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revision 1.436, Sun Feb 5 01:08:16 2006 UTC revision 1.437, Thu Feb 9 19:34:26 2006 UTC
# Line 11338  Line 11338 
11338             @fids;             @fids;
11339  }  }
11340    
11341    
11342    # RAE. Sometimes we want to do the building tree for all genomes, not just complete ones.
11343    # Therefore, I broke this into two sections, one that should retain all the function of
11344    # build_tree_of_complete and the other that does the calculation
11345    
11346    
11347  sub build_tree_of_complete {  sub build_tree_of_complete {
11348      my($self,$min_for_label) = @_;      my($self,$min_for_label) = @_;
11349        return $self->buld_tee_of_all($min_for_label, "complete");
11350    }
11351    
11352    sub build_tree_of_all {
11353        my($self, $min_for_label, $complete)=@_;
11354      my(@last,@tax,$i,$prefix,$lev,$genome,$tax);      my(@last,@tax,$i,$prefix,$lev,$genome,$tax);
11355    
11356      $min_for_label = $min_for_label ? $min_for_label : 10;      $min_for_label = $min_for_label ? $min_for_label : 10;
# Line 11349  Line 11360 
11360      @last = ();      @last = ();
11361    
11362    
11363      foreach $genome (grep { $_ !~ /^99999/ } $self->sort_genomes_by_taxonomy($self->genomes("complete")))      foreach $genome (grep { $_ !~ /^99999/ } $self->sort_genomes_by_taxonomy($self->genomes($complete)))
11364      {      {
11365          $tax = $self->taxonomy_of($genome);          $tax = $self->taxonomy_of($genome);
11366          @tax = split(/\s*;\s*/,$tax);          @tax = split(/\s*;\s*/,$tax);
# Line 11397  Line 11408 
11408      }      }
11409  }  }
11410    
11411    sub taxonomic_groups_of_all {
11412        my($self,$min_for_labels) = @_;
11413    
11414        my($tree,undef) = $self->build_tree_of_all($min_for_labels);
11415        return &taxonomic_groups($tree);
11416    }
11417    
11418  sub taxonomic_groups_of_complete {  sub taxonomic_groups_of_complete {
11419      my($self,$min_for_labels) = @_;      my($self,$min_for_labels) = @_;
11420    

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