Provided by: libbio-perl-perl_1.7.2-3_all bug

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)