bio::factory::ftlocationfactory(3pm) [debian man page]
Bio::Factory::FTLocationFactory(3pm) User Contributed Perl Documentation Bio::Factory::FTLocationFactory(3pm) NAME
Bio::Factory::FTLocationFactory - A FeatureTable Location Parser SYNOPSIS
# parse a string into a location object $loc = Bio::Factory::FTLocationFactory->from_string("join(100..200, 400..500"); DESCRIPTION
Implementation of string-encoded location parsing for the Genbank feature table encoding of locations. 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 CONTRIBUTORS
Jason Stajich, jason-at-bioperl-dot-org Chris Fields, cjfields-at-uiuc-dot-edu 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::Factory::FTLocationFactory->new(); Function: Builds a new Bio::Factory::FTLocationFactory object Returns : an instance of Bio::Factory::FTLocationFactory Args : 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. This implementation parses the Genbank feature table encoding of locations. Example : Returns : A Bio::LocationI implementing object. Args : A string. _parse_location Title : _parse_location Usage : $loc = $locfactory->_parse_location( $loc_string) Function: Parses the given location string and returns a location object with start() and end() and strand() set appropriately. Note that this method is private. Returns : A Bio::LocationI implementing object or undef on failure Args : location string perl v5.14.2 2012-03-02 Bio::Factory::FTLocationFactory(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)