bio::search::hsp::hmmer3hsp(3pm) [debian man page]
Bio::Search::HSP::hmmer3HSP(3pm) User Contributed Perl Documentation Bio::Search::HSP::hmmer3HSP(3pm) NAME
Bio::Search::HSP::hmmer3HSP - DESCRIPTION of Object SYNOPSIS
Give standard usage here DESCRIPTION
Describe the object here 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 - Thomas Sharpton Email thomas.sharpton@gmail.com Describe contact details here CONTRIBUTORS
Additional contributors names and emails here 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 = new Bio::Search::HSP::hmmer3HSP(); Function: Builds a new Bio::Search::HSP::hmmer3HSP object Returns : an instance of Bio::Search::HSP::hmmer3HSP Args : get_aln Title : get_aln Usage : my $aln = $hsp->gel_aln Function: Returns a Bio::SimpleAlign representing the HSP alignment Returns : Bio::SimpleAlign Args : none perl v5.14.2 2012-03-02 Bio::Search::HSP::hmmer3HSP(3pm)
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Bio::Search::HSP::WABAHSP(3pm) User Contributed Perl Documentation Bio::Search::HSP::WABAHSP(3pm) NAME
Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments SYNOPSIS
# use this object as you would a GenericHSP # a few other methods have been added including state DESCRIPTION
This object implements a few of the extra methods such as hmmstate_string which returns the HMM state representation for the WABA alignment. We also must implement a method to calculate homology_string since it is not returned by the algorithm in the machine readable format. 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 _ new Title : new Usage : my $obj = Bio::Search::HSP::WABAHSP->new(); Function: Builds a new Bio::Search::HSP::WABAHSP object Returns : Bio::Search::HSP::WABAHSP Args : -hmmstate_seq => the string representing the state output from WABA hmmstate_string Title : hmmstate_string Usage : my $hmmseq = $wabahsp->hmmstate_string(); Function: Get/Set the WABA HMM stateseq Returns : string Args : [optional] string homology_string Title : homolgy_string Usage : my $homology_str = $hsp->homology_string(); Function: Homology string must be calculated for a WABA HSP so we can do so here and cache the result so it is only done once Returns : string Args : none perl v5.14.2 2012-03-02 Bio::Search::HSP::WABAHSP(3pm)