Bio::Search::Hit BlastHit
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Summary
Bio::Search::Hit::BlastHit - Blast-specific subclass of Bio::Search::Hit::GenericHit
Package variables
No package variables defined.
Included modules
Bio::Search::SearchUtils
Inherit
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.
Methods
newDescriptionCode
iterationDescriptionCode
found_againDescriptionCode
Methods description
newcode    nextTop
 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.
iterationcodeprevnextTop
 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_againcodeprevnextTop
 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( $hit->found_again()) { ... }; Returns : Boolean, true (1) if the hit has been found in a previous PSI-BLAST iteration. Returns false (0 or undef) for hits that have not occurred in a previous PSI-BLAST iteration. Argument : Boolean (1 or 0). Only used for setting. Throws : none
See Also : iteration()
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($iter,$found) = $self->_rearrange([qw(ITERATION 
                                            FOUND_AGAIN
                                           )], @args);

  defined $iter   && $self->iteration($iter);
  defined $found  && $self->found_again($found);

  return $self;
}
iterationdescriptionprevnextTop
sub iteration {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_psiblast_iteration'} = $value;
    }
    return $self->{'_psiblast_iteration'};
}
found_againdescriptionprevnextTop
sub found_again {
   my $self = shift;
   return $self->{'_found_again'} = shift if @_;
   return $self->{'_found_again'};
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich and Steve ChervitzTop
Email jason@bioperl.org
Email sac@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _