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


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.


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.


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


 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.


 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()


 Title     : found_again
 Usage     : $hit->found_again;
 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()