use Bio::Tools::Run::Phylo::PAML::Evolver;

  my $evolver = Bio::Tools::Run::Phylo::PAML::Evolver->new();

  # Get a $tree object somehow
  $evolver->tree($tree);

  # FIXME: evolver generates a tree (first run with option 1 or 2)?

  # One or more alns are created
  my @alns = $evolver->run();

  ####

  # Or with all the data coming from a previous PAML run
  my $parser = Bio::Tools::Phylo::PAML->new
    (
     -file => "$inputfile",
    );
  my $result = $parser->next_result();
  my $tree = $result->next_tree;
  $evolver->tree($tree);
  my @codon_freqs = $result->get_CodonFreqs();
  $evolver->set_CodonFreqs(\@codon_freqs);

  my $val = $evolver->prepare();

  # FIXME: something similar for nucleotide frequencies:
  # Option (5) Simulate nucleotide data sets (use MCbase.dat)?

  # FIXME: something similar for aa parameters:
  # Option (7) Simulate amino acid data sets (use MCaa.dat)?

  # FIXME: With an initial RootSeq.txt

 
    $MINNAMELEN = 25;
    $PROGRAMNAME = 'evolver' . ($^O =~ /mswin/i ?'.exe':'');
    if( defined $ENV{'PAMLDIR'} ) {
	$PROGRAM = Bio::Root::IO->catfile($ENV{'PAMLDIR'},$PROGRAMNAME). ($^O =~ /mswin/i ?'.exe':'');;
    }
   
    # valid values for parameters, the default one is always
    # the first one in the array
    # much of the documentation here is lifted directly from the MCcodon.dat
    # example file provided with the package

    # Evolver calls time for seed: SetSeed(i==-1?(int)time(NULL):i);
    my $rand = int(time);
    #     my $rand = int(rand(999999));
    %VALIDVALUES = 
        ( 

         # FIXME: there should be a 6-7-8 option that fits MCcodon or MCbase or MCaa
         'outfmt'    => [0,1], 
         #     0           * 0:paml format (mc.paml); 1:paup format (mc.paup)
         # random number seed (odd number)
         # FIXME: set seed to null here and ask for it later?
         'seed' => "$rand",
         # numseq can actually be calculated from the tree external nodes
         # nucleotide sites
         'nuclsites' => '1000',
         # replicates
         'replicates' => '1',
         # tree length; use -1 if tree has absolute branch lengths
         # Note that tree length and branch lengths under the codon model are
         # measured by the expected number of nucleotide substitutions per codon
         # (see Goldman & Yang 1994).  For amino acid models, they are defined as
         # the expected number of amino acid changes per amino acid site.
         'tree_length' => '1.5',
         # omega
         # FIXME: if one wants to call for different omegas (NSsites),
         # right now it has to be done like:
         # $evolver->set_parameter(omega,"3\n0.2\t0.3\t0.5\n0.5\t0.9\t3.2\n");
         # 3            * number of site classes, followed by frequencies and omega's.
         #   0.6    0.3   0.1 # Freqs
         #   0.1    0.8   3.2 # Omegas
         'omega' => '0.3',
         # kappa
         'kappa' => '5',
         # FIXME: this only for MCbase.dat ?
         # model: 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85, 5:T92, 6:TN93, 7:REV
         # FIXME: this applies to only some models?
         # 10 5 1 2 3 * kappa or rate parameters in model
         # FIXME: this applies to only MCbase.dat ?
         # 0.5  4     * <alpha>  <#categories for discrete gamma>
        ); # end of validvalues

        return 'evolver';

        return Bio::Root::IO->catfile($ENV{PAMLDIR}) if $ENV{PAMLDIR};

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
#   $self->{'_branchLengths'} = 0;
  my ($tree, $st, $params, $exe)
      = $self->_rearrange([qw(TREE SAVE_TEMPFILES PARAMS EXECUTABLE)],
				    @args);
  defined $tree && $self->tree($tree);
  defined $st  && $self->save_tempfiles($st);
  defined $exe && $self->executable($exe);

  $self->set_default_parameters();
  if( defined $params ) {
      if( ref($params) !~ /HASH/i ) { 
	  $self->warn("Must provide a valid hash ref for parameter -FLAGS");
      } else {
	  map { $self->set_parameter($_, $$params{$_}) } keys %$params;
      }
  }
  return $self;

   my ($self,$aln,$tree) = @_;
   # FIXME: To consider: to have save_tempfiles always TRUE by default
   # or simply never delete
   unless ( $self->save_tempfiles ) {
       # brush so we don't get plaque buildup ;)
       $self->cleanup();
   }
   $tree = $self->tree unless $tree;
   my ($tempdir) = $self->tempdir();

   # FIXME:
   # If multiple replicates, evolver gives:
   # A file with a concatenation of sequential phylips separated by a
   # double return which gets correctly parsed by AlignIO next_aln

   # Or a concatenation of paup entries with tags separating them which
   # wont get correctly parsed with current AlignIO (failed with
   # nexus)

   # FIXME: To consider: force phylip outfmt and split the files if
   # replicates > 1

   #    if( ! ref($aln) && -e $aln ) { 
   #        $tempseqfile = $aln;
   #    } else { 
   #        ($tempseqFH,$tempseqfile) = $self->io->tempfile
   # 	   ('-dir' => $tempdir, 
   # 	    UNLINK => ($self->save_tempfiles ? 0 : 1));
   #        my $alnout = Bio::AlignIO->new('-format'      => 'phylip',
   # 				     '-fh'          => $tempseqFH,
   #                                      '-interleaved' => 0,
   #                                      '-idlength'    => $MINNAMELEN > $aln->maxdisplayname_length() ? $MINNAMELEN : $aln->maxdisplayname_length() +1);
   #        $alnout->write_aln($aln);
   #        $alnout->close();
   #        undef $alnout;   
   #        close($tempseqFH);
   #    }
   # now let's print the MCcodon.dat file.
   # many of the these programs are finicky about what the filename is 
   # and won't even run without the properly named file.  Ack
   
   # FIXME: we should do the appropriate here if we are simulating codons, nts o aa.
   my $evolver_ctl = "$tempdir/MCcodon.dat";
   my $evolverfh;
   open($evolverfh, ">$evolver_ctl") or $self->throw("cannot open $evolver_ctl for writing");
   # FIXME: params follow an order in the control file, they are not a hash. Do we have an
   # clean example of this in bioperl-run?
   my %params = $self->get_parameters;
   print $evolverfh "$params{outfmt}\n";
   print $evolverfh "$params{seed}\n";
   # FIXME: call get_leaf_nodes to count only leafs - relates to newick onlyleafids bug
   # my $numseq = scalar($tree->get_nodes);
   my $numseq = scalar($tree->get_leaf_nodes);
   print $evolverfh "$numseq ";
   print $evolverfh "$params{nuclsites} ";
   print $evolverfh "$params{replicates}\n\n";
   print $evolverfh "$params{tree_length}\n";
   # FIXME: do #1:#n branch tagging magic here
   # FIXME: this pre flush stuff is for appending mode
   my $treeout = Bio::TreeIO->new
       ('-format' => 'newick',
        '-fh'     => $evolverfh,
        -PRE =>'>>',
        '-flush',
       );
#    $treeout->bootstrap_style('nointernalids');
   $treeout->write_tree($tree);
   # Appending mode to add more control file contents here
   open($evolverfh, ">>$evolver_ctl") or $self->throw("cannot open $evolver_ctl for writing");
   print $evolverfh "\n$params{omega}\n";
   print $evolverfh "$params{kappa}\n";
   # Print codon freqs here or defaults (below)
   my @codon_freqs = $self->get_CodonFreqs();
   foreach my $firstbase (@codon_freqs) {
       foreach my $element (@$firstbase) {
           print $evolverfh "  $element";
       }
       print $evolverfh "\n";
   }

   # FIXME: codon freqs or nt freqs should always come from an object?
   # Silly printing the default codonfreqs in the default
   # MCcodon.dat provided by PAML
   unless (@codon_freqs) {
       print $evolverfh 
       "0.00983798  0.01745548  0.00222048  0.01443315\n",
       "0.00844604  0.01498576  0.00190632  0.01239105\n",
       "0.01064012  0.01887870  0           0\n",
       "0.00469486  0.00833007  0           0.00688776\n",
       "0.01592816  0.02826125  0.00359507  0.02336796\n",
       "0.01367453  0.02426265  0.00308642  0.02006170\n",
       "0.01722686  0.03056552  0.00388819  0.02527326\n",
       "0.00760121  0.01348678  0.00171563  0.01115161\n",
       "0.01574077  0.02792876  0.00355278  0.02309304\n",
       "0.01351366  0.02397721  0.00305010  0.01982568\n",
       "0.01702419  0.03020593  0.00384245  0.02497593\n",
       "0.00751178  0.01332811  0.00169545  0.01102042\n",
       "0.02525082  0.04480239  0.00569924  0.03704508\n",
       "0.02167816  0.03846344  0.00489288  0.03180369\n",
       "0.02730964  0.04845534  0.00616393  0.04006555\n",
       "0.01205015  0.02138052  0.00271978  0.01767859\n";
   }
   print $evolverfh "\n// end of file.\n";
   close($evolverfh);
   # FIXME: what do we return in prepare?
   # return

    my $self = shift;
    # FIXME: We should look for the stuff we prepared in the prepare method here
    my $rc = (1);
    {
        my $exit_status;
        my ($tmpdir) = $self->tempdir();
        chdir($tmpdir);
        my $evolverexe = $self->executable();
        $self->throw("unable to find or run executable for 'evolver'") unless $evolverexe && -e $evolverexe && -x _;
        open(RUN, "$evolverexe 6 MCcodon.dat |") or $self->throw("Cannot open exe $evolverexe");
        my @output = <RUN>;
        $exit_status = close(RUN);
        $self->error_string(join('',@output));
        if ( (grep { /\berr(or)?: /io } @output)  || !$exit_status) {
            $self->warn("There was an error - see error_string for the program output");
            $rc = 0;
        }
        # FIXME - hardcoded mc.paml
        unless ($self->indel) {
            my $in  = Bio::AlignIO->new('-file'   => "$tmpdir/mc.paml", 
                                        '-format' => 'phylip');
            my $aln = $in->next_aln();
            $self->alignment($aln);
        }
    }
    return $rc;

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

   my ($self,$aln) = @_;

   if( defined $aln ) { 
       if( -e $aln ) { 
	   $self->{'_alignment'} = $aln;
       } elsif( !ref($aln) || ! $aln->isa('Bio::Align::AlignI') ) { 
	   $self->warn("Must specify a valid Bio::Align::AlignI object to the alignment function not $aln");
	   return undef;
       } else {
	   $self->{'_alignment'} = $aln;
       }
   }
   return  $self->{'_alignment'};

   my ($self, $tree, %params) = @_;
   if( defined $tree ) { 
       if( ! ref($tree) || ! $tree->isa('Bio::Tree::TreeI') ) { 
	   $self->warn("Must specify a valid Bio::Tree::TreeI object to the alignment function");
       }
       $self->{'_tree'} = $tree;
       # FIXME: I think we dont need this in Evolver
#        if ( defined $params{'_branchLengths'} ) {
# 	 my $ubl = $params{'_branchLengths'};
# 	 if ($ubl !~ m/^(0|1|2)$/) {
# 	   $self->throw("The branchLengths parameter to tree() must be 0 (ignore), 1 (initial values) or 2 (fixed values) only");
# 	 }
# 	 $self->{'_branchLengths'} = $ubl;
#        }
   }
   return $self->{'_tree'};

   my ($self) = @_;
   # we're returning a copy of this
   return %{ $self->{'_evolverparams'} };

   my ($self,$param,$value) = @_;
   unless ($self->{'no_param_checks'} == 1) {
       if ( ! defined $VALIDVALUES{$param} ) { 
           $self->warn("unknown parameter $param will not be set unless you force by setting no_param_checks to true");
           return 0;
       } 
       if ( ref( $VALIDVALUES{$param}) =~ /ARRAY/i &&
            scalar @{$VALIDVALUES{$param}} > 0 ) {
       
           unless ( grep { $value eq $_ } @{ $VALIDVALUES{$param} } ) {
               $self->warn("parameter $param specified value $value is not recognized, please see the documentation and the code for this module or set the no_param_checks to a true value");
               return 0;
           }
       }
   }
   $self->{'_evolverparams'}->{$param} = $value;
   return 1;

   my ($self,$keepold) = @_;
   $keepold = 0 unless defined $keepold;
   
   while( my ($param,$val) = each %VALIDVALUES ) {
       # skip if we want to keep old values and it is already set
       next if( defined $self->{'_evolverparams'}->{$param} && $keepold);
       if(ref($val)=~/ARRAY/i ) {
	   $self->{'_evolverparams'}->{$param} = $val->[0];
       }  else { 
	   $self->{'_evolverparams'}->{$param} = $val;
       }
   }

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

    my $self = shift;

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

   my ($self) = @_;
   return @{$self->{'_codonfreqs'} || []};

    my $self= shift;
    unless ( $self->save_tempfiles ) {
	$self->cleanup();
    }
    $self->SUPER::DESTROY();

    my $self = shift;

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


1;

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

  http://bioperl.org/bioperl-bugs/

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

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

 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

 Title   : cleanup
 Usage   : $evolver->cleanup();
 Function: Will cleanup the tempdir directory after a PAML run
 Returns : none
 Args    : none

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