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

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