Bio/SeqFeature/Similarity.pm

   1 #
   2 # BioPerl module for Bio::SeqFeature::Similarity
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Hilmar Lapp <hlapp@gmx.net>
   7 #
   8 # Copyright Hilmar Lapp
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::SeqFeature::Similarity - A sequence feature based on similarity
  17
  18 =head1 SYNOPSIS
  19
  20     # obtain a similarity feature somehow
  21     print "significance: ", $sim_fea->significance(), "\n";
  22     print "bit score: ", $sim_fea->bits(), "\n";
  23     print "score: ", $sim_fea->score(), "\n";
  24     print "fraction of identical residues: ", $sim_fea->frac_identical(), "\n";
  25
  26 =head1 DESCRIPTION
  27
  28 This module is basically a sequence features based on similarity, and therefore
  29 has support for measures assessing the similarity.
  30
  31 Everything else is inherited from L<Bio::SeqFeature::Generic>.
  32
  33 =head1 FEEDBACK
  34
  35 =head2 Mailing Lists
  36
  37 User feedback is an integral part of the evolution of this
  38 and other Bioperl modules. Send your comments and suggestions preferably
  39  to one of the Bioperl mailing lists.
  40 Your participation is much appreciated.
  41
  42   bioperl-l@bioperl.org                  - General discussion
  43   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  44
  45 =head2 Support
  46
  47 Please direct usage questions or support issues to the mailing list:
  48
  49 I<bioperl-l@bioperl.org>
  50
  51 rather than to the module maintainer directly. Many experienced and
  52 reponsive experts will be able look at the problem and quickly
  53 address it. Please include a thorough description of the problem
  54 with code and data examples if at all possible.
  55
  56 =head2 Reporting Bugs
  57
  58 Report bugs to the Bioperl bug tracking system to help us keep track
  59 the bugs and their resolution.  Bug reports can be submitted via the
  60 web:
  61
  62   https://github.com/bioperl/bioperl-live/issues
  63
  64 =head1 AUTHOR - Hilmar Lapp
  65
  66 Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com
  67
  68 =head1 APPENDIX
  69
  70 The rest of the documentation details each of the object
  71 methods. Internal methods are usually preceded with a _
  72
  73 =cut
  74
  75
  76 # Let the code begin...
  77
  78
  79 package Bio::SeqFeature::Similarity;
  80 use strict;
  81
  82
  83 use base qw(Bio::SeqFeature::Generic);
  84
  85 sub new {
  86     my ( $caller, @args) = @_;
  87     my ($self) = $caller->SUPER::new(@args);
  88
  89     my ($primary,$evalue, $bits, $frac,$seqlen,$seqdesc) =
  90         $self->_rearrange([qw(PRIMARY
  91                               EXPECT
  92                               BITS
  93                               FRAC
  94                               SEQLENGTH
  95                               SEQDESC
  96                               )],@args);
  97
  98     defined $evalue && $self->significance($evalue);
  99     defined $bits   && $self->bits($bits);
 100     defined $frac   && $self->frac_identical($frac);
 101     defined $seqlen && $self->seqlength($seqlen);
 102     defined $seqdesc && $self->seqdesc($seqdesc);
 103     $primary  = 'similarity' unless defined $primary;
 104     $self->primary_tag($primary) unless( defined $self->primary_tag() );
 105     $self->strand(0) unless( defined $self->strand() );
 106
 107     return $self;
 108 }
 109
 110 =head2 significance
 111
 112  Title   : significance
 113  Usage   : $evalue = $obj->significance();
 114            $obj->significance($evalue);
 115  Function:
 116  Returns :
 117  Args    :
 118
 119
 120 =cut
 121
 122 sub significance {
 123     return shift->_tag_value('signif', @_);
 124 }
 125
 126 =head2 bits
 127
 128  Title   : bits
 129  Usage   : $bits = $obj->bits();
 130            $obj->bits($value);
 131  Function:
 132  Returns :
 133  Args    :
 134
 135
 136 =cut
 137
 138 sub bits {
 139     return shift->_tag_value('Bits', @_);
 140 }
 141
 142 =head2 frac_identical
 143
 144  Title   : frac_identical
 145  Usage   : $fracid = $obj->frac_identical();
 146            $obj->frac_identical($value);
 147  Function:
 148  Returns :
 149  Args    :
 150
 151
 152 =cut
 153
 154 sub frac_identical {
 155     return shift->_tag_value('FracId', @_);
 156 }
 157
 158 =head2 seqlength
 159
 160  Title   : seqlength
 161  Usage   : $len = $obj->seqlength();
 162            $obj->seqlength($len);
 163  Function:
 164  Returns :
 165  Args    :
 166
 167
 168 =cut
 169
 170 sub seqlength {
 171     return shift->_tag_value('SeqLength', @_);
 172 }
 173
 174 =head2 seqdesc
 175
 176  Title   : seqdesc
 177  Usage   : $desc = $obj->seqdesc();
 178            $obj->seqdesc($desc);
 179  Function: At present this method is a shorthand for
 180            $obj->annotation()->description().
 181
 182            Note that this is not stored in the tag system and hence will
 183            not be included in the return value of gff_string().
 184  Returns :
 185  Args    :
 186
 187
 188 =cut
 189
 190 sub seqdesc {
 191     my ( $self, $value ) = @_;
 192
 193     if ( defined $value ) {
 194         my $v = Bio::Annotation::SimpleValue->new();
 195         $v->value($value);
 196         $self->annotation->add_Annotation( 'description', $v );
 197     }
 198     my ($v) = $self->annotation()->get_Annotations('description');
 199     return defined $v ? $v->value : undef;
 200 }
 201
 202 #
 203 # Everything else is just inherited from SeqFeature::Generic.
 204 #
 205
 206 1;