Bio/TreeIO/tabtree.pm

   1 #
   2 # BioPerl module for Bio::TreeIO::tabtree
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Jason Stajich <jason@bioperl.org>
   7 #
   8 # Copyright Jason Stajich
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::TreeIO::tabtree - A simple output format which displays a tree as an ASCII drawing
  17
  18 =head1 SYNOPSIS
  19
  20   use Bio::TreeIO;
  21   my $in = Bio::TreeIO->new(-file => 'input', -format => 'newick');
  22   my $out = Bio::TreeIO->new(-file => '>output', -format => 'tabtree');
  23
  24   while( my $tree = $in->next_tree ) {
  25       $out->write_tree($tree);
  26   }
  27
  28 =head1 DESCRIPTION
  29
  30 This is a made up format just for outputting trees as an ASCII drawing.
  31
  32 =head1 FEEDBACK
  33
  34 =head2 Mailing Lists
  35
  36 User feedback is an integral part of the evolution of this and other
  37 Bioperl modules. Send your comments and suggestions preferably to
  38 the Bioperl mailing list.  Your participation is much appreciated.
  39
  40   bioperl-l@bioperl.org                  - General discussion
  41   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  42
  43 =head2 Support
  44
  45 Please direct usage questions or support issues to the mailing list:
  46
  47 I<bioperl-l@bioperl.org>
  48
  49 rather than to the module maintainer directly. Many experienced and
  50 reponsive experts will be able look at the problem and quickly
  51 address it. Please include a thorough description of the problem
  52 with code and data examples if at all possible.
  53
  54 =head2 Reporting Bugs
  55
  56 Report bugs to the Bioperl bug tracking system to help us keep track
  57 of the bugs and their resolution. Bug reports can be submitted via the
  58 web:
  59
  60   https://github.com/bioperl/bioperl-live/issues
  61
  62 =head1 AUTHOR - Jason Stajich
  63
  64 Email jason@bioperl.org
  65
  66 =head1 APPENDIX
  67
  68 The rest of the documentation details each of the object methods.
  69 Internal methods are usually preceded with a _
  70
  71 =cut
  72
  73
  74 # Let the code begin...
  75
  76
  77 package Bio::TreeIO::tabtree;
  78 use strict;
  79
  80 # Object preamble - inherits from Bio::Root::Root
  81
  82
  83
  84 use base qw(Bio::TreeIO);
  85
  86 =head2 new
  87
  88  Title   : new
  89  Usage   : my $obj = Bio::TreeIO::tabtree->new();
  90  Function: Builds a new Bio::TreeIO::tabtree object
  91  Returns : Bio::TreeIO::tabtree
  92  Args    :
  93
  94
  95 =cut
  96
  97 sub new {
  98   my($class,@args) = @_;
  99
 100   my $self = $class->SUPER::new(@args);
 101
 102 }
 103
 104 =head2 write_tree
 105
 106  Title   : write_tree
 107  Usage   : $treeio->write_tree($tree);
 108  Function: Write a tree out to data stream in newick/phylip format
 109  Returns : none
 110  Args    : Bio::Tree::TreeI object
 111
 112 =cut
 113
 114 sub write_tree{
 115    my ($self,$tree) = @_;
 116    my $line = _write_tree_Helper($tree->get_root_node,"");
 117    $self->_print($line. "\n");
 118    $self->flush if $self->_flush_on_write && defined $self->_fh;
 119    return;
 120 }
 121
 122 sub _write_tree_Helper {
 123     my ($node,$indent) = @_;
 124     return unless defined $node;
 125
 126     my @d = $node->each_Descendent();
 127     my $line = "";
 128     my ($i,$lastchild) = (0,scalar @d - 1);
 129     for my $n ( @d ) {
 130         if( $n->is_Leaf ) {
 131             $line .= sprintf("%s| \n%s\\-%s\n",
 132                              $indent,$indent,$n->id || '');
 133         } else {
 134             $line .= sprintf("$indent|  %s\n",( $n->id ?
 135                                                sprintf("(%s)",$n->id) : ''));
 136         }
 137         my $new_indent = $indent . (($i == $lastchild) ? "| " : "  ");
 138         if( $n != $node ) {
 139             # avoid the unlikely case of cycles
 140             $line .= _write_tree_Helper($n,$new_indent);
 141         }
 142     }
 143     return $line;
 144 }
 145
 146 =head2 next_tree
 147
 148  Title   : next_tree
 149  Usage   :
 150  Function: Sorry not possible with this format
 151  Returns : none
 152  Args    : none
 153
 154
 155 =cut
 156
 157 sub next_tree{
 158     $_[0]->throw("Sorry the format 'tabtree' can only be used as an output format at this time");
 159 }
 160
 161 1;