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1 # $Id: SimpleValue.pm,v 1.9.2.1 2003/03/10 22:04:56 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Annotation::SimpleValue
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4 #
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5 # Cared for by bioperl <bioperl-l@bio.perl.org>
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6 #
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7 # Copyright bioperl
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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::Annotation::SimpleValue - A simple scalar
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::Annotation::SimpleValue;
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20 use Bio::Annotation::Collection;
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21
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22 my $col = new Bio::Annotation::Collection;
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23 my $sv = new Bio::Annotation::SimpleValue(-value => 'someval');
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24 $col->add_Annotation('tagname', $sv);
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25
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26 =head1 DESCRIPTION
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27
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28 Scalar value annotation object
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29
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30 =head1 FEEDBACK
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31
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32 =head2 Mailing Lists
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33
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34 User feedback is an integral part of the evolution of this and other
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35 Bioperl modules. Send your comments and suggestions preferably to one
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36 of the Bioperl mailing lists. Your participation is much appreciated.
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37
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38 bioperl-l@bioperl.org - General discussion
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39 http://bio.perl.org/MailList.html - About the mailing lists
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40
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41 =head2 Reporting Bugs
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42
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43 Report bugs to the Bioperl bug tracking system to help us keep track
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44 the bugs and their resolution. Bug reports can be submitted via email
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45 or the web:
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46
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47 bioperl-bugs@bioperl.org
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48 http://bugzilla.bioperl.org/
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49
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50 =head1 AUTHOR - bioperl
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51
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52 Email bioperl-l@bio.perl.org
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53
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54 Describe contact details here
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55
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56 =head1 APPENDIX
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57
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58 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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59
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60 =cut
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61
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62
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63 # Let the code begin...
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64
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65
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66 package Bio::Annotation::SimpleValue;
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67 use vars qw(@ISA);
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68 use strict;
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69
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70 # Object preamble - inherits from Bio::Root::Root
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71
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72 use Bio::AnnotationI;
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73 #use Bio::Ontology::TermI;
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74 use Bio::Root::Root;
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75
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76 @ISA = qw(Bio::Root::Root Bio::AnnotationI);
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77
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78 =head2 new
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79
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80 Title : new
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81 Usage : my $sv = new Bio::Annotation::SimpleValue;
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82 Function: Instantiate a new SimpleValue object
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83 Returns : Bio::Annotation::SimpleValue object
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84 Args : -value => $value to initialize the object data field [optional]
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85 -tagname => $tag to initialize the tagname [optional]
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86 -tag_term => ontology term representation of the tag [optional]
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87
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88 =cut
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89
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90 sub new{
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91 my ($class,@args) = @_;
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92
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93 my $self = $class->SUPER::new(@args);
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94
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95 my ($value,$tag,$term) =
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96 $self->_rearrange([qw(VALUE TAGNAME TAG_TERM)], @args);
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97
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98 # set the term first
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99 defined $term && $self->tag_term($term);
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100 defined $value && $self->value($value);
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101 defined $tag && $self->tagname($tag);
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102
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103 return $self;
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104 }
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105
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106
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107 =head1 AnnotationI implementing functions
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108
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109 =cut
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110
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111 =head2 as_text
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112
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113 Title : as_text
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114 Usage : my $text = $obj->as_text
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115 Function: return the string "Value: $v" where $v is the value
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116 Returns : string
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117 Args : none
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118
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119
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120 =cut
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121
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122 sub as_text{
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123 my ($self) = @_;
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124
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125 return "Value: ".$self->value;
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126 }
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127
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128 =head2 hash_tree
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129
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130 Title : hash_tree
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131 Usage : my $hashtree = $value->hash_tree
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132 Function: For supporting the AnnotationI interface just returns the value
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133 as a hashref with the key 'value' pointing to the value
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134 Returns : hashrf
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135 Args : none
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136
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137
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138 =cut
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139
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140 sub hash_tree{
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141 my ($self) = @_;
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142
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143 my $h = {};
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144 $h->{'value'} = $self->value;
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145 }
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146
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147 =head2 tagname
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148
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149 Title : tagname
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150 Usage : $obj->tagname($newval)
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151 Function: Get/set the tagname for this annotation value.
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152
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153 Setting this is optional. If set, it obviates the need to
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154 provide a tag to AnnotationCollection when adding this
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155 object.
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156
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157 Example :
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158 Returns : value of tagname (a scalar)
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159 Args : new value (a scalar, optional)
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160
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161
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162 =cut
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163
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164 sub tagname{
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165 my $self = shift;
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166
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167 # check for presence of an ontology term
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168 if($self->{'_tag_term'}) {
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169 # keep a copy in case the term is removed later
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170 $self->{'tagname'} = $_[0] if @_;
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171 # delegate to the ontology term object
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172 return $self->tag_term->name(@_);
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173 }
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174 return $self->{'tagname'} = shift if @_;
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175 return $self->{'tagname'};
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176 }
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177
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178
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179 =head1 Specific accessors for SimpleValue
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180
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181 =cut
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182
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183 =head2 value
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184
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185 Title : value
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186 Usage : $obj->value($newval)
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187 Function: Get/Set the value for simplevalue
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188 Returns : value of value
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189 Args : newvalue (optional)
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190
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191
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192 =cut
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193
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194 sub value{
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195 my ($self,$value) = @_;
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196
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197 if( defined $value) {
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198 $self->{'value'} = $value;
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199 }
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200 return $self->{'value'};
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201 }
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202
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203 =head2 tag_term
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204
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205 Title : tag_term
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206 Usage : $obj->tag_term($newval)
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207 Function: Get/set the L<Bio::Ontology::TermI> object representing
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208 the tag name.
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209
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210 This is so you can specifically relate the tag of this
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211 annotation to an entry in an ontology. You may want to do
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212 this to associate an identifier with the tag, or a
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213 particular category, such that you can better match the tag
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214 against a controlled vocabulary.
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215
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216 This accessor will return undef if it has never been set
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217 before in order to allow this annotation to stay
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218 light-weight if an ontology term representation of the tag
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219 is not needed. Once it is set to a valid value, tagname()
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220 will actually delegate to the name() of this term.
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221
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222 Example :
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223 Returns : a L<Bio::Ontology::TermI> compliant object, or undef
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224 Args : on set, new value (a L<Bio::Ontology::TermI> compliant
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225 object or undef, optional)
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226
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227
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228 =cut
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229
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230 sub tag_term{
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231 my $self = shift;
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232
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233 return $self->{'_tag_term'} = shift if @_;
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234 return $self->{'_tag_term'};
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235 }
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236
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237 1;
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