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

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-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 = new Bio::Search::HSP::PSLHSP();
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)