Bio::Search::Result
PullResultI
Summary
Bio::Search::Result::PullResultI - Bio::Search::Result::ResultI interface for
'pull' parsers
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# This is an interface and cannot be instantiated
# typically one gets Results from a SearchIO stream
use Bio::SearchIO;
my $io = new Bio::SearchIO(-format => 'hmmer_pull',
-file => 't/data/hmmpfam.out');
my $result = $io->next_result;
while( $hit = $result->next_hit()) {
# enter code here for hit processing
}
my $id = $result->query_name();
my $desc = $result->query_description();
my $dbname = $result->database_name();
my $size = $result->database_letters();
my $num_entries = $result->database_entries();
my $gap_ext = $result->get_parameter('gapext');
my @params = $result->available_parameters;
my $kappa = $result->get_statistic('kappa');
my @statnames = $result->available_statistics;
Description
Bio::Search::Result::ResultI objects are data structures containing
the results from the execution of a search algorithm. As such, it may
contain various algorithm specific information as well as details of
the execution, but will contain a few fundamental elements, including
the ability to return Bio::Search::Hit::HitI objects.
PullResultI is for fast implementations that only do parsing work on the result
data when you actually request information by calling one of the ResultI
methods.
Many methods of ResultI are implemented in a way suitable for inheriting classes
that use Bio::PullParserI. It only really makes sense for PullResult modules to
be created by (and have as a -parent) SearchIO modules written using
PullParserI.
Methods
Methods description
Title : _setup
Usage : $self->_setup(@args)
Function: Implementers should call this to setup common fields and deal with
common arguments to new().
Returns : n/a
Args : @args received in new(). |
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 |
Title : query_name
Usage : $id = $result->query_name();
Function: Get the string identifier of the query used by the
algorithm that performed the search.
Returns : a string.
Args : none |
Title : query_accession
Usage : $id = $result->query_accession();
Function: Get the accession (if available) for the query sequence
Returns : a string
Args : none |
Title : query_length
Usage : $id = $result->query_length();
Function: Get the length of the query sequence used in the search.
Returns : a number
Args : none |
Title : query_description
Usage : $id = $result->query_description();
Function: Get the description of the query sequence
used in the search.
Returns : a string
Args : none |
Title : database_name
Usage : $name = $result->database_name()
Function: Used to obtain the name of the database that the query was searched
against by the algorithm.
Returns : a scalar string
Args : none |
Title : database_letters
Usage : $size = $result->database_letters()
Function: Used to obtain the size of database that was searched against.
Returns : a scalar integer (units specific to algorithm, but probably the
total number of residues in the database, if available) or undef if
the information was not available to the Processor object.
Args : none |
Title : database_entries
Usage : $num_entries = $result->database_entries()
Function: Used to obtain the number of entries contained in the database.
Returns : a scalar integer representing the number of entities in the database
or undef if the information was not available.
Args : none |
Title : algorithm
Usage : my $r_type = $result->algorithm
Function: Obtain the name of the algorithm used to obtain the Result
Returns : string (e.g., BLASTP)
Args : [optional] scalar string to set value |
Title : algorithm_version
Usage : my $r_version = $result->algorithm_version
Function: Obtain the version of the algorithm used to obtain the Result
Returns : string (e.g., 2.1.2)
Args : [optional] scalar string to set algorithm version value |
Title : algorithm_reference
Usage : $obj->algorithm_reference($newval)
Function:
Returns : value of the literature reference for the algorithm
Args : newvalue (optional)
Comments: The default implementation in ResultI returns an empty string
rather than throwing a NotImplemented exception, since
the ref may not always be available and is not critical. |
Title : num_hits
Usage : my $hitcount= $result->num_hits
Function: returns the number of hits for this query result
Returns : integer
Args : none |
Title : hits
Usage : my @hits = $result->hits
Function: Returns the HitI objects contained within this Result
Returns : Array of Bio::Search::Hit::HitI objects
Args : none
See Also: Bio::Search::Hit::HitI |
Usage : $nohits = $blast->no_hits_found();
Function : 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
Args : none |
Title : rewind
Usage : $result->rewind;
Function: Allow one to reset the Hit iterator to the beginning
Since this is an in-memory implementation
Returns : none
Args : none |
Title : get_parameter
Usage : my $gap_ext = $result->get_parameter('gapext')
Function: Returns the value for a specific parameter used
when running this result
Returns : string
Args : name of parameter (string) |
Title : available_parameters
Usage : my @params = $result->available_parameters
Function: Returns the names of the available parameters
Returns : Return list of available parameters used for this result
Args : none |
Title : add_parameter
Usage : $report->add_parameter('gapext', 11);
Function: Adds a parameter
Returns : none
Args : key - key value name for this parama
value - value for this parameter |
Title : get_statistic
Usage : my $gap_ext = $result->get_statistic('kappa')
Function: Returns the value for a specific statistic available
from this result
Returns : string
Args : name of statistic (string) |
Title : available_statistics
Usage : my @statnames = $result->available_statistics
Function: Returns the names of the available statistics
Returns : Return list of available statistics used for this result
Args : none |
Title : add_statistic
Usage : $report->add_statistic('lambda', 2.3);
Function: Adds a statistic
Returns : none
Args : key - key value name for this statistic
value - value for this statistic |
Methods code
sub _setup
{ my ($self, @args) = @_;
$self->_fields( { ( next_hit => undef,
num_hits => undef,
hits => undef,
no_hits_found => undef,
query_name => undef,
query_accession => undef,
query_length => undef,
query_description => undef ) } );
my ($parent, $chunk, $params, $stats) = $self->_rearrange([qw(PARENT
CHUNK
PARAMETERS
STATISTICS)],
@args);
$self->throw("Need -parent or -chunk to be defined") unless $parent || $chunk;
$self->parent($parent) if $parent;
if ($chunk) {
my ($io, $start, $end) = (undef, 0, undef);
if (ref($chunk) eq 'ARRAY') {
($io, $start, $end) = @{$chunk};
}
else {
$io = $chunk;
}
$self->chunk($io, -start => $start, -end => $end);
}
if (defined $params) {
if (ref($params) !~ /hash/i) {
$self->throw("Must specify a hash reference with the the parameter '-parameters");
}
while (my ($key,$value) = each %{$params}) {
$self->add_parameter($key, $value);
}
}
if (defined $stats) {
if (ref($stats) !~ /hash/i) {
$self->throw("Must specify a hash reference with the the parameter '-statistics");
}
while (my ($key,$value) = each %{$stats}) {
$self->add_statistic($key, $value);
}
}} | sub next_hit
{ return shift->get_field('next_hit');} | sub query_name
{ return shift->get_field('query_name');} | sub query_accession
{ return shift->get_field('query_accession');} | sub query_length
{ return shift->get_field('query_length');} | sub query_description
{ return shift->get_field('query_description');} | sub database_name
{ return shift->get_field('database_name');} | sub database_letters
{ return shift->get_field('database_letters');} | sub database_entries
{ return shift->get_field('database_entries');} | sub algorithm
{ return shift->get_field('algorithm');} | sub algorithm_version
{ return shift->get_field('algorithm_version');} | sub algorithm_reference
{ my ($self) = @_;
return ''; } | sub num_hits
{ return shift->get_field('num_hits');} | sub hits
{ return shift->get_field('hits');} | sub no_hits_found
{ return shift->get_field('no_hits_found');} | sub rewind
{ shift->throw_not_implemented(); } | sub get_parameter
{ my ($self, $param) = @_;
$param || return;
return unless defined $self->{_parameters};
return $self->{_parameters}->get_parameter($param);} | sub available_parameters
{ my $self = shift;
return () unless defined $self->{_parameters};
return $self->{_parameters}->available_parameters;} | sub add_parameter
{ my ($self, $key, $value) = @_;
unless (exists $self->{_parameters}) {
$self->{_parameters} = new Bio::Tools::Run::GenericParameters;
}
$self->{_parameters}->set_parameter($key => $value);} | sub get_statistic
{ my ($self, $stat) = @_;
$stat || return;
return unless defined $self->{_statistics};
return $self->{_statistics}->get_statistic($stat);} | sub available_statistics
{ my $self = shift;
return () unless defined $self->{_statistics};
return $self->{_statistics}->available_statistics;} | sub add_statistic
{ my ($self, $key, $value) = @_;
unless (exists $self->{_statistics}) {
$self->{_statistics} = new Bio::Search::GenericStatistics;
}
$self->{_statistics}->set_statistic($key => $value);} | General documentation
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
Copyright (c) 2006 Sendu Bala.
This software is provided "as is" without warranty of any kind.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : sort_hits
Usage : $result->sort_hits(\&sort_function)
Function : Sorts the available hit objects by a user-supplied function.
Defaults to sort by descending score.
Returns : n/a
Args : A coderef for the sort function. See the documentation on the Perl
sort() function for guidelines on writing sort functions.
Note : To access the special variables $a and $b used by the Perl sort()
function the user function must access Bio::Search::Result::ResultI namespace.
For example, use :
$result->sort_hits(sub{$Bio::Search::Result::ResultI::a->length <=>
$Bio::Search::Result::ResultI::b->length});
NOT $result->sort_hits($a->length <=>$b->length);