Bio::SearchIO::fasta(3pm)				User Contributed Perl Documentation				 Bio::SearchIO::fasta(3pm)

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.

perl v5.14.2							    2012-03-02						 Bio::SearchIO::fasta(3pm)