Bio::Search::Result HMMERResult
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Summary
Bio::Search::Result::HMMERResult - A Result object for HMMER results
Package variables
No package variables defined.
Inherit
Bio::Search::Result::GenericResult
Synopsis
    use Bio::Search::Result::HMMERResult;
my $result = Bio::Search::Result::HMMERResult->new
( -hmm_name => 'pfam',
-sequence_file => 'roa1.pep',
-hits => \@hits);
# generally we use Bio::SearchIO to build these objects use Bio::SearchIO; my $in = Bio::SearchIO->new(-format => 'hmmer', -file => 'result.hmmer'); while( my $result = $in->next_result ) { print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n"; }
Description
This is a specialization of Bio::Search::Result::GenericResult.
There are a few extra methods, specifically sequence_file,
hmm_name, next_models, and models.
Methods
newDescriptionCode
hmm_nameDescriptionCode
sequence_fileDescriptionCode
next_modelDescriptionCode
modelsDescriptionCode
rewindDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Search::Result::HMMERResult->new();
Function: Builds a new Bio::Search::Result::HMMERResult object
Returns : Bio::Search::Result::HMMERResult
Args : -hmm_name => string, name of hmm file
-sequence_file => name of the sequence file
plus Bio::Search::Result::GenericResult parameters
           -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)
-program_reference => literature reference string for this algorithm
hmm_namecodeprevnextTop
 Title   : hmm_name
Usage : $obj->hmm_name($newval)
Function: Get/Set the value of hmm_name
Returns : value of hmm_name
Args : newvalue (optional)
sequence_filecodeprevnextTop
 Title   : sequence_file
Usage : $obj->sequence_file($newval)
Function: Get/Set the value of sequence_file
Returns : value of sequence_file
Args : newvalue (optional)
next_modelcodeprevnextTop
 Title   : next_model
Usage : my $domain = $result->next_model
Function: Returns the next domain - this
is an alias for next_hit
Returns : Bio::Search::Hit::HitI object
Args : none
modelscodeprevnextTop
 Title   : models
Usage : my @domains = $result->models;
Function: Returns the list of HMM models seen - this
is an alias for hits()
Returns : Array of Bio::Search::Hit::HitI objects
Args : none
rewindcodeprevnextTop
 Title   : rewind
Usage : $result->rewind;
Function: Allow one to reset the Hit iteration to the beginning
Since this is an in-memory implementation
Returns : none
Args : none
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;
  my $self = $class->SUPER::new(@args);
  
  my ($hmm,$seqfile) = $self->_rearrange([qw(HMM_NAME SEQUENCE_FILE)],
					 @args);
  
  defined( $seqfile) && $self->sequence_file($seqfile);
  defined( $hmm) && $self->hmm_name($hmm);

  return $self;
}
hmm_namedescriptionprevnextTop
sub hmm_name {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_hmm_name'} = $value;
    }
    return $self->{'_hmm_name'};
}
sequence_filedescriptionprevnextTop
sub sequence_file {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_sequence_file'} = $value;
    }
    return $self->{'_sequence_file'};
}
next_modeldescriptionprevnextTop
sub next_model {
shift->next_hit
}
modelsdescriptionprevnextTop
sub models {
shift->hits
}
rewinddescriptionprevnextTop
sub rewind {
   my ($self) = @_;
   $self->{'_hitindex'} = 0;
}
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 StajichTop
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::Search::Result::GenericResult inherited methodsTop
algorithmTop
 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_versionTop
 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
Bio::Search::Result::ResultI interface methodsTop
Bio::Search::Result::ResultI implementation
next_hitTop
 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_nameTop
 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_accessionTop
 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_lengthTop
 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_descriptionTop
 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_nameTop
 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_lettersTop
 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_entriesTop
 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_parameterTop
 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_parametersTop
 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_statisticTop
 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_statisticsTop
 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
Bio::Search::Result::GenericResult specific methodsTop
add_hitTop
 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_parameterTop
 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_statisticTop
 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_hitsTop
 Title   : num_hits
Usage : my $hitcount= $result->num_hits
Function: returns the number of hits for this query result
Returns : integer
Args : none
hitsTop
 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
program_referenceTop
 Title   : program_reference
Usage : $obj->program_reference($newval)
Function:
Returns : value of the literature reference for the algorithm
Args : newvalue (optional)