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Bio::Search::HSP::PSLHUser)Contributed Perl DocumenBio::Search::HSP::PSLHSP(3)

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)

perl v5.32.1			  2019-12-07	   Bio::Search::HSP::PSLHSP(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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