NAME

Bio::Search::Result::PullResultI - Bio::Search::Result::ResultI interface for 'pull' parsers

SYNOPSIS

    # This is an interface and cannot be instantiated

    # typically one gets Results from a SearchIO stream
    use Bio::SearchIO;
    my $io = Bio::SearchIO->new(-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.

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 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

Support

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 Bugs

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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR Sendu Bala

Email bix@sendu.me.uk

COPYRIGHT

DISCLAIMER

This software is provided "as is" without warranty of any kind.

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

_setup

 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().

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    : none

sort_hits

 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);

query_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    : none

query_accession

 Title   : query_accession
 Usage   : $id = $result->query_accession();
 Function: Get the accession (if available) for the query sequence
 Returns : a string
 Args    : none

query_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    : none

query_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    : none

database_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    : none

database_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    : none

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    : none

algorithm

 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

algorithm_version

 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

algorithm_reference

 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.

num_hits

 Title   : num_hits
 Usage   : my $hitcount= $result->num_hits
 Function: returns the number of hits for this query result
 Returns : integer
 Args    : none

hits

 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

no_hits_found

 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

rewind

 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

get_parameter

 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)

available_parameters

 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

add_parameter

 Title   : add_parameter
 Usage   : $result->add_parameter('gapext', 11);
 Function: Adds a parameter
 Returns : none
 Args    : key  - key value name for this parama
           value - value for this parameter

get_statistic

 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)

available_statistics

 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

add_statistic

 Title   : add_statistic
 Usage   : $result->add_statistic('lambda', 2.3);
 Function: Adds a statistic
 Returns : none
 Args    : key  - key value name for this statistic
           value - value for this statistic