NAME

       Bio::Search::HSP::WABAHSP - HSP object suitable for describing WABA alignments

SYNOPSIS

       # use this object as you would a GenericHSP # a few other methods have been added
       including state

DESCRIPTION

       This object implements a few of the extra methods such as hmmstate_string which returns
       the HMM state representation for the WABA alignment.  We also must implement a method to
       calculate homology_string since it is not returned by the algorithm in the machine
       readable format.

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 - 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 = Bio::Search::HSP::WABAHSP->new();
        Function: Builds a new Bio::Search::HSP::WABAHSP object
        Returns : Bio::Search::HSP::WABAHSP
        Args    : -hmmstate_seq => the string representing the state output from WABA

   hmmstate_string
        Title   : hmmstate_string
        Usage   : my $hmmseq = $wabahsp->hmmstate_string();
        Function: Get/Set the WABA HMM stateseq
        Returns : string
        Args    : [optional] string

   homology_string
        Title   : homolgy_string
        Usage   : my $homology_str = $hsp->homology_string();
        Function: Homology string must be calculated for a WABA HSP so we can do
                  so here and cache the result so it is only done once
        Returns : string
        Args    : none