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Viewing changes to Bio/Matrix/PSM/SiteMatrix.pm

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (1.2.3 upstream)
  • Revision ID: james.westby@ubuntu.com-20090310071911-fukqzw54pyb1f0bd
Tags: 1.6.0-2
https://launchpad.net/bugs/324001
* Removed patch system (not used):
  - removed instuctions in debian/rules;
  - removed quilt from Build-Depends in debian/control.
* Re-enabled tests:
  - uncommented test command in debian/rules;
  - uncommented previously missing build-dependencies in debian/control.
  - Re-enabled tests and uncommented build-dependencies accordingly.
* Removed libmodule-build-perl and libtest-harness-perl from
  Build-Depends-Indep (provided by perl-modules).
* Better cleaning of empty directories using find -type d -empty -delete
  instead of rmdir in debian/rules (LP: #324001).

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Bio/Matrix/PSM/SiteMatrix.pm
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# $Id: SiteMatrix.pm,v 1.31.4.3 2006/10/02 23:10:22 sendu Exp $
 
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# $Id: SiteMatrix.pm 11480 2007-06-14 14:16:21Z sendu $
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#---------------------------------------------------------
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=head1 NAME
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  my %param=(-pA=>$a,-pC=>$c,-pG=>$g,-pT=>$t,
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             -lA=>$la, -lC=>$lc,-lG=>$lg,-lT=>$l,
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             -IC=>$ic,-e_val=>$score, -id=>$mid);
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  my $site=new Bio::Matrix::PSM::SiteMatrix(%param);
 
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  my $site=Bio::Matrix::PSM::SiteMatrix->new(%param);
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  #Or get it from a file:
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  use Bio::Matrix::PSM::IO;
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  my $psmIO= new Bio::Matrix::PSM::IO(-file=>$file, -format=>'transfac');
 
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  my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'transfac');
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  while (my $psm=$psmIO->next_psm) {
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    #Now we have a Bio::Matrix::PSM::Psm object, 
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    # see Bio::Matrix::PSM::PsmI for details
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=head2 new
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 Title   : new
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 Usage   : my $site=new Bio::Matrix::PSM::SiteMatrix(-pA=>$a,-pC=>$c,
 
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 Usage   : my $site=Bio::Matrix::PSM::SiteMatrix->new(-pA=>$a,-pC=>$c,
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                                                     -pG=>$g,-pT=>$t,
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                                                     -IC=>$ic,
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                                                     -e_val=>$score,