bio::factory::locationfactoryi(3pm) [debian man page]
Bio::Factory::LocationFactoryI(3pm) User Contributed Perl Documentation Bio::Factory::LocationFactoryI(3pm) NAME
Bio::Factory::LocationFactoryI - A factory interface for generating locations from a string SYNOPSIS
# Do not use directly, see Bio::Factory::LocationFactory for example use Bio::Factory::FTLocationFactory; my $locfact = Bio::Factory::FTLocationFactory->new(); my $location = $locfact->from_string("1..200"); print $location->start(), " ", $location->end(), " ", $location->strand," "; DESCRIPTION
An interface for Location Factories which generate Bio::LocationI objects from a string. 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 - Hilmar Lapp Email hlapp at gmx.net APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ from_string Title : from_string Usage : $loc = $locfactory->from_string("100..200"); Function: Parses the given string and returns a Bio::LocationI implementing object representing the location encoded by the string. Different implementations may support different encodings. An example of a commonly used encoding is the Genbank feature table encoding of locations. Example : Returns : A Bio::LocationI implementing object. Args : A string. perl v5.14.2 2012-03-02 Bio::Factory::LocationFactoryI(3pm)
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Bio::Location::AvWithinCoordPolicy(3pm) User Contributed Perl Documentation Bio::Location::AvWithinCoordPolicy(3pm) NAME
Bio::Location::AvWithinCoordPolicy - class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise SYNOPSIS
See Bio::Location::CoordinatePolicyI DESCRIPTION
CoordinatePolicyI implementing objects are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for it. This class will compute the coordinates such that for fuzzy locations of type WITHIN and BETWEEN the average of the two limits will be returned, and for all other locations it will return the widest possible range, but by using some common sense. This means that e.g. locations like "<5..100" (start before position 5) will return 5 as start (returned values have to be positive integers). FEEDBACK
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Hilmar Lapp, Jason Stajich Email <hlapp-at-gmx-dot-net>, <jason-at-bioperl-dot-org> APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ start Title : start Usage : $start = $policy->start($location); Function: Get the integer-valued start coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. end Title : end Usage : $end = $policy->end($location); Function: Get the integer-valued end coordinate of the given location as computed by this computation policy. Returns : A positive integer number. Args : A Bio::LocationI implementing object. perl v5.14.2 2012-03-02 Bio::Location::AvWithinCoordPolicy(3pm)