Raw content of Bio::Map::CytoMarker
<![CDATA[# $Id: CytoMarker.pm,v 1.3 2002/10/22 07:45:15 lapp Exp $
#
# BioPerl module for Bio::Map::CytoMarker
#
# 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::Map::CytoMarker - An object representing a marker.
=head1 SYNOPSIS
$o_usat = new Bio::Map::CytoMarker(-name=>'Chad Super Marker 2',
-position => $pos);
=head1 DESCRIPTION
This object handles markers with a positon in a cytogenetic map known.
This marker will have a name and a position.
=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/MailList.shtml - 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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Heikki Lehvaslaiho
Email heikki@ebi.ac.uk
=head1 CONTRIBUTORS
Chad Matsalla bioinformatics1@dieselwurks.com
Lincoln Stein lstein@cshl.org
Jason Stajich 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::Map::CytoMarker;
use vars qw(@ISA);
use strict;
use Bio::Map::Marker;
use Bio::Map::CytoPosition;
use Bio::RangeI;
@ISA = qw(Bio::Map::Marker Bio::RangeI );
=head2 Bio::Map::MarkerI methods
=cut
=head2 get_position_object
Title : get_position_class
Usage : my $pos = $marker->get_position_object();
Function: To get an object of the default Position class
for this Marker. Subclasses should redefine this method.
The Position needs to be L<Bio::Map::PositionI>.
Returns : L<Bio::Map::CytoPosition>
Args : none
=cut
sub get_position_object {
my ($self) = @_;
return new Bio::Map::CytoPosition();
}
=head2 Comparison methods
The numeric values for cutogeneic loctions go from the p tip of
chromosome 1, down to the q tip and similarly throgh consecutive
chromosomes, through X and end the the q tip of X. See
L<Bio::Map::CytoPosition::cytorange> for more details.
The numeric values for cytogenetic positions are ranges of type
L<Bio::Range>, so MarkerI type of operators (equals, less_than,
greater_than) are not very meaningful, but they might be of some use
combined with L<Bio::RangeI> methods (overlaps, contains, equals,
intersection, union). equals(), present in both interfaces is treated
as a more precice RangeI method.
CytoMarker has a method L<get_chr> which might turn out to be useful
in this context.
The L<less_than> and L<greater_than> methods are implemented by
comparing the end values of the range, so you better first check that
markers do not overlap, or you get an opposite result than expected.
The numerical values are not metric, so avarages are not meaningful.
Note: These methods always return a value. A false value (0) might
mean that you have not set the position! Check those warnings.
=cut
=head2 Bio::Map::MarkerI comparison methods
=cut
=head2 tuple
Title : tuple
Usage : ($me, $you) = $self->_tuple($compare)
Function: Utility method to extract numbers and test for missing values.
Returns : two ranges or tuple of -1
Args : Bio::Map::MappableI or Bio::Map::PositionI
=cut
=head2 less_than
Title : less_than
Usage : if( $mappable->less_than($m2) ) ...
Function: Tests if a position is less than another position
Returns : boolean
Args : Bio::Map::MappableI or Bio::Map::PositionI
=cut
sub less_than {
my ($self,$compare) = @_;
my ($me, $you) = $self->tuple($compare);
return 0 if $me == -1 or $you == -1 ;
$me = $me->end;
$you = $you->start;
print STDERR "me=$me, you=$you\n" if $self->verbose > 0;
return $me < $you;
}
=head2 greater_than
Title : greater_than
Usage : if( $mappable->greater_than($m2) ) ...
Function: Tests if position is greater than another position
Returns : boolean
Args : Bio::Map::MappableI or Bio::Map::PositionI
=cut
sub greater_than {
my ($self,$compare) = @_;
my ($me, $you) = $self->tuple($compare);
return 0 if $me == -1 or $you == -1 ;
$me = $me->start;
$you = $you->end;
print STDERR "me=$me, you=$you\n" if $self->verbose > 0;
return $me > $you;
}
=head2 RangeI methods
=cut
=head2 equals
Title : equals
Usage : if( $mappable->equals($mapable2)) ...
Function: Test if a position is equal to another position
Returns : boolean
Args : Bio::Map::MappableI or Bio::Map::PositionI
=cut
sub equals {
my ($self,$compare) = @_;
my ($me, $you) = $self->tuple($compare);
return 0 unless $me->isa('Bio::RangeI') and $you->isa('Bio::RangeI');
return $me->equals($you);
}
=head2 overlaps
Title : overlaps
Usage : if($r1->overlaps($r2)) { do stuff }
Function : tests if $r2 overlaps $r1
Args : a range to test for overlap with
Returns : true if the ranges overlap, false otherwise
Inherited: Bio::RangeI
=cut
sub overlaps {
my ($self,$compare) = @_;
my ($me, $you) = $self->tuple($compare);
return 0 unless $me->isa('Bio::RangeI') and $you->isa('Bio::RangeI');
return $me->overlaps($you);
}
=head2 contains
Title : contains
Usage : if($r1->contains($r2) { do stuff }
Function : tests wether $r1 totaly contains $r2
Args : a range to test for being contained
Returns : true if the argument is totaly contained within this range
Inherited: Bio::RangeI
=cut
sub contains {
my ($self,$compare) = @_;
my ($me, $you) = $self->tuple($compare);
return 0 unless $me->isa('Bio::RangeI') and $you->isa('Bio::RangeI');
print STDERR "me=", $me->start. "-", $me->end, " ",
"you=", $you->start. "-", $you->end, "\n"
if $self->verbose > 0;
return $me->contains($you);
}
=head2 intersection
Title : intersection
Usage : ($start, $stop, $strand) = $r1->intersection($r2)
Function : gives the range that is contained by both ranges
Args : a range to compare this one to
Returns : nothing if they do not overlap, or the range that they do overlap
Inherited: Bio::RangeI::intersection
=cut
sub intersection {
my ($self,$compare) = @_;
my ($me, $you) = $self->tuple($compare);
return 0 unless $me->isa('Bio::RangeI') and $you->isa('Bio::RangeI');
return $me->intersection($you);
}
=head2 union
Title : union
Usage : ($start, $stop, $strand) = $r1->union($r2);
: ($start, $stop, $strand) = Bio::Range->union(@ranges);
Function : finds the minimal range that contains all of the ranges
Args : a range or list of ranges to find the union of
Returns : the range containing all of the ranges
Inherited: Bio::RangeI::union
=cut
sub union {
my ($self,$compare) = @_;
my ($me, $you) = $self->tuple($compare);
return 0 unless $me->isa('Bio::RangeI') and $you->isa('Bio::RangeI');
return $me->union($you);
}
=head2 New methods
=cut
=head2 get_chr
Title : get_chr
Usage : my $mychr = $marker->get_chr();
Function: Read only method for the chromosome string of the location.
A shotrcut to $marker->position->chr().
Returns : chromosome value
Args : [optional] new chromosome value
=cut
sub get_chr {
my ($self) = @_;
return undef unless $self->position;
return $self->position->chr;
}
1;
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