Bio/SeqFeature/Similarity.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::SeqFeature::Similarity
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Hilmar Lapp <hlapp@gmx.net>
   8 #
   9 # Copyright Hilmar Lapp
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::SeqFeature::Similarity - A sequence feature based on similarity
  18
  19 =head1 SYNOPSIS
  20
  21     # obtain a similarity feature somehow
  22     print "significance: ", $sim_fea->significance(), "\n";
  23     print "bit score: ", $sim_fea->bits(), "\n";
  24     print "score: ", $sim_fea->score(), "\n";
  25     print "fraction of identical residues: ", $sim_fea->frac_identical(), "\n";
  26
  27 =head1 DESCRIPTION
  28
  29 This module is basically a sequence features based on similarity, and therefore
  30 has support for measures assessing the similarity.
  31
  32 Everything else is inherited from L<Bio::SeqFeature::Generic>.
  33
  34 =head1 FEEDBACK
  35
  36 =head2 Mailing Lists
  37
  38 User feedback is an integral part of the evolution of this
  39 and other Bioperl modules. Send your comments and suggestions preferably
  40  to one of the Bioperl mailing lists.
  41 Your participation is much appreciated.
  42
  43   bioperl-l@bioperl.org                  - General discussion
  44   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  45
  46 =head2 Support
  47
  48 Please direct usage questions or support issues to the mailing list:
  49
  50 L<bioperl-l@bioperl.org>
  51
  52 rather than to the module maintainer directly. Many experienced and
  53 reponsive experts will be able look at the problem and quickly
  54 address it. Please include a thorough description of the problem
  55 with code and data examples if at all possible.
  56
  57 =head2 Reporting Bugs
  58
  59 Report bugs to the Bioperl bug tracking system to help us keep track
  60 the bugs and their resolution.  Bug reports can be submitted via the
  61 web:
  62
  63   http://bugzilla.open-bio.org/
  64
  65 =head1 AUTHOR - Hilmar Lapp
  66
  67 Email hlapp@gmx.net or hilmar.lapp@pharma.novartis.com
  68
  69 =head1 APPENDIX
  70
  71 The rest of the documentation details each of the object
  72 methods. Internal methods are usually preceded with a _
  73
  74 =cut
  75
  76
  77 # Let the code begin...
  78
  79
  80 package Bio::SeqFeature::Similarity;
  81 use strict;
  82
  83
  84 use base qw(Bio::SeqFeature::Generic);
  85
  86 sub new {
  87     my ( $caller, @args) = @_;
  88     my ($self) = $caller->SUPER::new(@args);
  89
  90     my ($primary,$evalue, $bits, $frac,$seqlen,$seqdesc) =
  91         $self->_rearrange([qw(PRIMARY
  92                               EXPECT
  93                               BITS
  94                               FRAC
  95                               SEQLENGTH
  96                               SEQDESC
  97                               )],@args);
  98
  99     defined $evalue && $self->significance($evalue);
 100     defined $bits   && $self->bits($bits);
 101     defined $frac   && $self->frac_identical($frac);
 102     defined $seqlen && $self->seqlength($seqlen);
 103     defined $seqdesc && $self->seqdesc($seqdesc);
 104     $primary  = 'similarity' unless defined $primary;
 105     $self->primary_tag($primary) unless( defined $self->primary_tag() );
 106     $self->strand(0) unless( defined $self->strand() );
 107
 108     return $self;
 109 }
 110
 111 =head2 significance
 112
 113  Title   : significance
 114  Usage   : $evalue = $obj->significance();
 115            $obj->significance($evalue);
 116  Function:
 117  Returns :
 118  Args    :
 119
 120
 121 =cut
 122
 123 sub significance {
 124     return shift->_tag_value('signif', @_);
 125 }
 126
 127 =head2 bits
 128
 129  Title   : bits
 130  Usage   : $bits = $obj->bits();
 131            $obj->bits($value);
 132  Function:
 133  Returns :
 134  Args    :
 135
 136
 137 =cut
 138
 139 sub bits {
 140     return shift->_tag_value('Bits', @_);
 141 }
 142
 143 =head2 frac_identical
 144
 145  Title   : frac_identical
 146  Usage   : $fracid = $obj->frac_identical();
 147            $obj->frac_identical($value);
 148  Function:
 149  Returns :
 150  Args    :
 151
 152
 153 =cut
 154
 155 sub frac_identical {
 156     return shift->_tag_value('FracId', @_);
 157 }
 158
 159 =head2 seqlength
 160
 161  Title   : seqlength
 162  Usage   : $len = $obj->seqlength();
 163            $obj->seqlength($len);
 164  Function:
 165  Returns :
 166  Args    :
 167
 168
 169 =cut
 170
 171 sub seqlength {
 172     return shift->_tag_value('SeqLength', @_);
 173 }
 174
 175 =head2 seqdesc
 176
 177  Title   : seqdesc
 178  Usage   : $desc = $obj->seqdesc();
 179            $obj->seqdesc($desc);
 180  Function: At present this method is a shorthand for
 181            $obj->annotation()->description().
 182
 183            Note that this is not stored in the tag system and hence will
 184            not be included in the return value of gff_string().
 185  Returns :
 186  Args    :
 187
 188
 189 =cut
 190
 191 sub seqdesc {
 192     my ($self, $value) = @_;
 193
 194     if( defined $value ) {
 195         my $v = Bio::Annotation::SimpleValue->new();
 196         $v->value($value);
 197         $self->annotation->add_Annotation('description',$v);
 198     }
 199     my ($v) = $self->annotation()->get_Annotations('description');
 200     return defined $v ? $v->value : undef;
 201 }
 202
 203 #
 204 # Everything else is just inherited from SeqFeature::Generic.
 205 #
 206
 207 1;