--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/CPT/ParameterGroup.pm	Mon Jun 05 02:50:07 2023 +0000
@@ -0,0 +1,161 @@
+package CPT::ParameterGroup;
+use Moose;
+use strict;
+use warnings;
+use autodie;
+
+# A special type of a ParameterCollection (could probably be a child...ohwell)
+use Moose::Util::TypeConstraints;
+#subtype 'TypeStr', as 'Str', where { $_ eq 'xor' || $_ eq 'or' || $_ eq 'and' };
+# Replaced with the enum
+
+has 'name' => ( is => 'rw', isa => 'Str');
+has 'description' => ( is => 'rw', isa => 'Str');
+has 'validator' => ( is => 'rw', isa => enum([qw(xor or and)]));
+has 'options' => ( is => 'rw', isa => 'ArrayRef[HashRef]' );
+
+
+sub validate {
+	die 'Unimplemented';
+}
+
+
+
+sub set_data {
+	my ($self, $hash_ref) = @_;
+	my %d = %{$hash_ref};
+	$self->name($d{name});
+	$self->description($d{description});
+	$self->validator($d{validator});
+	$self->options($d{options});
+}
+
+
+
+sub getopt {
+	my ($self) = @_;
+	die 'unimplemented';
+}
+
+sub flattenOptionsArray{
+	my ($self) = @_;
+	my @opts;
+	push(@opts, [sprintf("Option Group: %s\n%s\n[%s]", $self->name(), $self->description(), $self->_formatted_choice_str)]);
+	require CPT::ParameterCollection;
+	my $pC = CPT::ParameterCollection->new();
+	foreach(@{$self->options()}){
+		my %z = %{$_};
+		my $group_name = $z{group};
+		my @group_opts = @{$z{options}};
+		push(@opts, [sprintf("Subgroup: %s", $group_name)]);
+		foreach(@group_opts){
+			my $p = $pC->_coerce_param($_);
+			push(@opts, $p->getOptionsArray());
+		}
+	}
+	return \@opts;
+}
+
+sub _formatted_choice_str{
+	my ($self) = @_;
+	if($self->validator() eq 'xor'){
+		return 'Please only use options from ONE of the groups below, and no more';
+	}elsif($self->validator() eq 'or'){
+		return 'Please only use options from at least ONE of the groups below';
+	}elsif($self->validator() eq 'and'){
+		return 'Please ensure values/defaults are specified for ALL of the options in the groups below';
+	}
+	return undef;
+}
+
+
+sub populate_from_getopt {
+	my ( $self, $opt ) = @_;
+	die 'unimplemented';
+}
+
+no Moose;
+1;
+
+__END__
+
+=pod
+
+=encoding UTF-8
+
+=head1 NAME
+
+CPT::ParameterGroup
+
+=head1 VERSION
+
+version 1.99.4
+
+=head2 validate
+
+	$pC->validate();
+
+calls the validate method, which loops through and checks that user values line up with the validate method in each and every slot.
+
+Currently unimplemented!
+
+=head2 getopt
+
+	my @getopt_compatible_array = $pC->getopt()
+
+Returns a getopt compatible array by looping through the array and simply returning array objects, and calling the getOptionsArray method on CPT::Parameter::* objects
+
+=head2 populate_from_getopt
+
+	$parameterCollection->populate_from_getopt($opt);
+
+Populate the ->value() from getopt. This is the special sauce of this portion of the module. 
+Our test case for this function is the connector choice problem.
+
+{ 
+        name => 'Data Source #1',
+        description => "FASTA data source for our script",
+        type => 'xor', # must select only from one subgroup
+        options => [
+            {
+                group => 'Chado Custom',
+                options => [
+                    [ 'host' => 'Hostname', { required => 1, validate => 'Str' } ],
+                    [ 'user' => 'Username', { required => 1, validate => 'Str' } ],
+                    [ 'pass' => 'Password', { required => 1, validate => 'Str' } ],
+                    [ 'name' => 'Database name', { required => 1, validate => 'Str' } ],
+                    [ 'organism' => 'organism name', { required => 1, validate => 'Str' } ],
+                    [ 'landmark' => 'landmark name', { required => 1, validate => 'Str' } ],
+                ]
+            },
+            {
+                group => 'Chado GMOD pre-defined connector',
+                options => [
+                    [ 'conn=s' => 'Connection Nickname', { required => 1, validate => 'Str' } ],
+                ]
+            },
+            {
+                group => 'File',
+                options => [
+                    [ 'file|f=' => 'Input file', { required => 1, validate => 'File/Input' } ],
+                ]
+            },
+
+        ]
+    },
+
+This should intelligently set parameters in $opt based on the passed data. The real question is how to handle password....
+
+=head1 AUTHOR
+
+Eric Rasche <rasche.eric@yandex.ru>
+
+=head1 COPYRIGHT AND LICENSE
+
+This software is Copyright (c) 2014 by Eric Rasche.
+
+This is free software, licensed under:
+
+  The GNU General Public License, Version 3, June 2007
+
+=cut