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1 # $Id: Comment.pm,v 1.8 2002/09/25 18:11:33 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Annotation::Comment
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4 #
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5 # Cared for by Ewan Birney <birney@ebi.ac.uk>
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6 #
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7 # Copyright Ewan Birney
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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::Comment - A comment object, holding text
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16
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17 =head1 SYNOPSIS
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18
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19
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20 $comment = Bio::Annotation::Comment->new();
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21 $comment->text("This is the text of this comment");
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22 $annotation->add_Annotation('comment', $comment);
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23
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24
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25 =head1 DESCRIPTION
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26
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27 A holder for comments in annotations, just plain text. This is a very simple
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28 object, and justifiably so.
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29
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30 =head1 CONTACT
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31
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32 Describe contact details here
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33
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34 =head1 APPENDIX
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35
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36 The rest of the documentation details each of the object
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37 methods. Internal methods are usually preceded with a _
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38
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39 =cut
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40
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41
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42 # Let the code begin...
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43
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44 package Bio::Annotation::Comment;
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45 use vars qw(@ISA);
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46 use strict;
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47
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48 use Bio::Root::Root;
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49 use Bio::AnnotationI;
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50
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51 @ISA = qw(Bio::Root::Root Bio::AnnotationI);
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52
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53 =head2 new
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54
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55 Title : new
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56 Usage : $comment = Bio::Annotation::Comment->new( '-text' => 'some text for this comment');
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57 Function: This returns a new comment object, optionally with
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58 text filed
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59 Example :
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60 Returns : a Bio::Annotation::Comment object
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61 Args : a hash with -text optionally set
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62
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63
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64 =cut
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65
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66
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67 sub new {
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68 my($class,@args) = @_;
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69
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70 my $self = $class->SUPER::new(@args);
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71 my ($text,$tag) = $self->_rearrange([qw(TEXT TAGNAME)], @args);
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72
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73 defined $text && $self->text($text);
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74 defined $tag && $self->tagname($tag);
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75
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76 return $self;
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77 }
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78
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79 =head1 AnnotationI implementing functions
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80
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81 =cut
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82
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83 =head2 as_text
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84
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85 Title : as_text
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86 Usage :
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87 Function:
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88 Example :
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89 Returns :
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90 Args :
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91
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92
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93 =cut
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94
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95 sub as_text{
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96 my ($self) = @_;
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97
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98 return "Comment: ".$self->text;
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99 }
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100
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101 =head2 hash_tree
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102
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103 Title : hash_tree
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104 Usage :
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105 Function:
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106 Example :
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107 Returns :
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108 Args :
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109
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110
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111 =cut
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112
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113 sub hash_tree{
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114 my ($self) = @_;
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115
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116 my $h = {};
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117 $h->{'text'} = $self->text;
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118 }
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119
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120 =head2 tagname
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121
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122 Title : tagname
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123 Usage : $obj->tagname($newval)
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124 Function: Get/set the tagname for this annotation value.
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125
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126 Setting this is optional. If set, it obviates the need to provide
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127 a tag to Bio::AnnotationCollectionI when adding this object. When
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128 obtaining an AnnotationI object from the collection, the collection
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129 will set the value to the tag under which it was stored unless the
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130 object has a tag stored already.
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131 Example :
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132 Returns : value of tagname (a scalar)
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133 Args : new value (a scalar, optional)
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134
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135
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136 =cut
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137
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138 sub tagname{
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139 my ($self,$value) = @_;
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140 if( defined $value) {
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141 $self->{'tagname'} = $value;
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142 }
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143 return $self->{'tagname'};
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144 }
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145
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146 =head1 Specific accessors for Comments
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147
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148 =cut
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149
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150
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151 =head2 text
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152
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153 Title : text
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154 Usage : $value = $self->text($newval)
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155 Function: get/set for the text field. A comment object
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156 just holds a single string which is accessible through
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157 this method
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158 Example :
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159 Returns : value of text
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160 Args : newvalue (optional)
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161
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162
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163 =cut
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164
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165 sub text{
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166 my ($self,$value) = @_;
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167 if( defined $value) {
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168 $self->{'text'} = $value;
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169 }
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170 return $self->{'text'};
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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
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176 1;
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