NAME
Bio::Search::HSP::PSLHSP - A HSP for PSL output
SYNOPSIS
# get a PSLHSP somehow (SearchIO::psl)DESCRIPTION
This is a HSP for PSL output so we can handle seq_inds differently.
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 listsSupport
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/issuesAUTHOR - Jason Stajich
Email jason-at-bioperl-dot-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::PSLHSP->new();
Function: Builds a new Bio::Search::HSP::PSLHSP object
Returns : an instance of Bio::Search::HSP::PSLHSP
Args : -gapblocks => arrayref of gap locations which are [start,length]
of gapsgap_blocks
Title : gap_blocks
Usage : $obj->gap_blocks($seqtype,$blocks)
Function: Get/Set the gap blocks
Returns : value of gap_blocks (a scalar)
Args : sequence type - 'query' or 'hit'
blocks - arrayref of block start,lengthmismatches
Title : mismatches
Usage : $obj->mismatches($newval)
Function: Get/Set the number of mismatches
Returns : value of mismatches (a scalar)
Args : on set, new value (a scalar or undef, optional)