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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::Alignment::MAFFT 3pm"
.TH Bio::Tools::Run::Alignment::MAFFT 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::Alignment::MAFFT \- run the MAFFT alignment tools
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  # Build a MAFFT alignment factory
\&  $factory = Bio::Tools::Run::Alignment::MAFFT\->new(@params);
\&
\&  # Pass the factory a list of sequences to be aligned.
\&  $inputfilename = \*(Aqt/cysprot.fa\*(Aq;
\&  # $aln is a SimpleAlign object.
\&  $aln = $factory\->align($inputfilename);
\&
\&  # or where @seq_array is an array of Bio::Seq objects
\&  $seq_array_ref = \e@seq_array;
\&  $aln = $factory\->align($seq_array_ref);
\&
\&  #There are various additional options available.
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
You can get \s-1MAFFT\s0 from <http://mafft.cbrc.jp/alignment/software/>.
\&\*(L"fftnsi\*(R" is the default method for Mafft version 4 in this
implementation.
.PP
See Bio::Tools::Run::Alignment::Clustalw for a description on how to
specify parameters to the underlying alignment program. See the \s-1MAFFT\s0
manual page for a description of the \s-1MAFFT\s0 parameters.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/MailList.html \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \-  Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason\-at\-bioperl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory\->program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS "executable"
.IX Subsection "executable"
.Vb 6
\& Title   : executable
\& Usage   : my $exe = $blastfactory\->executable(\*(Aqblastall\*(Aq);
\& Function: Finds the full path to the \*(Aqcodeml\*(Aq 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
.Ve
.SS "program_path"
.IX Subsection "program_path"
.Vb 5
\& 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
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns:  string
\& Args    :
.Ve
.SS "error_string"
.IX Subsection "error_string"
.Vb 5
\& 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)
.Ve
.SS "version"
.IX Subsection "version"
.Vb 6
\& Title   : version
\& Usage   : exit if $prog\->version() < 1.8
\& Function: Determine the version number of the program
\& Example :
\& Returns : float or undef
\& Args    : none
.Ve
.SS "run"
.IX Subsection "run"
.Vb 6
\& Title   : run
\& Usage   : my $output = $application\->run(\e@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
.Ve
.SS "align"
.IX Subsection "align"
.Vb 10
\& Title   : align
\& Usage   :
\&    $inputfilename = \*(Aqt/data/cysprot.fa\*(Aq;
\&    $aln = $factory\->align($inputfilename);
\&or
\&    $seq_array_ref = \e@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.
.Ve
.SS "_run"
.IX Subsection "_run"
.Vb 8
\& 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
.Ve
.SS "_setinput"
.IX Subsection "_setinput"
.Vb 6
\& 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
.Ve
.SS "_setparams"
.IX Subsection "_setparams"
.Vb 6
\& 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
.Ve
.SS "methods"
.IX Subsection "methods"
.Vb 5
\& Title   : methods
\& Usage   : my @methods = $self\->methods()
\& Function: Get/Set Alignment methods \- NOT VALIDATED
\& Returns : array of strings
\& Args    : arrayref of strings
.Ve
.SS "_version6"
.IX Subsection "_version6"
.Vb 6
\& Title   : _version6
\& Usage   : Internal function, not to be called directly
\& Function: Check if the version of MAFFT is 6
\& Example :
\& Returns : Boolean
\& Args    : None
.Ve
.SH "Bio::Tools::Run::BaseWrapper methods"
.IX Header "Bio::Tools::Run::BaseWrapper methods"
.SS "no_param_checks"
.IX Subsection "no_param_checks"
.Vb 6
\& 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)
.Ve
.SS "save_tempfiles"
.IX Subsection "save_tempfiles"
.Vb 5
\& Title   : save_tempfiles
\& Usage   : $obj\->save_tempfiles($newval)
\& Function:
\& Returns : value of save_tempfiles
\& Args    : newvalue (optional)
.Ve
.SS "outfile_name"
.IX Subsection "outfile_name"
.Vb 6
\& 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
.Ve
.SS "tempdir"
.IX Subsection "tempdir"
.Vb 5
\& 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
.Ve
.SS "cleanup"
.IX Subsection "cleanup"
.Vb 5
\& Title   : cleanup
\& Usage   : $mafft\->cleanup();
\& Function: Will cleanup the tempdir directory
\& Returns : none
\& Args    : none
.Ve
.SS "io"
.IX Subsection "io"
.Vb 5
\& Title   : io
\& Usage   : $obj\->io($newval)
\& Function:  Gets a L<Bio::Root::IO> object
\& Returns : L<Bio::Root::IO>
\& Args    : none
.Ve