Raw content of Bio::Location::Atomic
<![CDATA[# $Id: Atomic.pm,v 1.6 2002/12/01 00:05:20 jason Exp $
#
# BioPerl module for Bio::Location::Atomic
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Location::Atomic - Implementation of a Atomic Location on a Sequence
=head1 SYNOPSIS
use Bio::Location::Atomic;
my $location = new Bio::Location::Atomic(-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, $location->end;
}
=head1 DESCRIPTION
This is an implementation of Bio::LocationI to manage simple location
information on a Sequence.
=head1 FEEDBACK
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Location::Atomic;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::LocationI;
@ISA = qw(Bio::Root::Root Bio::LocationI);
sub new {
my ($class, @args) = @_;
my $self = {};
bless $self,$class;
my ($v,$start,$end,$strand,$seqid) = $self->_rearrange([qw(VERBOSE
START
END
STRAND
SEQ_ID)],@args);
defined $v && $self->verbose($v);
defined $strand && $self->strand($strand);
defined $start && $self->start($start);
defined $end && $self->end($end);
if( defined $self->start && defined $self->end &&
$self->start > $self->end && $self->strand != -1 ) {
$self->warn("When building a location, start ($start) is expected to be less than end ($end), ".
"however it was not. Switching start and end and setting strand to -1");
$self->strand(-1);
my $e = $self->end;
my $s = $self->start;
$self->start($e);
$self->end($s);
}
$seqid && $self->seq_id($seqid);
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) = @_;
$self->min_start($value) if( defined $value );
return $self->SUPER::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) = @_;
$self->min_end($value) if( defined $value );
return $self->SUPER::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
sub strand {
my ($self, $value) = @_;
if ( defined $value ) {
if ( $value eq '+' ) { $value = 1; }
elsif ( $value eq '-' ) { $value = -1; }
elsif ( $value eq '.' ) { $value = 0; }
elsif ( $value != -1 && $value != 1 && $value != 0 ) {
$self->throw("$value is not a valid strand info");
}
$self->{'_strand'} = $value
}
# let's go ahead and force to '0' if
# we are requesting the strand without it
# having been set previously
return $self->{'_strand'} || 0;
}
=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) = @_;
return abs($self->end() - $self->start()) + 1;
}
=head2 min_start
Title : min_start
Usage : my $minstart = $location->min_start();
Function: Get minimum starting location of feature startpoint
Returns : integer or undef if no minimum starting point.
Args : none
=cut
sub min_start {
my ($self,$value) = @_;
if(defined($value)) {
$self->{'_start'} = $value;
}
return $self->{'_start'};
}
=head2 max_start
Title : max_start
Usage : my $maxstart = $location->max_start();
Function: Get maximum starting location of feature startpoint.
In this implementation this is exactly the same as min_start().
Returns : integer or undef if no maximum starting point.
Args : none
=cut
sub max_start {
my ($self,@args) = @_;
return $self->min_start(@args);
}
=head2 start_pos_type
Title : start_pos_type
Usage : my $start_pos_type = $location->start_pos_type();
Function: Get start position type (ie <,>, ^).
In this implementation this will always be 'EXACT'.
Returns : type of position coded as text
('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none
=cut
sub start_pos_type {
my($self) = @_;
return 'EXACT';
}
=head2 min_end
Title : min_end
Usage : my $minend = $location->min_end();
Function: Get minimum ending location of feature endpoint
Returns : integer or undef if no minimum ending point.
Args : none
=cut
sub min_end {
my($self,$value) = @_;
if(defined($value)) {
$self->{'_end'} = $value;
}
return $self->{'_end'};
}
=head2 max_end
Title : max_end
Usage : my $maxend = $location->max_end();
Function: Get maximum ending location of feature endpoint
In this implementation this is exactly the same as min_end().
Returns : integer or undef if no maximum ending point.
Args : none
=cut
sub max_end {
my($self,@args) = @_;
return $self->min_end(@args);
}
=head2 end_pos_type
Title : end_pos_type
Usage : my $end_pos_type = $location->end_pos_type();
Function: Get end position type (ie <,>, ^)
In this implementation this will always be 'EXACT'.
Returns : type of position coded as text
('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none
=cut
sub end_pos_type {
my($self) = @_;
return 'EXACT';
}
=head2 location_type
Title : location_type
Usage : my $location_type = $location->location_type();
Function: Get location type encoded as text
Returns : string ('EXACT', 'WITHIN', 'BETWEEN')
Args : none
=cut
sub location_type {
my ($self) = @_;
return 'EXACT';
}
=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
sub is_remote {
my $self = shift;
if( @_ ) {
my $value = shift;
$self->{'is_remote'} = $value;
}
return $self->{'is_remote'};
}
=head2 each_Location
Title : each_Location
Usage : @locations = $locObject->each_Location($order);
Function: Conserved function call across Location:: modules - will
return an array containing the component Location(s) in
that object, regardless if the calling object is itself a
single location or one containing sublocations.
Returns : an array of Bio::LocationI implementing objects - for
Simple locations, the return value is just itself.
Args :
=cut
sub each_Location {
my ($self) = @_;
return ($self);
}
=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) = @_;
if( $self->start == $self->end ) {
return $self->start;
}
my $str = $self->start . ".." . $self->end;
if( $self->strand == -1 ) {
$str = sprintf("complement(%s)", $str);
}
return $str;
}
sub trunc {
my ($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::Atomic->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::Atomic->new();
$out->start($newstart);
$out->end($newend);
$out->strand($newstrand);
$out->seq_id();
}
return $out;
}
1;
]]>