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1 # $Id: InterProTerm.pm,v 1.4.2.2 2003/03/25 12:32:16 heikki Exp $
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2 #
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3 # BioPerl module for Bio::Ontology::InterProTerm
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4 #
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5 # Cared for by Peter Dimitrov <dimitrov@gnf.org>
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6 #
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7 # Copyright Peter Dimitrov
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8 # (c) Peter Dimitrov, dimitrov@gnf.org, 2002.
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9 # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
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10 #
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11 # You may distribute this module under the same terms as perl itself.
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12 # Refer to the Perl Artistic License (see the license accompanying this
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13 # software package, or see http://www.perl.com/language/misc/Artistic.html)
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14 # for the terms under which you may use, modify, and redistribute this module.
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15 #
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16 # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
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17 # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
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18 # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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19 #
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20 # POD documentation - main docs before the code
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21
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22 =head1 NAME
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23
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24 InterProTerm - Implementation of InterProI term interface
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25
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26 =head1 SYNOPSIS
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27
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28 my $term = Bio::Ontology::InterProTerm->new( -interpro_id => "IPR000001",
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29 -name => "Kringle",
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30 -definition => "Kringles are autonomous structural domains ...",
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31 -ontology => "Domain"
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32 );
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33 print $term->interpro_id(), "\n";
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34 print $term->name(), "\n";
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35 print $term->definition(), "\n";
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36 print $term->is_obsolete(), "\n";
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37 print $term->ontology->name(), "\n";
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38
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39 =head1 DESCRIPTION
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40
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41 This is a simple extension of L<Bio::Ontology::Term> for InterPro terms.
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42
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43 =head1 FEEDBACK
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44
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45 =head2 Mailing Lists
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46
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47 User feedback is an integral part of the evolution of this and other
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48 Bioperl modules. Send your comments and suggestions preferably to
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49 the Bioperl mailing list. Your participation is much appreciated.
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50
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51 bioperl-l@bioperl.org - General discussion
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52 http://bioperl.org/MailList.shtml - About the mailing lists
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53
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54 =head2 Reporting Bugs
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55
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56 Report bugs to the Bioperl bug tracking system to help us keep track
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57 of the bugs and their resolution. Bug reports can be submitted via
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58 email or the web:
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59
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60 bioperl-bugs@bioperl.org
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61 http://bugzilla.bioperl.org/
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62
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63 =head1 AUTHOR - Peter Dimitrov
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64
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65 Email dimitrov@gnf.org
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66
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67 =head1 CONTRIBUTORS
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68
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69 Additional contributors names and emails here
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70
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71 =head1 APPENDIX
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72
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73 The rest of the documentation details each of the object methods.
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74 Internal methods are usually preceded with a _
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75
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76 =cut
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77
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78
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79 # Let the code begin...
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80
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81
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82 package Bio::Ontology::InterProTerm;
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83 use vars qw(@ISA);
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84 use strict;
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85
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86 use Bio::Ontology::Term;
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87 use Bio::Annotation::Reference;
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88
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89 use constant INTERPRO_ID_DEFAULT => "IPR000000";
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90
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91 @ISA = qw( Bio::Ontology::Term );
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92
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93 =head2 new
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94
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95 Title : new
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96 Usage : $term = Bio::Ontology::InterProTerm->new( -interpro_id => "IPR000002",
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97 -name => "Cdc20/Fizzy",
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98 -definition => "The Cdc20/Fizzy region is almost always ...",
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99 -ontology => "Domain"
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100 );
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101
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102 Function: Creates a new Bio::Ontology::InterProTerm.
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103 Example :
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104 Returns : A new Bio::Ontology::InterProTerm object.
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105 Args :
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106 -interpro_id => the InterPro ID of the term. Has the form IPRdddddd, where dddddd is a zero-padded six digit number
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107 -name => the name of this InterPro term [scalar]
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108 -definition => the definition/abstract of this InterPro term [scalar]
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109 -ontology => ontology of InterPro terms [Bio::Ontology::OntologyI]
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110 -comment => a comment [scalar]
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111
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112 =cut
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113
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114 sub new{
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115 my ($class, @args) = @_;
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116 my $self = $class->SUPER::new(@args);
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117
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118 my ( $interpro_id,
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119 $short_name)
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120 = $self->_rearrange( [qw( INTERPRO_ID
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121 SHORT_NAME
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122 )
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123 ], @args );
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124
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125 $interpro_id && $self->interpro_id( $interpro_id );
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126 $short_name && $self->short_name( $short_name );
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127
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128 return $self;
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129 }
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130
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131 =head2 init
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132
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133 Title : init
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134 Usage : $term->init();
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135 Function: Initializes this InterProTerm to all "" and empty lists.
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136 Example :
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137 Returns :
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138 Args :
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139
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140
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141 =cut
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142
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143 sub init{
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144 my $self = shift;
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145
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146 # first call the inherited version to properly chain up the hierarchy
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147 $self->SUPER::init(@_);
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148
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149 # then only initialize what we implement ourselves here
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150 $self->interpro_id( INTERPRO_ID_DEFAULT );
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151 $self->short_name("");
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152
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153 }
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154
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155 =head2 _check_interpro_id
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156
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157 Title : _check_interpro_id
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158 Usage :
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159 Function: Performs simple check in order to validate that its argument has the form IPRdddddd, where dddddd is a zero-padded six digit number.
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160 Example :
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161 Returns : Returns its argument if valid, otherwise throws exception.
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162 Args : String
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163
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164
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165 =cut
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166
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167 sub _check_interpro_id{
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168 my ($self, $value) = @_;
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169
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170 $self->throw( "InterPro ID ".$value." is incorrect\n" )
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171 unless ( $value =~ /^IPR\d{6}$/ ||
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172 $value eq INTERPRO_ID_DEFAULT );
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173
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174 return $value;
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175 }
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176
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177 =head2 interpro_id
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178
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179 Title : interpro_id
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180 Usage : $obj->interpro_id($newval)
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181 Function: Set/get for the interpro_id of this InterProTerm
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182 Example :
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183 Returns : value of interpro_id (a scalar)
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184 Args : new value (a scalar, optional)
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185
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186
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187 =cut
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188
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189 sub interpro_id{
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190 my ($self, $value) = @_;
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191
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192 if( defined $value) {
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193 $value = $self->_check_interpro_id($value);
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194 }
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195
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196 return $self->identifier($value);
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197 }
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198
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199 =head2 short_name
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200
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201 Title : short_name
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202 Usage : $obj->short_name($newval)
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203 Function: Set/get for the short name of this InterProTerm.
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204 Example :
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205 Returns : value of short_name (a scalar)
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206 Args : new value (a scalar, optional)
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207
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208
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209 =cut
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210
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211 sub short_name{
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212 my ($self, $value) = @_;
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213
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214 if( defined $value) {
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215 $self->{'short_name'} = $value ? $value : undef;
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216 }
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217
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218 return $self->{'short_name'};
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219 }
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220
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221 =head2 protein_count
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222
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223 Title : protein_count
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224 Usage : $obj->protein_count($newval)
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225 Function: Set/get for the protein count of this InterProTerm.
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226 Example :
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227 Returns : value of protein_count (a scalar)
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228 Args : new value (a scalar, optional)
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229
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230
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231 =cut
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232
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233 sub protein_count{
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234 my ($self,$value) = @_;
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235
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236 if( defined $value) {
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237 $self->{'protein_count'} = $value ? $value : undef;
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238 }
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239
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240 return $self->{'protein_count'};
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241 }
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242
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243 =head2 get_references
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244
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245 Title : get_references
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246 Usage :
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247 Function: Get the references for this InterPro term.
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248 Example :
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249 Returns : An array of L<Bio::Annotation::Reference> objects
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250 Args :
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251
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252
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253 =cut
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254
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255 sub get_references{
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256 my $self = shift;
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257
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258 return @{$self->{"_references"}} if exists($self->{"_references"});
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259 return ();
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260 }
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261
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262 =head2 add_reference
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263
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264 Title : add_reference
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265 Usage :
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266 Function: Add one or more references to this InterPro term.
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267 Example :
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268 Returns :
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269 Args : One or more L<Bio::Annotation::Reference> objects.
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270
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271
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272 =cut
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273
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274 sub add_reference{
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275 my $self = shift;
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276
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277 $self->{"_references"} = [] unless exists($self->{"_references"});
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278 push(@{$self->{"_references"}}, @_);
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279 }
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280
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281 =head2 remove_references
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282
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283 Title : remove_references
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284 Usage :
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285 Function: Remove all references for this InterPro term.
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286 Example :
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287 Returns : The list of previous references as an array of
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288 L<Bio::Annotation::Reference> objects.
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289 Args :
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290
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291
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292 =cut
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293
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294 sub remove_references{
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295 my $self = shift;
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296
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297 my @arr = $self->get_references();
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298 $self->{"_references"} = [];
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299 return @arr;
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300 }
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301
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302 =head2 get_members
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303
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304 Title : get_members
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305 Usage : @arr = get_members()
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306 Function: Get the list of member(s) for this object.
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307 Example :
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308 Returns : An array of Bio::Annotation::DBLink objects
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309 Args :
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310
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311
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312 =cut
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313
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314 sub get_members{
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315 my $self = shift;
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316
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317 return @{$self->{'_members'}} if exists($self->{'_members'});
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318 return ();
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319 }
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320
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321 =head2 add_member
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322
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323 Title : add_member
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324 Usage :
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325 Function: Add one or more member(s) to this object.
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326 Example :
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327 Returns :
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328 Args : One or more Bio::Annotation::DBLink objects.
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329
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330
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331 =cut
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332
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333 sub add_member{
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334 my $self = shift;
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335
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336 $self->{'_members'} = [] unless exists($self->{'_members'});
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337 push(@{$self->{'_members'}}, @_);
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338 }
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339
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340 =head2 remove_members
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341
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342 Title : remove_members
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343 Usage :
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344 Function: Remove all members for this class.
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345 Example :
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346 Returns : The list of previous members as an array of
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347 Bio::Annotation::DBLink objects.
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348 Args :
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349
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350
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351 =cut
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352
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353 sub remove_members{
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354 my $self = shift;
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355
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356 my @arr = $self->get_members();
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357 $self->{'_members'} = [];
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358 return @arr;
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359 }
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360
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361 =head2 get_examples
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362
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363 Title : get_examples
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364 Usage : @arr = get_examples()
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365 Function: Get the list of example(s) for this object.
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366
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367 This is an element of the InterPro xml schema.
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368
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369 Example :
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370 Returns : An array of Bio::Annotation::DBLink objects
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371 Args :
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372
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373
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374 =cut
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375
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376 sub get_examples{
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377 my $self = shift;
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378
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379 return @{$self->{'_examples'}} if exists($self->{'_examples'});
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380 return ();
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381 }
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382
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383 =head2 add_example
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384
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385 Title : add_example
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386 Usage :
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387 Function: Add one or more example(s) to this object.
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388
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389 This is an element of the InterPro xml schema.
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390
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391 Example :
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392 Returns :
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393 Args : One or more Bio::Annotation::DBLink objects.
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394
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395
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396 =cut
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397
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398 sub add_example{
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399 my $self = shift;
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400
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401 $self->{'_examples'} = [] unless exists($self->{'_examples'});
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402 push(@{$self->{'_examples'}}, @_);
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403 }
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404
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405 =head2 remove_examples
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406
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407 Title : remove_examples
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408 Usage :
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409 Function: Remove all examples for this class.
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410
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411 This is an element of the InterPro xml schema.
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412
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413 Example :
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414 Returns : The list of previous examples as an array of
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415 Bio::Annotation::DBLink objects.
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416 Args :
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417
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418
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419 =cut
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420
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421 sub remove_examples{
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422 my $self = shift;
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423
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424 my @arr = $self->get_examples();
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425 $self->{'_examples'} = [];
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426 return @arr;
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427 }
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428
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429 =head2 get_external_documents
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430
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431 Title : get_external_documents
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432 Usage : @arr = get_external_documents()
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433 Function: Get the list of external_document(s) for this object.
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434
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435 This is an element of the InterPro xml schema.
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436
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437 Example :
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438 Returns : An array of Bio::Annotation::DBLink objects
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439 Args :
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440
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441
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442 =cut
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443
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444 sub get_external_documents{
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445 my $self = shift;
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446
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447 return @{$self->{'_external_documents'}} if exists($self->{'_external_documents'});
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448 return ();
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449 }
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450
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451 =head2 add_external_document
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452
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453 Title : add_external_document
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454 Usage :
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455 Function: Add one or more external_document(s) to this object.
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456
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457 This is an element of the InterPro xml schema.
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458
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459 Example :
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460 Returns :
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461 Args : One or more Bio::Annotation::DBLink objects.
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462
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463
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464 =cut
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465
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466 sub add_external_document{
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467 my $self = shift;
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468
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469 $self->{'_external_documents'} = [] unless exists($self->{'_external_documents'});
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470 push(@{$self->{'_external_documents'}}, @_);
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471 }
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472
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473 =head2 remove_external_documents
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474
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475 Title : remove_external_documents
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476 Usage :
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477 Function: Remove all external_documents for this class.
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478
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479 This is an element of the InterPro xml schema.
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480
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481 Example :
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482 Returns : The list of previous external_documents as an array of
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483 Bio::Annotation::DBLink objects.
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484 Args :
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485
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486
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487 =cut
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488
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489 sub remove_external_documents{
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490 my $self = shift;
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491
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492 my @arr = $self->get_external_documents();
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493 $self->{'_external_documents'} = [];
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494 return @arr;
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495 }
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496
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497 =head2 class_list
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498
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499 Title : class_list
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500 Usage : $obj->class_list($newval)
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501 Function: Set/get for class list element of the InterPro xml schema
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502 Example :
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503 Returns : reference to an array of Bio::Annotation::DBLink objects
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504 Args : reference to an array of Bio::Annotation::DBLink objects
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505
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506
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507 =cut
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508
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509 sub class_list{
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510 my ($self, $value) = @_;
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511
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512 if( defined $value) {
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513 $self->{'class_list'} = $value;
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514 }
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515
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516 return $self->{'class_list'};
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517 }
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518
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519 =head2 to_string
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520
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521 Title : to_string()
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522 Usage : print $term->to_string();
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523 Function: to_string method for InterPro terms.
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524 Returns : A string representation of this InterPro term.
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525 Args :
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526
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527 =cut
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528
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529 sub to_string {
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|
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530 my($self) = @_;
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531 my $s = "";
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532
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533 $s .= "-- InterPro id:\n";
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534 $s .= $self->interpro_id()."\n";
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535 if (defined $self->name) {
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536 $s .= "-- Name:\n";
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537 $s .= $self->name()."\n";
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538 $s .= "-- Definition:\n";
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|
|
539 $s .= $self->definition()."\n";
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|
|
540 $s .= "-- Category:\n";
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|
|
541 if ( defined( $self->ontology() ) ) {
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|
|
542 $s .= $self->ontology()->name()."\n";
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|
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543 } else {
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|
|
544 $s .= "\n";
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|
|
545 }
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|
|
546 $s .= "-- Version:\n";
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|
|
547 $s .= $self->version()."\n";
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|
|
548 $s .= "-- Is obsolete:\n";
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|
|
549 $s .= $self->is_obsolete()."\n";
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|
|
550 $s .= "-- Comment:\n";
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|
|
551 $s .= $self->comment()."\n";
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|
|
552 if (defined $self->references) {
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|
|
553 $s .= "-- References:\n";
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|
|
554 foreach my $ref ( @{$self->references} ) {
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|
|
555 $s .= $ref->authors."\n".$ref->title."\n".$ref->location."\n\n";
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|
|
556 };
|
|
|
557 $s .= "\n";
|
|
|
558 }
|
|
|
559 if (defined $self->member_list) {
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|
|
560 $s .= "-- Member List:\n";
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|
|
561 foreach my $ref ( @{$self->member_list} ) {
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|
|
562 $s .= $ref->database."\t".$ref->primary_id."\n";
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|
|
563 };
|
|
|
564 $s .= "\n";
|
|
|
565 }
|
|
|
566 if (defined $self->external_doc_list) {
|
|
|
567 $s .= "-- External Document List:\n";
|
|
|
568 foreach my $ref ( @{$self->external_doc_list} ) {
|
|
|
569 $s .= $ref->database."\t".$ref->primary_id."\n";
|
|
|
570 };
|
|
|
571 $s .= "\n";
|
|
|
572 }
|
|
|
573 if (defined $self->examples) {
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|
|
574 $s .= "-- Examples:\n";
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|
|
575 foreach my $ref ( @{$self->examples} ) {
|
|
|
576 $s .= $ref->database."\t".$ref->primary_id."\t".$ref->comment."\n";
|
|
|
577 };
|
|
|
578 $s .= "\n";
|
|
|
579 }
|
|
|
580 if (defined $self->class_list) {
|
|
|
581 $s .= "-- Class List:\n";
|
|
|
582 foreach my $ref ( @{$self->class_list} ) {
|
|
|
583 $s .= $ref->primary_id."\n";
|
|
|
584 };
|
|
|
585 $s .= "\n";
|
|
|
586 }
|
|
|
587 if ($self->get_secondary_ids) {
|
|
|
588 $s .= "-- Secondary IDs:\n";
|
|
|
589 foreach my $ref ( $self->get_secondary_ids() ) {
|
|
|
590 $s .= $ref."\n";
|
|
|
591 };
|
|
|
592 $s .= "\n";
|
|
|
593 }
|
|
|
594 }
|
|
|
595 else {
|
|
|
596 $s .= "InterPro term not fully instantiated\n";
|
|
|
597 }
|
|
|
598 return $s;
|
|
|
599 }
|
|
|
600
|
|
|
601 =head1 Deprecated methods
|
|
|
602
|
|
|
603 These are here for backwards compatibility.
|
|
|
604
|
|
|
605 =cut
|
|
|
606
|
|
|
607 =head2 secondary_ids
|
|
|
608
|
|
|
609 Title : secondary_ids
|
|
|
610 Usage : $obj->secondary_ids($newval)
|
|
|
611 Function: This is deprecated. Use get_secondary_ids() or
|
|
|
612 add_secondary_id() instead.
|
|
|
613 Example :
|
|
|
614 Returns : reference to an array of strings
|
|
|
615 Args : reference to an array of strings
|
|
|
616
|
|
|
617
|
|
|
618 =cut
|
|
|
619
|
|
|
620 sub secondary_ids{
|
|
|
621 my $self = shift;
|
|
|
622 my @ids;
|
|
|
623
|
|
|
624 $self->warn("secondary_ids is deprecated. Use ".
|
|
|
625 "get_secondary_ids/add_secondary_id instead.");
|
|
|
626
|
|
|
627 # set mode?
|
|
|
628 if(@_) {
|
|
|
629 my $sids = shift;
|
|
|
630 if($sids) {
|
|
|
631 $self->add_secondary_id(@$sids);
|
|
|
632 @ids = @$sids;
|
|
|
633 } else {
|
|
|
634 # we interpret setting to undef as removing the array
|
|
|
635 $self->remove_secondary_ids();
|
|
|
636 }
|
|
|
637 } else {
|
|
|
638 # no; get mode
|
|
|
639 @ids = $self->get_secondary_ids();
|
|
|
640 }
|
|
|
641 return \@ids;
|
|
|
642 }
|
|
|
643
|
|
|
644 1;
|
