Bio::Map CytoMarker
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Summary
Bio::Map::CytoMarker - An object representing a marker.
Package variables
No package variables defined.
Included modules
Bio::Map::CytoPosition
Inherit
Bio::Map::Marker
Synopsis
  $o_usat = Bio::Map::CytoMarker->new(-name=>'Chad Super Marker 2',
-position => $pos);
Description
This object handles markers with a positon in a cytogenetic map known.
This marker will have a name and a position.
Methods
get_position_objectDescriptionCode
get_chrDescriptionCode
Methods description
get_position_objectcode    nextTop
 Title   : get_position_class
Usage : my $position = $marker->get_position_object();
Function: To get an object of the default Position class
for this Marker. Subclasses should redefine this method.
The Position returned needs to be a Bio::Map::PositionI with
-element set to self.
Returns : Bio::Map::PositionI
Args : none for an 'empty' PositionI object, optionally
Bio::Map::MapI and value string to set the Position's -map and -value
attributes.
get_chrcodeprevnextTop
 Title   : get_chr
Usage : my $mychr = $marker->get_chr();
Function: Read only method for the chromosome string of the location.
A shortcut to $marker->position->chr().
Returns : chromosome value
Args : [optional] new chromosome value
Methods code
get_position_objectdescriptionprevnextTop
sub get_position_object {
   my ($self, $map, $value) = @_;
   $map ||= $self->default_map;
   if ($value) {
	  $self->throw("Value better be scalar, not [$value]") unless ref($value) eq '';
   }
   
   my $pos = Bio::Map::CytoPosition->new();
   $pos->map($map) if $map;
   $pos->value($value) if $value;
   $pos->element($self);
   return $pos;
}
get_chrdescriptionprevnextTop
sub get_chr {
    my ($self) = @_;
    return unless $self->position;
    return $self->position->chr;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Heikki Lehvaslaiho Top
Email heikki-at-bioperl-dot-org
CONTRIBUTORSTop
Chad Matsalla bioinformatics1@dieselwurks.com
Lincoln Stein lstein@cshl.org
Jason Stajich jason@bioperl.org
Sendu Bala bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::Map::MarkerI methodsTop
Comparison methodsTop
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
Bio::Map::CytoPosition::cytorange for more details.
New methodsTop