lib/CXGN/Phylo/OrganismTree.pm

   1 =head1 NAME
   2
   3 CXGN::Phylo::OrgnanismTree - an object to handle SGN organism  trees
   4
   5 =head1 USAGE
   6
   7  my $tree = CXGN::Phylo::OrganismTree->new();
   8  my $root = $tree->get_root();
   9  my $node = $root->add_child();
  10  $node->set_name("I'm a child node");
  11  $node->set_link("http://solgenomics.net/");
  12  my $child_node = $node->add_child();
  13  $child_node->set_name("I'm a grand-child node");
  14  print $tree->generate_newick();
  15
  16 =head1 DESCRIPTION
  17
  18 This is a subcass of L<CXGN::Phylo::Tree>
  19
  20
  21
  22 =head1 AUTHORS
  23
  24  Naama Menda (nm249@cornell.edu)
  25
  26
  27 =cut
  28
  29 use strict;
  30
  31
  32 #use CXGN::Page;
  33 #use CXGN::Page::FormattingHelpers qw/tooltipped_text/;
  34 use CXGN::DB::DBICFactory;
  35 use CXGN::Chado::Organism;
  36 use CXGN::Tools::WebImageCache;
  37 use CXGN::Phylo::Node;
  38
  39 package CXGN::Phylo::OrganismTree;
  40
  41 use base qw / CXGN::Phylo::Tree / ;
  42
  43 =head2 function new()
  44
  45   Synopsis:     my $t = CXGN::Phylo::OrganismTree->new($schema)
  46   Arguments:    $schema object
  47   Returns:      an instance of a Tree object.
  48   Side effects: creates the object and initializes some parameters.
  49   Description:
  50
  51 =cut
  52
  53 sub new {
  54     my $class = shift;
  55     my $schema = shift || die "NO SCHEMA OBJECT PROVIDED!!\n";
  56
  57     my $self = $class->SUPER::new();
  58
  59     $self->set_schema($schema);
  60
  61     return $self;
  62 }
  63
  64
  65
  66 #######
  67
  68
  69 =head2 recursive_children
  70
  71  Usage: $self->recursive_children($nodes_hashref, $organism, $node, $is_root)
  72  Desc:  recursively add child nodes starting from root.
  73  Ret:   nothing
  74  Args:  $nodes_hashref (organism_id => CXGN::Chado::Organism), $organism object for your root, $node object for your root, 1 (boolean)
  75  Side Effects: sets name, label, link, tooltip for nodes, highlites leaf nodes.
  76  Example:
  77
  78 =cut
  79
  80
  81 sub recursive_children {
  82     my $self=shift;
  83     my $nodes=shift;
  84     my $o= shift; #CXGN::Chado::Organism object
  85     my $n = shift; # CXGN::Phylo::Node object
  86  my $species_cache=shift;
  87  my $is_root=shift;
  88
  89     $n->set_name($o->get_species());
  90     my $orgkey ="".$o->get_organism_id()."";
  91     $n->get_label()->set_link("/chado/organism.pl?organism_id=" . $o->get_organism_id());
  92     my $content=$species_cache->get($orgkey);
  93     $content=~ s/\?/<br\/>/g;
  94     $n->set_tooltip($n->get_name());
  95     $n->set_onmouseover("javascript:showPopUp('popup','".$content."','<b>".$o->get_species()."</b>')");
  96     $n->set_onmouseout("javascript:hidePopUp('popup');");
  97     $n->get_label()->set_name(" ".$o->get_species());
  98     $n->get_label()->set_onmouseover("javascript:showPopUp('popup','".$content."','<b>".$o->get_species()."</b>')");
  99     $n->get_label()->set_onmouseout("javascript:hidePopUp('popup');");
 100     $n->set_species($n->get_name());
 101     $n->set_hide_label(0);
 102     $n->get_label()->set_hidden(0);
 103
 104     my @cl=$n->get_children();
 105
 106
 107     my @children = $o->get_direct_children;
 108     foreach my $child (@children) {
 109
 110         if ( exists( $nodes->{$child->get_organism_id() } ) && defined( $nodes->{$child->get_organism_id()} ) ) {
 111
 112             my $new_node=$n->add_child();
 113             $self->recursive_children($nodes, $child, $new_node,$species_cache);
 114         }
 115     }
 116     if ($n->is_leaf()  ) { $n->set_hilited(1) ; }
 117 }
 118
 119
 120 =head2 find_recursive_parent
 121
 122  Usage: $self->find_recursive_parent($organism, $nodes_hashref)
 123  Desc:  populate $nodes_hashref  (organism_id=> CXGN::Chado::organism) with recursive parent organisms
 124  Ret:   $nodes_hashref
 125  Args:  $organism object, $nodes_hashref
 126  Side Effects: none
 127  Example:
 128
 129 =cut
 130
 131
 132
 133 sub find_recursive_parent {
 134     my $self=shift;
 135     my $organism=shift ;
 136     my $nodes= shift; # hash ref
 137
 138     my $parent = $organism->get_parent;
 139     if ($parent) {
 140         my $id = $parent->get_organism_id();
 141
 142         if (!$nodes->{$id} ) {
 143             $nodes->{$id} = $parent ;
 144             $self->find_recursive_parent($parent, $nodes);
 145         }
 146     }
 147     else { return; }
 148     return $nodes;
 149 }
 150
 151
 152 =head2 build_tree
 153
 154  Usage:  $self->build_tree($root_species_name, $species_hashref,$speciesinfo_cache)
 155  Desc:   builds an organism tree starting from $root with a list of species
 156  Ret:    a newick representation of the tree
 157  Args:   $root_species_name, $species_hashref
 158  Side Effects:  sets tree nodes names and lables, and renders the tree  (see L<CXGN::Phylo::Renderer> )
 159                 calls $tree->generate_newick($root_node, 1)
 160  Example:
 161
 162 =cut
 163
 164 sub build_tree  {
 165
 166     my $self=shift;
 167     my $root= shift; #'Solanaceae';
 168
 169     my $species_hash=  shift;
 170     my $species_cache= shift;
 171
 172     my $schema = $self->get_schema();
 173     my $root_o = CXGN::Chado::Organism->new_with_species($schema, $root);
 174     my $root_o_id = $root_o->get_organism_id();
 175     my $organism_link =   "/chado/organism.pl?organism_id=";
 176
 177     my $nodes=();
 178
 179
 180     my $root_node = $self->get_root();#CXGN::Phylo::Node->new();
 181
 182
 183     foreach my $s (keys %$species_hash ) {
 184
 185         my $o =  CXGN::Chado::Organism->new_with_species($schema, $s);
 186         if ($o) {
 187             my $organism_id = $o->get_organism_id();
 188             #if ($organism_id != $species_hash->{$s} ) {
 189         #
 190         #    }
 191             $nodes->{$organism_id}=$o;
 192             $nodes = $self->find_recursive_parent($o, $nodes);
 193         } else {
 194             $self->d( "NO ORGANISM FOUND FOR SPECIES $s  !!!!!!!!!!!\n\n");
 195         }
 196     }
 197
 198     $self->recursive_children( $nodes,  $nodes->{$root_o_id}, $root_node , $species_cache,1) ;
 199
 200     $self->set_show_labels(1);
 201
 202
 203     $root_node->set_name($root_o->get_species());
 204     $root_node->set_link($organism_link . $root_o_id);
 205     $self->set_root($root_node);
 206
 207     $self->d( "FOUND organism " . $nodes->{$root_o_id} . " root node: " .  $root_node->get_name() . "\n\n");
 208
 209     my $newick= $self->generate_newick($root_node, 1);
 210
 211
 212     $self->standard_layout();
 213
 214     my $renderer = CXGN::Phylo::PNG_tree_renderer->new($self);
 215
 216     my $leaf_count= $self->get_leaf_count();
 217     my $image_height =   $leaf_count*20  > 120  ? $leaf_count*20  : 120 ;
 218
 219     $self->get_layout->set_image_height($image_height);
 220     $self->get_layout->set_image_width(800);
 221     $self->get_layout->set_top_margin(20);
 222     $self->set_renderer($renderer);
 223     #$tree->get_layout->layout();
 224     $self->get_renderer->render();
 225
 226     return $newick;
 227 }
 228
 229
 230
 231
 232 ##########
 233 return 1##
 234 ##########