Topic/phylo orthologs1

lib/CXGN/Phylo/IdTaxonMap.pm

@@ -0,0 +1,70 @@
+package CXGN::Phylo::IdTaxonMap;
+
+use strict;
+use List::Util qw ( min max sum );
+
+my %default_map =
+  (
+   '^AT' => 'arabidopsis',
+   '^Bradi' => 'brachypodium',
+   '^(?:X_)?\d{5}[.]m\d{6}' => 'castorbean', # can have X_ prefix or not
+   '^GSVIV' => 'grape',
+   '^(?:GRMZM|AC\d{6})' => 'maize',
+   '^IMGA[|_](?:Medtr|AC|CU)' => 'medicago',
+   '^evm' => 'papaya',
+   '^POPTR' => 'poplar',
+   '^LOC_Os' => 'rice',
+   '^jgi_Selmo' => 'selaginella',
+   '^Sb' => 'sorghum',
+   '^Glyma' => 'soybean',
+   '^Solyc' => 'tomato'
+  );
+
+
+sub  new {
+  my $class = shift;
+  my $arg = shift; # hash ref, keys are regular expressions, values are corresponding taxon names.
+  my $args= {};
+  my $self = bless $args, $class;
+
+  my %map = ();
+  foreach (keys %default_map) {
+    $map{$_} = $default_map{$_};
+  }
+
+  foreach (keys %$arg) {
+    $map{$_} = $arg->{$_};
+  }
+
+  $self->{map} = \%map;
+  return $self;
+}
+
+sub get_map{
+  my $self = shift;
+  return $self->{map};
+}
+
+
+sub add_idregex_taxonname{
+  my $self = shift;
+  my $idregex = shift;
+  my $taxonname = shift;
+  $self->{map}->{$idregex} = $taxonname;
+}
+
+
+sub id_to_taxonname{
+  my $self = shift;
+  my $id = shift;
+
+  my $map = $self->get_map();
+  foreach (keys %$map) {
+#   print "id regex: $_\n";
+    return $map->{$_} if($id =~ /$_/);
+  }
+  warn "No taxon name found for id: $id\n";
+  return;
+}
+
+1;

lib/CXGN/Phylo/Layout.pm

@@ -357,8 +357,7 @@ sub _layout_vertical {
     my $total_leaves = $self->get_tree()->get_leaf_count();
     my $image_height = $self->get_image_height();
     if ($total_leaves < 1) { return; }
-    my $vertical_gap = ($image_height - $self->get_top_margin() - $self->get_bottom_margin()) / ($total_leaves);
-
+    my $vertical_gap = ($total_leaves > 1)?($image_height - $self->get_top_margin() - $self->get_bottom_margin()) / ($total_leaves-1): 0;
     # the leaf nodes should be easy.
     # traverse the tree, find all the leaves, and set the vertical
     # coordinate in the leaves to an increasing value with step $vertical_gap.