Raw content of Bio::Location::Simple
<![CDATA[# $Id: Simple.pm,v 1.31 2002/10/22 07:38:35 lapp Exp $
#
# BioPerl module for Bio::Location::Simple
# Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Location::Simple - Implementation of a Simple Location on a Sequence
=head1 SYNOPSIS
use Bio::Location::Simple;
my $location = new Bio::Location::Simple(-start => 1, -end => 100,
-strand => 1 );
if( $location->strand == -1 ) {
printf "complement(%d..%d)\n", $location->start, $location->end;
} else {
printf "%d..%d\n", $location->start, $location->end;
}
=head1 DESCRIPTION
This is an implementation of Bio::LocationI to manage exact location
information on a Sequence: '22' or '12..15' or '16^17'.
You can test the type of the location using lenght() function () or
directly location_type() which can one of two values: 'EXACT' or
'IN-BETWEEN'.
=head1 FEEDBACK
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Heikki Lehvaslaiho
Email heikki@ebi.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Location::Simple;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::Location::Atomic;
@ISA = qw( Bio::Location::Atomic );
BEGIN {
use vars qw( %RANGEENCODE %RANGEDECODE );
%RANGEENCODE = ('\.\.' => 'EXACT',
'\^' => 'IN-BETWEEN' );
%RANGEDECODE = ('EXACT' => '..',
'IN-BETWEEN' => '^' );
}
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($locationtype) = $self->_rearrange([qw(LOCATION_TYPE)],@args);
$locationtype && $self->location_type($locationtype);
return $self;
}
=head2 start
Title : start
Usage : $start = $loc->start();
Function: get/set the start of this range
Returns : the start of this range
Args : optionaly allows the start to be set
: using $loc->start($start)
=cut
sub start {
my ($self, $value) = @_;
$self->{'_start'} = $value if defined $value ;
$self->throw("Only adjacent residues when location type ".
"is IN-BETWEEN. Not [". $self->{'_start'}. "] and [".
$self->{'_end'}. "]" )
if defined $self->{'_start'} && defined $self->{'_end'} &&
$self->location_type eq 'IN-BETWEEN' &&
($self->{'_end'} - 1 != $self->{'_start'});
return $self->{'_start'};
}
=head2 end
Title : end
Usage : $end = $loc->end();
Function: get/set the end of this range
Returns : the end of this range
Args : optionaly allows the end to be set
: using $loc->end($start)
=cut
sub end {
my ($self, $value) = @_;
$self->{'_end'} = $value if defined $value ;
$self->throw("Only adjacent residues when location type ".
"is IN-BETWEEN. Not [". $self->{'_start'}. "] and [".
$self->{'_end'}. "]" )
if defined $self->{'_start'} && defined $self->{'_end'} &&
$self->location_type eq 'IN-BETWEEN' &&
($self->{'_end'} - 1 != $self->{'_start'});
return $self->{'_end'};
}
=head2 strand
Title : strand
Usage : $strand = $loc->strand();
Function: get/set the strand of this range
Returns : the strandidness (-1, 0, +1)
Args : optionaly allows the strand to be set
: using $loc->strand($strand)
=cut
=head2 length
Title : length
Usage : $len = $loc->length();
Function: get the length in the coordinate space this location spans
Example :
Returns : an integer
Args : none
=cut
sub length {
my ($self) = @_;
if ($self->location_type eq 'IN-BETWEEN' ) {
return 0;
} else {
return abs($self->end - $self->start) + 1;
}
}
=head2 min_start
Title : min_start
Usage : my $minstart = $location->min_start();
Function: Get minimum starting location of feature startpoint
Returns : integer or undef if no minimum starting point.
Args : none
=cut
=head2 max_start
Title : max_start
Usage : my $maxstart = $location->max_start();
Function: Get maximum starting location of feature startpoint.
In this implementation this is exactly the same as min_start().
Returns : integer or undef if no maximum starting point.
Args : none
=cut
=head2 start_pos_type
Title : start_pos_type
Usage : my $start_pos_type = $location->start_pos_type();
Function: Get start position type (ie <,>, ^).
Returns : type of position coded as text
('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN', 'IN-BETWEEN')
Args : none
=cut
=head2 min_end
Title : min_end
Usage : my $minend = $location->min_end();
Function: Get minimum ending location of feature endpoint
Returns : integer or undef if no minimum ending point.
Args : none
=cut
=head2 max_end
Title : max_end
Usage : my $maxend = $location->max_end();
Function: Get maximum ending location of feature endpoint
In this implementation this is exactly the same as min_end().
Returns : integer or undef if no maximum ending point.
Args : none
=cut
=head2 end_pos_type
Title : end_pos_type
Usage : my $end_pos_type = $location->end_pos_type();
Function: Get end position type (ie <,>, ^)
Returns : type of position coded as text
('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN', 'IN-BETWEEN')
Args : none
=cut
=head2 location_type
Title : location_type
Usage : my $location_type = $location->location_type();
Function: Get location type encoded as text
Returns : string ('EXACT' or 'IN-BETWEEN')
Args : 'EXACT' or '..' or 'IN-BETWEEN' or '^'
=cut
sub location_type {
my ($self, $value) = @_;
if( defined $value || ! defined $self->{'_location_type'} ) {
$value = 'EXACT' unless defined $value;
$value = uc $value;
if (! defined $RANGEDECODE{$value}) {
$value = '\^' if $value eq '^';
$value = '\.\.' if $value eq '..';
$value = $RANGEENCODE{$value};
}
$self->throw("Did not specify a valid location type. [$value] is no good")
unless defined $value;
$self->{'_location_type'} = $value;
}
$self->throw("Only adjacent residues when location type ".
"is IN-BETWEEN. Not [". $self->{'_start'}. "] and [".
$self->{'_end'}. "]" )
if $self->{'_location_type'} eq 'IN-BETWEEN' &&
defined $self->{'_start'} &&
defined $self->{'_end'} &&
($self->{'_end'} - 1 != $self->{'_start'});
return $self->{'_location_type'};
}
=head2 is_remote
Title : is_remote
Usage : $self->is_remote($newval)
Function: Getset for is_remote value
Returns : value of is_remote
Args : newvalue (optional)
=cut
=head2 to_FTstring
Title : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none
=cut
sub to_FTstring {
my($self) = @_;
my $str;
if( $self->start == $self->end ) {
return $self->start;
}
$str = $self->start . $RANGEDECODE{$self->location_type} . $self->end;
if($self->is_remote() && $self->seq_id()) {
$str = $self->seq_id() . ":" . $str;
}
if( $self->strand == -1 ) {
$str = "complement(".$str.")";
}
return $str;
}
#
# not tested
#
sub trunc {
my ($self,$start,$end,$relative_ori) = @_;
my $newstart = $self->start - $start+1;
my $newend = $self->end - $start+1;
my $newstrand = $relative_ori * $self->strand;
my $out;
if( $newstart < 1 || $newend > ($end-$start+1) ) {
$out = Bio::Location::Simple->new();
$out->start($self->start);
$out->end($self->end);
$out->strand($self->strand);
$out->seq_id($self->seqid);
$out->is_remote(1);
} else {
$out = Bio::Location::Simple->new();
$out->start($newstart);
$out->end($newend);
$out->strand($newstrand);
$out->seq_id();
}
return $out;
}
1;
]]>