Bio::Search::HSP::WABAUser3Contributed Perl DocumeBio::Search::HSP::WABAHSP(3)NAMEBio::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)