[Bioperl-guts-l] bioperl-live/Bio/Tools/Phylo PAML.pm,1.45,1.46

Christopher John Fields cjfields at dev.open-bio.org
Sat Aug 5 23:55:09 EDT 2006


Update of /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo
In directory dev.open-bio.org:/tmp/cvs-serv20553/Bio/Tools/Phylo

Modified Files:
	PAML.pm 
Log Message:
Bug 1883

Index: PAML.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/Phylo/PAML.pm,v
retrieving revision 1.45
retrieving revision 1.46
diff -C2 -d -r1.45 -r1.46
*** PAML.pm	4 Aug 2006 19:06:04 -0000	1.45
--- PAML.pm	6 Aug 2006 03:55:07 -0000	1.46
***************
*** 247,250 ****
--- 247,251 ----
      my $seqtype = $self->{'_summary'}->{'seqtype'};
      if ($seqtype eq 'CODONML' || $seqtype eq 'AAML') {
+         my $has_model_line = 0;
  	while (defined ($_ = $self->_readline)) {
  	    if ($seqtype eq 'CODONML' && 
***************
*** 261,268 ****
  		# %data = $self->_parse_PairwiseAA;
  		# last;	    
! 	    } elsif (m/^Model\s+(\d+)/ ) { 
  		$self->_pushback($_);
  		my $model = $self->_parse_NSsitesBatch;
  		push @{$data{'-NSsitesresults'}}, $model;
  	    } elsif ( m/for each branch/ ) {
  		my %branch_dnds = $self->_parse_branch_dnds;
--- 262,272 ----
  		# %data = $self->_parse_PairwiseAA;
  		# last;	    
! 	    } elsif (m/^Model\s+(\d+)/ ||
!                      ((!$has_model_line && m/^TREE/) &&
!                      $seqtype eq 'CODONML')) {
  		$self->_pushback($_);
  		my $model = $self->_parse_NSsitesBatch;
  		push @{$data{'-NSsitesresults'}}, $model;
+                 $has_model_line = 1;
  	    } elsif ( m/for each branch/ ) {
  		my %branch_dnds = $self->_parse_branch_dnds;
***************
*** 923,927 ****
  	next if /^\s+$/;
  	
! 	next unless( $okay || /^Model\s+\d+/ );
  	if( /^Model\s+(\d+)/ ) {
  	    if( $okay ) {
--- 927,931 ----
  	next if /^\s+$/;
  	
! 	next unless( $okay || /^Model\s+\d+/ || /^TREE/);
  	if( /^Model\s+(\d+)/ ) {
  	    if( $okay ) {



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