bio::map::linkageposition(3pm) [debian man page]
Bio::Map::LinkagePosition(3pm) User Contributed Perl Documentation Bio::Map::LinkagePosition(3pm) NAME
Bio::Map::LinkagePosition - Create a Position for a Marker that will be placed on a Bio::Map::LinkageMap SYNOPSIS
use Bio::Map::Position; my $position = Bio::Map::LinkagePosition->new(-positions => 1, -distance => 22.1 ); # can get listing of positions my @positions = $position->each_position; DESCRIPTION
Position for a Bio::Map::MarkerI compliant object that will be placed on a Bio::Map::LinkageMap. See Bio::Map::MarkerI and Bio::Map::LinkageMap for details 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 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 _ new Title : new Usage : my $obj = Bio::Map::LinkagePosition->new(-positions => $position, -distance => $distance); Function: Builds a new Bio::Map::LinkagePosition object Returns : Bio::Map::LinkagePosition Args : -order => the relative order of this marker on a linkage map -positions => positions on a map Bio::Map::PositionI methods order Title : order Usage : $o_position->order($order) my $order = $o_position->order() Function: get/set the order position of this position in a map Returns : int Args : none to get, int to set perl v5.14.2 2012-03-02 Bio::Map::LinkagePosition(3pm)
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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)