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Viewing changes to Bio/LiveSeq/Mutator.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/LiveSeq/Mutator.pm
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# $Id: Mutator.pm,v 1.33.4.3 2006/10/02 23:10:21 sendu Exp $
 
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# $Id: Mutator.pm 11480 2007-06-14 14:16:21Z sendu $
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#
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# bioperl module for Bio::LiveSeq::Mutator
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#
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    if ($len == 1 and $refstring =~ /[^\.\-\*\?]/ and 
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        $varstring  =~ /[^\.\-\*\?]/ ) { #point
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        $mutation = new Bio::LiveSeq::Mutation (-seq => $varstring,
 
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        $mutation = Bio::LiveSeq::Mutation->new(-seq => $varstring,
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                                                -pos => $pos,
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                                                );
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    }
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    elsif ( $refstring =~ /^[^\.\-\*\?]+$/ and 
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            $varstring  !~ /^[^\.\-\*\?]+$/ ) { # deletion
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        $mutation = new Bio::LiveSeq::Mutation (-pos => $pos,
 
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        $mutation = Bio::LiveSeq::Mutation->new(-pos => $pos,
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                                                -len => $len
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                                                );
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    }
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    elsif ( $refstring !~ /^[^\.\-\*\?]+$/ and 
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            $varstring  =~ /^[^\.\-\*\?]+$/ ) { # insertion
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        $mutation = new Bio::LiveSeq::Mutation (-seq => $varstring,
 
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        $mutation = Bio::LiveSeq::Mutation->new(-seq => $varstring,
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                                                -pos => $pos,
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                                                -len => 0
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                                                );
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    } else { # complex
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        $mutation = new Bio::LiveSeq::Mutation (-seq => $varstring,
 
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        $mutation = Bio::LiveSeq::Mutation->new(-seq => $varstring,
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                                                -pos => $pos,
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                                                -len => $len
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                                                );