[Bioperl-guts-l] bioperl commit

[Jason Stajich]

Tue Feb  4 13:36:37 EST 2003
Update of /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo
In directory dev:/tmp/cvs-serv26157/Bio/Tools/Phylo

Modified Files:
	PAML.pm 
Log Message:
deal with slightly different format and the NOTE: information
bioperl-live/Bio/Tools/Phylo PAML.pm,1.11,1.12
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo/PAML.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /tmp/T0xgayhZ	2003-02-04 13:36:37.660011081 -0500
+++ /tmp/T1ygayhZ	2003-02-04 13:36:37.670010286 -0500
@@ -518,11 +518,12 @@
     }
     my $seqct = 0;
     my @seqs;
-    while( defined ($_ = $self->_readline ) ) {
+    while( defined ($_ = $self->_readline ) ) {	
 	last if( /^\s+$/ && exists $self->{'_summary'}->{'ngmatrix'} );
-	next if( /^\s+$/ );
+	next if( /^\s+$/ || /^NOTE:/i );
 	chomp;
 	my ($seq,$rest) = split(/\s+/,$_,2);
+	$rest = '' unless defined $rest; # get rid of empty messages
 	my $j = 0;
 	if( $self->{'_summary'}->{'seqtype'} eq 'YN00') {
 	    push @seqs, Bio::PrimarySeq->new(-display_id => $seq);