Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::SearchIO::sim4 - parser for Sim4 alignments

SYNOPSIS

         # do not use this module directly, it is a driver for SearchIO
         use Bio::SearchIO;
         my $searchio = Bio::SearchIO->new(-file => 'results.sim4',
                                          -format => 'sim4');

         while ( my $result = $searchio->next_result ) {
             while ( my $hit = $result->next_hit ) {
                 while ( my $hsp = $hit->next_hsp ) {
                     # ...
                 }
             }
         }

DESCRIPTION

       This is a driver for the SearchIO system for parsing Sim4.
       http://globin.cse.psu.edu/html/docs/sim4.html

       Cannot parse LAV or 'exon file' formats (A=2 or A=5)

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org

CONTRIBUTORS

       Luc Gauthier (lgauthie@hotmail.com)

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::sim4->new();
        Function: Builds a new Bio::SearchIO::sim4 object
        Returns : an instance of Bio::SearchIO::sim4
        Args    :

   next_result
        Title   : next_result
        Usage   : my $result = $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 '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: 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

   _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().