Ewan Birney

NAME

Bio::Factory::BlastHitFactory - Factory for Bio::Search::Hit::BlastHit objects

SYNOPSIS

    use Bio::Factory::BlastHitFactory;

    my $hit_fact = Bio::Factory::BlastHitFactory->new();

    my $hit = $hit_fact->create_hit( %parameters );

See documentation for create_hit() for information about %parameters.

DESCRIPTION

This module encapsulates code for creating Bio::Search::Hit::BlastHit and Bio::Search::HSP::BlastHSP objects from traditional BLAST report data (i.e., non-XML formatted).

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 one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                - General discussion
  http://bio.perl.org/MailList.html    - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR

Steve Chervitz <sac@bioperl.org>

See the FEEDBACK section for where to send bug reports and comments.

COPYRIGHT

Copyright (c) 2001 Steve Chervitz. All Rights Reserved.

DISCLAIMER

This software is provided "as is" without warranty of any kind.

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

create_hit

 Title   : create_hit
 Usage   : $hit = $factory->create_hit( %params );
 Function: Creates a new Bio::Search::Hit::BlastHit object given 
           raw BLAST report data, formatted in traditional BLAST report format.
 Returns : A single Bio::Search::Hit::BlastHit object
 Args    : Named parameters to be passed to the BlastHit object.
           Parameter keys are case-insensitive.
           See Bio::Search::Hit::BlastHit::new() documentation for 
           details about these parameters.
           The only additional parameter required is:
              -RESULT    => a Bio::Search::Result::BlastResult object.
           From this result object, the program, query length, 
           and iteration are obtained and passed on to the BlastHit.