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# $Id: Feature.pm,v 1.5.4.1 2006/10/02 23:10:35 sendu Exp $
#
# BioPerl module for Bio::Tools::Primer::Feature
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
HideShow 58 lines of Pod
=head1 NAME
Bio::Tools::Primer::Feature - position of a single primer
=head1 SYNOPSIS
    use Bio::Tools::Primer::Feature;
    my $pf = Bio::Tools::Primer::Feature->new( -start => $start, -end => $end, -strand => $strand);
    $pf->attach_seq($seq);
    # is a SeqFeatureI
    print "primer starts at ",$pf->start," with sequence ",$pf->seq->seq(),"\n";
    # helper functions
    print "GC percentage ",$pf->gc(),"\n";
    print "has inversion of size 4 at ",$pf->inversion(4),"\n";
=head1 DESCRIPTION
Primer Features represents one primer in a primer pair. This object is
mainly for designing primers, and probably principly used in the
primer design system
=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
the Bioperl mailing list.  Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Ewan Birney
Email birney-at-ebi.ac.uk
=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::Tools::Primer::Feature;
use base qw(Bio::SeqFeature::Generic);
sub new {
    my ( $caller, @args) = @_;   
    my ($self) = $caller->SUPER::new(@args); 
    # done - we hope
    return $self;
}
sub gc_percent {
    my $self = shift;
    my $seq = $self->seq();
    if( !defined $seq ) {
        $self->throw("Primer feature has no attached sequence, can't calculate GC");
    }
    my $str = $seq->seq();
    my $count = $str =~ tr/GCgc/GCgc/;
    return $count*100.0 / $seq->length;
}
sub inversion {
    my $self = shift;
    my $size = shift;
    if( !defined $size ) {
        $self->throw("Must have size paramter in inversion");
    }
    my $seq = $self->seq();
    if( !defined $seq ) {
        $self->throw("Primer feature has no attached sequence, can't calculate inversion");
    }
    my $len = $seq->length - $size;
    my $str = $seq->seq();
    foreach my $i ( 0 .. $len ) {
        my $revstr = substr($str,$i,$size);
        my $orig = $revstr;
        $revstr = reverse $revstr;
        $revstr = s/[^ATGCNatgcn]/N/g;
        $revstr =~ tr/ATGCNatgcn/TACGNtacgn/;
        if( $str =~ /$revstr/ ) {
            return $orig;
        }
    }
    return;
}
1;