bio::factory::analysisi(3pm) [debian man page]
Bio::Factory::AnalysisI(3pm) User Contributed Perl Documentation Bio::Factory::AnalysisI(3pm) NAME
Bio::Factory::AnalysisI - An interface to analysis tool factory SYNOPSIS
This is an interface module - you do not instantiate it. Use Bio::Tools::Run::AnalysisFactory module: use Bio::Tools::Run::AnalysisFactory; my $list = Bio::Tools::Run::AnalysisFactory->new->available_analyses; DESCRIPTION
This interface contains all public methods for showing available analyses and for creating objects representing them. 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
Martin Senger (martin.senger@gmail.com) COPYRIGHT
Copyright (c) 2003, Martin Senger and EMBL-EBI. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. DISCLAIMER
This software is provided "as is" without warranty of any kind. SEE ALSO
o http://www.ebi.ac.uk/Tools/webservices/soaplab/guide APPENDIX
This is actually the main documentation... If you try to call any of these methods directly on this "Bio::Factory::AnalysisI" object you will get a not implemented error message. You need to call them on a "Bio::Tools::Run::AnalysisFactory" object instead. available_categories Usage : $factory->available_categories; Returns : an array reference with the names of available categories Args : none The analysis tools may be grouped into categories by their functional similarity, or by the similar data types they deal with. This method shows all available such categories. available_analyses Usage : $factory->available_analyses; $factory->available_analyses ($category); Returns : an array reference with the names of all available analyses, or the analyses available in the given '$category' Args : none || category_name Show available analyses. Their names usually consist of category analysis names, separated by "::". create_analysis Usage : $factory->create_analysis ($name); Returns : a Bio::Tools::Run::Analyis object Args : analysis name A real factory method creating an analysis object. The created object gets all access and location information from the factory object. perl v5.14.2 2012-03-02 Bio::Factory::AnalysisI(3pm)
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Bio::Tools::Run::Profile(3pm) User Contributed Perl Documentation Bio::Tools::Run::Profile(3pm) NAME
Bio::Tools::Run::Profile SYNOPSIS
Build a Profile factory # $paramfile is the full path to the seg binary file my @params = ('DB',$dbfile,'PROGRAM',$paramfile); my $factory = Bio::Tools::Run::Profile->new($param); # Pass the factory a Bio::PrimarySeqI object # @feats is an array of Bio::SeqFeature::Generic objects my @feats = $factory->run($seq); DESCRIPTION
Wrapper module for the pfscan program 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 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: http://redmine.open-bio.org/projects/bioperl/ AUTHOR - Balamurugan Kumarasamy Email: fugui@worf.fugu-sg.org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ program_name Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None program_dir Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args : new Title : new Usage : my $factory= Bio::Tools::Run::Profile->new($param); Function: creates a new Profile factory Returns: Bio::Tools::Run::Profile Args : predict_protein_features Title : predict_protein_features Usage : DEPRECATED. Use $factory->run($seq) instead. Function: Runs Profile and creates an array of featrues Returns : An array of L<Bio::SeqFeature::FeaturePair> objects Args : A Bio::PrimarySeqI run Title : run Usage : my @feats = $factory->run($seq) Function: Runs Profile Returns : An array of L<Bio::SeqFeature::FeaturePair> objects Args : A Bio::PrimarySeqI _input Title : _input Usage : $factory->_input($seqFile) Function: get/set for input file Returns : Args : _run Title : _run Usage : $factory->_run() Function: Makes a system call and runs pfscan Returns : An array of L<Bio::SeqFeature::FeaturePair> objects Args : _writeSeqFile Title : _writeSeqFile Usage : $factory->_writeSeqFile($seq) Function: Creates a file from the given seq object Returns : A string(filename) Args : Bio::PrimarySeqI perl v5.12.3 2011-06-18 Bio::Tools::Run::Profile(3pm)