NAME¶
Bio::Search::Result::CrossMatchResult - CrossMatch-specific subclass of
Bio::Search::Result::GenericResult
SYNOPSIS¶
# Working with iterations (CrossMatch results)
$result->next_iteration();
$result->num_iterations();
$result->iteration();
$result->iterations();
# See Bio::Search::Result::GenericResult for information about working with
Results.
# See Bio::Search::Iteration::IterationI # for details about working with
iterations.
# TODO: # * Show how to configure a SearchIO stream so that it generates #
CrossMatchResult objects.
DESCRIPTION¶
This object is a subclass of Bio::Search::Result::GenericResult 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 _
new¶
Title : new
Usage : my $obj = Bio::Search::Result::CrossMatchResult->new();
Function: Builds a new Bio::Search::Result::CrossMatchResult object
Returns : Bio::Search::Result::CrossMatchResult
Args : See Bio::Search::Result::GenericResult();
The following parameters are specific to CrossMatchResult:
-iterations => array ref of Bio::Search::Iteration::IterationI objects
-inclusion_threshold => e-value threshold for inclusion in the
CrossMatch score matrix model (blastpgp)
hits¶
This method overrides Bio::Search::Result::GenericResult::hits to take into
account the possibility of multiple iterations, as occurs in CrossMatch
reports.
If there are multiple iterations, all 'new' hits for all iterations are
returned. These are the hits that did not occur in a previous iteration.
See Also: Bio::Search::Result::GenericResult::hits
next_hit¶
This method overrides Bio::Search::Result::GenericResult::next_hit to take into
account the possibility of multiple iterations, as occurs in CrossMatch
reports.
If there are multiple iterations, calling
next_hit() traverses the all of
the hits, old and new, for each iteration, calling
next_hit() on each
iteration.
See Also: Bio::Search::Iteration::GenericIteration::next_hit
num_hits¶
This method overrides Bio::Search::Result::GenericResult::num_hits to take into
account the possibility of multiple iterations, as occurs in CrossMatch
reports.
If there are multiple iterations, calling
num_hits() returns the number
of 'new' hits for each iteration. These are the hits that did not occur in a
previous iteration.
See Also: Bio::Search::Result::GenericResult::num_hits
add_iteration¶
Title : add_iteration
Usage : $report->add_iteration($iteration)
Function: Adds a IterationI to the stored list of iterations
Returns : Number of IterationI currently stored
Args : Bio::Search::Iteration::IterationI
next_iteration¶
Title : next_iteration
Usage : while( $it = $result->next_iteration()) { ... }
Function: Returns the next Iteration object, representing all hits
found within a given CrossMatch iteration.
Returns : a Bio::Search::Iteration::IterationI object or undef if there are no more.
Args : none
iteration¶
Usage : $iteration = $blast->iteration( $number );
Purpose : Get an IterationI object for the specified iteration
in the search result (CrossMatch).
Returns : Bio::Search::Iteration::IterationI object
Throws : Bio::Root::NoSuchThing exception if $number is not within
range of the number of iterations in this report.
Argument : integer (optional, if not specified get the last iteration)
First iteration = 1
num_iterations¶
Usage : $num_iterations = $blast->num_iterations;
Purpose : Get the number of iterations in the search result (CrossMatch).
Returns : Total number of iterations in the report
Argument : none (read-only)
number_of_iterations¶
Same as num_iterations.
round¶
Same as iteration.
iterations¶
Title : iterations
Usage : my @iterations = $result->iterations
Function: Returns the IterationI objects contained within this Result
Returns : Array of L<Bio::Search::Iteration::IterationI> objects
Args : none
no_hits_found¶
Usage : $nohits = $blast->no_hits_found( $iteration_number );
Purpose : Get boolean indicator indicating whether or not any hits
were present in the report.
This is NOT the same as determining the number of hits via
the hits() method, which will return zero hits if there were no
hits in the report or if all hits were filtered out during the parse.
Thus, this method can be used to distinguish these possibilities
for hitless reports generated when filtering.
Returns : Boolean
Argument : (optional) integer indicating the iteration number (CrossMatch)
If iteration number is not specified and this is a CrossMatch result,
then this method will return true only if all iterations had
no hits found.
set_no_hits_found¶
Usage : $blast->set_no_hits_found( $iteration_number );
Purpose : Set boolean indicator indicating whether or not any hits
were present in the report.
Returns : n/a
Argument : (optional) integer indicating the iteration number (CrossMatch)
_next_iteration_index¶
Title : _next_iteration_index
Usage : private
rewind¶
Title : rewind
Usage : $result->rewind;
Function: Allow one to reset the Iteration iterator to the beginning
Since this is an in-memory implementation
Returns : none
Args : none
inclusion_threshold¶
Title : inclusion_threshold
Usage : my $incl_thresh = $result->inclusion_threshold; (read-only)
Function: Gets the e-value threshold for inclusion in the CrossMatch
score matrix model (blastpgp) that was used for generating the report
being parsed.
Returns : number (real) or undef if not a CrossMatch report.
Args : none