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Viewing changes to Bio/Symbol/ProteinAlphabet.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/Symbol/ProteinAlphabet.pm
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# $Id: ProteinAlphabet.pm,v 1.7.2.1 2006/10/02 23:10:31 sendu Exp $
 
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# $Id: ProteinAlphabet.pm 11480 2007-06-14 14:16:21Z sendu $
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#
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# BioPerl module for Bio::Symbol::ProteinAlphabet
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#
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=head1 SYNOPSIS
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    use Bio::Symbol::ProteinAlphabet;
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    my $alpha = new Bio::Symbol::ProteinAlphabet();
 
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    my $alpha = Bio::Symbol::ProteinAlphabet->new();
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    foreach my $symbol ( $alpha->symbols ) {
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        print "symbol is $symbol\n";
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    }
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=head2 new
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 Title   : new
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 Usage   : my $obj = new Bio::Symbol::ProteinAlphabet();
 
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 Usage   : my $obj = Bio::Symbol::ProteinAlphabet->new();
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 Function: Builds a new Bio::Symbol::ProteinAlphabet object 
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 Returns : Bio::Symbol::ProteinAlphabet
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 Args    :
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  foreach my $let ( keys %codes  ) {  
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      if( scalar @{$codes{$let}} != 1) { push @left, $let; next; }
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      $symbols{$let} = new Bio::Symbol::Symbol(-name => $aa{$let},
 
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      $symbols{$let} = Bio::Symbol::Symbol->new(-name => $aa{$let},
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                                               -token => $let);      
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  }
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  foreach my $l ( @left ) {
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      foreach my $sym ( @{$codes{$l}} ) {
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          push @subsym, $symbols{$sym};
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      }
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      my $alpha = new Bio::Symbol::Alphabet(-symbols => \@subsym);
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      $symbols{$l} = new Bio::Symbol::Symbol(-name => $aa{$l},
 
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      my $alpha = Bio::Symbol::Alphabet->new(-symbols => \@subsym);
 
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      $symbols{$l} = Bio::Symbol::Symbol->new(-name => $aa{$l},
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                                               -token => $l,
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                                               -matches => $alpha,
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                                               -symbols => \@subsym);