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Viewing changes to Bio/Matrix/PSM/IO/mast.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/IO/mast.pm
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# $Id: mast.pm,v 1.21.4.2 2006/10/02 23:10:22 sendu Exp $
 
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# $Id: mast.pm 11480 2007-06-14 14:16:21Z sendu $
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=head1 NAME
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=head2 new
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 Title   : new
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 Usage   : my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'mast', 
 
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 Usage   : my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'mast', 
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                                                                               -file=>$file);
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 Function: Associates a file with the appropriate parser
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 Throws  : Throws if the file passed is in HTML format or if 
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                        warn "Malformed data found: $line\n";
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                        next;
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                }
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                $instances{$id}=new Bio::Matrix::PSM::InstanceSite (-id=>$id,
 
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                $instances{$id}=Bio::Matrix::PSM::InstanceSite->new(-id=>$id,
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                                                                                                                                                          -desc=>$key,
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                                                                                                                                                          -score=>$eval, 
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                                                                                                                                                          -width=>$len,
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        my $width=$index{$id};
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    #We don't know the sequence, but we know the length
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        my $seq='N' x ($width*$self->{_factor}); #Future version will have to parse Section tree nad get the real seq
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        my $instance=new Bio::Matrix::PSM::InstanceSite 
 
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        my $instance=Bio::Matrix::PSM::InstanceSite->new 
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            ( -id=>"$id\@$sid", 
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              -mid=>$id, 
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              -accession_number=>$sid,
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        push @instances,$instance;
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        $pos+=$index{$id}*$self->{_factor};
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    }
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    my $psm= new Bio::Matrix::PSM::Psm (-instances=> \@instances, 
 
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    my $psm= Bio::Matrix::PSM::Psm->new(-instances=> \@instances, 
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                                        -e_val    => $eval, 
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                                        -id       => $sid);
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    $self->_pushback($line);