Manual Reference Pages - BIO::SEARCH::HSP::PSLHSP (3)
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 _
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]
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
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)
|perl v5.20.3 ||BIO::SEARCH::HSP::PSLHSP (3) ||2016-04-05 |
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