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1 # $Id: GOterm.pm,v 1.12.2.4 2003/07/03 00:41:40 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Ontology::GOterm
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4 #
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5 # Cared for by Christian M. Zmasek <czmasek@gnf.org> or <cmzmasek@yahoo.com>
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6 #
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7 # (c) Christian M. Zmasek, czmasek@gnf.org, 2002.
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8 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
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9 #
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10 # You may distribute this module under the same terms as perl itself.
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11 # Refer to the Perl Artistic License (see the license accompanying this
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12 # software package, or see http://www.perl.com/language/misc/Artistic.html)
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13 # for the terms under which you may use, modify, and redistribute this module.
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14 #
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15 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
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16 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
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17 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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18 #
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19 # You may distribute this module under the same terms as perl itself
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20
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21 # POD documentation - main docs before the code
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22
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23
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24 =head1 NAME
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25
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26 GOterm - representation of GO terms
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27
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28 =head1 SYNOPSIS
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29
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30 $term = Bio::Ontology::GOterm->new
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31 ( -go_id => "GO:0016847",
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32 -name => "1-aminocyclopropane-1-carboxylate synthase",
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33 -definition => "Catalysis of ...",
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34 -is_obsolete => 0,
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35 -comment => "" );
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36
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37 $term->add_definition_references( @refs );
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38 $term->add_secondary_GO_ids( @ids );
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39 $term->add_aliases( @aliases );
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40
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41 foreach my $dr ( $term->each_definition_reference() ) {
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42 print $dr, "\n";
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43 }
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44
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45 # etc.
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46
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47 =head1 DESCRIPTION
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48
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49 This is "dumb" class for GO terms (it provides no functionality related to graphs).
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50 Implements Bio::Ontology::TermI.
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51
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52 =head1 FEEDBACK
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53
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54 =head2 Mailing Lists
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55
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56 User feedback is an integral part of the evolution of this and other
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57 Bioperl modules. Send your comments and suggestions preferably to one
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58 of the Bioperl mailing lists. Your participation is much appreciated.
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59
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60 bioperl-l@bioperl.org - General discussion
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61 http://bio.perl.org/MailList.html - About the mailing lists
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62
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63 =head2 Reporting Bugs
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64
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65 Report bugs to the Bioperl bug tracking system to help us keep track
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66 the bugs and their resolution. Bug reports can be submitted via email
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67 or the web:
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68
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69 bioperl-bugs@bio.perl.org
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70 http://bugzilla.bioperl.org/
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71
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72 =head1 AUTHOR
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73
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74 Christian M. Zmasek
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75
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76 Email: czmasek@gnf.org or cmzmasek@yahoo.com
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77
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78 WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
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79
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80 Address:
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81
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82 Genomics Institute of the Novartis Research Foundation
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83 10675 John Jay Hopkins Drive
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84 San Diego, CA 92121
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85
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86 =head1 APPENDIX
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87
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88 The rest of the documentation details each of the object
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89 methods.
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90
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91 =cut
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92
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93
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94 # Let the code begin...
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95
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96 package Bio::Ontology::GOterm;
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97 use vars qw( @ISA );
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98 use strict;
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99 use Bio::Ontology::Term;
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100
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101 use constant GOID_DEFAULT => "GO:0000000";
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102 use constant TRUE => 1;
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103 use constant FALSE => 0;
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104
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105 @ISA = qw( Bio::Ontology::Term );
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106
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107
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108
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109
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110 =head2 new
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111
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112 Title : new
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113 Usage : $term = Bio::Ontology::GOterm->new( -go_id => "GO:0016847",
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114 -name => "1-aminocyclopropane-1-carboxylate synthase",
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115 -definition => "Catalysis of ...",
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116 -is_obsolete => 0,
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117 -comment => "" );
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118 Function: Creates a new Bio::Ontology::GOterm.
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119 Returns : A new Bio::Ontology::GOterm object.
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120 Args : -go_id => the goid of this GO term [GO:nnnnnnn]
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121 or [nnnnnnn] (nnnnnnn is a zero-padded
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122 integer of seven digits)
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123 -name => the name of this GO term [scalar]
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124 -definition => the definition of this GO term [scalar]
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125 -ontology => the ontology for this term (a
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126 Bio::Ontology::OntologyI compliant object)
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127 -version => version information [scalar]
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128 -is_obsolete => the obsoleteness of this GO term [0 or 1]
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129 -comment => a comment [scalar]
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130
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131 =cut
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132
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133 sub new {
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134
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135 my( $class,@args ) = @_;
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136
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137 my $self = $class->SUPER::new( @args );
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138
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139 my ( $GO_id )
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140 = $self->_rearrange( [ qw( GO_ID ) ], @args );
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141
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142 $GO_id && $self->GO_id( $GO_id );
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143
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144
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145 return $self;
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146
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147 } # new
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148
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149
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150 =head2 init
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151
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152 Title : init()
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153 Usage : $term->init();
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154 Function: Initializes this GOterm to all "" and empty lists.
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155 Returns :
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156 Args :
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157
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158 =cut
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159
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160 sub init {
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161
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162 my $self = shift;
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163
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164 # first call the inherited version to properly chain up the hierarchy
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165 $self->SUPER::init(@_);
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166
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167 # then only initialize what we implement ourselves here
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168 #$self->GO_id( GOID_DEFAULT );
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169
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170 } # init
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171
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172
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173
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174
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175 =head2 GO_id
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176
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177 Title : GO_id
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178 Usage : $term->GO_id( "GO:0003947" );
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179 or
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180 print $term->GO_id();
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181 Function: Set/get for the goid of this GO term.
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182
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183 This is essentially an alias to identifier(), with added
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184 format checking.
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185
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186 Returns : The goid [GO:nnnnnnn].
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187 Args : The goid [GO:nnnnnnn] or [nnnnnnn] (nnnnnnn is a
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188 zero-padded integer of seven digits) (optional).
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189
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190 =cut
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191
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192 sub GO_id {
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193 my $self = shift;
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194 my $value;
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195
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196 if ( @_ ) {
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197 $value = $self->_check_go_id( shift );
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198 unshift(@_, $value);
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199 }
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200
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201 return $self->identifier( @_ );
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202
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203 } # GO_id
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204
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205
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206 =head2 get_secondary_GO_ids
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207
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208 Title : get_secondary_GO_ids
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209 Usage : @ids = $term->get_secondary_GO_ids();
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210 Function: Returns a list of secondary goids of this Term.
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211
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212 This is aliased to remove_secondary_ids().
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213
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214 Returns : A list of secondary goids [array of [GO:nnnnnnn]]
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215 (nnnnnnn is a zero-padded integer of seven digits).
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216 Args :
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217
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218 =cut
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219
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220 sub get_secondary_GO_ids {
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221 return shift->get_secondary_ids(@_);
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222 } # get_secondary_GO_ids
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223
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224
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225 =head2 add_secondary_GO_id
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226
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227 Title : add_secondary_GO_id
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228 Usage : $term->add_secondary_GO_id( @ids );
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229 or
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230 $term->add_secondary_GO_id( $id );
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231 Function: Pushes one or more secondary goids into
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232 the list of secondary goids.
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233
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234 This is aliased to remove_secondary_ids().
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235
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236 Returns :
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237 Args : One secondary goid [GO:nnnnnnn or nnnnnnn] or a list
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238 of secondary goids [array of [GO:nnnnnnn or nnnnnnn]]
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239 (nnnnnnn is a zero-padded integer of seven digits).
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240
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241 =cut
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242
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243 sub add_secondary_GO_id {
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244 return shift->add_secondary_id(@_);
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245 } # add_secondary_GO_id
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246
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247
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248 =head2 remove_secondary_GO_ids
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249
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250 Title : remove_secondary_GO_ids()
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251 Usage : $term->remove_secondary_GO_ids();
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252 Function: Deletes (and returns) the secondary goids of this Term.
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253
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254 This is aliased to remove_secondary_ids().
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255
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256 Returns : A list of secondary goids [array of [GO:nnnnnnn]]
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257 (nnnnnnn is a zero-padded integer of seven digits).
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258 Args :
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259
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260 =cut
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261
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262 sub remove_secondary_GO_ids {
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263 return shift->remove_secondary_ids(@_);
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264 } # remove_secondary_GO_ids
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265
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266
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267
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268
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269 =head2 to_string
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270
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271 Title : to_string()
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272 Usage : print $term->to_string();
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273 Function: to_string method for GO terms.
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274 Returns : A string representation of this GOterm.
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275 Args :
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276
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277 =cut
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278
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279 sub to_string {
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280 my( $self ) = @_;
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281
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282 my $s = "";
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283
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284 $s .= "-- GO id:\n";
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285 $s .= ($self->GO_id() || '')."\n";
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286 $s .= "-- Name:\n";
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287 $s .= ($self->name() || '') ."\n";
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288 $s .= "-- Definition:\n";
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289 $s .= ($self->definition() || '') ."\n";
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290 $s .= "-- Category:\n";
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291 if ( defined( $self->ontology() ) ) {
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292 $s .= $self->ontology()->name()."\n";
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293 }
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294 else {
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295 $s .= "\n";
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296 }
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297 $s .= "-- Version:\n";
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298 $s .= ($self->version() || '') ."\n";
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299 $s .= "-- Is obsolete:\n";
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300 $s .= $self->is_obsolete()."\n";
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301 $s .= "-- Comment:\n";
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302 $s .= ($self->comment() || '') ."\n";
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303 $s .= "-- Definition references:\n";
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304 $s .= $self->_array_to_string( $self->get_dblinks() )."\n";
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305 $s .= "-- Secondary GO ids:\n";
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306 $s .= $self->_array_to_string( $self->get_secondary_GO_ids() )."\n";
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307 $s .= "-- Aliases:\n";
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308 $s .= $self->_array_to_string( $self->get_synonyms() );
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309
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310 return $s;
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311
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312 } # to_string
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313
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314
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315
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316
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317 # Title : _check_go_id
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318 # Function: Checks whether the argument is [GO:nnnnnnn].
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319 # If "GO:" is not present, it adds it.
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320 # Returns : The canonical GO id.
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321 # Args : The value to be checked.
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322 sub _check_go_id {
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323 my ( $self, $value ) = @_;
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324 unless ( $value =~ /^(GO:)?\d{7}$/ || $value eq GOID_DEFAULT ) {
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325 $self->throw( "Found [" . $value
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326 . "] where [GO:nnnnnnn] or [nnnnnnn] expected" );
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327 }
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328 unless ( $value =~ /^GO:/ ) {
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329 $value = "GO:".$value;
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330 }
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331 return $value;
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332 } # _check_go_id
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333
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334
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335
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336 # Title : _array_to_string
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337 # Function:
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338 # Returns :
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339 # Args :
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340 sub _array_to_string {
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341 my( $self, @value ) = @_;
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342
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343 my $s = "";
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344
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345 for ( my $i = 0; $i < scalar( @value ); ++$i ) {
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346 if ( ! ref( $value[ $i ] ) ) {
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347 $s .= "#" . $i . "\n-- " . $value[ $i ] . "\n";
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348 }
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349 }
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350
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351 return $s;
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352
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353 } # _array_to_string
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354
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355 #################################################################
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356 # aliases or forwards to maintain backward compatibility
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357 #################################################################
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358
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359 *each_secondary_GO_id = \&get_secondary_GO_ids;
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360 *add_secondary_GO_ids = \&add_secondary_GO_id;
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361
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362 1;
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