Bio::Search::Result
GenericResult
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Summary
Bio::Search::Result::GenericResult - Generic Implementation of Bio::Search::Result::ResultI interface applicable to most search results.
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# typically one gets Results from a SearchIO stream
use Bio::SearchIO;
my $io = new Bio::SearchIO(-format => 'blast',
-file => 't/data/HUMBETGLOA.tblastx');
while( my $result = $io->next_result) {
# process all search results within the input stream
while( my $hit = $result->next_hits()) {
# insert code here for hit processing
}
}
use Bio::Search::Result::GenericResult;
my @hits = (); # would be a list of Bio::Search::Hit::HitI objects
# typically these are created from a Bio::SearchIO stream
my $result = new Bio::Search::Result::GenericResult
( -query_name => 'HUMBETGLOA',
-query_accession => ''
-query_description => 'Human haplotype C4 beta-globin gene, complete cds.'
-query_length => 3002
-database_name => 'ecoli.aa'
-database_letters => 4662239,
-database_entries => 400,
-parameters => { 'e' => '0.001' },
-statistics => { 'kappa' => 0.731 },
-algorithm => 'blastp',
-algorithm_version => '2.1.2',
);
my $id = $result->query_name();
my $desc = $result->query_description();
my $name = $result->database_name();
my $size = $result->database_letters();
my $num_entries = $result->database_entries();
my $gap_ext = $result->get_parameter('e');
my @params = $result->available_parameters;
my $kappa = $result->get_statistic('kappa');
my @statnames = $result->available_statistics;
Description
This object is an implementation of the Bio::Search::Result::ResultI
interface and provides a generic place to store results from a
sequence database search.
Methods
Methods description
Title : _nexthitindex
Usage : private |
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 |
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 : add_statistic
Usage : $report->add_statistic('lambda', 2.3);
Function: Adds a parameter
Returns : none
Args : key - key value name for this parama
value - value for this parameter |
Title : algorithm
Usage : my $r_type = $hsp->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_reference
Usage : $obj->algorithm_reference($newval)
Function:
Returns : string containing literature reference for the algorithm
Args : newvalue string (optional)
Comments: Formerly named program_reference(), which is still supported
for backwards compatibility. |
Title : algorithm_version
Usage : my $r_version = $hsp->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 : available_parameters
Usage : my @params = $report->available_paramters
Function: Returns the names of the available parameters
Returns : Return list of available parameters used for this report
Args : none |
Title : available_statistics
Usage : my @statnames = $report->available_statistics
Function: Returns the names of the available statistics
Returns : Return list of available statistics used for this report
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 : [optional] new integer for the number of sequence entries in the db |
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 : [optional] new scalar integer for number of letters in db |
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 : [optional] new string for the db name |
Title : get_parameter
Usage : my $gap_ext = $report->get_parameter('gapext')
Function: Returns the value for a specific parameter used
when running this report
Returns : string
Args : name of parameter (string) |
Title : get_statistic
Usage : my $gap_ext = $report->get_statistic('kappa')
Function: Returns the value for a specific statistic available
from this report
Returns : string
Args : name of statistic (string) |
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 |
Title : new
Usage : my $obj = new Bio::Search::Result::GenericResult();
Function: Builds a new Bio::Search::Result::GenericResult object
Returns : Bio::Search::Result::GenericResult
Args : -query_name => Name of query Sequence
-query_accession => Query accession number (if available)
-query_description => Description of query sequence
-query_length => Length of query sequence
-database_name => Name of database
-database_letters => Number of residues in database
-database_entries => Number of entries in database
-parameters => hash ref of search parameters (key => value)
-statistics => hash ref of search statistics (key => value)
-algorithm => program name (blastx)
-algorithm_version => version of the algorithm (2.1.2)
-algorithm_reference => literature reference string for this algorithm |
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 : num_hits
Usage : my $hitcount= $result->num_hits
Function: returns the number of hits for this query result
Returns : integer
Args : none |
Title : query_accession
Usage : $id = $result->query_accession();
Function: Get the accession (if available) for the query sequence
Returns : a string
Args : [optional] new string value for accession |
Title : query_description
Usage : $id = $result->query_description();
Function: Get the description of the query sequence
used in the search.
Returns : a string
Args : [optional] new string for the query description |
Title : query_length
Usage : $id = $result->query_length();
Function: Get the length of the query sequence
used in the search.
Returns : a number
Args : [optional] new integer value for query length |
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 : [optional] new string value for query name |
Title : rewind
Usage : $result->rewind;
Function: Allow one to reset the Hit iteration to the beginning
Since this is an in-memory implementation
Returns : none
Args : none |
Title : to_string
Usage : print $blast->to_string;
Function: Returns a string representation for the Blast result.
Primarily intended for debugging purposes.
Example : see usage
Returns : A string of the form:
[GenericResult] <analysis_method> query=<name> <description> db=<database
e.g.:
[GenericResult] BLASTP query=YEL060C vacuolar protease B, db=PDBUNIQ
Args : None |
Methods code
sub _nexthitindex
{ my ($self,@args) = @_;
return $self->{'_hitindex'}++;} | sub add_hit
{ my ($self,$s) = @_;
if( $s->isa('Bio::Search::Hit::HitI') ) {
push @{$self->{'_hits'}}, $s;
} else {
$self->warn("Passed in " .ref($s).
" as a Hit which is not a Bio::Search::HitI... skipping");
}
return scalar @{$self->{'_hits'}};} | sub add_parameter
{ my ($self,$key,$value) = @_;
$self->{'_parameters'}->{$key} = $value;} | sub add_statistic
{ my ($self,$key,$value) = @_;
$self->{'_statistics'}->{$key} = $value;
return;} | sub algorithm
{ my ($self,$value) = @_;
my $previous = $self->{'_algorithm'};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_algorithm'} = $value;
}
return $previous;} | sub algorithm_reference
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'algorithm_reference'} = $value;
}
return $self->{'algorithm_reference'};} | sub algorithm_version
{ my ($self,$value) = @_;
my $previous = $self->{'_algorithm_version'};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_algorithm_version'} = $value;
}
return $previous;} | sub available_parameters
{ my ($self) = @_;
return keys %{$self->{'_parameters'}};} | sub available_statistics
{ my ($self) = @_;
return keys %{$self->{'_statistics'}};} | sub database_entries
{ my ($self,$value) = @_;
my $previous = $self->{'_dbentries'};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_dbentries'} = $value;
}
return $previous;} | sub database_letters
{ my ($self,$value) = @_;
my $previous = $self->{'_dbletters'};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_dbletters'} = $value;
}
return $previous;} | sub database_name
{ my ($self,$value) = @_;
my $previous = $self->{'_dbname'};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_dbname'} = $value;
}
return $previous;} | sub get_parameter
{ my ($self,$name) = @_;
return $self->{'_parameters'}->{$name};} | sub get_statistic
{ my ($self,$key) = @_;
return $self->{'_statistics'}->{$key};} | sub hits
{ my ($self) = shift;
my @hits = ();
if( ref $self->{'_hits'}) {
@hits = @{$self->{'_hits'}};
}
return @hits;} | sub iterations
{
my ($self, $num ) = @_;
if( defined $num ) {
$self->{'_iterations'} = $num;
}
return $self->{'_iterations'};
} | sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_hits'} = [];
$self->{'_hitindex'} = 0;
$self->{'_statistics'} = {};
$self->{'_parameters'} = {};
my ($qname,$qacc,$qdesc,$qlen,
$dbname,$dblet,$dbent,$params,
$stats, $hits, $algo, $algo_v,
$prog_ref, $algo_r) = $self->_rearrange([qw(QUERY_NAME
QUERY_ACCESSION
QUERY_DESCRIPTION
QUERY_LENGTH
DATABASE_NAME
DATABASE_LETTERS
DATABASE_ENTRIES
PARAMETERS
STATISTICS
HITS
ALGORITHM
ALGORITHM_VERSION
PROGRAM_REFERENCE
ALGORITHM_REFERENCE
)],@args);
$algo_r ||= $prog_ref;
defined $algo && $self->algorithm($algo);
defined $algo_v && $self->algorithm_version($algo_v);
defined $algo_r && $self->algorithm_reference($algo_r);
defined $qname && $self->query_name($qname);
defined $qacc && $self->query_accession($qacc);
defined $qdesc && $self->query_description($qdesc);
defined $qlen && $self->query_length($qlen);
defined $dbname && $self->database_name($dbname);
defined $dblet && $self->database_letters($dblet);
defined $dbent && $self->database_entries($dbent);
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);
}
}
if( defined $hits ) {
$self->throw("Must define arrayref of Hits when initializing a $class\n") unless ref($hits) =~ /array/i;
foreach my $s ( @$hits ) {
$self->add_hit($s);
}
}
return $self;} | sub next_hit
{ my ($self,@args) = @_;
my $index = $self->_nexthitindex;
return undef if $index > scalar @{$self->{'_hits'}};
return $self->{'_hits'}->[$index];} | sub no_hits_found
{
my ($self, $round) = @_;
my $result = 0;
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 $result;
} | sub num_hits
{ my ($self) = shift;
if (not defined $self->{'_hits'}) {
$self->throw("Can't get Hits: data not collected.");
}
return scalar(@{$self->{'_hits'}});} | sub psiblast
{
my ($self, $val ) = @_;
if( $val ) {
$self->{'_psiblast'} = 1;
}
return $self->{'_psiblast'};
} | sub query_accession
{ my ($self,$value) = @_;
my $previous = $self->{'_queryacc'};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_queryacc'} = $value;
}
return $previous;} | sub query_description
{ my ($self,$value) = @_;
my $previous = $self->{'_querydesc'};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_querydesc'} = $value;
}
return $previous;} | sub query_length
{ my ($self,$value) = @_;
my $previous = $self->{'_querylength'};
if( defined $value || ! defined $previous ) {
$value = $previous = 0 unless defined $value;
$self->{'_querylength'} = $value;
}
return $previous;} | sub query_name
{ my ($self,$value) = @_;
my $previous = $self->{'_queryname'};
if( defined $value || ! defined $previous ) {
$value = $previous = '' unless defined $value;
$self->{'_queryname'} = $value;
}
return $previous;} | sub rewind
{ my ($self) = @_;
$self->{'_hitindex'} = 0;} | sub set_no_hits_found
{
my ($self, $round) = @_;
$round ||= 1;
$self->{"_iteration_$round"}->{'_no_hits_found'} = 1;
} | sub to_string
{
my $self = shift;
my $str = "[GenericResult] " . $self->algorithm . " query=" . $self->query_name . " " . $self->query_description .", db=" . $self->database_name;
return $str;
}
1;
} | General documentation
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/MailList.shtml - About the mailing lists
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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
| AUTHOR - Jason Stajich and Steve Chervitz | Top |
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
| Bio::Search::Result::ResultI interface methods | Top |
Bio::Search::Result::ResultI implementation
Bio::Search::Result::GenericResult specific methods