Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Search::Hit::BlastHit - 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()