Bio::Search::Result BlastResult
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Summary
Bio::Search::Result::BlastResult - Blast-specific subclass of Bio::Search::Result::GenericResult
Package variables
No package variables defined.
Included modules
Bio::Search::BlastStatistics
Inherit
Bio::Search::Result::GenericResult
Synopsis
    # Working with iterations (PSI-BLAST results)
$result->next_iteration(); $result->num_iterations(); $result->iteration(); $result->iterations();
# See Bio::Search::Result::GenericResult for information about working with Results.
# See Bio::Search::Iteration::IterationI
# for details about working with iterations.
# TODO:
# * Show how to configure a SearchIO stream so that it generates
# BlastResult objects.
Description
This object is a subclass of Bio::Search::Result::GenericResult
and provides some operations that facilitate working with BLAST
and PSI-BLAST results.
For general information about working with Results, see
Bio::Search::Result::GenericResult.
Methods
newDescriptionCode
hitsDescriptionCode
next_hitDescriptionCode
num_hitsDescriptionCode
add_hitDescriptionCode
add_iterationDescriptionCode
next_iterationDescriptionCode
iterationDescriptionCode
num_iterationsDescriptionCode
number_of_iterationsDescriptionCode
roundDescriptionCode
iterationsDescriptionCode
psiblastDescriptionCode
no_hits_foundDescriptionCode
set_no_hits_foundDescriptionCode
_next_iteration_indexDescriptionCode
rewindDescriptionCode
inclusion_thresholdDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Search::Result::BlastResult->new();
Function: Builds a new Bio::Search::Result::BlastResult object
Returns : Bio::Search::Result::BlastResult
Args : See Bio::Search::Result::GenericResult();
The following parameters are specific to BlastResult:
-iterations => array ref of Bio::Search::Iteration::IterationI objects
-inclusion_threshold => e-value threshold for inclusion in the
PSI-BLAST score matrix model (blastpgp)
hitscodeprevnextTop
 Title   : hits
Usage : my @hits = $result->hits
Function: Returns the available hits for this Result
Returns : Array of Bio::Search::Hit::HitI objects
Args : none
Note : This method overrides Bio::Search::Result::GenericResult::hits to
take into account the possibility of multiple iterations, as occurs
in PSI-BLAST reports.
If there are multiple iterations, all 'new' hits for all iterations
are returned. These are the hits that did not occur in a previous
iteration.
See Also: Bio::Search::Result::GenericResult::hits
next_hitcodeprevnextTop
 Title   : next_hit
Usage : while( $hit = $result->next_hit()) { ... }
Function: Returns the next available Hit object, representing potential
matches between the query and various entities from the database.
Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
Args : none
Note : This method overrides Bio::Search::Result::GenericResult::next_hit
to take into account the possibility of multiple iterations, as
occurs in PSI-BLAST reports.
If there are multiple iterations, calling next_hit() traverses the all of the hits, old and new, for each iteration, calling next_hit() on each iteration. See Also: Bio::Search::Iteration::GenericIteration::next_hit
num_hitscodeprevnextTop
 Title   : num_hits
Usage : my $hitcount= $result->num_hits
Function: returns the number of hits for this query result
Returns : integer
Args : none
Note : This method overrides Bio::Search::Result::GenericResult::num_hits
to take into account the possibility of multiple iterations, as
occurs in PSI-BLAST reports.
If there are multiple iterations, calling num_hits() returns the number of 'new' hits for each iteration. These are the hits that did not occur in a previous iteration. See Also: Bio::Search::Result::GenericResult::num_hits
add_hitcodeprevnextTop
 Title   : add_hit
Usage : $report->add_hit($hit)
Function: Adds a HitI to the stored list of hits
Returns : Number of HitI currently stored
Args : Bio::Search::Hit::HitI
add_iterationcodeprevnextTop
 Title   : add_iteration
Usage : $report->add_iteration($iteration)
Function: Adds a IterationI to the stored list of iterations
Returns : Number of IterationI currently stored
Args : Bio::Search::Iteration::IterationI
next_iterationcodeprevnextTop
 Title   : next_iteration
Usage : while( $it = $result->next_iteration()) { ... }
Function: Returns the next Iteration object, representing all hits
found within a given PSI-Blast iteration.
Returns : a Bio::Search::Iteration::IterationI object or undef if there are no more.
Args : none
iterationcodeprevnextTop
 Usage     : $iteration = $blast->iteration( $number );
Purpose : Get an IterationI object for the specified iteration
in the search result (PSI-BLAST).
Returns : Bio::Search::Iteration::IterationI object
Throws : Bio::Root::NoSuchThing exception if $number is not within
range of the number of iterations in this report.
Argument : integer (optional, if not specified get the last iteration)
First iteration = 1
num_iterationscodeprevnextTop
 Usage     : $num_iterations = $blast->num_iterations; 
Purpose : Get the number of iterations in the search result (PSI-BLAST).
Returns : Total number of iterations in the report
Argument : none (read-only)
number_of_iterationscodeprevnextTop
 Usage     : $num_iterations = $blast->number_of_iterations; 
Purpose : Get the number of iterations in the search result (PSI-BLAST).
Returns : Total number of iterations in the report
Argument : none (read-only)
Note : Alias of num_iterations.
roundcodeprevnextTop
 Usage     : $round = $blast->round( $number );
Purpose : Get an IterationI object for the specified iteration
in the search result (PSI-BLAST).
Returns : Bio::Search::Iteration::IterationI object
Throws : Bio::Root::NoSuchThing exception if $number is not within
range of the number of iterations in this report.
Argument : integer (optional, if not specified get the last iteration)
First iteration = 1
Note : Alias of iteration.
iterationscodeprevnextTop
 Title   : iterations
Usage : my @iterations = $result->iterations
Function: Returns the IterationI objects contained within this Result
Returns : Array of Bio::Search::Iteration::IterationI objects
Args : none
psiblastcodeprevnextTop
 Usage     : if( $blast->psiblast ) { ... }
Purpose : Set/get a boolean indicator whether or not the report
is a PSI-BLAST report.
Returns : 1 if PSI-BLAST, undef if not.
Argument : 1 (when setting)
no_hits_foundcodeprevnextTop
 Usage     : $nohits = $blast->no_hits_found( $iteration_number );
Purpose : Get boolean indicator indicating whether or not any hits
were present in the report.
This is NOT the same as determining the number of hits via the hits() method, which will return zero hits if there were no hits in the report or if all hits were filtered out during the parse. Thus, this method can be used to distinguish these possibilities for hitless reports generated when filtering. Returns : Boolean Argument : (optional) integer indicating the iteration number (PSI-BLAST) If iteration number is not specified and this is a PSI-BLAST result, then this method will return true only if all iterations had no hits found.
set_no_hits_foundcodeprevnextTop
 Usage     : $blast->set_no_hits_found( $iteration_number ); 
Purpose : Set boolean indicator indicating whether or not any hits
were present in the report.
Returns : n/a
Argument : (optional) integer indicating the iteration number (PSI-BLAST)
_next_iteration_indexcodeprevnextTop
 Title   : _next_iteration_index
Usage : private
rewindcodeprevnextTop
 Title   : rewind
Usage : $result->rewind;
Function: Allow one to reset the Iteration iterator to the beginning
Since this is an in-memory implementation
Returns : none
Args : none
inclusion_thresholdcodeprevnextTop
 Title   : inclusion_threshold
Usage : my $incl_thresh = $result->inclusion_threshold; (read-only)
Function: Gets the e-value threshold for inclusion in the PSI-BLAST
score matrix model (blastpgp) that was used for generating the report
being parsed.
Returns : number (real) or undef if not a PSI-BLAST report.
Args : none
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);

  $self->{'_iterations'} = [];
  $self->{'_iteration_index'} = 0;
  $self->{'_iteration_count'} = 0;

  my( $iters, $ithresh ) = $self->_rearrange([qw(ITERATIONS
                                                 INCLUSION_THRESHOLD)],@args);

  $self->{'_inclusion_threshold'} = $ithresh;  # This is a read-only variable
if( defined $iters ) { $self->throw("Must define arrayref of Iterations when initializing a $class\n") unless ref($iters) =~ /array/i; foreach my $i ( @{$iters} ) { $self->add_iteration($i); } } else { # This shouldn't get called with the new SearchIO::blast.
print STDERR "BlastResult::new(): Not adding iterations.\n"; $self->{'_no_iterations'} = 1; } return $self;
}
hitsdescriptionprevnextTop
sub hits {
   my ($self) = shift;
   if ($self->{'_no_iterations'}) {
       return $self->SUPER::hits;
   }
   my @hits = ();
   foreach my $it ($self->iterations) {
       push @hits, $it->hits;
   }
   return @hits;
}
next_hitdescriptionprevnextTop
sub next_hit {
    my ($self,@args) = @_;
    if ($self->{'_no_iterations'}) {
        return $self->SUPER::next_hit(@args);
    }

    my $iter_index;
    if (not defined $self->{'_last_hit'}) {
        $iter_index = $self->{'_iter_index'} = $self->_next_iteration_index;
    } else {
        $iter_index = $self->{'_iter_index'};
    }

    return if $iter_index >= scalar @{$self->{'_iterations'}};

    my $it = $self->{'_iterations'}->[$iter_index];
    my $hit = $self->{'_last_hit'} = $it->next_hit;

    return defined($hit) ? $hit : $self->next_hit;
}
num_hitsdescriptionprevnextTop
sub num_hits {
   my ($self) = shift;
   if ($self->{'_no_iterations'}) {
       return $self->SUPER::num_hits;
   }
   if (not defined $self->{'_iterations'}) {
       $self->throw("Can't get Hits: data not collected.");
    }
    return scalar( $self->hits );
}
add_hitdescriptionprevnextTop
sub add_hit {
    my ($self,$hit) = @_;
    my $iter = $self->iteration;
    if( $hit->isa('Bio::Search::Hit::HitI') ) { 
	return $iter->add_hit(-hit => $hit);
    } else { 
        $self->throw("Passed in a " .ref($hit). 
                     " as a Iteration which is not a Bio::Search::Hit::HitI.");
    }
    return $iter->num_hits;
}
add_iterationdescriptionprevnextTop
sub add_iteration {
    my ($self,$i) = @_;
    if( $i->isa('Bio::Search::Iteration::IterationI') ) { 
        push @{$self->{'_iterations'}}, $i;
        $self->{'_iteration_count'}++;
    } else { 
        $self->throw("Passed in a " .ref($i). 
                     " as a Iteration which is not a Bio::Search::Iteration::IterationI.");
    }
    return scalar @{$self->{'_iterations'}};
}
next_iterationdescriptionprevnextTop
sub next_iteration {
    my ($self) = @_;

   unless($self->{'_iter_queue_started'}) {
       $self->{'_iter_queue'} = [$self->iterations()];
       $self->{'_iter_queue_started'} = 1;
   }
   return shift @{$self->{'_iter_queue'}};
}
iterationdescriptionprevnextTop
sub iteration {
    my ($self,$num) = @_;
    $num = scalar @{$self->{'_iterations'}} unless defined $num;
    unless ($num >= 1 and $num <= scalar $self->{'_iteration_count'}) {
        $self->throw(-class=>'Bio::Root::NoSuchThing',
                     -text=>"No such iteration number: $num. Valid range=1-$self->{'_iteration_count'}",
                     -value=>$num);
    }
    return $self->{'_iterations'}->[$num-1];
}
num_iterationsdescriptionprevnextTop
sub num_iterations {
 shift->{'_iteration_count'}
}
number_of_iterationsdescriptionprevnextTop
sub number_of_iterations {
 shift->num_iterations
}
rounddescriptionprevnextTop
sub round {
 shift->iteration(@_)
}
iterationsdescriptionprevnextTop
sub iterations {
     my $self = shift;
    my @its = ();
    if( ref($self->{'_iterations'}) =~ /ARRAY/i ) {
       @its = @{$self->{'_iterations'}};
    }
    return @its;
}
psiblastdescriptionprevnextTop
sub psiblast {
#----------------
my ($self, $val ) = @_; if( $val ) { $self->{'_psiblast'} = 1; } return $self->{'_psiblast'};
}
no_hits_founddescriptionprevnextTop
sub no_hits_found {
    my ($self, $round) = @_;

    my $result = 0;   # final return value of this method.
# Watch the double negative!
# result = 0 means "yes hits were found"
# result = 1 means "no hits were found" (for the indicated iteration or all iterations)
# If a iteration was not specified and there were multiple iterations,
# this method should return true only if all iterations had no hits found.
if( not defined $round ) { if( $self->{'_iterations'} > 1) { $result = 1; foreach my $i( 1..$self->{'_iterations'} ) { if( not defined $self->{"_iteration_$i"}->{'_no_hits_found'} ) { $result = 0; last; } } } else { $result = $self->{"_iteration_1"}->{'_no_hits_found'}; } } else { $result = $self->{"_iteration_$round"}->{'_no_hits_found'}; } return $result;
}
set_no_hits_founddescriptionprevnextTop
sub set_no_hits_found {
    my ($self, $round) = @_;
    $round ||= 1;
    $self->{"_iteration_$round"}->{'_no_hits_found'} = 1;
}
_next_iteration_indexdescriptionprevnextTop
sub _next_iteration_index {
   my ($self,@args) = @_;
   return $self->{'_iteration_index'}++;
}
rewinddescriptionprevnextTop
sub rewind {
   my $self = shift;
   $self->SUPER::rewind(@_);
   $self->{'_iteration_index'} = 0;
   foreach ($self->iterations) {
       $_->rewind;
   }
}
inclusion_thresholddescriptionprevnextTop
sub inclusion_threshold {
    my $self = shift;
    return $self->{'_inclusion_threshold'};
}

1;
}
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 - Steve ChervitzTop
Email sac@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _