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.\" ========================================================================
.\"
.IX Title "Bio::Search::HSP::WABAHSP 3pm"
.TH Bio::Search::HSP::WABAHSP 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::Search::HSP::WABAHSP \- HSP object suitable for describing WABA alignments
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
# use this object as you would a GenericHSP
# a few other methods have been added including state
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object implements a few of the extra methods such as
hmmstate_string which returns the \s-1HMM\s0 state representation for the
\&\s-1WABA\s0 alignment.  We also must implement a method to calculate
homology_string since it is not returned by the algorithm in the
machine readable format.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason@bioperl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 5
\& 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
.Ve
.SS "hmmstate_string"
.IX Subsection "hmmstate_string"
.Vb 5
\& Title   : hmmstate_string
\& Usage   : my $hmmseq = $wabahsp\->hmmstate_string();
\& Function: Get/Set the WABA HMM stateseq
\& Returns : string
\& Args    : [optional] string
.Ve
.SS "homology_string"
.IX Subsection "homology_string"
.Vb 6
\& 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
.Ve