Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches

SYNOPSIS

           # get a Set object probably from the results object
           print "Bits score over set ",$set->bits," evalue ",$set->evalue,"\n";

           foreach $domain ( $set->each_Domain ) {
               print "Domain start ",$domain->start," end ",$domain->end,"\n";
           }

DESCRIPTION

       Represents a set of HMMER domains hitting one sequence. HMMER reports two different
       scores, a per sequence total score (and evalue) and a per domain score and evalue. This
       object represents a collection of the same domain with the sequence bits score and evalue.
       (these attributes are also on the per domain scores, which you can get there).

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 - Ewan Birney

       Email birney-at-ebi.ac.uk

APPENDIX

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

   add_Domain
        Title   : add_Domain
        Usage   : $set->add_Domain($domain)
        Function: adds the domain to the list
        Returns : nothing
        Args    : A Bio::Tools::HMMER::Domain object

   each_Domain
        Title   : each_Domain
        Usage   : foreach $domain ( $set->each_Domain() )
        Function: returns an array of domain objects in this set
        Returns : array
        Args    : none

   name
        Title   : name
        Usage   : $obj->name($newval)
        Function:
        Example :
        Returns : value of name
        Args    : newvalue (optional)

   desc
        Title   : desc
        Usage   : $obj->desc($newval)
        Function:
        Example :
        Returns : value of desc
        Args    : newvalue (optional)

   accession
        Title   : accession
        Usage   : $obj->accession($newval)
        Function:
        Example :
        Returns : value of accession
        Args    : newvalue (optional)

   bits
        Title   : bits
        Usage   : $obj->bits($newval)
        Function:
        Example :
        Returns : value of bits
        Args    : newvalue (optional)

   evalue
        Title   : evalue
        Usage   : $obj->evalue($newval)
        Function:
        Example :
        Returns : value of evalue
        Args    : newvalue (optional)