Bio::Search::HSP::WABAHSP(3)

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.

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AUTHOR - Jason Stajich
Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS
Additional contributors names and emails here

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 = new Bio::Search::HSP::WABAHSP();
 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