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Bio::Search::HSP::WABAHSP(3) User Contributed Perl Documentation 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.

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.                  - General discussion  - About the mailing lists

Please direct usage questions or support issues to the mailing list:
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.

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:


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
2019-01-01 perl v5.28.1

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