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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::Factory::TreeFactoryI(3pm) 			User Contributed Perl Documentation			   Bio::Factory::TreeFactoryI(3pm)

NAME
Bio::Factory::TreeFactoryI - Factory Interface for getting and writing trees from/to a data stream SYNOPSIS
# get a $factory from somewhere Bio::TreeIO likely my $treeio = Bio::TreeIO->new(-format => 'newick', #this is phylip/newick format -file => 'file.tre'); my $treeout = Bio::TreeIO->new(-format => 'nexus', -file => ">file.nexus"); # convert tree formats from newick/phylip to nexus while(my $tree = $treeio->next_tree) { $treeout->write_tree($tree); } DESCRIPTION
This interface describes the minimal functions needed to get and write trees from a data stream. It is implemented by the Bio::TreeIO factory. 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 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_tree Title : next_tree Usage : my $tree = $factory->next_tree; Function: Get a tree from the factory Returns : L<Bio::Tree::TreeI> Args : none write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Writes a tree onto the stream Returns : none Args : L<Bio::Tree::TreeI> perl v5.14.2 2012-03-02 Bio::Factory::TreeFactoryI(3pm)
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