diff variant_effect_predictor/Bio/Tree/NodeNHX.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tree/NodeNHX.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,171 @@
+# $Id: NodeNHX.pm,v 1.5.2.1 2003/09/14 19:00:35 jason Exp $
+#
+# BioPerl module for Bio::Tree::NodeNHX
+#
+# Cared for by Aaron Mackey <[e-mail]>
+#
+# Copyright Aaron Mackey
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags
+
+=head1 SYNOPSIS
+
+    use Bio::Tree::NodeNHX;
+    my $nodeA = new Bio::Tree::NodeNHX();
+    my $nodeL = new Bio::Tree::NodeNHX();
+    my $nodeR = new Bio::Tree::NodeNHX();
+
+    my $node = new Bio::Tree::NodeNHX();
+    $node->add_Descendents($nodeL);
+    $node->add_Descendents($nodeR);
+
+    print "node is not a leaf \n" if( $node->is_leaf);
+
+=head1 DESCRIPTION
+
+Makes a Tree Node with NHX tags, suitable for building a Tree.  See
+L<Bio::Tree::Node> for a full list of functionality.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list.  Your participation is much appreciated.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+the web:
+
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Aaron Mackey
+
+Email [e-mail]
+
+=head1 CONTRIBUTORS
+
+The NHX (New Hampshire eXtended) format was created by Chris Zmasek,
+and is described at:
+
+  http://www.genetics.wustl.edu/eddy/forester/NHX.html
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+package Bio::Tree::NodeNHX;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Tree::Node;
+
+@ISA = qw(Bio::Tree::Node);
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Tree::NodeNHX();
+ Function: Builds a new Bio::Tree::NodeNHX object
+ Returns : Bio::Tree::NodeNHX
+ Args    : -left          => pointer to Left descendent (optional)
+           -right         => pointer to Right descenent (optional)
+	   -branch_length => branch length [integer] (optional)
+           -bootstrap     => value   bootstrap value (string)
+           -description   => description of node
+           -id            => unique id for node
+           -nhx           => hashref of NHX tags and values
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+
+  my $self = $class->SUPER::new(@args);
+  my ($nhx) = $self->_rearrange([qw(NHX)], @args);
+  $self->nhx_tag($nhx);
+  return $self;
+}
+
+sub DESTROY {
+    my ($self) = @_;
+    # try to insure that everything is cleaned up
+    $self->SUPER::DESTROY();
+    if( defined $self->{'_desc'} &&
+	ref($self->{'_desc'}) =~ /ARRAY/i ) {
+	while( my ($nodeid,$node) = each %{ $self->{'_desc'} } ) {
+	    $node->{'_ancestor'} = undef; # insure no circular references
+	    $node->DESTROY();
+	    $node = undef;
+	}
+	$self->{'_desc'} = {};
+    }
+}
+
+sub to_string{
+   my ($self) = @_;
+   return sprintf("%s%s%s",
+		  defined $self->id ? $self->id : '',
+		  defined $self->branch_length ? ':' . 
+		  $self->branch_length : ' ',
+		  '[' . join(":", "&&NHX", 
+			     map { "$_=" .join(',',
+					       $self->get_tag_values($_))}
+		 $self->get_all_tags() ) . ']'
+		  );
+}
+
+=head2 nhx_tag
+
+ Title   : nhx_tag
+ Usage   : my $tag = $nodenhx->nhx_tag(%tags);
+ Function: Set tag-value pairs for NHX nodes
+ Returns : none
+ Args    : hashref to update the tags/value pairs
+           OR 
+           with a scalar value update the bootstrap value by default
+
+
+=cut
+
+sub nhx_tag {
+    my ($self, $tags) = @_;
+    if (defined $tags && (ref($tags) =~ /HASH/i)) {
+	while( my ($tag,$val) = each %$tags ) {
+	    if( ref($val) =~ /ARRAY/i ) {
+		for my $v ( @$val ) {
+		    $self->add_tag_value($tag,$v);
+		}
+	    } else {
+		$self->add_tag_value($tag,$val);
+	    }
+	}
+	if (exists $tags->{'B'}) {
+	    $self->bootstrap($tags->{'B'});
+	}
+    } elsif (defined $tags and ! ref ($tags)) {
+	print STDERR "here with $tags\n";
+        # bootstrap by default
+	$self->bootstrap($tags);
+    }
+}
+
+1;