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revision 1.22, Fri Jun 29 16:22:37 2007 UTC revision 1.23, Fri Jun 29 16:31:35 2007 UTC
# Line 1774  Line 1774 
1774  }  }
1775    
1776  sub display {  sub display {
1777      my ($self,$gd, $fid, $gd_window_size) = @_;      my ($self,$gd, $fid, $gd_window_size, $compare_or_coupling) = @_;
1778    
1779      my $fig = new FIG;      my $fig = new FIG;
1780      my $all_regions = [];      my $all_regions = [];
# Line 1818  Line 1818 
1818      my %all_genes;      my %all_genes;
1819      my %all_genomes;      my %all_genomes;
1820      foreach my $feature (@$target_gene_features){ $all_genes{$feature} = 1;}      foreach my $feature (@$target_gene_features){ $all_genes{$feature} = 1;}
     my $compare_regions_flag = 1; # set it for compare regions view (0 -> no view, 1-> yes view)  
     my $functional_coupling_flag = 0; # set functional coupling for view (0 -> no view, 1-> yes view)  
1821    
1822      if ($functional_coupling_flag == 1)      if ($compare_or_coupling == 0)
1823      {      {
1824          my @coup = grep { $_->[1]} $fig->coupling_and_evidence($fid,5000,1e-10,4,1);          my @coup = grep { $_->[1]} $fig->coupling_and_evidence($fid,5000,1e-10,4,1);
1825    
# Line 1864  Line 1862 
1862          }          }
1863      }      }
1864    
1865      if ($compare_regions_flag)      elsif ($compare_or_coupling == 1)
1866      {      {
1867          # make a hash of genomes that are phylogenetically close          # make a hash of genomes that are phylogenetically close
1868          #my $close_threshold = ".26";          #my $close_threshold = ".26";

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