Provided by: libbio-perl-perl_1.7.2-2_all bug


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


           # 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.


       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


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AUTHOR - Shin Leong



       Additional contributors names and emails here


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        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

        Title   : _alignment
        Usage   : private

        Title   : _parse
        Usage   : private

        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