Bio::S...hResult(3pm)

✨ NAME ✨

Bio::Search::Result::CrossMatchResult — okay so this is the CrossMatch-specific subclass of Bio::Search::Result::GenericResult, bestie. 🎀

(and yeah, this is the Bio::S...hResult(3pm) page — just so you know where you landed 💅)

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🦋 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.

and yeah that TODO is literally still a TODO, no cap 🙈 the docs said "we'll get to it" and then simply did not.

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🌸 DESCRIPTION 🌸

This object is a subclass of Bio::Search::Result::GenericResult, and it serves up some operations that make working with CrossMatch and CrossMatch results actually bearable, fr fr. 🫶

For the general tea about working with Results, go read Bio::Search::Result::GenericResult. ✨

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💌 FEEDBACK 💌

🫶 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules — like, the glow-up is a whole group project, and your participation is much appreciated. 🥹 Send your comments and suggestions preferably to the Bioperl mailing list:

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 so we can keep track of the bugs and their resolution — we love a paper trail, periodt. Bug reports can be submitted via the web:

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

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👑 AUTHOR - Shin Leong

Email sleong@watson.wustl.edu 💖

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🌈 CONTRIBUTORS

Additional contributors names and emails here ✨

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⭐ APPENDIX ⭐

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

🍓 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 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

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and that's the whole page, bestie 💖 this was perl v5.32.1, dated 2021-08-15 — go forth and iterate responsibly 🧚✨