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