← Back to branch summary

~ubuntu-branches/ubuntu/saucy/bioperl/saucy-proposed

« back to all changes in this revision

Viewing changes to Bio/Matrix/PSM/ProtPsm.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).

Show diffs side-by-side

added added

removed removed

Lines of Context:
Bio/Matrix/PSM/ProtPsm.pm
1
1
#---------------------------------------------------------
2
 
# $Id: ProtPsm.pm,v 1.8.4.1 2006/10/02 23:10:22 sendu Exp $
 
2
# $Id: ProtPsm.pm 11480 2007-06-14 14:16:21Z sendu $
3
3
 
4
4
#ISA ProtMatrix, HAS InstanceSite
5
5
 
12
12
  use Bio::Matrix::PSM::IO;
13
13
 
14
14
  #To get a ProtPsm object from a file use the Psm parser:
15
 
  my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'psiblast', -file=>$file);
 
15
  my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'psiblast', -file=>$file);
16
16
 
17
17
  # Now go through all entities in the file with next_psm, which
18
18
  # returns a Psm object see Bio::Matrix::PSM::IO for detailed