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Manual Reference Pages  -  BIO::SEARCH::HSP::PSLHSP (3)

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NAME

Bio::Search::HSP::PSLHSP - A HSP for PSL output

CONTENTS

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)



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perl v5.20.3 BIO::SEARCH::HSP::PSLHSP (3) 2016-04-05

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