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Bio::SearchIO::sim4(3)User Contributed Perl DocumentatioBio::SearchIO::sim4(3)

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:

	 http://bugzilla.open-bio.org/

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().

perl v5.14.1			  2011-07-22		Bio::SearchIO::sim4(3)
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