Provided by: libbio-perl-perl_1.7.6-3_all bug


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


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


       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.


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AUTHOR - Jason Stajich



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

        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

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