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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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