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1 # $Id: tabtree.pm,v 1.6 2002/10/22 07:45:25 lapp Exp $
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2 #
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3 # BioPerl module for Bio::TreeIO::tabtree
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::TreeIO::tabtree - A simple output format which displays a tree as an ASCII drawing
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::TreeIO;
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20 my $in = new Bio::TreeIO(-file => 'input', -format => 'newick');
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21 my $out = new Bio::TreeIO(-file => '>output', -format => 'tabtree');
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22
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23 while( my $tree = $in->next_tree ) {
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24 $out->write_tree($tree);
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25 }
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26
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27 =head1 DESCRIPTION
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28
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29 This is a made up format just for outputting trees as an ASCII drawing.
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30
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31 =head1 FEEDBACK
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32
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33 =head2 Mailing Lists
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34
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35 User feedback is an integral part of the evolution of this and other
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36 Bioperl modules. Send your comments and suggestions preferably to
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37 the Bioperl mailing list. Your participation is much appreciated.
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38
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39 bioperl-l@bioperl.org - General discussion
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40 http://bioperl.org/MailList.shtml - About the mailing lists
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41
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42 =head2 Reporting Bugs
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43
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44 Report bugs to the Bioperl bug tracking system to help us keep track
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45 of the bugs and their resolution. Bug reports can be submitted via
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46 email or the web:
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47
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48 bioperl-bugs@bioperl.org
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49 http://bugzilla.bioperl.org/
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50
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51 =head1 AUTHOR - Jason Stajich
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52
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53 Email jason@bioperl.org
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54
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55 Describe contact details here
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56
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57 =head1 CONTRIBUTORS
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58
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59 Additional contributors names and emails here
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60
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61 =head1 APPENDIX
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62
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63 The rest of the documentation details each of the object methods.
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64 Internal methods are usually preceded with a _
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65
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66 =cut
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67
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68
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69 # Let the code begin...
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70
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71
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72 package Bio::TreeIO::tabtree;
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73 use vars qw(@ISA);
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74 use strict;
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75
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76 # Object preamble - inherits from Bio::Root::Root
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77
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78 use Bio::TreeIO;
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79
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80
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81 @ISA = qw(Bio::TreeIO );
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82
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83 =head2 new
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84
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85 Title : new
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86 Usage : my $obj = new Bio::TreeIO::tabtree();
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87 Function: Builds a new Bio::TreeIO::tabtree object
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88 Returns : Bio::TreeIO::tabtree
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89 Args :
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90
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91
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92 =cut
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93
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94 sub new {
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95 my($class,@args) = @_;
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96
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97 my $self = $class->SUPER::new(@args);
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98
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99 }
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100
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101 =head2 write_tree
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102
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103 Title : write_tree
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104 Usage : $treeio->write_tree($tree);
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105 Function: Write a tree out to data stream in newick/phylip format
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106 Returns : none
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107 Args : Bio::Tree::TreeI object
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108
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109 =cut
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110
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111 sub write_tree{
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112 my ($self,$tree) = @_;
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113 my @data = _write_tree_Helper($tree->get_root_node,0);
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114 $self->_print(join("\n", @data), "\n");
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115 $self->flush if $self->_flush_on_write && defined $self->_fh;
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116 return;
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117 }
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118
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119 sub _write_tree_Helper {
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120 my ($node,$depth) = @_;
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121 return () if (!defined $node);
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122
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123 my @data;
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124 my @d = $node->each_Descendent();
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125
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126 push @data,sprintf("%s%s","\t"x$depth,
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127 $node->to_string);
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128 if( @d ) {
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129 my $c = 0;
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130 foreach my $n ( @d ) {
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131 push @data, _write_tree_Helper($n,$depth+1);
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132 }
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133 }
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134
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135 return @data;
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136 }
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137
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138 =head2 next_tree
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139
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140 Title : next_tree
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141 Usage :
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142 Function: Sorry not possible with this format
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143 Returns : none
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144 Args : none
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145
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146
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147 =cut
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148
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149 sub next_tree{
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150 $_[0]->throw("Sorry the format 'tabtree' can only be used as an output format at this time");
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151 }
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152
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153 1;
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