man Bio::Search::Hit::BlastHit (3): Blast-specific subclass of Bio::Search::Hit::GenericHit

SYNOPSIS

use Bio::Search::Hit::BlastHit;
my $hit = Bio::Search::Hit::BlastHit->new(-algorithm => 'blastp');

# See Bio::Search::Hit::GenericHit for information about working with Hits.

# TODO: Describe how to configure a SearchIO stream so that it generates # GenericHit objects.

DESCRIPTION

This object is a subclass of Bio::Search::Hit::GenericHit and provides some operations that facilitate working with BLAST and PSI-BLAST Hits.

For general information about working with Hits, see Bio::Search::Hit::GenericHit.

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 - Jason Stajich and Steve Chervitz

Email [email protected] Email [email protected]

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::Hit::GenericHit->new();
 Function: Builds a new Bio::Search::Hit::GenericHit object 
 Returns : Bio::Search::Hit::GenericHit
 Args    : See Bio::Search::Hit::GenericHit() for other args.
           Here are the BLAST-specific args that can be used when
           creating BlastHit objects:
           -iteration    => integer for the PSI-Blast iteration number
           -found_again  => boolean, true if hit appears in a 
                            "previously found" section of a PSI-Blast report.

iteration

 Usage     : $hit->iteration( $iteration_num );
 Purpose   : Gets the iteration number in which the Hit was found.
 Example   : $iteration_num = $sbjct->iteration();
 Returns   : Integer greater than or equal to 1
             Non-PSI-BLAST reports will report iteration as 1, but this number
             is only meaningful for PSI-BLAST reports.
 Argument  : iteration_num (optional, used when setting only)
 Throws    : none

found_again

 Title     : found_again
 Usage     : $hit->found_again;
             $hit->found_again(1);
 Purpose   : Gets a boolean indicator whether or not the hit has
             been found in a previous iteration.
             This is only applicable to PSI-BLAST reports.
              This method indicates if the hit was reported in the 
              "Sequences used in model and found again" section of the
              PSI-BLAST report or if it was reported in the
              "Sequences not found previously or not previously below threshold"
              section of the PSI-BLAST report. Only for hits in iteration > 1.
 Example   : if( $hit->found_again()) { ... };
 Returns   : Boolean, true (1) if the hit has been found in a 
             previous PSI-BLAST iteration.
             Returns false (0 or undef) for hits that have not occurred in a
             previous PSI-BLAST iteration.
 Argument  : Boolean (1 or 0). Only used for setting.
 Throws    : none