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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-03-10 07:19:11 UTC
  • mfrom: (3.1.2 squeeze)
  • Revision ID: james.westby@ubuntu.com-20090310071911-ever3si2bbzx1iks
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/Search/HSP/HSPI.pm
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#-----------------------------------------------------------------
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# $Id: HSPI.pm,v 1.36.4.2 2006/10/02 23:10:24 sendu Exp $
 
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# $Id: HSPI.pm 15084 2008-12-03 22:31:23Z cjfields $
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#
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# BioPerl module for Bio::Search::HSP::HSPI
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#
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 Title    : gaps
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 Usage    : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
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 Function : Get the number of gaps in the query, hit, or total alignment.
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 Returns  : Integer, number of gaps or 0 if none
 
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 Function : Get the number of gap charcters in the query, hit, or total alignment.
 
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 Returns  : Integer, number of gap characters or 0 if none
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 Args     : 'query' = num conserved / length of query seq (without gaps)
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            'hit'   = num conserved / length of hit seq (without gaps)
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            'total' = num conserved / length of alignment (with gaps)
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=cut
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#-------
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sub seq {
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#-------
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    my($self,$seqType) = @_; 
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    $seqType ||= 'query';
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    $seqType = 'sbjct' if $seqType eq 'hit';
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    }
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    require Bio::LocatableSeq;
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    my $id = $seqType =~ /^q/i ? $self->query->seq_id : $self->hit->seq_id;
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    new Bio::LocatableSeq (-ID    => $id,
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                           -SEQ   => $str,
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                           -START => $self->start($seqType),
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                           -END   => $self->end($seqType),
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                           -STRAND=> $self->strand($seqType),
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                           -DESC  => "$seqType sequence ",
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                           );
 
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    return Bio::LocatableSeq->new(  -ID        => $id,
 
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                                    -SEQ       => $str,
 
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                                    -START     => $self->start($seqType),
 
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                                    -END       => $self->end($seqType),
 
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                                    -STRAND    => $self->strand($seqType),
 
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                                    -FORCE_NSE => $id ? 0 : 1,
 
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                                    -DESC      => "$seqType sequence " );
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}
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=head2 seq_str