[Bioperl-guts-l] bioperl-live/t SimpleAlign.t,1.46,1.47

Jason Stajich jason at dev.open-bio.org
Tue Dec 12 16:36:58 EST 2006


Update of /home/repository/bioperl/bioperl-live/t
In directory dev.open-bio.org:/tmp/cvs-serv5362/t

Modified Files:
	SimpleAlign.t 
Log Message:
add features to alignments to allow for better NEXUS integration

Index: SimpleAlign.t
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/t/SimpleAlign.t,v
retrieving revision 1.46
retrieving revision 1.47
diff -C2 -d -r1.46 -r1.47
*** SimpleAlign.t	25 Sep 2006 16:21:26 -0000	1.46
--- SimpleAlign.t	12 Dec 2006 21:36:56 -0000	1.47
***************
*** 3,7 ****
  ## $Id$
  use strict;
! use constant NUMTESTS => 75;
  use vars qw($DEBUG);
  $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
--- 3,7 ----
  ## $Id$
  use strict;
! use constant NUMTESTS => 85;
  use vars qw($DEBUG);
  $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
***************
*** 20,23 ****
--- 20,26 ----
  use_ok('Bio::AlignIO');
  use_ok('Bio::Root::IO');
+ use_ok('Bio::SeqFeature::Generic');
+ use_ok('Bio::Location::Simple');
+ use_ok('Bio::Location::Split');
  
  my ($str, $aln, @seqs, $seq);
***************
*** 304,306 ****
  }
  
! 1;
\ No newline at end of file
--- 307,356 ----
  }
  
! # test for Bio::SimpleAlign annotation method and 
! # Bio::FeatureHolder stuff
! 
! $aln = Bio::SimpleAlign->new;
! for my $seqset ( [qw(one AGAGGAT)], [qw(two AGACGAT) ], [qw(three AGAGGTT)]) {
!     $aln->add_seq(Bio::LocatableSeq->new(-id => $seqset->[0],
! 					 -seq => $seqset->[1]));
! }
! 
! is $aln->no_sequences, 3, 'added 3 seqs';
! 
! $aln->add_SeqFeature(Bio::SeqFeature::Generic->new(-start => 1,
! 						   -end   => 1,
! 						   -primary_tag => 'charLabel',
! 						   ));
! $aln->add_SeqFeature(Bio::SeqFeature::Generic->new(-start => 3,
! 						   -end   => 3,
! 						   -primary_tag => 'charLabel',
! 
! 						   ));
! is($aln->feature_count, 2, 'first 2 features added');
! 
! my $splitloc =Bio::Location::Split->new;
! $splitloc->add_sub_Location(Bio::Location::Simple->new(-start => 2,
! 						       -end   => 3));
! 
! $splitloc->add_sub_Location(Bio::Location::Simple->new(-start => 5,
! 						       -end   => 6));
! 						     
! $aln->add_SeqFeature(Bio::SeqFeature::Generic->new(-location =>$splitloc,
! 						   -primary_tag => 'charLabel',
! 						   ));
! 
! is($aln->feature_count, 3, '3rd feature added');
! 
! #get a slice as defined by the feature
! my $i = 0;
! my @slice_lens = qw(1 1 2 2);
! for my $feature ( $aln->get_SeqFeatures ) {
!     for my $loc ( $feature->location->each_Location ) {
! 	my $fslice = $aln->slice($loc->start, $loc->end);
! 	is($fslice->length, $slice_lens[$i++], "slice $i len");
!     }
! }
! 
! # test for Binary/Morphological/Mixed data
! 
! 1;



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