[Bioperl-guts-l] bioperl-live/Bio Species.pm,1.47,1.48

Christopher John Fields cjfields at dev.open-bio.org
Tue Jan 30 00:39:09 EST 2007


Update of /home/repository/bioperl/bioperl-live/Bio
In directory dev.open-bio.org:/tmp/cvs-serv613

Modified Files:
	Species.pm 
Log Message:
Bugs 2197, 2092

Index: Species.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Species.pm,v
retrieving revision 1.47
retrieving revision 1.48
diff -C2 -d -r1.47 -r1.48
*** Species.pm	1 Dec 2006 18:51:46 -0000	1.47
--- Species.pm	30 Jan 2007 05:39:07 -0000	1.48
***************
*** 164,168 ****
          # (lineage may have subspecies, species, genus ...)
          my $name = $self->node_name;
!         if ($name && ($name ne $vals[0] && $name ne $vals[1]) && $name ne "$vals[1] $vals[0]") {
              if ($name =~ /^$vals[1] $vals[0]\s*(.+)/) {
                  # just assume the problem is someone tried to make a Bio::Species starting at subspecies
--- 164,168 ----
          # (lineage may have subspecies, species, genus ...)
          my $name = $self->node_name;
!         if ($name && ($name !~ m{$vals[0]} && $name !~ m{$vals[1]}) && $name !~ m{$vals[1] $vals[0]}) {
              if ($name =~ /^$vals[1] $vals[0]\s*(.+)/) {
                  # just assume the problem is someone tried to make a Bio::Species starting at subspecies
***************
*** 172,176 ****
              }
              else {
!                 $self->throw("The supplied lineage does not start near '$name' (I was supplied '".join(" | ", @vals)."')");
              }
          }
--- 172,176 ----
              }
              else {
!                 $self->warn("The supplied lineage does not start near '$name' (I was supplied '".join(" | ", @vals)."')");
              }
          }



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