bio::map::positionwithsequence(3pm) [debian man page]
Bio::Map::PositionWithSequence(3pm) User Contributed Perl Documentation Bio::Map::PositionWithSequence(3pm) NAME
Bio::Map::PositionWithSequence - A position with a sequence. SYNOPSIS
use Bio::Map::PositionWithSequence; my $pos = Bio::Map::PositionWithSequence->new(-map => $map, -element => $element, -start => 0, -seq => 'ATGC'); DESCRIPTION
Have a position with a sequence, eg. define what the binding site sequence of a certain transcription factor binding site is by modelling it as one of these objects with the -element assigned to a Bio::Map::TranscriptionFactor instance. 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 - Sendu Bala Email bix@sendu.me.uk 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::PositionWithSequence->new(); Function: Builds a new Bio::Map::PositionWithSequence object Returns : Bio::Map::PositionWithSequence Args : -map => Bio::Map::GeneMap object -element => Bio::Map::Gene object -relative => Bio::Map::GeneRelative object -seq => string, length of this string will set the length of this position's range * If this position has no range, or if a single value can describe the range * -value => scalar : something that describes the single point position or range of this Position, most likely an int * Or if this position has a range, at least two of * -start => int : value of the start co-ordinate -end => int : value of the end co-ordinate -length => int : length of the range seq Title : seq Usage : my $string = $obj->seq(); Function: Get/set the sequence as a string of letters. Returns : scalar Args : Optionally on set the new value (a string). An optional second argument presets the alphabet (otherwise it will be guessed). perl v5.14.2 2012-03-02 Bio::Map::PositionWithSequence(3pm)
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Bio::Map::MarkerI(3pm) User Contributed Perl Documentation Bio::Map::MarkerI(3pm) NAME
Bio::Map::MarkerI - Interface for basic marker functionality SYNOPSIS
# do not use this module directly # See Bio::Map::Marker for an example of # implementation. DESCRIPTION
A Marker is a Bio::Map::Mappable with some properties particular to markers. It also offers a number of convienience methods to make dealing with map elements easier. 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 - Jason Stajich Email jason@bioperl.org CONTRIBUTORS
Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org Chad Matsalla bioinformatics1@dieselwurks.com 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 _ 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. position Title : position Usage : my $position = $mappable->position(); $mappable->position($position); Function: Get/Set the Position of this Marker (where it is on which map), purging all other positions before setting. Returns : L<Bio::Map::PositionI> Args : Bio::Map::PositionI OR Bio::Map::MapI AND scalar OR scalar, but only if the marker has a default map positions Title : positions Usage : $marker->positions([$pos1, $pos2, $pos3]); Function: Add multiple Bio::Map::PositionI to this marker Returns : n/a Args : array ref of $map/value tuples or array ref of Bio::Map::PositionI default_map Title : default_map Usage : my $map = $marker->default_map(); Function: Get/Set the default map for the marker. Returns : L<Bio::Map::MapI> Args : [optional] new L<Bio::Map::MapI> in_map Title : in_map Usage : if ( $marker->in_map($map) ) {} Function: Tests if this marker is found on a specific map Returns : boolean Args : a map unique id OR Bio::Map::MapI perl v5.14.2 2012-03-02 Bio::Map::MarkerI(3pm)