[NET-294] Add quickperms from PALM

+nla/+edge/+permutationMethods/Base.m

@@ -1,5 +1,5 @@
 classdef Base
     methods (Abstract)
-        permuted_input_struct = permute(obj, orig_input_struct)
+        permuted_input_struct = permute(obj, orig_input_struct, permutation_number)
     end
 end

+nla/+edge/+permutationMethods/BehaviorVec.m

@@ -1,6 +1,6 @@
 classdef BehaviorVec < nla.edge.permutationMethods.Base
     methods
-        function permuted_input_struct = permute(obj, orig_input_struct)
+        function permuted_input_struct = permute(obj, orig_input_struct, ~)
             permuted_input_struct = orig_input_struct;
             permuted_behavior = nla.helpers.permuteVector(orig_input_struct.behavior);
             permuted_input_struct.behavior = permuted_behavior;

+nla/+edge/+permutationMethods/FCWildBootstrap.m

@@ -1,6 +1,6 @@
 classdef FCWildBootstrap < nla.edge.permutationMethods.Base
     methods
-        function permuted_input_struct = permute(obj, orig_input_struct)
+        function permuted_input_struct = permute(obj, orig_input_struct, ~)
             permuted_input_struct = orig_input_struct;
             permuted_input_struct.func_conn = orig_input_struct.func_conn.copy();
             fcData = permuted_input_struct.func_conn.v';

+nla/+edge/+permutationMethods/None.m

@@ -1,6 +1,6 @@
 classdef None < nla.edge.permutationMethods.Base
     methods
-        function permuted_input_struct = permute(~, orig_input_struct)
+        function permuted_input_struct = permute(~, orig_input_struct, ~)
             permuted_input_struct = orig_input_struct;
         end
     end

+nla/+edge/+permutationMethods/Quickperms.m

@@ -0,0 +1,41 @@
+classdef Quickperms < nla.edge.permutationMethods.Base
+    %QUICKPERMS Implementation of Palm's quickperms method
+    %
+    %
+
+    properties
+    end
+
+    methods
+        function obj = Quickperms()
+        end
+
+        function permuted_input_struct = permute(obj, orig_input_struct, permutation)
+            permuted_input_struct = orig_input_struct;
+            permuted_input_struct.behavior = orig_input_struct.behavior(orig_input_struct.permutations(:, permutation));
+        end
+
+        function orig_input_struct = createPermutations(obj, orig_input_struct, number_permutations)
+            [rows, columns] = size(orig_input_struct.permutation_groups);
+            unique_values = unique(orig_input_struct.permutation_groups(:, columns));
+            if ismember(0, unique_values)
+                orig_input_struct.permutation_groups(:, columns) = orig_input_struct.permutation_groups(:, columns) + 1;
+                unique_values = unique(orig_input_struct.permutation_groups(:, columns));
+            end
+            counts = containers.Map(unique_values, ones(1, numel(unique_values)));
+            last_column = zeros(rows, 1);
+            for row_num = 1:rows
+                last_column(row_num) = counts(orig_input_struct.permutation_groups(row_num, columns));
+                counts(orig_input_struct.permutation_groups(row_num, columns)) = counts(orig_input_struct.permutation_groups(row_num, columns)) + 1;
+            end
+            % Check if all values in first column of permutation struct are single value
+            if ~all(orig_input_struct.permutation_groups(:, 1) == orig_input_struct.permutation_groups(1, 1))
+                all_ones = -1 .* ones(rows, 1);
+                orig_input_struct.permutation_groups = [all_ones orig_input_struct.permutation_groups];
+            end
+            orig_input_struct.permutation_groups = [orig_input_struct.permutation_groups last_column];
+            [permutations, ~] = nla.lib.palm_quickperms(orig_input_struct.behavior, orig_input_struct.permutation_groups, number_permutations);
+            orig_input_struct.permutations = permutations;
+        end
+    end
+end