NAME

       Bio::Tools::Run::Alignment::DBA - Object for the alignment of two sequences using the DNA
       Block Aligner program.

SYNOPSIS

         use Bio::Tools::Run::Alignment::DBA;

         #  Build a dba alignment factory
         my @params = ('matchA' => 0.75,
                        'matchB' => '0.55',
                        'dymem' =>'linear');
         my $factory = Bio::Tools::Run::Alignment::DBA->new(@params);

         #  Pass the factory a filename with 2 sequences to be aligned.
         $inputfilename = 't/data/dbaseq.fa';
         # @hsps is an array of GenericHSP objects
         my @hsps = $factory->align($inputfilename);

         # or
         my @files = ('t/data/dbaseq1.fa','t/data/dbaseq2.fa');
         my @hsps = $factory->align(\@files);

         # or where @seq_array is an array of Bio::Seq objects
         $seq_array_ref = \@seq_array;
         my @hsps = $factory->align($seq_array_ref);

DESCRIPTION

       DNA Block Aligner program (DBA) was developed by Ewan Birney. DBA is part of the Wise
       package available at <http://www.sanger.ac.uk/software/wise2>.

       You will need to enable dba to find the dba program. This can be done in a few different
       ways:

       1. Define an environmental variable WISEDIR:

         export WISEDIR =/usr/local/share/wise2.2.0

       2. Include a definition of an environmental variable WISEDIR in every script that will use
       DBA.pm:

         $ENV{WISEDIR} = '/usr/local/share/wise2.2.20';

       3. Make sure that the dba application is in your PATH.

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://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 the bugs and their
       resolution.  Bug reports can be submitted via the web:

         http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Shawn Hoon

       Email shawnh@fugu-sg.org

APPENDIX

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

   program_name
        Title   : program_name
        Usage   : $factory>program_name()
        Function: holds the program name
        Returns:  string
        Args    : None

   program_dir
        Title   : program_dir
        Usage   : $factory->program_dir(@params)
        Function: returns the program directory, obtained from ENV variable.
        Returns:  string
        Args    :

   version
        Title   : version
        Usage   : exit if $prog->version() < 1.8
        Function: Determine the version number of the program
        Example :
        Returns : float or undef
        Args    : none

   align
        Title   : align
        Usage   :
                   $inputfilename = 't/data/seq.fa';
                   @hsps = $factory->align($inputfilename);
                 or
                   #@seq_array is array of Seq objs
                   $seq_array_ref = \@seq_array;
                   @hsps = $factory->align($seq_array_ref);
                 or
                   my @files = ('t/data/seq1.fa','t/data/seq2.fa');
                   @hsps = $factory->align(\@files);
        Function: Perform a DBA  alignment

        Returns : An array of Bio::Search::HSP::GenericHSP objects
        Args    : Name of a file containing a set of 2 fasta sequences
                  or else a reference to an array  to 2  Bio::Seq objects.
                  or else a reference to an array of 2 file
                     names containing 1 fasta sequence each

        Throws an exception if argument is not either a string (eg a
        filename) or a reference to an array of 2 Bio::Seq objects.  If
        argument is string, throws exception if file corresponding to string
        name can not be found. If argument is Bio::Seq array, throws
        exception if less than two sequence objects are in array.

   _run
        Title   :  _run
        Usage   :  Internal function, not to be called directly
        Function:   makes actual system call to dba program
        Example :
        Returns : nothing; dba  output is written to a temp file
        Args    : Name of a file containing a set of unaligned fasta sequences
                  and hash of parameters to be passed to dba

   _parse_results
        Title   :  __parse_results
        Usage   :  Internal function, not to be called directly
        Function:  Parses dba output
        Example :
        Returns : an reference to an array of GenericHSPs
        Args    : the name of the output file

   _setinput()
        Title   :  _setinput
        Usage   :  Internal function, not to be called directly
        Function:   Create input file for dba program
        Example :
        Returns : name of file containing dba data input
        Args    : Seq or Align object reference or input file name

   _setparams()
        Title   :  _setparams
        Usage   :  Internal function, not to be called directly
        Function:   Create parameter inputs for dba program
        Example :
        Returns : parameter string to be passed to dba
                  during align or profile_align
        Args    : name of calling object

   _query_seq()
        Title   :  _query_seq
        Usage   :  Internal function, not to be called directly
        Function:  get/set for the query sequence
        Example :
        Returns :
        Args    :

   _subject_seq()
        Title   :  _subject_seq
        Usage   :  Internal function, not to be called directly
        Function:  get/set for the subject sequence
        Example :
        Returns :

        Args    :