Manual Reference Pages - BIO::SEARCH::HSP::WABAHSP (3)
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
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