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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy, David Paleino, Charles Plessy
  • Date: 2008-07-02 11:24:48 UTC
  • mfrom: (1.1.1 upstream)
  • Revision ID: james.westby@ubuntu.com-20080702112448-2kphz1t3xwqyi9jv
Tags: 2.0.0-1
http://bugs.debian.org/479323
[ David Paleino ]
* Updated to Standards-Version 3.8.0 (no changes needed)

[ Charles Plessy ]
* New upstream release (Closes: #479323)
  Quoting the upstream changelog:
  o Modified exonerate to work in Client:Server mode
  o Fixed --refine to work with SDP alignments
  o Disabled codegen warnings from bootstrapper during compilation
  o Added --geneticcode option for using alternative genetic codes
  o Added --splice5 and --splice3 to allow alternative splice site PSSMs
  o Fixed several bugs when scanning query sequences (eg. --forcescan query)
  o Fixed to report query on forward strand whenever possible.
  o Fixed --ryo sequence dumping with --bestn
  o Fixed a bug with missing seeds when using --annotation
  o Changed license to GPLv3
  o Added protein2dna:bestfit and protein2genome:bestfit models
    (works with exhaustive alignment only)
* Updated my email address.
* debian/control:
  - Building on glib-2.0 instead of 1.2.
  - Added a build dependancy on libreadline5-dev.
  - Augmented the long description and changed the short.
  - Added a build dependency on CDBS.
* debian/copyright made machine-readable.
* debian/rules switched to cdbs.
* debian/dirs: removed.

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src/c4/opair.c
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*  C4 dynamic programming library - code for optimal pairs       *
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*                                                                *
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*  Guy St.C. Slater..   mailto:guy@ebi.ac.uk                     *
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*  Copyright (C) 2000-2006.  All Rights Reserved.                *
 
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*  Copyright (C) 2000-2008.  All Rights Reserved.                *
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*                                                                *
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*  This source code is distributed under the terms of the        *
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*  GNU Lesser General Public License. See the file COPYING       *
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*  or http://www.fsf.org/copyleft/lesser.html for details        *
 
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*  GNU General Public License, version 3. See the file COPYING   *
 
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*  or http://www.gnu.org/licenses/gpl.txt for details            *
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*                                                                *
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*  If you use this code, please keep this notice intact.         *
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*                                                                *
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/**/
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OPair *OPair_create(Optimal *optimal,
 
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OPair *OPair_create(Optimal *optimal, SubOpt *subopt,
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                    gint query_length, gint target_length, gpointer user_data){
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    register OPair *opair = g_new(OPair, 1);
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    g_assert(optimal);
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    g_assert(target_length >= 0);
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    opair->optimal = Optimal_share(optimal);
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    opair->user_data = user_data;
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    opair->subopt = SubOpt_create(query_length, target_length);
 
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    opair->subopt = SubOpt_share(subopt);
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    opair->region = Region_create(0, 0, query_length, target_length);
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    opair->prev_score = C4_IMPOSSIBLY_HIGH_SCORE;
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    return opair;
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                                  opair->user_data, threshold,
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                                  opair->subopt);
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    if(alignment){
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        SubOpt_add_alignment(opair->subopt, alignment);
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        if(alignment->score > opair->prev_score)
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            g_warning("Score [%d] greater than previous [%d]",
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                      alignment->score, opair->prev_score);