Provided by: libbio-perl-perl_1.7.2-3_all
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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AUTHOR - Jason Stajich
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)