NAME

       Bio::Tools::Run::Alignment::MAFFT - run the MAFFT alignment tools

SYNOPSIS

         # Build a MAFFT alignment factory
         $factory = Bio::Tools::Run::Alignment::MAFFT->new(@params);

         # Pass the factory a list of sequences to be aligned.
         $inputfilename = 't/cysprot.fa';
         # $aln is a SimpleAlign object.
         $aln = $factory->align($inputfilename);

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

         #There are various additional options available.

DESCRIPTION

       You can get MAFFT from <http://mafft.cbrc.jp/alignment/software/>.  "fftnsi" is the
       default method for Mafft version 4 in this implementation.

       See Bio::Tools::Run::Alignment::Clustalw for a description on how to specify parameters to
       the underlying alignment program. See the MAFFT manual page for a description of the MAFFT
       parameters.

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/MailList.html - 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 - Jason Stajich

       Email jason-at-bioperl.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

   executable
        Title   : executable
        Usage   : my $exe = $blastfactory->executable('blastall');
        Function: Finds the full path to the 'codeml' executable
        Returns : string representing the full path to the exe
        Args    : [optional] name of executable to set path to
                  [optional] boolean flag whether or not warn when exe is not found

   program_path
        Title   : program_path
        Usage   : my $path = $factory->program_path();
        Function: Builds path for executable
        Returns : string representing the full path to the exe
        Args    : none

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

   error_string
        Title   : error_string
        Usage   : $obj->error_string($newval)
        Function: Where the output from the last analysis run is stored.
        Returns : value of error_string
        Args    : newvalue (optional)

   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

   run
        Title   : run
        Usage   : my $output = $application->run(\@seqs);
        Function: Generic run of an application
        Returns : Bio::SimpleAlign object
        Args    : array ref of Bio::PrimarySeqI objects OR
                  filename of sequences to run with

   align
        Title   : align
        Usage   :
           $inputfilename = 't/data/cysprot.fa';
           $aln = $factory->align($inputfilename);
       or
           $seq_array_ref = \@seq_array;
           # @seq_array is an array of Seq objs
           $aln = $factory->align($seq_array_ref);
        Function: Perform a multiple sequence alignment
        Returns : Reference to a SimpleAlign object containing the
                  sequence alignment.
        Args    : Name of a file containing a set of unaligned fasta sequences
                  or else an array of references to Bio::Seq objects.

        Throws an exception if argument is not either a string (eg a
        filename) or a reference to an array of 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 tcoffee program
        Example :
        Returns : nothing; tcoffee output is written to a
                  temporary file OR specified output file
        Args    : Name of a file containing a set of unaligned fasta sequences
                  and hash of parameters to be passed to tcoffee

   _setinput
        Title   :  _setinput
        Usage   :  Internal function, not to be called directly
        Function:  Create input file for mafft programs
        Example :
        Returns : name of file containing mafft 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 mafft program
        Example :
        Returns : parameter string to be passed to mafft program
        Args    : name of calling object

   methods
        Title   : methods
        Usage   : my @methods = $self->methods()
        Function: Get/Set Alignment methods - NOT VALIDATED
        Returns : array of strings
        Args    : arrayref of strings

   _version6
        Title   : _version6
        Usage   : Internal function, not to be called directly
        Function: Check if the version of MAFFT is 6
        Example :
        Returns : Boolean
        Args    : None

Bio::Tools::Run::BaseWrapper methods

   no_param_checks
        Title   : no_param_checks
        Usage   : $obj->no_param_checks($newval)
        Function: Boolean flag as to whether or not we should
                  trust the sanity checks for parameter values
        Returns : value of no_param_checks
        Args    : newvalue (optional)

   save_tempfiles
        Title   : save_tempfiles
        Usage   : $obj->save_tempfiles($newval)
        Function:
        Returns : value of save_tempfiles
        Args    : newvalue (optional)

   outfile_name
        Title   : outfile_name
        Usage   : my $outfile = $mafft->outfile_name();
        Function: Get/Set the name of the output file for this run
                  (if you wanted to do something special)
        Returns : string
        Args    : [optional] string to set value to

   tempdir
        Title   : tempdir
        Usage   : my $tmpdir = $self->tempdir();
        Function: Retrieve a temporary directory name (which is created)
        Returns : string which is the name of the temporary directory
        Args    : none

   cleanup
        Title   : cleanup
        Usage   : $mafft->cleanup();
        Function: Will cleanup the tempdir directory
        Returns : none
        Args    : none

   io
        Title   : io
        Usage   : $obj->io($newval)
        Function:  Gets a L<Bio::Root::IO> object
        Returns : L<Bio::Root::IO>
        Args    : none