Bio::Search::Hit::BlastHit(3)

NAME
Bio::Search::Hit::BlastHit - 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.

  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 - Jason Stajich and Steve Chervitz
Email jason@bioperl.org Email sac@bioperl.org

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

See Also : found_again()

  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

See Also : iteration()