Bio::Search::HSP::WABAHSP man page on Pidora

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Bio::Search::HSP::WABAUser3Contributed Perl DocumeBio::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.

FEEDBACK
   Mailing Lists
       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.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

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

       bioperl-l@bioperl.org

       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.

   Reporting Bugs
       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:

	 http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

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 = 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

   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

perl v5.14.1			  2011-07-22	  Bio::Search::HSP::WABAHSP(3)
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