/usr/share/perl5/Bio/LiveSeq/Range.pm is in libbio-perl-perl 1.6.923-1.
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# bioperl module for Bio::LiveSeq::Range
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Joseph Insana <insana@ebi.ac.uk> <jinsana@gmx.net>
#
# Copyright Joseph Insana
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::LiveSeq::Range - Range abstract class for LiveSeq
=head1 SYNOPSIS
# documentation needed
=head1 DESCRIPTION
This is used as parent for exon and intron classes.
=head1 AUTHOR - Joseph A.L. Insana
Email: Insana@ebi.ac.uk, jinsana@gmx.net
=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::LiveSeq::Range;
use strict;
use base qw(Bio::LiveSeq::SeqI);
=head2 new
Title : new
Usage : $range1 = Bio::LiveSeq::Range->new(-seq => $obj_ref,
-start => $beginlabel,
-end => $endlabel, -strand => 1);
Function: generates a new Bio::LiveSeq::Range
Returns : reference to a new object of class Range
Errorcode -1
Args : two labels, an obj_ref and an integer
strand 1=forward strand, strand -1=reverse strand
if strand not specified, it defaults to 1
the -seq argument must point to the underlying DNA LiveSeq object
=cut
sub new {
my ($thing, %args) = @_;
my $class = ref($thing) || $thing;
my ($obj,%range);
my ($seq,$start,$end,$strand)=($args{-seq},$args{-start},$args{-end},$args{-strand});
$obj = \%range;
$obj = bless $obj, $class;
unless ($seq->valid($start)) {
$obj->warn("$class not initialised because start label not valid");
return (-1);
}
unless ($seq->valid($end)) {
$obj->warn("$class not initialised because end label not valid");
return (-1);
}
unless (defined $strand) {
$strand = 1;
}
if (($strand != 1)&&($strand != -1)) {
$obj->warn("$class not initialised because strand identifier not valid. Use 1 (forward strand) or -1 (reverse strand).");
return (-1);
}
if ($start eq $end) {
$obj->warn("$class reports: start and end label are the same....");
} else {
unless ($seq->follows($start,$end,$strand)==1) {
$obj->warn("Fatal: end label $end doesn't follow start label $start for strand $strand!");
return (-1);
}
}
#if ($strand == 1) {
# unless ($seq->is_downstream($start,$end)==1) {
# croak "Fatal: end label not downstream of start label for forward strand!";
# }
#} else {
# unless ($seq->is_upstream($start,$end)==1) {
# croak "Fatal: end label not upstream of start label for reverse strand!";
# }
#}
$obj->{'seq'}=$seq;
$obj->{'start'}=$start;
$obj->{'end'}=$end;
$obj->{'strand'}=$strand;
return $obj;
}
=head2 valid
Title : valid
Usage : $boolean = $obj->valid($label)
Function: tests if a label exists AND is part of the object
Returns : boolean
Args : label
=cut
1;
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