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

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)