package Bio::Tools::Run::Alignment::TCoffee;
$Bio::Tools::Run::Alignment::TCoffee::VERSION = '1.7.4';
use utf8;
use strict;
use warnings;

use vars qw($AUTOLOAD @ISA $PROGRAM_NAME $PROGRAM_DIR %DEFAULTS
            @TCOFFEE_PARAMS @TCOFFEE_SWITCHES @OTHER_SWITCHES %OK_FIELD
            );

use Cwd;
use Bio::Seq;
use Bio::SeqIO;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::Root::IO;
use Bio::Factory::ApplicationFactoryI;
use Bio::Tools::Run::WrapperBase;

@ISA = qw(Bio::Tools::Run::WrapperBase
          Bio::Factory::ApplicationFactoryI);

# ABSTRACT: Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program
# AUTHOR: Jason Stajich <jason@bioperl.org>
# AUTHOR: Peter Schattner <schattner@alum.mit.edu>
# OWNER: Jason Stajich <jason@bioperl.org>
# OWNER: Peter Schattner <schattner@alum.mit.edu>
# LICENSE: Perl_5


# You will need to enable TCoffee to find the tcoffee program. This can be done
# in (at least) twp ways:
#  1. define an environmental variable TCOFFEE:
#        export TCOFFEEDIR=/home/progs/tcoffee   or
#  2. include a definition of an environmental variable TCOFFEEDIR
#      in every script that will
#     use Bio::Tools::Run::Alignment::TCoffee.pm.
#        BEGIN {$ENV{TCOFFEEDIR} = '/home/progs/tcoffee'; }

BEGIN {
    $PROGRAM_NAME = 't_coffee';
    $PROGRAM_DIR = $ENV{'TCOFFEEDIR'};
    %DEFAULTS = ( 'MATRIX' => 'blosum',
                  'OUTPUT' => 'clustalw',
                  'AFORMAT'=> 'msf',
                  'METHODS' => [qw(lalign_id_pair clustalw_pair)]
                );


    @TCOFFEE_PARAMS = qw(IN TYPE PARAMETERS DO_NORMALISE EXTEND
                         DP_MODE KTUPLE NDIAGS DIAG_MODE SIM_MATRIX
                         MATRIX GAPOPEN GAPEXT COSMETIC_PENALTY TG_MODE
                         WEIGHT SEQ_TO_ALIGN NEWTREE USETREE TREE_MODE
                         OUTFILE OUTPUT CASE CPU OUT_LIB OUTORDER SEQNOS
                         RUN_NAME CONVERT
                         );

    @TCOFFEE_SWITCHES = qw(QUICKTREE);

    @OTHER_SWITCHES = qw(QUIET ALIGN KEEPDND);

# Authorize attribute fields
    foreach my $attr ( @TCOFFEE_PARAMS, @TCOFFEE_SWITCHES, @OTHER_SWITCHES ) {
        $OK_FIELD{$attr}++; }
}


sub program_name {
    return $PROGRAM_NAME;
}


sub program_dir {
    return $PROGRAM_DIR;
}

sub new {
    my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($attr, $value);

    while (@args) {
        $attr =   shift @args;
        $value =  shift @args;
        next if( $attr =~ /^-/); # don't want named parameters
        $self->$attr($value);
    }
    $self->matrix($DEFAULTS{'MATRIX'}) unless( $self->matrix );
    $self->output($DEFAULTS{'OUTPUT'}) unless( $self->output );
    $self->methods($DEFAULTS{'METHODS'}) unless $self->methods;
    # $self->aformat($DEFAULTS{'AFORMAT'}) unless $self->aformat;

    return $self;
}

sub AUTOLOAD {
    my $self = shift;
    my $attr = $AUTOLOAD;
    $attr =~ s/.*:://;
    $attr = uc $attr;
    # aliasing
    $attr = 'OUTFILE' if $attr eq 'OUTFILE_NAME';
    $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};

    $self->{$attr} = shift if @_;
    return $self->{$attr};
}


sub error_string{
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'error_string'} = $value;
    }
    return $self->{'error_string'};

}


sub version {
    my ($self) = @_;
    my $exe;
    return undef unless $exe = $self->executable;
    my $string = `$exe -quiet=stdout 2>&1` ;
    $string =~ /Version_([\d.]+)/;
    return $1 || undef;

}


sub _major_minor_version {
    my ($self) = @_;
    my $version = $self->version;
    $version =~ s/(\d+\.\d+)[\D].*$/$1/;
    return $version;
}


sub run{
   my ($self,@args) = @_;
   my ($type,$seq,$profile) = $self->_rearrange([qw(TYPE
                                                    SEQ
                                                    PROFILE)],
                                                @args);
   if( $type =~ /align/i ) {
       return $self->align($seq);
   } elsif( $type =~ /profile/i ) {
       return $self->profile_align($profile,$seq);
   } else {
       $self->warn("unrecognized alignment type $type\n");
   }
   return undef;
}


sub align {
    my ($self,$input) = @_;
    # Create input file pointer
    $self->io->_io_cleanup();
    my ($infilename,$type) = $self->_setinput($input);
    if (!$infilename) {
        $self->throw("Bad input data or less than 2 sequences in $input !");
    }

    my $param_string = $self->_setparams();

    # run tcoffee
    return $self->_run('align', [$infilename,$type], $param_string);
}

#################################################


sub profile_align {
    my $self = shift;
    my $input1 = shift;
    my $input2 = shift;

    my ($temp,$infilename1,$infilename2,$type1,$type2,$input,$seq);

    $self->io->_io_cleanup();
    # Create input file pointers
    ($infilename1,$type1) = $self->_setinput($input1);
    ($infilename2,$type2) = $self->_setinput($input2);
    unless ($type1) {
        $self->throw("Unknown type for first argument");
    }
    unless ($type2) {
        $self->throw("Unknown type for second argument")
    }

    if (!$infilename1 || !$infilename2) {
     $self->throw("Bad input data: $input1 or $input2 !");
    }

    my $param_string = $self->_setparams();
    # run tcoffee
    my $aln = $self->_run('profile-aln',
                          [$infilename1,$type1],
                          [$infilename2,$type2],
                          $param_string)
            ;
}
#################################################


sub _run {
    my ($infilename, $infile1,$infile2) = ('','','');
    my $self = shift;
    my $command = shift;
    my $instring;
    if ($command =~ /align/) {
        my $infile = shift ;
        my $type;
        ($infilename,$type) = @$infile;
        $instring =  '-in='.join(',',($infilename, 'X'.$self->matrix,
                          $self->methods));
    }
    if ($command =~ /profile/) {
        my $in1 = shift ;
        my $in2 = shift ;
        my ($type1,$type2);
        ($infile1,$type1) = @$in1;
        ($infile2,$type2) = @$in2;
        # in later versions (tested on 5.72 and 7.54) the API for profile
        # alignment changed. This attempts to do the right thing for older
        # versions but corrects for newer ones
        if ($self->_major_minor_version
            && $self->_major_minor_version < 5) {
            # this breaks severely on newer TCoffee (>= v5)
            unless (($self->matrix =~ /none/i) || ($self->matrix =~ /null/i) ) {
                $instring = '-in='.join(',',
                                ($type2.$infile2),
                                'X'.$self->matrix,
                                (map {'M'.$_} $self->methods)
                                );
                $instring .= ' -profile='.$infile1;
            } else {
                $instring = '-in='.join(',',(
                            $type1.$infile1,
                            $type2.$infile2,
                            (map {'M'.$_} $self->methods)
                                            )
                                        );
            }
        } else {
            if ($type2 eq 'S') {
                # second infile is a sequence, not an alignment
                $instring .= ' -profile='.join(',',$infile1);
                $instring .= ' -seq='.join(',',$infile2);
            } else {
                $instring .= ' -profile='.join(',',$infile1,$infile2);
            }
            $instring .= ' -matrix='.$self->matrix unless (($self->matrix =~ /none/i) || ($self->matrix =~ /null/i)) ;
            $instring .= ' -method='.join(',',$self->methods) if ($self->methods) ;
        }
    }
    my $param_string = shift;
#    my ($paramfh,$parameterFile) = $self->io->tempfile;
#    print $paramfh ( "$instring\n-output=gcg$param_string") ;
#    close($paramfh);
#    my $commandstring = "t_coffee -output=gcg -parameters $parameterFile" ;    ##MJL

    my $commandstring = $self->executable." $instring $param_string";

    #$self->debug( "tcoffee command = $commandstring \n");

    my $status = system($commandstring);
    my $outfile = $self->outfile();

    if( !-e $outfile || -z $outfile ) {
        $self->warn( "TCoffee call crashed: $? [command $commandstring]\n");
        return undef;
    }

    # retrieve alignment (Note: MSF format for AlignIO = GCG format of
    # tcoffee)

    my $in  = Bio::AlignIO->new('-file' => $outfile, '-format' =>
                                $self->output);
    my $aln = $in->next_aln();

    # Replace file suffix with dnd to find name of dendrogram file(s) to delete
    if( ! $self->keepdnd ) {
        foreach my $f ( $infilename, $infile1, $infile2 ) {
            next if( !defined $f || $f eq '');
            $f =~ s/\.[^\.]*$// ;
            # because TCoffee writes these files to the CWD
            if( $Bio::Root::IO::PATHSEP ) {
                my @line = split(/$Bio::Root::IO::PATHSEP/, $f);
                $f = pop @line;
            } else {
                (undef, undef, $f) = File::Spec->splitpath($f);
            }
            unlink $f .'.dnd' if( $f ne '' );
        }
    }
    return $aln;
}



sub _setinput {
    my ($self,$input) = @_;
    my ($infilename, $seq, $temp, $tfh);
    #  If $input is not a reference it better be the name of a
    # file with the sequence/ alignment data...
    my $type = '';
    if (! ref $input) {
        # check that file exists or throw
        $infilename = $input;
        unless (-e $input) {return 0;}
        # let's peek and guess
        open(my $IN,$infilename) || $self->throw("Cannot open $infilename");
        my $header = <$IN>;
        if( $header =~ /^\s+\d+\s+\d+/ ||
            $header =~ /Pileup/i ||
            $header =~ /clustal/i ) { # phylip
            $type = 'A';
        }

        # On some systems, having filenames with / in them (ie. a file in a
        # directory) causes t-coffee to completely fail. It warns on all systems.
        # The -no_warning option solves this, but there is still some strange
        # bug when doing certain profile-related things. This is magically solved
        # by copying the profile file to a temp file in the current directory, so
        # it its filename supplied to t-coffee contains no /
        # (It's messy here - I just do this to /all/ input files to most easily
        #  catch all variants of providing a profile - it may only be the last
        #  form (isa("Bio::PrimarySeqI")) that causes a problem?)

        my (undef, undef, $adjustedfilename) = File::Spec->splitpath($infilename);
        if ($adjustedfilename ne $infilename) {
            my ($fh, $tempfile) = $self->io->tempfile(-dir => cwd());
            seek($IN, 0, 0);
            while (<$IN>) {
                print $fh $_;
            }
            close($fh);
            (undef, undef, $tempfile) = File::Spec->splitpath($tempfile);
            $infilename = $tempfile;
            $type = 'S';
        }

        close($IN);
        return ($infilename,$type);
    } elsif (ref($input) =~ /ARRAY/i ) {
        #  $input may be an array of BioSeq objects...
        #  Open temporary file for both reading & writing of array
        ($tfh,$infilename) = $self->io->tempfile(-dir => cwd());
        (undef, undef, $infilename) = File::Spec->splitpath($infilename);
        if( ! ref($input->[0]) ) {
            $self->warn("passed an array ref which did not contain objects to _setinput");
            return undef;
        } elsif( $input->[0]->isa('Bio::PrimarySeqI') ) {
            $temp =  Bio::SeqIO->new('-fh' => $tfh,
                         '-format' => 'fasta');
            my $ct = 1;
            foreach $seq (@$input) {
                return 0 unless ( ref($seq) &&
                          $seq->isa("Bio::PrimarySeqI") );
                if( ! defined $seq->display_id ||
                    $seq->display_id =~ /^\s+$/) {
                    $seq->display_id( "Seq".$ct++);
                }
                $temp->write_seq($seq);
            }
            $temp->close();
            undef $temp;
            close($tfh);
            $tfh = undef;
            $type = 'S';
        } elsif( $input->[0]->isa('Bio::Align::AlignI' ) ) {
            $temp =  Bio::AlignIO->new('-fh' => $tfh,
                           '-format' => $self->aformat);
            foreach my $aln (@$input) {
                next unless ( ref($aln) &&
                          $aln->isa("Bio::Align::AlignI") );
                $temp->write_aln($aln);
            }
            $temp->close();
            undef $temp;
            close($tfh);
            $tfh = undef;
            $type = 'A';
        }  else {
            $self->warn( "got an array ref with 1st entry ".
                 $input->[0].
                 " and don't know what to do with it\n");
        }
        return ($infilename,$type);
        #  $input may be a SimpleAlign object.
    } elsif ( $input->isa("Bio::Align::AlignI") ) {
        #  Open temporary file for both reading & writing of SimpleAlign object
        ($tfh, $infilename) = $self->io->tempfile(-dir => cwd());
        (undef, undef, $infilename) = File::Spec->splitpath($infilename);
        $temp =  Bio::AlignIO->new(-fh=>$tfh,
                       '-format' => 'clustalw');
        $temp->write_aln($input);
        close($tfh);
        undef $tfh;
        return ($infilename,'A');
    }

    #  or $input may be a single BioSeq object (to be added to
    # a previous alignment)
    elsif ( $input->isa("Bio::PrimarySeqI")) {
        #  Open temporary file for both reading & writing of BioSeq object
        ($tfh,$infilename) = $self->io->tempfile(-dir => cwd());
        (undef, undef, $infilename) = File::Spec->splitpath($infilename);
        $temp =  Bio::SeqIO->new(-fh=> $tfh, '-format' =>'Fasta');
        $temp->write_seq($input);
        $temp->close();
        close($tfh);
        undef $tfh;
        return ($infilename,'S');
    } else {
        $self->warn("Got $input and don't know what to do with it\n");
    }
    return 0;
}



sub _setparams {
    my ($self) = @_;
    my ($attr, $value,$param_string);
    $param_string = '';
    my $laststr;
    for  $attr ( @TCOFFEE_PARAMS ) {
        $value = $self->$attr();
        next unless (defined $value);
        my $attr_key = lc $attr;
        if( $attr_key =~ /matrix/ ) {
            $self->{'_in'} = [ "X".lc($value) ];
        } else {
            $attr_key = ' -'.$attr_key;
            $param_string .= $attr_key .'='.$value;
        }
   }
    for  $attr ( @TCOFFEE_SWITCHES) {
        $value = $self->$attr();
        next unless ($value);
        my $attr_key = lc $attr; #put switches in format expected by tcoffee
        $attr_key = ' -'.$attr_key;
        $param_string .= $attr_key ;
    }

    # Set default output file if no explicit output file selected
    unless ($self->outfile ) {
        my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir());
        close($tfh);
        undef $tfh;
        $self->outfile($outfile);
        $param_string .= " -outfile=$outfile" ;
    }

    if ($self->quiet() || $self->verbose < 0) { $param_string .= ' -quiet';}

    # -no_warning is required on some systems with certain versions or failure
    # is guaranteed
    if ($self->_major_minor_version >= 4
        && $self->_major_minor_version < 4.7) {
        $param_string .= ' -no_warning';
    }

    return $param_string;
}


sub aformat{
    my $self = shift;
    $self->{'_aformat'} = shift if @_;
    return $self->{'_aformat'};
}



sub methods{
   my ($self) = shift;

   @{$self->{'_methods'}} = @{shift || []} if @_;
   return @{$self->{'_methods'} || []};
}










1;

__END__

=pod

=encoding UTF-8

=head1 NAME

Bio::Tools::Run::Alignment::TCoffee - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program

=head1 VERSION

version 1.7.4

=head1 SYNOPSIS

  # Build a tcoffee alignment factory
  @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
  $factory = Bio::Tools::Run::Alignment::TCoffee->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);

  # Or one can pass the factory a pair of (sub)alignments
  #to be aligned against each other, e.g.:

  # where $aln1 and $aln2 are Bio::SimpleAlign objects.
  $aln = $factory->profile_align($aln1,$aln2);

  # Or one can pass the factory an alignment and one or more
  # unaligned sequences to be added to the alignment. For example:

  # $seq is a Bio::Seq object.
  $aln = $factory->profile_align($aln1,$seq);

  #There are various additional options and input formats available.
  #See the DESCRIPTION section that follows for additional details.

=head1 DESCRIPTION

Note: this DESCRIPTION only documents the (Bio)perl interface to
TCoffee.

=head2 Helping the module find your executable

You will need to enable TCoffee to find the t_coffee program. This
can be done in (at least) three ways:

 1. Make sure the t_coffee executable is in your path so that
    which t_coffee returns a t_coffee executable on your system.

 2. Define an environmental variable TCOFFEEDIR which is a dir
    which contains the 't_coffee' app:
    In bash
    export TCOFFEEDIR=/home/username/progs/T-COFFEE_distribution_Version_1.37/bin
    In csh/tcsh
    setenv TCOFFEEDIR /home/username/progs/T-COFFEE_distribution_Version_1.37/bin

 3. Include a definition of an environmental variable TCOFFEEDIR in
    every script that will use this TCoffee wrapper module.
    BEGIN { $ENV{TCOFFEDIR} = '/home/username/progs/T-COFFEE_distribution_Version_1.37/bin' }
    use Bio::Tools::Run::Alignment::TCoffee;

If you are running an application on a webserver make sure the
webserver environment has the proper PATH set or use the options 2 or
3 to set the variables.

=head1 INTERNAL METHODS

=head2 _numeric_version

Version "numbers" are not numeric values.  In the case of T-Coffee,
they have an hash component at their end.  This was not the case in
older releases.  We use the first two numeric parts to do different
things though.  See also issue #1.

=head2 _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

=head2 _setinput

 Title   :  _setinput
 Usage   :  Internal function, not to be called directly
 Function:  Create input file for tcoffee program
 Example :
 Returns : name of file containing tcoffee data input AND
           type of file (if known, S for sequence, L for sequence library,
           A for sequence alignment)
 Args    : Seq or Align object reference or input file name

=head2 _setparams

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

=head1 PARAMETERS FOR ALIGNMENT COMPUTATION

There are a number of possible parameters one can pass in TCoffee.
One should really read the online manual for the best explanation of
all the features.  See
http://igs-server.cnrs-mrs.fr/~cnotred/Documentation/t_coffee/t_coffee_doc.html

These can be specified as parameters when instantiating a new TCoffee
object, or through get/set methods of the same name (lowercase).

=head2 IN

 Title       : IN
 Description : (optional) input filename, this is specified when
               align so should not use this directly unless one
               understand TCoffee program very well.

=head2 TYPE

 Title       : TYPE
 Args        : [string] DNA, PROTEIN
 Description : (optional) set the sequence type, guessed automatically
               so should not use this directly

=head2 PARAMETERS

 Title       : PARAMETERS
 Description : (optional) Indicates a file containing extra parameters

=head2 EXTEND

 Title       : EXTEND
 Args        : 0, 1, or positive value
 Default     : 1
 Description : Flag indicating that library extension should be
               carried out when performing multiple alignments, if set
               to 0 then extension is not made, if set to 1 extension
               is made on all pairs in the library.  If extension is
               set to another positive value, the extension is only
               carried out on pairs having a weigth value superior to
               the specified limit.

=head2 DP_NORMALISE

 Title       : DP_NORMALISE
 Args        : 0 or positive value
 Default     : 1000
 Description : When using a value different from 0, this flag sets the
               score of the highest scoring pair to 1000.

=head2 DP_MODE

 Title       : DP_MODE
 Args        : [string] gotoh_pair_wise, myers_miller_pair_wise,
               fasta_pair_wise cfasta_pair_wise
 Default     : cfast_fair_wise
 Description : Indicates the type of dynamic programming used by
               the program

    gotoh_pair_wise : implementation of the gotoh algorithm
    (quadratic in memory and time)

    myers_miller_pair_wise : implementation of the Myers and Miller
    dynamic programming algorithm ( quadratic in time and linear in
    space). This algorithm is recommended for very long sequences. It
    is about 2 time slower than gotoh. It only accepts tg_mode=1.

    fasta_pair_wise: implementation of the fasta algorithm. The
    sequence is hashed, looking for ktuples words. Dynamic programming
    is only carried out on the ndiag best scoring diagonals. This is
    much faster but less accurate than the two previous.

    cfasta_pair_wise : c stands for checked. It is the same
    algorithm. The dynamic programming is made on the ndiag best
    diagonals, and then on the 2*ndiags, and so on until the scores
    converge. Complexity will depend on the level of divergence of the
    sequences, but will usually be L*log(L), with an accuracy
    comparable to the two first mode ( this was checked on BaliBase).

=head2 KTUPLE

 Title       : KTUPLE
 Args        : numeric value
 Default     : 1 or 2 (1 for protein, 2 for DNA )

 Description : Indicates the ktuple size for cfasta_pair_wise dp_mode
               and fasta_pair_wise. It is set to 1 for proteins, and 2
               for DNA. The alphabet used for protein is not the 20
               letter code, but a mildly degenerated version, where
               some residues are grouped under one letter, based on
               physicochemical properties:
               rk, de, qh, vilm, fy (the other residues are
               not degenerated).

=head2 NDIAGS

 Title       : NDIAGS
 Args        : numeric value
 Default     : 0
 Description : Indicates the number of diagonals used by the
               fasta_pair_wise algorithm. When set to 0,
               n_diag=Log (length of the smallest sequence)

=head2 DIAG_MODE

 Title       : DIAG_MODE
 Args        : numeric value
 Default     : 0


 Description : Indicates the manner in which diagonals are scored
              during the fasta hashing.

              0 indicates that the score of a diagonal is equal to the
              sum of the scores of the exact matches it contains.


              1 indicates that this score is set equal to the score of
              the best uninterrupted segment

              1 can be useful when dealing with fragments of sequences.

=head2 SIM_MATRIX

 Title       : SIM_MATRIX
 Args        : string
 Default     : vasiliky
 Description : Indicates the manner in which the amino acid is being
               degenerated when hashing. All the substitution matrix
               are acceptable. Categories will be defined as sub-group
               of residues all having a positive substitution score
               (they can overlap).

               If you wish to keep the non degenerated amino acid
               alphabet, use 'idmat'

=head2 MATRIX

 Title       : MATRIX
 Args        :
 Default     :
 Description : This flag is provided for compatibility with
               ClustalW. Setting matrix = 'blosum' is equivalent to
               -in=Xblosum62mt , -matrix=pam is equivalent to
               in=Xpam250mt . Apart from this, the rules are similar
               to those applying when declaring a matrix with the
               -in=X fl

=head2 GAPOPEN

 Title       : GAPOPEN
 Args        : numeric
 Default     : 0
 Description : Indicates the penalty applied for opening a gap. The
               penalty must be negative. If you provide a positive
               value, it will automatically be turned into a negative
               number. We recommend a value of 10 with pam matrices,
               and a value of 0 when a library is used.

=head2 GAPEXT

 Title       : GAPEXT
 Args        : numeric
 Default     : 0
 Description : Indicates the penalty applied for extending a gap.

=head2 COSMETIC_PENALTY

 Title       : COSMETIC_PENALTY
 Args        : numeric
 Default     : 100
 Description : Indicates the penalty applied for opening a gap. This
               penalty is set to a very low value. It will only have
               an influence on the portions of the alignment that are
               unalignable. It will not make them more correct, but
               only more pleasing to the eye ( i.e. Avoid stretches of
               lonely residues).

               The cosmetic penalty is automatically turned off if a
               substitution matrix is used rather than a library.

=head2 TG_MODE

 Title       : TG_MODE
 Args        : 0,1,2
 Default     : 1
 Description : (Terminal Gaps)
               0: indicates that terminal gaps must be panelized with
                  a gapopen and a gapext penalty.
               1: indicates that terminal gaps must be penalized only
                  with a gapext penalty
               2: indicates that terminal gaps must not be penalized.

=head2 WEIGHT

 Title       : WEIGHT
 Args        : sim or sim_<matrix_name or matrix_file> or integer value
 Default     : sim


 Description : Weight defines the way alignments are weighted when
               turned into a library.

               sim indicates that the weight equals the average
                   identity within the match residues.

               sim_matrix_name indicates the average identity with two
                   residues regarded as identical when their
                   substitution value is positive. The valid matrices
                   names are in matrices.h (pam250mt) . Matrices not
                   found in this header are considered to be
                   filenames. See the format section for matrices. For
                   instance, -weight=sim_pam250mt indicates that the
                   grouping used for similarity will be the set of
                   classes with positive substitutions. Other groups
                   include

                       sim_clustalw_col ( categories of clustalw
                       marked with :)

                       sim_clustalw_dot ( categories of clustalw
                       marked with .)


               Value indicates that all the pairs found in the
               alignments must be given the same weight equal to
               value. This is useful when the alignment one wishes to
               turn into a library must be given a pre-specified score
               (for instance if they come from a structure
               super-imposition program). Value is an integer:

                       -weight=1000

  Note       : Weight only affects methods that return an alignment to
               T-Coffee, such as ClustalW. On the contrary, the
               version of Lalign we use here returns a library where
               weights have already been applied and are therefore
               insensitive to the -weight flag.

=head2 SEQ_TO_ALIGN

 Title       : SEQ_TO_ALIGN
 Args        : filename
 Default     : no file - align all the sequences

 Description : You may not wish to align all the sequences brought in
               by the -in flag. Supplying the seq_to_align flag allows
               for this, the file is simply a list of names in Fasta
               format.

               However, note that library extension will be carried out
               on all the sequences.

=head1 PARAMETERS FOR TREE COMPUTATION AND OUTPUT

=head2 NEWTREE

 Title       : NEWTREE
 Args        : treefile
 Default     : no file
 Description : Indicates the name of the new tree to compute. The
               default will be <sequence_name>.dnd, or <run_name.dnd>.
               Format is Phylip/Newick tree format

=head2 USETREE

 Title       : USETREE
 Args        : treefile
 Default     : no file specified
 Description : This flag indicates that rather than computing a new
               dendrogram, t_coffee can use a pre-computed one. The
               tree files are in phylips format and compatible with
               ClustalW. In most cases, using a pre-computed tree will
               halve the computation time required by t_coffee. It is
               also possible to use trees output by ClustalW or
               Phylips. Format is Phylips tree format

=head2 TREE_MODE

 Title       : TREE_MODE
 Args        : slow, fast, very_fast
 Default     : very_fast
 Description : This flag indicates the method used for computing the
               dendrogram.
               slow : the chosen dp_mode using the extended library,
               fast : The fasta dp_mode using the extended library.
               very_fast: The fasta dp_mode using pam250mt.

=head2 QUICKTREE

 Title       : QUICKTREE
 Args        :
 Default     :
 Description : This flag is kept for compatibility with ClustalW.
               It indicates that:  -tree_mode=very_fast

=head1 PARAMETERS FOR ALIGNMENT OUTPUT

=head2 OUTFILE

 Title       : OUTFILE
 Args        : out_aln file, default, no
 Default     : default ( yourseqfile.aln)
 Description : indicates name of output alignment file

=head2 OUTPUT

 Title       : OUTPUT
 Args        : format1, format2
 Default     : clustalw
 Description : Indicated format for outputting outputfile
               Supported formats are:

               clustalw_aln, clustalw: ClustalW format.
               gcg, msf_aln : Msf alignment.
               pir_aln : pir alignment.
               fasta_aln : fasta alignment.
               phylip : Phylip format.
               pir_seq : pir sequences (no gap).
               fasta_seq : fasta sequences (no gap).
    As well as:
                score_html : causes the output to be a reliability
                             plot in HTML
                score_pdf : idem in PDF.
                score_ps : idem in postscript.

    More than one format can be indicated:
                -output=clustalw,gcg, score_html

=head2 CASE

 Title       : CASE
 Args        : upper, lower
 Default     : upper
 Description : triggers choice of the case for output

=head2 CPU

 Title       : CPU
 Args        : value
 Default     : 0
 Description : Indicates the cpu time (micro seconds) that must be
               added to the t_coffee computation time.

=head2 OUT_LIB

 Title       : OUT_LIB
 Args        : name of library, default, no
 Default     : default
 Description : Sets the name of the library output. Default implies
               <run_name>.tc_lib

=head2 OUTORDER

 Title       : OUTORDER
 Args        : input or aligned
 Default     : input
 Description : Sets the name of the library output. Default implies
               <run_name>.tc_lib

=head2 SEQNOS

 Title       : SEQNOS
 Args        : on or off
 Default     : off
 Description : Causes the output alignment to contain residue numbers
               at the end of each line:

=head1 PARAMETERS FOR GENERIC OUTPUT

=head2 RUN_NAME

 Title       : RUN_NAME
 Args        : your run name
 Default     :
 Description : This flag causes the prefix <your sequences> to be
               replaced by <your run name> when renaming the default
               files.

=head2 ALIGN

 Title       : ALIGN
 Args        :
 Default     :
 Description : Indicates that the program must produce the
               alignment. This flag is here for compatibility with
               ClustalW

=head2 QUIET

 Title       : QUIET
 Args        : stderr, stdout, or filename, or nothing
 Default     : stderr
 Description : Redirects the standard output to either a file.
              -quiet on its own redirect the output to /dev/null.

=head2 CONVERT

 Title       : CONVERT
 Args        :
 Default     :
 Description : Indicates that the program must not compute the
               alignment but simply convert all the sequences,
               alignments and libraries into the format indicated with
               -output. This flag can also be used if you simply want
               to compute a library ( i.e. You have an alignment and
               you want to turn it into a library).

=head2 program_name

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

=head2 program_dir

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

=head2 error_string

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

=head2 version

 Title   : version
 Usage   : $prog->version()
 Function: Determine the version number of the program
 Example :
 Returns : string
 Args    : none

=head2 run

 Title   : run
 Usage   : my $output = $application->run(-seq     => $seq,
                                          -profile => $profile,
                                          -type    => 'profile-aln');
 Function: Generic run of an application
 Returns : Bio::SimpleAlign object
 Args    : key-value parameters allowed for TCoffee runs AND
           -type     => profile-aln or alignment for profile alignments or
                        just multiple sequence alignment
           -seq      => either Bio::PrimarySeqI object OR
                        array ref of Bio::PrimarySeqI objects OR
                        filename of sequences to run with
           -profile  => profile to align to, if this is an array ref
                        will specify the first two entries as the two
                        profiles to align to each other

=head2 align

 Title   : align
 Usage   :
        $inputfilename = 't/data/cysprot.fa';
        $aln = $factory->align($inputfilename);
or
        $seq_array_ref = \@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.

=head2 profile_align

 Title   : profile_align
 Usage   :
 Function: Perform an alignment of 2 (sub)alignments
 Example :
 Returns : Reference to a SimpleAlign object containing the (super)alignment.
 Args    : Names of 2 files containing the subalignments
           or references to 2 Bio::SimpleAlign objects.
 Note    : Needs to be updated to run with newer TCoffee code, which
           allows more than two profile alignments.

Throws an exception if arguments are not either strings (eg filenames)
or references to SimpleAlign objects.

=head2 aformat

 Title   : aformat
 Usage   : my $alignmentformat = $self->aformat();
 Function: Get/Set alignment format
 Returns : string
 Args    : string

=head2 methods

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

=head1 Bio::Tools::Run::BaseWrapper methods

=head2 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)

=head2 save_tempfiles

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

=head2 outfile_name

 Title   : outfile_name
 Usage   : my $outfile = $tcoffee->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

=head2 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

=head2 cleanup

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

=head2 io

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

=head1 FEEDBACK

=head2 Mailing lists

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.

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

=head2 Support

Please direct usage questions or support issues to the mailing list:
I<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.

=head2 Reporting bugs

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

  https://github.com/bioperl/bio-tools-run-alignment-tcoffee/issues

=head1 AUTHORS

Jason Stajich <jason@bioperl.org>

Peter Schattner <schattner@alum.mit.edu>

=head1 COPYRIGHT

This software is copyright (c) by Jason Stajich <jason@bioperl.org>, and by Peter Schattner <schattner@alum.mit.edu>.

This software is available under the same terms as the perl 5 programming language system itself.

=cut
