 @@ cdef class OBIView_NUC_SEQS(OBIView):
         cdef Obiview_p view
         cdef OBIDMS_column column
         cdef OBIDMS_column_p column_p
-        cdef OBIDMS_column_p* column_pp
         cdef OBIDMS_column_header_p header
         cdef str column_n
  
@@ -551,20 +514,9 @@ cdef class OBIView_NUC_SEQS(OBIView):
         if obi_view_delete_column(view, 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?):
+        # Remove instance from the dictionary
         (self.columns).pop(column_name)
-        (self.columns_pp).pop(column_name)
         
-        i = 0
-        while i < view.column_count :
-            column_pp = <OBIDMS_column_p*> ((view.columns)+i)
-            column_p = <OBIDMS_column_p> (view.columns)[i]
-            header = (column_p).header
-            col_name = bytes2str(header.name)
-            col_capsule = PyCapsule_New(column_pp, NULL, NULL)
-            (self.columns_pp)[col_name] = col_capsule
-            i+=1
-
         for column_n in self.columns :
             (self.columns[column_n]).update_pointer()
 
@@ -572,7 +524,7 @@ cdef class OBIView_NUC_SEQS(OBIView):
     def __getitem__(self, object item) :
         if type(item) == str :
             return (self.columns)[item]
-        elif type(item) == int :     # TODO int?
+        elif type(item) == int :
             return OBI_Nuc_Seq_Stored(self, item)
     
     
@@ -607,7 +559,7 @@ cdef class OBIView_line :
             elif value_type == bool :
                 value_obitype = 'OBI_BOOL'            
             elif value_type == str :
-                if only_ATGC(str2bytes(value)) :    # TODO
+                if only_ATGC(str2bytes(value)) :    # TODO detect IUPAC?
                     value_obitype = 'OBI_SEQ'
                 elif len(value) == 1 :
                     value_obitype = 'OBI_CHAR'
@@ -691,17 +643,17 @@ cdef class OBIDMS :
         return all_views[view_name]
 
 
-    cpdef dict read_views(self) :    # TODO function that prints the dic nicely and function that prints 1 view. Add column type in col ref
+    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
+        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)
@@ -718,7 +670,7 @@ cdef class OBIDMS :
             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))     # TODO move this function in utils or somethings
+            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 :

python/obitools3/obidms/_obidmscolumn_float.pxd

@@ -1,12 +1,13 @@
 #cython: language_level=3
 
-from .capi.obitypes cimport index_t
+from .capi.obitypes cimport index_t, obifloat_t
 from ._obidms       cimport OBIDMS_column, OBIDMS_column_multi_elts
 
 
 cdef class OBIDMS_column_float(OBIDMS_column):
     cpdef object get_line(self, index_t line_nb)
     cpdef set_line(self, index_t line_nb, object value)
+    cpdef list bool_list_from_compare(self, obifloat_t value, int comp)
 
 cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
     cpdef object get_item(self, index_t line_nb, str element_name)

python/obitools3/obidms/_obidmscolumn_float.pyx

@@ -5,7 +5,9 @@ from .capi.obiview      cimport obi_column_get_obifloat_with_elt_name_in_view, \
                                 obi_column_set_obifloat_with_elt_name_in_view, \
                                 obi_column_set_obifloat_with_elt_idx_in_view
 from .capi.obierrno     cimport obi_errno
-from .capi.obitypes     cimport OBIFloat_NA, obifloat_t
+from .capi.obitypes     cimport OBIFloat_NA, obifloat_t, byte_t
+from .capi.obidmscolumn cimport obi_float_column_greater_than   # TODO need to be in view...
+
 
 from obitools3.utils cimport str2bytes
 
@@ -30,6 +32,22 @@ cdef class OBIDMS_column_float(OBIDMS_column):
         if obi_column_set_obifloat_with_elt_idx_in_view(self.view, (self.pointer)[0], line_nb, 0, <obifloat_t> value) < 0:
             raise Exception("Problem setting a value in a column")
 
+    cpdef list bool_list_from_compare(self, obifloat_t value, int comp):
+        cdef list    result_p
+        cdef byte_t* result_c
+        cdef int     i
+        result_p = []
+        if comp == 4 :
+            result_c = obi_float_get_bool_list_from_compare_in_view(self.view, (self.pointer)[0], value, GREATER_THAN)
+        else :
+            raise Exception("Comparison not handled")
+        for i in range(self.get_nb_lines_used()) :
+            result_p.append(<int> result_c[i])
+            print(result_p[i])
+        free(result_c)
+        return result_p
+
+
 
 cdef class OBIDMS_column_multi_elts_float(OBIDMS_column_multi_elts):
 

src/obiavl.c

@@ -2217,3 +2217,8 @@ index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_blob_p value)
 }
 
 
+const char* obi_avl_group_get_name(OBIDMS_avl_group_p avl_group)
+{
+	return avl_group->name;
+}
+

src/obiavl.h

@@ -410,5 +410,18 @@ Obi_blob_p obi_avl_group_get(OBIDMS_avl_group_p avl_group, index_t idx);
 index_t obi_avl_group_add(OBIDMS_avl_group_p avl_group, Obi_blob_p value);
 
 
+/**
+ * @brief Recovers the name of an AVL group.
+ *
+ * @param avl_group A pointer on the AVL group structure.
+ *
+ * @returns A pointer on the name of the AVL group.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+const char* obi_avl_group_get_name(OBIDMS_avl_group_p avl_group);
+
+
 #endif /* OBIAVL_H_ */
 

src/obiblob_indexer.c

@@ -22,19 +22,21 @@
 #define DEBUG_LEVEL 0	// TODO has to be defined somewhere else (cython compil flag?)
 
 
-//inline int obi_indexer_exists(OBIDMS_p dms, const char* name);
+inline int obi_indexer_exists(OBIDMS_p dms, const char* name);
 
-//inline Obi_indexer_p obi_indexer(OBIDMS_p dms, const char* name);
+inline Obi_indexer_p obi_indexer(OBIDMS_p dms, const char* name);
 
-//inline Obi_indexer_p obi_create_indexer(OBIDMS_p dms, const char* name);
+inline Obi_indexer_p obi_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_open_indexer(OBIDMS_p dms, const char* name);
 
-//inline int obi_close_indexer(Obi_indexer_p indexer);
+inline int obi_close_indexer(Obi_indexer_p indexer);
 
-//inline index_t obi_indexer_add(Obi_indexer_p indexer, Obi_blob_p value);
+inline index_t obi_indexer_add(Obi_indexer_p indexer, Obi_blob_p value);
 
-//inline Obi_blob_p obi_indexer_get(Obi_indexer_p indexer, index_t idx);
+inline Obi_blob_p obi_indexer_get(Obi_indexer_p indexer, index_t idx);
+
+inline const char* obi_indexer_get_name(Obi_indexer_p indexer);
 
 
 char* obi_build_indexer_name(const char* column_name, obiversion_t column_version)

src/obiblob_indexer.h

@@ -47,7 +47,10 @@ typedef OBIDMS_avl_group_p Obi_indexer_p; 		/**< Typedef to refer to the pointer
  * @since April 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-#define obi_indexer_exists obi_avl_exists
+inline int obi_indexer_exists(OBIDMS_p dms, const char* name)
+{
+	return obi_avl_exists(dms, name);
+}
 
 
 /**
@@ -62,7 +65,10 @@ typedef OBIDMS_avl_group_p Obi_indexer_p; 		/**< Typedef to refer to the pointer
  * @since April 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-#define obi_indexer obi_avl_group
+inline Obi_indexer_p obi_indexer(OBIDMS_p dms, const char* name)
+{
+	return obi_avl_group(dms, name);
+}
 
 
 /**
@@ -77,7 +83,10 @@ typedef OBIDMS_avl_group_p Obi_indexer_p; 		/**< Typedef to refer to the pointer
  * @since April 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-#define obi_create_indexer obi_create_avl_group
+inline Obi_indexer_p obi_create_indexer(OBIDMS_p dms, const char* name)
+{
+	return obi_create_avl_group(dms, name);
+}
 
 
 /**
@@ -92,7 +101,10 @@ typedef OBIDMS_avl_group_p Obi_indexer_p; 		/**< Typedef to refer to the pointer
  * @since April 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-#define obi_open_indexer obi_open_avl_group
+inline Obi_indexer_p obi_open_indexer(OBIDMS_p dms, const char* name)
+{
+	return obi_open_avl_group(dms, name);
+}
 
 
 /**
@@ -106,7 +118,10 @@ typedef OBIDMS_avl_group_p Obi_indexer_p; 		/**< Typedef to refer to the pointer
  * @since April 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-#define obi_close_indexer obi_close_avl_group
+inline int obi_close_indexer(Obi_indexer_p indexer)
+{
+	return obi_close_avl_group(indexer);
+}
 
 
 /**
@@ -121,7 +136,10 @@ typedef OBIDMS_avl_group_p Obi_indexer_p; 		/**< Typedef to refer to the pointer
  * @since April 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-#define obi_indexer_add obi_avl_group_add
+inline index_t obi_indexer_add(Obi_indexer_p indexer, Obi_blob_p value)
+{
+	return obi_avl_group_add(indexer, value);
+}
 
 
 /**
@@ -135,7 +153,26 @@ typedef OBIDMS_avl_group_p Obi_indexer_p; 		/**< Typedef to refer to the pointer
  * @since April 2016
  * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-#define obi_indexer_get obi_avl_group_get
+inline Obi_blob_p obi_indexer_get(Obi_indexer_p indexer, index_t idx)
+{
+	return obi_avl_group_get(indexer, idx);
+}
+
+
+/**
+ * @brief Recovers the name of an indexer.
+ *
+ * @param indexer A pointer on the indexer.
+ *
+ * @returns A pointer on the name of the indexer.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+inline const char* obi_indexer_get_name(Obi_indexer_p indexer)
+{
+	return obi_avl_group_get_name(indexer);
+}
 
 
 /**

src/obidms.c

@@ -18,6 +18,7 @@
 #include <fcntl.h>
 #include <sys/types.h>
 #include <dirent.h>
+#include <unistd.h>
 
 #include "obidms.h"
 #include "obierrno.h"
@@ -202,14 +203,14 @@ int create_dms_infos_file(int dms_file_descriptor, const char* dms_name)
  *
  **********************************************************************/
 
-int obi_dms_exists(const char* dms_name)
+int obi_dms_exists(const char* dms_path)
 {
     struct stat buffer;
 	char*       directory_name;
     int 		check_dir;
 
 	// Build and check the directory name
-    directory_name = build_directory_name(dms_name);
+    directory_name = build_directory_name(dms_path);
 	if (directory_name == NULL)
 		return -1;
 
@@ -224,14 +225,15 @@ int obi_dms_exists(const char* dms_name)
 }
 
 
-OBIDMS_p obi_create_dms(const char* dms_name)
+OBIDMS_p obi_create_dms(const char* dms_path)
 {
-	char* directory_name;
-	DIR*  dms_dir;
-	int   dms_file_descriptor;
+	char*  directory_name;
+	DIR*   dms_dir;
+	int    dms_file_descriptor;
+	size_t i, j;
 
 	// Build and check the directory name
-	directory_name = build_directory_name(dms_name);
+	directory_name = build_directory_name(dms_path);
 	if (directory_name == NULL)
 		return NULL;
 
@@ -278,22 +280,32 @@ OBIDMS_p obi_create_dms(const char* dms_name)
 		return NULL;
 	}
 
+	// Isolate the dms name
+	j = 0;
+	for (i=0; i<strlen(dms_path); i++)
+	{
+		if (dms_path[i] == '/')
+			j = i+1;
+		i++;
+	}
+
 	// Create the informations file
-	if (create_dms_infos_file(dms_file_descriptor, dms_name) < 0)
+	if (create_dms_infos_file(dms_file_descriptor, dms_path+j) < 0)
 		return NULL;
 
-	return obi_open_dms(dms_name);
+	return obi_open_dms(dms_path);
 }
 
 
-OBIDMS_p obi_open_dms(const char* dms_name)
+OBIDMS_p obi_open_dms(const char* dms_path)
 {
 	OBIDMS_p	dms;
-	char*	 	directory_name;
+	char*	 	relative_directory_path;
 	char* 		infos_file_name;
 	int			infos_file_descriptor;
 	bool		little_endian_dms;
 	bool 		little_endian_platform;
+	size_t		i, j;
 
 	dms = NULL;
 
@@ -307,18 +319,37 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 	}
 
 	// Build and check the directory name
-	directory_name = build_directory_name(dms_name);
-	if (directory_name == NULL)
+	relative_directory_path = build_directory_name(dms_path);
+	if (relative_directory_path == NULL)
 	{
 		free(dms);
 		return NULL;
 	}
 
-	strncpy(dms->directory_name, directory_name, OBIDMS_MAX_NAME);
-	free(directory_name);
+	// Build and store the absolute path to the DMS
+	if (getcwd(dms->directory_path, MAX_PATH_LEN) == NULL)
+	{
+		obi_set_errno(OBIDMS_UNKNOWN_ERROR);
+		obidebug(1, "\nError getting the absolute path to the current working directory");
+		free(relative_directory_path);
+		return NULL;
+	}
+	strcat(dms->directory_path, "/");
+	strcat(dms->directory_path, relative_directory_path);
+	free(relative_directory_path);
+
+	// Isolate and store the dms name
+	j = 0;
+	for (i=0; i<strlen(dms_path); i++)
+	{
+		if (dms_path[i] == '/')
+			j = i+1;
+		i++;
+	}
+	strcpy(dms->dms_name, dms_path+j);
 
 	// Try to open the directory
-	dms->directory = opendir(dms->directory_name);
+	dms->directory = opendir(dms->directory_path);
 	if (dms->directory == NULL)
 	{
 		switch (errno)
@@ -355,7 +386,7 @@ OBIDMS_p obi_open_dms(const char* dms_name)
 	}
 
 	// Open informations file to check endianness
-	infos_file_name = build_infos_file_name(dms_name);
+	infos_file_name = build_infos_file_name(dms->dms_name);
 	infos_file_descriptor = openat(dms->dir_fd, infos_file_name, O_RDONLY, 0777);
 	if (infos_file_descriptor < 0)
 	{
@@ -551,7 +582,7 @@ Obi_indexer_p obi_dms_get_indexer_from_list(OBIDMS_p dms, const char* indexer_na
 
 	for (i=0; i < (indexers_list->nb_opened_indexers); i++)
 	{
-		if (!strcmp(((indexers_list->indexers)[i])->name, indexer_name))	// TODO get_name function indexer
+		if (!strcmp(obi_indexer_get_name((indexers_list->indexers)[i]), indexer_name))
 		{	// Found the indexer already opened, return it
 			return (indexers_list->indexers)[i];
 		}
@@ -561,7 +592,7 @@ Obi_indexer_p obi_dms_get_indexer_from_list(OBIDMS_p dms, const char* indexer_na
 }
 
 
-void obi_dms_list_indexer(OBIDMS_p dms, Obi_indexer_p indexer)
+void obi_dms_list_indexer(OBIDMS_p dms, Obi_indexer_p indexer)  	// TODO add check if indexer already in list?
 {
 	*(((dms->opened_indexers)->indexers)+((dms->opened_indexers)->nb_opened_indexers)) = indexer;
 	((dms->opened_indexers)->nb_opened_indexers)++;
@@ -577,7 +608,7 @@ int obi_dms_unlist_indexer(OBIDMS_p dms, Obi_indexer_p indexer)
 
 	for (i=0; i < indexers_list->nb_opened_indexers; i++)
 	{
-		if (!strcmp(((indexers_list->indexers)[i])->name, indexer->name))	// TODO get_name function indexer
+		if (!strcmp(obi_indexer_get_name((indexers_list->indexers)[i]), indexer->name))
 		{	// Found the indexer. Rearrange list
 			(indexers_list->nb_opened_indexers)--;
 			(indexers_list->indexers)[i] = (indexers_list->indexers)[indexers_list->nb_opened_indexers];
@@ -602,15 +633,7 @@ char* obi_dms_get_dms_path(OBIDMS_p dms)
 		return NULL;
 	}
 
-	if (getcwd(full_path, MAX_PATH_LEN) == NULL)	// TODO store when opening
-	{
-		obi_set_errno(OBI_UTILS_ERROR);
-		obidebug(1, "\nError getting the path to a file or directory");
-		return NULL;
-	}
-
-	strcat(full_path, "/");
-	strcat(full_path, dms->directory_name);
+	strcpy(full_path, dms->directory_path);
 
 	return full_path;
 }

src/obidms.h

@@ -78,9 +78,14 @@ typedef struct Opened_indexers_list {
  * and opening of an OBITools Data Management System (DMS)
  */
 typedef struct OBIDMS {
+	char					dms_name[OBIDMS_MAX_NAME+1];		/** The name of the DMS.
+																 */
 	char					directory_name[OBIDMS_MAX_NAME+1];	/**< The name of the directory
 																 *   containing the DMS.
 																 */
+	char					directory_path[MAX_PATH_LEN];     	/**< The absolute path of the directory
+																 *   containing the DMS.
+																 */
 	DIR*					directory;							/**< A directory entry usable to
 																 *   refer and scan the database directory.
 																 */
@@ -105,7 +110,7 @@ typedef struct OBIDMS {
 /**
  * @brief Checks if an OBIDMS exists.
  *
- * @param dms_name A pointer to a C string containing the name of the database.
+ * @param dms_path A pointer to a C string containing the path to the database.
  *
  * @returns An integer value indicating the status of the database.
  * @retval 1 if the database exists.
@@ -115,7 +120,7 @@ typedef struct OBIDMS {
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-int obi_dms_exists(const char* dms_name);
+int obi_dms_exists(const char* dms_path);
 
 
 /**
@@ -127,7 +132,7 @@ int obi_dms_exists(const char* dms_name);
  *
  * A directory to store Obiblob indexers is also created.
  *
- * @param dms_name A pointer to a C string containing the name of the database.
+ * @param dms_path A pointer to a C string containing the path to the database.
  *                 The actual directory name used to store the DMS will be
  *                 `<dms_name>.obidms`.
  *
@@ -144,7 +149,7 @@ OBIDMS_p obi_create_dms(const char* dms_name);
 /**
  * @brief Opens an existing OBITools Data Management instance (OBIDMS).
  *
- * @param dms_name A pointer to a C string containing the name of the database.
+ * @param dms_path A pointer to a C string containing the path to the database.
  *
  * @returns A pointer to an OBIDMS structure describing the opened DMS.
  * @retval NULL if an error occurred.
@@ -153,7 +158,7 @@ OBIDMS_p obi_create_dms(const char* dms_name);
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-OBIDMS_p obi_open_dms(const char* dms_name);
+OBIDMS_p obi_open_dms(const char* dms_path);
 
 
 /**
@@ -162,7 +167,7 @@ OBIDMS_p obi_open_dms(const char* dms_name);
  * If the database already exists, this function opens it, otherwise it
  * creates a new database.
  *
- * @param dms_name A pointer to a C string containing the name of the database.
+ * @param dms_path A pointer to a C string containing the path to the database.
  *
  * @returns A pointer to an OBIDMS structure describing the OBIDMS.
  * @retval NULL if an error occurred.
@@ -171,7 +176,7 @@ OBIDMS_p obi_open_dms(const char* dms_name);
  * @since May 2015
  * @author Eric Coissac (eric.coissac@metabarcoding.org)
  */
-OBIDMS_p obi_dms(const char* dms_name);
+OBIDMS_p obi_dms(const char* dms_path);
 
 
 /**
@@ -230,6 +235,8 @@ OBIDMS_column_p obi_dms_get_column_from_list(OBIDMS_p dms, const char* column_na
 /**
  * @brief Adds a column identified by its name and its version number in the list of opened columns.
  *
+ * @warning obi_dms_get_column_from_list() should be used first to check if the column isn't already listed.
+ *
  * @param dms The OBIDMS.
  * @param column A pointer on the column that should be added in the list of opened columns.
  *
@@ -269,6 +276,8 @@ Obi_indexer_p obi_dms_get_indexer_from_list(OBIDMS_p dms, const char* indexer_na
 /**
  * @brief Adds an indexer identified by its name in the list of opened indexers.
  *
+ * @warning obi_dms_get_indexer_from_list() should be used first to check if the indexer isn't already listed.
+ *
  * @param dms The OBIDMS.
  * @param indexer A pointer on the indexer that should be added in the list of opened indexers.
  *
@@ -291,9 +300,19 @@ int obi_dms_unlist_indexer(OBIDMS_p dms, Obi_indexer_p indexer);
 
 
 /**
- * Function meant to disappear soon
+ * @brief Gets the full path to the DMS.
+ *
+ * @warning The returned pointer has to be freed by the caller.
+ *
+ * @param dms The DMS.
+ *
+ * @returns A pointer to the full path.
+ * @retval NULL if an error occurred.
+ *
+ * @since April 2016
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
  */
-char* obi_dms_get_path(OBIDMS_p dms);
+char* obi_dms_get_dms_path(OBIDMS_p dms);
 
 
 /**

src/obidmscolumn_float.c

@@ -63,3 +63,27 @@ obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t
 	return obi_column_get_obifloat_with_elt_idx(column, line_nb, element_idx);
 }
 
+
+small_bool_t* obi_float_get_bool_list_from_compare(OBIDMS_column_p column, obifloat_t value, OBIDMS_column_p line_selection, Comp_type_t comp)	// TODO openMP, get index or bool list
+{
+	small_bool_t* bool_vector;
+	index_t i;
+	index_t nb_elements;
+
+	nb_elements = (column->header)->lines_used * (column->header)->nb_elements_per_line;	// TODO how are vector lines handled?
+	bool_vector = (small_bool_t*) malloc(nb_elements * sizeof(small_bool_t));
+
+	// TODO check if line_selection == NULL
+	// Check and case comps
+
+	if (comp == GREATER_THAN)
+	{
+		for (i=0; i<nb_elements; i++)
+		{
+			bool_vector[i] = (*(((obifloat_t*) (column->data)) + i)) > value;	// TODO get through function, depends on vector lines problem
+		}
+	}
+
+	return bool_vector;
+}
+

src/obidmscolumn_float.h

@@ -95,5 +95,8 @@ int obi_column_set_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_n
 obifloat_t obi_column_get_obifloat_with_elt_name(OBIDMS_column_p column, index_t line_nb, const char* element_name);
 
 
+small_bool_t* obi_float_get_bool_list_from_compare(OBIDMS_column_p column, obifloat_t value, OBIDMS_column_p line_selection, Comp_type_t comp);
+
+
 #endif /* OBIDMSCOLUMN_FLOAT_H_ */
 

src/obiview.c

@@ -311,7 +311,7 @@ OBIDMS_column_p clone_column_in_view(Obiview_p view, const char* column_name)
 {
 	int i;
 	OBIDMS_column_p current_line_selection = NULL;
-	OBIDMS_column_p column;
+	OBIDMS_column_p column = NULL;
 	OBIDMS_column_p column_buffer;
 
 	// Check that the view is not read-only
@@ -1401,6 +1401,12 @@ obifloat_t obi_column_get_obifloat_with_elt_name_in_view(Obiview_p view, OBIDMS_
 	return obi_column_get_obifloat_with_elt_idx_in_view(view, column, line_nb, element_idx);
 }
 
+
+small_bool_t* obi_float_get_bool_list_from_compare_in_view(Obiview_p view, OBIDMS_column_p column, obifloat_t value, Comp_type_t comp)
+{
+	return obi_float_get_bool_list_from_compare(view, column, value, view->line_selection, comp);
+}
+
 /****************************************/