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Usage of search facilities
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Bio::SearchIO::hmmer3(3pm) User Contributed Perl Documentation Bio::SearchIO::hmmer3(3pm) NAME
Bio::SearchIO::hmmer3 - 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::SearchIO::Hmmer3->new(); Function: Builds a new Bio::SearchIO::Hmmer3 object Returns : an instance of Bio::SearchIO::Hmmer3 Args : -fh/-file => HMMER filename -format => 'hmmer3' next_result Title : next_result Usage : my $hit = $searchio->next_result; Function: Returns the next Result from a search Returns : Bio::Search::Result::ResultI object Args : none start_element Title : start_element Usage : $eventgenerator->start_element Function: Handles a start event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' end_element Title : end_element Usage : $eventgeneartor->end_element Function: Handles and end element event Returns : none Args : hashref with at least 2 keys 'Data' and 'Name' element Title : element Usage : $eventhandler->element({'Name' => $name, 'Data' => $str}); Function: Convienence method that calls start_element, characters, end_element Returns : none Args : Hash ref with the keys 'Name' and 'Data' characters Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string within_element Title : within_element Usage : if( $eventgenerator->within_element( $element ) ) {} Function: Test if we are within a particular element This is different than 'in' because within can be tested for a whole block Returns : boolean Args : string element name in_element Title : in_element Usage : if( $eventgenerator->in_element( $element ) ) {} Function: Test if we are in a particular element This is different than 'within' because 'in' only tests its immediate parent Returns : boolean Args : string element name start_document Title : start_document Usage : $eventgenerator->start_document Function: Handle a start document event Returns : none Args : none end_document Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none result_count Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results processed Returns : interger Args : none perl v5.14.2 2012-03-02 Bio::SearchIO::hmmer3(3pm)
