Bio::Search::HSP::PSLHSP - A HSP for PSL output # get a PSLHSP somehow (SearchIO::psl) This is a HSP for PSL output so we can handle seq_inds differently.

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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.bioperl.org/ Email jason-at-bioperl-dot-org Describe contact details here Additional contributors names and emails here 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)