[Bio] / FigKernelPackages / proml.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/proml.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.2, Sat Jan 13 03:22:44 2007 UTC revision 1.4, Sat Jan 13 17:15:28 2007 UTC
# Line 427  Line 427 
427      #  Returned trees have our labels, and branch lengths that are in % change,      #  Returned trees have our labels, and branch lengths that are in % change,
428      #  not the more usual expected number per position:      #  not the more usual expected number per position:
429    
430      my @trees = map { gjonewicklib::newick_rescale_branches( $_, 0.01 );      my @trees = map { gjonewicklib::newick_relabel_nodes( $_, \%id ) } @trees;
                       gjonewicklib::newick_relabel_nodes( $_, \%id )  
                     }  
                 @trees;  
431    
432      if ( $tree_format =~ m/overbeek/i )      if ( $tree_format =~ m/overbeek/i )
433      {      {
# Line 478  Line 475 
475    
476      my $kmin = 1 / ( gjonewicklib::newick_tree_length( $tree ) || 1 );      my $kmin = 1 / ( gjonewicklib::newick_tree_length( $tree ) || 1 );
477    
478      print STDERR "Length = ", gjonewicklib::newick_tree_length( $tree ), "; kmin = $kmin\n"; ## DEBUG ##  #   print STDERR "Length = ", gjonewicklib::newick_tree_length( $tree ), "; kmin = $kmin\n"; ## DEBUG ##
479    
480      #  Generate "rate variation" by rescaling the supplied tree.  We could use a      #  Generate "rate variation" by rescaling the supplied tree.  We could use a
481      #  finer grain estimator, then categorize the inferred values.  This might      #  finer grain estimator, then categorize the inferred values.  This might
# Line 535  Line 532 
532                             map  { [ $_, @{ shift @results }[1] ] }  # get the likelihoods                             map  { [ $_, @{ shift @results }[1] ] }  # get the likelihoods
533                             @cat_vals;                             @cat_vals;
534    
535              printf STDERR "%6d  %2d => %12.4f\n", $i+1, @$best; ## DEBUG ##  #           printf STDERR "%6d  %2d => %12.4f\n", $i+1, @$best; ## DEBUG ##
536              push @categories, $best->[0];              push @categories, $best->[0];
537              push @weights,    1;              push @weights,    1;
538          }          }

Legend:
Removed from v.1.2  
changed lines
  Added in v.1.4

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3