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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.

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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.

44
Makefile Normal file
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@ -0,0 +1,44 @@
EXEC=sumatra
SUMATRA_SRC= sumatra.c \
mtcompare_sumatra.c
SUMATRA_OBJ= $(patsubst %.c,%.o,$(SUMATRA_SRC))
SRCS= $(SUMATRA_SRC)
LIB= -lfasta -llcs -lfile -lutils -lz -lm
include ./global.mk
all: $(EXEC)
########
#
# sumatra compilation
#
########
# executable compilation and link
sumatra: $(SUMATRA_OBJ) $(LIBFASTA) $(LIBLCS) $(LIBFILE) $(LIBUTILS)
$(CC) $(LDFLAGS) -o $@ -pthread $(SUMATRA_OBJ) $(LIBFASTAPATH) $(LIBLCSPATH) $(LIBFILEPATH) $(LIBUTILSPATH) $(LIB)
########
#
# project management
#
########
clean:
rm -f *.o
rm -f *.P
rm -f $(EXEC)
$(MAKE) -C ../sumalibs/libfasta clean
$(MAKE) -C ../sumalibs/liblcs clean
$(MAKE) -C ../sumalibs/libfile clean
$(MAKE) -C ../sumalibs/libutils clean

45
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LIBFASTAPATH = -L../sumalibs/libfasta
LIBLCSPATH = -L../sumalibs/liblcs
LIBFILEPATH = -L../sumalibs/libfile
LIBUTILSPATH = -L../sumalibs/libutils
LIBFASTA = ../sumalibs/libfasta/libfasta.a
LIBLCS = ../sumalibs/liblcs/liblcs.a
LIBFILE = ../sumalibs/libfile/libfile.a
LIBUTILS = ../sumalibs/libutils/libutils.a
CC=gcc
LDFLAGS=
ifeq ($(CC),gcc)
CFLAGS = -O3 -s -DOMP_SUPPORT -fopenmp -w
else
CFLAGS = -O3 -w
endif
default: all
%.o: %.c
$(CC) $(CFLAGS) -c -o $@ $< $(LIB)
########
#
# libraries compilation
#
########
../sumalibs/libfasta/libfasta.a:
$(MAKE) -C ../sumalibs/libfasta
../sumalibs/liblcs/liblcs.a:
$(MAKE) -C ../sumalibs/liblcs
../sumalibs/libfile/libfile.a:
$(MAKE) -C ../sumalibs/libfile
../sumalibs/libutils/libutils.a:
$(MAKE) -C ../sumalibs/libutils

317
mtcompare_sumatra.c Normal file
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/*
* mtcompare.c
*
* Created on: 17 ao<61>t 2010
* Authors: Eric Coissac, Celine Mercier
*/
#include <pthread.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include "sumatra.h"
#include "../sumalibs/libfasta/sequence.h"
#include "../sumalibs/libutils/utilities.h"
#include "../sumalibs/liblcs/upperband.h"
#include "../sumalibs/liblcs/sse_banded_LCS_alignment.h"
typedef struct {
int32_t tocompute; // next line to compute
int64_t computed; // count of alignment computed
int32_t thread_count; // count of active thread
int32_t tokill;
pthread_t *threads;
pthread_mutex_t m_tocompute;
pthread_mutex_t m_thread_count;
pthread_mutex_t m_incharge;
pthread_mutex_t m_print;
pthread_mutex_t m_tokill;
pthread_mutex_t m_finished;
int32_t lineset;
int64_t pairs;
fastaSeqCount *db1;
fastaSeqCount *db2;
BOOL normalize;
BOOL lcsmode;
int reference;
BOOL extradata;
BOOL always;
double threshold;
int16_t** addresses;
int16_t** iseqs1;
int16_t** iseqs2;
int sizeForSeqs;
} thread_control_t;
void printLine(fastaSeqPtr seq1, fastaSeqPtr seq2, int32_t seqcount, double *score, BOOL extradata, int64_t pairs)
{
int j;
for (j=0; j < seqcount; j++,seq2++,score++)
printResults(seq1,seq2,*score,extradata,pairs,(*score >=0));
}
void *computeline(void* c)
{
thread_control_t *control=(thread_control_t*)c;
int32_t line;
int32_t start;
int32_t end;
int32_t threadid;
int32_t i,j;
double *score;
double *scores;
fastaSeqPtr db2;
fastaSeqPtr db1;
fastaSeqPtr sq2;
fastaSeqPtr sq1;
char* s1;
int l1;
int LCSmin;
threadid = control->thread_count++;
pthread_mutex_unlock(&(control->m_thread_count));
db1 = control->db1->fastaSeqs;
if (control->db2)
{
end = control->db2->count;
db2 = control->db2->fastaSeqs;
}
else
{
end = control->db1->count;
db2 = control->db1->fastaSeqs;
}
scores = (double*)malloc(end * sizeof(double));
while (control->tocompute < control->db1->count)
{
pthread_mutex_lock(&(control->m_tocompute));
line = control->tocompute;
pthread_mutex_unlock(&(control->m_incharge));
if (line < control->db1->count)
{
for (i=0,sq1=db1+line; i < control->lineset && (i+line) < control->db1->count; i++,sq1++)
{
s1 = sq1->sequence;
l1 = sq1->length;
start = (control->db2) ? 0:line+i+1;
for (score=scores,j=start; j < end ; j++,score++)
{
sq2=db2+j;
filtersSumatra(sq1, sq2, control->threshold, control->normalize, control->reference, control->lcsmode, score, &LCSmin);
if (control->always || (*score == -1.0))
{
*score = alignForSumathings(s1, *((control->iseqs1)+threadid), sq2->sequence, *((control->iseqs2)+threadid), l1, sq2->length,
control->normalize, control->reference, control->lcsmode, *((control->addresses)+threadid), control->sizeForSeqs, LCSmin);
if (!control->always && (((*score < control->threshold) && (control->lcsmode || control->normalize)) || ((!control->lcsmode && !control->normalize) && (*score > control->threshold))))
*score = -1.0;
else if (!control->lcsmode && control->normalize)
*score = 1.0 - *score;
}
else if (*score == -2.0)
*score = -1.0;
}
pthread_mutex_lock(&(control->m_print));
printLine(sq1,db2+start,end-start,scores,control->extradata,control->pairs);
pthread_mutex_unlock(&(control->m_print));
}
}
}
pthread_mutex_unlock(&(control->m_incharge));
free(scores);
pthread_mutex_lock(&(control->m_finished));
control->tokill=threadid;
pthread_mutex_unlock(&(control->m_tokill));
return (void*)threadid;
}
int mt_compare_sumatra(fastaSeqCount *db1, fastaSeqCount *db2, double threshold, BOOL normalize, int reference, BOOL lcsmode, BOOL extradata, int n)
{
int64_t pairs;
thread_control_t control;
int32_t i;
int lmax, lmax1;
int lmin, lmin1;
if (db2==NULL)
{
fprintf(stderr,"Pairwise alignment of one database against itself\n");
pairs = (int64_t)(db1->count - 1) * (int64_t)db1->count /2;
}
else
{
fprintf(stderr,"Pairwise alignment of two databases\n");
pairs = (int64_t)db1->count * (int64_t)db2->count;
}
fprintf(stderr,"Count of alignment to do : %lld\n",pairs);
control.addresses = (int16_t**) malloc(n*sizeof(int16_t*));
control.iseqs1 = (int16_t**) malloc(n*sizeof(int16_t*));
control.iseqs2 = (int16_t**) malloc(n*sizeof(int16_t*));
calculateMaxAndMinLenDB(*db1, &lmax, &lmin);
if (!(db2==NULL))
{
calculateMaxAndMinLenDB(*db2, &lmax1, &lmin1);
if (lmax1 > lmax)
lmax = lmax1;
if (lmin1 < lmin)
lmin = lmin1;
}
for (i=0; i < n; i++)
control.sizeForSeqs = prepareTablesForSumathings(lmax, lmin, threshold, normalize, reference, lcsmode, (control.addresses)+i, (control.iseqs1)+i, (control.iseqs2)+i);
control.db1 = db1;
control.db2 = db2;
control.tocompute = 0;
control.normalize = normalize;
control.reference = reference;
control.extradata = extradata;
control.threshold = threshold;
control.lcsmode = lcsmode;
control.computed = 0;
control.thread_count = 0;
control.pairs = pairs;
if (n > control.db1->count/2)
n = control.db1->count/2;
control.lineset = control.db1->count / n / 2;
if (threshold > 0)
{
fprintf(stderr,"Compute exact LCS only for score > %lf\n", threshold);
control.always = FALSE;
}
else
control.always=TRUE;
if (pthread_mutex_init(&(control.m_thread_count),NULL))
{
fprintf(stderr,"m_thread_count mutex init error\n");
exit(1);
}
if (pthread_mutex_init(&(control.m_tocompute),NULL))
{
fprintf(stderr,"m_tocompute mutex init error\n");
exit(1);
}
if (pthread_mutex_init(&(control.m_incharge),NULL))
{
fprintf(stderr,"m_incharge mutex init error\n");
exit(1);
}
if (pthread_mutex_init(&(control.m_print),NULL))
{
fprintf(stderr,"m_print mutex init error\n");
exit(1);
}
if (pthread_mutex_init(&(control.m_tokill),NULL))
{
fprintf(stderr,"m_tokill mutex init error\n");
exit(1);
}
if (pthread_mutex_init(&(control.m_finished),NULL))
{
fprintf(stderr,"m_finished mutex init error\n");
exit(1);
}
control.threads = (pthread_t*)malloc(n * sizeof(pthread_t));
if (!control.threads)
{
fprintf(stderr,"Cannot allocate memory for threads\n");
exit(2);
}
pthread_mutex_lock(&(control.m_thread_count));
pthread_mutex_lock(&(control.m_tocompute));
pthread_mutex_lock(&(control.m_incharge));
pthread_mutex_unlock(&(control.m_print));
pthread_mutex_lock(&(control.m_tokill));
pthread_mutex_unlock(&(control.m_finished));
fprintf(stderr,"\n");
for (i=0; i < n; i++)
{
fprintf(stderr,"Initializing thread...");
if (pthread_create(control.threads+i,NULL,computeline,&control))
{
fprintf(stderr," : thread %d Error\n",i);
exit(3);
}
pthread_mutex_lock(&(control.m_thread_count));
fprintf(stderr," : thread %d Ok\n",control.thread_count);
}
pthread_mutex_unlock(&(control.m_thread_count));
for (control.tocompute=0;
control.tocompute < db1->count+1;
control.tocompute+=control.lineset)
{
pthread_mutex_unlock(&(control.m_tocompute));
pthread_mutex_lock(&(control.m_incharge));
}
pthread_mutex_unlock(&(control.m_tocompute));
fprintf(stderr,"\n");
for (i=0; i < n; i++)
{
pthread_mutex_lock(&(control.m_tokill));
fprintf(stderr,"Joining thread %d...",control.tokill);
pthread_mutex_unlock(&(control.m_tocompute));
pthread_join(control.threads[control.tokill],NULL);
fprintf(stderr," : Ok\n");
pthread_mutex_unlock(&(control.m_finished));
}
// Freeing
for (i=0; i < n; i++)
{
free((*((control.iseqs1)+i))-(control.sizeForSeqs)+lmax);
free((*((control.iseqs2)+i))-(control.sizeForSeqs)+lmax);
}
free(control.iseqs1);
free(control.iseqs2);
if ((reference == ALILEN) && ((lcsmode && normalize) || (!lcsmode)))
{
for (i=0; i < n; i++)
free(*((control.addresses)+i));
free(control.addresses);
}
return 0;
}

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/*
* mtcompare_sumatra.h
*
* Created on: 12 mars 2013
* Author: celinemercier
*/
#ifndef MTCOMPARE_SUMATRA_H_
#define MTCOMPARE_SUMATRA_H_
int mt_compare_sumatra(fastaSeqCount *db1, fastaSeqCount *db2, double threshold, BOOL normalize, int reference, BOOL lcsmode, BOOL extradata, int n);
#endif /* MTCOMPARE_SUMATRA_H_ */

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/**
* FileName: sumatra.c
* Authors: Eric Coissac, Celine Mercier
* Description: computation of pairwise similarities of DNA sequences
* **/
#include "sumatra.h"
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <math.h>
#include <string.h>
#include <sys/time.h>
#include "../sumalibs/libfasta/sequence.h"
#include "../sumalibs/liblcs/upperband.h"
#include "../sumalibs/liblcs/sse_banded_LCS_alignment.h"
#include "../sumalibs/libutils/utilities.h"
#include "mtcompare_sumatra.h"
#define VERSION "1.0.02"
/* ----------------------------------------------- */
/* printout help */
/* ----------------------------------------------- */
#define PP fprintf(stdout,
static void PrintHelp()
{
PP "-----------------------------------------------------------------------------------------------------------------------------\n");
PP " SUMATRA Version %s\n", VERSION);
PP "-----------------------------------------------------------------------------------------------------------------------------\n");
PP " Synopsis : sumatra computes all the pairwise LCS (Longest Common Subsequence) scores\n");
PP " of one nucleotide dataset or between two nucleotide datasets.\n");
PP " Usage: sumatra [options] <dataset1> [dataset2]\n");
PP "-----------------------------------------------------------------------------------------------------------------------------\n");
PP " Options:\n\n");
PP " -h : [H]elp - print <this> help\n\n");
PP " -l : Reference sequence length is the shortest. \n\n");
PP " -L : Reference sequence length is the largest. \n\n");
PP " -a : Reference sequence length is the alignment length (default). \n\n");
PP " -n : Score is normalized by reference sequence length (default).\n\n");
PP " -r : Raw score, not normalized. \n\n");
PP " -d : Score is expressed in distance (default: score is expressed in similarity). \n\n");
PP " -t ##.## : Score threshold. If the score is normalized and expressed in similarity (default),\n");
PP " it is an identity, e.g. 0.95 for an identity of 95%%. If the score is normalized\n");
PP " and expressed in distance, it is (1.0 - identity), e.g. 0.05 for an identity of 95%%.\n");
PP " If the score is not normalized and expressed in similarity, it is the length of the\n");
PP " Longest Common Subsequence. If the score is not normalized and expressed in distance,\n");
PP " it is (reference length - LCS length).\n");
PP " Only sequence pairs with a similarity above ##.## are printed. Default: 0.00 \n");
PP " (no threshold).\n\n");
PP " -p ## : Number of threads used for computation (default=1).\n\n");
PP " -g : n's are replaced with a's (default: sequences with n's are discarded).\n");
PP " -x : Adds four extra columns with the count and length of both sequences.\n");
PP "-----------------------------------------------------------------------------------------------------------------------------\n");
PP " First argument : the nucleotide dataset to analyze\n\n");
PP " Second argument : optionally the second nucleotide dataset\n");
PP "-----------------------------------------------------------------------------------------------------------------------------\n");
PP " Results table description : \n");
PP " column 1 : Identifier sequence 1\n");
PP " column 2 : Identifier sequence 2\n");
PP " column 3 : Score\n");
PP " column 4 : Count of sequence 1 (only with option -x)\n");
PP " column 5 : Count of sequence 2 (only with option -x)\n");
PP " column 6 : Length of sequence 1 (only with option -x)\n");
PP " column 7 : Length of sequence 2 (only with option -x)\n");
PP "-----------------------------------------------------------------------------------------------------------------------------\n");
PP " http://metabarcoding.org/sumatra\n");
PP "-----------------------------------------------------------------------------------------------------------------------------\n\n");
}
#undef PP
/* ----------------------------------------------- */
/* printout usage and exit */
/* ----------------------------------------------- */
#define PP fprintf(stderr,
static void ExitUsage(stat)
int stat;
{
PP "usage: sumatra [-l|L|a|n|r|d|g|x] [-t threshold_value] [-p number of threads] dataset1 [dataset2]\n");
PP "type \"sumatra -h\" for help\n");
if (stat)
exit(stat);
}
#undef PP
void printResults(fastaSeqPtr seq1,fastaSeqPtr seq2,
double score,
BOOL extradata,
int64_t pairs,
BOOL print)
{
static struct timeval start;
static struct timeval lastprint;
static BOOL first=TRUE;
static uint64_t aligned=0;
struct timeval current;
double fraction;
time_t fulltime;
time_t remaintime;
double elapsedtime;
int32_t day;
int32_t hour;
int32_t minute;
int32_t seconde;
aligned++;
if (first)
{
first=FALSE;
gettimeofday(&start,NULL);
lastprint=start;
}
gettimeofday(&current,NULL);
if (current.tv_sec!=lastprint.tv_sec)
{
lastprint=current;
fraction = (double)aligned/(double)pairs;
elapsedtime = difftime(current.tv_sec,start.tv_sec);
fulltime = elapsedtime / fraction;
remaintime = (time_t)difftime(fulltime,(time_t)elapsedtime);
fprintf(stderr,
"Computed %lld / %lld -> %5.2lf%%",
aligned, pairs, fraction*100.
);
seconde = fulltime % 60;
minute = fulltime / 60;
hour = minute / 60;
minute = minute % 60;
day = hour / 24;
hour = hour % 24;
if (day)
fprintf(stderr,
", estimated computation time = %3d days %02d:%02d:%02d",
day,
hour,
minute,
seconde
);
else
fprintf(stderr,
", estimated computation time = %02d:%02d:%02d",
hour,
minute,
seconde
);
seconde = remaintime % 60;
minute = remaintime / 60;
hour = minute / 60;
minute = minute % 60;
day = hour / 24;
hour = hour % 24;
if (day)
fprintf(stderr,
", about %3d days %02d:%02d:%02d remaining \r",
day,
hour,
minute,
seconde
);
else
fprintf(stderr,
", about %02d:%02d:%02d remaining \r",
hour,
minute,
seconde
);
}
if (print)
{
if (extradata)
printf("%s\t%s\t%lf\t%d\t%d\t%d\t%d\n", seq1->accession_id,
seq2->accession_id,
score,
seq1->count,
seq2->count,
seq1->length,
seq2->length
);
else
printf("%s\t%s\t%lf\n", seq1->accession_id,
seq2->accession_id,
score);
}
}
int compare1(fastaSeqCount db1, double threshold, BOOL normalize, int reference, BOOL lcsmode, BOOL extradata)
{
BOOL always = TRUE;
int64_t pairs = (int64_t)(db1.count - 1) * (int64_t)db1.count /2;
BOOL print;
double score;
int32_t i,j;
char* s1;
char* s2;
int l1;
int l2;
int16_t* iseq1;
int16_t* iseq2;
int16_t* address;
int sizeForSeqs;
int lmax, lmin;
int LCSmin;
fprintf(stderr,"Pairwise alignments of one dataset against itself\n");
fprintf(stderr,"Count of alignments to do : %lld\n",pairs);
if (threshold > 0)
{
fprintf(stderr,"Computing for scores > %lf\n",threshold);
always = FALSE;
}
calculateMaxAndMinLenDB(db1, &lmax, &lmin);
sizeForSeqs = prepareTablesForSumathings(lmax, lmin, threshold, normalize, reference, lcsmode, &address, &iseq1, &iseq2);
for (i=0; i < db1.count; i++) // ...??
for (j=i+1; j < db1.count; j++)
{
print = FALSE;
filtersSumatra(db1.fastaSeqs+i, db1.fastaSeqs+j, threshold, normalize, reference, lcsmode, &score, &LCSmin);
if (score >= 0) // identical sequences
print = TRUE;
else if (always || (score == -1.0)) // filter passed or no threshold
{
s1 = (db1.fastaSeqs+i)->sequence;
l1 = (db1.fastaSeqs+i)->length;
s2 = (db1.fastaSeqs+j)->sequence;
l2 = (db1.fastaSeqs+j)->length;
score = alignForSumathings(s1, iseq1, s2, iseq2, l1, l2, normalize, reference, lcsmode, address, sizeForSeqs, LCSmin);
print = always || (((normalize || lcsmode) && (score >= threshold)) || ((!lcsmode && !normalize) && (score <= threshold)));
if (print && !lcsmode && normalize)
score = 1.0 - score;
}
printResults(db1.fastaSeqs+i, db1.fastaSeqs+j, score, extradata, pairs, print);
}
free(iseq1-sizeForSeqs+lmax);
free(iseq2-sizeForSeqs+lmax);
return 0;
}
int compare2(fastaSeqCount db1, fastaSeqCount db2, double threshold, BOOL normalize, int reference, BOOL lcsmode, BOOL extradata)
{
BOOL always = TRUE;
int64_t pairs = (int64_t)(db1.count) * (int64_t)(db2.count);
BOOL print;
double score;
int32_t i,j;
char* s1;
char* s2;
int l1;
int l2;
int16_t* iseq1;
int16_t* iseq2;
int16_t* address;
int sizeForSeqs;
int lmax;
int lmax1;
int lmin;
int lmin1;
int LCSmin;
fprintf(stderr,"Pairwise alignments of two datasets\n");
fprintf(stderr,"Count of alignments to do : %lld\n",pairs);
if (threshold > 0)
{
fprintf(stderr,"Computing for scores > %lf\n",threshold);
always = FALSE;
}
calculateMaxAndMinLenDB(db1, &lmax, &lmin);
calculateMaxAndMinLenDB(db2, &lmax1, &lmin1);
if (lmax1 > lmax)
lmax = lmax1;
if (lmin1 < lmin)
lmin = lmin1;
sizeForSeqs = prepareTablesForSumathings(lmax, lmin, threshold, normalize, reference, lcsmode, &address, &iseq1, &iseq2);
for (i=0; i < db1.count; i++)
for (j=0; j < db2.count; j++)
{
print = FALSE;
filtersSumatra(db1.fastaSeqs+i, db2.fastaSeqs+j, threshold, normalize, reference, lcsmode, &score, &LCSmin);
if (score >= 0) // identical sequences
print = TRUE;
else if (always || (score == -1.0)) // filter passed or no threshold
{
s1 = (db1.fastaSeqs+i)->sequence;
l1 = (db1.fastaSeqs+i)->length;
s2 = (db2.fastaSeqs+j)->sequence;
l2 = (db2.fastaSeqs+j)->length;
score = alignForSumathings(s1, iseq1, s2, iseq2, l1, l2, normalize, reference, lcsmode, address, sizeForSeqs, LCSmin);
print = always || (((normalize || lcsmode) && (score >= threshold)) || ((!lcsmode && !normalize) && (score <= threshold)));
if (print && !lcsmode && normalize)
score = 1.0 - score;
}
printResults(db1.fastaSeqs+i, db2.fastaSeqs+j, score, extradata, pairs, print);
}
free(iseq1-sizeForSeqs+lmax);
free(iseq2-sizeForSeqs+lmax);
return 0;
}
int main(int argc, char **argv)
{
int32_t carg = 0;
int32_t errflag = 0;
BOOL normalize = TRUE;
BOOL lcsmode = TRUE;
int reference = ALILEN;
BOOL extradata = FALSE;
BOOL onlyATGC = TRUE;
double threshold = 0.0;
int ndb = 0;
int nproc = 1;
fastaSeqCount db1;
fastaSeqCount db2;
while ((carg = getopt(argc, argv, "hlLanrdt:p:gx")) != -1) {
switch (carg) {
/* -------------------- */
case 'h': /* help */
/* -------------------- */
PrintHelp();
exit(0);
break;
/* -------------------------------------------------- */
case 'l': /* Normalize LCS/Error by the shortest sequence length*/
/* -------------------------------------------------- */
reference=MINLEN;
break;
/* -------------------------------------------------- */
case 'L': /* Normalize LCS/Error by the largest sequence length */
/* -------------------------------------------------- */
reference=MAXLEN;
break;
/* -------------------------------------------------- */
case 'a': /* Normalize LCS/Error by the alignment length */
/* -------------------------------------------------- */
reference=ALILEN;
break;
/* -------------------------------------------------- */
case 'n': /* Normalize LCS by the reference length */
/* -------------------------------------------------- */
normalize=TRUE;
break;
/* -------------------------------------------------- */
case 'r': /* No normalization */
/* -------------------------------------------------- */
normalize=FALSE;
break;
/* -------------------------------------------------- */
case 'd': /* Score is expressed in distance */
/* -------------------------------------------------- */
lcsmode=FALSE;
break;
/* ------------------------------------------------------------------- */
case 't': /* Prints only pairs with similarity higher than (threshold) */
/* ------------------------------------------------------------------- */
sscanf(optarg,"%lf",&threshold);
break;
/* -------------------------------------------------- */
case 'p': /* number of processors to use */
/* -------------------------------------------------- */
sscanf(optarg,"%d",&nproc);
break;
/* -------------------------------------------------- */
case 'x': /* Print extra data (node weight, lseq1, lseq2) */
/* -------------------------------------------------- */
extradata=TRUE;
break;
/* -------------------------------------------------- */
case 'g': /* replace n's with a's in sequences */
/* -------------------------------------------------- */
onlyATGC=FALSE;
break;
case '?': /* bad option */
errflag++;
break;
}
}
ndb = argc - optind;
if (ndb < 1)
errflag++;
if (errflag)
ExitUsage(errflag);
fprintf(stderr,"===============================================================\n");
fprintf(stderr," SUMATRA version %s\n",VERSION);
#ifdef __SSE2__
fprintf(stderr,"Alignment using SSE2 code\n");
#else
fprintf(stderr,"Alignment using standard code, SSE2 unavailable\n");
#endif
fprintf(stderr,"===============================================================\n");
if (normalize && (threshold > 1.0))
{
fprintf(stderr, "\nERROR : Please specify a threshold included between 0.0 and 1.0 when normalizing scores.\n\n");
exit(1);
}
fprintf(stderr,"Reading dataset 1...");
db1 = seq_readAllSeq2(argv[optind], TRUE, onlyATGC);
fprintf(stderr,"\n%d sequences\n",db1.count);
if (!onlyATGC)
(void)cleanDB(db1);
addCounts(&db1);
if (threshold>0)
(void)hashDB(db1);
optind++;
if (ndb == 2)
{
fprintf(stderr,"Reading dataset 2...");
db2 = seq_readAllSeq2(argv[optind], TRUE, onlyATGC);
fprintf(stderr,"\n%d sequences\n",db2.count);
if (!onlyATGC)
(void)cleanDB(db2);
addCounts(&db2);
if (threshold>0)
(void)hashDB(db2);
}
if (!lcsmode && normalize && (threshold > 0))
threshold = 1.0 - threshold;
if (ndb==1)
{
if (nproc==1)
compare1(db1, threshold, normalize, reference, lcsmode, extradata);
else
mt_compare_sumatra(&db1, NULL, threshold, normalize, reference, lcsmode, extradata, nproc);
}
else
{
if (nproc==1)
compare2(db1, db2, threshold, normalize, reference, lcsmode, extradata);
else
mt_compare_sumatra(&db1, &db2, threshold, normalize, reference, lcsmode, extradata, nproc);
}
fprintf(stderr,"\nDone.\n\n");
return 0;
}

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/*
* sumatra.h
*
* Created on: 8 ao<61>t 2010
* Author: coissac
*/
#ifndef SUMATRA_H_
#define SUMATRA_H_
#include "../sumalibs/libfasta/sequence.h"
void printResults(fastaSeqPtr seq1, fastaSeqPtr seq2, double score, BOOL extradata, int64_t pairs, BOOL print);
#endif /* SUMATRA_H_ */

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