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Viewing changes to Bio/AlignIO/msf.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/AlignIO/msf.pm
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# $Id: msf.pm,v 1.22.4.3 2006/10/02 23:10:12 sendu Exp $
 
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# $Id: msf.pm 14883 2008-09-16 18:27:31Z jason $
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#
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# BioPerl module for Bio::AlignIO::msf
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#   based on the Bio::SeqIO::msf module
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                        $seqname = $name;
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                        $start = 1;
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                        $str = $hash{$name};
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                        $str =~ s/[^A-Za-z]//g;
 
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                        $str =~ s/[^0-9A-Za-z$Bio::LocatableSeq::OTHER_SYMBOLS]//g;
 
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                        $end = length($str);
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                }
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                $seq = new Bio::LocatableSeq(-seq   => $hash{$name},
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                                                                                          -id    => $seqname,
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                                                                                          -start => $start,
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                                                                                          -end   => $end,
 
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                $seq = Bio::LocatableSeq->new(-seq   => $hash{$name},
 
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                                              -id    => $seqname,
 
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                                              -start => $start,
 
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                                              -end   => $end,
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                                                                                         );
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                $aln->add_seq($seq);
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                $self->_print (sprintf("\n%s   MSF: %d  Type: %s  %s  Check: 00 ..\n\n",
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                               $name,  $aln->no_sequences, $type, $date));
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    my $seqCountFormat = "%".($maxname > 20 ? $maxname + 2: 22)."s%-27d%27d\n";
 
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    my $seqNameFormat  = "%-".($maxname > 20 ? $maxname : 20)."s  ";
 
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                foreach $seq ( $aln->each_seq() ) {
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                        $name = $aln->displayname($seq->get_nse());
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                        $miss = $maxname - length ($name);
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        while( $count < $length ) {
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                        # there is another block to go!
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                        $self->_print (sprintf("%22s%-27d%27d\n",' ',$count+1,$count+50));
 
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                        $self->_print (sprintf($seqCountFormat,' ',$count+1,$count+50));
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                        foreach $name  ( @arr ) {
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                                $self->_print (sprintf("%-20s  ",$name));
 
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                                $self->_print (sprintf($seqNameFormat,$name));
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                                $tempcount = $count;
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                                $index = 0;