NAME
Bio::Search::Result::HMMERResult - A Result object for HMMER results
SYNOPSIS
use Bio::Search::Result::HMMERResult;
my $result = new Bio::Search::Result::HMMERResult
( -hmm_name => 'pfam',
-sequence_file => 'roa1.pep',
-hits => \@hits);
# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = new Bio::SearchIO(-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.
FEEDBACK
Mailing Lists
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 listsReporting Bugs
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:
http://bugzilla.open-bio.org/AUTHOR - Jason Stajich
Email jason@bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = new Bio::Search::Result::HMMERResult();
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 fileplus 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 algorithmhmm_name
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_file
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_model
Title : next_model
Usage : my $domain = $result->next_model
Function: Returns the next domain - this
is an alias for next_hit
Returns : L<Bio::Search::Hit::HitI> object
Args : nonemodels
Title : models
Usage : my @domains = $result->models;
Function: Returns the list of HMM models seen - this
is an alias for hits()
Returns : Array of L<Bio::Search::Hit::HitI> objects
Args : noneBio::Search::Result::GenericResult inherited methods
algorithm
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 valuealgorithm_version
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 valueBio::Search::Result::ResultI interface methods
Bio::Search::Result::ResultI implementation
next_hit
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 : nonequery_name
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 namequery_accession
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 accessionquery_length
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 lengthquery_description
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 descriptiondatabase_name
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 namedatabase_letters
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_entries
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 dbget_parameter
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_parameters
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 : noneget_statistic
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_statistics
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 : noneBio::Search::Result::GenericResult specific methods
add_hit
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::HitIrewind
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 : noneadd_parameter
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 parameteradd_statistic
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 parameternum_hits
Title : num_hits
Usage : my $hitcount= $result->num_hits
Function: returns the number of hits for this query result
Returns : integer
Args : nonehits
Title : hits
Usage : my @hits = $result->hits
Function: Returns the available hits for this Result
Returns : Array of L<Bio::Search::Hit::HitI> objects
Args : noneprogram_reference
Title : program_reference
Usage : $obj->program_reference($newval)
Function:
Returns : value of the literature reference for the algorithm
Args : newvalue (optional)