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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:

	 https://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-08	  Bio::Search::HSP::WABAHSP(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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