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1 # $Id: Similarity.pm,v 1.10 2002/11/01 21:39:05 jason Exp $
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2 #
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3 # BioPerl module for Bio::SeqFeature::Similarity
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4 #
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5 # Cared for by Hilmar Lapp <hlapp@gmx.net>
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6 #
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7 # Copyright Hilmar Lapp
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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::SeqFeature::Similarity - A sequence feature based on similarity
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16
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17 =head1 SYNOPSIS
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18
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19 # obtain a similarity feature somehow
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20 print "significance: ", $sim_fea->significance(), "\n";
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21 print "bit score: ", $sim_fea->bits(), "\n";
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22 print "score: ", $sim_fea->score(), "\n";
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23 print "fraction of identical residues: ", $sim_fea->frac_identical(), "\n";
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24
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25 =head1 DESCRIPTION
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26
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27 This module is basically a sequence features based on similarity, and therefore
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28 has support for measures assessing the similarity.
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29
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30 Everything else is inherited from L<Bio::SeqFeature::Generic>.
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31
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32 =head1 FEEDBACK
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33
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34 =head2 Mailing Lists
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35
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36 User feedback is an integral part of the evolution of this
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37 and other Bioperl modules. Send your comments and suggestions preferably
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38 to one of the Bioperl mailing lists.
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39 Your participation is much appreciated.
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40
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41 bioperl-l@bioperl.org - General discussion
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42 http://bio.perl.org/MailList.html - About the mailing lists
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43
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44 =head2 Reporting Bugs
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45
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46 Report bugs to the Bioperl bug tracking system to help us keep track
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47 the bugs and their resolution.
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48 Bug reports can be submitted via email or the web:
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49
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50 bioperl-bugs@bio.perl.org
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51 http://bugzilla.bioperl.org/
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52
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53 =head1 AUTHOR - Hilmar Lapp
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54
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55 Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com
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56
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57 Describe contact details here
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58
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59 =head1 APPENDIX
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60
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61 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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62
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63 =cut
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64
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65
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66 # Let the code begin...
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67
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68
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69 package Bio::SeqFeature::Similarity;
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70 use vars qw(@ISA);
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71 use strict;
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72
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73 use Bio::SeqFeature::Generic;
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74
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75 @ISA = qw(Bio::SeqFeature::Generic);
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76
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77 sub new {
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78 my ( $caller, @args) = @_;
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79 my ($self) = $caller->SUPER::new(@args);
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80
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81 my ($primary,$evalue, $bits, $frac,$seqlen,$seqdesc) =
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82 $self->_rearrange([qw(PRIMARY
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83 EXPECT
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84 BITS
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85 FRAC
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86 SEQDESC
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87 SEQLENGTH
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88 )],@args);
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89
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90 defined $evalue && $self->significance($evalue);
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91 defined $bits && $self->bits($bits);
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92 defined $frac && $self->frac_identical($frac);
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93 defined $seqlen && $self->seqlength($seqlen);
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94 defined $seqdesc && $self->seqdesc($seqdesc);
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95 $primary = 'similarity' unless defined $primary;
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96 $self->primary_tag($primary) unless( defined $self->primary_tag() );
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97 $self->strand(0) unless( defined $self->strand() );
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98
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99 return $self;
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100 }
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101
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102 =head2 significance
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103
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104 Title : significance
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105 Usage : $evalue = $obj->significance();
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106 $obj->significance($evalue);
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107 Function:
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108 Returns :
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109 Args :
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110
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111
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112 =cut
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113
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114 sub significance {
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115 my ($self, $value) = @_;
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116
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117 return $self->_tag_value('signif', $value);
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118 }
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119
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120 =head2 bits
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121
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122 Title : bits
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123 Usage : $bits = $obj->bits();
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124 $obj->bits($value);
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125 Function:
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126 Returns :
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127 Args :
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128
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129
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130 =cut
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131
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132 sub bits {
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133 my ($self, $value) = @_;
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134
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135 return $self->_tag_value('Bits', $value);
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136 }
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137
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138 =head2 frac_identical
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139
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140 Title : frac_identical
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141 Usage : $fracid = $obj->frac_identical();
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142 $obj->frac_identical($value);
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143 Function:
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144 Returns :
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145 Args :
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146
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147
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148 =cut
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149
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150 sub frac_identical {
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151 my ($self, $value) = @_;
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152
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153 return $self->_tag_value('FracId', $value);
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154 }
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155
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156 =head2 seqlength
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157
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158 Title : seqlength
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159 Usage : $len = $obj->seqlength();
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160 $obj->seqlength($len);
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161 Function:
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162 Returns :
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163 Args :
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164
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165
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166 =cut
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167
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168 sub seqlength {
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169 my ($self, $value) = @_;
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170
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171 return $self->_tag_value('SeqLength', $value);
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172 }
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173
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174 =head2 seqdesc
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175
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176 Title : seqdesc
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177 Usage : $desc = $obj->seqdesc();
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178 $obj->seqdesc($desc);
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179 Function: At present this method is a shorthand for
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180 $obj->annotation()->description().
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181
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182 Note that this is not stored in the tag system and hence will
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183 not be included in the return value of gff_string().
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184 Returns :
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185 Args :
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186
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187
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188 =cut
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189
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190 sub seqdesc {
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191 my ($self, $value) = @_;
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192
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193 if( defined $value ) {
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194 my $v = Bio::Annotation::SimpleValue->new();
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195 $v->value($value);
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196 $self->annotation->add_Annotation('description',$v);
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197 }
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198 my ($v) = $self->annotation()->get_Annotations('description');
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199 return $v ? $v->value : undef;
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200 }
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201
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202 #
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203 # Everything else is just inherited from SeqFeature::Generic.
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204 #
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205
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206 1;
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