Bio::Search::HSP::PSLHSP.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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)