| Bio::Search::Hit::BlastHit(3pm) | User Contributed Perl Documentation | Bio::Search::Hit::BlastHit(3pm) |
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;
$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()
| 2021-08-15 | perl v5.32.1 |