NAME

       Bio::SearchIO::hmmer2 - A parser for HMMER output (hmmpfam, hmmsearch)

SYNOPSIS

           # do not use this class directly it is available through Bio::SearchIO
           use Bio::SearchIO;
           my $in = Bio::SearchIO->new(-format => 'hmmer2',
                                      -file   => 't/data/L77119.hmmer');
           while( my $result = $in->next_result ) {
               # this is a Bio::Search::Result::HMMERResult object
               print $result->query_name(), " for HMM ", $result->hmm_name(), "\n";
               while( my $hit = $result->next_hit ) {
                   print $hit->name(), "\n";
                   while( my $hsp = $hit->next_hsp ) {
                       print "length is ", $hsp->length(), "\n";
                   }
               }
           }

DESCRIPTION

       This object implements a parser for HMMER output.

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-at-bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   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 element event
        Returns : none
        Args    : hashref with at least 2 keys 'Data' and 'Name'

   end_element
        Title   : start_element
        Usage   : $eventgenerator->end_element
        Function: Handles an 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: Convience 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 immediete 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 we have processed
        Returns : integer
        Args    : none