debian man page for bio::searchio::cross_match

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

NAME
       Bio::SearchIO::cross_match - CrossMatch-specific subclass of Bio::SearchIO

SYNOPSIS
	   # Working with iterations (CrossMatch results)
	   my $searchIO = Bio::SearchIO->new( -format => 'cross_match',
				   -file   => "$file.screen.out" )
	   while(my $r = $searchIO->next_result) {
	     while(my $hit = $r->next_hit) {
	       while(my $hsp = $hit->next_hsp) {
		  #Do the processing here.
	       }
	     }
	   }
       # See Bio::SearchIO for information about working with Results.

       # See Bio::SearchIO # for details about working with Bio::SearchIO.

DESCRIPTION
       This object is a subclass of Bio::SearchIO and provides some operations that facilitate working with CrossMatch and CrossMatch results.

       For general information about working with Results, see Bio::Search::Result::GenericResult.

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 - Shin Leong
       Email sleong@watson.wustl.edu

CONTRIBUTORS
       Additional contributors names and emails here

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	: $result = stream->next_result
	Function: Reads the next ResultI object from the stream and returns it.

		  Certain driver modules may encounter entries in the stream that
		  are either misformatted or that use syntax not yet understood
		  by the driver. If such an incident is recoverable, e.g., by
		  dismissing a feature of a feature table or some other non-mandatory
		  part of an entry, the driver will issue a warning. In the case
		  of a non-recoverable situation an exception will be thrown.
		  Do not assume that you can resume parsing the same stream after
		  catching the exception. Note that you can always turn recoverable
		  errors into exceptions by calling $stream->verbose(2) (see
		  Bio::Root::RootI POD page).
	Returns : A Bio::Search::Result::ResultI object
	Args	: n/a

       See Bio::Root::RootI

   _alignment
	Title	: _alignment
	Usage	: private

   _parse
	Title	: _parse
	Usage	: private

   result_count
	Title	: result_count
	Usage	: $num = $stream->result_count;
	Function: Gets the number of CrossMatch results that have been parsed.
	Returns : integer
	Args	: none
	Throws	: none

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