bio::map::cytomarker(3pm) [debian man page]
Bio::Map::CytoMarker(3pm) User Contributed Perl Documentation Bio::Map::CytoMarker(3pm) NAME
Bio::Map::CytoMarker - An object representing a 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. FEEDBACK
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/wiki/Mailing_lists - About the mailing lists Support 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 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 the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org CONTRIBUTORS
Chad Matsalla bioinformatics1@dieselwurks.com Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org Sendu Bala bix@sendu.me.uk APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ Bio::Map::MarkerI methods get_position_object 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 L<Bio::Map::PositionI> with -element set to self. Returns : L<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. 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 Bio::Map::CytoPosition::cytorange for more details. New methods get_chr 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 perl v5.14.2 2012-03-02 Bio::Map::CytoMarker(3pm)
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Bio::Map::OrderedPositionWithDistance(3pm) User Contributed Perl Documentation Bio::Map::OrderedPositionWithDistance(3pm) NAME
Bio::Map::OrderedPositionWithDistance - Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. SYNOPSIS
use Bio::Map::OrderedPositionWithDistance; # the first marker in the sequence my $position = Bio::Map::OrderedPositionWithDistance->new(-positions => 1, -distance => 22.3 ); # the second marker in the sequence, 15.6 units from the fist one my $position2 = Bio::Map::OrderedPositionWithDistance->new(-positions => 2, -distance => 15.6 ); # the third marker in the sequence, coincidental with the second # marker my $position3 = Bio::Map::OrderedPositionWithDistance->new(-positions => 3, -distance => 0 ); DESCRIPTION
This object is an implementation of the PositionI interface and the Position object handles the specific values of a position. OrderedPositionWithDistance is intended to be slightly more specific then Position but only specific enough for a parser from the MarkerIO subsystem to create and then pass to a client application to bless into the proper type. For an example of how this is intended to work, see the Mapmaker.pm. No units are assumed here - units are handled by context of which Map a position is placed in. Se Bio::Map::Position for additional information. FEEDBACK
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/wiki/Mailing_lists - About the mailing lists Support 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 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 the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Chad Matsalla Email bioinformatics1@dieselwurks.com CONTRIBUTORS
Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $obj = Bio::Map::OrderedPositionWithDistance->new(); Function: Builds a new Bio::Map::OrderedPositionWithDistance object Returns : Bio::Map::OrderedPositionWithDistance Args : -positions - Should be a single value representing the order of this marker within the list of markers -distance - The distance this marker is from the marker before it. 0 reflects coincidentality. distance($new_distance) Title : distance($new_distance) Usage : $position->distance(new_distance) _or_ $position->distance() Function: get/set the distance of this position from the previous marker Returns : A scalar representing the current distance for this position. Args : If $new_distance is provided the distance of this Position will be set to $new_distance perl v5.14.2 2012-03-02 Bio::Map::OrderedPositionWithDistance(3pm)