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lib/Bio/Phylo/Beagle.pm  view on Meta::CPAN

 Title   : update_transition_matrices
 Usage   : $beagle->update_transition_matrices( %args )
 Function: Calculate a list of transition probability matrices
 Returns : error code
 Args    : -index  => Optional: Index of eigen-decomposition buffer
           -deriv1 => Optional: List of indices of first derivative matrices to update
           -deriv2 => Optional: List of indices of second derivative matrices to update

=cut

sub update_transition_matrices {
    $logger->info("@_");
    my $self = shift;
    my %args = looks_like_hash @_;
        
    # create node and edge arrays
    my $tree = $self->get_tree;        
    my ( @nodeIndices, @edgeLengths );
    my $nodeIndex = 0;
    $tree->visit_depth_first(
        '-post' => sub {

lib/Bio/Phylo/Beagle.pm  view on Meta::CPAN

 Title   : update_partials
 Usage   : $beagle->update_partials( %args )
 Function: Calculate or queue for calculation partials using a list of operations
 Returns : error code
 Args    : -operations => Bio::Phylo::BeagleOperations::Array
           -count      => Number of operations (input)
           -index      => Index number of scaleBuffer to store accumulated factors (input)

=cut

sub update_partials {
    $logger->info("@_");
    my $self = shift;
    if ( my %args = looks_like_hash @_ ) {
        
        my $operations = $args{'-operations'} || throw 'BadArgs' => 'Need -operations argument';
        my $count      = $args{'-count'}      || throw 'BadArgs' => 'Need -count argument';
        my $index      = $args{'-index'}      || throw 'BadArgs' => 'Need -index argument';
        
        # /**
        #  * @brief Calculate or queue for calculation partials using a list of operations