Bio::Search::HSP::PSLHSP(3pm)

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 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-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 gaps

  gap_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,length

  mismatches
 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)