Bio::Tools::Phylo::Molphy Result
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Summary
Bio::Tools::Phylo::Molphy::Result - container for data parsed from a ProtML run
Package variables
No package variables defined.
Inherit
Bio::Root::Root
Synopsis
  # do not use this object directly, you will get it back as part of a 
# Molphy parser
use Bio::Tools::Phylo::Molphy;
my $parser = Bio::Tools::Phylo::Molphy->new(-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 = Bio::TreeIO->new(-format => "newick"); $out->write_tree($trees[0]); # writing only the 1st tree }
Description
A container for data parsed from a ProtML run.
Methods
newDescriptionCode
modelDescriptionCode
substitution_matrixDescriptionCode
transition_probability_matrixDescriptionCode
residue_frequenciesDescriptionCode
next_treeDescriptionCode
rewind_tree_iterator
No description
Code
add_treeDescriptionCode
search_spaceDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Tools::Phylo::Molphy::Result->new();
Function: Builds a new Bio::Tools::Phylo::Molphy::Result object
Returns : Bio::Tools::Phylo::Molphy::Result
Args :
modelcodeprevnextTop
 Title   : model
Usage : $obj->model($newval)
Function:
Returns : value of model
Args : newvalue (optional)
substitution_matrixcodeprevnextTop
 Title   : substitution_matrix
Usage : my $smat = $result->subsitution_matrix;
Function: Get the relative substitution matrix calculated in the ML procedure
Returns : reference to hash of hashes where key is the aa/nt name and value
is another hash ref which contains keys for all the aa/nt
possibilities
Args : none
transition_probability_matrixcodeprevnextTop
 Title   : transition_probability_matrix
Usage : my $matrixref = $molphy->transition_probablity_matrix();
Function: Gets the observed transition probability matrix
Returns : hash of hashes of aa/nt transition to each other aa/nt
Args : Transition matrix type, typically
'1PAM-1.0e05' or '1PAM-1.0e07'
residue_frequenciescodeprevnextTop
 Title   : residue_frequencies
Usage : my %data = $molphy->residue_frequencies()
Function: Get the modeled and expected frequencies for
each of the residues in the sequence
Returns : hash of either aa (protml) or nt (nucml) frequencies
each key will point to an array reference where
1st slot is model's expected frequency
2nd slot is observed frequency in the data
$hash{'A'}->[0] =
Args : none
next_treecodeprevnextTop
 Title   : next_tree
Usage : my $tree = $factory->next_tree;
Function: Get the next tree from the factory
Returns : Bio::Tree::TreeI
Args : none
add_treecodeprevnextTop
 Title   : add_tree
Usage : $result->add_tree($tree);
Function: Adds a tree
Returns : integer which is the number of trees stored
Args : Bio::Tree::TreeI
search_spacecodeprevnextTop
 Title   : search_space
Usage : $obj->search_space($newval)
Function:
Returns : value of search_space
Args : newvalue (optional)
Methods code
newdescriptionprevnextTop
sub new {
  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 provide 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 $self;
}
modeldescriptionprevnextTop
sub model {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'model'} = $value;
    }
    return $self->{'model'};
}
substitution_matrixdescriptionprevnextTop
sub substitution_matrix {
   my ($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 $self->{'_substitution_matrix'};
}
transition_probability_matrixdescriptionprevnextTop
sub transition_probability_matrix {
   my ($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};
}
residue_frequenciesdescriptionprevnextTop
sub residue_frequencies {
   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'}};
}
next_treedescriptionprevnextTop
sub next_tree {
   my ($self,@args) = @_;
   return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef;
}
rewind_tree_iteratordescriptionprevnextTop
sub rewind_tree_iterator {
    shift->{'_treeiterator'} = 0;
}
add_treedescriptionprevnextTop
sub add_tree {
   my ($self,$tree) = @_;
   if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) {
       push @{$self->{'_trees'}},$tree;
   }
   return scalar @{$self->{'_trees'}};
}
search_spacedescriptionprevnextTop
sub search_space {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'search_space'} = $value;
    }
    return $self->{'search_space'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
rewind_treeTop
 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