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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 à 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-à-vis its staff, any and all
measures required to ensure respect of said intellectual property rights
of the Holder and/or Contributors.
Article 7 - RELATED SERVICES
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 préside à
sa rédaction:
* d'une part, le respect des principes de diffusion des logiciels
libres: accès au code source, droits étendus conférés aux
utilisateurs,
* d'autre part, la désignation d'un droit applicable, le droit
français, auquel elle est conforme, tant au regard du droit de la
responsabilité civile que du droit de la propriété 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 à l'Energie Atomique - CEA, établissement public de
recherche à caractère scientifique, technique et industriel, dont le
siège est situé 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris.
Centre National de la Recherche Scientifique - CNRS, établissement
public à caractère scientifique et technologique, dont le siège est
situé 3 rue Michel-Ange, 75794 Paris cedex 16.
Institut National de Recherche en Informatique et en Automatique -
INRIA, établissement public à caractère scientifique et technologique,
dont le siège est situé Domaine de Voluceau, Rocquencourt, BP 105, 78153
Le Chesnay cedex.
Préambule
Ce contrat est une licence de logiciel libre dont l'objectif est de
conférer aux utilisateurs la liberté de modification et de
redistribution du logiciel régi par cette licence dans le cadre d'un
modèle de diffusion en logiciel libre.
L'exercice de ces libertés est assorti de certains devoirs à la charge
des utilisateurs afin de préserver ce statut au cours des
redistributions ultérieures.
L'accessibilité au code source et les droits de copie, de modification
et de redistribution qui en découlent ont pour contrepartie de n'offrir
aux utilisateurs qu'une garantie limitée et de ne faire peser sur
l'auteur du logiciel, le titulaire des droits patrimoniaux et les
concédants successifs qu'une responsabilité restreinte.
A cet égard l'attention de l'utilisateur est attirée sur les risques
associés au chargement, à l'utilisation, à la modification et/ou au
développement et à la reproduction du logiciel par l'utilisateur étant
donné sa spécificité de logiciel libre, qui peut le rendre complexe à
manipuler et qui le réserve donc à des développeurs ou des
professionnels avertis possédant des connaissances informatiques
approfondies. Les utilisateurs sont donc invités à charger et tester
l'adéquation du logiciel à leurs besoins dans des conditions permettant
d'assurer la sécurité de leurs systèmes et/ou de leurs données et, plus
généralement, à l'utiliser et l'exploiter dans les mêmes conditions de
sécurité. Ce contrat peut être reproduit et diffusé librement, sous
réserve de le conserver en l'état, sans ajout ni suppression de clauses.
Ce contrat est susceptible de s'appliquer à tout logiciel dont le
titulaire des droits patrimoniaux décide de soumettre l'exploitation aux
dispositions qu'il contient.
Article 1 - DEFINITIONS
Dans ce contrat, les termes suivants, lorsqu'ils seront écrits avec une
lettre capitale, auront la signification suivante:
Contrat: désigne le présent contrat de licence, ses éventuelles versions
postérieures et annexes.
Logiciel: désigne le logiciel sous sa forme de Code Objet et/ou de Code
Source et le cas échéant sa documentation, dans leur état au moment de
l'acceptation du Contrat par le Licencié.
Logiciel Initial: désigne le Logiciel sous sa forme de Code Source et
éventuellement de Code Objet et le cas échéant sa documentation, dans
leur état au moment de leur première diffusion sous les termes du Contrat.
Logiciel Modifié: désigne le Logiciel modifié par au moins une
Contribution.
Code Source: désigne l'ensemble des instructions et des lignes de
programme du Logiciel et auquel l'accès est nécessaire en vue de
modifier le Logiciel.
Code Objet: désigne les fichiers binaires issus de la compilation du
Code Source.
Titulaire: désigne le ou les détenteurs des droits patrimoniaux d'auteur
sur le Logiciel Initial.
Licencié: désigne le ou les utilisateurs du Logiciel ayant accepté le
Contrat.
Contributeur: désigne le Licencié auteur d'au moins une Contribution.
Concédant: désigne le Titulaire ou toute personne physique ou morale
distribuant le Logiciel sous le Contrat.
Contribution: désigne l'ensemble des modifications, corrections,
traductions, adaptations et/ou nouvelles fonctionnalités intégrées dans
le Logiciel par tout Contributeur, ainsi que tout Module Interne.
Module: désigne un ensemble de fichiers sources y compris leur
documentation qui permet de réaliser des fonctionnalités ou services
supplémentaires à ceux fournis par le Logiciel.
Module Externe: désigne tout Module, non dérivé du Logiciel, tel que ce
Module et le Logiciel s'exécutent dans des espaces d'adressage
différents, l'un appelant l'autre au moment de leur exécution.
Module Interne: désigne tout Module lié au Logiciel de telle sorte
qu'ils s'exécutent dans le même espace d'adressage.
GNU GPL: désigne la GNU General Public License dans sa version 2 ou
toute version ultérieure, telle que publiée par Free Software Foundation
Inc.
Parties: désigne collectivement le Licencié et le Concédant.
Ces termes s'entendent au singulier comme au pluriel.
Article 2 - OBJET
Le Contrat a pour objet la concession par le Concédant au Licencié d'une
licence non exclusive, cessible et mondiale du Logiciel telle que
définie ci-après à l'article 5 pour toute la durée de protection des droits
portant sur ce Logiciel.
Article 3 - ACCEPTATION
3.1 L'acceptation par le Licencié des termes du Contrat est réputée
acquise du fait du premier des faits suivants:
* (i) le chargement du Logiciel par tout moyen notamment par
téléchargement à partir d'un serveur distant ou par chargement à
partir d'un support physique;
* (ii) le premier exercice par le Licencié de l'un quelconque des
droits concédés par le Contrat.
3.2 Un exemplaire du Contrat, contenant notamment un avertissement
relatif aux spécificités du Logiciel, à la restriction de garantie et à
la limitation à un usage par des utilisateurs expérimentés a été mis à
disposition du Licencié préalablement à son acceptation telle que
définie à l'article 3.1 ci dessus et le Licencié reconnaît en avoir pris
connaissance.
Article 4 - ENTREE EN VIGUEUR ET DUREE
4.1 ENTREE EN VIGUEUR
Le Contrat entre en vigueur à la date de son acceptation par le Licencié
telle que définie en 3.1.
4.2 DUREE
Le Contrat produira ses effets pendant toute la durée légale de
protection des droits patrimoniaux portant sur le Logiciel.
Article 5 - ETENDUE DES DROITS CONCEDES
Le Concédant concède au Licencié, qui accepte, les droits suivants sur
le Logiciel pour toutes destinations et pour la durée du Contrat dans
les conditions ci-après détaillées.
Par ailleurs, si le Concédant détient ou venait à détenir un ou
plusieurs brevets d'invention protégeant tout ou partie des
fonctionnalités du Logiciel ou de ses composants, il s'engage à ne pas
opposer les éventuels droits conférés par ces brevets aux Licenciés
successifs qui utiliseraient, exploiteraient ou modifieraient le
Logiciel. En cas de cession de ces brevets, le Concédant s'engage à
faire reprendre les obligations du présent alinéa aux cessionnaires.
5.1 DROIT D'UTILISATION
Le Licencié est autorisé à utiliser le Logiciel, sans restriction quant
aux domaines d'application, étant ci-après précisé 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'exécution, ou le stockage du
Logiciel sur tout support.
3. la possibilité d'en observer, d'en étudier, ou d'en tester le
fonctionnement afin de déterminer les idées et principes qui sont
à la base de n'importe quel élément de ce Logiciel; et ceci,
lorsque le Licencié effectue toute opération de chargement,
d'affichage, d'exécution, 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 résultant.
Le Licencié est autorisé à apporter toute Contribution au Logiciel sous
réserve de mentionner, de façon explicite, son nom en tant qu'auteur de
cette Contribution et la date de création 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 marché à titre
onéreux ou gratuit, un ou des exemplaires du Logiciel par tout procédé.
Le Licencié est autorisé à distribuer des copies du Logiciel, modifié ou
non, à des tiers dans les conditions ci-après détaillées.
5.3.1 DISTRIBUTION DU LOGICIEL SANS MODIFICATION
Le Licencié est autorisé à distribuer des copies conformes du Logiciel,
sous forme de Code Source ou de Code Objet, à condition que cette
distribution respecte les dispositions du Contrat dans leur totalité et
soit accompagnée:
1. d'un exemplaire du Contrat,
2. d'un avertissement relatif à la restriction de garantie et de
responsabilité du Concédant telle que prévue aux articles 8
et 9,
et que, dans le cas où seul le Code Objet du Logiciel est redistribué,
le Licencié permette aux futurs Licenciés d'accéder facilement au Code
Source complet du Logiciel en indiquant les modalités d'accès, étant
entendu que le coût additionnel d'acquisition du Code Source ne devra
pas excéder le simple coût de transfert des données.
5.3.2 DISTRIBUTION DU LOGICIEL MODIFIE
Lorsque le Licencié apporte une Contribution au Logiciel, les conditions
de distribution du Logiciel Modifié en résultant sont alors soumises à
l'intégralité des dispositions du Contrat.
Le Licencié est autorisé à distribuer le Logiciel Modifié, sous forme de
code source ou de code objet, à condition que cette distribution
respecte les dispositions du Contrat dans leur totalité et soit
accompagnée:
1. d'un exemplaire du Contrat,
2. d'un avertissement relatif à la restriction de garantie et de
responsabilité du Concédant telle que prévue aux articles 8
et 9,
et que, dans le cas où seul le code objet du Logiciel Modifié est
redistribué, le Licencié permette aux futurs Licenciés d'accéder
facilement au code source complet du Logiciel Modifié en indiquant les
modalités d'accès, étant entendu que le coût additionnel d'acquisition
du code source ne devra pas excéder le simple coût de transfert des données.
5.3.3 DISTRIBUTION DES MODULES EXTERNES
Lorsque le Licencié a développé un Module Externe les conditions du
Contrat ne s'appliquent pas à ce Module Externe, qui peut être distribué
sous un contrat de licence différent.
5.3.4 COMPATIBILITE AVEC LA LICENCE GNU GPL
Le Licencié peut inclure un code soumis aux dispositions d'une des
versions de la licence GNU GPL dans le Logiciel modifié ou non et
distribuer l'ensemble sous les conditions de la même version de la
licence GNU GPL.
Le Licencié peut inclure le Logiciel modifié 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 même version de la licence GNU GPL.
Article 6 - PROPRIETE INTELLECTUELLE
6.1 SUR LE LOGICIEL INITIAL
Le Titulaire est détenteur 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 faculté de modifier les conditions de
diffusion de ce Logiciel Initial.
Le Titulaire s'engage à ce que le Logiciel Initial reste au moins régi
par le Contrat et ce, pour la durée visée à l'article 4.2.
6.2 SUR LES CONTRIBUTIONS
Le Licencié qui a développé une Contribution est titulaire sur celle-ci
des droits de propriété intellectuelle dans les conditions définies par
la législation applicable.
6.3 SUR LES MODULES EXTERNES
Le Licencié qui a développé un Module Externe est titulaire sur celui-ci
des droits de propriété intellectuelle dans les conditions définies par
la législation applicable et reste libre du choix du contrat régissant
sa diffusion.
6.4 DISPOSITIONS COMMUNES
Le Licencié s'engage expressément:
1. à ne pas supprimer ou modifier de quelque manière que ce soit les
mentions de propriété intellectuelle apposées sur le Logiciel;
2. à reproduire à l'identique lesdites mentions de propriété
intellectuelle sur les copies du Logiciel modifié ou non.
Le Licencié s'engage à ne pas porter atteinte, directement ou
indirectement, aux droits de propriété intellectuelle du Titulaire et/ou
des Contributeurs sur le Logiciel et à prendre, le cas échéant, à
l'égard de son personnel toutes les mesures nécessaires pour assurer le
respect des dits droits de propriété intellectuelle du Titulaire et/ou
des Contributeurs.
Article 7 - SERVICES ASSOCIES
7.1 Le Contrat n'oblige en aucun cas le Concédant à la réalisation de
prestations d'assistance technique ou de maintenance du Logiciel.
Cependant le Concédant 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 déterminés dans un acte séparé. Ces actes de
maintenance et/ou assistance technique n'engageront que la seule
responsabilité du Concédant qui les propose.
7.2 De même, tout Concédant est libre de proposer, sous sa seule
responsabilité, à ses licenciés une garantie, qui n'engagera que lui,
lors de la redistribution du Logiciel et/ou du Logiciel Modifié et ce,
dans les conditions qu'il souhaite. Cette garantie et les modalités
financières de son application feront l'objet d'un acte séparé entre le
Concédant et le Licencié.
Article 8 - RESPONSABILITE
8.1 Sous réserve des dispositions de l'article 8.2, le Licencié a la
faculté, sous réserve de prouver la faute du Concédant concerné, de
solliciter la réparation du préjudice direct qu'il subirait du fait du
Logiciel et dont il apportera la preuve.
8.2 La responsabilité du Concédant est limitée aux engagements pris en
application du Contrat et ne saurait être engagée en raison notamment:
(i) des dommages dus à l'inexécution, totale ou partielle, de ses
obligations par le Licencié, (ii) des dommages directs ou indirects
découlant de l'utilisation ou des performances du Logiciel subis par le
Licencié et (iii) plus généralement d'un quelconque dommage indirect. En
particulier, les Parties conviennent expressément que tout préjudice
financier ou commercial (par exemple perte de données, perte de
bénéfices, perte d'exploitation, perte de clientèle ou de commandes,
manque à gagner, trouble commercial quelconque) ou toute action dirigée
contre le Licencié par un tiers, constitue un dommage indirect et
n'ouvre pas droit à réparation par le Concédant.
Article 9 - GARANTIE
9.1 Le Licencié reconnaît que l'état actuel des connaissances
scientifiques et techniques au moment de la mise en circulation du
Logiciel ne permet pas d'en tester et d'en vérifier toutes les
utilisations ni de détecter l'existence d'éventuels défauts. L'attention
du Licencié a été attirée sur ce point sur les risques associés au
chargement, à l'utilisation, la modification et/ou au développement et à
la reproduction du Logiciel qui sont réservés à des utilisateurs avertis.
Il relève de la responsabilité du Licencié de contrôler, par tous
moyens, l'adéquation du produit à ses besoins, son bon fonctionnement et
de s'assurer qu'il ne causera pas de dommages aux personnes et aux biens.
9.2 Le Concédant déclare de bonne foi être en droit de concéder
l'ensemble des droits attachés au Logiciel (comprenant notamment les
droits visés à l'article 5).
9.3 Le Licencié reconnaît que le Logiciel est fourni "en l'état" par le
Concédant sans autre garantie, expresse ou tacite, que celle prévue à
l'article 9.2 et notamment sans aucune garantie sur sa valeur commerciale,
son caractère sécurisé, innovant ou pertinent.
En particulier, le Concédant ne garantit pas que le Logiciel est exempt
d'erreur, qu'il fonctionnera sans interruption, qu'il sera compatible
avec l'équipement du Licencié et sa configuration logicielle ni qu'il
remplira les besoins du Licencié.
9.4 Le Concédant ne garantit pas, de manière expresse ou tacite, que le
Logiciel ne porte pas atteinte à un quelconque droit de propriété
intellectuelle d'un tiers portant sur un brevet, un logiciel ou sur tout
autre droit de propriété. Ainsi, le Concédant exclut toute garantie au
profit du Licencié contre les actions en contrefaçon qui pourraient être
diligentées au titre de l'utilisation, de la modification, et de la
redistribution du Logiciel. Néanmoins, si de telles actions sont
exercées contre le Licencié, le Concédant lui apportera son aide
technique et juridique pour sa défense. Cette aide technique et
juridique est déterminée au cas par cas entre le Concédant concerné et
le Licencié dans le cadre d'un protocole d'accord. Le Concédant dégage
toute responsabilité quant à l'utilisation de la dénomination du
Logiciel par le Licencié. Aucune garantie n'est apportée quant à
l'existence de droits antérieurs sur le nom du Logiciel et sur
l'existence d'une marque.
Article 10 - RESILIATION
10.1 En cas de manquement par le Licencié aux obligations mises à sa
charge par le Contrat, le Concédant pourra résilier de plein droit le
Contrat trente (30) jours après notification adressée au Licencié et
restée sans effet.
10.2 Le Licencié dont le Contrat est résilié n'est plus autorisé à
utiliser, modifier ou distribuer le Logiciel. Cependant, toutes les
licences qu'il aura concédées antérieurement à la résiliation du Contrat
resteront valides sous réserve qu'elles aient été effectuées en
conformité avec le Contrat.
Article 11 - DISPOSITIONS DIVERSES
11.1 CAUSE EXTERIEURE
Aucune des Parties ne sera responsable d'un retard ou d'une défaillance
d'exécution du Contrat qui serait dû à un cas de force majeure, un cas
fortuit ou une cause extérieure, telle que, notamment, le mauvais
fonctionnement ou les interruptions du réseau électrique ou de
télécommunication, la paralysie du réseau liée à une attaque
informatique, l'intervention des autorités gouvernementales, les
catastrophes naturelles, les dégâts des eaux, les tremblements de terre,
le feu, les explosions, les grèves et les conflits sociaux, l'état de
guerre...
11.2 Le fait, par l'une ou l'autre des Parties, d'omettre en une ou
plusieurs occasions de se prévaloir d'une ou plusieurs dispositions du
Contrat, ne pourra en aucun cas impliquer renonciation par la Partie
intéressée à s'en prévaloir ultérieurement.
11.3 Le Contrat annule et remplace toute convention antérieure, écrite
ou orale, entre les Parties sur le même objet et constitue l'accord
entier entre les Parties sur cet objet. Aucune addition ou modification
aux termes du Contrat n'aura d'effet à l'égard des Parties à moins
d'être faite par écrit et signée par leurs représentants dûment habilités.
11.4 Dans l'hypothèse où une ou plusieurs des dispositions du Contrat
s'avèrerait contraire à une loi ou à un texte applicable, existants ou
futurs, cette loi ou ce texte prévaudrait, et les Parties feraient les
amendements nécessaires pour se conformer à cette loi ou à ce texte.
Toutes les autres dispositions resteront en vigueur. De même, la
nullité, pour quelque raison que ce soit, d'une des dispositions du
Contrat ne saurait entraîner la nullité de l'ensemble du Contrat.
11.5 LANGUE
Le Contrat est rédigé en langue française et en langue anglaise, ces
deux versions faisant également foi.
Article 12 - NOUVELLES VERSIONS DU CONTRAT
12.1 Toute personne est autorisée à copier et distribuer des copies de
ce Contrat.
12.2 Afin d'en préserver la cohérence, le texte du Contrat est protégé
et ne peut être modifié que par les auteurs de la licence, lesquels se
réservent le droit de publier périodiquement des mises à jour ou de
nouvelles versions du Contrat, qui posséderont chacune un numéro
distinct. Ces versions ultérieures seront susceptibles de prendre en
compte de nouvelles problématiques rencontrées par les logiciels libres.
12.3 Tout Logiciel diffusé sous une version donnée du Contrat ne pourra
faire l'objet d'une diffusion ultérieure que sous la même version du
Contrat ou une version postérieure, sous réserve des dispositions de
l'article 5.3.4.
Article 13 - LOI APPLICABLE ET COMPETENCE TERRITORIALE
13.1 Le Contrat est régi par la loi française. Les Parties conviennent
de tenter de régler à l'amiable les différends ou litiges qui
viendraient à se produire par suite ou à l'occasion du Contrat.
13.2 A défaut d'accord amiable dans un délai de deux (2) mois à compter
de leur survenance et sauf situation relevant d'une procédure d'urgence,
les différends ou litiges seront portés par la Partie la plus diligente
devant les Tribunaux compétents de Paris.
Version 2.0 du 2006-09-05.

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CC=gcc
LDFLAGS=
CFLAGS = -O3 -w
default: all
%.o: %.c
$(CC) $(CFLAGS) -c -o $@ $< $(LIB)

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libfasta/Makefile Normal file
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SOURCES = fasta_header_parser.c \
fasta_seq_writer.c \
fasta_header_handler.c \
header_mem_handler.c \
sequence.c
SRCS=$(SOURCES)
OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
LIBFILE = libfasta.a
RANLIB = ranlib
include ../global.mk
all: $(LIBFILE)
fasta_header_parser.c: fasta_header_parser.l
flex -Pheader_yy -t $< > $@
dic_parser.c: dic_parser.l
lex -Phashtable_yy -t $< > $@
clean:
rm -rf $(OBJECTS) $(LIBFILE)
rm -f *.a
$(LIBFILE): $(OBJECTS)
ar -cr $@ $?
$(RANLIB) $@

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#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "sequence.h"
#include "fasta_header_parser.h"
#include "fasta_header_handler.h"
char* char_header_add_field(char* header, char* name, char* value)
{
int lheader = strlen(header);
header = (char*) realloc(header, (lheader+strlen(name)+strlen(value)+4)*sizeof(char));
if (header[lheader-1] == '.')
{
strcpy(header+lheader-1,";");
strcpy(header+lheader," ");
strcpy(header+lheader+1,name);
strcpy(header+lheader+1+strlen(name),"=");
strcpy(header+lheader+1+strlen(name)+1,value);
}
else
{
strcpy(header+lheader,";");
strcpy(header+lheader+1," ");
strcpy(header+lheader+2,name);
strcpy(header+lheader+2+strlen(name),"=");
strcpy(header+lheader+2+strlen(name)+1,value);
}
return header;
}
char* fastaSeqPtr_header_add_field(fastaSeqPtr seq, char* name, char* value)
{
int lheader = strlen(seq->rawheader);
int i;
char* buffer;
char* rawheader;
rawheader = (char*) malloc((lheader+strlen(name)+strlen(value)+5)*sizeof(char));
strcpy(rawheader, seq->rawheader);
buffer = calloc(lheader, sizeof(char));
i=0;
while ((rawheader[i] != ' ') && (rawheader[i] != 0))
i++;
if (rawheader[i] == ' ')
strcpy(buffer, rawheader+i);
else
strcpy(rawheader+i, " ");
i++;
strcpy(rawheader+i,name);
strcpy(rawheader+i+strlen(name),"=");
strcpy(rawheader+i+strlen(name)+1,value);
strcpy(rawheader+i+strlen(name)+1+strlen(value),";");
strcpy(rawheader+i+strlen(name)+1+strlen(value)+1, buffer);
free(buffer);
return(rawheader);
}
element_from_header* table_header_add_field(element_from_header* header, char* name, char* value)
{
int nbf;
nbf = atoi(header[0].value);
nbf++;
header = (element_from_header*) realloc(header, (nbf+1)*sizeof(element_from_header));
header[nbf].name = (char*) malloc((1+strlen(name))*sizeof(char));
strcpy(header[nbf].name, name);
header[nbf].value = (char*) malloc((1+strlen(value))*sizeof(char));
strcpy(header[nbf].value, value);
sprintf(header[0].value, "%d", nbf);
return(header);
}
void free_header_table(element_from_header* header)
{
int i;
int nbf = atoi(header[0].value);
for (i = 0; i <= nbf; i++)
{
free((header[i]).name);
free((header[i]).value);
}
free(header);
}
char* getItemFromHeader(char* name, element_from_header* header)
{
char* value = 0;
int nbf;
int i;
nbf = atoi(header[0].value);
for (i = 1; i <= nbf; i++)
{
if (strcmp(header[i].name,name)==0)
value = header[i].value;
}
return value;
}
void changeValue(element_from_header* header, char* name, char* newValue)
{
int i;
int nbf = atoi(header[0].value);
for (i = 1; i <= nbf; i++)
{
if (strcmp(header[i].name, name)==0)
{
header[i].value = realloc(header[i].value, (1+strlen(newValue))*sizeof(char));
strcpy(header[i].value, newValue);
}
}
}

23
libfasta/fasta_header_handler.h Normal file
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#ifndef FASTA_HEADER_HANDLER_H_
#define FASTA_HEADER_HANDLER_H_
#include "sequence.h"
char* char_header_add_field(char*,char*,char*);
char* fastaSeqPtr_header_add_field(fastaSeqPtr seq, char* name, char* value);
element_from_header* table_header_add_dic(element_from_header* header, char* name, struct hashtable *hashtab);
element_from_header* table_header_add_field(element_from_header* header, char* name, char* value);
void free_header_table(element_from_header*);
char* getItemFromHeader(char*, element_from_header*);
void changeValue(element_from_header* header, char* name, char* newValue);
#endif

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libfasta/fasta_header_parser.h Normal file
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#ifndef FASTA_HEADER_PARSER_H_
#define FASTA_HEADER_PARSER_H_
typedef struct {
char *name;
void *value;
}element_from_header;
element_from_header* header_parser_main(char*);
#endif

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libfasta/fasta_header_parser.l Normal file
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/*
* Add -ll in Makefile if you modify this file to convert to .c
*/
%x REGID
%x REGNAME
%x REGVAL
%{
#include <stdlib.h>
#include <string.h>
#include "header_mem_handler.h"
#include "fasta_header_handler.h"
#define MEMALLOCATED 10
#define BUFFER 5
#define YY_DECL int header_parser(int *nbf, int *memory_allocated, element_from_header **p_header)
%}
WORD [[:alnum:]:\-.{},'_()\#\[\]\|\&\"\'\/\%\+]+
WORDID [[:alnum:]:\-.{},'_()\#\[\]\|\&\"\'\/\%\+=;]+
SUP >
EOL \n
SEP ;
SPACE [[:blank:]]+
EQUAL =
%%
int i;
int size_needed;
int free_size;
char* field;
<INITIAL>{SUP} {
/*printf("\n<INITIAL>{SUP},%s",yytext);*/
BEGIN(REGID);
}
<INITIAL,REGID>{WORDID} {
i=0;
field = malloc_field(&free_size);
(*p_header)[*nbf].name = (char*) malloc(3*sizeof(char));
strcpy(((*p_header)[*nbf]).name,"id");
size_needed = strlen(yytext)+1;
(*p_header)[*nbf].value = (char*) malloc(sizeof(char)*size_needed);
strcpy(((*p_header)[*nbf]).value,yytext);
(*nbf)++;
}
<INITIAL,REGID>{SPACE} {
BEGIN(REGNAME);
}
<REGNAME>{WORD} {
/*fprintf(stderr,"\n<REGNAME>{WORD} **%s**",yytext);*/
field = store_in_field(field,yytext,&free_size,&i);
}
<REGNAME>{SPACE} {
/*fprintf(stderr,"\n<REGNAME>{SPACE} **%s**",yytext);*/
if (i != 0)
field = store_in_field(field,yytext,&free_size,&i);
}
<REGNAME>{EQUAL} {
/*fprintf(stderr,"\n<REGNAME>{EQUAL},%s",yytext);*/
field = store_in_header_table(field, &((*p_header)[*nbf].name), &free_size, &i);
BEGIN(REGVAL);
}
<REGNAME>{SEP} {
/*fprintf(stderr,"\n<REGNAME>{SEP},%s",yytext);*/
(*p_header)[*nbf].name = (char*) malloc(19*sizeof(char));
strcpy((*p_header)[*nbf].name,"definition");
field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
BEGIN(REGNAME);
}
<REGVAL>{WORD} {
/*fprintf(stderr,"\n<REGVAL>{WORD} **%s**\n",yytext);*/
field = store_in_field(field,yytext,&free_size,&i);
}
<REGVAL>{SPACE} {
/*fprintf(stderr,"\n<REGVAL>{SPACE} **%s**\n",yytext);*/
field = store_in_field(field,yytext,&free_size,&i);
}
<REGVAL>{SEP} {
/*fprintf(stderr,"\n<REGVAL>{SEP},%s\n",yytext);*/
field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
BEGIN(REGNAME);
}
<REGVAL>{EQUAL} {
/*fprintf(stderr, "\nWarning : separator ';' probably missing in header after %s",(*p_header)[*nbf].name);*/
}
<REGVAL><<EOF>> {
field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
end_header_table(p_header, *nbf);
free(field);
BEGIN(INITIAL);
return 0;
}
<REGNAME><<EOF>> {
/*(*p_header)[*nbf].name = (char*) malloc(sizeof(char)*19);
strcpy((*p_header)[*nbf].name,"other_informations");
field = store_in_header_table(field, &((*p_header)[*nbf].value), &free_size, &i);
p_header = check_and_realloc_mem_in_header_table(p_header, nbf, memory_allocated);
*/
end_header_table(p_header, *nbf);
free(field);
BEGIN(INITIAL);
return 0;
}
%%
int header_yywrap()
{
return 1;
}
element_from_header* header_parser_main(char *h)
{
int nbfields,memory_allocated;
element_from_header* header;
char* nbfields_n;
char* nbfields_v;
nbfields_n = (char*) malloc(9*sizeof(char));
nbfields_v = (char*) malloc(5*sizeof(char));
memory_allocated=MEMALLOCATED;
nbfields=1;
strcpy(nbfields_n, "nbfields");
strcpy(nbfields_v, "1");
header = (element_from_header*) malloc(memory_allocated * sizeof(element_from_header));
header[0].name = nbfields_n;
header[0].value = nbfields_v;
YY_BUFFER_STATE state;
state=yy_scan_string(h);
header_parser(&nbfields, &memory_allocated, &header);
yy_delete_buffer(state);
return header;
}

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#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "sequence.h"
#include "fasta_header_parser.h"
void printOnlySeqFromFastaSeqPtr(fastaSeqPtr seq, FILE* output)
{
char nuc;
int n=60;
int l = strlen(seq->sequence);
for (n=60; n<l; n+=60)
{
nuc = seq->sequence[n];
seq->sequence[n]=0;
fprintf(output,"%s\n",seq->sequence+n-60);
seq->sequence[n]=nuc;
}
fprintf(output,"%s\n",seq->sequence+n-60);
}
void printOnlySeqFromChar(char* seq, FILE* output)
{
char nuc;
int n=60;
int l = strlen(seq);
for (n=60; n<l; n+=60)
{
nuc = seq[n];
seq[n]=0;
fprintf(output,"%s\n",seq+n-60);
seq[n]=nuc;
}
fprintf(output,"%s\n",seq+n-60);
}
void printOnlyHeaderFromFastaSeqPtr(fastaSeqPtr seq, FILE* output)
{
fprintf(output,">%s\n",seq->rawheader);
}
void printOnlyHeaderFromTable(element_from_header* header, FILE* output)
{
int i;
int nbf;
nbf = atoi(header[0].value);
fprintf(output,">%s ",header[1].value);
for (i = 2; i <= nbf; i++)
{
if (strcmp(header[i].name, "definition") != 0)
{
fprintf(output,"%s",header[i].name);
fprintf(output,"=");
fprintf(output,"%s; ",header[i].value);
}
}
if (strcmp(header[nbf].name, "definition") == 0)
fprintf(output,"%s; ",header[nbf].value);
fprintf(output,"\n");
}
void printHeaderAndSeqFromFastaSeqPtr(fastaSeqPtr seq, FILE* output)
{
printOnlyHeaderFromFastaSeqPtr(seq, output);
printOnlySeqFromFastaSeqPtr(seq, output);
}

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#ifndef FASTA_SEQ_WRITER_H_
#define FASTA_SEQ_WRITER_H_
#include "sequence.h"
void printOnlySeqFromFastaSeqPtr(fastaSeqPtr, FILE*);
void printOnlySeqFromChar(char*, FILE*);
void printOnlyHeaderFromFastaSeqPtr(fastaSeqPtr, FILE*);
void printOnlyHeaderFromTable(element_from_header*, FILE*);
void printHeaderAndSeqFromFastaSeqPtr(fastaSeqPtr, FILE*);
#endif

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#include <stdio.h>
#include <stdlib.h>
#include "header_mem_handler.h"
#include <string.h>
#define FIELD_BUFFER 1024
char* malloc_field(int *free_size)
{
char* field = (char*) malloc(sizeof(char) * FIELD_BUFFER);
field[0] = 0;
(*free_size) = FIELD_BUFFER;
return field;
}
int check_mem_field(int size_needed)
{
int number_of_chunks_to_alloc;
number_of_chunks_to_alloc = size_needed / FIELD_BUFFER + 1;
return number_of_chunks_to_alloc;
}
char* realloc_field(int number_of_chunks_to_alloc, char* field)
{
int size_needed;
size_needed = number_of_chunks_to_alloc * FIELD_BUFFER;
field = realloc(field, (size_needed)*sizeof(char));
return field;
}
char* check_and_realloc_field(char* field, int size_needed, int* free_size)
{
size_needed = size_needed + strlen(field);
int number_of_chunks_to_alloc = check_mem_field(size_needed);
if (strlen(field)>0)
field = realloc_field(number_of_chunks_to_alloc, field);
else
{
free(field);
field = malloc(number_of_chunks_to_alloc * FIELD_BUFFER);
}
(*free_size) = number_of_chunks_to_alloc*FIELD_BUFFER - size_needed + 1;
return field;
}
char* store_in_field(char* field, char* yytext, int* free_size, int* i)
{
int size_needed;
size_needed = strlen(yytext)+1;
if (size_needed > (*free_size))
field = check_and_realloc_field(field, size_needed, free_size);
else
(*free_size) = (*free_size) - size_needed + 1;
strcpy(&(field[(*i)]),yytext);
(*i) = (*i)+size_needed-1;
return field;
}
char* store_in_header_table(char* field, char** storing_place, int* free_size, int* i)
{
int size_needed;
size_needed = strlen(field)+1;
*storing_place = (char*) malloc(size_needed*sizeof(char));
strcpy(*storing_place,field);
(*i)=0;
free(field);
field = malloc_field(free_size);
return field;
}
element_from_header** check_and_realloc_mem_in_header_table(element_from_header** p_header, int* nbf, int* memory_allocated)
{
(*nbf)++;
if (*nbf == *memory_allocated)
{
(*memory_allocated)++;
*p_header = (element_from_header*) realloc(*p_header, (*memory_allocated) * sizeof(element_from_header));
}
return p_header;
}
void end_header_table(element_from_header** p_header, int nbf)
{
nbf = nbf - 1;
//fprintf(stderr, "nbf = %d", nbf);
sprintf((*p_header)->value, "%d", nbf);
}

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#ifndef HEADER_MEM_HANDLER_H_
#define HEADER_MEM_HANDLER_H_
#include "fasta_header_parser.h"
char* malloc_field(int*);
int check_mem_field(int);
char* realloc_field(int, char*);
char* check_and_realloc_field(char*, int, int*);
char* store_in_field(char*, char*, int*, int*);
char* store_in_header_table(char*, char**, int*, int*);
element_from_header** check_and_realloc_mem_in_header_table(element_from_header**, int*, int*);
void end_header_table(element_from_header** p_header, int nbf);
#endif

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/**
* FileName: sequence.c
* Authors: Tiayyba Riaz, Celine Mercier
* Description: C file for sequence reading and parsing
* **/
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include "../libutils/utilities.h"
#include "sequence.h"
#include "../libfile/fileHandling.h"
#include "fasta_header_handler.h"
#include "fasta_header_parser.h"
/*
* Function Name: seq_getNext(FILE *fp, char *fieldDelim)
* Description: Gets the next sequence from file by calling another function, passes the sequence
* to other function to get the header elements and nucleotide suquence into a strcuture of
* type fastaSeq and returns a pointer to this newly populated structure.
*/
fastaSeqPtr seq_getNext(FILE *fp, char *fieldDelim, BOOL isStandardSeq, BOOL onlyATGC)
{
char *seq;
char *header;
char *strTemp;
fastaSeqPtr seqElem;
int seqLen;
seq = seq_readNextFromFilebyLine(fp);
if (seq == NULL) return NULL;
/* Find header separator \n, if not found return NULL */
strTemp = strchr(seq, '\n');
if(strTemp == NULL)
return NULL;
seqLen = strlen(strTemp);
header = (char*) util_malloc(1+(strlen(seq) - seqLen)*sizeof(char), __FILE__, __LINE__);
/* Separate header in header variable */
strncpy(header, seq, strTemp - seq);
header[strTemp - seq] = '\0';
/* Get memory for new sequence structure element */
seqElem = (fastaSeqPtr) util_malloc(sizeof(fastaSeq), __FILE__, __LINE__);
/* Parse header and assign values to structure fields */
seq_fillHeader(header, fieldDelim, seqElem);
/* Get clean sequence and assign to structure field */
if (isStandardSeq)
if (onlyATGC)
seq_fillSeqOnlyATGC(strTemp, seqElem, seqLen);
else
seq_fillSeq(strTemp, seqElem, seqLen);
else
seq_fillDigitSeq(strTemp, seqElem, seqLen);
/* Type cast the char * seq to void pointer and deallocate the memory pointed by this */
util_free((void *)seq);
/* Return new sequence structure element */
return seqElem;
}
char *seq_readNextFromFilebyLine(FILE* fp)
{
char newc = '\0';
BOOL seqCompleted = FALSE;
int length = 500;
int32_t len;
char tempstr[length];
char* buffer;
if (feof(fp)) return NULL;
newc = file_nextChar(fp);
if (newc != '>') ungetc(newc, fp);
buffer = util_malloc(1*sizeof(char), __FILE__, __LINE__);
buffer[0] = '\0';
while(!seqCompleted)
{
newc = file_nextChar(fp);
if(newc == '>' || newc == '\0')
{
seqCompleted = TRUE;
if (newc == '>')
ungetc(newc, fp); // Make sure next time we start from sequence delimiter >
}
else
{
ungetc(newc, fp);
if(file_nextLine( fp, tempstr, length) != NULL)
{
len = strlen(tempstr) + strlen(buffer) + 1;
buffer = util_realloc(buffer, len, __FILE__, __LINE__);
strcat(buffer, tempstr);
}
else
{
seqCompleted = TRUE;
}
}
}
return buffer;
}
/*
* Function Name: seq_fillHeader(char* header, char *fieldDelim, fastaSeqPtr seqElem)
*/
void seq_fillHeader(char* header, char *fieldDelim, fastaSeqPtr seqElem)
{
char* IdEnd;
int IdSize;
seqElem->rawheader = strdup(header);
IdEnd = strchr(header, ' ');
if (IdEnd == NULL)
IdSize = strlen(header);
else
IdSize = strlen(header) - strlen(IdEnd);
seqElem->accession_id = (char*) util_malloc(1+IdSize*sizeof(char), __FILE__, __LINE__);
strncpy(seqElem->accession_id, header, IdSize);
(seqElem->accession_id)[IdSize] = '\0';
}
/*
* Function Name: seq_fillSeq(char *seq, fastaSeqPtr seqElem)
* Description: Parses the whole sequences for actual nucleotide sequences and stores that
* sequence in the field of structure 'seqElem' .
*/
void seq_fillSeq(char *seq, fastaSeqPtr seqElem, int seqLen)
{
char* seqTemp;
char c;
int32_t index = 0, seqIndex = 0, len = strlen(seq);
char* seqAlphabets = "acgtACGT-nN";
seqTemp = (char*) util_malloc(seqLen*sizeof(char), __FILE__, __LINE__);
while (index < len)
{
c = seq[index++];
if (strchr(seqAlphabets, c) != NULL)
seqTemp[seqIndex++] = tolower(c);
}
seqTemp[seqIndex] = '\0';
seqElem->length=seqIndex;
seqElem->sequence = strdup(seqTemp);
}
void seq_fillSeqOnlyATGC(char *seq, fastaSeqPtr seqElem, int seqLen)
{
char* seqTemp;
char c;
int32_t index = 0, seqIndex = 0, len = strlen(seq);
char* seqAlphabets = "acgtACGT";
int notAllATGC = 0;
seqTemp = (char*) util_malloc(seqLen*sizeof(char), __FILE__, __LINE__);
while (index < len)
{
c = seq[index++];
if (strchr(seqAlphabets, c) != NULL)
seqTemp[seqIndex++] = tolower(c);
else if (c != '\n')
notAllATGC = 1;
}
if (notAllATGC)
seqTemp[0] = '\0';
else
{
seqTemp[seqIndex] = '\0';
seqElem->length=seqIndex;
}
seqElem->sequence = strdup(seqTemp);
}
void seq_fillDigitSeq(char *seq, fastaSeqPtr seqElem, int seqLen)
{
char* seqTemp;
char c;
int32_t index = 0, seqIndex = 0, len = strlen(seq);
seqTemp = (char*) util_malloc(seqLen*sizeof(char), __FILE__, __LINE__);
while (index < len)
{
c = seq[index++];
if ((c >= '0' && c <= '9') || c == ' ')
seqTemp[seqIndex++] = c;
/*else
{
printf("Error in input file");
exit(0);
}*/
}
seqTemp[seqIndex] = '\0';
seqElem->sequence = strdup(seqTemp);
}
fastaSeqCount seq_readAllSeq2(char *fileName, BOOL isStandardSeq, BOOL onlyATGC)
{
FILE* fp;
fastaSeqPtr seqPtr;
fastaSeqPtr seqPtrAr;
int32_t counter = 0;
int32_t slots = 1000;
fastaSeqCount allseqs;
int32_t discarded=0;
fp = file_open(fileName, TRUE);
if (fp == NULL)
{
fprintf(stderr, "\nCould not open file.\n");
exit(1);
}
exitIfEmptyFile(fp);
seqPtrAr = (fastaSeqPtr) util_malloc(slots*sizeof(fastaSeq), __FILE__, __LINE__);
seqPtr = seq_getNext(fp, " ", isStandardSeq, onlyATGC);
while (seqPtr != NULL)
{
if (counter == slots)
{
slots += 1000;
seqPtrAr = (fastaSeqPtr)util_realloc(seqPtrAr, slots*sizeof(fastaSeq), __FILE__, __LINE__);
}
if ((seqPtr->sequence)[0] != '\0')
seqPtrAr[counter++] = *seqPtr;
else
discarded++;
util_free((void *)seqPtr);
seqPtr = seq_getNext(fp, " ", isStandardSeq, onlyATGC);
}
fclose(fp);
if (counter != slots)
seqPtrAr = (fastaSeqPtr)util_realloc(seqPtrAr, counter*sizeof(fastaSeq), __FILE__, __LINE__);
allseqs.count = counter;
allseqs.fastaSeqs = seqPtrAr;
if (discarded)
fprintf(stderr, "\nDiscarded %d sequences that did not contain only 'AaTtGgCc' characters.", discarded);
return allseqs;
}
int32_t seq_findSeqByAccId (char *accid, fastaSeqCountPtr allseqs)
{
int32_t i;
for (i = 0; i < allseqs->count; i++)
{
if (strcmp (accid, allseqs->fastaSeqs[i].accession_id) == 0)
return i;
}
return -1;
}
void seq_printSeqs (fastaSeqCountPtr allseq)
{
int32_t i;
for (i = 0; i < allseq->count; i++)
//for (i = 0; i < 4; i++)
{
if (allseq->fastaSeqs[i].sequence == NULL) continue;
if (allseq->fastaSeqs[i].rawheader)
printf (">%s\n", allseq->fastaSeqs[i].rawheader);
else
printf (">%s\n", allseq->fastaSeqs[i].accession_id);
printf ("%s\n", allseq->fastaSeqs[i].sequence);
}
}
int cleanDB(fastaSeqCount db) // replace not a/t/g/c with a's
{
int32_t i;
char *seq;
BOOL changed;
int32_t seqchanged=0;
int32_t nucchanged=0;
fprintf(stderr,"Cleaning dataset...");
for (i=0; i < db.count;i++)
{
changed=FALSE;
for (seq = db.fastaSeqs[i].sequence; *seq!=0; seq++)
{
if (*seq!='a' && *seq!='c' && *seq!='g' && *seq!='t')
{
changed=TRUE;
nucchanged++;
*seq='a';
}
}
if (changed)
seqchanged++;
}
if (seqchanged)
fprintf(stderr," : %d nucleotides substituted in %d sequences\n",nucchanged,seqchanged);
else
fprintf(stderr," : Done\n");
return(db.count);
}
void addCounts(fastaSeqCount* db)
{
int s;
char* count;
element_from_header* header;
char* count_n;
char* count_v;
count_n = (char*) malloc(6*sizeof(char));
count_v = (char*) malloc(2*sizeof(char));
strcpy(count_n, "count");
strcpy(count_v, "1");
for (s=0; s < db->count; s++)
{
header = header_parser_main(db->fastaSeqs[s].rawheader);
count = getItemFromHeader("count", header);
if (count == 0) // no count field
{
header = table_header_add_field(header, count_n, count_v);
db->fastaSeqs[s].count = 1;
}
else
db->fastaSeqs[s].count = atoi(count);
db->fastaSeqs[s].header = header;
}
}
int uniqSeqsVector(fastaSeqCount* db, fastaSeqPtr** uniqSeqs)
{
int i, j, k;
*(*(uniqSeqs)) = db->fastaSeqs;
db->fastaSeqs[0].uniqHead = TRUE;
i = 0;
k = 1;
for (j=1; j < db->count; j++)
{
if (strcmp(db->fastaSeqs[i].sequence, db->fastaSeqs[j].sequence) == 0)
{
db->fastaSeqs[i].count += db->fastaSeqs[j].count;
db->fastaSeqs[j].uniqHead = FALSE;
}
else
{
db->fastaSeqs[j].uniqHead = TRUE;
*(*(uniqSeqs)+k) = (db->fastaSeqs)+j;
k++;
i = j;
}
}
return(k);
}
void calculateMaxAndMinLen(fastaSeqPtr* db, int n, int* lmax, int* lmin)
{
int i;
int l;
*lmax = 0;
for (i=0; i < n; i++)
{
l = (*(db+i))->length;
if (l > *lmax)
*lmax = l;
}
*lmin = *lmax;
for (i=0; i < n; i++)
{
l = (*(db+i))->length;
if (l < *lmin)
*lmin = l;
}
}
void calculateMaxAndMinLenDB(fastaSeqCount db, int* lmax, int* lmin)
{
int i;
int l;
*lmax = 0;
for (i=0; i < db.count; i++)
{
l = ((db.fastaSeqs)+i)->length;
if (l > *lmax)
*lmax = l;
}
*lmin = *lmax;
for (i=0; i < db.count; i++)
{
l = ((db.fastaSeqs)+i)->length;;
if (l < *lmin)
*lmin = l;
}
}
int sortSeqsWithCounts(const void **s1, const void **s2)
{
return(((fastaSeqPtr) *s2)->count - ((fastaSeqPtr) *s1)->count);
}
int reverseSortSeqsWithCounts(const void **s1, const void **s2)
{
return(((fastaSeqPtr) *s1)->count - ((fastaSeqPtr) *s2)->count);
}

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/**
* FileName: sequence.h
* Authors: Tiayyba Riaz, Celine Mercier
* Description: Prototypes and other declarations for sequences
* **/
#ifndef SEQUENCE_H_
#define SEQUENCE_H_
#include <stdint.h>
#include <stdio.h>
#include "../libutils/utilities.h"
#include "fasta_header_parser.h"
typedef struct {
char* accession_id; // identifier
char *rawheader; // not parsed header
element_from_header* header; // parsed header
char *sequence; // DNA sequence itself
int32_t length; // DNA sequence's length
int32_t count; // abundance of the sequence
unsigned char *table; // 4mer occurrence table build using function buildTable
int32_t over; // count of 4mer with occurrences greater than 255 (overflow)
struct fastaSeqPtr* next; // next unique sequence for example
BOOL cluster_center; // whether the sequence is a cluster center or not
int32_t cluster_weight; // cluster weight when sequence is cluster center
int32_t cluster_weight_unique_ids; // cluster weight when sequence is cluster center, counting the number sequence records
double score; // score with cluster center for example
struct fastaSeqPtr* center; // pointer to the sequence's cluster center
int32_t center_index; // index of the sequence's cluster center
BOOL uniqHead; // whether the sequence is a unique head or not
char* columns_BIOM; // to print in BIOM format
int columns_BIOM_size; // size allocated for columns_BIOM
char* line_OTU_table; // to print in OTU table format
int line_OTU_table_size; // size allocated for line_OTU_table
struct hashtable *sample_counts; // sample counts for sumaclean
}fastaSeq,*fastaSeqPtr;
typedef struct {
int32_t count;
fastaSeqPtr fastaSeqs;
}fastaSeqCount, *fastaSeqCountPtr;
fastaSeqPtr seq_getNext(FILE *fp, char *fieldDelim, BOOL isStandardSeq, BOOL onlyATGC);
char *seq_readNextFromFilebyLine(FILE* fp);
void seq_fillSeq(char *seq, fastaSeqPtr seqElem, int seqLen);
void seq_fillSeqOnlyATGC(char *seq, fastaSeqPtr seqElem, int seqLen);
void seq_fillDigitSeq(char *seq, fastaSeqPtr seqElem, int seqLen);
void seq_fillHeader(char* header, char *fieldDelim, fastaSeqPtr seqElem);
fastaSeqCount seq_readAllSeq2(char *fileName, BOOL isStandardSeq, BOOL onlyATGC);
int32_t seq_findSeqByAccId (char *accid, fastaSeqCountPtr allseqs);
void seq_printSeqs (fastaSeqCountPtr allseq);
int cleanDB(fastaSeqCount);
void addCounts(fastaSeqCount* db);
int uniqSeqsVector(fastaSeqCount* db, fastaSeqPtr** uniqSeqs);
void calculateMaxAndMinLen(fastaSeqPtr* db, int n, int* lmax, int* lmin);
void calculateMaxAndMinLenDB(fastaSeqCount db, int* lmax, int* lmin);
int sortSeqsWithCounts(const void **s1, const void **s2);
int reverseSortSeqsWithCounts(const void **s1, const void **s2);
void readSampleCounts(fastaSeqCount* db, char* key_name);
#endif /*SEQUENCE_H_*/

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SOURCES = fileHandling.c
SRCS=$(SOURCES)
OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
LIBFILE= libfile.a
RANLIB=ranlib
include ../global.mk
all: $(LIBFILE)
clean:
rm -rf $(OBJECTS) $(LIBFILE)
rm -f *.P
rm -f *.a
$(LIBFILE): $(OBJECTS)
ar -cr $@ $?
$(RANLIB) $@

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/**
* FileName: fileHandling.c
* Authors: Tiayyba Riaz, Celine Mercier
* Description: C file for file handling functions
* **/
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include "../libutils/utilities.h"
/*
* Function Name: fileOpen(char* fileName, BOOL abortOnError)
* Description: Opens the file and returns the pointer to file object
*/
FILE *file_open(char* fileName, BOOL abortOnError)
{
FILE* fp;
if (fileName == NULL && abortOnError)
ERRORABORT(FILE_OPENING_ERROR, "File name not given.");
if (fileName == NULL)
return NULL;
fp = fopen(fileName, "r");
return fp;
}
FILE *file_openrw(char* fileName, BOOL abortOnError)
{
FILE* fp;
if (fileName == NULL && abortOnError)
ERRORABORT(FILE_OPENING_ERROR, "File name not given.");
if (fileName == NULL)
return NULL;
fp = fopen(fileName, "w+");
return fp;
}
/*
* Function Name: fileNextChar(FILE* fp)
* Description: Reads the file and returns next character, if file is null or its end of file, returns \¯.
*/
char file_nextChar(FILE* fp)
{
if (fp == NULL)
return '\0';
if(feof(fp))
return '\0';
return (char) fgetc(fp);
}
/*
* Function Name: *fileNextLine(FILE *fp, char *buffer, int32_t bufferSize)
* Description: Reads the file and returns next line, if file is null or its end of file, returns \¯.
*/
char *file_nextLine(FILE *fp, char *buffer, int32_t bufferSize)
{
if(fp == NULL)
return NULL;
if(feof(fp))
return NULL;
return fgets(buffer, bufferSize, fp);
}
void exitIfEmptyFile(FILE *file)
{
long savedOffset = ftell(file);
fseek(file, 0, SEEK_END);
if (ftell(file) == 0)
{
fprintf(stderr, "\nInput file is empty.\n");
exit(1);
}
fseek(file, savedOffset, SEEK_SET);
}

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/**
* FileName: fileHandling.h
* Authors: Tiayyba Riaz, Celine Mercier
* Description: Header file for file handling functions
* **/
#ifndef FILEHANDLING_H_
#define FILEHANDLING_H_
#include "../libutils/utilities.h"
/* Prototypes */
FILE *file_open(char* fileName, BOOL abortOnError);
char file_nextChar(FILE* fp);
char *file_nextLine(FILE *fp, char *buffer, int32_t bufferSize);
FILE *file_openrw(char* fileName, BOOL abortOnError);
void exitIfEmptyFile(FILE *file);
#endif /*FILEHANDLING_H_*/

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SOURCES = sse_banded_LCS_alignment.c \
upperband.c
SRCS=$(SOURCES)
OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
LIBFILE= liblcs.a
RANLIB=ranlib
include ../global.mk
all: $(LIBFILE)
clean:
rm -rf $(OBJECTS) $(LIBFILE)
rm -f *.P
rm -f *.a
$(LIBFILE): $(OBJECTS)
ar -cr $@ $?
$(RANLIB) $@

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#include "_lcs.h"
#include <string.h>
#include <stdlib.h>
#include <limits.h>
#include <stdio.h>
// Allocate a band allowing to align sequences of length : 'length'
column_t* allocateColumn(int length,column_t *column, bool mode8bits)
{
int size;
bool newc = false;
// The band length should be equal to the length
// of the sequence + 7 for taking into account its
// shape
size = (length+1) * ((mode8bits) ? sizeof(int8_t):sizeof(int16_t));
// If the pointer to the old column is NULL we allocate
// a new column
if (column==NULL)
{
column = malloc(sizeof(column_t));
if (!column)
return NULL;
column->size = 0;
column->data.shrt=NULL;
column->score.shrt=NULL;
newc = true;
}
// Otherwise we check if its size is sufficient
// or if it should be extended
if (size > column->size)
{
int16_t *old = column->data.shrt;
int16_t *olds= column->score.shrt;
column->data.shrt = malloc(size);
column->score.shrt= malloc(size);
if (column->data.shrt==NULL || column->score.shrt==NULL)
{
fprintf(stderr,"Allocation Error on column for a size of %d\n" , size);
column->data.shrt = old;
column->score.shrt= olds;
if (newc)
{
free(column);
column=NULL;
return NULL;
}
return NULL;
}
else
column->size = size;
}
return column;
}
void freeColumn(column_p column)
{
if (column)
{
if (column->data.shrt)
free(column->data.shrt);
if (column->score.shrt)
free(column->score.shrt);
free(column);
}
}
int fastLCSScore(const char* seq1, const char* seq2,column_pp column,int32_t* lpath)
{
return fastLCSScore16(seq1,seq2,column,lpath);
}
int simpleLCS(const char* seq1, const char* seq2,column_pp ppcolumn,int32_t* lpath)
{
int lseq1,lseq2; // length of the both sequences
int lcs;
int itmp; // tmp variables for swap
const char* stmp; //
int32_t *score;
int32_t *path;
column_t *column;
int32_t i,j;
int32_t sl,su,sd;
int32_t pl,pu,pd;
// Made seq1 the longest sequences
lseq1=strlen(seq1);
lseq2=strlen(seq2);
if (lseq1 < lseq2)
{
itmp=lseq1;
lseq1=lseq2;
lseq2=itmp;
stmp=seq1;
seq1=seq2;
seq2=stmp;
}
lseq1++;
lseq2++;
// a band sized to the smallest sequence is allocated
if (ppcolumn)
column = *ppcolumn;
else
column=NULL;
column = allocateColumn(lseq1*2,column,0);
score = (int32_t*) column->score.shrt;
path = (int32_t*) column->data.shrt;
memset(score,0,lseq1 * sizeof(int32_t));
for (j=0; j < lseq1; j++)
path[j]=j;
for (i=1; i< lseq2; i++)
{
sl=0;
pl=i;
for (j=1; j < lseq1; j++)
{
sd=score[j-1] + (seq2[i-1]==seq1[j-1] ? 1:0);
pd=path[j-1] + 1;
su=score[j];
pu=path[j] + 1;
score[j-1]=sl;
if (su > sl) sl=su, pl=pu;
if (sd > sl) sl=sd, pl=pd;
}
}
lcs = sl;
if(lpath) *lpath=pl;
if (ppcolumn)
*ppcolumn=column;
else
freeColumn(column);
return lcs;
}

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#include "_lcs.h"
#include <string.h>
#include <stdlib.h>
#include <limits.h>
#include <stdio.h>
#define VSIZE (8)
#define VTYPE vInt16
#define STYPE int16_t
#define CMENB shrt
#define VMODE false
#define FASTLCSSCORE fastLCSScore16
#define INSERT_REG _MM_INSERT_EPI16
#define EXTRACT_REG _MM_EXTRACT_EPI16
#define EQUAL_REG _MM_CMPEQ_EPI16
#define GREATER_REG _MM_CMPGT_EPI16
#define SMALLER_REG _MM_CMPLT_EPI16
#define ADD_REG _MM_ADD_EPI16
#define SUB_REG _MM_SUB_EPI16
#define AND_REG _MM_AND_SI128
#define ANDNOT_REG _MM_ANDNOT_SI128
#define OR_REG _MM_OR_SI128
#define SET_CONST _MM_SET1_EPI16
#define GET_MAX _MM_MAX_EPI16
#define GET_MIN _MM_MIN_EPI16
#define MIN_SCORE INT16_MIN
#define MAX_SCORE 32000
#include "_lcs_fast.h"

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#include "_lcs.h"
#include <string.h>
#include <stdlib.h>
#include <limits.h>
#include <stdio.h>
#define VSIZE (16)
#define VTYPE vInt8
#define STYPE int8_t
#define CMENB byte
#define VMODE true
#define FASTLCSSCORE fastLCSScore8
#define INSERT_REG _MM_INSERT_EPI8
#define EXTRACT_REG _MM_EXTRACT_EPI8
#define EQUAL_REG _MM_CMPEQ_EPI8
#define GREATER_REG _MM_CMPGT_EPI8
#define SMALLER_REG _MM_CMPLT_EPI8
#define ADD_REG _MM_ADD_EPI8
#define SUB_REG _MM_SUB_EPI8
#define AND_REG _MM_AND_SI128
#define ANDNOT_REG _MM_ANDNOT_SI128
#define OR_REG _MM_OR_SI128
#define SET_CONST _MM_SET1_EPI8
#define GET_MAX _MM_MAX_EPI8
#define GET_MIN _MM_MIN_EPI8
#define MIN_SCORE INT8_MIN
#define MAX_SCORE 127
#include "_lcs_fast.h"

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#include "../libsse/_sse.h"
#define bool char
#define false (1==0)
#define true (1==1)
typedef struct {
int16_t size;
union { int16_t *shrt;
int8_t *byte;
} data;
union { int16_t *shrt;
int8_t *byte;
} score;
} column_t, **column_pp, *column_p;
column_p allocateColumn(int length,column_t *column, bool mode8bits);
void freeColumn(column_p column);
int fastLCSScore16(const char* seq1, const char* seq2,column_pp ppcolumn,int32_t* lpath);
int fastLCSScore8(const char* seq1, const char* seq2,column_pp ppcolumn,int32_t* lpath);
int simpleLCS(const char* seq1, const char* seq2,column_pp ppcolumn,int32_t* lpath);
int fastLCSScore(const char* seq1, const char* seq2,column_pp column,int32_t* lpath);

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/*
* Print a SSE register for debug purpose
*/
#ifdef __SSE2__
static void printreg(VTYPE r)
{
STYPE a0,a1,a2,a3,a4,a5,a6,a7;
#if VMODE
STYPE a8,a9,a10,a11,a12,a13,a14,a15;
#endif
a0= EXTRACT_REG(r,0);
a1= EXTRACT_REG(r,1);
a2= EXTRACT_REG(r,2);
a3= EXTRACT_REG(r,3);
a4= EXTRACT_REG(r,4);
a5= EXTRACT_REG(r,5);
a6= EXTRACT_REG(r,6);
a7= EXTRACT_REG(r,7);
#if VMODE
a8= EXTRACT_REG(r,8);
a9= EXTRACT_REG(r,9);
a10= EXTRACT_REG(r,10);
a11= EXTRACT_REG(r,11);
a12= EXTRACT_REG(r,12);
a13= EXTRACT_REG(r,13);
a14= EXTRACT_REG(r,14);
a15= EXTRACT_REG(r,15);
#endif
printf( "a00 :-> %7d %7d %7d %7d "
" %7d %7d %7d %7d "
#if VMODE
"%7d %7d %7d %7d "
" %7d %7d %7d %7d "
#endif
"\n"
, a0,a1,a2,a3,a4,a5,a6,a7
#if VMODE
, a8,a9,a10,a11,a12,a13,a14,a15
#endif
);
}
/*
* set position p of a SSE register with the value v
*/
static inline VTYPE insert_reg(VTYPE r, STYPE v, int p)
{
switch (p) {
case 0: return INSERT_REG(r,v,0);
case 1: return INSERT_REG(r,v,1);
case 2: return INSERT_REG(r,v,2);
case 3: return INSERT_REG(r,v,3);
case 4: return INSERT_REG(r,v,4);
case 5: return INSERT_REG(r,v,5);
case 6: return INSERT_REG(r,v,6);
case 7: return INSERT_REG(r,v,7);
#if VMODE
case 8: return INSERT_REG(r,v,8);
case 9: return INSERT_REG(r,v,9);
case 10: return INSERT_REG(r,v,10);
case 11: return INSERT_REG(r,v,11);
case 12: return INSERT_REG(r,v,12);
case 13: return INSERT_REG(r,v,13);
case 14: return INSERT_REG(r,v,14);
case 15: return INSERT_REG(r,v,15);
#endif
}
return _MM_SETZERO_SI128();
}
static inline STYPE extract_reg(VTYPE r, int p)
{
switch (p) {
case 0: return EXTRACT_REG(r,0);
case 1: return EXTRACT_REG(r,1);
case 2: return EXTRACT_REG(r,2);
case 3: return EXTRACT_REG(r,3);
case 4: return EXTRACT_REG(r,4);
case 5: return EXTRACT_REG(r,5);
case 6: return EXTRACT_REG(r,6);
case 7: return EXTRACT_REG(r,7);
#if VMODE
case 8: return EXTRACT_REG(r,8);
case 9: return EXTRACT_REG(r,9);
case 10: return EXTRACT_REG(r,10);
case 11: return EXTRACT_REG(r,11);
case 12: return EXTRACT_REG(r,12);
case 13: return EXTRACT_REG(r,13);
case 14: return EXTRACT_REG(r,14);
case 15: return EXTRACT_REG(r,15);
#endif
}
return 0;
}
#define GET_H_SYMBOLE(s,p) ((p && p < lseq1) ? (s)[(p)-1]:255)
#define GET_V_SYMBOLE(s,p) ((p && p < lseq2) ? (s)[(p)-1]:0)
#define LSHIFT_SCORE(r) { r = _MM_SLLI_SI128((r),sizeof(STYPE)); }
#define SET_H_SYMBOLE(r,p,s) { r = insert_reg((r),(STYPE)GET_H_SYMBOLE(seq1,(s)),(p)); }
#define PUSH_V_SYMBOLE(r,s) { r = insert_reg(_MM_SLLI_SI128((r),sizeof(STYPE)),(STYPE)GET_V_SYMBOLE(seq2,(s)),0); }
#define EQUAL(f1,f2) _MM_AND_SI128(EQUAL_REG((f1),(f2)),SET_CONST(1))
int FASTLCSSCORE(const char* seq1, const char* seq2,column_pp ppcolumn,int32_t* lpath)
{
int lseq1,lseq2; // length of the both sequences
int itmp; // tmp variables for swap
const char* stmp; //
int nbands; // Number of bands of width eight in the score matrix
int lastband; // width of the last band
// Register for scanning the score matrix
VTYPE minus1;
VTYPE minus2;
VTYPE current;
VTYPE left;
VTYPE top;
VTYPE diag;
VTYPE sminus1;
VTYPE sminus2;
VTYPE scurrent;
VTYPE sleft;
VTYPE stop;
VTYPE sdiag;
VTYPE way;
VTYPE onevect;
VTYPE maxvect;
VTYPE fhseq; // The fragment of the horizontal sequence
// to consider for aligment
VTYPE fvseq; // The fragment of the horizontal sequence
// to consider for aligment
VTYPE match;
int band;
int line;
int limit;
int lcs;
int h;
int i;
column_t *column;
// Made seq1 the longest sequences
lseq1=strlen(seq1);
lseq2=strlen(seq2);
if (lseq1 < 10 || lseq2 < 10)
return simpleLCS(seq1,seq2,ppcolumn,lpath);
if (lseq1 < lseq2)
{
itmp=lseq1;
lseq1=lseq2;
lseq2=itmp;
stmp=seq1;
seq1=seq2;
seq2=stmp;
}
// we add one to both lengths for taking into
// account the extra line and column in the score
// matrix
lseq1++;
lseq2++;
// a band sized to the smallest sequence is allocated
if (ppcolumn)
column = *ppcolumn;
else
column=NULL;
column = allocateColumn(lseq2,column,VMODE);
// Check memory allocation
if (column == NULL)
return -1;
for (i=0; i<lseq2;i++)
{
column->data.CMENB[i]=MIN_SCORE;
column->score.CMENB[i]=-1;
}
nbands = lseq1 / VSIZE; // You have VSIZE element in one SSE register
// Alignment will be realized in nbands
lastband = lseq1 - (nbands * VSIZE); // plus one of width lastband except if
// lastband==0
if (lastband) nbands++;
else lastband=VSIZE;
lastband--;
// printf("seq1 : %s seq2 : %s\n",seq1,seq2);
minus2 = SET_CONST(MIN_SCORE);
minus1 = _MM_SETZERO_SI128();
sminus1= _MM_SETZERO_SI128();
sminus2= _MM_SETZERO_SI128();
onevect= SET_CONST(1);
maxvect= SET_CONST(MAX_SCORE);
h=0;
fhseq = _MM_SETZERO_SI128();
fvseq = _MM_SETZERO_SI128();
//
// Beginning of the first band
//
for (line = 0; line < VSIZE; line++,h++) // avant VSIZE - 1
{
// printf("line= %4d h= %4d\n",line,h);
SET_H_SYMBOLE(fhseq,line,h)
PUSH_V_SYMBOLE(fvseq,line)
minus2 = insert_reg(minus2,0,h);
minus1 = insert_reg(minus1,MIN_SCORE,line); // 0 avant
match = EQUAL(fhseq,fvseq);
if (lpath)
{
sminus2 = insert_reg(sminus2,line-1,line); // Je ne suis pas certain de l'initialisation
sminus1 = insert_reg(sminus1,0,line);
}
// printreg(fvseq);
// printreg(fhseq);
// printreg(match);
// printf("================================\n");
current = minus1; // The best score is the upper one
// It cannot be the best as set to MIN_SCORE
left = minus1;
// printf("Vert = "); printreg(current);
LSHIFT_SCORE(minus1) // I shift minus1 so now I'll compare with the left position
minus1=insert_reg(minus1,(column)->data.CMENB[line],0);
top=minus1;
if (lpath)
{
sleft=sminus1; // I store the path length corresponding to the upper path
LSHIFT_SCORE(sminus1) // I shift to prepare the score coming from the left side
sminus1=insert_reg(sminus1,(column)->score.CMENB[line],0);
stop=sminus1;
sdiag=sminus2;
}
// printf("Horz = "); printreg(minus1);
current = GET_MAX(current,minus1); // Look for the best between upper and left
// printf("BstHV= "); printreg(current);
//
// printf("Diag = "); printreg(ADD_REG(minus2,match));
diag=minus2;
// minus2 = ; // Minus2 contains the diagonal score, so I add the match reward
// Diag score are setup to 0 so this one will win on the first iteration
current = GET_MAX(current,ADD_REG(minus2,match));
if (lpath)
{
// printf("\n");
// printf("current: ");
// printreg(current);
// printf("current: ");
// printreg(SUB_REG(current,match));
// printf("diag : ");
// printreg(diag);
// printf("left : ");
// printreg(left);
// printf("top : ");
// printreg(top);
way = EQUAL_REG(SUB_REG(current,match),diag);
scurrent= OR_REG(AND_REG(way,sdiag),
ANDNOT_REG(way,maxvect));
// printf("sdiag : ");
// printreg(scurrent);
way = EQUAL_REG(current,left);
scurrent= GET_MIN(scurrent,OR_REG(AND_REG(way,sleft),
ANDNOT_REG(way,maxvect)));
// printf("sleft : ");
// printreg(scurrent);
way = EQUAL_REG(current,top);
scurrent= GET_MIN(scurrent,OR_REG(AND_REG(way,stop),
ANDNOT_REG(way,maxvect)));
// printf("stop : ");
// printreg(scurrent);
scurrent= ADD_REG(scurrent,onevect);
sminus2=sminus1;
sminus1=scurrent;
}
// printf("line %d :Best = ",line); printreg(current);
//
// printf("================================\n");
minus2=minus1;
minus1=current;
// printf("min2 = "); printreg(minus2);
// printf("min1 = "); printreg(minus1);
// printf("================================\n");
// printf("\n");
// printf("sdiag : ");
// printreg(sminus2);
// printf("scur : ");
// printreg(scurrent);
// printf("current: ");
// printreg(current);
// printf("%8s\n",seq1);
// printf("%8s\n",seq2);
// printf("================================\n");
} ///// <<<<<<<<------- Fin du debut de la premiere bande
// printf("================================\n");
(column)->data.CMENB[lseq2-VSIZE+line]=EXTRACT_REG(current,VSIZE-1);
if (lpath)
(column)->score.CMENB[lseq2-VSIZE+line]=EXTRACT_REG(scurrent,VSIZE-1);
for (band=0; band < nbands; band++)
{
// SET_H_SYMBOLE(fhseq,line,h)
// minus2 = insert_reg(minus2,0,line);
// minus1 = insert_reg(minus1,MIN_SCORE,line); // 0 avant
// h++;
for (; line < lseq2; line++)
{
// printf("Je tourne avec line= %d \n",line);
PUSH_V_SYMBOLE(fvseq,line)
match = EQUAL(fhseq,fvseq);
// printreg(fvseq);
// printreg(fhseq);
// printreg(match);
// printf("================================\n");
current = minus1;
left = minus1;
// Store the last current score in extra column
(column)->data.CMENB[line-VSIZE]=EXTRACT_REG(current,VSIZE-1);
LSHIFT_SCORE(minus1)
minus1=insert_reg(minus1,(column)->data.CMENB[line],0);
top = minus1;
// printf("Vert = "); printreg(current);
if (lpath)
{
sleft= sminus1;
(column)->score.CMENB[line-VSIZE]=EXTRACT_REG(scurrent,VSIZE-1);
LSHIFT_SCORE(sminus1)
sminus1=insert_reg(sminus1,(column)->score.CMENB[line],0);
stop=sminus1;
sdiag=sminus2;
}
// printf("line = %d --> get = %d\n",line,(column)->data.CMENB[line]);
// printf("Horz = "); printreg(minus1);
current = GET_MAX(current,minus1);
diag=minus2;
current = GET_MAX(current,ADD_REG(minus2,match));
if (lpath)
{
// printf("\n");
// printf("current: ");
// printreg(current);
// printf("current: ");
// printreg(SUB_REG(current,match));
// printf("diag : ");
// printreg(diag);
// printf("left : ");
// printreg(left);
// printf("top : ");
// printreg(top);
way = EQUAL_REG(SUB_REG(current,match),diag);
scurrent= OR_REG(AND_REG(way,sdiag),
ANDNOT_REG(way,maxvect));
// printf("sdiag : ");
// printreg(scurrent);
way = EQUAL_REG(current,left);
scurrent= GET_MIN(scurrent,OR_REG(AND_REG(way,sleft),
ANDNOT_REG(way,maxvect)));
// printf("sleft : ");
// printreg(scurrent);
way = EQUAL_REG(current,top);
scurrent= GET_MIN(scurrent,OR_REG(AND_REG(way,stop),
ANDNOT_REG(way,maxvect)));
// printf("stop : ");
// printreg(scurrent);
scurrent= ADD_REG(scurrent,onevect);
sminus2=sminus1;
sminus1=scurrent;
}
minus2=minus1;
minus1=current;
// printf("\n");
// printf("sdiag : ");
// printreg(sminus2);
// printf("scur : ");
// printreg(scurrent);
// printf("current: ");
// printreg(current);
// printf("%8s\n",seq1);
// printf("%8s\n",seq2);
}
// printf("================================\n");
// end of the band and beginnig of the next one
limit=(band==(nbands-1)) ? lastband:VSIZE;
for (line = 0; line < limit; line++,h++)
{
// printf("Je fini avec line= %d \n",line);
SET_H_SYMBOLE(fhseq,line,h)
PUSH_V_SYMBOLE(fvseq,line)
minus2 = insert_reg(minus2,MIN_SCORE,line);
minus1 = insert_reg(minus1,MIN_SCORE,line);
current = minus1;
left=minus1;
match = EQUAL(fhseq,fvseq);
if (lpath)
{
sminus2 = insert_reg(sminus2,lseq2-VSIZE+line,line);
sminus1 = insert_reg(sminus1,h,line);
sleft= sminus1;
}
// printf("\n");
// printf("fhseq = "); printreg(fhseq);
// printf("fvseq = "); printreg(fvseq);
// printf("----------------------------------------------------------------\n");
// printf("match = "); printreg(match);
(column)->data.CMENB[lseq2-VSIZE+line]=EXTRACT_REG(current,VSIZE-1);
LSHIFT_SCORE(minus1)
minus1=insert_reg(minus1,(column)->data.CMENB[line],0);
top=minus1;
current = GET_MAX(current,minus1);
if (lpath)
{
(column)->score.CMENB[lseq2-VSIZE+line]=EXTRACT_REG(scurrent,VSIZE-1);
LSHIFT_SCORE(sminus1)
sminus1=insert_reg(sminus1,(column)->score.CMENB[line],0);
stop=sminus1;
sdiag=sminus2;
way = EQUAL_REG(current,minus1);
scurrent= OR_REG(AND_REG(way,sminus1),
ANDNOT_REG(way,scurrent));
}
diag=minus2;
current = GET_MAX(current,ADD_REG(minus2,match));
if (lpath)
{
way = EQUAL_REG(SUB_REG(current,match),diag);
scurrent= OR_REG(AND_REG(way,sdiag),
ANDNOT_REG(way,maxvect));
way = EQUAL_REG(current,left);
scurrent= GET_MIN(scurrent,OR_REG(AND_REG(way,sleft),
ANDNOT_REG(way,maxvect)));
way = EQUAL_REG(current,top);
scurrent= GET_MIN(scurrent,OR_REG(AND_REG(way,stop),
ANDNOT_REG(way,maxvect)));
scurrent= ADD_REG(scurrent,onevect);
sminus2=sminus1;
sminus1=scurrent;
}
// printf("currt = "); printreg(current);
minus2=minus1;
minus1=current;
// printf("\n");
// printf("sdiag : ");
// printreg(sminus2);
// printf("scur : ");
// printreg(scurrent);
// printf("current: ");
// printreg(current);
// printf("%8s\n",seq1);
// printf("%8s\n",seq2);
// printf("Je stocke line= %d la valeur %d\n",lseq2-VSIZE+line,(column)->data.CMENB[lseq2-VSIZE+line]);
}
}
// printf("\n");
// printf("line = %d, h= %d, lastband = %d\n",line,h,lastband);
// printf("currt = "); printreg(current);
lcs = extract_reg(current,lastband);
if(lpath)
*lpath= extract_reg(scurrent,lastband);
// printf("lastband = %d (%d) lcs = %d\n",lastband,lseq2,lcs);
if (ppcolumn)
*ppcolumn=column;
else
freeColumn(column);
return lcs;
}
#else
int FASTLCSSCORE(const char* seq1, const char* seq2,column_pp ppcolumn,int32_t* lpath)
{
return simpleLCS(seq1,seq2,ppcolumn,lpath);
}
#endif /* __SSE2__ */

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/*
* banded_LCS_alignment.c
*
* Created on: 7 nov. 2012
* Author: merciece
*/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "../libutils/utilities.h"
typedef struct {
int score;
int l_path;
}infos;
int calculateScore(char nuc1, char nuc2)
{
return(nuc1 == nuc2);
}
infos** banded_align(char *seq1, char *seq2, int l1, int l2, int bandLengthRight, int bandLengthLeft)
{
int i, j;
//int c;
//double id;
int start, end;
int diag_score, delete, insert, mismatch;
int l_path, l_path_i, l_path_d;
int bestScore;
int mismatch_margin;
int stop;
int diag_index;
infos **matrix;
l1++;
l2++;
mismatch_margin = bandLengthLeft; // the biggest one
diag_index = l1-l2; // diagonal index
stop=0;
//fprintf(stderr,"\nseq1 = %s, seq2=%s, bandLengthR = %d, bandLengthL = %d", seq1, seq2, bandLengthRight, bandLengthLeft);
// Matrix initialization~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
matrix = (infos**) malloc(l1 * sizeof(infos*));
for (i = 0; i < l1; i++)
matrix[i] = (infos*) malloc(l2 * sizeof(infos));
for (i = 0; i < l1; i++)
for (j = 0; j < l2; j++)
{
matrix[i][j].score = 0;
matrix[i][j].l_path = 0;
}
for (i = 0; i < l1; i++)
matrix[i][0].l_path = i;
for (j = 0; j < l2; j++)
matrix[0][j].l_path = j;
// Matrix initialized~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
for (i = 1; i < l1; i++)
{
start = i - bandLengthLeft;
if (start < 1)
start = 1;
end = i+bandLengthRight+1;
if (end > l2)
end = l2;
for (j = start; j < end; j++)
{
delete = matrix[i-1][j].score;
l_path_d = matrix[i-1][j].l_path + 1;
insert = matrix[i][j-1].score;
l_path_i = matrix[i][j-1].l_path + 1;
mismatch = 0;
diag_score = calculateScore(seq1[i-1], seq2[j-1]);
bestScore = matrix[i-1][j-1].score + diag_score;
l_path = matrix[i-1][j-1].l_path + 1;
if (diag_score == 0) // mismatch
mismatch = 1;
if ((insert > bestScore) || ((insert == bestScore) && (l_path_i < l_path)))
{
bestScore = matrix[i][j-1].score;
l_path = l_path_i;
mismatch = 0;
}
if ((delete > bestScore) || ((delete == bestScore) && (l_path_d < l_path)))
{
bestScore = delete;
l_path = l_path_d;
mismatch = 0;
}
/*if (((i-j) - diag_index == 0) && (mismatch == 1))
{
//fprintf(stderr, "\nR = %d, L = %d\n", bandLengthRight, bandLengthLeft);
if (bandLengthRight+bandLengthLeft == 0)
{
stop = 1;
//fprintf(stderr, "\nBREAKING LOOPS\n");
break;
}
if (bandLengthRight != 0)
bandLengthRight = bandLengthRight - 1;
if (bandLengthLeft != 0)
bandLengthLeft = bandLengthLeft - 1;
}*/
(matrix[i][j]).score = bestScore;
(matrix[i][j]).l_path = l_path;
}
//if ((bandLengthRight + bandLengthLeft == 0) && ((matrix[i][j].l_path - matrix[i][j].score) > mismatch_margin))
if (stop==1)
break;
}
return(matrix);
}
void calculateBandLength(int l1, int l2, double threshold, int* bandLengthRight, int* bandLengthLeft)
{
(*bandLengthLeft) = round(-l1 * threshold + l1);
(*bandLengthRight) = round(-l1 * threshold + l2);
// fprintf(stderr,"\nR=%d, L=%d", (*bandLengthRight), (*bandLengthLeft));
}
double calculateId(infos** matrix, int len1, int len2)
{
double id;
int l_ali;
int l_lcs;
l_lcs = matrix[len1][len2].score;
l_ali = matrix[len1][len2].l_path;
if (l_lcs == 0)
id = 0.0;
else
id = (double) l_lcs / (double) l_ali;
//fprintf(stderr, "\n%d, %d\n", l_lcs, l_ali);
return(id);
}
double banded_lcs_align(int16_t* seq1, int16_t* seq2, int l1, int l2, double threshold, BOOL n, int ref, BOOL lcsmode, int16_t* address)
{
double id;
int bandLengthRight, bandLengthLeft;
int i,j;
char* s1;
char* s2;
s1 = (char*) malloc(l1*sizeof(char)+1);
s2 = (char*) malloc(l2*sizeof(char)+1);
for (i=l1-1, j=0; i>=0, j<l1; i--, j++)
*(s1+i) = (char) *(seq1+j);
for (i=0; i<l2; i++)
*(s2+i) = (char) *(seq2+i);
*(s1+l1) = 0;
*(s2+l2) = 0;
//fprintf(stderr, "\nl1=%d, %s\nl2=%d, %s\n", l1, s1, l2, s2);
infos** matrix;
calculateBandLength(l1, l2, threshold, &bandLengthRight, &bandLengthLeft);
matrix = banded_align(s1, s2, l1, l2, bandLengthRight, bandLengthLeft);
/*fprintf(stderr, "\n");
for (i = 0; i <= l1; i++)
{
fprintf(stderr, "\n");
for (j = 0; j <= l2; j++)
fprintf(stderr, "%d/%d\t", matrix[i][j].score, matrix[i][j].l_path); //matrix[i][j].stop);
}
fprintf(stderr, "\n");*/
id = calculateId(matrix, l1, l2);
for (i = 0; i <= l1; i++)
free(matrix[i]);
free(matrix);
free(s1);
free(s2);
//fprintf(stderr, "\nscore = %lf\n", id);
return(id);
}

9
liblcs/banded_LCS_alignment.h Normal file
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@@ -0,0 +1,9 @@
/*
* banded_LCS_alignment.h
*
* Created on: november 8, 2012
* Author: mercier
*/
double banded_lcs_align(int16_t* seq1, int16_t* seq2, int l1, int l2, double threshold, BOOL n, int ref, BOOL lcsmode, int16_t* address);

724
liblcs/sse_banded_LCS_alignment.c Normal file
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@@ -0,0 +1,724 @@
/*
* sse_banded_LCS_alignment.c
*
* Created on: 7 nov. 2012
* Author: celine mercier
*/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <stdint.h>
#include "../libutils/utilities.h"
#include "../libsse/_sse.h"
/*static void printreg(__m128i r)
{
int16_t a0,a1,a2,a3,a4,a5,a6,a7;
a0= _MM_EXTRACT_EPI16(r,0);
a1= _MM_EXTRACT_EPI16(r,1);
a2= _MM_EXTRACT_EPI16(r,2);
a3= _MM_EXTRACT_EPI16(r,3);
a4= _MM_EXTRACT_EPI16(r,4);
a5= _MM_EXTRACT_EPI16(r,5);
a6= _MM_EXTRACT_EPI16(r,6);
a7= _MM_EXTRACT_EPI16(r,7);
fprintf(stderr, "a00 :-> %7d %7d %7d %7d "
" %7d %7d %7d %7d "
"\n"
, a0,a1,a2,a3,a4,a5,a6,a7
);
}
*/
static inline int extract_reg(__m128i r, int p)
{
switch (p) {
case 0: return(_MM_EXTRACT_EPI16(r,0));
case 1: return(_MM_EXTRACT_EPI16(r,1));
case 2: return(_MM_EXTRACT_EPI16(r,2));
case 3: return(_MM_EXTRACT_EPI16(r,3));
case 4: return(_MM_EXTRACT_EPI16(r,4));
case 5: return(_MM_EXTRACT_EPI16(r,5));
case 6: return(_MM_EXTRACT_EPI16(r,6));
case 7: return(_MM_EXTRACT_EPI16(r,7));
}
return(0);
}
void sse_banded_align_lcs_and_ali_len(int16_t* seq1, int16_t* seq2, int l1, int l2, int bandLengthLeft, int bandLengthTotal, int16_t* address, double* lcs_length, int* ali_length)
{
register int j;
int k1, k2;
int max, diff;
int l_reg, l_loc;
int line;
int numberOfRegistersPerLine;
int numberOfRegistersFor3Lines;
BOOL even_line;
BOOL odd_line;
BOOL even_BLL;
BOOL odd_BLL;
um128* SSEregisters;
um128* p_diag;
um128* p_gap1;
um128* p_gap2;
um128* p_diag_j;
um128* p_gap1_j;
um128* p_gap2_j;
um128 current;
um128* l_ali_SSEregisters;
um128* p_l_ali_diag;
um128* p_l_ali_gap1;
um128* p_l_ali_gap2;
um128* p_l_ali_diag_j;
um128* p_l_ali_gap1_j;
um128* p_l_ali_gap2_j;
um128 l_ali_current;
um128 nucs1;
um128 nucs2;
um128 scores;
um128 boolean_reg;
// Initialisations
odd_BLL = bandLengthLeft & 1;
even_BLL = !odd_BLL;
max = INT16_MAX - l1;
numberOfRegistersPerLine = bandLengthTotal / 8;
numberOfRegistersFor3Lines = 3 * numberOfRegistersPerLine;
SSEregisters = (um128*) calloc(numberOfRegistersFor3Lines * 2, sizeof(um128));
l_ali_SSEregisters = SSEregisters + numberOfRegistersFor3Lines;
// preparer registres SSE
for (j=0; j<numberOfRegistersFor3Lines; j++)
l_ali_SSEregisters[j].i = _MM_LOAD_SI128(address+j*8);
p_diag = SSEregisters;
p_gap1 = SSEregisters+numberOfRegistersPerLine;
p_gap2 = SSEregisters+2*numberOfRegistersPerLine;
p_l_ali_diag = l_ali_SSEregisters;
p_l_ali_gap1 = l_ali_SSEregisters+numberOfRegistersPerLine;
p_l_ali_gap2 = l_ali_SSEregisters+2*numberOfRegistersPerLine;
// Loop on diagonals = 'lines' :
for (line=2; line <= l1+l2; line++)
{
odd_line = line & 1;
even_line = !odd_line;
// loop on the registers of a line :
for (j=0; j < numberOfRegistersPerLine; j++)
{
p_diag_j = p_diag+j;
p_gap1_j = p_gap1+j;
p_gap2_j = p_gap2+j;
p_l_ali_diag_j = p_l_ali_diag+j;
p_l_ali_gap1_j = p_l_ali_gap1+j;
p_l_ali_gap2_j = p_l_ali_gap2+j;
// comparing nucleotides for diagonal scores :
// k1 = position of the 1st nucleotide to align for seq1 and k2 = position of the 1st nucleotide to align for seq2
if (odd_line && odd_BLL)
k1 = (line / 2) + ((bandLengthLeft+1) / 2) - j*8;
else
k1 = (line / 2) + (bandLengthLeft/2) - j*8;
k2 = line - k1 - 1;
nucs1.i = _MM_LOADU_SI128(seq1+l1-k1);
nucs2.i = _MM_LOADU_SI128(seq2+k2);
/* fprintf(stderr, "\nnucs, r %d, k1 = %d, k2 = %d\n", j, k1, k2);
printreg(nucs1.i);
printreg(nucs2.i);
*/
// computing diagonal score :
scores.i = _MM_AND_SI128(_MM_CMPEQ_EPI16(nucs1.i, nucs2.i), _MM_SET1_EPI16(1));
current.i = _MM_ADDS_EPU16(p_diag_j->i, scores.i);
// Computing alignment length
l_ali_current.i = p_l_ali_diag_j->i;
boolean_reg.i = _MM_CMPGT_EPI16(p_gap1_j->i, current.i);
l_ali_current.i = _MM_OR_SI128(
_MM_AND_SI128(p_l_ali_gap1_j->i, boolean_reg.i),
_MM_ANDNOT_SI128(boolean_reg.i, l_ali_current.i));
current.i = _MM_OR_SI128(
_MM_AND_SI128(p_gap1_j->i, boolean_reg.i),
_MM_ANDNOT_SI128(boolean_reg.i, current.i));
boolean_reg.i = _MM_AND_SI128(
_MM_CMPEQ_EPI16(p_gap1_j->i, current.i),
_MM_CMPLT_EPI16(p_l_ali_gap1_j->i, l_ali_current.i));
l_ali_current.i = _MM_OR_SI128(
_MM_AND_SI128(p_l_ali_gap1_j->i, boolean_reg.i),
_MM_ANDNOT_SI128(boolean_reg.i, l_ali_current.i));
current.i = _MM_OR_SI128(
_MM_AND_SI128(p_gap1_j->i, boolean_reg.i),
_MM_ANDNOT_SI128(boolean_reg.i, current.i));
boolean_reg.i = _MM_CMPGT_EPI16(p_gap2_j->i, current.i);
l_ali_current.i = _MM_OR_SI128(
_MM_AND_SI128(p_l_ali_gap2_j->i, boolean_reg.i),
_MM_ANDNOT_SI128(boolean_reg.i, l_ali_current.i));
current.i = _MM_OR_SI128(
_MM_AND_SI128(p_gap2_j->i, boolean_reg.i),
_MM_ANDNOT_SI128(boolean_reg.i, current.i));
boolean_reg.i = _MM_AND_SI128(
_MM_CMPEQ_EPI16(p_gap2_j->i, current.i),
_MM_CMPLT_EPI16(p_l_ali_gap2_j->i, l_ali_current.i));
l_ali_current.i = _MM_OR_SI128(
_MM_AND_SI128(p_l_ali_gap2_j->i, boolean_reg.i),
_MM_ANDNOT_SI128(boolean_reg.i, l_ali_current.i));
current.i = _MM_OR_SI128(
_MM_AND_SI128(p_gap2_j->i, boolean_reg.i),
_MM_ANDNOT_SI128(boolean_reg.i, current.i));
/* fprintf(stderr, "\nline = %d", line);
fprintf(stderr, "\nDiag, r %d : ", j);
printreg((*(p_diag_j)).i);
fprintf(stderr, "Gap1 : ");
printreg((*(p_gap1_j)).i);
fprintf(stderr, "Gap2 : ");
printreg((*(p_gap2_j)).i);
fprintf(stderr, "current : ");
printreg(current.i);
fprintf(stderr, "L ALI\nDiag r %d : ", j);
printreg((*(p_l_ali_diag_j)).i);
fprintf(stderr, "Gap1 : ");
printreg((*(p_l_ali_gap1_j)).i);
fprintf(stderr, "Gap2 : ");
printreg((*(p_l_ali_gap2_j)).i);
fprintf(stderr, "current : ");
printreg(l_ali_current.i);
*/
// diag = gap1 and gap1 = current
p_diag_j->i = p_gap1_j->i;
p_gap1_j->i = current.i;
// l_ali_diag = l_ali_gap1 and l_ali_gap1 = l_ali_current+1
p_l_ali_diag_j->i = p_l_ali_gap1_j->i;
p_l_ali_gap1_j->i = _MM_ADD_EPI16(l_ali_current.i, _MM_SET1_EPI16(1));
}
// shifts for gap2, to do only once all the registers of a line have been computed Copier gap2 puis le charger depuis la copie?
for (j=0; j < numberOfRegistersPerLine; j++)
{
if ((odd_line && even_BLL) || (even_line && odd_BLL))
{
p_gap2[j].i = _MM_LOADU_SI128((p_gap1[j].s16)-1);
p_l_ali_gap2[j].i = _MM_LOADU_SI128((p_l_ali_gap1[j].s16)-1);
if (j == 0)
{
p_gap2[j].i = _MM_INSERT_EPI16(p_gap2[j].i, 0, 0);
p_l_ali_gap2[j].i = _MM_INSERT_EPI16(p_l_ali_gap2[j].i, max, 0);
}
}
else
{
p_gap2[j].i = _MM_LOADU_SI128(p_gap1[j].s16+1);
p_l_ali_gap2[j].i = _MM_LOADU_SI128(p_l_ali_gap1[j].s16+1);
if (j == numberOfRegistersPerLine - 1)
{
p_gap2[j].i = _MM_INSERT_EPI16(p_gap2[j].i, 0, 7);
p_l_ali_gap2[j].i = _MM_INSERT_EPI16(p_l_ali_gap2[j].i, max, 7);
}
}
}
// end shifts for gap2
}
/* /// Recovering LCS and alignment lengths \\\ */
// finding the location of the results in the registers :
diff = l1-l2;
if ((diff & 1) && odd_BLL)
l_loc = (int) floor((double)(bandLengthLeft) / (double)2) - floor((double)(diff) / (double)2);
else
l_loc = (int) floor((double)(bandLengthLeft) / (double)2) - ceil((double)(diff) / (double)2);
l_reg = (int)floor((double)l_loc/(double)8.0);
//fprintf(stderr, "\nl_reg = %d, l_loc = %d\n", l_reg, l_loc);
l_loc = l_loc - l_reg*8;
// extracting the results from the registers :
*lcs_length = extract_reg(p_gap1[l_reg].i, l_loc);
*ali_length = extract_reg(p_l_ali_gap1[l_reg].i, l_loc) - 1;
// freeing the registers
free(SSEregisters);
}
double sse_banded_align_just_lcs(int16_t* seq1, int16_t* seq2, int l1, int l2, int bandLengthLeft, int bandLengthTotal)
{
register int j;
int k1, k2;
int diff;
int l_reg, l_loc;
int16_t l_lcs;
int line;
int numberOfRegistersPerLine;
int numberOfRegistersFor3Lines;
BOOL even_line;
BOOL odd_line;
BOOL even_BLL;
BOOL odd_BLL;
um128* SSEregisters;
um128* p_diag;
um128* p_gap1;
um128* p_gap2;
um128* p_diag_j;
um128* p_gap1_j;
um128* p_gap2_j;
um128 current;
um128 nucs1;
um128 nucs2;
um128 scores;
// Initialisations
odd_BLL = bandLengthLeft & 1;
even_BLL = !odd_BLL;
numberOfRegistersPerLine = bandLengthTotal / 8;
numberOfRegistersFor3Lines = 3 * numberOfRegistersPerLine;
SSEregisters = malloc(numberOfRegistersFor3Lines * sizeof(um128));
// preparer registres SSE
for (j=0; j<numberOfRegistersFor3Lines; j++)
(*(SSEregisters+j)).i = _MM_SETZERO_SI128();
p_diag = SSEregisters;
p_gap1 = SSEregisters+numberOfRegistersPerLine;
p_gap2 = SSEregisters+2*numberOfRegistersPerLine;
// Loop on diagonals = 'lines' :
for (line=2; line <= l1+l2; line++)
{
odd_line = line & 1;
even_line = !odd_line;
// loop on the registers of a line :
for (j=0; j < numberOfRegistersPerLine; j++)
{
p_diag_j = p_diag+j;
p_gap1_j = p_gap1+j;
p_gap2_j = p_gap2+j;
// comparing nucleotides for diagonal scores :
// k1 = position of the 1st nucleotide to align for seq1 and k2 = position of the 1st nucleotide to align for seq2
if (odd_line && odd_BLL)
k1 = (line / 2) + ((bandLengthLeft+1) / 2) - j*8;
else
k1 = (line / 2) + (bandLengthLeft/2) - j*8;
k2 = line - k1 - 1;
nucs1.i = _MM_LOADU_SI128(seq1+l1-k1);
nucs2.i = _MM_LOADU_SI128(seq2+k2);
// computing diagonal score :
scores.i = _MM_AND_SI128(_MM_CMPEQ_EPI16(nucs1.i, nucs2.i), _MM_SET1_EPI16(1));
current.i = _MM_ADDS_EPU16((*(p_diag_j)).i, scores.i);
// current = max(gap1, current)
current.i = _MM_MAX_EPI16((*(p_gap1_j)).i, current.i);
// current = max(gap2, current)
current.i = _MM_MAX_EPI16((*(p_gap2_j)).i, current.i);
// diag = gap1 and gap1 = current
(*(p_diag_j)).i = (*(p_gap1_j)).i;
(*(p_gap1_j)).i = current.i;
}
// shifts for gap2, to do only once all the registers of a line have been computed
for (j=0; j < numberOfRegistersPerLine; j++)
{
if ((odd_line && even_BLL) || (even_line && odd_BLL))
{
(*(p_gap2+j)).i = _MM_LOADU_SI128(((*(p_gap1+j)).s16)-1);
if (j == 0)
{
(*(p_gap2+j)).i = _MM_INSERT_EPI16((*(p_gap2+j)).i, 0, 0);
}
}
else
{
(*(p_gap2+j)).i = _MM_LOADU_SI128(((*(p_gap1+j)).s16)+1);
if (j == numberOfRegistersPerLine - 1)
{
(*(p_gap2+j)).i = _MM_INSERT_EPI16((*(p_gap2+j)).i, 0, 7);
}
}
}
// end shifts for gap2
}
/* /// Recovering LCS and alignment lengths \\\ */
// finding the location of the results in the registers :
diff = l1-l2;
if ((diff & 1) && odd_BLL)
l_loc = (int) floor((double)(bandLengthLeft) / (double)2) - floor((double)(diff) / (double)2);
else
l_loc = (int) floor((double)(bandLengthLeft) / (double)2) - ceil((double)(diff) / (double)2);
l_reg = (int)floor((double)l_loc/(double)8.0);
//fprintf(stderr, "\nl_reg = %d, l_loc = %d\n", l_reg, l_loc);
l_loc = l_loc - l_reg*8;
// extracting LCS from the registers :
l_lcs = extract_reg((*(p_gap1+l_reg)).i, l_loc);
// freeing the registers
free(SSEregisters);
return((double) l_lcs);
}
inline void calculateBandLengths(int l1, int l2, int* bandLengthRight, int* bandLengthLeft, int LCSmin)
{
(*bandLengthLeft) = l1 - LCSmin;
(*bandLengthRight) = l2 - LCSmin;
}
int calculateLCSmin(int l1, int l2, double threshold, BOOL normalize, int reference, BOOL lcsmode)
{
int LCSmin;
if (threshold > 0)
{
if (normalize)
{
if (reference == MINLEN)
LCSmin = threshold*l2;
else // ref = maxlen or alilen
LCSmin = threshold*l1;
}
else if (lcsmode)
LCSmin = threshold;
else if ((reference == MINLEN)) // not lcsmode
LCSmin = l2 - threshold;
else // not lcsmode and ref = maxlen or alilen
LCSmin = l1 - threshold;
}
else
LCSmin = 0;
return(LCSmin);
}
int calculateSSEBandLength(int bandLengthRight, int bandLengthLeft)
{
// *bandLengthTotal= (double) floor(bandLengthRight + bandLengthLeft) / 2.0 + 1;
int bandLengthTotal= (double)(bandLengthRight + bandLengthLeft) / 2.0 + 1.0;
return (bandLengthTotal & (~ (int)7)) + (( bandLengthTotal & (int)7) ? 8:0); // Calcule le multiple de 8 superieur
}
int calculateSizeToAllocate(int maxLen, int minLen, int LCSmin)
{
int size;
int notUsed;
calculateBandLengths(maxLen, minLen, &notUsed, &size, LCSmin); // max size = max left band length * 2
//fprintf(stderr, "\nsize for address before %8 = %d", size);
size*= 2;
size = (size & (~ (int)7)) + (( size & (int)7) ? 8:0); // Calcule le multiple de 8 superieur
size*= 3;
size+= 16;
//fprintf(stderr, "\nsize for address = %d", size);
return(size*sizeof(int16_t));
}
void iniSeq(int16_t* seq, int size, int16_t iniValue)
{
int16_t *target=seq;
int16_t *end = target + (size_t)size;
for (; target < end; target++)
*target = iniValue;
}
void putSeqInSeq(int16_t* seq, char* s, int l, BOOL reverse)
{
int16_t *target=seq;
int16_t *end = target + (size_t)l;
char *source=s;
if (reverse)
for (source=s + (size_t)l-1; target < end; target++, source--)
*target=*source;
else
for (; target < end; source++,target++)
*target=*source;
}
void initializeAddressWithGaps(int16_t* address, int bandLengthTotal, int bandLengthLeft, int l1)
{
int i;
int address_00, x_address_10, address_01, address_01_shifted;
int numberOfRegistersPerLine;
int bm;
int value=INT16_MAX-l1;
numberOfRegistersPerLine = bandLengthTotal / 8;
bm = bandLengthLeft%2;
for (i=0; i < (3*numberOfRegistersPerLine*8); i++)
address[i] = value;
// 0,0 set to 1 and 0,1 and 1,0 set to 2
address_00 = bandLengthLeft / 2;
x_address_10 = address_00 + bm - 1;
address_01 = numberOfRegistersPerLine*8 + x_address_10;
address_01_shifted = numberOfRegistersPerLine*16 + address_00 - bm;
// fill address_00, address_01,+1, address_01_shifted,+1
address[address_00] = 1;
address[address_01] = 2;
address[address_01+1] = 2;
address[address_01_shifted] = 2;
address[address_01_shifted+1] = 2;
}
double sse_banded_lcs_align(int16_t* seq1, int16_t* seq2, int l1, int l2, BOOL normalize, int reference, BOOL lcsmode, int16_t* address, int LCSmin)
{
double id;
int bandLengthRight, bandLengthLeft, bandLengthTotal;
int ali_length;
//fprintf(stderr, "\nl1 = %d, l2 = %d\n", l1, l2);
calculateBandLengths(l1, l2, &bandLengthRight, &bandLengthLeft, LCSmin);
//fprintf(stderr, "\nBLL = %d, BLR = %d, LCSmin = %d\n", bandLengthLeft, bandLengthRight, LCSmin);
bandLengthTotal = calculateSSEBandLength(bandLengthRight, bandLengthLeft);
//fprintf(stderr, "\nBLT = %d\n", bandLengthTotal);
if ((reference == ALILEN) && (normalize || !lcsmode))
{
initializeAddressWithGaps(address, bandLengthTotal, bandLengthLeft, l1);
sse_banded_align_lcs_and_ali_len(seq1, seq2, l1, l2, bandLengthLeft, bandLengthTotal, address, &id, &ali_length);
}
else
id = sse_banded_align_just_lcs(seq1, seq2, l1, l2, bandLengthLeft, bandLengthTotal);
//fprintf(stderr, "\nid before normalizations = %f", id);
//fprintf(stderr, "\nlcs = %f, ali = %d\n", id, ali_length);
if (!lcsmode && !normalize)
switch(reference) {
case ALILEN: id = ali_length - id;
break;
case MAXLEN: id = l1 - id;
break;
case MINLEN: id = l2 - id;
}
//fprintf(stderr, "\n2>>> %f, %d\n", id, ali_length);
if (normalize)
switch(reference) {
case ALILEN: id = id / (double) ali_length;
break;
case MAXLEN: id = id / (double) l1;
break;
case MINLEN: id = id / (double) l2;
}
//fprintf(stderr, "\nid = %f\n", id);
return(id);
}
double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, BOOL normalize, int reference, BOOL lcsmode, int16_t** address, int* buffer_size, int16_t** iseq1,
int16_t** iseq2, int* buffer_sizeS)
{
double id;
int l1;
int l2;
int lmax, lmin;
int sizeToAllocateForBand;
int maxBLL, notUsed;
int sizeToAllocateForSeqs;
int LCSmin;
l1 = strlen(seq1);
l2 = strlen(seq2);
if (l2 > l1)
{
lmax = l1;
lmin = l2;
}
else
{
lmax = l2;
lmin = l1;
}
if (!lcsmode && (normalize==TRUE))
{
threshold = 1.0 - threshold;
}
LCSmin = calculateLCSmin(lmax, lmin, threshold, normalize, reference, lcsmode);
// Allocating space for matrix band if the alignment must be computed
if ((reference == ALILEN) && ((lcsmode && normalize) || (!lcsmode))) // checking if alignment must be computed
{
sizeToAllocateForBand = calculateSizeToAllocate(lmax, lmin, LCSmin);
if (sizeToAllocateForBand > (*buffer_size))
{
// reallocating if needed
address = reallocA16Address(*address, sizeToAllocateForBand);
}
}
// Allocating space for the int16_t arrays representing the sequences
calculateBandLengths(lmax, lmin, &notUsed, &maxBLL, LCSmin);
sizeToAllocateForSeqs = 2*maxBLL+lmax;
if (sizeToAllocateForSeqs > *buffer_sizeS)
{
(*(iseq1)) = realloc((*(iseq1)), sizeToAllocateForSeqs*sizeof(int16_t));
(*(iseq2)) = realloc((*(iseq2)), sizeToAllocateForSeqs*sizeof(int16_t));
}
iniSeq(*(iseq1), maxBLL, 0);
iniSeq(*(iseq2), maxBLL, 255);
*(iseq1) = *(iseq1)+maxBLL;
*(iseq2) = *(iseq2)+maxBLL;
// longest seq must be first argument of sse_align function
if (l2 > l1)
{
putSeqInSeq((*(iseq1)), seq2, l2, TRUE);
putSeqInSeq((*(iseq2)), seq1, l1, FALSE);
id = sse_banded_lcs_align(*(iseq1), *(iseq2), l2, l1, normalize, reference, lcsmode, *address, LCSmin);
}
else
{
putSeqInSeq((*(iseq1)), seq1, l1, TRUE);
putSeqInSeq((*(iseq2)), seq2, l2, FALSE);
id = sse_banded_lcs_align(*(iseq1), *(iseq2), l1, l2, normalize, reference, lcsmode, *address, LCSmin);
}
return(id);
}
int prepareTablesForSumathings(int lmax, int lmin, double threshold, BOOL normalize, int reference, BOOL lcsmode,
int16_t** address, int16_t** iseq1, int16_t** iseq2)
{
int sizeToAllocateForBand;
int maxBLL;
int notUsed;
int sizeToAllocateForSeqs;
int LCSmin;
LCSmin = calculateLCSmin(lmax, lmin, threshold, normalize, reference, lcsmode);
// Allocating space for matrix band if the alignment must be computed
if ((reference == ALILEN) && (normalize || !lcsmode)) // checking if alignment must be computed
{
sizeToAllocateForBand = calculateSizeToAllocate(lmax, lmin, LCSmin);
(*(address)) = getA16Address(sizeToAllocateForBand);
}
// Allocating space for the int16_t arrays representing the sequences
calculateBandLengths(lmax, lmin, &notUsed, &maxBLL, LCSmin);
sizeToAllocateForSeqs = 2*maxBLL+lmax;
(*(iseq1)) = malloc(sizeToAllocateForSeqs*sizeof(int16_t));
(*(iseq2)) = malloc(sizeToAllocateForSeqs*sizeof(int16_t));
iniSeq(*(iseq1), maxBLL, 0);
iniSeq(*(iseq2), maxBLL, 255);
*(iseq1) = *(iseq1)+maxBLL;
*(iseq2) = *(iseq2)+maxBLL;
return(maxBLL+lmax);
}
double alignForSumathings(char* seq1, int16_t* iseq1, char* seq2, int16_t* iseq2, int l1, int l2,
BOOL normalize, int reference, BOOL lcsmode, int16_t* address, int sizeForSeqs, int LCSmin)
{
double id;
iniSeq(iseq1, sizeForSeqs, 0);
iniSeq(iseq2, sizeForSeqs, 255);
if (l2 > l1)
{
putSeqInSeq(iseq1, seq2, l2, TRUE);
putSeqInSeq(iseq2, seq1, l1, FALSE);
id = sse_banded_lcs_align(iseq1, iseq2, l2, l1, normalize, reference, lcsmode, address, LCSmin);
}
else
{
putSeqInSeq(iseq1, seq1, l1, TRUE);
putSeqInSeq(iseq2, seq2, l2, FALSE);
id = sse_banded_lcs_align(iseq1, iseq2, l1, l2, normalize, reference, lcsmode, address, LCSmin);
}
return(id);
}

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/*
* sse_banded_LCS_alignment.h
*
* Created on: november 29, 2012
* Author: mercier
*/
#ifndef SSE_BANDED_LCS_ALIGNMENT_H_
#define SSE_BANDED_LCS_ALIGNMENT_H_
#include <stdint.h>
double sse_banded_lcs_align(int16_t* seq1, int16_t* seq2, int l1, int l2, BOOL normalize, int reference, BOOL lcsmode, int16_t* address, int LCSmin);
int calculateSizeToAllocate(int maxLen, int minLen, int LCSmin);
void calculateThresholdFromErrorNumber(int error, int length, double* threshold);
void iniSeq(int16_t* seq, int size, int16_t iniValue);
void putSeqInSeq(int16_t* seq, char* s, int l, BOOL reverse);
double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, BOOL normalize, int reference, BOOL lcsmode, int16_t** address, int* buffer_size, int16_t** iseq1,
int16_t** iseq2, int* buffer_sizeS);
int prepareTablesForSumathings(int lmax, int lmin, double threshold, BOOL normalize, int reference, BOOL lcsmode,
int16_t** address, int16_t** iseq1, int16_t** iseq2);
double alignForSumathings(char* seq1, int16_t* iseq1, char* seq2, int16_t* iseq2, int l1, int l2, BOOL normalize,
int reference, BOOL lcsmode, int16_t* address, int sizeForSeqs, int LCSmin);
int calculateLCSmin(int l1, int l2, double threshold, BOOL normalize, int reference, BOOL lcsmode);
#endif

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#include "../libsse/_sse.h"
#include <stdio.h>
#include <math.h>
#include "../libutils/utilities.h"
#include "../libfasta/sequence.h"
#include "sse_banded_LCS_alignment.h"
inline static uchar_v hash4m128(uchar_v frag)
{
uchar_v words;
vUInt8 mask_03= _MM_SET1_EPI8(0x03); // charge le registre avec 16x le meme octet
vUInt8 mask_FC= _MM_SET1_EPI8(0xFC);
frag.m = _MM_SRLI_EPI64(frag.m,1); // shift logic a droite sur 2 x 64 bits
frag.m = _MM_AND_SI128(frag.m,mask_03); // and sur les 128 bits
words.m= _MM_SLLI_EPI64(frag.m,2);
words.m= _MM_AND_SI128(words.m,mask_FC);
frag.m = _MM_SRLI_SI128(frag.m,1);
words.m= _MM_OR_SI128(words.m,frag.m);
words.m= _MM_SLLI_EPI64(words.m,2);
words.m= _MM_AND_SI128(words.m,mask_FC);
frag.m = _MM_SRLI_SI128(frag.m,1);
words.m= _MM_OR_SI128(words.m,frag.m);
words.m= _MM_SLLI_EPI64(words.m,2);
words.m= _MM_AND_SI128(words.m,mask_FC);
frag.m = _MM_SRLI_SI128(frag.m,1);
words.m= _MM_OR_SI128(words.m,frag.m);
return words;
}
#ifdef __SSE2__
inline static int anyzerom128(vUInt8 data)
{
vUInt8 mask_00= _MM_SETZERO_SI128();
uint64_v tmp;
tmp.m = _MM_CMPEQ_EPI8(data,mask_00);
return (int)(tmp.c[0]!=0 || tmp.c[1]!=0);
}
#else
inline static int anyzerom128(vUInt8 data)
{
int i;
um128 tmp;
tmp.i = data;
for (i=0;i<8;i++)
if (tmp.s8[i]==0)
return 1;
return 0;
}
#endif
inline static void dumpm128(unsigned short *table,vUInt8 data)
{
memcpy(table,&data,16);
}
/**
* Compute 4mer occurrence table from a DNA sequence
*
* sequence : a pointer to the null terminated nuc sequence
* table : a pointer to a 256 cells unisgned char table for
* storing the occurrence table
* count : pointer to an int value used as a return value
* containing the global word counted
*
* returns the number of words observed in the sequence with a
* count greater than 255.
*/
int buildTable(const char* sequence, unsigned char *table, int *count)
{
int overflow = 0;
int wc=0;
int i;
vUInt8 mask_00= _MM_SETZERO_SI128();
uchar_v frag;
uchar_v words;
uchar_v zero;
char* s;
s=(char*)sequence;
memset(table,0,256*sizeof(unsigned char));
// encode ascii sequence with A : 00 C : 01 T: 10 G : 11
for(frag.m=_MM_LOADU_SI128((vUInt8*)s);
! anyzerom128(frag.m);
s+=12,frag.m=_MM_LOADU_SI128((vUInt8*)s))
{
words= hash4m128(frag);
// printf("%d %d %d %d\n",words.c[0],words.c[1],words.c[2],words.c[3]);
if (table[words.c[0]]<255) table[words.c[0]]++; else overflow++;
if (table[words.c[1]]<255) table[words.c[1]]++; else overflow++;
if (table[words.c[2]]<255) table[words.c[2]]++; else overflow++;
if (table[words.c[3]]<255) table[words.c[3]]++; else overflow++;
if (table[words.c[4]]<255) table[words.c[4]]++; else overflow++;
if (table[words.c[5]]<255) table[words.c[5]]++; else overflow++;
if (table[words.c[6]]<255) table[words.c[6]]++; else overflow++;
if (table[words.c[7]]<255) table[words.c[7]]++; else overflow++;
if (table[words.c[8]]<255) table[words.c[8]]++; else overflow++;
if (table[words.c[9]]<255) table[words.c[9]]++; else overflow++;
if (table[words.c[10]]<255) table[words.c[10]]++; else overflow++;
if (table[words.c[11]]<255) table[words.c[11]]++; else overflow++;
wc+=12;
}
zero.m=_MM_CMPEQ_EPI8(frag.m,mask_00);
//printf("frag=%d %d %d %d\n",frag.c[0],frag.c[1],frag.c[2],frag.c[3]);
//printf("zero=%d %d %d %d\n",zero.c[0],zero.c[1],zero.c[2],zero.c[3]);
words = hash4m128(frag);
if (zero.c[0]+zero.c[1]+zero.c[2]+zero.c[3]==0)
for(i=0;zero.c[i+3]==0;i++,wc++)
if (table[words.c[i]]<255) table[words.c[i]]++; else overflow++;
if (count) *count=wc;
return overflow;
}
static inline vUInt16 partialminsum(vUInt8 ft1,vUInt8 ft2)
{
vUInt8 mini;
vUInt16 minilo;
vUInt16 minihi;
vUInt8 mask_00= _MM_SETZERO_SI128();
mini = _MM_MIN_EPU8(ft1,ft2);
minilo = _MM_UNPACKLO_EPI8(mini,mask_00);
minihi = _MM_UNPACKHI_EPI8(mini,mask_00);
return _MM_ADDS_EPU16(minilo,minihi);
}
int compareTable(unsigned char *t1, int over1, unsigned char* t2, int over2)
{
vUInt8 ft1;
vUInt8 ft2;
vUInt8 *table1=(vUInt8*)t1;
vUInt8 *table2=(vUInt8*)t2;
ushort_v summini;
int i;
int total;
ft1 = _MM_LOADU_SI128(table1);
ft2 = _MM_LOADU_SI128(table2);
summini.m = partialminsum(ft1,ft2);
table1++;
table2++;
for (i=1;i<16;i++,table1++,table2++)
{
ft1 = _MM_LOADU_SI128(table1);
ft2 = _MM_LOADU_SI128(table2);
summini.m = _MM_ADDS_EPU16(summini.m,partialminsum(ft1,ft2));
}
// Finishing the sum process
summini.m = _MM_ADDS_EPU16(summini.m,_MM_SRLI_SI128(summini.m,8)); // sum the 4 firsts with the 4 lasts
summini.m = _MM_ADDS_EPU16(summini.m,_MM_SRLI_SI128(summini.m,4));
total = summini.c[0]+summini.c[1];
total+= (over1 < over2) ? over1:over2;
return total;
}
int threshold4(int wordcount,double identity)
{
int error;
int lmax;
wordcount+=3;
error = (int)floor((double)wordcount * ((double)1.0-identity));
lmax = (wordcount - error) / (error + 1);
if (lmax < 4)
return 0;
return (lmax - 3) \
* (error + 1) \
+ ((wordcount - error) % (error + 1));
}
int thresholdLCS4(int32_t reflen,int32_t lcs)
{
int nbfrag;
int smin;
int R;
int common;
nbfrag = (reflen - lcs)*2 + 1;
smin = lcs/nbfrag;
R = lcs - smin * nbfrag;
common = MAX(smin - 2,0) * R + MAX(smin - 3,0) * (nbfrag - R);
return common;
}
int hashDB(fastaSeqCount db)
{
int32_t i;
int32_t count;
fprintf(stderr,"Indexing dataset...");
for (i=0; i < db.count;i++)
{
db.fastaSeqs[i].table = util_malloc((256)*sizeof(unsigned char), __FILE__, __LINE__);
db.fastaSeqs[i].over = buildTable((const char*)(db.fastaSeqs[i].sequence),
db.fastaSeqs[i].table,
&count);
}
fprintf(stderr," : Done\n");
return db.count;
}
BOOL isPossible(fastaSeqPtr seq1, fastaSeqPtr seq2, double threshold, BOOL normalize, int reference, BOOL lcsmode)
{
int32_t reflen;
int32_t maxlen;
int32_t lcs;
int32_t mincount;
if (seq1->length < 12 || seq2->length < 12)
return TRUE;
maxlen = MAX(seq1->length,seq2->length);
if (reference==ALILEN || reference==MAXLEN)
reflen = maxlen;
else
reflen = MIN(seq1->length,seq2->length);
if (normalize)
{
if (! lcsmode)
threshold = 1. - threshold;
lcs = (int32_t)ceil((double)reflen * threshold);
}
else
{
if (! lcsmode)
threshold = reflen - threshold;
lcs = (int32_t) threshold;
}
if (lcs > MIN(seq1->length,seq2->length))
return FALSE;
mincount = thresholdLCS4(maxlen,lcs);
return compareTable(seq1->table,seq1->over,seq2->table,seq2->over) >=mincount;
}
BOOL isPossibleSumathings(fastaSeqPtr seq1, fastaSeqPtr seq2, int l1, int l2, double threshold, BOOL normalize, int reference, BOOL lcsmode)
{ // optimized version of the filter for sumaclust and sumatra
int32_t reflen;
int32_t lcs;
int32_t mincount;
if (l1 < 12 || l2 < 12)
return TRUE;
if (reference==ALILEN || reference==MAXLEN)
reflen = l1;
else
reflen = l2;
if (normalize)
lcs = (int32_t)ceil((double)reflen * threshold);
else
{
if (! lcsmode)
threshold = reflen - threshold;
lcs = (int32_t) threshold;
}
mincount = thresholdLCS4(l1,lcs);
return compareTable(seq1->table,seq1->over,seq2->table,seq2->over) >=mincount;
}
void filters(fastaSeqPtr seq1, fastaSeqPtr seq2, double threshold, BOOL normalize, int reference, BOOL lcsmode, double* score, int* LCSmin)
{ // score takes value -1 if filters are passed. score must be initialized in calling function.
int l1;
int l2;
l1 = seq1->length;
l2 = seq2->length;
if (l1 >= l2)
{
*LCSmin = calculateLCSmin(l1, l2, threshold, normalize, reference, lcsmode);
if (l2 >= *LCSmin)
{
if (isPossibleSumathings(seq1, seq2, l1, l2, threshold, normalize, reference, lcsmode)) // 4-mers filter
*score = -1.0;
}
}
else
{
*LCSmin = calculateLCSmin(l2, l1, threshold, normalize, reference, lcsmode);
if (l1 >= *LCSmin)
{
if (isPossibleSumathings(seq2, seq1, l2, l1, threshold, normalize, reference, lcsmode)) // 4-mers filter
*score = -1.0;
}
}
}
void filtersSumatra(fastaSeqPtr seq1, fastaSeqPtr seq2, double threshold, BOOL normalize, int reference, BOOL lcsmode, double* score, int* LCSmin)
{ // score takes value -2 if filters are not passed, -1 if filters are passed and >= 0 with max score if the 2 sequences are identical.
int l1;
int l2;
l1 = seq1->length;
*score = -2.0;
if (strcmp(seq1->sequence, seq2->sequence) == 0) // the 2 sequences are identical
{
if (lcsmode && normalize)
*score = 1.0;
else if (!lcsmode)
*score = 0.0;
else
*score = l1;
}
else if (threshold != 0)
{
l2 = seq2->length;
if (l1 >= l2)
{
*LCSmin = calculateLCSmin(l1, l2, threshold, normalize, reference, lcsmode);
if (l2 >= *LCSmin)
{
if (isPossibleSumathings(seq1, seq2, l1, l2, threshold, normalize, reference, lcsmode)) // 4-mers filter
*score = -1.0;
}
}
else
{
*LCSmin = calculateLCSmin(l2, l1, threshold, normalize, reference, lcsmode);
if (l1 >= *LCSmin)
{
if (isPossibleSumathings(seq2, seq1, l2, l1, threshold, normalize, reference, lcsmode)) // 4-mers filter
*score = -1.0;
}
}
}
else
*LCSmin = 0;
}

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#ifndef UPPERBAND_H_
#define UPPERBAND_H_
int buildTable(const char *sequence, unsigned char *table, int *count);
int compareTable(unsigned char *t1, int over1, unsigned char* t2, int over2);
int threshold4(int wordcount,double identity);
int thresholdLCS4(int32_t reflen,int32_t lcs);
int hashDB(fastaSeqCount);
BOOL isPossible(fastaSeqPtr, fastaSeqPtr, BOOL, int, double, BOOL);
BOOL isPossibleSumathings(fastaSeqPtr seq1, fastaSeqPtr seq2, int l1, int l2, double threshold, BOOL normalize, int reference, BOOL lcsmode);
void filters(fastaSeqPtr seq1, fastaSeqPtr seq2, double threshold, BOOL normalize, int reference, BOOL lcsmode, double* score, int* LCSmin);
void filtersSumatra(fastaSeqPtr seq1, fastaSeqPtr seq2, double threshold, BOOL normalize, int reference, BOOL lcsmode, double* score, int* LCSmin);
#endif

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#ifndef _SSE_H_
#define _SSE_H_
#include <string.h>
#include <inttypes.h>
#ifdef __SSE2__
#include <xmmintrin.h>
#else
typedef long long __m128i __attribute__ ((__vector_size__ (16), __may_alias__));
#endif /* __SSE2__ */
#ifndef MAX
#define MAX(x,y) (((x)>(y)) ? (x):(y))
#define MIN(x,y) (((x)<(y)) ? (x):(y))
#endif
#define ALIGN __attribute__((aligned(16)))
typedef __m128i vUInt8;
typedef __m128i vInt8;
typedef __m128i vUInt16;
typedef __m128i vInt16;
typedef __m128i vUInt64;
typedef union
{
__m128i i;
int64_t s64[ 2];
int16_t s16[ 8];
int8_t s8 [16];
uint8_t u8 [16];
uint16_t u16[8 ];
uint32_t u32[4 ];
uint64_t u64[2 ];
} um128;
typedef union
{
vUInt8 m;
uint8_t c[16];
} uchar_v;
typedef union
{
vUInt16 m;
uint16_t c[8];
} ushort_v;
typedef union
{
vUInt64 m;
uint64_t c[2];
} uint64_v;
#ifdef __SSE2__
static inline int8_t _s2_extract_epi8(__m128i r, const int p)
{
#define ACTIONP(r,x) return _mm_extract_epi16(r,x) & 0xFF
#define ACTIONI(r,x) return _mm_extract_epi16(r,x) >> 8
switch (p) {
case 0: ACTIONP(r,0);
case 1: ACTIONI(r,0);
case 2: ACTIONP(r,1);
case 3: ACTIONI(r,1);
case 4: ACTIONP(r,2);
case 5: ACTIONI(r,2);
case 6: ACTIONP(r,3);
case 7: ACTIONI(r,3);
case 8: ACTIONP(r,4);
case 9: ACTIONI(r,4);
case 10: ACTIONP(r,5);
case 11: ACTIONI(r,5);
case 12: ACTIONP(r,6);
case 13: ACTIONI(r,6);
case 14: ACTIONP(r,7);
case 15: ACTIONI(r,7);
}
#undef ACTIONP
#undef ACTIONI
return 0;
}
static inline __m128i _s2_max_epi8(__m128i a, __m128i b)
{
__m128i mask = _mm_cmpgt_epi8( a, b );
a = _mm_and_si128 (a,mask );
b = _mm_andnot_si128(mask,b);
return _mm_or_si128(a,b);
}
static inline __m128i _s2_min_epi8(__m128i a, __m128i b)
{
__m128i mask = _mm_cmplt_epi8( a, b );
a = _mm_and_si128 (a,mask );
b = _mm_andnot_si128(mask,b);
return _mm_or_si128(a,b);
}
static inline __m128i _s2_insert_epi8(__m128i r, int b, const int p)
{
#define ACTIONP(r,x) return _mm_insert_epi16(r,(_mm_extract_epi16(r,x) & 0xFF00) | (b & 0x00FF),x)
#define ACTIONI(r,x) return _mm_insert_epi16(r,(_mm_extract_epi16(r,x) & 0x00FF) | ((b << 8)& 0xFF00),x)
switch (p) {
case 0: ACTIONP(r,0);
case 1: ACTIONI(r,0);
case 2: ACTIONP(r,1);
case 3: ACTIONI(r,1);
case 4: ACTIONP(r,2);
case 5: ACTIONI(r,2);
case 6: ACTIONP(r,3);
case 7: ACTIONI(r,3);
case 8: ACTIONP(r,4);
case 9: ACTIONI(r,4);
case 10: ACTIONP(r,5);
case 11: ACTIONI(r,5);
case 12: ACTIONP(r,6);
case 13: ACTIONI(r,6);
case 14: ACTIONP(r,7);
case 15: ACTIONI(r,7);
}
#undef ACTIONP
#undef ACTIONI
return _mm_setzero_si128();
}
// Fill a SSE Register with 16 time the same 8bits integer value
#define _MM_SET1_EPI8(x) _mm_set1_epi8(x)
#define _MM_INSERT_EPI8(r,x,i) _s2_insert_epi8((r),(x),(i))
#define _MM_CMPEQ_EPI8(x,y) _mm_cmpeq_epi8((x),(y))
#define _MM_CMPGT_EPI8(x,y) _mm_cmpgt_epi8((x),(y))
#define _MM_CMPLT_EPI8(x,y) _mm_cmplt_epi8((x),(y))
#define _MM_MAX_EPI8(x,y) _s2_max_epi8((x),(y))
#define _MM_MIN_EPI8(x,y) _s2_min_epi8((x),(y))
#define _MM_ADD_EPI8(x,y) _mm_add_epi8((x),(y))
#define _MM_SUB_EPI8(x,y) _mm_sub_epi8((x),(y))
#define _MM_EXTRACT_EPI8(r,p) _s2_extract_epi8((r),(p))
#define _MM_MIN_EPU8(x,y) _mm_min_epu8((x),(y))
// Fill a SSE Register with 8 time the same 16bits integer value
#define _MM_SET1_EPI16(x) _mm_set1_epi16(x)
#define _MM_INSERT_EPI16(r,x,i) _mm_insert_epi16((r),(x),(i))
#define _MM_CMPEQ_EPI16(x,y) _mm_cmpeq_epi16((x),(y))
#define _MM_CMPGT_EPI16(x,y) _mm_cmpgt_epi16((x),(y))
#define _MM_CMPGT_EPU16(x,y) _mm_cmpgt_epu16((x),(y)) // n'existe pas ??
#define _MM_CMPLT_EPI16(x,y) _mm_cmplt_epi16((x),(y))
#define _MM_MAX_EPI16(x,y) _mm_max_epi16((x),(y))
#define _MM_MIN_EPI16(x,y) _mm_min_epi16((x),(y))
#define _MM_ADD_EPI16(x,y) _mm_add_epi16((x),(y))
#define _MM_SUB_EPI16(x,y) _mm_sub_epi16((x),(y))
#define _MM_EXTRACT_EPI16(r,p) _mm_extract_epi16((r),(p))
#define _MM_UNPACKLO_EPI8(a,b) _mm_unpacklo_epi8((a),(b))
#define _MM_UNPACKHI_EPI8(a,b) _mm_unpackhi_epi8((a),(b))
#define _MM_ADDS_EPU16(x,y) _mm_adds_epu16((x),(y))
// Multiplication
#define _MM_MULLO_EPI16(x,y) _mm_mullo_epi16((x), (y))
#define _MM_SRLI_EPI64(r,x) _mm_srli_epi64((r),(x))
#define _MM_SLLI_EPI64(r,x) _mm_slli_epi64((r),(x))
// Set a SSE Register to 0
#define _MM_SETZERO_SI128() _mm_setzero_si128()
#define _MM_AND_SI128(x,y) _mm_and_si128((x),(y))
#define _MM_ANDNOT_SI128(x,y) _mm_andnot_si128((x),(y))
#define _MM_OR_SI128(x,y) _mm_or_si128((x),(y))
#define _MM_XOR_SI128(x,y) _mm_xor_si128((x),(y))
#define _MM_SLLI_SI128(r,s) _mm_slli_si128((r),(s))
#define _MM_SRLI_SI128(r,s) _mm_srli_si128((r),(s))
// Load a SSE register from an unaligned address
#define _MM_LOADU_SI128(x) _mm_loadu_si128(x)
// Load a SSE register from an aligned address (/!\ not defined when SSE not available)
#define _MM_LOAD_SI128(x) _mm_load_si128(x)
// #define _MM_UNPACKLO_EPI8(x,y) _mm_unpacklo_epi8((x),(y))
#else /* __SSE2__ Not defined */
static inline __m128i _em_set1_epi8(int x)
{
um128 a;
x&=0xFF;
a.s8[0]=x;
a.s8[1]=x;
a.u16[1]=a.u16[0];
a.u32[1]=a.u32[0];
a.u64[1]=a.u64[0];
return a.i;
}
static inline __m128i _em_insert_epi8(__m128i r, int x, const int i)
{
um128 a;
a.i=r;
a.s8[i]=x & 0xFF;
return a.i;
}
static inline __m128i _em_cmpeq_epi8(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s8[z]=(x.s8[z]==y.s8[z]) ? 0xFF:0
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
R(8);
R(9);
R(10);
R(11);
R(12);
R(13);
R(14);
R(15);
#undef R
return r.i;
}
static inline __m128i _em_cmpgt_epi8(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s8[z]=(x.s8[z]>y.s8[z]) ? 0xFF:0
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
R(8);
R(9);
R(10);
R(11);
R(12);
R(13);
R(14);
R(15);
#undef R
return r.i;
}
static inline __m128i _em_cmplt_epi8(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s8[z]=(x.s8[z]<y.s8[z]) ? 0xFF:0
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
R(8);
R(9);
R(10);
R(11);
R(12);
R(13);
R(14);
R(15);
#undef R
return r.i;
}
static inline __m128i _em_max_epi8(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s8[z]=MAX(x.s8[z],y.s8[z])
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
R(8);
R(9);
R(10);
R(11);
R(12);
R(13);
R(14);
R(15);
#undef R
return r.i;
}
static inline __m128i _em_min_epi8(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s8[z]=MIN(x.s8[z],y.s8[z])
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
R(8);
R(9);
R(10);
R(11);
R(12);
R(13);
R(14);
R(15);
#undef R
return r.i;
}
static inline __m128i _em_add_epi8(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s8[z]=x.s8[z]+y.s8[z]
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
R(8);
R(9);
R(10);
R(11);
R(12);
R(13);
R(14);
R(15);
#undef R
return r.i;
}
static inline __m128i _em_sub_epi8(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s8[z]=x.s8[z]+y.s8[z]
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
R(8);
R(9);
R(10);
R(11);
R(12);
R(13);
R(14);
R(15);
#undef R
return r.i;
}
static inline int _em_extract_epi8(__m128i r, const int i)
{
um128 a;
a.i=r;
return a.s8[i] & 0xFF;
}
static inline __m128i _em_min_epu8(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.u8[z]=MIN(x.u8[z],y.u8[z])
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
R(8);
R(9);
R(10);
R(11);
R(12);
R(13);
R(14);
R(15);
#undef R
return r.i;
}
static inline __m128i _em_set1_epi16(int x)
{
um128 a;
x&=0xFFFF;
a.s16[0]=x;
a.s16[1]=x;
a.u32[1]=a.u32[0];
a.u64[1]=a.u64[0];
return a.i;
}
static inline __m128i _em_insert_epi16(__m128i r, int x, const int i)
{
um128 a;
a.i=r;
a.s16[i]=x & 0xFFFF;
return a.i;
}
static inline __m128i _em_cmpeq_epi16(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s16[z]=(x.s16[z]==y.s16[z]) ? 0xFFFF:0
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
#undef R
return r.i;
}
static inline __m128i _em_cmpgt_epi16(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s16[z]=(x.s16[z]>y.s16[z]) ? 0xFFFF:0
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
#undef R
return r.i;
}
static inline __m128i _em_cmplt_epi16(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s16[z]=(x.s16[z]<y.s16[z]) ? 0xFFFF:0
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
#undef R
return r.i;
}
static inline __m128i _em_max_epi16(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s16[z]=MAX(x.s16[z],y.s16[z])
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
#undef R
return r.i;
}
static inline __m128i _em_min_epi16(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s16[z]=MIN(x.s16[z],y.s16[z])
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
#undef R
return r.i;
}
static inline __m128i _em_add_epi16(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s16[z]=x.s16[z]+y.s16[z]
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
#undef R
return r.i;
}
static inline __m128i _em_sub_epi16(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s16[z]=x.s16[z]+y.s16[z]
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
#undef R
return r.i;
}
static inline int _em_extract_epi16(__m128i r, const int i)
{
um128 a;
a.i=r;
return a.s16[i] & 0xFFFF;
}
static inline __m128i _em_unpacklo_epi8(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s16[z]=(((int16_t)(y.s8[z])) << 8) | (int16_t)(x.s8[z])
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
#undef R
return r.i;
}
static inline __m128i _em_unpackhi_epi8(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.s16[z]=(((int16_t)(y.s8[z+8])) << 8) | (int16_t)(x.s8[z+8])
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
#undef R
return r.i;
}
static inline __m128i _em_adds_epu16(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.u16[z]=x.u16[z]+y.u16[z]
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
#undef R
return r.i;
}
static inline __m128i _em_srli_epi64(__m128i a, int b)
{
um128 x;
x.i=a;
x.s64[0]>>=b;
x.s64[1]>>=b;
return x.i;
}
static inline __m128i _em_slli_epi64(__m128i a, int b)
{
um128 x;
x.i=a;
x.s64[0]<<=b;
x.s64[1]<<=b;
return x.i;
}
static inline __m128i _em_setzero_si128()
{
um128 x;
x.s64[0]=x.s64[1]=0;
return x.i;
}
static inline __m128i _em_and_si128(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.u64[z]=x.u64[z] & y.u64[z]
R(0);
R(1);
#undef R
return r.i;
}
static inline __m128i _em_andnot_si128(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.u64[z]=(~x.u64[z]) & y.u64[z]
R(0);
R(1);
#undef R
return r.i;
}
static inline __m128i _em_or_si128(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.u64[z]=x.u64[z] | y.u64[z]
R(0);
R(1);
#undef R
return r.i;
}
static inline __m128i _em_xor_si128(__m128i a, __m128i b)
{
um128 x;
um128 y;
um128 r;
x.i=a;
y.i=b;
#define R(z) r.u64[z]=x.u64[z] ^ y.u64[z]
R(0);
R(1);
#undef R
return r.i;
}
static inline __m128i _em_slli_si128(__m128i a, int b)
{
um128 x;
x.i=a;
#define R(z) x.u8[z]=(z>=b) ? x.u8[z-b]:0
R(15);
R(14);
R(13);
R(12);
R(11);
R(10);
R(9);
R(8);
R(7);
R(6);
R(5);
R(4);
R(3);
R(2);
R(1);
R(0);
#undef R
return x.i;
}
static inline __m128i _em_srli_si128(__m128i a, int b)
{
um128 x;
x.i=a;
#define R(z) x.u8[z]=((b+z) > 15) ? 0:x.u8[z+b]
R(0);
R(1);
R(2);
R(3);
R(4);
R(5);
R(6);
R(7);
R(8);
R(9);
R(10);
R(11);
R(12);
R(13);
R(14);
R(15);
#undef R
return x.i;
}
inline static __m128i _em_loadu_si128(__m128i const *P)
{
um128 tmp;
um128 *pp=(um128*)P;
tmp.u8[0]=(*pp).u8[0];
tmp.u8[1]=(*pp).u8[1];
tmp.u8[2]=(*pp).u8[2];
tmp.u8[3]=(*pp).u8[3];
tmp.u8[4]=(*pp).u8[4];
tmp.u8[5]=(*pp).u8[5];
tmp.u8[6]=(*pp).u8[6];
tmp.u8[7]=(*pp).u8[7];
tmp.u8[8]=(*pp).u8[8];
tmp.u8[9]=(*pp).u8[9];
tmp.u8[10]=(*pp).u8[10];
tmp.u8[11]=(*pp).u8[11];
tmp.u8[12]=(*pp).u8[12];
tmp.u8[13]=(*pp).u8[13];
tmp.u8[14]=(*pp).u8[14];
tmp.u8[15]=(*pp).u8[15];
return tmp.i;
}
#define _MM_SET1_EPI8(x) _em_set1_epi8(x)
#define _MM_INSERT_EPI8(r,x,i) _em_insert_epi8((r),(x),(i))
#define _MM_CMPEQ_EPI8(x,y) _em_cmpeq_epi8((x),(y))
#define _MM_CMPGT_EPI8(x,y) _em_cmpgt_epi8((x),(y))
#define _MM_CMPLT_EPI8(x,y) _em_cmplt_epi8((x),(y))
#define _MM_MAX_EPI8(x,y) _em_max_epi8((x),(y))
#define _MM_MIN_EPI8(x,y) _em_min_epi8((x),(y))
#define _MM_ADD_EPI8(x,y) _em_add_epi8((x),(y))
#define _MM_SUB_EPI8(x,y) _em_sub_epi8((x),(y))
#define _MM_EXTRACT_EPI8(r,p) _em_extract_epi8((r),(p))
#define _MM_MIN_EPU8(x,y) _em_min_epu8((x),(y))
#define _MM_SET1_EPI16(x) _em_set1_epi16(x)
#define _MM_INSERT_EPI16(r,x,i) _em_insert_epi16((r),(x),(i))
#define _MM_CMPEQ_EPI16(x,y) _em_cmpeq_epi16((x),(y))
#define _MM_CMPGT_EPI16(x,y) _em_cmpgt_epi16((x),(y))
#define _MM_CMPLT_EPI16(x,y) _em_cmplt_epi16((x),(y))
#define _MM_MAX_EPI16(x,y) _em_max_epi16((x),(y))
#define _MM_MIN_EPI16(x,y) _em_min_epi16((x),(y))
#define _MM_ADD_EPI16(x,y) _em_add_epi16((x),(y))
#define _MM_SUB_EPI16(x,y) _em_sub_epi16((x),(y))
#define _MM_EXTRACT_EPI16(r,p) _em_extract_epi16((r),(p))
#define _MM_UNPACKLO_EPI8(a,b) _em_unpacklo_epi8((a),(b))
#define _MM_UNPACKHI_EPI8(a,b) _em_unpackhi_epi8((a),(b))
#define _MM_ADDS_EPU16(x,y) _em_adds_epu16((x),(y))
#define _MM_SRLI_EPI64(r,x) _em_srli_epi64((r),(x))
#define _MM_SLLI_EPI64(r,x) _em_slli_epi64((r),(x))
#define _MM_SETZERO_SI128() _em_setzero_si128()
#define _MM_AND_SI128(x,y) _em_and_si128((x),(y))
#define _MM_ANDNOT_SI128(x,y) _em_andnot_si128((x),(y))
#define _MM_OR_SI128(x,y) _em_or_si128((x),(y))
#define _MM_XOR_SI128(x,y) _em_xor_si128((x),(y))
#define _MM_SLLI_SI128(r,s) _em_slli_si128((r),(s))
#define _MM_SRLI_SI128(r,s) _em_srli_si128((r),(s))
#define _MM_LOADU_SI128(x) _em_loadu_si128(x)
#define _MM_LOAD_SI128(x) _em_loadu_si128(x)
#endif /* __SSE2__ */
#define _MM_NOT_SI128(x) _MM_XOR_SI128((x),(_MM_SET1_EPI8(0xFFFF)))
#endif

BIN
libutils/.DS_Store vendored Normal file
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25
libutils/Makefile Normal file
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@@ -0,0 +1,25 @@
SOURCES = utilities.c \
debug.c
SRCS=$(SOURCES)
OBJECTS= $(patsubst %.c,%.o,$(SOURCES))
LIBFILE= libutils.a
RANLIB=ranlib
include ../global.mk
all: $(LIBFILE)
clean:
rm -rf $(OBJECTS) $(LIBFILE)
rm -f *.P
rm -f *.a
$(LIBFILE): $(OBJECTS)
ar -cr $@ $?
$(RANLIB) $@

32
libutils/debug.c Normal file
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@@ -0,0 +1,32 @@
/*
* debug.c
*
* Created on: 4 sept. 2012
* Author: coissac
*/
#include <stdlib.h>
#include <inttypes.h>
#include "debug.h"
char* int2bin(int64_t i,size_t bits)
{
static char str[65];
uint64_t u;
if (bits > 64)
return NULL;
str[bits] = 0;
// type punning because signed shift is implementation-defined
u = *(unsigned *)&i;
for(; bits--; u >>= 1)
str[bits] = u & 1 ? '1' : '0';
return str;
}

25
libutils/debug.h Normal file
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@@ -0,0 +1,25 @@
/*
* debug.h
*
* Created on: 4 sept. 2012
* Author: coissac
*/
#ifndef DEBUG_H_
#define DEBUG_H_
#ifdef DEBUG
#undef DEBUG
#endif
#ifdef DEBUG_ON
#define DEBUG(format,...) fprintf(stderr,"[%s:%d] : "format"\n",__FILE__,__LINE__,__VA_ARGS__)
#else
#define DEBUG(format,...)
#endif
#include <stdint.h>
char * int2bin(int64_t i,size_t bits);
#endif /* DEBUG_H_ */

230
libutils/utilities.c Normal file
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@@ -0,0 +1,230 @@
/**
* FileName: utilities.c
* Author: Tiayyba Riaz
* Description: C file for miscellenious functions and macros
* **/
#include "utilities.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
/*
* Function Name: errorAbort(int errorCode, char* errorMsg, char* fileName, int lineNumber)
* Description: Reports an error on standard error and aborts
*/
void errorAbort(int32_t errorCode, char* errorMsg, char* fileName, int32_t lineNumber)
{
fprintf(stderr,"Error %d in file %s line %d : %s\n",
errorCode,
fileName,
lineNumber,
errorMsg);
abort();
}
void *util_malloc(size_t chunksize, const char *filename, int32_t line)
{
void * chunk;
chunk = calloc(1,chunksize);
if (!chunk)
errorAbort(MEM_ALLOC_ERROR,"Could not allocate memory.",filename,line);
return chunk;
}
/*
* Function Name: util_realloc(void *chunk, int32_t newsize, const char *filename, int32_t line)
* Description: Overloading realloc funstion, changes the size of the memory object pointed to by chunk
* to the size specified by newsize. If memory cannot be allocated, gives the error on stderr and aborts.
*/
void *util_realloc(void *chunk, size_t newsize, const char *filename, int32_t line)
{
void *newchunk;
newchunk = realloc(chunk,newsize);
if (!newchunk)
{
errorAbort(MEM_ALLOC_ERROR,"Could not allocate memory.",filename,line);
}
return newchunk;
}
/*
* Function Name: util_free(void *chunk)
* Description: Returns the memory specified by chunk back to operating syste.
*/
void util_free(void *chunk)
{
free(chunk);
}
BOOL util_findInArr(int32_t tempArr[], int seqNo, int32_t noOfSeqs)
{
int index;
for(index = 0; index < noOfSeqs; index++)
{
if(tempArr[index] == seqNo) return TRUE;
}
return FALSE;
}
/**
*
* String handling utilities
*
**/
/*
* Function Name: str_chopAtDelim(char *dest, char *src, char *delim, BOOL includeDelim)
* Description: chops the string startig from source to the delimeter specified.
*/
char *str_chopAtDelim(char *dest, char *src, char *delim, BOOL includeDelim)
{
char *temp;
int32_t len;
/* returns a pointer to the first occurance of delim in src*/
temp = strstr(src, delim);
if (temp == NULL)
return NULL;
if (includeDelim)
{
/* temp - src + strlen(delim) -> a string between src and delimeter including delimeter*/
len = temp - src + strlen(delim);
strncpy(dest, src, len);
}
else
{
len = temp - src;
strncpy(dest, src, temp - src);
}
dest[len] = '\0';
return dest;
}
/*
* Function Name: str_sepNameValue(char *name, char *value, char *src, char *delim)
* Description: .
*/
void str_sepNameValue(char *name, char *value, char *src, char *delim)
{
char *temp;
temp = strstr(src, delim);
if(temp != NULL)
{
strncpy(name, src, temp - src);
strcpy(value, temp + strlen(delim));
}
else
{
strcpy(name, src);
strcpy(value, "");
}
}
/*
* Function Name: str_removeSpaces(char *src)
* Description: Removes the spaces from the start and end of the string.
*/
int str_isSpace (char ch)
{
switch (ch)
{
case ' ':
case '\t':
case '\n':
return 1;
}
return 0;
}
void str_removeSpaces(char *src)
{
int32_t start = 0, end = strlen(src) - 1;
int32_t index = 0;
if (src == NULL || end < 0) return;
while(str_isSpace(src[start]) && start < end) start++;
while(str_isSpace(src[end]) && end > start) end--;
if ( start == end && src[start] == ' ')
{
src[0] = '\0';
return;
}
if (start > 0)
{
while(start <= end)
{
src[index] = src[start];
index++;
start++;
}
src[index] = '\0';
return;
}
src[end+1] = '\0';
}
/*
* Function Name: str_strrstr(char *src, char *delim)
* Description: Searches the position of last occurence of string delim in src.
*/
char *str_strrstr(char *src, char *delim)
{
char *last, *next;
next = strstr(src, delim);
last = next;
while(next != NULL)
{
last = next;
next = strstr(last + 1, delim);
}
return last;
}
void* getA16Address(int size)
{
void* address;
address = (void*) malloc(size);
while ((((long long unsigned int) (address))%16) != 0)
address++;
return(address);
}
void** reallocA16Address(void** address, int size)
{
if (*(address) == NULL)
*(address) = malloc(size);
*(address) = realloc(address, size);
while ((((long long unsigned int) (*(address)))%16) != 0)
(*(address))++;
return(address);
}

56
libutils/utilities.h Normal file
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/**
* FileName: utilities.h
* Author: Tiayyba Riaz
* Description: Header file for miscellenious functions and macros
* **/
#ifndef UTILITIES_H_
#define UTILITIES_H_
#include <stdint.h>
#include <stdio.h>
#include <time.h>
//static char *basecodes = "00100020000000000003000000";
//#define BASEIDX(ch) basecodes[ch - 'a'] - 48
#ifndef MAX
#define MAX(x,y) (((x)>(y)) ? (x):(y))
#define MIN(x,y) (((x)<(y)) ? (x):(y))
#endif
typedef char BOOL;
#define TRUE (3==3)
#define FALSE (!TRUE)
#define ALILEN (0)
#define MAXLEN (1)
#define MINLEN (2)
/* Error Codes */
#define FILE_OPENING_ERROR (1)
#define MEM_ALLOC_ERROR (2)
/* Prototypes */
void errorAbort(int32_t code, char* errorMsg, char* fileName, int32_t lineNumber);
char *str_strrstr(char *src, char *delim);
void str_removeSpaces(char *src);
void str_sepNameValue(char *name, char *value, char *src, char *delim);
char *str_chopAtDelim(char *dest, char *src, char *delim, BOOL includeDelim);
void util_free(void *chunk);
void *util_realloc(void *chunk, size_t newsize, const char *filename, int32_t line);
void *util_malloc(size_t chunksize, const char *filename, int32_t line);
BOOL util_findInArr(int32_t tempArr[], int seqNo, int32_t noOfSeqs);
void* getA16Address(int size);
void** reallocA16Address(void** address, int size);
/* Macros */
#define ERRORABORT(code, msg) errorAbort((code), (msg), __FILE__, __LINE__)
#endif /*UTILITIES_H_*/