diff variant_effect_predictor/Bio/TreeIO/tabtree.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/TreeIO/tabtree.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,153 @@
+# $Id: tabtree.pm,v 1.6 2002/10/22 07:45:25 lapp Exp $
+#
+# BioPerl module for Bio::TreeIO::tabtree
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::TreeIO::tabtree - A simple output format which displays a tree as an ASCII drawing
+
+=head1 SYNOPSIS
+
+  use Bio::TreeIO;
+  my $in = new Bio::TreeIO(-file => 'input', -format => 'newick');
+  my $out = new Bio::TreeIO(-file => '>output', -format => 'tabtree');
+
+  while( my $tree = $in->next_tree ) {
+      $out->write_tree($tree);
+  }
+
+=head1 DESCRIPTION
+
+This is a made up format just for outputting trees as an ASCII drawing.
+
+=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
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Jason Stajich
+
+Email [e-mail]
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails here
+
+=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::TreeIO::tabtree;
+use vars qw(@ISA);
+use strict;
+
+# Object preamble - inherits from Bio::Root::Root
+
+use Bio::TreeIO;
+
+
+@ISA = qw(Bio::TreeIO );
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::TreeIO::tabtree();
+ Function: Builds a new Bio::TreeIO::tabtree object 
+ Returns : Bio::TreeIO::tabtree
+ Args    :
+
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+
+  my $self = $class->SUPER::new(@args);
+
+}
+
+=head2 write_tree
+
+ Title   : write_tree
+ Usage   : $treeio->write_tree($tree);
+ Function: Write a tree out to data stream in newick/phylip format
+ Returns : none
+ Args    : Bio::Tree::TreeI object
+
+=cut
+
+sub write_tree{
+   my ($self,$tree) = @_;      
+   my @data = _write_tree_Helper($tree->get_root_node,0);
+   $self->_print(join("\n", @data), "\n");   
+   $self->flush if $self->_flush_on_write && defined $self->_fh;
+   return;
+}
+
+sub _write_tree_Helper {
+    my ($node,$depth) = @_;
+    return () if (!defined $node);
+
+    my @data;
+    my @d = $node->each_Descendent();
+
+    push @data,sprintf("%s%s","\t"x$depth,
+		       $node->to_string);
+    if( @d ) {
+	my $c = 0;
+	foreach my $n ( @d ) {
+	    push @data, _write_tree_Helper($n,$depth+1);
+	}
+    }
+
+    return @data;
+}
+
+=head2 next_tree
+
+ Title   : next_tree
+ Usage   : 
+ Function: Sorry not possible with this format
+ Returns : none
+ Args    : none
+
+
+=cut
+
+sub next_tree{
+    $_[0]->throw("Sorry the format 'tabtree' can only be used as an output format at this time");
+}
+
+1;