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

   $self->{'_params'}{$param} = $value;
   return 1;
}

=head2 set_default_parameters

 Title   : set_default_parameters
 Usage   : $obj->set_default_parameters();
 Function: (Re)set the default parameters from the defaults
           (the first value in each array in the valid_values() array)
 Returns : none
 Args    : none


=cut


sub set_default_parameters {
    my ($self) = @_;
    my @validvals = $self->valid_values();
    foreach my $elem (@validvals) {
        keys %$elem; #reset hash iterator
        my ($param,$val) = each %$elem;
        if (ref($val)=~/ARRAY/i ) {
            unless (ref($val->[0])=~/HASH/i) {
                push @{ $self->{'_orderedparams'} }, {$param, $val->[0]};
            } else {
                $val = $val->[0];
            }
        }
        if ( ref($val) =~ /HASH/i ) {
            my $prevparam;
            while (defined($val)) {
                last unless (ref($val) =~ /HASH/i);
                last unless (defined($param));
                $prevparam = $param;
                ($param,$val) = each %{$val};
                push @{ $self->{'_orderedparams'} }, {$prevparam, $param};
                push @{ $self->{'_orderedparams'} }, {$param, $val} if (defined($val));
            }
        } elsif (ref($val) !~ /HASH/i && ref($val) !~ /ARRAY/i) {
            push @{ $self->{'_orderedparams'} }, {$param, $val};
        }
    }
}


=head2 update_ordered_parameters

 Title   : update_ordered_parameters
 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};
      }
   }
}

=head2 outfile_name

 Title   : outfile_name
 Usage   : my $outfile = $hyphy->outfile_name();
 Function: Get/Set the name of the output file for this run
           (if you wanted to do something special)
 Returns : string
 Args    : [optional] string to set value to


=cut

sub outfile_name {
   my $self = shift;
   if( @_ ) {
      return $self->{'_params'}->{'outfile'} = shift @_;
   }
   return $self->{'_params'}->{'outfile'};
}

=head2 version

 Title   : version
 Usage   : $obj->version()
 Function:  Returns the version string from HYPHY
 Returns : string
 Args    : none


=cut

sub version {
    my $self = shift;
    my $tempdir = $self->tempdir;
    if (defined $self->{'_version'}) {
        return $self->{'_version'};
    }
    # if it's not already defined, write out a small batchfile to return the version string, then clean up.
    my $versionbf = "$tempdir/version.bf";
    open(WRAPPER, ">", $versionbf) or $self->throw("cannot open $versionbf for writing");
    print WRAPPER qq{GetString (versionString, HYPHY_VERSION, 2);\nfprintf (stdout, versionString);};
    close(WRAPPER);
    my $exe = $self->executable();
    unless ($exe && -e $exe && -x _) {
        $self->throw("unable to find or run executable for 'HYPHY'");
    }
    my $commandstring = $exe . " BASEPATH=" . $self->program_dir . " " . $versionbf;
    open(RUN, "$commandstring |") or $self->throw("Cannot open exe $exe");
    my $output = <RUN>;