/ 
bioperl-1.0
/ Bio::Search::Result::BlastResult

NAME

Bio::Search::Result::BlastResult - A top-level BLAST Report object

SYNOPSIS

The construction of BlastResult objects is performed by by the Bio::SearchIO::psiblast parser. Therefore, you do not need to use Bio::Search::Result::BlastResult) directly. If you need to construct BlastHits directly, see the new() function for details.

For Bio::SearchIO BLAST parsing usage examples, see the examples/search-blast directory of the Bioperl distribution.

DESCRIPTION

This module supports BLAST versions 1.x and 2.x, gapped and ungapped, and PSI-BLAST.

DEPENDENCIES

Bio::Search::Result::BlastResult.pm is a concrete class that inherits from Bio::Root::Root and Bio::Search::Result::ResultI. It relies on two other modules:

Bio::Search::Hit::BlastHit

Encapsulates a single a single BLAST hit.

Bio::Search::GenericDatabase

Provides an interface to a blast database metadata.

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 one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org              - General discussion
http://bio.perl.org/MailList.html  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

bioperl-bugs@bio.perl.org                   
http://bio.perl.org/bioperl-bugs/

AUTHOR

Steve Chervitz <sac@bioperl.org>

See the FEEDBACK section for where to send bug reports and comments.

ACKNOWLEDGEMENTS

This software was originally developed in the Department of Genetics at Stanford University. I would also like to acknowledge my colleagues at Affymetrix for useful feedback.

COPYRIGHT

Copyright (c) 2001 Steve Chervitz. All Rights Reserved.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

APPENDIX

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

next_hit

See Bio::Search::Result::ResultI::next_hit() for documentation

query_name

See Bio::Search::Result::ResultI::query_name() for documentation

query_length

See Bio::Search::Result::ResultI::query_length() for documentation

query_description

See Bio::Search::Result::ResultI::query_description() for documentation

analysis_method

See Bio::AnalysisResultI::analysis_method() for documentation

This implementation ensures that the name matches /blast/i.

analysis_method_version

See Bio::AnalysisResultI::analysis_method_version() for documentation

analysis_query

See Bio::AnalysisResultI::analysis_query() for documentation

analysis_subject

Usage     : $blastdb = $result->analyis_subject();
Purpose   : Get a Bio::Search::DatabaseI object containing
            information about the database used in the BLAST analysis.
Returns   : Bio::Search::DatabaseI object.
Argument  : n/a

next_feature

Title   : next_feature
Usage   : while( my $feat = $blast_result->next_feature ) { # do something }
Function: Returns the next feature available in the analysis result, or
          undef if there are no more features.
Example :
Returns : A Bio::SeqFeatureI compliant object, in this case, 
          each Bio::Search::HSP::BlastHSP object within each BlastHit.
Args    : None

to_string

Title   : to_string
Usage   : print $blast->to_string;
Function: Returns a string representation for the Blast result. 
          Primarily intended for debugging purposes.
Example : see usage
Returns : A string of the form:
          [BlastResult] <analysis_method> query=<name> <description> db=<database
          e.g.:
          [BlastResult] BLASTP query=YEL060C vacuolar protease B, db=PDBUNIQ 
Args    : None

add_hit

Usage     : $blast->add_hit( $hit );
Purpose   : Adds a hit object to the collection of hits in this BLAST result.
Returns   : n/a
Argument  : A Bio::Search::Hit::HitI object
Comments  : For PSI-BLAST, hits from all iterations are lumped together.
            For any given hit, you can determine the iteration in which it was
            found by checking $hit->iteration().

is_signif

Usage     : $blast->is_signif();
Purpose   : Determine if the BLAST report contains significant hits.
Returns   : Boolean
Argument  : n/a
Comments  : BLAST reports without significant hits but with defined
          : significance criteria will throw exceptions during construction.
          : This obviates the need to check significant() for
          : such objects.

matrix

Usage     : $blast_object->matrix();
Purpose   : Get the name of the scoring matrix used.
          : This is extracted from the report.
Argument  : n/a
Returns   : string or undef if not defined
Comments  : TODO: Deprecate this and implement get_parameter('matrix').

raw_statistics

Usage     : @stats = $blast_result->raw_statistics();
Purpose   : Get the raw, unparsed statistical parameter section of the Blast report.
            This is the section at the end after the last HSP alignment.
Argument  : n/a
Returns   : Array of strings

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 deteriming 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 (PSI-BLAST)
            If iteration number is not specified and this is a PSI-BLAST 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 (PSI-BLAST)

iterations

Usage     : $num_iterations = $blast->iterations;  (get)
            $blast->iterations($num_iterations);   (set)
Purpose   : Set/get the number of iterations in the Blast Report (PSI-BLAST).
Returns   : Total number of iterations in the report
Argument  : integer  (when setting)

psiblast

Usage     : if( $blast->psiblast ) { ... }
Purpose   : Set/get a boolean indicator whether or not the report 
            is a PSI-BLAST report.
Returns   : 1 if PSI-BLAST, undef if not.
Argument  : 1 (when setting)