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.
email@example.com - General discussion http://bioperl.org/wiki/Mailing_lists - 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