NAME

Bio::Search::Result::INFERNALResult - A Result object for INFERNAL results

SYNOPSIS

    # typically one gets Results from a SearchIO stream
    use Bio::SearchIO;
    my $io = Bio::SearchIO->new(-format => 'infernal',
                                -file   => 't/data/cmsearch_output.txt');
    while( my $result = $io->next_result ) {
        while( my $hit = $result->next_hit ) {
          print join(" ", $result->query_name, $result->algorithm, $result->num_hits), "\n";
        }
    }

DESCRIPTION

This object is a specialization of Bio::Search::Result::GenericResult. There is one extra method called cm_name.

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 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 of the bugs and their resolution. Bug reports can be submitted via the web:

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

AUTHOR - Paul Cantalupo

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 = Bio::Search::Result::INFERNALResult->new();
 Function: Builds a new Bio::Search::Result::INFERNALResult object
 Returns : Bio::Search::Result::INFERNALResult
 Args    : -cm_name    => string, name of covariance model (CM) file.
           plus Bio::Search::Result::GenericResult parameters

cm_name

 Title   : cm_name
 Usage   : $obj->cm_name($newvalue)
 Function: Get/Set value of the covariance model file name (cm_name)
 Returns : value of cm_name
 Args    : newvalue (optional)