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Viewing changes to Bio/Matrix/PSM/PsmI.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/PsmI.pm
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# $Id: PsmI.pm,v 1.8.4.1 2006/10/02 23:10:22 sendu Exp $
 
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# $Id: PsmI.pm 11480 2007-06-14 14:16:21Z sendu $
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#---------------------------------------------------------
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#ISA SiteMatrix, HAS InstanceSite
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  use Bio::Matrix::PSM::IO;
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  # To get a Psm object from a file use the Psm parser:
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  my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'meme', -file=>$file);
 
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  my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'meme', -file=>$file);
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  # Now go through all entities in the file with next_psm, which
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  # returns a Psm object see Bio::Matrix::PSM::IO for detailed
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   }
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  # or create from memmory:
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  my $psm= new Bio::Matrix::PSM::Psm( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT,
 
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  my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,-pT=>\@pT,
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                                      -id=>$id,
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                                      -instances=>$instances, -e_val=>$e_val,
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                                      -IC=>$ic, -width=>$width, -sites=>$sites)
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=head2 new
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 Title   : new
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 Usage   : my $psm= new Bio::Matrix::PSM::Psm( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,
 
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 Usage   : my $psm= Bio::Matrix::PSM::Psm->new( -pA=>\@pA,-pC=>\@pC,-pG=>\@pG,
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                                               -pT=>\@pT,-id=>$id,
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                                               -instances=>$instances, 
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                                               -e_val=>$e_val,