# do not use this object directly, you will get it back as part of a 
  # Molphy parser
  use Bio::Tools::Phylo::Molphy;
  my $parser = new Bio::Tools::Phylo::Molphy(-file => 'output.protml');
  while( my $r = $parser->next_result ) {
    # r is a Bio::Tools::Phylo::Molphy::Result object

    # print the model name
    print $r->model, "\n";

    # get the substitution matrix
    # this is a hash of 3letter aa codes -> 3letter aa codes representing
    # substitution rate
    my $smat = $r->substitution_matrix;
    print "Arg -> Gln substitution rate is %d\n", 
          $smat->{'Arg'}->{'Gln'}, "\n";

    # get the transition probablity matrix
    # this is a hash of 3letter aa codes -> 3letter aa codes representing
    # transition probabilty
    my $tmat = $r->transition_probability_matrix;
    print "Arg -> Gln transition probablity is %.2f\n", 
          $tmat->{'Arg'}->{'Gln'}, "\n";

    # get the frequency for each of the residues
    my $rfreqs = $r->residue_frequencies;

    foreach my $residue ( keys %{$rfreqs} ) {
       printf "residue %s  expected freq: %.2f observed freq: %.2f\n",
              $residue,$rfreqs->{$residue}->[0], $rfreqs->{$residue}->[1];
    }

    my @trees;
    while( my $t = $r->next_tree ) {
        push @trees, $t;
    }

    print "search space is ", $r->search_space, "\n",
          "1st tree score is ", $trees[0]->score, "\n";

    # writing to STDOUT, use -file => '>filename' to specify a file
    my $out = new Bio::TreeIO(-format => "newick");
    $out->write_tree($trees[0]); # writing only the 1st tree
  }

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

  my $self = $class->SUPER::new(@args);
  my ($trees,$smat,$freq,
      $model, $sspace,
      ) = $self->_rearrange([qw(TREES SUBSTITUTION_MATRIX
				FREQUENCIES
				MODEL SEARCH_SPACE)], @args);

  if( $trees ) {
      if(ref($trees) !~ /ARRAY/i ) { 
	  $self->warn("Must have provided a valid array reference to initialize trees");
      } else {
	  foreach my $t ( @$trees ) {
	      $self->add_tree($t);
	  }
      }
  }
  # initialize things through object methods to be a good 
  # little OO programmer
  if( ref($smat) =~ /HASH/i ) {
      $self->substitution_matrix($smat);
  }
  if( ref($freq) =~ /HASH/i ) {
      $self->residue_frequencies($freq);
  }
  
  $model && $self->model($model); 
  $sspace && $self->search_space($sspace);
  $self->{'_treeiterator'} = 0;

  return $self;

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

   my ($self,$val) = @_;
   if(defined $val ) { 
       if( ref($val) =~ /HASH/ ) {
	   foreach my $v (values %{$val} ) {
	       if( ref($v) !~ /HASH/i ) { 
		   $self->warn("Must be a valid hashref of hashrefs for substition_matrix");
		   return;
	       }
	   }
	   $self->{'_substitution_matrix'} = $val;
       } else { 
	   $self->warn("Must be a valid hashref of hashrefs for substition_matrix");
	   return;
       }
   }
   return $self->{'_substitution_matrix'};

   my ($self,$type,$val) = @_;
   $type = '1PAM-1.0e7' unless defined $type;
   if(defined $val ) { 
       if( ref($val) =~ /HASH/ ) {
	   foreach my $v (values %{$val} ) {
	       if( ref($v) !~ /HASH/i ) { 
		   $self->warn("Must be a valid hashref of hashrefs for transition_probability_matrix");
		   return;
	       }
	   } 
	   $self->{'_TPM'}->{$type} = $val;
       } else { 
	   $self->warn("Must be a valid hashref of hashrefs for transition_probablity_matrix");
	   return;
       }
   }

   # fix this for nucml where there are 2 values (one is just a transformation
   # of the either, but how to represent?)
   return $self->{'_TPM'}->{$type};

   my ($self,$val) = @_;
   if(defined $val ) { 
       if( ref($val) =~ /HASH/ ) {
	   $self->{'_residue_frequencies'} = $val;
       } else { 
	   $self->warn("Must be a valid hashref of hashrefs for residue_frequencies");
       }
   }
   return %{$self->{'_residue_frequencies'}};

   my ($self,@args) = @_;
   return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef;

    shift->{'_treeiterator'} = 0;

   my ($self,$tree) = @_;
   if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) {
       push @{$self->{'_trees'}},$tree;
   }
   return scalar @{$self->{'_trees'}};

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

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  http://bugzilla.open-bio.org/

 Title   : rewind_tree_iterator
 Usage   : $result->rewind_tree()
 Function: Rewinds the tree iterator so that next_tree can be 
           called again from the beginning
 Returns : none
 Args    : none