diff variant_effect_predictor/Bio/SeqFeature/Similarity.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqFeature/Similarity.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,206 @@
+# $Id: Similarity.pm,v 1.10 2002/11/01 21:39:05 jason Exp $
+#
+# BioPerl module for Bio::SeqFeature::Similarity
+#
+# Cared for by Hilmar Lapp <[e-mail]>
+#
+# Copyright Hilmar Lapp
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::SeqFeature::Similarity - A sequence feature based on similarity
+
+=head1 SYNOPSIS
+
+    # obtain a similarity feature somehow
+    print "significance: ", $sim_fea->significance(), "\n";
+    print "bit score: ", $sim_fea->bits(), "\n";
+    print "score: ", $sim_fea->score(), "\n";
+    print "fraction of identical residues: ", $sim_fea->frac_identical(), "\n";
+
+=head1 DESCRIPTION
+
+This module is basically a sequence features based on similarity, and therefore
+has support for measures assessing the similarity.
+
+Everything else is inherited from L<Bio::SeqFeature::Generic>.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this
+and other Bioperl modules. Send your comments and suggestions preferably
+ to one of the Bioperl mailing lists.
+Your participation is much appreciated.
+
+  [e-mail]          - General discussion
+  http://bio.perl.org/MailList.html             - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+ the bugs and their resolution.
+ Bug reports can be submitted via email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Hilmar Lapp
+
+Email [e-mail] or [e-mail]
+
+Describe contact details here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::SeqFeature::Similarity;
+use vars qw(@ISA);
+use strict;
+
+use Bio::SeqFeature::Generic;
+
+@ISA = qw(Bio::SeqFeature::Generic);
+
+sub new {
+    my ( $caller, @args) = @_;   
+    my ($self) = $caller->SUPER::new(@args); 
+
+    my ($primary,$evalue, $bits, $frac,$seqlen,$seqdesc) =
+	$self->_rearrange([qw(PRIMARY
+			      EXPECT
+			      BITS
+			      FRAC
+			      SEQDESC
+			      SEQLENGTH				      
+			      )],@args);
+
+    defined $evalue && $self->significance($evalue);
+    defined $bits   && $self->bits($bits);
+    defined $frac   && $self->frac_identical($frac);
+    defined $seqlen && $self->seqlength($seqlen);
+    defined $seqdesc && $self->seqdesc($seqdesc);
+    $primary  = 'similarity' unless defined $primary;
+    $self->primary_tag($primary) unless( defined $self->primary_tag() );
+    $self->strand(0) unless( defined $self->strand() );
+
+    return $self;
+}
+
+=head2 significance
+
+ Title   : significance
+ Usage   : $evalue = $obj->significance();
+           $obj->significance($evalue);
+ Function: 
+ Returns : 
+ Args    : 
+
+
+=cut
+
+sub significance {
+    my ($self, $value) = @_;
+
+    return $self->_tag_value('signif', $value);
+}
+
+=head2 bits
+
+ Title   : bits
+ Usage   : $bits = $obj->bits();
+           $obj->bits($value);
+ Function: 
+ Returns : 
+ Args    : 
+
+
+=cut
+
+sub bits {
+    my ($self, $value) = @_;
+
+    return $self->_tag_value('Bits', $value);
+}
+
+=head2 frac_identical
+
+ Title   : frac_identical
+ Usage   : $fracid = $obj->frac_identical();
+           $obj->frac_identical($value);
+ Function: 
+ Returns : 
+ Args    : 
+
+
+=cut
+
+sub frac_identical {
+    my ($self, $value) = @_;
+
+    return $self->_tag_value('FracId', $value);
+}
+
+=head2 seqlength
+
+ Title   : seqlength
+ Usage   : $len = $obj->seqlength();
+           $obj->seqlength($len);
+ Function: 
+ Returns : 
+ Args    : 
+
+
+=cut
+
+sub seqlength {
+    my ($self, $value) = @_;
+
+    return $self->_tag_value('SeqLength', $value);
+}
+
+=head2 seqdesc
+
+ Title   : seqdesc
+ Usage   : $desc = $obj->seqdesc();
+           $obj->seqdesc($desc);
+ Function: At present this method is a shorthand for 
+           $obj->annotation()->description().
+
+           Note that this is not stored in the tag system and hence will
+           not be included in the return value of gff_string().
+ Returns : 
+ Args    : 
+
+
+=cut
+
+sub seqdesc {
+    my ($self, $value) = @_;
+
+    if( defined $value ) { 
+	my $v = Bio::Annotation::SimpleValue->new();
+	$v->value($value);
+	$self->annotation->add_Annotation('description',$v);
+    }
+    my ($v) = $self->annotation()->get_Annotations('description');
+    return $v ? $v->value : undef;
+}
+
+#
+# Everything else is just inherited from SeqFeature::Generic.
+#
+
+1;