[Bioperl-guts-l] bioperl-live/Bio/TreeIO nexus.pm,1.16,1.17

Christopher John Fields cjfields at dev.open-bio.org
Tue Mar 6 22:46:58 EST 2007


Update of /home/repository/bioperl/bioperl-live/Bio/TreeIO
In directory dev.open-bio.org:/tmp/cvs-serv11298/Bio/TreeIO

Modified Files:
	nexus.pm 
Log Message:
bug 2205

Index: nexus.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/TreeIO/nexus.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** nexus.pm	6 Mar 2007 21:56:36 -0000	1.16
--- nexus.pm	7 Mar 2007 03:46:56 -0000	1.17
***************
*** 152,157 ****
                  my $trans = $1;
                  for my $n ( split( /\s*,\s*/, $trans ) ) {
!                     my ( $id, $tag ) = split( /\s+/, $n );
!                     $translate{$id} = $tag;
                  }
              }
--- 152,160 ----
                  my $trans = $1;
                  for my $n ( split( /\s*,\s*/, $trans ) ) {
!                     if ($n  =~ /^\s*(\S+)\s+(.+)$/) {
!                         my ($id,$tag) = ($1,$2);
!                         $tag =~ s/\s+$//;  # remove the extra spaces of the last taxon
!                         $translate{$id} = $tag;
!                     }
                  }
              }
***************
*** 160,164 ****
              }
              while (
!                 $trees =~ /\s+tree\s+(\S+)\s*\=
               \s*(?:\[\S+\])?\s*([^\;]+;)\s*/igx
                )
--- 163,167 ----
              }
              while (
!                 $trees =~ /\s+tree\s+\*?\s*(\S+)\s*\=
               \s*(?:\[\S+\])?\s*([^\;]+;)\s*/igx
                )



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