[Bioperl-guts-l] bioperl-live/Bio/Graphics FeatureBase.pm, 1.21, 1.22

Scott Cain scain at dev.open-bio.org
Thu Feb 1 13:19:12 EST 2007


Update of /home/repository/bioperl/bioperl-live/Bio/Graphics
In directory dev.open-bio.org:/tmp/cvs-serv11498/Graphics

Modified Files:
	FeatureBase.pm 
Log Message:
adding is_circular to Graphics::FeatureBase because it is required by Bio::PrimarySeqI; adding more flexible functionality to SeqIO::chadoxml while introducing a -flybase_compat arg to allow it to continue to work like they expect


Index: FeatureBase.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/FeatureBase.pm,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** FeatureBase.pm	30 Jan 2007 22:41:34 -0000	1.21
--- FeatureBase.pm	1 Feb 2007 18:19:09 -0000	1.22
***************
*** 111,114 ****
--- 111,117 ----
    }
  
+   # is_circular is needed for Bio::PrimarySeqI compliance
+   $self->{i_circular} = $arg{-is_circular} || 0;
+ 
    # fix start, stop
    if (defined $self->{stop} && defined $self->{start}
***************
*** 226,229 ****
--- 229,241 ----
  }
  
+ #is_circular is needed for Bio::PrimarySeqI
+ sub is_circular {
+   my $self = shift;
+   my $d = $self->{is_circular};
+   $self->{is_circular} = shift if @_;
+   $d;
+ }
+ 
+ 
  sub seq {
    my $self = shift;



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