Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::SearchIO::fasta - A SearchIO parser for FASTA results

SYNOPSIS

         # Do not use this object directly, use it through the SearchIO system
          use Bio::SearchIO;
          my $searchio = Bio::SearchIO->new(-format => 'fasta',
                           -file   => 'report.FASTA');
          while( my $result = $searchio->next_result ) {
           # ... do what you would normally doi with Bio::SearchIO.
          }

DESCRIPTION

       This object contains the event based parsing code for FASTA format reports.  It creates
       Bio::Search::HSP::FastaHSP objects instead of Bio::Search::HSP::GenericHSP for the HSP
       objects.

       This module will parse -m 9 -d 0 output as well as default m 1 output from FASTA as well
       as SSEARCH.

       Also see the SearchIO HOWTO: http://bioperl.open-bio.org/wiki/HOWTO:SearchIO
       <http://bioperl.open-bio.org/wiki/HOWTO:SearchIO>.

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, Aaron Mackey, William Pearson

       Email jason-at-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::SearchIO::fasta->new();
        Function: Builds a new Bio::SearchIO::fasta object
        Returns : Bio::SearchIO::fasta
        Args    : -idlength - set ID length to something other
                              than the default (6), this is only
                              necessary if you have compiled FASTA
                              with a new default id length to display
                              in the HSP alignment blocks

   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

   _mode
        Title   : _mode
        Usage   : $obj->_mode($newval)
        Function:
        Example :
        Returns : value of _mode
        Args    : newvalue (optional)

   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 'in' because within can be tested
                  for a whole block.
        Returns : boolean
        Args    : string element name

   start_document
        Title   : start_document
        Usage   : $eventgenerator->start_document
        Function: Handles 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

   idlength
        Title   : idlength
        Usage   : $obj->idlength($newval)
        Function: Internal storage of the length of the ID desc
                  in the HSP alignment blocks.  Defaults to
                  $IDLENGTH class variable value
        Returns : value of idlength
        Args    : newvalue (optional)

   result_count
        Title   : result_count
        Usage   : my $count = $searchio->result_count
        Function: Returns the number of results we have processed
        Returns : integer
        Args    : none

   _will_handle
        Title   : _will_handle
        Usage   : Private method. For internal use only.
                     if( $self->_will_handle($type) ) { ... }
        Function: Provides an optimized way to check whether or not an element of a
                  given type is to be handled.
        Returns : Reference to EventHandler object if the element type is to be handled.
                  undef if the element type is not to be handled.
        Args    : string containing type of element.

       Optimizations:

       1.
         Using the cached pointer to the EventHandler to minimize repeated lookups.

       2.
         Caching the will_handle status for each type that is encountered so that it only need be
         checked by calling handler->will_handle($type) once.

       This does not lead to a major savings by itself (only 5-10%).  In combination with other
       optimizations, or for large parse jobs, the savings good be significant.

       To test against the unoptimized version, remove the parentheses from around the third term
       in the ternary " ? : " operator and add two calls to $self->_eventHandler().

   _processHits
        Title   : _processHits
        Usage   : Private method. For internal use only.
        Function: Process/report any hits/hsps we saw in the top table, not in alignments.
        Returns : nothing.
        Args    : array of hits to process.