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lib/Bio/Tools/Run/Phylo/Hyphy/Base.pm  view on Meta::CPAN

 Usage   : $hyphy->update_ordered_parameters(0);
 Function: (Re)set the default parameters from the defaults
           (the first value in each array in the
           %VALIDVALUES class variable)
 Returns : none
 Args    : boolean: keep existing parameter values


=cut

sub update_ordered_parameters {
   my ($self) = @_;
   for (my $i=0; $i < scalar(@{$self->{'_orderedparams'}}); $i++) {
      my ($param,$val) = each %{$self->{'_orderedparams'}[$i]};
      if (exists $self->{'_params'}{$param}) {
         $self->{'_orderedparams'}[$i] = {$param, $self->{'_params'}{$param}};
      } else {
         $self->{'_orderedparams'}[$i] = {$param, $val};
      }
   }
}

lib/Bio/Tools/Run/Phylo/Hyphy/BatchFile.pm  view on Meta::CPAN

=head2 update_ordered_parameters

 Title   : update_ordered_parameters
 Usage   : $BatchFile->update_ordered_parameters();
 Function: updates all of the parameters needed for the ordered input redirect in HBL.
 Returns : nothing
 Args    : none

=cut

sub update_ordered_parameters {
    my ($self) = @_;
    unless (defined ($self->{'_params'}{'order'})) {
        $self->throw("No ordered parameters for HYPHY were defined.");
    }
    for (my $i=0; $i< scalar @{$self->{'_params'}{'order'}}; $i++) {
        my $item = @{$self->{'_params'}{'order'}}[$i];
        #FIXME: update_ordered_parameters should be more flexible. It should be able to tell what type of object $item is and, if necessary, create a temp file for it.
        if (ref ($item) =~ m/Bio::SimpleAlign/) {
            $item = $self->{'_params'}{'tempalnfile'};
        } elsif (ref ($item) =~ m/Bio::Tree::Tree/) {