Bio::Tools::Phylo::Molphy
Result
Toolbar
Summary
Bio::Tools::Phylo::Molphy::Result - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
Give standard usage here
Description
Describe the object here
Methods
Methods description
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 |
Title : model
Usage : $obj->model($newval)
Function:
Returns : value of model
Args : newvalue (optional) |
Title : new
Usage : my $obj = new Bio::Tools::Phylo::Molphy::Result();
Function: Builds a new Bio::Tools::Phylo::Molphy::Result object
Returns : Bio::Tools::Phylo::Molphy::Result
Args : |
Title : next_tree
Usage : my $tree = $factory->next_tree;
Function: Get the next tree from the factory
Returns : Bio::Tree::TreeI
Args : none |
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 |
Title : search_space
Usage : $obj->search_space($newval)
Function:
Returns : value of search_space
Args : newvalue (optional) |
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 |
Title : transition_probability_matrix
Usage : my $matrixref = $molphy->transition_probablity_matrix();
Function: Gets the observed transition probability matrix
Returns : hash of hashes of aa/nt transition to each other aa/nt
Args : none |
Methods code
sub add_tree
{ my ($self,$tree) = @_;
if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) {
push @{$self->{'_trees'}},$tree;
}
return scalar @{$self->{'_trees'}};} | sub model
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'model'} = $value;
}
return $self->{'model'};} | sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($trees,
$smat,$tmat,$freq,
$model, $sspace,
) = $self->_rearrange([qw(TREES SUBSTITUTION_MATRIX
TRANSITION_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);
}
}
}
if( ref($smat) =~ /HASH/i ) {
$self->substitution_matrix($smat);
}
if( ref($tmat) =~ /HASH/i ) {
$self->transition_probability_matrix($tmat);
}
if( ref($freq) =~ /HASH/i ) {
$self->residue_frequencies($freq);
}
$model && $self->model($model);
$sspace && $self->search_space($sspace);
$self->{'_treeiterator'} = 0;
return $self;} | sub next_tree
{ my ($self,@args) = @_;
return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef;} | 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'}};} | sub rewind_tree_iterator
{ shift->{'_treeiterator'} = 0;} | sub search_space
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'search_space'} = $value;
}
return $self->{'search_space'};
}
1;} | sub substitution_matrix
{ my ($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 undef;
}
}
$self->{'_substitution_matrix'} = $val;
} else {
$self->warn("Must be a valid hashref of hashrefs for substition_matrix");
return undef;
}
}
return $self->{'_substitution_matrix'};} | sub transition_probability_matrix
{ my ($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 transition_probability_matrix");
return undef;
}
}
$self->{'_TPM'} = $val;
} else {
$self->warn("Must be a valid hashref of hashrefs for transition_probablity_matrix");
return undef;
}
}
return $self->{'_TPM'};} | General documentation
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/MailList.shtml - About the mailing lists
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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
| AUTHOR - Jason Stajich | Top |
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
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