Raw content of Bio::Map::CytoMarker # $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;