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.\" ========================================================================
.\"
.IX Title "Bio::SearchIO::cross_match 3pm"
.TH Bio::SearchIO::cross_match 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::SearchIO::cross_match \- CrossMatch\-specific subclass of Bio::SearchIO
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 10
\&    # Working with iterations (CrossMatch results)
\&    my $searchIO = Bio::SearchIO\->new( \-format => \*(Aqcross_match\*(Aq,
\&                            \-file   => "$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.
\&        }
\&      }
\&    }
.Ve
.PP
See Bio::SearchIO for details about working with Bio::SearchIO.
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object is a subclass of Bio::SearchIO
and provides some operations that facilitate working with CrossMatch
and CrossMatch results.
.PP
For general information about working with Results, see 
Bio::Search::Result::GenericResult.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Shin Leong"
.IX Header "AUTHOR - Shin Leong"
Email sleong@watson.wustl.edu
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Additional contributors names and emails here
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "next_result"
.IX Subsection "next_result"
.Vb 3
\& 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
.Ve
.PP
See Bio::Root::RootI
.SS "_alignment"
.IX Subsection "_alignment"
.Vb 2
\& Title   : _alignment
\& Usage   : private
.Ve
.SS "_parse"
.IX Subsection "_parse"
.Vb 2
\& Title   : _parse
\& Usage   : private
.Ve
.SS "result_count"
.IX Subsection "result_count"
.Vb 6
\& 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
.Ve