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
Bio::Search::GenericStatistics
Bio::Tools::Run::GenericParameters
Inherit
Bio::Root::Root Bio::Search::Result::ResultI
Synopsis
    # typically one gets Results from a SearchIO stream
use Bio::SearchIO;
my $io = Bio::SearchIO->new(-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_hit ) {
# 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 = Bio::Search::Result::GenericResult->new ( -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;
# TODO: Show how to configure a SearchIO stream so that it generates
# GenericResult objects.
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.
Unless you're writing a parser, you won't ever need to create a
GenericResult or any other ResultI-implementing object. If you use
the SearchIO system, ResultI objects are created automatically from
a SearchIO stream which returns Bio::Search::Result::ResultI objects.
For documentation on what you can do with GenericResult (and other ResultI
objects), please see the API documentation in
Bio::Search::Result::ResultI.
Methods
newDescriptionCode
algorithmDescriptionCode
algorithm_versionDescriptionCode
next_hitDescriptionCode
query_nameDescriptionCode
query_accessionDescriptionCode
query_giDescriptionCode
query_lengthDescriptionCode
query_descriptionDescriptionCode
database_nameDescriptionCode
database_lettersDescriptionCode
database_entriesDescriptionCode
get_parameterDescriptionCode
available_parametersDescriptionCode
get_statisticDescriptionCode
available_statisticsDescriptionCode
add_hitDescriptionCode
hit_factoryDescriptionCode
rewindDescriptionCode
_nexthitindexDescriptionCode
add_parameterDescriptionCode
add_statisticDescriptionCode
num_hitsDescriptionCode
hitsDescriptionCode
algorithm_referenceDescriptionCode
program_referenceDescriptionCode
ridDescriptionCode
no_hits_foundDescriptionCode
set_no_hits_foundDescriptionCode
to_stringDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Search::Result::GenericResult->new();
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
-hits => array ref of Bio::Search::Hit::HitI objects
-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
-rid => value of the BLAST Request ID (eg. RID: ZABJ4EA7014)
-hit_factory => Bio::Factory::ObjectFactoryI capable of making
Bio::Search::Hit::HitI objects
algorithmcodeprevnextTop
 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
algorithm_versioncodeprevnextTop
 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
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
query_namecodeprevnextTop
 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
query_accessioncodeprevnextTop
 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
query_gicodeprevnextTop
 Title   : query_gi
Usage : $acc = $hit->query_gi();
Function: Retrieve the NCBI Unique ID (aka the GI #),
if available, for the query
Returns : a scalar string (empty string if not set)
Args : none
query_lengthcodeprevnextTop
 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
query_descriptioncodeprevnextTop
 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
database_namecodeprevnextTop
 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
database_letterscodeprevnextTop
 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
database_entriescodeprevnextTop
 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
get_parametercodeprevnextTop
 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)
available_parameterscodeprevnextTop
 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
get_statisticcodeprevnextTop
 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)
available_statisticscodeprevnextTop
 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
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
hit_factorycodeprevnextTop
 Title   : hit_factory
Usage : $hit->hit_factory($hit_factory)
Function: Get/set the factory used to build HitI objects if necessary.
Returns : Bio::Factory::ObjectFactoryI
Args : Bio::Factory::ObjectFactoryI
rewindcodeprevnextTop
 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
_nexthitindexcodeprevnextTop
 Title   : _nexthitindex
Usage : private
add_parametercodeprevnextTop
 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
add_statisticcodeprevnextTop
 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
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
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
algorithm_referencecodeprevnextTop
 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.
program_referencecodeprevnextTop
 Title   : program_reference
Usage : $obj->program_reference()
Function:
Returns : string containing literature reference for the algorithm
Args :
Comments: Deprecated - use algorithm_reference() instead.
ridcodeprevnextTop
 Title   : rid
Usage : $obj->rid($newval)
Function:
Returns : value of the BLAST Request ID (eg. RID: ZABJ4EA7014)
Args : newvalue (optional)
Comments: The default implementation in ResultI returns an empty string
rather than throwing a NotImplemented exception, since
the RID may not always be available and is not critical.
See: (1) http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/rid.html
(2) http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node63.html
no_hits_foundcodeprevnextTop
See documentation in Bio::Search::Result::ResultI::no_hits_found()
set_no_hits_foundcodeprevnextTop
See documentation in Bio::Search::Result::ResultI::set_no_hits_found()
to_stringcodeprevnextTop
 Title   : to_string
Usage : print $blast->to_string;
Function: Returns a string representation for the Blast result.
Primarily intended for debugging purposes.
Example : see usage
Returns : A string of the form:
[GenericResult] <analysis_method> query=<name> <description> db=<database
e.g.:
[GenericResult] BLASTP query=YEL060C vacuolar protease B, db=PDBUNIQ
Args : None
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

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

  $self->{'_hits'} = [];
  $self->{'_hitindex'} = 0;
  $self->{'_statistics'} = Bio::Search::GenericStatistics->new();
  $self->{'_parameters'} = Bio::Tools::Run::GenericParameters->new();

  my ($qname,$qacc,$qdesc,$qlen, $qgi,
      $dbname,$dblet,$dbent,$params,   
      $stats, $hits, $algo, $algo_v,
      $prog_ref, $algo_r, $rid, $hit_factory) = $self->_rearrange([qw(QUERY_NAME
                                                  QUERY_ACCESSION
                                                  QUERY_DESCRIPTION
                                                  QUERY_LENGTH
                                                  QUERY_GI
                                                  DATABASE_NAME
                                                  DATABASE_LETTERS
                                                  DATABASE_ENTRIES
                                                  PARAMETERS
                                                  STATISTICS
                                                  HITS
                                                  ALGORITHM
                                                  ALGORITHM_VERSION
                                                  PROGRAM_REFERENCE
                                                  ALGORITHM_REFERENCE
                                                  RID
                                                  HIT_FACTORY
                                                 )],@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 $rid && $self->rid($rid);

  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 $qgi   && $self->query_gi($qgi);
  defined $dbname && $self->database_name($dbname);
  defined $dblet  && $self->database_letters($dblet);
  defined $dbent  && $self->database_entries($dbent);

  defined $hit_factory && $self->hit_factory($hit_factory);
  
  if( defined $params ) {
      if( ref($params) !~ /hash/i ) {
          $self->throw("Must specify a hash reference with the parameter '-parameters");
      }
      while( my ($key,$value) = each %{$params} ) {
          $self->{'_parameters'}->set_parameter($key   =>   $value);
               # $self->add_parameter($key,$value);
} } if( defined $stats ) { if( ref($stats) !~ /hash/i ) { $self->throw("Must specify a hash reference with the parameter '-statistics"); } while( my ($key,$value) = each %{$stats} ) { $self->{'_statistics'}->set_statistic($key => $value); # $self->add_statistic($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 $self;
}
algorithmdescriptionprevnextTop
sub algorithm {
    my ($self,$value) = @_;
    my $previous = $self->{'_algorithm'};
    if( defined $value || ! defined $previous ) { 
        $value = $previous = '' unless defined $value;
        $self->{'_algorithm'} = $value;
    } 
    return $previous;
}
algorithm_versiondescriptionprevnextTop
sub algorithm_version {
    my ($self,$value) = @_;
    my $previous = $self->{'_algorithm_version'};
    if( defined $value || ! defined $previous ) { 
        $value = $previous = '' unless defined $value;
        $self->{'_algorithm_version'} = $value;
    } 

    return $previous;
}
next_hitdescriptionprevnextTop
sub next_hit {
    my ($self,@args) = @_;
    my $index = $self->_nexthitindex;
    return if $index > scalar @{$self->{'_hits'}};
    
    my $hit = $self->{'_hits'}->[$index];
    if (ref($hit) eq 'HASH') {
        my $factory = $self->hit_factory || $self->throw("Tried to get a Hit, but it was a hash ref and we have no hit factory");
        $hit = $factory->create_object(%{$hit});
        $self->{'_hits'}->[$index] = $hit;
        delete $self->{_hashes}->{$index};
    }
    return $hit;
}
query_namedescriptionprevnextTop
sub query_name {
    my ($self,$value) = @_;
    my $previous = $self->{'_queryname'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{'_queryname'} = $value;
    } 
    return $previous;
}
query_accessiondescriptionprevnextTop
sub query_accession {
    my ($self,$value) = @_;
    my $previous = $self->{'_queryacc'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{'_queryacc'} = $value;
    } 
    return $previous;
}
query_gidescriptionprevnextTop
sub query_gi {
    my ($self,$value) = @_;
    if( defined $value ) {
        $self->{'_query_gi'} = $value;
    } else {
        $self->{'_query_gi'} = $self->query_name =~ m{^gi\|(\d+)} ? $1 : '';
    } 
    return $self->{'_query_gi'};
}
query_lengthdescriptionprevnextTop
sub query_length {
    my ($self,$value) = @_;
    my $previous = $self->{'_querylength'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = 0 unless defined $value;
        $self->{'_querylength'} = $value;
    } 
    return $previous;
}
query_descriptiondescriptionprevnextTop
sub query_description {
    my ($self,$value) = @_;
    my $previous = $self->{'_querydesc'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{'_querydesc'} = $value;
    } 
    return $previous;
}
database_namedescriptionprevnextTop
sub database_name {
    my ($self,$value) = @_;
    my $previous = $self->{'_dbname'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{'_dbname'} = $value;
    } 
    return $previous;
}
database_lettersdescriptionprevnextTop
sub database_letters {
    my ($self,$value) = @_;
    my $previous = $self->{'_dbletters'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{'_dbletters'} = $value;
    } 
    return $previous;
}
database_entriesdescriptionprevnextTop
sub database_entries {
    my ($self,$value) = @_;
    my $previous = $self->{'_dbentries'};
    if( defined $value || ! defined $previous ) {
        $value = $previous = '' unless defined $value;
        $self->{'_dbentries'} = $value;
    } 
    return $previous;
}
get_parameterdescriptionprevnextTop
sub get_parameter {
   my ($self,$name) = @_;
   return $self->{'_parameters'}->get_parameter($name);
}
available_parametersdescriptionprevnextTop
sub available_parameters {
   my ($self) = @_;
   return $self->{'_parameters'}->available_parameters;
}
get_statisticdescriptionprevnextTop
sub get_statistic {
   my ($self,$key) = @_;
   return $self->{'_statistics'}->get_statistic($key);
}
available_statisticsdescriptionprevnextTop
sub available_statistics {
   my ($self) = @_;
   return $self->{'_statistics'}->available_statistics;
}
add_hitdescriptionprevnextTop
sub add_hit {
    my ($self,$s) = @_;
    if (ref($s) eq 'HASH' || $s->isa('Bio::Search::Hit::HitI') ) {
        push @{$self->{'_hits'}}, $s;
    }
    else { 
        $self->throw("Passed in " .ref($s)." as a Hit which is not a Bio::Search::HitI.");
    }
    
    if (ref($s) eq 'HASH') {
        $self->{_hashes}->{$#{$self->{'_hits'}}} = 1;
    }
    return scalar @{$self->{'_hits'}};
}
hit_factorydescriptionprevnextTop
sub hit_factory {
    my $self = shift;
    if (@_) { $self->{_hit_factory} = shift }
    return $self->{_hit_factory} || return;
}
rewinddescriptionprevnextTop
sub rewind {
   my ($self) = @_;
   $self->{'_hitindex'} = 0;
}
_nexthitindexdescriptionprevnextTop
sub _nexthitindex {
   my ($self,@args) = @_;
   return $self->{'_hitindex'}++;
}
add_parameterdescriptionprevnextTop
sub add_parameter {
   my ($self,$key,$value) = @_;
   $self->{'_parameters'}->set_parameter($key => $value);
}
add_statisticdescriptionprevnextTop
sub add_statistic {
   my ($self,$key,$value) = @_;
   $self->{'_statistics'}->set_statistic($key => $value);
   return;
}
num_hitsdescriptionprevnextTop
sub num_hits {
   my ($self) = shift;
   if (not defined $self->{'_hits'}) {
       $self->throw("Can't get Hits: data not collected.");
    }
    return scalar(@{$self->{'_hits'}});
}
hitsdescriptionprevnextTop
sub hits {
    my ($self) = shift;
    
    foreach my $i (keys %{$self->{_hashes} || {}}) {
        my $factory = $self->hit_factory || $self->throw("Tried to get a Hit, but it was a hash ref and we have no hit factory");
        $self->{'_hits'}->[$i] = $factory->create_object(%{$self->{'_hits'}->[$i]});
        delete $self->{_hashes}->{$i};
    }
    
    my @hits = ();
    if (ref $self->{'_hits'}) {
        @hits = @{$self->{'_hits'}};
    }
    return @hits;
}
algorithm_referencedescriptionprevnextTop
sub algorithm_reference {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'algorithm_reference'} = $value;
    }
    return $self->{'algorithm_reference'};
}
program_referencedescriptionprevnextTop
sub program_reference {
 shift->algorithm_reference(@_);
}
riddescriptionprevnextTop
sub rid {
    my ($self,$value) = @_;
    if( defined $value) {
	   $self->{'rid'} = $value;
	}
	return $self->{'rid'};
}
no_hits_founddescriptionprevnextTop
sub no_hits_found {
    my $self = shift;

    # Watch the double negative! 
# result = 0 means "yes hits were found"
# result = 1 means "no hits were found"
return $self->{'_no_hits_found'};
}
set_no_hits_founddescriptionprevnextTop
sub set_no_hits_found {
    my $self = shift;
    $self->{'_no_hits_found'} = 1;
}
to_stringdescriptionprevnextTop
sub to_string {
    my $self = shift;
    my $str = ref($self) . ", algorithm= " . $self->algorithm . ", query=" . $self->query_name . " " . $self->query_description .", db=" . $self->database_name;
    return $str;
}

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 - Jason Stajich and Steve ChervitzTop
Email jason@bioperl.org
Email sac@bioperl.org
CONTRIBUTORSTop
Sendu Bala, bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::Search::Result::ResultI interface methodsTop
Bio::Search::Result::ResultI implementation
Bio::Search::Report Top
Bio::Search::Result::GenericResult specific methods