[Bioperl-guts-l] bioperl-live/Bio SimpleAlign.pm,1.88,1.89

Heikki Lehvaslaiho heikki at pub.open-bio.org
Wed Sep 21 10:26:14 EDT 2005


Update of /home/repository/bioperl/bioperl-live/Bio
In directory pub.open-bio.org:/tmp/cvs-serv10080

Modified Files:
	SimpleAlign.pm 
Log Message:
remove_gaps() did not use the passed gap_char argument.
Enabled it but added a note to use gap_char() and remove_columns.
Resolves bug #1868


Index: SimpleAlign.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SimpleAlign.pm,v
retrieving revision 1.88
retrieving revision 1.89
diff -C2 -d -r1.88 -r1.89
*** SimpleAlign.pm	4 Aug 2005 18:16:59 -0000	1.88
--- SimpleAlign.pm	21 Sep 2005 14:26:12 -0000	1.89
***************
*** 896,899 ****
--- 896,902 ----
                          indicates that only all-gaps columns should be deleted
  
+ Used from method L<remove_columns> in most cases. Set gap character
+ using L<gap_char()|gap_char>.
+ 
  =cut
  
***************
*** 902,908 ****
      my $gap_line;
      if ($all_gaps_columns) {
!         $gap_line = $self->all_gap_line;
      } else {
!         $gap_line = $self->gap_line;
      }
      my $aln = $self->new;
--- 905,911 ----
      my $gap_line;
      if ($all_gaps_columns) {
!         $gap_line = $self->all_gap_line($gapchar);
      } else {
!         $gap_line = $self->gap_line($gapchar);
      }
      my $aln = $self->new;



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