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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::Alignment::Amap 3pm"
.TH Bio::Tools::Run::Alignment::Amap 3pm "2018-09-14" "perl v5.26.2" "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::Amap \- Object for the calculation of an
iterative multiple sequence alignment from a set of unaligned
sequences or alignments using the Amap (2.0) program
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&  # Build a muscle alignment factory
\&  $factory = Bio::Tools::Run::Alignment::Amap\->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);
\&
\&  # Or one can pass the factory a pair of (sub)alignments
\&  #to be aligned against each other, e.g.:
\&
\&  #There are various additional options and input formats available.
\&  #See the DESCRIPTION section that follows for additional details.
\&
\&  #To run amap with training, try something like:
\&
\&  #First round to generate train.params
\&  $factory = Bio::Tools::Run::Alignment::Amap\->new
\&      (
\&       \*(Aqiterative\-refinement\*(Aq  => \*(Aq1000\*(Aq,
\&       \*(Aqconsistency\*(Aq   => \*(Aq5\*(Aq,
\&       \*(Aqpre\-training\*(Aq => \*(Aq20\*(Aq,
\&       \*(Aqemissions\*(Aq => \*(Aq\*(Aq,
\&       \*(Aqverbose\*(Aq => \*(Aq\*(Aq,
\&       \*(Aqtrain\*(Aq   => "$dir/$subdir/$outdir/train.params",
\&      );
\&  $factory\->outfile_name("$dir/$subdir/$outdir/train.params");
\&
\&  #Second round to use train.params to get a high qual alignment
\&
\&  $seq_array_ref = \e@seq_array;
\&  $aln = $factory\->align($seq_array_ref);
\&  $aln = \*(Aq\*(Aq;
\&  $factory = \*(Aq\*(Aq;
\&
\&  $factory = Bio::Tools::Run::Alignment::Amap\->new
\&      (
\&       \*(Aqiterative\-refinement\*(Aq  => \*(Aq1000\*(Aq,
\&       \*(Aqconsistency\*(Aq   => \*(Aq5\*(Aq,
\&       \*(Aqpre\-training\*(Aq => \*(Aq20\*(Aq,
\&       \*(Aqverbose\*(Aq => \*(Aq\*(Aq,
\&       \*(Aqparamfile\*(Aq   => "$dir/$subdir/$outdir/train.params",
\&      );
\&  $factory\->outfile_name("$dir/$subdir/$outdir/outfile.afa");
\&  $aln = $factory\->align($seq_array_ref);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Amap uses a Sequence Annealing algorithm which is an incremental
method for building multiple alignments. You can get it and see
information about it at this \s-1URL\s0 http://bio.math.berkeley.edu/amap/
.SS "Helping the module find your executable"
.IX Subsection "Helping the module find your executable"
\&\s-1FIXME:\s0 Amap uses the same parameters as Probcons, plus a few others. I
haven't had time to check all the changes from the Probcons.pm
runnable. Feel free to do it.
.PP
You will need to enable Amap to find the amap program. This can be
done in (at least) three ways:
.PP
.Vb 8
\&  1. Make sure the amap executable is in your path (i.e. 
\&     \*(Aqwhich amap\*(Aq returns a valid program
\&  2. define an environmental variable AMAPDIR which points to a 
\&     directory containing the \*(Aqamap\*(Aq app:
\&   In bash 
\&        export AMAPDIR=/home/progs/amap   or
\&   In csh/tcsh
\&        setenv AMAPDIR /home/progs/amap
\&
\&  3. include a definition of an environmental variable AMAPDIR 
\&      in every script that will
\&     BEGIN {$ENV{AMAPDIR} = \*(Aq/home/progs/amap\*(Aq; }
\&     use Bio::Tools::Run::Alignment::Amap;
.Ve
.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/wiki/Mailing_lists  \- 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 \-  Albert Vilella"
.IX Header "AUTHOR - Albert Vilella"
Email foo@bar.com
.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 "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 "new"
.IX Subsection "new"
.Vb 5
\& Title   : new
\& Usage   : my $amap = Bio::Tools::Run::Alignment::Amap\->new();
\& Function: Constructor
\& Returns : Bio::Tools::Run::Alignment::Amap
\& Args    : \-outfile_name => $outname
.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    : Arrayref of Bio::PrimarySeqI objects or
\&           a filename to run on
.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 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 amap program
\& Example :
\& Returns : nothing; amap 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 amap
.Ve
.SS "_setinput"
.IX Subsection "_setinput"
.Vb 6
\& Title   :  _setinput
\& Usage   :  Internal function, not to be called directly        
\& Function:  Create input file for amap program
\& Example :
\& Returns : name of file containing amap data input AND
\& Args    : Arrayref of Seqs or input file name
.Ve
.SS "_setparams"
.IX Subsection "_setparams"
.Vb 7
\& Title   :  _setparams
\& Usage   :  Internal function, not to be called directly        
\& Function:  Create parameter inputs for amap program
\& Example :
\& Returns : parameter string to be passed to amap
\&           during align or profile_align
\& Args    : name of calling object
.Ve
.SS "aformat"
.IX Subsection "aformat"
.Vb 5
\& Title   : aformat
\& Usage   : my $alignmentformat = $self\->aformat();
\& Function: Get/Set alignment format
\& Returns : string
\& Args    : string
.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 = $amap\->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   : $amap\->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