diff --git a/+TableBlock/delete_recursive.m b/+TableBlock/delete_recursive.m
index c73fb428b80f301ad51d4c394a4de77567d8c5a6..18268887ffc8125c28ef527afbde045592796a58 100644
--- a/+TableBlock/delete_recursive.m
+++ b/+TableBlock/delete_recursive.m
@@ -1,29 +1,20 @@
-         %% delete_recursive
-        % delete any lines that are unconnected and one end or both
-        % code from
-        % http://www.mathworks.com/matlabcentral/fileexchange/12352-delete-unconnected-lines
-        % Copyright (c) 2009, Per-Anders Ekström
-            function delete_recursive( line )
-            %DELETE_RECURSIVE( LINE )  Delete line if:
-            %   1) do not have any source-block
-            %   2) do not have any line-children AND no destination-block
-            %   otherwise go recursively through all eventual line-children
+%% delete_recursive
+function delete_recursive( line_handle )
+
+if get( line_handle, 'SrcPortHandle' ) < 0
+    delete_line( line_handle ) ;
+    return
+end
+LineChild = get( line_handle, 'LineChildren' ) ;
+if ~isempty( LineChild )
+    for i=1:length( LineChild )
+        obj.delete_recursive( LineChild( i ) )
+    end
+else
+    if get( line_handle, 'DstPortHandle' ) < 0
+        delete_line( line_handle ) ;
+    end
+end
+end
+
 
-                if get( line, 'SrcPortHandle' ) < 0
-                    delete_line( line ) ;
-                    return
-                end
-                LineChildren = get( line, 'LineChildren' ) ;
-                if isempty( LineChildren )
-                    if get( line, 'DstPortHandle' ) < 0
-                        delete_line( line ) ;
-                    end
-                else
-                    for i=1:length( LineChildren )
-                        obj.delete_recursive( LineChildren( i ) )
-                    end
-                end
-            end
-        % end copyright
-            
-        
diff --git a/+TableBlock/set_block_display.m b/+TableBlock/set_block_display.m
index d1ce718689e542997b6091e854f45376b2687279..cb6691e403cc728d55b28a668882944a9b4b2b0c 100644
--- a/+TableBlock/set_block_display.m
+++ b/+TableBlock/set_block_display.m
@@ -1,32 +1,34 @@
 %% set_block_display
-        %    update a block based on an inputed boolean value representing
-        %    the typecheck state.
-        % inputs:
-        %   block_handle:handle - handle block to update
-        %   checked:boolean - 0 if not typechecked, 1 if typechecked
-        % outputs:
-        %   none
-        function [] = set_block_display(block_handle,checked)
-            %if object.pvs_checked == 1
-                mask_string = [];
-                code_block = sprintf('%s/code',getfullname(block_handle));
-                in_handles=find_system(code_block, 'SearchDepth',1,'FindAll','On','FollowLinks','On','LookUnderMasks','All','BlockType','Inport');
-                for i = 1:size(in_handles,1)
-                    mask_string = [mask_string 'port_label(''input'',' int2str(i) ',''' get_param(in_handles(i),'Name') ''');' ];
-                end
-                
-                out_handles=find_system(code_block, 'SearchDepth',1,'FindAll','On','FollowLinks','On','LookUnderMasks','All','BlockType','Outport');
-                for i = 1:size(out_handles,1)
-                    mask_string = [mask_string 'port_label(''output'',' int2str(i) ',''' get_param(out_handles(i),'Name') ''');' ];
-                end
-                
-                mask_string = [mask_string 'text(0.5, 0.9, ''Tabular Expression'', ''horizontalAlignment'', ''center'')'];
-              if checked == 0  
-                mask_string = [mask_string 'color(''red'')text(0.5, 0.1, ''Not Checked'', ''horizontalAlignment'', ''center'')'];
-              else
-                 mask_string = [mask_string 'color(''green'')text(0.5, 0.1, ''Checked'', ''horizontalAlignment'', ''center'')'];
+%    update a block based on an inputed boolean value representing
+%    the typecheck state.
+% inputs:
+%   block_handle:handle - handle block to update
+%   checked:boolean - 0 if not typechecked, 1 if typechecked
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = set_block_display(block_handle,checked)
+%if object.pvs_checked == 1
+mask_string = [];
+code_block = sprintf('%s/code',getfullname(block_handle));
+in_handles=find_system(code_block, 'SearchDepth',1,'FindAll','On','FollowLinks','On','LookUnderMasks','All','BlockType','Inport');
+for i = 1:size(in_handles,1)
+    mask_string = [mask_string 'port_label(''input'',' int2str(i) ',''' get_param(in_handles(i),'Name') ''');' ];
+end
+
+out_handles=find_system(code_block, 'SearchDepth',1,'FindAll','On','FollowLinks','On','LookUnderMasks','All','BlockType','Outport');
+for i = 1:size(out_handles,1)
+    mask_string = [mask_string 'port_label(''output'',' int2str(i) ',''' get_param(out_handles(i),'Name') ''');' ];
+end
+
+mask_string = [mask_string 'text(0.5, 0.9, ''Tabular Expression'', ''horizontalAlignment'', ''center'')'];
+if checked == 0
+    mask_string = [mask_string 'color(''red'')text(0.5, 0.1, ''Not Checked'', ''horizontalAlignment'', ''center'')'];
+else
+    mask_string = [mask_string 'color(''green'')text(0.5, 0.1, ''Checked'', ''horizontalAlignment'', ''center'')'];
+    
+end
+set_param(getfullname(block_handle),'MaskDisplay',mask_string);
+end
 
-              end
-                set_param(getfullname(block_handle),'MaskDisplay',mask_string);
-        end
-            
diff --git a/+TableBlock/set_code.m b/+TableBlock/set_code.m
index 1398710b2095738018226bdff185065620c69763..231f5361c606aaaea15010d9e761262d7ca18d4c 100644
--- a/+TableBlock/set_code.m
+++ b/+TableBlock/set_code.m
@@ -1,196 +1,188 @@
-        %% set_code
-        %    set the script of an embedded matlab block to an inputed
-        %    string of eml code, create the inputs and outputs for the
-        %    subsystem to connect to the eml block
-        % inputs:
-        %   block_handle:handle - handle block to update
-        %   code:string - eml code
-        %   function_name:string - name of the function
-        % outputs:
-        %   eml_handle:handle - handle of eml block, as this function may
-        %   create a new block.
-        function eml_handle = set_code(block_handle,code,function_name)
-         % unlink the block from the library, this is necessary if
-                % we
-                % want to change the subsystem of the block.
-                set_param(block_handle,'LinkStatus','none')
-
-
-                % determine if the name already exists in the model
-
-                if (~strcmp(get(block_handle,'Name'),function_name))
-                    try
-                    set_param(block_handle,'Name',function_name);
-                    catch exception
-                        msgbox(exception.message);
-                    end
-                end
-
-                % embedded matlab code block store code in stateflow states so
-                % we need to get the root hande
-                S = sfroot;
-
-                % get the path of the code block
-                code_block = sprintf('%s/code',getfullname(block_handle));
-                % determine if code block already exists
-                code_blocks = find_system(getfullname(block_handle),'LookUnderMasks','all','BlockType','SubSystem','Name','code');
-
-                % if the code block does not already exists we need to create a
-                % new one
-                if (isempty(code_blocks))
-                    code_blocks = add_block('simulink/User-Defined Functions/Embedded MATLAB Function',code_block);
-                end
-
-                eml_handle = code_blocks
-                % find the state of the code block and update it to the new
-                % code
-                myState = S.find('-isa','Stateflow.EMChart', '-and', 'Path', code_block); % find which one we want to edit
-
-                if (~isempty(myState))
-                    myState.Script =  sprintf('%s',code);
-                end
-
-                % delete any lines that are unconnected and one end or both
-                % code from
-                % http://www.mathworks.com/matlabcentral/fileexchange/12352-delete-unconnected-lines
-                % Copyright (c) 2009, Per-Anders Ekström
-                    % delete all the lines
-                    lines = find_system( getfullname(block_handle), ...
-                    'LookUnderMasks', 'all', ...
-                    'FindAll', 'on', ...
-                    'Type', 'line' ) ;
-
-
-                    % for each line, call delete_recursive if handle still exist
-                    for i=1:length( lines )
-                        if ishandle( lines( i ) )
-                            TableBlock.delete_recursive( lines( i ) )
-                        end
-                    end
-                % end copyright
-
-                % we need to determine which of the inports and outports we
-                % need to create and delete. Whenever we delete a port anything
-                % connected with this port is unconnected, other blocks, scopes
-                % etc. We would like to avoid this if possible because it can
-                % be quite annoying.
-
-                % First loop through all the inport blocks, if there does not
-                % exists an inport in the code block of the same name then
-                % delete the inport block
-                inports = find_system(getfullname(block_handle),'LookUnderMasks','all','SearchDepth',1,'FindAll','On','BlockType','Inport');
-                for i=1:size(inports,1)
-                    found = 0;
-                    in_handles=find_system(code_block, 'SearchDepth',1,'FindAll','On','FollowLinks','On','LookUnderMasks','All','BlockType','Inport');
-
-                    for j=1:size(in_handles,1)
-                        if strcmp(get_param(inports(i),'Name'),get_param(in_handles(j),'Name'))
-                            found = 1;
-                        end
-                    end
-
-                    if (~found)
-                        % old inport no longer exists
-                        delete_block(inports(i));
-                    end
-                end
-
-                % now we loop through all the inports in the code block if
-                % there is an inport block of the same name then connect them,
-                % else create a new inport block and connect them
-                in_handles=find_system(code_block, 'SearchDepth',1,'FindAll','On','FollowLinks','On','LookUnderMasks','All','BlockType','Inport');
-                for j = 1:size(in_handles,1)
-                    found = 0;
-                    inports = find_system(getfullname(block_handle),'LookUnderMasks','all','SearchDepth',1,'BlockType','Inport');
-                    for i = 1:size(inports,1)
-                        if strcmp(get_param(inports(i),'Name'),get_param(in_handles(j),'Name'))
-                            found = 1;
-
-                            % draw the line
-                            new_port_num = sprintf('%s/1',get_param(in_handles(j),'Name'));
-                            dest_port = sprintf('%s/%d','code',j);
-                            try
-                            add_line(getfullname(block_handle),new_port_num,dest_port);
-                            end
-                        end
-                    end
-                    if (~found)
-                       new_port = sprintf('%s/%s',getfullname(block_handle),get_param(in_handles(j),'Name'));
-                       add_block('simulink/Sources/In1',new_port)
-                       new_port_num = sprintf('%s/1',get_param(in_handles(j),'Name'));
-                    dest_port = sprintf('%s/%d','code',j);
-                    % sometimes line will be created automatically
-                    try       
-                    add_line(getfullname(block_handle),new_port_num,dest_port);
-                    end
-                    end
-
-
-                end
-
-
-                % Next we do the same thing with the outputs
-                outports = find_system(getfullname(block_handle),'LookUnderMasks','all','SearchDepth',1,'FindAll','On','BlockType','Outport');
-                for i=1:size(outports,1)
-                    found = 0;
-                    out_handles=find_system(code_block, 'SearchDepth',1,'FindAll','On','FollowLinks','On','LookUnderMasks','All','BlockType','Outport');
-
-                    for j=1:size(out_handles,1)
-                        if strcmp(get_param(outports(i),'Name'),get_param(out_handles(j),'Name'))
-                            found = 1;
-                        end
-                    end
-
-                    if (~found)
-                        % old inport no longer exists
-                        delete_block(outports(i));
-                    end
-                end
-
-                out_handles=find_system(code_block, 'SearchDepth',1,'FindAll','On','FollowLinks','On','LookUnderMasks','All','BlockType','Outport');
-                for j = 1:size(out_handles,1)
-                    found = 0;
-                    outports = find_system(getfullname(block_handle),'LookUnderMasks','all','SearchDepth',1,'BlockType','Outport');
-                    for i = 1:size(outports,1)
-                        if strcmp(get_param(outports(i),'Name'),get_param(out_handles(j),'Name'))
-                            found = 1;
-
-                            % draw the line
-                            new_port_num = sprintf('%s/1',get_param(out_handles(j),'Name'));
-                            dest_port = sprintf('%s/%d','code',j);
-                            try
-                            add_line(getfullname(block_handle),dest_port,new_port_num);
-                            end
-                        end
-                    end
-                    if (~found)
-                       new_port = sprintf('%s/%s',getfullname(block_handle),get_param(out_handles(j),'Name'));
-                       add_block('simulink/Sinks/Out1',new_port)
-                       new_port_num = sprintf('%s/1',get_param(out_handles(j),'Name'));
-                    dest_port = sprintf('%s/%d','code',j);
-                    try       
-                    add_line(getfullname(block_handle),dest_port,new_port_num);
-                    end
-                    end
-                end
-
-                % delete any lines that are unconnected and one end or both
-                % again sometimes extra lines are created
-                % code from
-                % http://www.mathworks.com/matlabcentral/fileexchange/12352-delete-unconnected-lines
-                % Copyright (c) 2009, Per-Anders Ekström
-                    % delete all the lines 
-                    lines = find_system( getfullname(block_handle), ...
-                        'LookUnderMasks', 'all', ...
-                        'FindAll', 'on', ...
-                        'Type', 'line' ) ;
-
-                    % for each line, call delete_recursive if handle still exist
-                    for i=1:length( lines )
-                        if ishandle( lines( i ) )
-                            TableBlock.delete_recursive( lines( i ) )
-                        end
-                    end   
-                % end copyright
-                
-        end
\ No newline at end of file
+%% set_code
+%    set the script of an embedded matlab block to an inputed
+%    string of eml code, create the inputs and outputs for the
+%    subsystem to connect to the eml block
+% inputs:
+%   block_handle:handle - handle block to update
+%   code:string - eml code
+%   function_name:string - name of the function
+% outputs:
+%   eml_handle:handle - handle of eml block, as this function may
+%   create a new block.
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function eml_handle = set_code(block_handle,code,function_name)
+% unlink the block from the library, this is necessary if
+% we
+% want to change the subsystem of the block.
+set_param(block_handle,'LinkStatus','none')
+
+
+% determine if the name already exists in the model
+
+if (~strcmp(get(block_handle,'Name'),function_name))
+    try
+        set_param(block_handle,'Name',function_name);
+    catch exception
+        msgbox(exception.message);
+    end
+end
+
+% embedded matlab code block store code in stateflow states so
+% we need to get the root hande
+S = sfroot;
+
+% get the path of the code block
+code_block = sprintf('%s/code',getfullname(block_handle));
+% determine if code block already exists
+code_blocks = find_system(getfullname(block_handle),'LookUnderMasks','all','BlockType','SubSystem','Name','code');
+
+% if the code block does not already exists we need to create a
+% new one
+if (isempty(code_blocks))
+    code_blocks = add_block('simulink/User-Defined Functions/Embedded MATLAB Function',code_block);
+end
+
+eml_handle = code_blocks
+% find the state of the code block and update it to the new
+% code
+myState = S.find('-isa','Stateflow.EMChart', '-and', 'Path', code_block); % find which one we want to edit
+
+if (~isempty(myState))
+    myState.Script =  sprintf('%s',code);
+end
+
+% delete any lines that are unconnected and one end or both
+% code from
+lines = find_system( getfullname(block_handle), ...
+    'LookUnderMasks', 'all', ...
+    'FindAll', 'on', ...
+    'Type', 'line' ) ;
+
+
+for i=1:length( lines )
+    if ishandle( lines( i ) )
+        TableBlock.delete_recursive( lines( i ) )
+    end
+end
+
+
+% we need to determine which of the inports and outports we
+% need to create and delete. Whenever we delete a port anything
+% connected with this port is unconnected, other blocks, scopes
+% etc. We would like to avoid this if possible because it can
+% be quite annoying.
+
+% First loop through all the inport blocks, if there does not
+% exists an inport in the code block of the same name then
+% delete the inport block
+inports = find_system(getfullname(block_handle),'LookUnderMasks','all','SearchDepth',1,'FindAll','On','BlockType','Inport');
+for i=1:size(inports,1)
+    found = 0;
+    in_handles=find_system(code_block, 'SearchDepth',1,'FindAll','On','FollowLinks','On','LookUnderMasks','All','BlockType','Inport');
+    
+    for j=1:size(in_handles,1)
+        if strcmp(get_param(inports(i),'Name'),get_param(in_handles(j),'Name'))
+            found = 1;
+        end
+    end
+    
+    if (~found)
+        % old inport no longer exists
+        delete_block(inports(i));
+    end
+end
+
+% now we loop through all the inports in the code block if
+% there is an inport block of the same name then connect them,
+% else create a new inport block and connect them
+in_handles=find_system(code_block, 'SearchDepth',1,'FindAll','On','FollowLinks','On','LookUnderMasks','All','BlockType','Inport');
+for j = 1:size(in_handles,1)
+    found = 0;
+    inports = find_system(getfullname(block_handle),'LookUnderMasks','all','SearchDepth',1,'BlockType','Inport');
+    for i = 1:size(inports,1)
+        if strcmp(get_param(inports(i),'Name'),get_param(in_handles(j),'Name'))
+            found = 1;
+            
+            % draw the line
+            new_port_num = sprintf('%s/1',get_param(in_handles(j),'Name'));
+            dest_port = sprintf('%s/%d','code',j);
+            try
+                add_line(getfullname(block_handle),new_port_num,dest_port);
+            end
+        end
+    end
+    if (~found)
+        new_port = sprintf('%s/%s',getfullname(block_handle),get_param(in_handles(j),'Name'));
+        add_block('simulink/Sources/In1',new_port)
+        new_port_num = sprintf('%s/1',get_param(in_handles(j),'Name'));
+        dest_port = sprintf('%s/%d','code',j);
+        % sometimes line will be created automatically
+        try
+            add_line(getfullname(block_handle),new_port_num,dest_port);
+        end
+    end
+    
+    
+end
+
+
+% Next we do the same thing with the outputs
+outports = find_system(getfullname(block_handle),'LookUnderMasks','all','SearchDepth',1,'FindAll','On','BlockType','Outport');
+for i=1:size(outports,1)
+    found = 0;
+    out_handles=find_system(code_block, 'SearchDepth',1,'FindAll','On','FollowLinks','On','LookUnderMasks','All','BlockType','Outport');
+    
+    for j=1:size(out_handles,1)
+        if strcmp(get_param(outports(i),'Name'),get_param(out_handles(j),'Name'))
+            found = 1;
+        end
+    end
+    
+    if (~found)
+        % old inport no longer exists
+        delete_block(outports(i));
+    end
+end
+
+out_handles=find_system(code_block, 'SearchDepth',1,'FindAll','On','FollowLinks','On','LookUnderMasks','All','BlockType','Outport');
+for j = 1:size(out_handles,1)
+    found = 0;
+    outports = find_system(getfullname(block_handle),'LookUnderMasks','all','SearchDepth',1,'BlockType','Outport');
+    for i = 1:size(outports,1)
+        if strcmp(get_param(outports(i),'Name'),get_param(out_handles(j),'Name'))
+            found = 1;
+            
+            % draw the line
+            new_port_num = sprintf('%s/1',get_param(out_handles(j),'Name'));
+            dest_port = sprintf('%s/%d','code',j);
+            try
+                add_line(getfullname(block_handle),dest_port,new_port_num);
+            end
+        end
+    end
+    if (~found)
+        new_port = sprintf('%s/%s',getfullname(block_handle),get_param(out_handles(j),'Name'));
+        add_block('simulink/Sinks/Out1',new_port)
+        new_port_num = sprintf('%s/1',get_param(out_handles(j),'Name'));
+        dest_port = sprintf('%s/%d','code',j);
+        try
+            add_line(getfullname(block_handle),dest_port,new_port_num);
+        end
+    end
+end
+
+% delete any lines that are unconnected and one end or both
+% again sometimes extra lines are created
+lines = find_system( getfullname(block_handle), ...
+    'LookUnderMasks', 'all', ...
+    'FindAll', 'on', ...
+    'Type', 'line' ) ;
+
+for i=1:length( lines )
+    if ishandle( lines( i ) )
+        TableBlock.delete_recursive( lines( i ) )
+    end
+end
+
+end
\ No newline at end of file
diff --git a/@Cell/cal_height.m b/@Cell/cal_height.m
index fb409ba2776c694612c33c4e86f340f2dfc465e5..329bfcebb8f928011953630d01fd0546de44cef3 100644
--- a/@Cell/cal_height.m
+++ b/@Cell/cal_height.m
@@ -3,24 +3,25 @@
 %    if the cell does not have a subgrid the height will be 1, else
 %    it will be the height of the subgrid.
 % inputs:
-%   object:Cell - Current Cell Object 
+%   object:Cell - Current Cell Object
 %   edit:boolean - 0 when not in edit mode, 1 in edit mode
 % outputs;
 %   h:double - height in number of cells
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function h = cal_height(object,edit)
-    h = 0;
-    if (isempty(object.subgrid))
-        h = 1;
-    else
-        for i=1:size(object.subgrid.cells,2)
-            h = h + cal_height(object.subgrid.cells(i),edit);
-        end
-        % edit button is half a cell high, if in edit mode increase
-        % by 0.5
-        if (edit == 1)
-            h = h + 0.5;
-        end
-
+h = 0;
+if (isempty(object.subgrid))
+    h = 1;
+else
+    for i=1:size(object.subgrid.cells,2)
+        h = h + cal_height(object.subgrid.cells(i),edit);
     end
+    % edit button is half a cell high, if in edit mode increase
+    % by 0.5
+    if (edit == 1)
+        h = h + 0.5;
+    end
+    
+end
 end
-       
\ No newline at end of file
diff --git a/@Cell/delete_Cell.m b/@Cell/delete_Cell.m
index 26c72d2ada47c516878971c8602b8b36b233a53b..caca6344d6890a9be719d3d115128125369ef4d0 100644
--- a/@Cell/delete_Cell.m
+++ b/@Cell/delete_Cell.m
@@ -1,28 +1,29 @@
- %% delete_Cell
-        %    deletes the current cell, will recursively delete any subgrids
-        %    if they exist.
-        % inputs:
-        %   object:Cell - Current Cell Object         
-        % outputs;
-        %   none
-        function [] = delete_Cell(object)
-            if(isempty(object.subgrid))
-                delete(object.grid_pb);
-                delete(object.cond);
-                object.cond = [];
-                object.grid_pb = [];
-                %delete(object);
-            else
-                % delete the subgrid
-                object.subgrid.deep_delete
-                if(ishghandle(object.grid_pb))
-                    delete(object.grid_pb);
-                end
-                delete(object.cond);
-                object.cond = [];
-                object.grid_pb = [];
-                %delete(object);
-            end
-        end
-        
-        
\ No newline at end of file
+%% delete_Cell
+%    deletes the current cell, will recursively delete any subgrids
+%    if they exist.
+% inputs:
+%   object:Cell - Current Cell Object
+% outputs;
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = delete_Cell(object)
+if(isempty(object.subgrid))
+    delete(object.grid_pb);
+    delete(object.cond);
+    object.cond = [];
+    object.grid_pb = [];
+    %delete(object);
+else
+    % delete the subgrid
+    object.subgrid.deep_delete
+    if(ishghandle(object.grid_pb))
+        delete(object.grid_pb);
+    end
+    delete(object.cond);
+    object.cond = [];
+    object.grid_pb = [];
+    %delete(object);
+end
+end
+
diff --git a/@Cell/flag_cell.m b/@Cell/flag_cell.m
index 2d10a581eec79712f423b04745aa51abf06f6125..3168646547d89924c71479497217ddf257a130f7 100644
--- a/@Cell/flag_cell.m
+++ b/@Cell/flag_cell.m
@@ -1,21 +1,22 @@
-        %% flag_cell
-        % mode
-        %   0 - normal
-        %   1 - red (error/false)
-        %   2 - green (ok/true)
-        function [] = flag_cell(object,mode)
-        
-            if (isempty(object.color))
-                object.color = get(object.cond,'BackgroundColor');
-            end
-            
-            if (mode == 0)
-                set(object.cond,'BackgroundColor',object.color);
-            elseif (mode == 1)
-                set(object.cond,'BackgroundColor',[0.92 0.65 0.65])
-            elseif (mode == 2)
-                set(object.cond,'BackgroundColor',[0.03 1.0 0.32]);
-            end
-        
-        end
-      
\ No newline at end of file
+%% flag_cell
+% mode
+%   0 - normal
+%   1 - red (error/false)
+%   2 - green (ok/true)
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = flag_cell(object,mode)
+
+if (isempty(object.color))
+    object.color = get(object.cond,'BackgroundColor');
+end
+
+if (mode == 0)
+    set(object.cond,'BackgroundColor',object.color);
+elseif (mode == 1)
+    set(object.cond,'BackgroundColor',[0.92 0.65 0.65])
+elseif (mode == 2)
+    set(object.cond,'BackgroundColor',[0.03 1.0 0.32]);
+end
+
+end
diff --git a/@Cell/get_pos.m b/@Cell/get_pos.m
index 8b826f7c736a6a8634e3a4a6643d45191299bea7..36d8e57fa1bd78f4b8b6289060bbdf52a9a90564 100644
--- a/@Cell/get_pos.m
+++ b/@Cell/get_pos.m
@@ -1,14 +1,15 @@
- 
-        %% get_pos
-        %    Returns the position of the edit box for the cell
-        % inputs:
-        %   object:Cell - Current Cell Object  
-        % outputs;
-        %   pos:[double double double double] - position of the cell
-        function pos = get_pos(object)
-            if (~isempty(object.cond))
-                pos = get(object.cond,'position');
-            end
-        end
-        
-        
\ No newline at end of file
+
+%% get_pos
+%    Returns the position of the edit box for the cell
+% inputs:
+%   object:Cell - Current Cell Object
+% outputs;
+%   pos:[double double double double] - position of the cell
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function pos = get_pos(object)
+if (~isempty(object.cond))
+    pos = get(object.cond,'position');
+end
+end
+
diff --git a/@Cell/new_Grid.m b/@Cell/new_Grid.m
index ea89b92abbd0e26334e8c43c43803084f706b992..2586ab7afc81057c06ad4f6db3d8b7d898caa797 100644
--- a/@Cell/new_Grid.m
+++ b/@Cell/new_Grid.m
@@ -1,19 +1,19 @@
- %% new_Grid
-        %    
-        % inputs:
-        %   object:Cell - Current Cell Object
-        % outputs;
-        %   
-        function [] = new_Grid(object)
-            object.subgrid = Grid(object.cell_index,object);
-            object.subgrid.new_Cell;
-            object.subgrid.new_Cell;
-            object.subgrid.set_rGrid(object.parent_grid.rGrid);
-            object.pb_flag = 0;
-            delete(object.grid_pb);
-            if(~isempty(object.parent_grid.rGrid))
-                object.parent_grid.rGrid.delete_g2s(object);
-            end
-        end
-        
-       
\ No newline at end of file
+%% new_Grid
+%
+% inputs:
+%   object:Cell - Current Cell Object
+% outputs;
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = new_Grid(object)
+object.subgrid = Grid(object.cell_index,object);
+object.subgrid.new_Cell;
+object.subgrid.new_Cell;
+object.subgrid.set_rGrid(object.parent_grid.rGrid);
+object.pb_flag = 0;
+delete(object.grid_pb);
+if(~isempty(object.parent_grid.rGrid))
+    object.parent_grid.rGrid.delete_g2s(object);
+end
+end
+
diff --git a/@Cell/pb_call.m b/@Cell/pb_call.m
index 78c30e051af000c5403adc03cf4e9ef87cf3a86c..cbbe776ff839ceac5621fedbd851dacca482160e 100644
--- a/@Cell/pb_call.m
+++ b/@Cell/pb_call.m
@@ -1,36 +1,37 @@
-     %% pb_call
-        %    callback function for the new subgrid button
-        % inputs:
-        %   object:Cell - Current Cell Object
-        %   src:double - Source of the callback
-        %   event:eventdata - Data of the eventcall
-        % outputs;
-        %   none
-        function [] = pb_call(object,src,event)
-            gui = get(src,'userdata');
-            
-            
-            
-            
-            object.new_Grid;
-            gui.reset_wh();
-            %gui.draw_grid2(gui.Grid2);
-            gui.draw_allgrids(0);
-            
-             if isempty(event) || event ~= 1
-
-                undo_data.action = 4;
-                undo_data.grid = object.subgrid;
-                undo_data.cell = object;
-                undo_data.text = [];
-                undo_data.subgrid = [];
-                
-                gui.undo_man.new_state(undo_data);
-             end
-            
-             gui.update_undoredo
-
-            
-        end
-        
-        
\ No newline at end of file
+%% pb_call
+%    callback function for the new subgrid button
+% inputs:
+%   object:Cell - Current Cell Object
+%   src:double - Source of the callback
+%   event:eventdata - Data of the eventcall
+% outputs;
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = pb_call(object,src,event)
+gui = get(src,'userdata');
+
+
+
+
+object.new_Grid;
+gui.reset_wh();
+%gui.draw_grid2(gui.Grid2);
+gui.draw_allgrids(0);
+
+if isempty(event) || event ~= 1
+    
+    undo_data.action = 4;
+    undo_data.grid = object.subgrid;
+    undo_data.cell = object;
+    undo_data.text = [];
+    undo_data.subgrid = [];
+    
+    gui.undo_man.new_state(undo_data);
+end
+
+gui.update_undoredo
+
+
+end
+
diff --git a/@Cell/set_pb.m b/@Cell/set_pb.m
index 93bbdc6a8e337608255adfeae869b2cfef4fc88a..66ed4e1d2cbad63ddf165c73969e3c006790ee73 100644
--- a/@Cell/set_pb.m
+++ b/@Cell/set_pb.m
@@ -1,22 +1,23 @@
 %% set_pb
-        %    create the new subgrid push button handle
-        % inputs:
-        %   object:Cell - Current Cell Object  
-        % outputs;
-        %   none
-        function [] = set_pb(object,fig,pos)
-            if(object.pb_flag == 1 && (isempty(object.grid_pb) || ~ishghandle(object.grid_pb)))
-            object.grid_pb = uicontrol('style','push',...
-                'units','pix',...
-                'string','+',...
-                'HorizontalAlign','left',...
-                'Parent',fig,...
-                'position',pos,...   
-                'callback',@(src,event)pb_call(object,src,event));
-            elseif (object.pb_flag == 1 && ~isempty(object.grid_pb))
-                    set(object.grid_pb,'Position',pos);
-                else
-                end
-        end
-        
-   
\ No newline at end of file
+%    create the new subgrid push button handle
+% inputs:
+%   object:Cell - Current Cell Object
+% outputs;
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = set_pb(object,fig,pos)
+if(object.pb_flag == 1 && (isempty(object.grid_pb) || ~ishghandle(object.grid_pb)))
+    object.grid_pb = uicontrol('style','push',...
+        'units','pix',...
+        'string','+',...
+        'HorizontalAlign','left',...
+        'Parent',fig,...
+        'position',pos,...
+        'callback',@(src,event)pb_call(object,src,event));
+elseif (object.pb_flag == 1 && ~isempty(object.grid_pb))
+    set(object.grid_pb,'Position',pos);
+else
+end
+end
+
diff --git a/@Cell/set_pos.m b/@Cell/set_pos.m
index f4f6bef93e954a6ab5b0bac9331498b521ee5600..c66650468ff5f16271c4e8eec566f92b6f3acd96 100644
--- a/@Cell/set_pos.m
+++ b/@Cell/set_pos.m
@@ -1,15 +1,17 @@
 %% set_pos
-        %    allows accessor to set the position of the edit box for the
-        %    cell.
-        % inputs:
-        %   object:Cell - Current Cell Object 
-        %   pos:[double double double double] - the new position of the
-        %   cell
-        % outputs;
-        %   none
-        function [] = set_pos(object,pos)
-            if (~isempty(object.cond))
-                set(object.cond,'position',pos);
-            end
-        end
-        
+%    allows accessor to set the position of the edit box for the
+%    cell.
+% inputs:
+%   object:Cell - Current Cell Object
+%   pos:[double double double double] - the new position of the
+%   cell
+% outputs;
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = set_pos(object,pos)
+if (~isempty(object.cond))
+    set(object.cond,'position',pos);
+end
+end
+
diff --git a/@Data/Data.m b/@Data/Data.m
index 8e9991fac95da495522ac95cb6a9847a49c89e38..0bb9f7fd880aed3db7ace9d262ce81900f18c044 100644
--- a/@Data/Data.m
+++ b/@Data/Data.m
@@ -1,3 +1,5 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 classdef Data < handle
     % This class will store the data for each table, ideally to seperate
     % out the data from the gui and logic.
@@ -30,7 +32,7 @@ classdef Data < handle
         end
         
     end
-      
+    
     
 end
 
diff --git a/@Data/clone.m b/@Data/clone.m
index 0c647c96bb2e1b557ecb83c19c2299fa347045ae..e8536b20fe5e3c3c111bc52cd4a7d776b1e3e553 100644
--- a/@Data/clone.m
+++ b/@Data/clone.m
@@ -1,41 +1,42 @@
- %% clone
-        %   creates copy of a data object, which involves copying
-        %   properties and calling individual clone functions on objects if
-        %   necessary.
-        % inputs:
-        %   object:Data - current object
-        %   handle:Data - the handle to the block
-        % outputs:
-        %   copy:Data - copy of the current block, perhaps with a new name
-        function copy = clone(object,handle)
-            % assume that dialog is closed
-            if ~object.valid
-                copy = [];
-                return;
-            end
-            copy = Data();
-            if ~isempty(handle)
-            copy.function_name =   get(handle,'Name');
-            else
-                copy.function_name = '';
-            end
-            copy.function_inputs = object.function_inputs;
-            copy.checked = object.checked;
-            copy.settings = object.settings;
-            copy.multi_mode = object.multi_mode;
-            
-            copy.Grid2 = Grid(2,[]);
-            copy.Grid1 = Grid(1,[]);
-            copy.Grid0 = RGrid(copy.Grid1,copy.Grid2);
-            copy.Grid1.set_rGrid(copy.Grid0);
-            copy.Grid2.set_rGrid(copy.Grid0);
-            
+%% clone
+%   creates copy of a data object, which involves copying
+%   properties and calling individual clone functions on objects if
+%   necessary.
+% inputs:
+%   object:Data - current object
+%   handle:Data - the handle to the block
+% outputs:
+%   copy:Data - copy of the current block, perhaps with a new name
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function copy = clone(object,handle)
+% assume that dialog is closed
+if ~object.valid
+    copy = [];
+    return;
+end
+copy = Data();
+if ~isempty(handle)
+    copy.function_name =   get(handle,'Name');
+else
+    copy.function_name = '';
+end
+copy.function_inputs = object.function_inputs;
+copy.checked = object.checked;
+copy.settings = object.settings;
+copy.multi_mode = object.multi_mode;
 
-            object.Grid2.clone(copy.Grid2,object.Grid2.grid_index,[])
-            object.Grid1.clone(copy.Grid1,object.Grid1.grid_index,[])
-            
-            object.copy_results(copy)
+copy.Grid2 = Grid(2,[]);
+copy.Grid1 = Grid(1,[]);
+copy.Grid0 = RGrid(copy.Grid1,copy.Grid2);
+copy.Grid1.set_rGrid(copy.Grid0);
+copy.Grid2.set_rGrid(copy.Grid0);
+
+
+object.Grid2.clone(copy.Grid2,object.Grid2.grid_index,[])
+object.Grid1.clone(copy.Grid1,object.Grid1.grid_index,[])
+
+object.copy_results(copy)
+
+end
 
-        end
-        
-        
\ No newline at end of file
diff --git a/@Data/copy_results.m b/@Data/copy_results.m
index 52c325021796cd25575d9f1f5e38b89637834929..27785ecb6f9f774a627cf49ac6783d7cca10923a 100644
--- a/@Data/copy_results.m
+++ b/@Data/copy_results.m
@@ -1,20 +1,21 @@
- %% copy_results
-        %   copy the results text of the current grid0 to a destination
-        %   Data's grid0 object.
-        % inputs:
-        %   object:Data - current object
-        %   dest:Data - destination object to save results text to, results
-        %   grid is assumed to already be set up.
-        % outputs:
-        %   none
-        function [] = copy_results(object,dest)
-            for i=1:size(dest.Grid0.Cells,2)
-                for j=1:size(object.Grid0.Cells,2)
-                    if (strcmp(object.Grid0.Cells(j).Cell1.cond_text,dest.Grid0.Cells(i).Cell1.cond_text) && strcmp(object.Grid0.Cells(j).Cell2.cond_text,dest.Grid0.Cells(i).Cell2.cond_text))
-                        dest.Grid0.Cells(i).result_text = object.Grid0.Cells(j).result_text;
-                    end
-                end
-            end
+%% copy_results
+%   copy the results text of the current grid0 to a destination
+%   Data's grid0 object.
+% inputs:
+%   object:Data - current object
+%   dest:Data - destination object to save results text to, results
+%   grid is assumed to already be set up.
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = copy_results(object,dest)
+for i=1:size(dest.Grid0.Cells,2)
+    for j=1:size(object.Grid0.Cells,2)
+        if (strcmp(object.Grid0.Cells(j).Cell1.cond_text,dest.Grid0.Cells(i).Cell1.cond_text) && strcmp(object.Grid0.Cells(j).Cell2.cond_text,dest.Grid0.Cells(i).Cell2.cond_text))
+            dest.Grid0.Cells(i).result_text = object.Grid0.Cells(j).result_text;
         end
-        
-   
\ No newline at end of file
+    end
+end
+end
+
diff --git a/@Data/getData.m b/@Data/getData.m
index 6eefdbb5ae2697992a391f435ef27c19596e0027..5bb6f0c545ada5a7605fd9bd32b7d554f9ee06da 100644
--- a/@Data/getData.m
+++ b/@Data/getData.m
@@ -1,22 +1,23 @@
-   %% getData
-        %   resturn individual properties to calling function
-        % inputs:
-        %   object:Data - current object
-        % outputs:
-        %   grid0:Grid - Results Grid
-        %   grid1:Grid - Left Grid
-        %   grid2:Grid - Top Grid
-        %   name:string - Function name
-        %   inputs:string - input string
-        %   checked:boolean - typecheck status
-        function [grid0, grid1, grid2, name, inputs, checked, multi] = getData(object)
-            grid0 = object.Grid0;
-            grid1 = object.Grid1;
-            grid2 = object.Grid2;
-            name = object.function_name;
-            inputs = object.function_inputs;
-            checked = object.checked;
-            multi = object.multi_mode;
-        end
-    
-    
\ No newline at end of file
+%% getData
+%   resturn individual properties to calling function
+% inputs:
+%   object:Data - current object
+% outputs:
+%   grid0:Grid - Results Grid
+%   grid1:Grid - Left Grid
+%   grid2:Grid - Top Grid
+%   name:string - Function name
+%   inputs:string - input string
+%   checked:boolean - typecheck status
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [grid0, grid1, grid2, name, inputs, checked, multi] = getData(object)
+grid0 = object.Grid0;
+grid1 = object.Grid1;
+grid2 = object.Grid2;
+name = object.function_name;
+inputs = object.function_inputs;
+checked = object.checked;
+multi = object.multi_mode;
+end
+
diff --git a/@Data/init.m b/@Data/init.m
index 2c20b6ce4345551d46bfbba5c0e781a85af4ad54..019fc8294a3e40f28663a8e5fe718bacb174403f 100644
--- a/@Data/init.m
+++ b/@Data/init.m
@@ -1,19 +1,20 @@
-  %% init
-        %   initialize the data to some default values and objects
-        % inputs:
-        %   object:Data - current object
-        % outputs:
-        %   none
-        function [] = init(object)
-            object.Grid2 = Grid(2,[]);
-            object.Grid1 = Grid(1,[]);
-            object.Grid0 = RGrid(object.Grid1,object.Grid2);
-            object.Grid1.set_rGrid(object.Grid0);
-            object.Grid2.set_rGrid(object.Grid0);
-            object.Grid2.new_Cell;
-            object.Grid1.new_Cell;
-            object.checked = 0;
-            object.multi_mode = 0;
-        end
-        
-     
\ No newline at end of file
+%% init
+%   initialize the data to some default values and objects
+% inputs:
+%   object:Data - current object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = init(object)
+object.Grid2 = Grid(2,[]);
+object.Grid1 = Grid(1,[]);
+object.Grid0 = RGrid(object.Grid1,object.Grid2);
+object.Grid1.set_rGrid(object.Grid0);
+object.Grid2.set_rGrid(object.Grid0);
+object.Grid2.new_Cell;
+object.Grid1.new_Cell;
+object.checked = 0;
+object.multi_mode = 0;
+end
+
diff --git a/@Data/save.m b/@Data/save.m
index b61ac014140510d4e33e02867467f818da741f1b..51ddaa5f737fe98ce8d9270a2419ff7677c81df3 100644
--- a/@Data/save.m
+++ b/@Data/save.m
@@ -1,10 +1,12 @@
-     %% save
-        %   saves the current data object to an external file
-        % inputs:
-        %   object:Data - current Data object
-        % outputs:
-        %   none
-        function [] = save(object)
-            filename = [ object.function_name '.table'];
-            save(filename,'object');
-        end
+%% save
+%   saves the current data object to an external file
+% inputs:
+%   object:Data - current Data object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = save(object)
+filename = [ object.function_name '.table'];
+save(filename,'object');
+end
diff --git a/@Data/setData.m b/@Data/setData.m
index 23628a9f7bee6d206bda2092686bfdf0acbe2f28..1083886b8f9667d7eed68c3aeee564d25b814887 100644
--- a/@Data/setData.m
+++ b/@Data/setData.m
@@ -1,23 +1,24 @@
-  %% setData
-        %   set the object properties, used when copying and other places
-        % inputs:
-        %   object:Data - current object
-        %   grid0:Grid - Results Grid
-        %   grid1:Grid - Left Grid
-        %   grid2:Grid - Top Grid
-        %   name:string - Function name
-        %   inputs:string - input string
-        %   checked:boolean - typecheck status
-        % outputs:
-        %   none
-        function [] = setData(object, grid0, grid1, grid2, name, inputs, checked, multi)
-            object.Grid0 = grid0;
-            object.Grid1 = grid1;
-            object.Grid2 = grid2;
-            object.function_name = name;
-            object.function_inputs = inputs;
-            object.checked = checked;
-            object.multi_mode = multi;
-        end
-        
-      
\ No newline at end of file
+%% setData
+%   set the object properties, used when copying and other places
+% inputs:
+%   object:Data - current object
+%   grid0:Grid - Results Grid
+%   grid1:Grid - Left Grid
+%   grid2:Grid - Top Grid
+%   name:string - Function name
+%   inputs:string - input string
+%   checked:boolean - typecheck status
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = setData(object, grid0, grid1, grid2, name, inputs, checked, multi)
+object.Grid0 = grid0;
+object.Grid1 = grid1;
+object.Grid2 = grid2;
+object.function_name = name;
+object.function_inputs = inputs;
+object.checked = checked;
+object.multi_mode = multi;
+end
+
diff --git a/@Data/setvalues.m b/@Data/setvalues.m
index 48f7b9eb935907fd4d233328caa75794cc21f90c..1af97742a04d01bcdb39c656af861afb627f3161 100644
--- a/@Data/setvalues.m
+++ b/@Data/setvalues.m
@@ -1,12 +1,13 @@
 %% setvalues
-        %   set the settings property to a settings object
-        % inputs:
-        %   object:Data - current object
-        %   settings:Settings - settings object to save
-        % outputs:
-        %   none
-        function [] = setvalues(object,settings)
-            object.settings = settings;
-        end
-        
-       
\ No newline at end of file
+%   set the settings property to a settings object
+% inputs:
+%   object:Data - current object
+%   settings:Settings - settings object to save
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = setvalues(object,settings)
+object.settings = settings;
+end
+
diff --git a/@Data/valid.m b/@Data/valid.m
index e2d19930fe9de2513d9601575b10da6d29a7cb17..244e401548514f88075bab2c619fa2b0673edccb 100644
--- a/@Data/valid.m
+++ b/@Data/valid.m
@@ -1,24 +1,25 @@
-    %% valid
-        %   determine if a given data object is valid for use or not
-        % inputs:
-        %   object:Data - current object
-        % outputs:
-        %   valid:boolean - 0 if not valid, 1 if valid
-        function valid = valid(object)
-            if isempty(object.Grid0)
-                valid = 0;
-                return
-            end
-            if isempty(object.Grid1)
-                valid = 0;
-                return
-            end
-            if isempty(object.Grid2)
-                valid = 0;
-                return
-            end
-            valid = 1;
-        
-        end
-        
-       
\ No newline at end of file
+%% valid
+%   determine if a given data object is valid for use or not
+% inputs:
+%   object:Data - current object
+% outputs:
+%   valid:boolean - 0 if not valid, 1 if valid
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function valid = valid(object)
+if isempty(object.Grid0)
+    valid = 0;
+    return
+end
+if isempty(object.Grid1)
+    valid = 0;
+    return
+end
+if isempty(object.Grid2)
+    valid = 0;
+    return
+end
+valid = 1;
+
+end
+
diff --git a/@EMLGenerator/EMLGenerator.m b/@EMLGenerator/EMLGenerator.m
index a51b82dce9b899b8b8dd1c1282e14f4dddccb752..24a4710de036481665ed794c6ed6c06c46b6a3f5 100644
--- a/@EMLGenerator/EMLGenerator.m
+++ b/@EMLGenerator/EMLGenerator.m
@@ -1,7 +1,9 @@
+
 classdef EMLGenerator < handle
     %UNTITLED Summary of this class goes here
     %   Detailed explanation goes here
-    
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification    
     properties
         data = [];
         datatype = [];
@@ -9,13 +11,13 @@ classdef EMLGenerator < handle
     end
     
     methods(Static)
-   revised_input = parse_inputs(input_string)
-         
+        revised_input = parse_inputs(input_string)
+        
         
         
         converted = type_convert(name,type,expression)
-         
-
+        
+        
         
     end
     
diff --git a/@EMLGenerator/generate_eml_code.m b/@EMLGenerator/generate_eml_code.m
index 3ae8eb2b1e3bbe1a0fa893fadc0153a1fcc534a0..4844f3412307e0a32f3ae8c20dde78e609465ef0 100644
--- a/@EMLGenerator/generate_eml_code.m
+++ b/@EMLGenerator/generate_eml_code.m
@@ -1,17 +1,18 @@
- %% generate_eml_code
-        %    generates the embedded matlab code by calling other methods in
-        %    this class
-        % inputs:
-        %   object:EMLGenerator - current object
-        % outputs:
-        %   code:string - string of eml code
-        function code = generate_eml_code(object)
-            code = [];
-            code = [code object.generate_preamble];
-            code = [code object.generate_eml_cond(object.data.Grid1,object.data.Grid2,0)];
-            
-        end
-        
-          
-        
-        
\ No newline at end of file
+%% generate_eml_code
+%    generates the embedded matlab code by calling other methods in
+%    this class
+% inputs:
+%   object:EMLGenerator - current object
+% outputs:
+%   code:string - string of eml code
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function code = generate_eml_code(object)
+code = [];
+code = [code object.generate_preamble];
+code = [code object.generate_eml_cond(object.data.Grid1,object.data.Grid2,0)];
+
+end
+
+
+
diff --git a/@EMLGenerator/generate_eml_cond.m b/@EMLGenerator/generate_eml_cond.m
index a70b27897a06e55ec0e48bdddfe9c963b9c543ae..11989d4be8b5e7371c37371b5b0c10dbb7ed6923 100644
--- a/@EMLGenerator/generate_eml_cond.m
+++ b/@EMLGenerator/generate_eml_cond.m
@@ -1,99 +1,101 @@
 %% generate_eml_cond
-        %    generate the embedded matlab for a conditon grid, recursive
-        %    function, will call horizontal generator if finds conditions
-        %    in that grid.
-        % inputs:
-        %   object:EMLGenerator - current object
-        %   g1:Grid - Grid 1
-        %   g2:Grid - Grid 2
-        %   depth:int - integer representing recursion dept for formating
-        %   use
-        % outputs:
-        %   code:string - string of eml code
-        function code = generate_eml_cond(object,g1,g2,depth)
-        
-        
-   
-        
-             space = '';
-            for i=1:depth
-                space = [space sprintf('  ')];
-            end
-          g1cond1 = g1.cells(1).cond_text;
-          g2cond1 = g2.cells(1).cond_text;
-          code = [];
-          %1D horizontal
-          if(~isempty(g1cond1) && isempty(g2cond1))
-              if object.data.multi_mode == 0
-            code = [code object.generate_eml_horizontal(g1,g2.cells(1),depth)];
-              else
-                  code = [code object.generate_eml_multi(g1,g2.cells(1),depth)];
-              end
-          % something in vertical column
-          else
+%    generate the embedded matlab for a conditon grid, recursive
+%    function, will call horizontal generator if finds conditions
+%    in that grid.
+% inputs:
+%   object:EMLGenerator - current object
+%   g1:Grid - Grid 1
+%   g2:Grid - Grid 2
+%   depth:int - integer representing recursion dept for formating
+%   use
+% outputs:
+%   code:string - string of eml code
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function code = generate_eml_cond(object,g1,g2,depth)
 
-            elsecell = [];
-            for i=1:size(g2.cells,2)
-                g2cond = g2.cells(i).cond_text;
-                % condition string of otherwise corresponds to an else
-                % statement, we allow this statement to be in any order
-                % in the cells of the grid, so we need to find where it
-                % is, if it exists.
-                if (strcmp(g2cond,'otherwise'))
-                    elsecell = g2.cells(i);
-                    found = 1;
-                    continue
-                end
-                if (i == 1)
-                    code = [code sprintf('%sif(%s)\n',space,(strtrim(char(g2.cells(i).cond_text))))];
-                else
-                    code = [code sprintf('%selseif(%s)\n',space,(strtrim(char(g2.cells(i).cond_text))))];
-                end
 
-                if(~isempty(g2.cells(i).subgrid))
-                    code = [code object.generate_eml_cond(g1,g2.cells(i).subgrid,depth+1)];
-                else
-                    if (~isempty(g1cond1))
-                        if object.data.multi_mode == 0
-                        code = [code object.generate_eml_horizontal(g1,g2.cells(i),depth+1)];
-                          else
-                              code = [code object.generate_eml_multi(g1,g2.cells(i),depth+1)];
-                          end
-                         %code = [code object.generate_eml_horizontal(g1,g2.cells(i),depth+1)];
-                    else    
-                        
-                        resultcell = object.data.Grid0.search_return(g1.cells(1),g2.cells(i));
-                        if(~isempty(resultcell))
-                                code = [code sprintf('%soutput = %s;\n',[space '  '],EMLGenerator.type_convert('output',object.datatype,strtrim(char(resultcell.result_text))))];
 
-                        else
-                        end
-                    end
-                end
-              
-            end
-           if(~isempty(elsecell))
-                 %resultcell = object.Grid0.search_return(elsecell,elsecell);
-                code = [code sprintf('%selse\n',space)];
 
-                if(~isempty(elsecell.subgrid))
-                    code = [code object.generate_eml_cond(g1,elsecell.subgrid,depth) sprintf('\n')];
+space = '';
+for i=1:depth
+    space = [space sprintf('  ')];
+end
+g1cond1 = g1.cells(1).cond_text;
+g2cond1 = g2.cells(1).cond_text;
+code = [];
+%1D horizontal
+if(~isempty(g1cond1) && isempty(g2cond1))
+    if object.data.multi_mode == 0
+        code = [code object.generate_eml_horizontal(g1,g2.cells(1),depth)];
+    else
+        code = [code object.generate_eml_multi(g1,g2.cells(1),depth)];
+    end
+    % something in vertical column
+else
+    
+    elsecell = [];
+    for i=1:size(g2.cells,2)
+        g2cond = g2.cells(i).cond_text;
+        % condition string of otherwise corresponds to an else
+        % statement, we allow this statement to be in any order
+        % in the cells of the grid, so we need to find where it
+        % is, if it exists.
+        if (strcmp(g2cond,'otherwise'))
+            elsecell = g2.cells(i);
+            found = 1;
+            continue
+        end
+        if (i == 1)
+            code = [code sprintf('%sif(%s)\n',space,(strtrim(char(g2.cells(i).cond_text))))];
+        else
+            code = [code sprintf('%selseif(%s)\n',space,(strtrim(char(g2.cells(i).cond_text))))];
+        end
+        
+        if(~isempty(g2.cells(i).subgrid))
+            code = [code object.generate_eml_cond(g1,g2.cells(i).subgrid,depth+1)];
+        else
+            if (~isempty(g1cond1))
+                if object.data.multi_mode == 0
+                    code = [code object.generate_eml_horizontal(g1,g2.cells(i),depth+1)];
                 else
-                    if (~isempty(g1cond1))
-                         code = [code object.generate_eml_horizontal(g1,elsecell,depth) sprintf('\n')];
-                    else    
+                    code = [code object.generate_eml_multi(g1,g2.cells(i),depth+1)];
+                end
+                %code = [code object.generate_eml_horizontal(g1,g2.cells(i),depth+1)];
+            else
                 
-                        resultcell = object.data.Grid0.search_return(g1.cells(1),elsecell);
-                        if(~isempty(resultcell))
-                             code = [code sprintf('%soutput = %s;\n',[space '  '],EMLGenerator.type_convert('output',object.datatype,strtrim(char(resultcell.result_text))))];
-                                
-                        end
-                    end
+                resultcell = object.data.Grid0.search_return(g1.cells(1),g2.cells(i));
+                if(~isempty(resultcell))
+                    code = [code sprintf('%soutput = %s;\n',[space '  '],EMLGenerator.type_convert('output',object.datatype,strtrim(char(resultcell.result_text))))];
+                    
+                else
                 end
+            end
+        end
+        
+    end
+    if(~isempty(elsecell))
+        %resultcell = object.Grid0.search_return(elsecell,elsecell);
+        code = [code sprintf('%selse\n',space)];
+        
+        if(~isempty(elsecell.subgrid))
+            code = [code object.generate_eml_cond(g1,elsecell.subgrid,depth) sprintf('\n')];
+        else
+            if (~isempty(g1cond1))
+                code = [code object.generate_eml_horizontal(g1,elsecell,depth) sprintf('\n')];
+            else
                 
-           end
-
-         code = [code sprintf('%send\n',space)];
-
-          end
-        end
\ No newline at end of file
+                resultcell = object.data.Grid0.search_return(g1.cells(1),elsecell);
+                if(~isempty(resultcell))
+                    code = [code sprintf('%soutput = %s;\n',[space '  '],EMLGenerator.type_convert('output',object.datatype,strtrim(char(resultcell.result_text))))];
+                    
+                end
+            end
+        end
+        
+    end
+    
+    code = [code sprintf('%send\n',space)];
+    
+end
+end
\ No newline at end of file
diff --git a/@EMLGenerator/generate_eml_horizontal.m b/@EMLGenerator/generate_eml_horizontal.m
index abc6d94ce42e12193e771bbc27b4b48a8934a3b9..f4d19ba2d4f0a22cb4c5464024525e1e205fc4b9 100644
--- a/@EMLGenerator/generate_eml_horizontal.m
+++ b/@EMLGenerator/generate_eml_horizontal.m
@@ -1,53 +1,54 @@
 %% generate_eml_horizontal
-        %    generate the embedded matlab code for grid1, seperated from
-        %    the code for grid2 since for a 2d table grid1 conditions will
-        %    be sub conditions of grid2 conditions
-        % inputs:
-        %   object:EMLGenerator - current object
-        %   g1:Grid - Grid 1
-        %   g2_cell:Cell - Cell for which grid1 is sub conditon of
-        %   depth:int - integer representing recursion dept for formating
-        %   use
-        % outputs:
-        %   code:string - string of eml code
-        function code = generate_eml_horizontal(object,g1,g2_cell,depth)
-            space = '';
-            for i=1:depth
-                space = [space sprintf('  ')];
-            end
-        code = [];
+%    generate the embedded matlab code for grid1, seperated from
+%    the code for grid2 since for a 2d table grid1 conditions will
+%    be sub conditions of grid2 conditions
+% inputs:
+%   object:EMLGenerator - current object
+%   g1:Grid - Grid 1
+%   g2_cell:Cell - Cell for which grid1 is sub conditon of
+%   depth:int - integer representing recursion dept for formating
+%   use
+% outputs:
+%   code:string - string of eml code
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function code = generate_eml_horizontal(object,g1,g2_cell,depth)
+space = '';
+for i=1:depth
+    space = [space sprintf('  ')];
+end
+code = [];
 
-            elsecell = [];
-            for i=1:size(g1.cells,2)
-                g1cond = g1.cells(i).cond_text;
-                % condition string of otherwise corresponds to an else
-                % statement, we allow this statement to be in any order
-                % in the cells of the grid, so we need to find where it
-                % is, if it exists.
-                if (strcmp(g1cond,'otherwise'))
-                    elsecell = g1.cells(i);
-                    found = 1;
-                    continue
-                end
-                if (i == 1)
-                    code = [code sprintf('%sif(%s)\n',space,strtrim(char(g1.cells(i).cond_text)))];
-                else
-                    code = [code sprintf('%selseif(%s)\n',space,strtrim(char(g1.cells(i).cond_text)))];
-                end
-                resultcell = object.data.Grid0.search_return(g1.cells(i),g2_cell);
-                if(~isempty(resultcell))
-                     code = [code sprintf('%soutput = %s;\n',[space '  '],EMLGenerator.type_convert('output',object.datatype,strtrim(char(resultcell.result_text))))];
-                                      
-                else
-                end
-            end
-            if(~isempty(elsecell))
-                 resultcell = object.data.Grid0.search_return(elsecell,g2_cell);
-                code = [code sprintf('%selse\n%soutput = %s;\n',space,[space '  '],EMLGenerator.type_convert('output',object.datatype,strtrim(char(resultcell.result_text))))];
+elsecell = [];
+for i=1:size(g1.cells,2)
+    g1cond = g1.cells(i).cond_text;
+    % condition string of otherwise corresponds to an else
+    % statement, we allow this statement to be in any order
+    % in the cells of the grid, so we need to find where it
+    % is, if it exists.
+    if (strcmp(g1cond,'otherwise'))
+        elsecell = g1.cells(i);
+        found = 1;
+        continue
+    end
+    if (i == 1)
+        code = [code sprintf('%sif(%s)\n',space,strtrim(char(g1.cells(i).cond_text)))];
+    else
+        code = [code sprintf('%selseif(%s)\n',space,strtrim(char(g1.cells(i).cond_text)))];
+    end
+    resultcell = object.data.Grid0.search_return(g1.cells(i),g2_cell);
+    if(~isempty(resultcell))
+        code = [code sprintf('%soutput = %s;\n',[space '  '],EMLGenerator.type_convert('output',object.datatype,strtrim(char(resultcell.result_text))))];
+        
+    else
+    end
+end
+if(~isempty(elsecell))
+    resultcell = object.data.Grid0.search_return(elsecell,g2_cell);
+    code = [code sprintf('%selse\n%soutput = %s;\n',space,[space '  '],EMLGenerator.type_convert('output',object.datatype,strtrim(char(resultcell.result_text))))];
+    
+end
+code = [code sprintf('%send\n',space)];
 
-            end
-            code = [code sprintf('%send\n',space)];
+end
 
-        end
-        
-        
\ No newline at end of file
diff --git a/@EMLGenerator/generate_preamble.m b/@EMLGenerator/generate_preamble.m
index fe56f3b747fcaa4c4a9f1117844c14a82e01cea8..6d819f0001845840ce58445e1466648ebed29483 100644
--- a/@EMLGenerator/generate_preamble.m
+++ b/@EMLGenerator/generate_preamble.m
@@ -1,68 +1,69 @@
 %% generate_preamble
-        %    generates the preamble for the eml code, the preamble is
-        %    everything before the first if statement, this is seperated
-        %    out to make the code simpler. 
-        % inputs:
-        %   object:EMLGenerator - current object
-        % outputs:
-        %   code:string - string of eml code
-        function code = generate_preamble(object)
-         
-                code = [];
-                function_name = EMLGenerator.parse_inputs(object.data.function_name);
-                %generate input list
-                parsed_input = EMLGenerator.parse_inputs(object.data.function_inputs);
-                input = [];
-                for i= 1:size(parsed_input,2)
-                    input = [input char(parsed_input{i}(1))];
-                    if i ~= size(parsed_input,2)
-                        input = [input ',']
-                    end
-                end
-                
-                output = [];
-                if (object.data.multi_mode == 1)
-                    for i=1:size(object.data.Grid1.cells,2)
-                         parsed_output = EMLGenerator.parse_inputs(strtrim(char(object.data.Grid1.cells(i).cond_text)));
+%    generates the preamble for the eml code, the preamble is
+%    everything before the first if statement, this is seperated
+%    out to make the code simpler.
+% inputs:
+%   object:EMLGenerator - current object
+% outputs:
+%   code:string - string of eml code
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function code = generate_preamble(object)
 
-                            output = [output char(parsed_output{1}(1))];
-                           
-                        if i ~= size(object.data.Grid1.cells,2)
-                        output = [output ',']
-                    end
-                    end
-                else
-                    output = 'output';
-                end
-                
-                code = sprintf('function [%s] = %s(%s)\n%s\n',output,char(function_name{1}(1)),input,'%%#eml');
-                % simulink forces you to have an output for all execution paths
-                % since it can't compute completness and disjointness we need
-                % to have a default value, if the user builds the table
-                % properly the default value will never be used. since
-                % different types might have a different default value, the
-                % temporary solution is just to use one of the outputs from our
-                % table, we will use the first cell because it is
-                % guaranteed to
-                % be filled in, regardless of the dimensionality of the table.
-                
-                if (object.data.multi_mode == 1)
-                    for i=1:size(object.data.Grid1.cells,2)
-                         parsed_output = EMLGenerator.parse_inputs(strtrim(char(object.data.Grid1.cells(i).cond_text)));
+code = [];
+function_name = EMLGenerator.parse_inputs(object.data.function_name);
+%generate input list
+parsed_input = EMLGenerator.parse_inputs(object.data.function_inputs);
+input = [];
+for i= 1:size(parsed_input,2)
+    input = [input char(parsed_input{i}(1))];
+    if i ~= size(parsed_input,2)
+        input = [input ',']
+    end
+end
 
-                            output_str = char(parsed_output{1}(1));
-                           
-                            code = [code sprintf('%s=%s;\n',output_str,EMLGenerator.type_convert(output_str,object.datatype,char(object.data.Grid0.Cells(i).result_text)))];
+output = [];
+if (object.data.multi_mode == 1)
+    for i=1:size(object.data.Grid1.cells,2)
+        parsed_output = EMLGenerator.parse_inputs(strtrim(char(object.data.Grid1.cells(i).cond_text)));
+        
+        output = [output char(parsed_output{1}(1))];
+        
+        if i ~= size(object.data.Grid1.cells,2)
+            output = [output ',']
+        end
+    end
+else
+    output = 'output';
+end
 
-                    end
-                    
-                else
-                    test  = 'output';
-                    output_string = EMLGenerator.type_convert(test,object.datatype,char(object.data.Grid0.Cells(1).result_text) );
-                      code = [code sprintf('output=%s;\n', output_string )];
+code = sprintf('function [%s] = %s(%s)\n%s\n',output,char(function_name{1}(1)),input,'%%#eml');
+% simulink forces you to have an output for all execution paths
+% since it can't compute completness and disjointness we need
+% to have a default value, if the user builds the table
+% properly the default value will never be used. since
+% different types might have a different default value, the
+% temporary solution is just to use one of the outputs from our
+% table, we will use the first cell because it is
+% guaranteed to
+% be filled in, regardless of the dimensionality of the table.
 
-                end
+if (object.data.multi_mode == 1)
+    for i=1:size(object.data.Grid1.cells,2)
+        parsed_output = EMLGenerator.parse_inputs(strtrim(char(object.data.Grid1.cells(i).cond_text)));
         
-        end
+        output_str = char(parsed_output{1}(1));
         
-       
\ No newline at end of file
+        code = [code sprintf('%s=%s;\n',output_str,EMLGenerator.type_convert(output_str,object.datatype,char(object.data.Grid0.Cells(i).result_text)))];
+        
+    end
+    
+else
+    test  = 'output';
+    output_string = EMLGenerator.type_convert(test,object.datatype,char(object.data.Grid0.Cells(1).result_text) );
+    code = [code sprintf('output=%s;\n', output_string )];
+    
+end
+
+end
+
diff --git a/@EMLGenerator/parse_inputs.m b/@EMLGenerator/parse_inputs.m
index da89204d669583db519bea9a2eb55026afa86498..94a43adebfae7954a897179e2e83846ca641b89f 100644
--- a/@EMLGenerator/parse_inputs.m
+++ b/@EMLGenerator/parse_inputs.m
@@ -1,51 +1,53 @@
 %% parse_inputs
-        %    parse an input string and return the list of inputs as a
-        %    matrix with accompaning type or indicating an error
-        % inputs:
-        %   input_string:string - string containing input string, comma
-        %   delimited list of variables, each variable may or may not be
-        %   followed by a colon then a type string.
-        % outputs:
-        %   revised_input:matrix - matrix containing parsed list, ex.
-        %   [{'x' 'int'};{'y'};{ 'z:{x:real|x>1}' }]
-        function revised_input = parse_inputs(input_string)
-            revised_input = [];
-            input_string2 = reshape(input_string',1,size(input_string,1)*size(input_string,2));
-           inputs = regexprep(input_string2,'\n','');
-           inputs = regexp(inputs,',','split');
-           
-           % need to be careful here because pvs dependant types can have
-           % :'s in them
-           
-           % find the first :, any thing before this is considered the
-           % variable any thing following is considered the type
-           c_locations = regexp(inputs,':','start');
-           for i= 1:size(inputs,2)
-               sub_input = [];
-                if size(c_locations{i},2) == 0
-                    sub_input{1} = inputs{i};
-                    new_inputs{i} = sub_input;
-                else
-                    sub_input{1} = inputs{i}(1:c_locations{i}(1)-1);
-                    sub_input{2} = inputs{i}(c_locations{i}(1)+1:end);
-                    new_inputs{i} = sub_input;
-                    %new_inputs{i}(1) = inputs{i}(1:c_locations{i}(1))
-                    %new_inputs{i}(2) = inputs{i}(c_locations{i}(1):end)
-                end
-           end
-           
-           %inputs = regexp(inputs,':','split')
-           
-           for i=1:size(new_inputs,2)
-                new_inputs{i}(1) = regexprep(new_inputs{i}(1),'\s','');
+%    parse an input string and return the list of inputs as a
+%    matrix with accompaning type or indicating an error
+% inputs:
+%   input_string:string - string containing input string, comma
+%   delimited list of variables, each variable may or may not be
+%   followed by a colon then a type string.
+% outputs:
+%   revised_input:matrix - matrix containing parsed list, ex.
+%   [{'x' 'int'};{'y'};{ 'z:{x:real|x>1}' }]
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function revised_input = parse_inputs(input_string)
+revised_input = [];
+input_string2 = reshape(input_string',1,size(input_string,1)*size(input_string,2));
+inputs = regexprep(input_string2,'\n','');
+inputs = regexp(inputs,',','split');
 
-                valid = regexp(new_inputs{i}(1),'[a-zA-Z][_a-zA-Z0-9]*','match');
-                if isempty(char(new_inputs{i}(1))) || ~strcmp(new_inputs{i}(1),valid{1})
-                    new_inputs{i}(2) = {'error'};
-                    %revised_input = cat(2,revised_input,[char(inputs{i}(1)); 'error'])
-                end
-           end 
-           if isempty(revised_input)
-               revised_input = new_inputs;
-           end
-        end
\ No newline at end of file
+% need to be careful here because pvs dependant types can have
+% :'s in them
+
+% find the first :, any thing before this is considered the
+% variable any thing following is considered the type
+c_locations = regexp(inputs,':','start');
+for i= 1:size(inputs,2)
+    sub_input = [];
+    if size(c_locations{i},2) == 0
+        sub_input{1} = inputs{i};
+        new_inputs{i} = sub_input;
+    else
+        sub_input{1} = inputs{i}(1:c_locations{i}(1)-1);
+        sub_input{2} = inputs{i}(c_locations{i}(1)+1:end);
+        new_inputs{i} = sub_input;
+        %new_inputs{i}(1) = inputs{i}(1:c_locations{i}(1))
+        %new_inputs{i}(2) = inputs{i}(c_locations{i}(1):end)
+    end
+end
+
+%inputs = regexp(inputs,':','split')
+
+for i=1:size(new_inputs,2)
+    new_inputs{i}(1) = regexprep(new_inputs{i}(1),'\s','');
+    
+    valid = regexp(new_inputs{i}(1),'[a-zA-Z][_a-zA-Z0-9]*','match');
+    if isempty(char(new_inputs{i}(1))) || ~strcmp(new_inputs{i}(1),valid{1})
+        new_inputs{i}(2) = {'error'};
+        %revised_input = cat(2,revised_input,[char(inputs{i}(1)); 'error'])
+    end
+end
+if isempty(revised_input)
+    revised_input = new_inputs;
+end
+end
\ No newline at end of file
diff --git a/@EMLGenerator/set_datatype.m b/@EMLGenerator/set_datatype.m
index b96a791649266a996da90f2d73e8fe3e22eb4552..50561bcd1e315edbb447b1efe78816214977a4f0 100644
--- a/@EMLGenerator/set_datatype.m
+++ b/@EMLGenerator/set_datatype.m
@@ -1,12 +1,13 @@
 %% set_datatype
-        %    set the datatype property based inputed string based on the simulink settings
-        % inputs:
-        %   object:EMLGenerator - current object
-        %   type:string - string of datatype conversion
-        % outputs:
-        %   none 
-        function [] = set_datatype(object,type)
-            object.datatype = type;
-        end
-        
-        
\ No newline at end of file
+%    set the datatype property based inputed string based on the simulink settings
+% inputs:
+%   object:EMLGenerator - current object
+%   type:string - string of datatype conversion
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = set_datatype(object,type)
+object.datatype = type;
+end
+
diff --git a/@EMLGenerator/type_convert.m b/@EMLGenerator/type_convert.m
index dcd3e157e4fbe452c09b2671197540120126e511..2a14d467a734fdacbcf1cd1cf667215e141d931b 100644
--- a/@EMLGenerator/type_convert.m
+++ b/@EMLGenerator/type_convert.m
@@ -6,6 +6,8 @@
 %   expression:string - string of the expression
 % outputs:
 %   converted:string - type conversion string
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function converted = type_convert(name,type,expression)
 if ~isempty(type)
     for i=1:size(type,1)
diff --git a/@GUI/GUI.m b/@GUI/GUI.m
index 31d072832f3de8c806dd0be91a527d172be64056..1acd5745f06b3a1678d465497cdf460e8583c709 100644
--- a/@GUI/GUI.m
+++ b/@GUI/GUI.m
@@ -1,5 +1,7 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 classdef GUI < handle
-   
+    
     
     properties
         % vertical grid
@@ -54,7 +56,7 @@ classdef GUI < handle
         TableBlk = [];
         saved = [];
         validation_report_handle = [];
-                multi_type = 0;
+        multi_type = 0;
         multi_mode = [];
         multi_grp = [];
         multi_opt_reg = [];
@@ -82,8 +84,8 @@ classdef GUI < handle
     end
     
     methods(Static)
-      msgbox_scroll(msg)
-          
+        msgbox_scroll(msg)
+        
     end
 end
 
diff --git a/@GUI/about_call.m b/@GUI/about_call.m
index f14fd25654dc3d033c5db23ba477fca4437f7c1f..91e4ed06957bcef9029833976b56b8e1cf6ffb3c 100644
--- a/@GUI/about_call.m
+++ b/@GUI/about_call.m
@@ -1,3 +1,11 @@
+%% about_call
+%   Displays a messagebox with information about the current
+% inputs:
+%   object:PVS_checker - GUI object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [] = about_call(object,src,event)
     msgbox(sprintf('Table Toolbox v%s\nCopyright 2010\nColin Eles\nMcMaster Center for Software Certification',object.version),'About Table Tool','modal');
 end
\ No newline at end of file
diff --git a/@GUI/check_call.m b/@GUI/check_call.m
index ab6cbbb671f90d4741c0d3ed688d01fe69b404ac..f4f0adca4b94c3e7e0ac8ebe7780d7411a76ea9b 100644
--- a/@GUI/check_call.m
+++ b/@GUI/check_call.m
@@ -1,32 +1,34 @@
-        %% check_call
-        %   callback function for check pushbutton. compiles a message of
-        %   the errors that were detected in each of the grids. outputs the
-        %   message to users via a msgbox.
-        % inputs:
-        %   object:GUI - current GUI object
-        %   src:double - source of the callback calling
-        %   event:eventdata - event that triggered the callback
-        % outputs:
-        %   none
-        function error = check_call(object,src,event)
-            error = 0;
-         
-            msg = object.check_inputs;
-            if (isempty(msg))
-                set(object.function_inputs_control,'BackgroundColor',[1 1 1])
-                msg = object.check_grid_condition(object.Grid2);
-                if object.multi_mode == 0
-                    msg = [msg object.check_grid_condition(object.Grid1)];
-                end
-                msg = [msg object.check_grid_result(object.Grid0)];
-            else
-                set(object.function_inputs_control,'BackgroundColor',[0.92 0.65 0.65])
-            end
-            
-            if ~isempty(msg)
-                msgbox(msg);
-                error = 1;
-            end
-            
-        end
-        
+%% check_call
+%   callback function for check pushbutton. compiles a message of
+%   the errors that were detected in each of the grids. outputs the
+%   message to users via a msgbox.
+% inputs:
+%   object:GUI - current GUI object
+%   src:double - source of the callback calling
+%   event:eventdata - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function error = check_call(object,src,event)
+error = 0;
+
+msg = object.check_inputs;
+if (isempty(msg))
+    set(object.function_inputs_control,'BackgroundColor',[1 1 1])
+    msg = object.check_grid_condition(object.Grid2);
+    if object.multi_mode == 0
+        msg = [msg object.check_grid_condition(object.Grid1)];
+    end
+    msg = [msg object.check_grid_result(object.Grid0)];
+else
+    set(object.function_inputs_control,'BackgroundColor',[0.92 0.65 0.65])
+end
+
+if ~isempty(msg)
+    msgbox(msg);
+    error = 1;
+end
+
+end
+
diff --git a/@GUI/check_grid_condition.m b/@GUI/check_grid_condition.m
index 3baa772bcf5f2ba0aae151bccd42e543b23c1f52..4cabe247f10c53ac249dc845caab61962eb68858 100644
--- a/@GUI/check_grid_condition.m
+++ b/@GUI/check_grid_condition.m
@@ -1,58 +1,60 @@
-        %% check_grid
-        %    check_grid will recursively loop through all the cells of a
-        %    grid and call the check_matlab_syntax function for each of the
-        %    strings in the cells. if there is an error the cell will
-        %    change colours to alert the user where the problem is.
-        % inputs:
-        %   object:GUI - current GUI object
-        %   grid:Grid - Grid object being checked
-        % outputs:
-        %   none
-        function msg = check_grid_condition(object,grid)
-            msg = [];
-            for i = 1:size(grid.cells,2)
-                
-                 error = '';
-                string = get(grid.cells(i).cond,'String');
-                
-                if ( strcmp(string,'') || isempty(string)) && i == 1 && isempty(grid.parent_grid) && size(grid.cells,2) == 1
-                    break
-                end
-                
-                % if the string is empty indicating that the table is 1
-                % dimensional or the string is "otherwise" skip the syntax
-                % checking.
-                if(~isempty(string) && ~strcmp(string,'otherwise'))
-                    error = object.check_matlab_syntax_condition(char(string),0);
-                end
-                 if isempty(error)
-                    if (strcmp(string,'') || isempty(string))
-                    error = 'Cell is empty';
-                    end
-                end
-                if ~isempty(error)
-                    % generate the message string
-                    msg = [msg sprintf('\n')];                    
-
-                    msg = [msg 'Condtion -> ' char(string) sprintf('\n')];
-                    msg = [msg error sprintf('\n')];
-
-                   % set tooltip string of cell to error msg
-                    set(grid.cells(i).cond,'TooltipString',error)
-                     % change background colour
-                    grid.cells(i).flag_cell(1);
-                else
-                    % reset tooltip and colour if no error found
-                    set(grid.cells(i).cond,'TooltipString','')
-                    grid.cells(i).flag_cell(0);
-                   
-
-                end
-                % recurse through subgrid
-                if(~isempty(grid.cells(i).subgrid))
-                    msg = [msg object.check_grid_condition(grid.cells(i).subgrid)];
-                end
-
-                   
-            end
+%% check_grid
+%    check_grid will recursively loop through all the cells of a
+%    grid and call the check_matlab_syntax function for each of the
+%    strings in the cells. if there is an error the cell will
+%    change colours to alert the user where the problem is.
+% inputs:
+%   object:GUI - current GUI object
+%   grid:Grid - Grid object being checked
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function msg = check_grid_condition(object,grid)
+msg = [];
+for i = 1:size(grid.cells,2)
+    
+    error = '';
+    string = get(grid.cells(i).cond,'String');
+    
+    if ( strcmp(string,'') || isempty(string)) && i == 1 && isempty(grid.parent_grid) && size(grid.cells,2) == 1
+        break
+    end
+    
+    % if the string is empty indicating that the table is 1
+    % dimensional or the string is "otherwise" skip the syntax
+    % checking.
+    if(~isempty(string) && ~strcmp(string,'otherwise'))
+        error = object.check_matlab_syntax_condition(char(string),0);
+    end
+    if isempty(error)
+        if (strcmp(string,'') || isempty(string))
+            error = 'Cell is empty';
         end
+    end
+    if ~isempty(error)
+        % generate the message string
+        msg = [msg sprintf('\n')];
+        
+        msg = [msg 'Condtion -> ' char(string) sprintf('\n')];
+        msg = [msg error sprintf('\n')];
+        
+        % set tooltip string of cell to error msg
+        set(grid.cells(i).cond,'TooltipString',error)
+        % change background colour
+        grid.cells(i).flag_cell(1);
+    else
+        % reset tooltip and colour if no error found
+        set(grid.cells(i).cond,'TooltipString','')
+        grid.cells(i).flag_cell(0);
+        
+        
+    end
+    % recurse through subgrid
+    if(~isempty(grid.cells(i).subgrid))
+        msg = [msg object.check_grid_condition(grid.cells(i).subgrid)];
+    end
+    
+    
+end
+end
diff --git a/@GUI/check_grid_result.m b/@GUI/check_grid_result.m
index c25622c9861966f38255efc8dfbe29e35a4f0958..9b54bb754f21672289f4c3f497b2ce7370d8d4bc 100644
--- a/@GUI/check_grid_result.m
+++ b/@GUI/check_grid_result.m
@@ -1,39 +1,41 @@
-        %% check_grid_result
-        %   Similar to above function check_grid_result, will loop through
-        % the cells of the output grid, unline check_grid, does not need to
-        % recurse.
-        % inputs:
-        %   object:GUI - current GUI object
-        %   grid:RGrid - RGrid object to be checked
-        % outputs:
-        %   none
-        function msg = check_grid_result(object,grid)
-            msg = [];
-            for i = 1:size(grid.Cells,2)
-                error = '';
-                string = get(grid.Cells(i).result,'String');
-                
-
-                error = object.check_matlab_syntax_condition(char(string),1);
-                if isempty(error)
-                    if (strcmp(string,'') || isempty(string))
-                    error = 'Cell is empty';
-                    end
-                end
-                if ~isempty(error)
-                     msg = [msg sprintf('\n')];                    
-
-                    msg = [msg 'Result -> ' char(string) sprintf('\n')];
-                    msg = [msg error sprintf('\n')];
-
-
-                    set(grid.Cells(i).result,'TooltipString',error)
-                    grid.Cells(i).flag_cell(1)
-                else
-                    set(grid.Cells(i).result,'TooltipString','')
-                    grid.Cells(i).flag_cell(0)
-                end
-                
-            end
+%% check_grid_result
+%   Similar to above function check_grid_result, will loop through
+% the cells of the output grid, unline check_grid, does not need to
+% recurse.
+% inputs:
+%   object:GUI - current GUI object
+%   grid:RGrid - RGrid object to be checked
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function msg = check_grid_result(object,grid)
+msg = [];
+for i = 1:size(grid.Cells,2)
+    error = '';
+    string = get(grid.Cells(i).result,'String');
+    
+    
+    error = object.check_matlab_syntax_condition(char(string),1);
+    if isempty(error)
+        if (strcmp(string,'') || isempty(string))
+            error = 'Cell is empty';
         end
+    end
+    if ~isempty(error)
+        msg = [msg sprintf('\n')];
         
+        msg = [msg 'Result -> ' char(string) sprintf('\n')];
+        msg = [msg error sprintf('\n')];
+        
+        
+        set(grid.Cells(i).result,'TooltipString',error)
+        grid.Cells(i).flag_cell(1)
+    else
+        set(grid.Cells(i).result,'TooltipString','')
+        grid.Cells(i).flag_cell(0)
+    end
+    
+end
+end
+
diff --git a/@GUI/check_inputs.m b/@GUI/check_inputs.m
index 2879c3c9db5b7781a2a4773d010d26347e6a08de..770f1d58e4f2fa6682288ee2148896a107949c55 100644
--- a/@GUI/check_inputs.m
+++ b/@GUI/check_inputs.m
@@ -1,21 +1,23 @@
 
-        
-      
-        %% check_inputs
-        %    ensure that the inputs are proper variable names, and that the
-        %    input string parses properly
-        % inputs:
-        %   object:GUI - current GUI object
-        % outputs:
-        %   error:string - error string if variable is not inputed properly
-        function error = check_inputs(object)
-            parsed_input = EMLGenerator.parse_inputs(get(object.function_inputs_control,'string'));
-            error = [];
-            for i=1:size(parsed_input,2)
-                if(size(parsed_input{i},2) == 2)
-                    if (strcmp(parsed_input{i}(2),'error'))
-                        error = [error sprintf('%s is not a valid variable name\n',char(parsed_input{i}(1))) ];
-                    end
-                end  
-            end
+
+
+%% check_inputs
+%    ensure that the inputs are proper variable names, and that the
+%    input string parses properly
+% inputs:
+%   object:GUI - current GUI object
+% outputs:
+%   error:string - error string if variable is not inputed properly
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function error = check_inputs(object)
+parsed_input = EMLGenerator.parse_inputs(get(object.function_inputs_control,'string'));
+error = [];
+for i=1:size(parsed_input,2)
+    if(size(parsed_input{i},2) == 2)
+        if (strcmp(parsed_input{i}(2),'error'))
+            error = [error sprintf('%s is not a valid variable name\n',char(parsed_input{i}(1))) ];
         end
+    end
+end
+end
diff --git a/@GUI/check_matlab_syntax_condition.m b/@GUI/check_matlab_syntax_condition.m
index 7e549cc3be1405b08e71687a2090d602c6b42c72..dc602838cf2b9e1c50cd712620092030acbfe4e9 100644
--- a/@GUI/check_matlab_syntax_condition.m
+++ b/@GUI/check_matlab_syntax_condition.m
@@ -1,61 +1,63 @@
-        %% check_matlab_syntax
-        %   this function will check that a string is valid matlab syntax
-        %   for the context that it is in. we need to build up the
-        %   expression which involves initiallizeing the input variables to
-        %   a dummy value and wraping an if statement around conditionals
-        % inputs:
-        %   object:GUI - current GUI object
-        %   string:string - string to be checked
-        %   result:boolean - false if the string is a conditoin true if
-        %       the string is an output statement
-        % outputs:
-        %   error:string - string containing the error message, empty if
-        %   there is no error
-        function error = check_matlab_syntax_condition(object,string,result)
-           % split the list of inputs to get inputs seperatly
-           
-           parsed_input = EMLGenerator.parse_inputs(get(object.function_inputs_control,'string'));
-           check_string = [];
-           
-           % initialize inputs to zero
-           % functions are assumed to be total, so 0 is just for 
-           % convienence
-           for i=1:size(parsed_input,2)
-                % set to zero
-                check_string = [check_string sprintf('%s=0;\n',char(parsed_input{i}(1)))];
-                
-                   
-           end
-           if ~result
-                % the string is a condition we need to evaulate it as it
-                % will be used in the code, as in order for an if statement
-                % to be valid the condition must evaulate to a numeric
-                % value not a structure or something else. we need to have
-                % the 1 in there as a dummy output, which is necesary for
-                % an if statement to be valid in matlab.
-                check_string = [check_string 'if (' string sprintf(')\n1;\nend')];
-           else
-               % the string is an output statement we can just evaulate the
-               % string on its own.
-               check_string = [check_string string ';' sprintf('\n')];
-           end
-           % attempt to evaluate the string catch the error.
-           try
-               eval(check_string);
-               error = [];
-           catch exception
-               error = exception.message;
-                % attempt to make one of the common errors slightly less
-                % cryptic.
-               if(strcmp(exception.identifier,'MATLAB:m_invalid_lhs_of_assignment'))
-                   error = [error sprintf('\nTo check equality use ==')];
-               end
-           end
-        end
-        
-        
-     
-        
-       
-
-        
+%% check_matlab_syntax
+%   this function will check that a string is valid matlab syntax
+%   for the context that it is in. we need to build up the
+%   expression which involves initiallizeing the input variables to
+%   a dummy value and wraping an if statement around conditionals
+% inputs:
+%   object:GUI - current GUI object
+%   string:string - string to be checked
+%   result:boolean - false if the string is a conditoin true if
+%       the string is an output statement
+% outputs:
+%   error:string - string containing the error message, empty if
+%   there is no error
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function error = check_matlab_syntax_condition(object,string,result)
+% split the list of inputs to get inputs seperatly
+
+parsed_input = EMLGenerator.parse_inputs(get(object.function_inputs_control,'string'));
+check_string = [];
+
+% initialize inputs to zero
+% functions are assumed to be total, so 0 is just for
+% convienence
+for i=1:size(parsed_input,2)
+    % set to zero
+    check_string = [check_string sprintf('%s=0;\n',char(parsed_input{i}(1)))];
+    
+    
+end
+if ~result
+    % the string is a condition we need to evaulate it as it
+    % will be used in the code, as in order for an if statement
+    % to be valid the condition must evaulate to a numeric
+    % value not a structure or something else. we need to have
+    % the 1 in there as a dummy output, which is necesary for
+    % an if statement to be valid in matlab.
+    check_string = [check_string 'if (' string sprintf(')\n1;\nend')];
+else
+    % the string is an output statement we can just evaulate the
+    % string on its own.
+    check_string = [check_string string ';' sprintf('\n')];
+end
+% attempt to evaluate the string catch the error.
+try
+    eval(check_string);
+    error = [];
+catch exception
+    error = exception.message;
+    % attempt to make one of the common errors slightly less
+    % cryptic.
+    if(strcmp(exception.identifier,'MATLAB:m_invalid_lhs_of_assignment'))
+        error = [error sprintf('\nTo check equality use ==')];
+    end
+end
+end
+
+
+
+
+
+
+
diff --git a/@GUI/check_output_consistent.m b/@GUI/check_output_consistent.m
index 232413fd496e0633b547d18ca0ed6c84dee1c404..c67e2f177a09586d417514d62fda0534791aeb3a 100644
--- a/@GUI/check_output_consistent.m
+++ b/@GUI/check_output_consistent.m
@@ -1,6 +1,6 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function result = check_output_consistent( object )
-%UNTITLED Summary of this function goes here
-%   Detailed explanation goes here
 output_block_types = object.output_data_type;
 
 output_table = {};
diff --git a/@GUI/close_fig.m b/@GUI/close_fig.m
index 1f86ab92e15070371faf95bdb6adb9edfe3b48a6..af3dcd9789cc1f1a34df85ae88825a893495f976 100644
--- a/@GUI/close_fig.m
+++ b/@GUI/close_fig.m
@@ -1,26 +1,28 @@
-        %% close_fig
-        %    callback function that is called whenever the close button is
-        %    pressed. 
-        % inputs:
-        %   object - current GUI object
-        %   src - source of the callback calling
-        %   event - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = close_fig(object,src,event)
-            if (object.validation_report_handle ~= 0)
-                delete(object.validation_report_handle)
-            end
-            object.save_data;
-            object.Data.open = 0;
-            object.Data.fig = [];
-            delete(object.fig);
-            % remove reference to the old figure.
-            object.fig = [];
-            % in simulink mode
-            if(object.mode == 1)
-                parent = get_param(object.block_handle,'Parent');
-                open_system(parent);
-            end
-        end
-            
+%% close_fig
+%    callback function that is called whenever the close button is
+%    pressed.
+% inputs:
+%   object - current GUI object
+%   src - source of the callback calling
+%   event - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = close_fig(object,src,event)
+if (object.validation_report_handle ~= 0)
+    delete(object.validation_report_handle)
+end
+object.save_data;
+object.Data.open = 0;
+object.Data.fig = [];
+delete(object.fig);
+% remove reference to the old figure.
+object.fig = [];
+% in simulink mode
+if(object.mode == 1)
+    parent = get_param(object.block_handle,'Parent');
+    open_system(parent);
+end
+end
+
diff --git a/@GUI/create_std_text.m b/@GUI/create_std_text.m
index e5a4ba36ff2cfc8aeff2e268d931d2ca5a4f9208..d930207220577c1706405e352aaef02236edea72 100644
--- a/@GUI/create_std_text.m
+++ b/@GUI/create_std_text.m
@@ -1,31 +1,29 @@
+%% create_std_text
+%   function will create an edit text box used for conditons and
+%   results. we want these to be consistent so its easier for it to
+%   be in one function.
+% inputs:
+%   obj:GUI - current GUI object
+%   Parent:double - handle to parent figure
+%   position:[double double double double] - position to place edit
+%       box in.
+% outputs:
+%   control:double - handle pointing to newly created uicontrol
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function control = create_std_text(object, Parent, position)
+control = uicontrol('style','edit',...
+    'Parent',Parent,...
+    'units','pix',...
+    'position',position,...
+    'min',0,'max',1,...  % This is the key to multiline edits.
+    'string',{''},...
+    'Max',2.0,...
+    'Clipping','on',...
+    'fontweight','bold',...
+    'BackgroundColor',[1 1 1],...
+    'horizontalalign','center',...
+    'KeyPressFcn',@(src,event)textbox_callback(object,src,event),...
+    'fontsize',11);
+end
 
-       
-        
-        %% create_std_text
-        %   function will create an edit text box used for conditons and
-        %   results. we want these to be consistent so its easier for it to
-        %   be in one function.
-        % inputs:
-        %   obj:GUI - current GUI object
-        %   Parent:double - handle to parent figure
-        %   position:[double double double double] - position to place edit
-        %       box in.
-        % outputs:
-        %   control:double - handle pointing to newly created uicontrol
-        function control = create_std_text(object, Parent, position)
-            control = uicontrol('style','edit',...
-                'Parent',Parent,...
-                'units','pix',...
-                'position',position,...
-                'min',0,'max',1,...  % This is the key to multiline edits.
-                'string',{''},...
-                'Max',2.0,...
-                'Clipping','on',...
-                'fontweight','bold',...
-                'BackgroundColor',[1 1 1],...
-                'horizontalalign','center',...
-                'KeyPressFcn',@(src,event)textbox_callback(object,src,event),...
-                'fontsize',11);
-        end
-       
-        
\ No newline at end of file
diff --git a/@GUI/draw_allgrids.m b/@GUI/draw_allgrids.m
index 14e33baa6a5e70100cfc455bbccfe0638e1059b8..9b7d5a3f98da13f16b9f6cd765694b31dd417688 100644
--- a/@GUI/draw_allgrids.m
+++ b/@GUI/draw_allgrids.m
@@ -1,15 +1,17 @@
-        %% draw_allgrids
-        %    function will call the draw methods for each of the 3 grids.
-        % inputs:
-        %   obj:GUI - current GUI object
-        %   load:boolean - 0 if grid is being refreshed, 1 if grid is being
-        %       loaded for the firs time.
-        % outputs:
-        %   none
-        function [] = draw_allgrids(object,load)
-            object.draw_grid2(object.Grid2,load);
-            object.draw_grid1(object.Grid1,load);
-            
-            object.draw_grid0(object.Grid0,load);
-        end
-        
+%% draw_allgrids
+%    function will call the draw methods for each of the 3 grids.
+% inputs:
+%   obj:GUI - current GUI object
+%   load:boolean - 0 if grid is being refreshed, 1 if grid is being
+%       loaded for the firs time.
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = draw_allgrids(object,load)
+object.draw_grid2(object.Grid2,load);
+object.draw_grid1(object.Grid1,load);
+
+object.draw_grid0(object.Grid0,load);
+end
+
diff --git a/@GUI/draw_grid0.m b/@GUI/draw_grid0.m
index 9c7f1172062da4666951292e2472eb10618f69ac..a49ed91657692ff75f1c57e198135e375ad7acd3 100644
--- a/@GUI/draw_grid0.m
+++ b/@GUI/draw_grid0.m
@@ -1,36 +1,38 @@
-        %% draw_grid0
-        %   function will draw the output grid onto the figure  
-        % inputs:
-        %   obj:GUI - current GUI object
-        %   grid:Grid - grid to be drawn, should be grid on left.
-        %   load:boolean - 0 if grid is being refreshed, 1 if grid is being
-        %       loaded for the firs time.
-        % outputs:
-        %   none
-        function [] = draw_grid0(object,grid,load)
-            % ensure that the results grid is up to date.
-            grid.refresh();
-            for i=1:size(grid.Cells,2)
-                % get the x coordinate from the associated top grid cell,
-                % get the y coordinate from the associated right grid cell.
-                pos1 = grid.Cells(i).Cell1.get_pos;
-                pos2 = grid.Cells(i).Cell2.get_pos;
-                pos = [0 0 0 0];
-                pos(1) = pos1(1);
-                pos(2) = pos2(2);
-                pos(3) = pos1(3);
-                pos(4) = pos2(4);
-                if isempty(grid.Cells(i).result) || ~ishandle(grid.Cells(i).result)%load == 1
-                    
-                    grid.Cells(i).result = object.create_std_text(object.fig,pos);
-                    % if we are loading the cell, try to restore the text
-                    % that was saved using save_results.
-                    if load == 1
-                        set(grid.Cells(i).result,'String',grid.Cells(i).result_text);
-                    end
-                else
-                    set(grid.Cells(i).result,'position',pos);
-                end
-            end
-        end
+%% draw_grid0
+%   function will draw the output grid onto the figure
+% inputs:
+%   obj:GUI - current GUI object
+%   grid:Grid - grid to be drawn, should be grid on left.
+%   load:boolean - 0 if grid is being refreshed, 1 if grid is being
+%       loaded for the firs time.
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = draw_grid0(object,grid,load)
+% ensure that the results grid is up to date.
+grid.refresh();
+for i=1:size(grid.Cells,2)
+    % get the x coordinate from the associated top grid cell,
+    % get the y coordinate from the associated right grid cell.
+    pos1 = grid.Cells(i).Cell1.get_pos;
+    pos2 = grid.Cells(i).Cell2.get_pos;
+    pos = [0 0 0 0];
+    pos(1) = pos1(1);
+    pos(2) = pos2(2);
+    pos(3) = pos1(3);
+    pos(4) = pos2(4);
+    if isempty(grid.Cells(i).result) || ~ishandle(grid.Cells(i).result)%load == 1
         
+        grid.Cells(i).result = object.create_std_text(object.fig,pos);
+        % if we are loading the cell, try to restore the text
+        % that was saved using save_results.
+        if load == 1
+            set(grid.Cells(i).result,'String',grid.Cells(i).result_text);
+        end
+    else
+        set(grid.Cells(i).result,'position',pos);
+    end
+end
+end
+
diff --git a/@GUI/draw_grid1.m b/@GUI/draw_grid1.m
index c166b841e5f5984fedb3d5bfe6e5808593e63217..c0fabc6d316869accde3b13122dac9c23f1dc7db 100644
--- a/@GUI/draw_grid1.m
+++ b/@GUI/draw_grid1.m
@@ -1,86 +1,88 @@
-        %% draw_grid1
-        %     Draws the grid on the top onto the figure. the current
-        %     assumption is that the top grid does not have any subgrids, 
-        % inputs:
-        %   obj:GUI - current GUI object
-        %   grid:Grid - grid to be drawn, should be grid on top.
-        %   load:boolean - 0 if grid is being refreshed, 1 if grid is being
-        %       loaded for the firs time.
-        % outputs:
-        %   none
-        function [] = draw_grid1(object,grid,load)
-            % assumption grid 1 has no subgrids
-            pos = [];
-            for i=1:size(grid.cells,2)
-                % if we are in edit mode we need to shift over the cells to
-                % accomidate for the new grid buttons in the left grid.
-                if(object.edit == 1)
-                    pb_space = grid.cells(i).grid_push_width;
-                else
-                    pb_space = 0;
-                end
-                figpos = get(object.fig,'position');
-
-                % check if grid2 is empty, currently grid 2 will never be
-                % empty, may change in future though.
-                if (isempty(object.Grid2))      
-                    pos = [grid.cells(i).condition_text_x grid.cells(i).condition_text_y grid.cells(i).condition_text_width grid.cells(i).condition_text_height];
-                else
-                    pos = [grid.cells(i).condition_text_x+grid.cells(i).condition_text_width*object.Grid2.max_width(1) figpos(4)-object.header_height-grid.cells(i).condition_text_y-grid.cells(i).condition_text_height grid.cells(i).condition_text_width grid.cells(i).condition_text_height];
-                end
-                % set the x coordinate of the cell
-                pos(1) = pos(1) + (i-1)*grid.cells(i).condition_text_width + grid.cells(i).condition_text_offset + pb_space;
-                % if the edit box does not exist create it, if it does
-                % adjust it's position.
-                if (isempty(grid.cells(i).cond) || ~ishandle(grid.cells(i).cond))%load == 1)
-                    grid.cells(i).cond = object.create_std_text(object.fig,pos);
-                    if (load == 1)
-                        set(grid.cells(i).cond,'String',grid.cells(i).cond_text); 
-                    end
-                else
-                    grid.cells(i).set_pos(pos);
-                end
-                
-                if(object.edit == 0)
-                    string = get(grid.cells(i).cond,'String')
-                   if(isempty(string))
-                       set(grid.cells(i).cond,'Visible','off');
-                   end
-                else
-                    set(grid.cells(i).cond,'Visible','on');
-                end
-            end
-            % if we are in edit mode, draw the new and delete buttons at
-            % the right of the last cell
-            if( object.edit == 1)
-                pos(1) = pos(1) + pos(3);
-                pos(2) = pos(2) + 20;
-                pos(4) = 20;
-                pos(3) = 60;
-                grid.set_pb(object.fig,pos);
-                pos(2) = pos(2) - 20;
-                
-                grid.set_delete_pb(object.fig,pos);
-                set(grid.delete_cell_pb,'userdata',object);
-                set(grid.new_cell_pb,'userdata',object);
-            else
-                delete(grid.new_cell_pb)
-                grid.new_cell_pb = [];
-                delete(grid.delete_cell_pb)
-                grid.delete_cell_pb = [];
-            end
-            if object.edit ==1 || load == 1
-                fig_pos = get(object.fig,'position');
-                if(pos(1)+pos(3)>fig_pos(3))
-                    fig_pos(3) = pos(1)+pos(3);
-                    set(object.fig,'position',fig_pos);
-                elseif (pos(1) + pos(3)<object.fig_width)
-                    fig_pos(3) = object.fig_width;
-                    set(object.fig,'position',fig_pos);
-                elseif (pos(1) + pos(3)<fig_pos(3) && pos(1) +pos(3) >object.fig_width)
-                    fig_pos(3) = pos(1)+pos(3);
-                    set(object.fig,'position',fig_pos);
-                end
-            end
+%% draw_grid1
+%     Draws the grid on the top onto the figure. the current
+%     assumption is that the top grid does not have any subgrids,
+% inputs:
+%   obj:GUI - current GUI object
+%   grid:Grid - grid to be drawn, should be grid on top.
+%   load:boolean - 0 if grid is being refreshed, 1 if grid is being
+%       loaded for the firs time.
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = draw_grid1(object,grid,load)
+% assumption grid 1 has no subgrids
+pos = [];
+for i=1:size(grid.cells,2)
+    % if we are in edit mode we need to shift over the cells to
+    % accomidate for the new grid buttons in the left grid.
+    if(object.edit == 1)
+        pb_space = grid.cells(i).grid_push_width;
+    else
+        pb_space = 0;
+    end
+    figpos = get(object.fig,'position');
+    
+    % check if grid2 is empty, currently grid 2 will never be
+    % empty, may change in future though.
+    if (isempty(object.Grid2))
+        pos = [grid.cells(i).condition_text_x grid.cells(i).condition_text_y grid.cells(i).condition_text_width grid.cells(i).condition_text_height];
+    else
+        pos = [grid.cells(i).condition_text_x+grid.cells(i).condition_text_width*object.Grid2.max_width(1) figpos(4)-object.header_height-grid.cells(i).condition_text_y-grid.cells(i).condition_text_height grid.cells(i).condition_text_width grid.cells(i).condition_text_height];
+    end
+    % set the x coordinate of the cell
+    pos(1) = pos(1) + (i-1)*grid.cells(i).condition_text_width + grid.cells(i).condition_text_offset + pb_space;
+    % if the edit box does not exist create it, if it does
+    % adjust it's position.
+    if (isempty(grid.cells(i).cond) || ~ishandle(grid.cells(i).cond))%load == 1)
+        grid.cells(i).cond = object.create_std_text(object.fig,pos);
+        if (load == 1)
+            set(grid.cells(i).cond,'String',grid.cells(i).cond_text);
+        end
+    else
+        grid.cells(i).set_pos(pos);
+    end
+    
+    if(object.edit == 0)
+        string = get(grid.cells(i).cond,'String')
+        if(isempty(string))
+            set(grid.cells(i).cond,'Visible','off');
         end
-        
+    else
+        set(grid.cells(i).cond,'Visible','on');
+    end
+end
+% if we are in edit mode, draw the new and delete buttons at
+% the right of the last cell
+if( object.edit == 1)
+    pos(1) = pos(1) + pos(3);
+    pos(2) = pos(2) + 20;
+    pos(4) = 20;
+    pos(3) = 60;
+    grid.set_pb(object.fig,pos);
+    pos(2) = pos(2) - 20;
+    
+    grid.set_delete_pb(object.fig,pos);
+    set(grid.delete_cell_pb,'userdata',object);
+    set(grid.new_cell_pb,'userdata',object);
+else
+    delete(grid.new_cell_pb)
+    grid.new_cell_pb = [];
+    delete(grid.delete_cell_pb)
+    grid.delete_cell_pb = [];
+end
+if object.edit ==1 || load == 1
+    fig_pos = get(object.fig,'position');
+    if(pos(1)+pos(3)>fig_pos(3))
+        fig_pos(3) = pos(1)+pos(3);
+        set(object.fig,'position',fig_pos);
+    elseif (pos(1) + pos(3)<object.fig_width)
+        fig_pos(3) = object.fig_width;
+        set(object.fig,'position',fig_pos);
+    elseif (pos(1) + pos(3)<fig_pos(3) && pos(1) +pos(3) >object.fig_width)
+        fig_pos(3) = pos(1)+pos(3);
+        set(object.fig,'position',fig_pos);
+    end
+end
+end
+
diff --git a/@GUI/draw_grid2.m b/@GUI/draw_grid2.m
index b8191c1b4544532f1e0a5a4d48ce450ff39e9212..a1f5f57e895bb4255ad63d8b0af26cf485505c00 100644
--- a/@GUI/draw_grid2.m
+++ b/@GUI/draw_grid2.m
@@ -1,164 +1,166 @@
-        %% draw_grid2
-        %    Draws the grid on the left onto the figure.
-        % inputs:
-        %   obj:GUI - current GUI object
-        %   grid:Grid - grid to be drawn, should be grid on left.
-        %   load:boolean - 0 if grid is being refreshed, 1 if grid is being
-        %       loaded for the firs time.
-        % outputs:
-        %   none
-        function [] = draw_grid2(object,grid,load)
-            if (~isempty(grid))
-                % generate a random pastel colour for the background, each
-                % grid has a different colour to help with readability
-                grid_color = [0.9+0.1*rand(1) 0.9+0.1*rand(1) 0.9+0.1*rand(1)];
-                for i=1:size(grid.cells,2)
-                    % check if the grid is the root grid
-                    if (~isempty(grid.parent_cell))
-                        % grid is not the root grid location is derived
-                        % from its parent.
-                        parent_pos = grid.parent_cell.get_pos;
-                        if i == 1
-                            % if we are at the first cell, location is the
-                            % same as the parent but shifted to the right
-                            % by one cell
-                            pos(3) = grid.cells(i).width * grid.cells(i).condition_text_width;
-                            pos(4) = grid.cells(i).height * grid.cells(i).condition_text_height;
-                            pos(1) = parent_pos(1) + parent_pos(3);
-                            pos(2) = parent_pos(2) + parent_pos(4) - pos(4);
-                        else
-                            % if we are not at the first cell, location is
-                            % the same as the previous cell but we shift
-                            % down by one cell
-                            prev_pos = grid.cells(i-1).get_pos;
-                            pos(3) = grid.cells(i).width * grid.cells(i).condition_text_width;
-                            pos(4) = grid.cells(i).height * grid.cells(i).condition_text_height;
-                            pos(1) = parent_pos(1) + parent_pos(3);
-                            pos(2) = prev_pos(2) - pos(4);
-                            grid_color = grid.cells(i-1).color;
-                            
-                        end
-                    else
-                        % grid is the root grid.
-                        % position of the first cell is based on
-                        % condition_text_x, and condition_text_y, as well
-                        % as the height of the figure and header.
-                        figpos = get(object.fig,'position');
-                        pos = [grid.cells(i).condition_text_x figpos(4)-object.header_height-grid.cells(i).condition_text_y grid.cells(i).condition_text_width grid.cells(i).condition_text_height];
-                        if i == 1
-                            pos(1) = pos(1);
-                            pos(4) = grid.cells(i).height * grid.cells(i).condition_text_height;
-
-                            pos(2) = pos(2)-pos(4)-grid.cells(i).condition_text_height-grid.cells(i).condition_text_offset;
-                            pos(3) = grid.cells(i).width * grid.cells(i).condition_text_width;
-                            pos(4) = grid.cells(i).height * grid.cells(i).condition_text_height;
-                        else
-                            prev_pos = grid.cells(i-1).get_pos;
-                            pos(3) = grid.cells(i).width * grid.cells(i).condition_text_width;
-                            pos(4) = grid.cells(i).height * grid.cells(i).condition_text_height;
-                            pos(1) = pos(1);
-                            pos(2) = prev_pos(2) - pos(4);
-                            grid_color = grid.cells(i-1).color;
-                        end
-                    end
-                    
-                    
-                    % if the edit box does not exist, ie. it is just being
-                    % created or we are loading the figure
-                    if (isempty(grid.cells(i).cond) || ~ishandle(grid.cells(i).cond))%load == 1)
-                        % create the new edit box
-                        grid.cells(i).cond = object.create_std_text(object.fig,pos);
-                        % if cell is the first in the grid use the new
-                        % colour, else take the colour of the previous cell
-                        % in the grid.
-                        if(i==1)
-                        set(grid.cells(i).cond,'BackgroundColor',grid_color);
-                        else
-                            set(grid.cells(i).cond,'BackgroundColor',get(grid.cells(i-1).cond,'BackgroundColor'))
-                        end
-                        grid.cells(i).color = grid_color;
-                        % if we are loading the cell set the string of the
-                        % edit box to be the value that we saved as a
-                        % result of calling save_conditions
-                        if (load == 1)
-                            set(grid.cells(i).cond,'String',grid.cells(i).cond_text);
-                        end
-                    else
-                        % if the edit box is already created change is
-                        % position to newly determined position.
-                        grid.cells(i).set_pos(pos);
-                    end
-                    % determine if we want to draw the new subgrid buttons,
-                    % which is located to the right of each of the leaf
-                    % cells.
-                    if(grid.cells(i).pb_flag == 1 && object.edit == 1)
-                        pb_pos = pos;
-                        pb_pos(1) = pos(1)+pos(3);
-                        pb_pos(3) = grid.cells(i).grid_push_width;
-                        if (ishghandle(grid.cells(i).grid_pb))
-                            set(grid.cells(i).grid_pb,'Visible','on');
-                        end
-                        grid.cells(i).set_pb(object.fig,pb_pos)
-                        set(grid.cells(i).grid_pb,'UserData',object);
-                    elseif(grid.cells(i).pb_flag == 1 && object.edit ~= 1)
-                        if (ishghandle(grid.cells(i).grid_pb))
-                        set(grid.cells(i).grid_pb,'Visible','off')
-                        end
-                    end
-                    
-                    delete_pb_pos = [];
-                   
-                    
-                    % detemine if we want to draw the new cell buttons,
-                    % which are located at the botton of the set of cells.
-                    if (i == size(grid.cells,2) && object.edit == 1)
-                        new_pb_pos = pos;
-                        new_pb_pos(4) = grid.cells(i).condition_text_height/2;
-                        new_pb_pos(3) = pos(3)/2;
-                        new_pb_pos(2) = pos(2) - new_pb_pos(4);
-                        if (ishghandle(grid.new_cell_pb))
-                            set(grid.new_cell_pb,'Visible','on');
-                        end
-                        grid.set_pb(object.fig,new_pb_pos);
-                        set(grid.new_cell_pb,'userdata',object);
-                        
-                        
-                        delete_pb_pos = new_pb_pos;
-                        delete_pb_pos(1) = new_pb_pos(1) + new_pb_pos(3);
-                        if (ishghandle(grid.delete_cell_pb))
-                            set(grid.delete_cell_pb,'Visible','on');
-                        end
-                        grid.set_delete_pb(object.fig,delete_pb_pos);
-                        set(grid.delete_cell_pb,'userdata',object);
-                    elseif (i == size(grid.cells,2) && object.edit ~= 1)
-
-                        if (ishghandle(grid.new_cell_pb))
-                            set(grid.new_cell_pb,'Visible','off');
-                        end
-
-                        if (ishghandle(grid.delete_cell_pb))
-                            set(grid.delete_cell_pb,'Visible','off');
-                        end
-                    end
-                    
-                    
-                    
-                    % recursively draw the subgrid of the cell if it
-                    % exists.
-                    object.draw_grid2(grid.cells(i).subgrid,load);
-                    
-                     if(object.edit == 0)
-                        string = get(grid.cells(i).cond,'String')
-                       if(isempty(string))
-                           set(grid.cells(i).cond,'Visible','off');
-                       end
-                    else
-                        set(grid.cells(i).cond,'Visible','on');
-                    end
-                    
-                end
+%% draw_grid2
+%    Draws the grid on the left onto the figure.
+% inputs:
+%   obj:GUI - current GUI object
+%   grid:Grid - grid to be drawn, should be grid on left.
+%   load:boolean - 0 if grid is being refreshed, 1 if grid is being
+%       loaded for the firs time.
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = draw_grid2(object,grid,load)
+if (~isempty(grid))
+    % generate a random pastel colour for the background, each
+    % grid has a different colour to help with readability
+    grid_color = [0.9+0.1*rand(1) 0.9+0.1*rand(1) 0.9+0.1*rand(1)];
+    for i=1:size(grid.cells,2)
+        % check if the grid is the root grid
+        if (~isempty(grid.parent_cell))
+            % grid is not the root grid location is derived
+            % from its parent.
+            parent_pos = grid.parent_cell.get_pos;
+            if i == 1
+                % if we are at the first cell, location is the
+                % same as the parent but shifted to the right
+                % by one cell
+                pos(3) = grid.cells(i).width * grid.cells(i).condition_text_width;
+                pos(4) = grid.cells(i).height * grid.cells(i).condition_text_height;
+                pos(1) = parent_pos(1) + parent_pos(3);
+                pos(2) = parent_pos(2) + parent_pos(4) - pos(4);
+            else
+                % if we are not at the first cell, location is
+                % the same as the previous cell but we shift
+                % down by one cell
+                prev_pos = grid.cells(i-1).get_pos;
+                pos(3) = grid.cells(i).width * grid.cells(i).condition_text_width;
+                pos(4) = grid.cells(i).height * grid.cells(i).condition_text_height;
+                pos(1) = parent_pos(1) + parent_pos(3);
+                pos(2) = prev_pos(2) - pos(4);
+                grid_color = grid.cells(i-1).color;
                 
-       
+            end
+        else
+            % grid is the root grid.
+            % position of the first cell is based on
+            % condition_text_x, and condition_text_y, as well
+            % as the height of the figure and header.
+            figpos = get(object.fig,'position');
+            pos = [grid.cells(i).condition_text_x figpos(4)-object.header_height-grid.cells(i).condition_text_y grid.cells(i).condition_text_width grid.cells(i).condition_text_height];
+            if i == 1
+                pos(1) = pos(1);
+                pos(4) = grid.cells(i).height * grid.cells(i).condition_text_height;
+                
+                pos(2) = pos(2)-pos(4)-grid.cells(i).condition_text_height-grid.cells(i).condition_text_offset;
+                pos(3) = grid.cells(i).width * grid.cells(i).condition_text_width;
+                pos(4) = grid.cells(i).height * grid.cells(i).condition_text_height;
+            else
+                prev_pos = grid.cells(i-1).get_pos;
+                pos(3) = grid.cells(i).width * grid.cells(i).condition_text_width;
+                pos(4) = grid.cells(i).height * grid.cells(i).condition_text_height;
+                pos(1) = pos(1);
+                pos(2) = prev_pos(2) - pos(4);
+                grid_color = grid.cells(i-1).color;
+            end
+        end
+        
+        
+        % if the edit box does not exist, ie. it is just being
+        % created or we are loading the figure
+        if (isempty(grid.cells(i).cond) || ~ishandle(grid.cells(i).cond))%load == 1)
+            % create the new edit box
+            grid.cells(i).cond = object.create_std_text(object.fig,pos);
+            % if cell is the first in the grid use the new
+            % colour, else take the colour of the previous cell
+            % in the grid.
+            if(i==1)
+                set(grid.cells(i).cond,'BackgroundColor',grid_color);
+            else
+                set(grid.cells(i).cond,'BackgroundColor',get(grid.cells(i-1).cond,'BackgroundColor'))
+            end
+            grid.cells(i).color = grid_color;
+            % if we are loading the cell set the string of the
+            % edit box to be the value that we saved as a
+            % result of calling save_conditions
+            if (load == 1)
+                set(grid.cells(i).cond,'String',grid.cells(i).cond_text);
+            end
+        else
+            % if the edit box is already created change is
+            % position to newly determined position.
+            grid.cells(i).set_pos(pos);
+        end
+        % determine if we want to draw the new subgrid buttons,
+        % which is located to the right of each of the leaf
+        % cells.
+        if(grid.cells(i).pb_flag == 1 && object.edit == 1)
+            pb_pos = pos;
+            pb_pos(1) = pos(1)+pos(3);
+            pb_pos(3) = grid.cells(i).grid_push_width;
+            if (ishghandle(grid.cells(i).grid_pb))
+                set(grid.cells(i).grid_pb,'Visible','on');
+            end
+            grid.cells(i).set_pb(object.fig,pb_pos)
+            set(grid.cells(i).grid_pb,'UserData',object);
+        elseif(grid.cells(i).pb_flag == 1 && object.edit ~= 1)
+            if (ishghandle(grid.cells(i).grid_pb))
+                set(grid.cells(i).grid_pb,'Visible','off')
+            end
+        end
+        
+        delete_pb_pos = [];
+        
+        
+        % detemine if we want to draw the new cell buttons,
+        % which are located at the botton of the set of cells.
+        if (i == size(grid.cells,2) && object.edit == 1)
+            new_pb_pos = pos;
+            new_pb_pos(4) = grid.cells(i).condition_text_height/2;
+            new_pb_pos(3) = pos(3)/2;
+            new_pb_pos(2) = pos(2) - new_pb_pos(4);
+            if (ishghandle(grid.new_cell_pb))
+                set(grid.new_cell_pb,'Visible','on');
+            end
+            grid.set_pb(object.fig,new_pb_pos);
+            set(grid.new_cell_pb,'userdata',object);
+            
+            
+            delete_pb_pos = new_pb_pos;
+            delete_pb_pos(1) = new_pb_pos(1) + new_pb_pos(3);
+            if (ishghandle(grid.delete_cell_pb))
+                set(grid.delete_cell_pb,'Visible','on');
+            end
+            grid.set_delete_pb(object.fig,delete_pb_pos);
+            set(grid.delete_cell_pb,'userdata',object);
+        elseif (i == size(grid.cells,2) && object.edit ~= 1)
+            
+            if (ishghandle(grid.new_cell_pb))
+                set(grid.new_cell_pb,'Visible','off');
+            end
+            
+            if (ishghandle(grid.delete_cell_pb))
+                set(grid.delete_cell_pb,'Visible','off');
             end
         end
         
+        
+        
+        % recursively draw the subgrid of the cell if it
+        % exists.
+        object.draw_grid2(grid.cells(i).subgrid,load);
+        
+        if(object.edit == 0)
+            string = get(grid.cells(i).cond,'String')
+            if(isempty(string))
+                set(grid.cells(i).cond,'Visible','off');
+            end
+        else
+            set(grid.cells(i).cond,'Visible','on');
+        end
+        
+    end
+    
+    
+end
+end
+
diff --git a/@GUI/edit_tog_call.m b/@GUI/edit_tog_call.m
index 5e8197cb9f23addc528fcd2b45ea9f6bcd02766c..a21215b3feafda67429d889f9a4cd2e0242c8a6b 100644
--- a/@GUI/edit_tog_call.m
+++ b/@GUI/edit_tog_call.m
@@ -1,21 +1,23 @@
-        %% edit_tog_call
-        %    callback function for when the edit button is clicked. when
-        %    edit is toggled we want to redraw the table with the edit
-        %    button visible or not visible
-        % inputs:
-        %   object - current GUI object
-        %   src - source of the callback calling
-        %   event - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = edit_tog_call(object,src,event)
-            % save the value of the edit toggle
-            value = get(src,'Value');
-            object.edit = value;
-            % reset the widths and heights of the grid then redraw all the
-            % grids.
-            object.reset_wh;
-            object.draw_allgrids(0);
-            
-        end
-        
+%% edit_tog_call
+%    callback function for when the edit button is clicked. when
+%    edit is toggled we want to redraw the table with the edit
+%    button visible or not visible
+% inputs:
+%   object - current GUI object
+%   src - source of the callback calling
+%   event - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = edit_tog_call(object,src,event)
+% save the value of the edit toggle
+value = get(src,'Value');
+object.edit = value;
+% reset the widths and heights of the grid then redraw all the
+% grids.
+object.reset_wh;
+object.draw_allgrids(0);
+
+end
+
diff --git a/@GUI/evaluate_counter.m b/@GUI/evaluate_counter.m
index 5fc7aa1dee4ba9dffd0391f70f8a66693f262c64..7fd54d33bdf227156a86a2c3dd48890c581ff3f2 100644
--- a/@GUI/evaluate_counter.m
+++ b/@GUI/evaluate_counter.m
@@ -1,18 +1,19 @@
-        %% evaluate_counter
-        %    function will call the evaluation function for a given counter
-        %    example.
-        % inputs:
-        %   object:GUI - current GUI object
-        %   counter:string - string representing the counter example, ie. 
-        %       'x = 3\ny = 5'
-        % outputs:
-        %   none
-        function [] = evaluate_counter(object,counter)
-            
-            problem = object.evaluate_counter_grid(object.Grid2, counter);
-            if(~problem)
-                object.evaluate_counter_grid(object.Grid1, counter)
-            end
-        end
-        
-        
\ No newline at end of file
+%% evaluate_counter
+%    function will call the evaluation function for a given counter
+%    example.
+% inputs:
+%   object:GUI - current GUI object
+%   counter:string - string representing the counter example, ie.
+%       'x = 3\ny = 5'
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = evaluate_counter(object,counter)
+
+problem = object.evaluate_counter_grid(object.Grid2, counter);
+if(~problem)
+    object.evaluate_counter_grid(object.Grid1, counter)
+end
+end
+
diff --git a/@GUI/evaluate_counter_grid.m b/@GUI/evaluate_counter_grid.m
index 19cb3edf4f15db9ad3e66374f2e6e1e9ff339925..1990023975100f072857cae61c6ece3145f47475 100644
--- a/@GUI/evaluate_counter_grid.m
+++ b/@GUI/evaluate_counter_grid.m
@@ -1,86 +1,88 @@
 %% evaluate_counter_grid
-        %    function will evaluate a counter example for a given grid.
-        % inputs:
-        %   object:GUI - current GUI object
-        %   grid:Grid - the grid to evaluate
-        %   counter:string - string representing the counter example, ie. 
-        %       'x = 3\ny = 5'
-        % outputs:
-        %   problem:boolean - 1 if grid has overlapping or underspecified
-        %       cells, 0 if not.
-        function problem = evaluate_counter_grid(object,grid,counter)
-        % split the list of inputs to get inputs seperatly
-           inputs = get(object.function_inputs_control,'String');
-           inputs2 = [];
-           for i=1:size(inputs,1)
-               inputs2 = [inputs2 inputs(i,:)]
-           end
-           inputs2 = regexprep(inputs2,'\s','');        
-           inputs = regexp(inputs2,',','split');
-           check_string = [];
-           
-           % keep track of the number of condtitions that evaulate to true
-           true_conds = 0;
-           sub_problem = 0;
-           problem = 0;
-           empty_cell = 0;
-           % initialize inputs to zero
-           % functions are assumed to be total, so 0 is just for 
-           % convienence
-           for i=1:size(inputs,2)
-                % set to zero
+%    function will evaluate a counter example for a given grid.
+% inputs:
+%   object:GUI - current GUI object
+%   grid:Grid - the grid to evaluate
+%   counter:string - string representing the counter example, ie.
+%       'x = 3\ny = 5'
+% outputs:
+%   problem:boolean - 1 if grid has overlapping or underspecified
+%       cells, 0 if not.
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function problem = evaluate_counter_grid(object,grid,counter)
+% split the list of inputs to get inputs seperatly
+inputs = get(object.function_inputs_control,'String');
+inputs2 = [];
+for i=1:size(inputs,1)
+    inputs2 = [inputs2 inputs(i,:)]
+end
+inputs2 = regexprep(inputs2,'\s','');
+inputs = regexp(inputs2,',','split');
+check_string = [];
+
+% keep track of the number of condtitions that evaulate to true
+true_conds = 0;
+sub_problem = 0;
+problem = 0;
+empty_cell = 0;
+% initialize inputs to zero
+% functions are assumed to be total, so 0 is just for
+% convienence
+for i=1:size(inputs,2)
+    % set to zero
+    
+    %need to parse the types out of the inputs
+    inputi = regexp(char(inputs(i)),'\w*','match','once');
+    check_string = [check_string sprintf('%s=0;\n',char(inputi))];
+end
+
+check_string = [check_string counter sprintf('\n')];
+for i=1:size(grid.cells,2)
+    condition_string = get(grid.cells(i).cond,'string');
+    if(~isempty(condition_string))
+        
+        eval([check_string  'result =(' char(condition_string) ');'])
+        if(result == 0)
+            grid.cells(i).flag_cell(1);
+        else
+            true_conds = true_conds + 1;
+            
+            grid.cells(i).flag_cell(2);
+        end
+    else
+        empty_cell = 1;
+    end
+end
+
+if (true_conds == 1)
+    for i=1:size(grid.cells,2)
+        condition_string = get(grid.cells(i).cond,'string');
+        if(~isempty(condition_string))
+            
+            eval([check_string  'result =(' char(condition_string) ');'])
+            if(result == 0)
+                grid.cells(i).flag_cell(1);
+            else
                 
-                %need to parse the types out of the inputs
-                inputi = regexp(char(inputs(i)),'\w*','match','once');
-                check_string = [check_string sprintf('%s=0;\n',char(inputi))];
-           end
-           
-           check_string = [check_string counter sprintf('\n')];
-           for i=1:size(grid.cells,2)
-                condition_string = get(grid.cells(i).cond,'string');
-                if(~isempty(condition_string))
-                   
-                    eval([check_string  'result =(' char(condition_string) ');'])
-                    if(result == 0)
-                        grid.cells(i).flag_cell(1);
-                    else
-                        true_conds = true_conds + 1;
-                        
-                        grid.cells(i).flag_cell(2);
-                    end
-                else
-                    empty_cell = 1;
+                if (~isempty(grid.cells(i).subgrid))
+                    sub_problem = object.evaluate_counter_grid(grid.cells(i).subgrid,counter);
                 end
-           end
-           
-           if (true_conds == 1)
-               for i=1:size(grid.cells,2)
-                    condition_string = get(grid.cells(i).cond,'string');
-                    if(~isempty(condition_string))
+                grid.cells(i).flag_cell(2);
+            end
+        else
+            empty_cell = 1;
+        end
+    end
+end
+
+
+if (true_conds ~= 1 || sub_problem == 1)
+    problem = 1;
+end
 
-                        eval([check_string  'result =(' char(condition_string) ');'])
-                        if(result == 0)
-                            grid.cells(i).flag_cell(1);
-                        else
+if (empty_cell)
+    problem = 0;
+end
 
-                            if (~isempty(grid.cells(i).subgrid))
-                                sub_problem = object.evaluate_counter_grid(grid.cells(i).subgrid,counter);
-                            end
-                            grid.cells(i).flag_cell(2);
-                        end
-                    else
-                        empty_cell = 1;
-                    end
-               end
-           end
-           
-           
-           if (true_conds ~= 1 || sub_problem == 1)
-               problem = 1;
-           end
-           
-           if (empty_cell)
-               problem = 0;
-           end
-           
-        end
\ No newline at end of file
+end
\ No newline at end of file
diff --git a/@GUI/help_call.m b/@GUI/help_call.m
index c295aad036d3e433a3f61cb0a1e620a2c4692b61..907b5836eeb59129ed010b8239fc678ba2ad1fba 100644
--- a/@GUI/help_call.m
+++ b/@GUI/help_call.m
@@ -1,3 +1,12 @@
+%% help_call
+%   opens up the help browser and displays the help file for this program
+% inputs:
+%   object:PVS_checker - PVS_checker object
+% outputs:
+%   status:boolean - 0 if pvs file has been checked, 1 if it has
+%   not
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [] = help_call(object,src,event)
     web(fullfile(fileparts(which('TTdiag')),'html','html','TT_help.html'),'-helpbrowser')
 end
\ No newline at end of file
diff --git a/@GUI/init.m b/@GUI/init.m
index d3b03b8d6d2127450578852f4fe89f308a503385..1050fcc98321de03e0bb4c31a26dcdefb24dce38 100644
--- a/@GUI/init.m
+++ b/@GUI/init.m
@@ -1,222 +1,223 @@
 %% init
-        %   initialize the gui
-        % inputs:
-        %   obj:GUI - GUI object
-        % outputs:
-        %   none
-        function [] = init(object)
-            
-            % create the handles for the gui objects
-            if object.mode == 1
-                name = get_param(object.block_handle,'Name');
-            elseif object.mode == 0
-                name = 'Table Tool';
-            end
-            % main figure
-            object.fig = figure('units','pixels',...
-                'position',[0 0 object.fig_width object.fig_height],...
-                'menubar','none',...
-                'name','Table Tool',...
-                'numbertitle','off',...
-                'resize','on',...
-                'Name',name,...
-                'CloseRequestFcn',@(src,event)close_fig(object,src,event),...
-                'ResizeFcn',@(src,event)resize_fig(object,src,event));
-          
-            
-            % edit button
-            object.edit_tog = uicontrol('style','toggle',...
-                'units','pix',...
-                'string','Edit',...
-                'HorizontalAlign','left',...
-                'Parent',object.fig,...
-                'Value',object.edit,...
-                'callback',@(src,event)edit_tog_call(object,src,event));
-            
-            % Save button
-            object.save_pb = uicontrol('style','push',...
-                'units','pix',...
-                'string','Save',...
-                'HorizontalAlign','left',...
-                'Parent',object.fig,...
-                'callback',@(src,event)save_call(object,src,event));
-            
-            % Close button
-            object.close_pb = uicontrol('style','push',...
-                'units','pix',...
-                'string','Close',...
-                'HorizontalAlign','left',...
-                'Parent',object.fig,...
-                'callback',@(src,event)close_fig(object,src,event));
-            
-            % Save external button
-            object.save_ext_pb = uicontrol('style','push',...
-                'units','pix',...
-                'string','Save Ext',...
-                'HorizontalAlign','left',...
-                'Parent',object.fig,...
-                'callback',@(src,event)save_ext_call(object,src,event));
-            
-            % PVS button
-            object.pvs_pb = uicontrol('style','push',...
-                'units','pix',...
-                'string','PVS',...
-                'HorizontalAlign','left',...
-                'Parent',object.fig,...
-                'callback',@(src,event)pvs_ext_call(object,src,event));
-            
-            % Check button
-            object.check_pb = uicontrol('style','push',...
-                'units','pix',...
-                'string','Check',...
-                'HorizontalAlign','left',...
-                'Parent',object.fig,...
-                'callback',@(src,event)check_call(object,src,event));
-            
-            % Input/Output button
-            object.input_pb = uicontrol('style','push',...
-                'units','pix',...
-                'string','Ports',...
-                'HorizontalAlign','left',...
-                'Parent',object.fig,...
-                'callback',@(src,event)input_call(object,src,event));
-            
-            % Settings button
-            object.settings_pb = uicontrol('style','push',...
-                'units','pix',...
-                'string','Settings',...
-                'HorizontalAlign','left',...
-                'Parent',object.fig,...
-                'callback',@(src,event)settings_call(object,src,event));
-            
-            % Expression Name Label
-            object.name_label = uicontrol('style','text',...
-                'string','Expression Name',...
-                'HorizontalAlign','right',...
-                'BackgroundColor',get(object.fig,'Color'));
-            
-            % Expression Name Edit box
-            object.function_name_control = uicontrol('style','edit',...
-                'units','pix',...
-                'Parent',object.fig,...
-                'HorizontalAlign','center',...
-                'FontWeight','bold',...
-                'FontSize',12,...
-                'Max',2.0,...
-                'KeyPressFcn',@(src,event)textbox_callback(object,src,event),...
-                'BackgroundColor',[1 1 1]);
-            
-            % input list label
-            object.input_label = uicontrol('style','text',...
-                'string','Inputs',...
-                'HorizontalAlign','right',...
-                'BackgroundColor',get(object.fig,'Color'));
-            
-            % input list edit box
-            object.function_inputs_control = uicontrol('style','edit',...
-                'units','pix',...
-                'Parent',object.fig,...
-                'HorizontalAlign','center',...
-                'FontWeight','bold',...
-                'Max',2.0,...
-                'FontSize',12,...
-                'KeyPressFcn',@(src,event)textbox_callback(object,src,event),...
-                'BackgroundColor',[1 1 1]);
-            
-            %object.multi_grp = uibuttongroup(...
-            %    'units','pix',...
-            %    'Parent',object.fig,...
-            %    'SelectionChangeFcn',@(src,event)multi_select_call(object,src,event));
-                
-            %object.multi_opt_out = uicontrol('style','radiobutton',...
-            %    'units','pix',...
-            %    'Parent',object.multi_grp,...
-            %    'HorizontalAlign','center',...
-            %    'FontWeight','bold',...
-            %    'String','Multiple Output',...
-            %    'FontSize',12,...
-            %    'BackgroundColor',[1 1 1]);
-            
-            %object.multi_opt_reg = uicontrol('style','radiobutton',...
-            %    'units','pix',...
-            %    'Parent',object.multi_grp,...
-            %    'HorizontalAlign','center',...
-            %    'FontWeight','bold',...
-            %    'String','One Output',...
-            %    'FontSize',12,...
-            %    'BackgroundColor',[1 1 1]);
-            
-            % load the function name and inputs
-            if (~isempty(object.function_name_text))
-                set(object.function_name_control,'String',object.function_name_text);
-            end
-            if (~isempty(object.function_inputs_text))
-                set(object.function_inputs_control,'String',object.function_inputs_text);
-            end
-            
-            
-            % Set up Menu
-            filemenu = uimenu('Label','File');
-            editmenu = uimenu('Label','Edit');
-            pvsmenu = uimenu('Label','PVS');
-            helpmenu = uimenu('Label','Help');
-            uimenu(filemenu,'Label','New','Accelerator','n','Callback',@(src,event)new_call(object,src,event));
-            uimenu(filemenu,'Label','Open...','Callback',@(src,event)open_call(object,src,event));
-            uimenu(filemenu,'Label','Save to Block','Separator','on','Accelerator','s','Callback',@(src,event)save_call(object,src,event));
-            uimenu(filemenu,'Label','Save to M-File','Callback',@(src,event)save_ext_call(object,src,event));
-            uimenu(filemenu,'Label','Close','Accelerator','w','Separator','on','Callback',@(src,event)close_fig(object,src,event));     
-            object.undo_opt = uimenu(editmenu,'Label','Undo','Accelerator','z','Callback',@(src,event)undo_call(object,src,event));
-            object.redo_opt = uimenu(editmenu,'Label','Redo','Accelerator','r','Callback',@(src,event)redo_call(object,src,event));
-            uimenu(editmenu,'Label','Show edit controls','Checked','on','Separator','on');
-            uimenu(editmenu,'Label','Ports and Data Manager','Accelerator','p','Callback',@(src,event)input_call(object,src,event));
-            multi_mode_menu = uimenu(editmenu,'Label','Output Mode');
-            object.multi_opt_reg = uimenu(multi_mode_menu,'Label','One Output','Callback',@(src,event)multi_select_call(object,src,event));
-            object.multi_opt_out = uimenu(multi_mode_menu,'Label','Multiple Outputs','Callback',@(src,event)multi_select_call(object,src,event));
-            uimenu(pvsmenu,'Label','Typecheck','Accelerator','t','Callback',@(src,event)pvs_ext_call(object,src,event));
-            uimenu(pvsmenu,'Label','PVS Settings','Callback',@(src,event)settings_call(object,src,event));
-            uimenu(pvsmenu,'Label','Check Status','Callback',@(src,event)prf_file_call(object,src,event));
-            uimenu(pvsmenu,'Label','Generate PVS file','Callback',@(src,event)pvs_file_call(object,src,event));
-
-            uimenu(helpmenu,'Label','Product Help','Callback',@(src,event)help_call(object,src,event));
-            uimenu(helpmenu,'Label','About Table Tool','Callback',@(src,event)about_call(object,src,event));
-            
-            object.set_command_pos;
-            object.reset_wh();
-            object.draw_allgrids(1);
-            object.saved = 1;
-            object.setPBenable;
-            
-            
-            object.settings = Settings();
-            if isfield(object.Data.settings,'set')
-                object.settings.setvalues(object.Data.settings);
-            else
-                object.settings.init();
-                
-            end
-            
-                        object.undo_man = UndoManager();
-
-            
-            
-            object.update_Statusbar;
-            object.update_multi_check_status;
-                        object.update_undoredo;
-
-            object.PVS = PVS_checker(object.Data);
-            object.EMLGen = EMLGenerator(object.Data);
-            
-            
-            
-            object.initialized = 1;
-            object.Data.open = 1;
-            object.Data.fig = object.fig;
-            
-            
-            
-            
-        end
-        
-        
-        
-        
\ No newline at end of file
+%   initialize the gui
+% inputs:
+%   obj:GUI - GUI object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = init(object)
+
+% create the handles for the gui objects
+if object.mode == 1
+    name = get_param(object.block_handle,'Name');
+elseif object.mode == 0
+    name = 'Table Tool';
+end
+% main figure
+object.fig = figure('units','pixels',...
+    'position',[0 0 object.fig_width object.fig_height],...
+    'menubar','none',...
+    'name','Table Tool',...
+    'numbertitle','off',...
+    'resize','on',...
+    'Name',name,...
+    'CloseRequestFcn',@(src,event)close_fig(object,src,event),...
+    'ResizeFcn',@(src,event)resize_fig(object,src,event));
+
+
+% edit button
+object.edit_tog = uicontrol('style','toggle',...
+    'units','pix',...
+    'string','Edit',...
+    'HorizontalAlign','left',...
+    'Parent',object.fig,...
+    'Value',object.edit,...
+    'callback',@(src,event)edit_tog_call(object,src,event));
+
+% Save button
+object.save_pb = uicontrol('style','push',...
+    'units','pix',...
+    'string','Save',...
+    'HorizontalAlign','left',...
+    'Parent',object.fig,...
+    'callback',@(src,event)save_call(object,src,event));
+
+% Close button
+object.close_pb = uicontrol('style','push',...
+    'units','pix',...
+    'string','Close',...
+    'HorizontalAlign','left',...
+    'Parent',object.fig,...
+    'callback',@(src,event)close_fig(object,src,event));
+
+% Save external button
+object.save_ext_pb = uicontrol('style','push',...
+    'units','pix',...
+    'string','Save Ext',...
+    'HorizontalAlign','left',...
+    'Parent',object.fig,...
+    'callback',@(src,event)save_ext_call(object,src,event));
+
+% PVS button
+object.pvs_pb = uicontrol('style','push',...
+    'units','pix',...
+    'string','PVS',...
+    'HorizontalAlign','left',...
+    'Parent',object.fig,...
+    'callback',@(src,event)pvs_ext_call(object,src,event));
+
+% Check button
+object.check_pb = uicontrol('style','push',...
+    'units','pix',...
+    'string','Check',...
+    'HorizontalAlign','left',...
+    'Parent',object.fig,...
+    'callback',@(src,event)check_call(object,src,event));
+
+% Input/Output button
+object.input_pb = uicontrol('style','push',...
+    'units','pix',...
+    'string','Ports',...
+    'HorizontalAlign','left',...
+    'Parent',object.fig,...
+    'callback',@(src,event)input_call(object,src,event));
+
+% Settings button
+object.settings_pb = uicontrol('style','push',...
+    'units','pix',...
+    'string','Settings',...
+    'HorizontalAlign','left',...
+    'Parent',object.fig,...
+    'callback',@(src,event)settings_call(object,src,event));
+
+% Expression Name Label
+object.name_label = uicontrol('style','text',...
+    'string','Expression Name',...
+    'HorizontalAlign','right',...
+    'BackgroundColor',get(object.fig,'Color'));
+
+% Expression Name Edit box
+object.function_name_control = uicontrol('style','edit',...
+    'units','pix',...
+    'Parent',object.fig,...
+    'HorizontalAlign','center',...
+    'FontWeight','bold',...
+    'FontSize',12,...
+    'Max',2.0,...
+    'KeyPressFcn',@(src,event)textbox_callback(object,src,event),...
+    'BackgroundColor',[1 1 1]);
+
+% input list label
+object.input_label = uicontrol('style','text',...
+    'string','Inputs',...
+    'HorizontalAlign','right',...
+    'BackgroundColor',get(object.fig,'Color'));
+
+% input list edit box
+object.function_inputs_control = uicontrol('style','edit',...
+    'units','pix',...
+    'Parent',object.fig,...
+    'HorizontalAlign','center',...
+    'FontWeight','bold',...
+    'Max',2.0,...
+    'FontSize',12,...
+    'KeyPressFcn',@(src,event)textbox_callback(object,src,event),...
+    'BackgroundColor',[1 1 1]);
+
+%object.multi_grp = uibuttongroup(...
+%    'units','pix',...
+%    'Parent',object.fig,...
+%    'SelectionChangeFcn',@(src,event)multi_select_call(object,src,event));
+
+%object.multi_opt_out = uicontrol('style','radiobutton',...
+%    'units','pix',...
+%    'Parent',object.multi_grp,...
+%    'HorizontalAlign','center',...
+%    'FontWeight','bold',...
+%    'String','Multiple Output',...
+%    'FontSize',12,...
+%    'BackgroundColor',[1 1 1]);
+
+%object.multi_opt_reg = uicontrol('style','radiobutton',...
+%    'units','pix',...
+%    'Parent',object.multi_grp,...
+%    'HorizontalAlign','center',...
+%    'FontWeight','bold',...
+%    'String','One Output',...
+%    'FontSize',12,...
+%    'BackgroundColor',[1 1 1]);
+
+% load the function name and inputs
+if (~isempty(object.function_name_text))
+    set(object.function_name_control,'String',object.function_name_text);
+end
+if (~isempty(object.function_inputs_text))
+    set(object.function_inputs_control,'String',object.function_inputs_text);
+end
+
+
+% Set up Menu
+filemenu = uimenu('Label','File');
+editmenu = uimenu('Label','Edit');
+pvsmenu = uimenu('Label','PVS');
+helpmenu = uimenu('Label','Help');
+uimenu(filemenu,'Label','New','Accelerator','n','Callback',@(src,event)new_call(object,src,event));
+uimenu(filemenu,'Label','Open...','Callback',@(src,event)open_call(object,src,event));
+uimenu(filemenu,'Label','Save to Block','Separator','on','Accelerator','s','Callback',@(src,event)save_call(object,src,event));
+uimenu(filemenu,'Label','Save to M-File','Callback',@(src,event)save_ext_call(object,src,event));
+uimenu(filemenu,'Label','Close','Accelerator','w','Separator','on','Callback',@(src,event)close_fig(object,src,event));
+object.undo_opt = uimenu(editmenu,'Label','Undo','Accelerator','z','Callback',@(src,event)undo_call(object,src,event));
+object.redo_opt = uimenu(editmenu,'Label','Redo','Accelerator','r','Callback',@(src,event)redo_call(object,src,event));
+uimenu(editmenu,'Label','Show edit controls','Checked','on','Separator','on');
+uimenu(editmenu,'Label','Ports and Data Manager','Accelerator','p','Callback',@(src,event)input_call(object,src,event));
+multi_mode_menu = uimenu(editmenu,'Label','Output Mode');
+object.multi_opt_reg = uimenu(multi_mode_menu,'Label','One Output','Callback',@(src,event)multi_select_call(object,src,event));
+object.multi_opt_out = uimenu(multi_mode_menu,'Label','Multiple Outputs','Callback',@(src,event)multi_select_call(object,src,event));
+uimenu(pvsmenu,'Label','Typecheck','Accelerator','t','Callback',@(src,event)pvs_ext_call(object,src,event));
+uimenu(pvsmenu,'Label','PVS Settings','Callback',@(src,event)settings_call(object,src,event));
+uimenu(pvsmenu,'Label','Check Status','Callback',@(src,event)prf_file_call(object,src,event));
+uimenu(pvsmenu,'Label','Generate PVS file','Callback',@(src,event)pvs_file_call(object,src,event));
+
+uimenu(helpmenu,'Label','Product Help','Callback',@(src,event)help_call(object,src,event));
+uimenu(helpmenu,'Label','About Table Tool','Callback',@(src,event)about_call(object,src,event));
+
+object.set_command_pos;
+object.reset_wh();
+object.draw_allgrids(1);
+object.saved = 1;
+object.setPBenable;
+
+
+object.settings = Settings();
+if isfield(object.Data.settings,'set')
+    object.settings.setvalues(object.Data.settings);
+else
+    object.settings.init();
+    
+end
+
+object.undo_man = UndoManager();
+
+
+
+object.update_Statusbar;
+object.update_multi_check_status;
+object.update_undoredo;
+
+object.PVS = PVS_checker(object.Data);
+object.EMLGen = EMLGenerator(object.Data);
+
+
+
+object.initialized = 1;
+object.Data.open = 1;
+object.Data.fig = object.fig;
+
+
+
+
+end
+
+
+
diff --git a/@GUI/input_call.m b/@GUI/input_call.m
index 536100fd9a0ab55423454be7054a6df145963ae6..01bc4297c5da79d4da4f3d88ad6697fed525ea42 100644
--- a/@GUI/input_call.m
+++ b/@GUI/input_call.m
@@ -1,22 +1,23 @@
-      %% input_call
-        %   function will open up the ports and data management window if
-        %   in simulink mode.
-        % inputs:
-        %   obj:GUI - GUI objecto
-        %   src:double - source of the callback calling
-        %   event:eventdata - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = input_call(object,src,event)
-            % make sure in simulink mode.
-            if object.mode == 1
-                eml_handle = object.save_call([],[]);
-               currentDir = pwd;
-                cd([matlabroot filesep 'toolbox' filesep 'stateflow' filesep 'stateflow' filesep 'private']);
-                fHandle = @eml_man;
-                cd(currentDir);
-                fHandle('edit_data_ports', sf('get', get_param(char(eml_handle),'UserData'), '.chart')) 
-            end
-        end
-        
-  
\ No newline at end of file
+%% input_call
+%   function will open up the ports and data management window if
+%   in simulink mode.
+% inputs:
+%   obj:GUI - GUI objecto
+%   src:double - source of the callback calling
+%   event:eventdata - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = input_call(object,src,event)
+% make sure in simulink mode.
+if object.mode == 1
+    eml_handle = object.save_call([],[]);
+    currentDir = pwd;
+    cd([matlabroot filesep 'toolbox' filesep 'stateflow' filesep 'stateflow' filesep 'private']);
+    fHandle = @eml_man;
+    cd(currentDir);
+    fHandle('edit_data_ports', sf('get', get_param(char(eml_handle),'UserData'), '.chart'))
+end
+end
+
diff --git a/@GUI/input_data_type.m b/@GUI/input_data_type.m
index 8baf7ac89859465acb0123d509851af388adce13..9f44f1c69825d49801d1f536321832084ab80dbf 100644
--- a/@GUI/input_data_type.m
+++ b/@GUI/input_data_type.m
@@ -8,6 +8,8 @@
 %   object:GUI - GUI objecto
 % outputs:
 %   type:string - string representation of the output type.
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function types = input_data_type(object)
 types = [];
 if (object.mode == 1)
diff --git a/@GUI/msgbox_scroll.m b/@GUI/msgbox_scroll.m
index b76a858609207e03b91d69a990d03cc39052441e..4874a1f6faf47d9e7b9941d4e1d82d55029302db 100644
--- a/@GUI/msgbox_scroll.m
+++ b/@GUI/msgbox_scroll.m
@@ -1,26 +1,28 @@
 %% msgbox_scroll
-        %    create a message box with a scrollable text area
-        % inputs:
-        %   msg:string - string to put into the message box
-        % outputs:
-        %   none
-        function [] = msgbox_scroll(msg)
-            fig = figure('units','pixels',...
-                'position',[0 0 700 500],...
-                'menubar','none',...
-                'name','PVS Report',...       
-                'numbertitle','off');
-            
-        uicontrol('style','edit',...
-                'units','pix',...
-                'Parent',fig,...
-                'HorizontalAlign','center',...
-                'FontWeight','bold',...
-                'FontSize',12,...
-                'Max',2.0,...
-                'HorizontalAlign','left',...
-                'String',msg,...
-                'Position',[1 1 698 498],...
-                'BackgroundColor',[1 1 1]);
-            
-        end
\ No newline at end of file
+%    create a message box with a scrollable text area
+% inputs:
+%   msg:string - string to put into the message box
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = msgbox_scroll(msg)
+fig = figure('units','pixels',...
+    'position',[0 0 700 500],...
+    'menubar','none',...
+    'name','PVS Report',...
+    'numbertitle','off');
+
+uicontrol('style','edit',...
+    'units','pix',...
+    'Parent',fig,...
+    'HorizontalAlign','center',...
+    'FontWeight','bold',...
+    'FontSize',12,...
+    'Max',2.0,...
+    'HorizontalAlign','left',...
+    'String',msg,...
+    'Position',[1 1 698 498],...
+    'BackgroundColor',[1 1 1]);
+
+end
\ No newline at end of file
diff --git a/@GUI/multi_select_call.m b/@GUI/multi_select_call.m
index e910a0bf25d2a89a73d82ef3b89db0f1b3ef2c80..772a59404304ed3121c12dfc8137892442255ae3 100644
--- a/@GUI/multi_select_call.m
+++ b/@GUI/multi_select_call.m
@@ -1,4 +1,5 @@
-
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [] = multi_select_call(object,src,event)
 label = get(src,'Label');
 if strcmp(label,'Multiple Outputs')
diff --git a/@GUI/new_call.m b/@GUI/new_call.m
index 6eb10d6f89b4d37f679df6d3e285db072f25292e..659e823f34ec644de53e75c5425884097063a6db 100644
--- a/@GUI/new_call.m
+++ b/@GUI/new_call.m
@@ -1,15 +1,16 @@
-       
-        %% new_call
-        %   callback for new button
-        % inputs:
-        %   obj:GUI - GUI objecto
-        %   src:double - source of the callback calling
-        %   event:eventdata - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = new_call(object,src,event)
-            TableToolMatlab
-        end
-        
-         
-    
\ No newline at end of file
+
+%% new_call
+%   callback for new button
+% inputs:
+%   obj:GUI - GUI objecto
+%   src:double - source of the callback calling
+%   event:eventdata - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = new_call(object,src,event)
+TableToolMatlab
+end
+
+
diff --git a/@GUI/open_call.m b/@GUI/open_call.m
index 0faaf08aaec469035ee71fec61e36a9bede46461..1729da750cff9687498d50a39ab62b0f43a1b512 100644
--- a/@GUI/open_call.m
+++ b/@GUI/open_call.m
@@ -1,17 +1,18 @@
 %% open_call
-        %   callback for the open option, will show a file picker and
-        %   attempt to load the file into a new window.
-        % inputs:
-        %   obj:GUI - GUI objecto
-        %   src:double - source of the callback calling
-        %   event:eventdata - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = open_call(object,src,event)
-               [FileName, PathName, FilterIndex] = uigetfile('*.table','Select pvs files');
-               if ~isempty(FileName)
-                TTdiag('Load',[PathName FileName]);
-               end
-        end
-        
-       
\ No newline at end of file
+%   callback for the open option, will show a file picker and
+%   attempt to load the file into a new window.
+% inputs:
+%   obj:GUI - GUI objecto
+%   src:double - source of the callback calling
+%   event:eventdata - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = open_call(object,src,event)
+[FileName, PathName, FilterIndex] = uigetfile('*.table','Select pvs files');
+if ~isempty(FileName)
+    TTdiag('Load',[PathName FileName]);
+end
+end
+
diff --git a/@GUI/output_data_type.m b/@GUI/output_data_type.m
index e1db24b90d364a270314e9c8ebe2a836aa0b191e..ee61f2f74e1bbee3bffd4e1ac579dce2c4a0b071 100644
--- a/@GUI/output_data_type.m
+++ b/@GUI/output_data_type.m
@@ -8,6 +8,8 @@
 %   object:GUI - GUI objecto
 % outputs:
 %   type:string - string representation of the output type.
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function types = output_data_type(object)
 types = [];
 if (object.mode == 1)
@@ -26,13 +28,7 @@ if (object.mode == 1)
                 typename = myState.Outputs(i).DataType;
             end
             types = [types;{myState.Outputs(i).Name, typename}]
-            %                         if strncmp(myState.Outputs.DataType,'Inherit',7);
-            %                             type = '';
-            %                         elseif strncmp(myState.Outputs.DataType,'boolean',7);
-            %                             type = 'logical';
-            %                         else
-            %                             type = myState.Outputs.DataType;
-            %                         end
+
         end
     else
         types = [];
diff --git a/@GUI/prf_file_call.m b/@GUI/prf_file_call.m
index 4f3798aa3cd4f4ac0503fe8671937540785f395b..73789bd264ef3f2213287402f36396fcc2b7b740 100644
--- a/@GUI/prf_file_call.m
+++ b/@GUI/prf_file_call.m
@@ -1,66 +1,67 @@
 %% prf_file_call
-        %   callback for the check status menu option, this function will
-        %   check the current status of the table, if the table has been
-        %   proven it will alert the user and update the status, if it has
-        %   not been proven it will alert the user.
-        % inputs:
-        %   obj:GUI - GUI objecto
-        %   src:double - source of the callback calling
-        %   event:eventdata - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = prf_file_call(object,src,event)
-            object.save_data;
-            % check if a pvs file exists
-            if (~exist([object.Data.function_name '.pvs'],'file'))
-                errordlg(['PVS theory file for this function does not exist' sprintf('\n') 'Nothing to check']);
-                return;
-            end
-            % check if prf file exists
-            if (~exist([object.Data.function_name '.prf'],'file'))
-                errordlg(['PVS proof (.prf) file for this function does not exist' sprintf('\n') 'Nothing to check']);
-                return;
-            end
-            % check if pvs file is different from current table
-            temp_pvs = [object.Data.function_name '_temp'];
-            object.PVS.generate_pvs_file(temp_pvs);
+%   callback for the check status menu option, this function will
+%   check the current status of the table, if the table has been
+%   proven it will alert the user and update the status, if it has
+%   not been proven it will alert the user.
+% inputs:
+%   obj:GUI - GUI objecto
+%   src:double - source of the callback calling
+%   event:eventdata - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = prf_file_call(object,src,event)
+object.save_data;
+% check if a pvs file exists
+if (~exist([object.Data.function_name '.pvs'],'file'))
+    errordlg(['PVS theory file for this function does not exist' sprintf('\n') 'Nothing to check']);
+    return;
+end
+% check if prf file exists
+if (~exist([object.Data.function_name '.prf'],'file'))
+    errordlg(['PVS proof (.prf) file for this function does not exist' sprintf('\n') 'Nothing to check']);
+    return;
+end
+% check if pvs file is different from current table
+temp_pvs = [object.Data.function_name '_temp'];
+object.PVS.generate_pvs_file(temp_pvs);
 
-            % read pvs theory on file
-            pvs1 = textread([object.Data.function_name '.pvs'], '%s', 'whitespace', '', 'bufsize', 268435456);
-            pvs2 = textread([temp_pvs '.pvs'], '%s', 'whitespace', '', 'bufsize', 268435456);
-            
-            if(size(pvs1{1},2) ~= size(pvs2{1},2))
-                errordlg(['pvs-theory file is different from the given graphical representation, ' sprintf('\n') ' you will need to reprove']);
-                return;
-            else
-              
-                    if ~all(pvs1{1} == pvs2{1})
-                        errordlg(['pvs-theory file is different from the given graphical representation, ' sprintf('\n') ' you will need to reprove']);
-                        return;
-                    end
-                    
-                
-            end
-            delete([temp_pvs '.pvs']);
+% read pvs theory on file
+pvs1 = textread([object.Data.function_name '.pvs'], '%s', 'whitespace', '', 'bufsize', 268435456);
+pvs2 = textread([temp_pvs '.pvs'], '%s', 'whitespace', '', 'bufsize', 268435456);
 
-            
-            status = object.PVS.check_status;
-            if (status ~= object.pvs_checked)
+if(size(pvs1{1},2) ~= size(pvs2{1},2))
+    errordlg(['pvs-theory file is different from the given graphical representation, ' sprintf('\n') ' you will need to reprove']);
+    return;
+else
+    
+    if ~all(pvs1{1} == pvs2{1})
+        errordlg(['pvs-theory file is different from the given graphical representation, ' sprintf('\n') ' you will need to reprove']);
+        return;
+    end
+    
+    
+end
+delete([temp_pvs '.pvs']);
 
-                object.pvs_checked = status;
-                object.update_Statusbar;
-                if (object.mode == 1)
-                    TableBlock.set_block_display(object.block_handle,object.pvs_checked)
-                end
 
-            end
+status = object.PVS.check_status;
+if (status ~= object.pvs_checked)
+    
+    object.pvs_checked = status;
+    object.update_Statusbar;
+    if (object.mode == 1)
+        TableBlock.set_block_display(object.block_handle,object.pvs_checked)
+    end
+    
+end
 
-            if (status == 1)
-                    msgbox('Table has been proven');
-                else
-                    msgbox('Table has not been proven');
-            end
+if (status == 1)
+    msgbox('Table has been proven');
+else
+    msgbox('Table has not been proven');
+end
+
+end
 
-        end
-        
-        
\ No newline at end of file
diff --git a/@GUI/pvs_ext_call.m b/@GUI/pvs_ext_call.m
index ae1c8ddc5a25ae8047714625449eecf14549d5e6..1c4e7890de0eb0b9990a35ffcafffc3b34292a55 100644
--- a/@GUI/pvs_ext_call.m
+++ b/@GUI/pvs_ext_call.m
@@ -1,44 +1,45 @@
-    %% pvs_ext_call
-        %   function will initiate the typechecking procedure for the table
-        % inputs:
-        %   obj:GUI - GUI objecto
-        %   src:double - source of the callback calling
-        %   event:eventdata - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = pvs_ext_call(object,src,event)
-        object.save_call([],[]);
-            object.save_data;
-            if (object.validation_report_handle ~= 0)
-                delete(object.validation_report_handle)
-            end
-            error = object.check_call;
-            
-            if(object.multi_mode == 0)
-            object.PVS.output_type = object.output_data_type;
-            
-            object.PVS.input_type = object.input_data_type;
-            end
-            
-            if (~error)
-                [check,result] = object.PVS.pvs_check;
-                if (check == 1)
-                       msgbox('table is valid')
-                elseif (check == 0 && strcmp(result,'canceled'))
-                    return;
-                else
-                    Valid_Report = ValidationReport(object);
-                    Valid_Report.set_results(result);
-                    Valid_Report.init();
-                end
-                object.pvs_checked = check;
-                object.update_Statusbar;
-                                if (object.mode == 1)
+%% pvs_ext_call
+%   function will initiate the typechecking procedure for the table
+% inputs:
+%   obj:GUI - GUI objecto
+%   src:double - source of the callback calling
+%   event:eventdata - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = pvs_ext_call(object,src,event)
+object.save_call([],[]);
+object.save_data;
+if (object.validation_report_handle ~= 0)
+    delete(object.validation_report_handle)
+end
+error = object.check_call;
 
-                TableBlock.set_block_display(object.block_handle,object.pvs_checked)
-                                end
-            end
+if(object.multi_mode == 0)
+    object.PVS.output_type = object.output_data_type;
+    
+    object.PVS.input_type = object.input_data_type;
+end
 
-        end
+if (~error)
+    [check,result] = object.PVS.pvs_check;
+    if (check == 1)
+        msgbox('table is valid')
+    elseif (check == 0 && strcmp(result,'canceled'))
+        return;
+    else
+        Valid_Report = ValidationReport(object);
+        Valid_Report.set_results(result);
+        Valid_Report.init();
+    end
+    object.pvs_checked = check;
+    object.update_Statusbar;
+    if (object.mode == 1)
         
-  
\ No newline at end of file
+        TableBlock.set_block_display(object.block_handle,object.pvs_checked)
+    end
+end
+
+end
+
diff --git a/@GUI/pvs_file_call.m b/@GUI/pvs_file_call.m
index ca9e4048af921656b64091ca7cf8d934fd15176c..70f2e8f47c22c80fb52b372215c43fa582c3a4a9 100644
--- a/@GUI/pvs_file_call.m
+++ b/@GUI/pvs_file_call.m
@@ -1,17 +1,18 @@
-    %% pvs_file_call
-        %   callback for the generate pvs file button, generates a pvs file
-        %   for the table, does not attempt to prove, overwrites.
-        % inputs:
-        %   obj:GUI - GUI objecto
-        %   src:double - source of the callback calling
-        %   event:eventdata - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = pvs_file_call(object,src,event)
-            object.save_data
-             object.PVS.generate_pvs_file(object.Data.function_name);
-            
-            
-        end
-        
-        
\ No newline at end of file
+%% pvs_file_call
+%   callback for the generate pvs file button, generates a pvs file
+%   for the table, does not attempt to prove, overwrites.
+% inputs:
+%   obj:GUI - GUI objecto
+%   src:double - source of the callback calling
+%   event:eventdata - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = pvs_file_call(object,src,event)
+object.save_data
+object.PVS.generate_pvs_file(object.Data.function_name);
+
+
+end
+
diff --git a/@GUI/redo_call.m b/@GUI/redo_call.m
index 25786563d86209f7f40470e022646b0835c245fe..81d50a507b4ade38aac79283dfea4194a3822de8 100644
--- a/@GUI/redo_call.m
+++ b/@GUI/redo_call.m
@@ -1,26 +1,28 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [] = redo_call(object,src,event)
 
 recalled_data = object.undo_man.redo;
- if isempty(recalled_data);
-     return;
- else
-     switch recalled_data.action
-         case 1
-             try
-             set(recalled_data.cell,'String',recalled_data.text);
-             catch exception
-             end
-         case 2
-             recalled_data.grid.pb_new_call(recalled_data.grid.new_cell_pb,1);
-         case 3
-             recalled_data.grid.pb_delete_call(recalled_data.grid.delete_cell_pb,1);
-         case 4
-             
-             %recalled_data.cell.pb_call(recalled_data.cell.grid_pb,1);
-             recalled_data.cell.subgrid = recalled_data.grid;
-             recalled_data.cell.subgrid = recalled_data.grid;
+if isempty(recalled_data);
+    return;
+else
+    switch recalled_data.action
+        case 1
+            try
+                set(recalled_data.cell,'String',recalled_data.text);
+            catch exception
+            end
+        case 2
+            recalled_data.grid.pb_new_call(recalled_data.grid.new_cell_pb,1);
+        case 3
+            recalled_data.grid.pb_delete_call(recalled_data.grid.delete_cell_pb,1);
+        case 4
+            
+            %recalled_data.cell.pb_call(recalled_data.cell.grid_pb,1);
+            recalled_data.cell.subgrid = recalled_data.grid;
+            recalled_data.cell.subgrid = recalled_data.grid;
             recalled_data.cell.pb_flag = 0;
-             if(~isempty(recalled_data.cell.parent_grid.rGrid))
+            if(~isempty(recalled_data.cell.parent_grid.rGrid))
                 recalled_data.cell.parent_grid.rGrid.delete_g2s(recalled_data.cell);
             end
             if(~isempty(recalled_data.grid.rGrid))
@@ -29,12 +31,12 @@ recalled_data = object.undo_man.redo;
             object.reset_wh();
             %gui.draw_grid2(gui.Grid2);
             object.draw_allgrids(1);
-             
-             
-         case 5
-             recalled_data.grid.pb_delete_call(recalled_data.grid.delete_cell_pb,1);
-     end
- end
- object.update_undoredo;
+            
+            
+        case 5
+            recalled_data.grid.pb_delete_call(recalled_data.grid.delete_cell_pb,1);
+    end
+end
+object.update_undoredo;
 
 end
\ No newline at end of file
diff --git a/@GUI/reset_wh.m b/@GUI/reset_wh.m
index 9cdb8f1d2e7004c288dea200c1612b76fdc524e2..d3fa2024ad5c69691763d46f0dab50b9bdc4acf2 100644
--- a/@GUI/reset_wh.m
+++ b/@GUI/reset_wh.m
@@ -1,14 +1,16 @@
-        %% reset_wh
-        %    function will call the set_widths and set_heights methods on
-        %    the left grid in the table. The height and width values are
-        %    used to draw the grid.
-        % inputs:
-        %   obj:GUI - current GUI object
-        % outputs:
-        %   none
-        function [] = reset_wh(object)
-            width = object.Grid2.max_width(1);
-            object.Grid2.set_widths(width);
-            object.Grid2.set_heights(object.edit);
-        end
-        
+%% reset_wh
+%    function will call the set_widths and set_heights methods on
+%    the left grid in the table. The height and width values are
+%    used to draw the grid.
+% inputs:
+%   obj:GUI - current GUI object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = reset_wh(object)
+width = object.Grid2.max_width(1);
+object.Grid2.set_widths(width);
+object.Grid2.set_heights(object.edit);
+end
+
diff --git a/@GUI/resize_fig.m b/@GUI/resize_fig.m
index a84a66c61bb72909f9941996a64af2091fcadc62..e56960b1ecc199e182e8d1393d21c5d81a3cae45 100644
--- a/@GUI/resize_fig.m
+++ b/@GUI/resize_fig.m
@@ -1,18 +1,19 @@
-   %% resize_fig
-        %    callback function that is called whenever the main figure is
-        %    resized. Ensures that the commands remain at the top of the
-        %    screen and the grid below them.
-        % inputs:
-        %   object:GUI - current GUI object
-        %   src:double - source of the callback calling
-        %   event:eventdata - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = resize_fig(object,src,event)
-            if(object.initialized == 1)
-                object.draw_allgrids(0);
-                object.set_command_pos;
-            end
-        end
-        
-       
\ No newline at end of file
+%% resize_fig
+%    callback function that is called whenever the main figure is
+%    resized. Ensures that the commands remain at the top of the
+%    screen and the grid below them.
+% inputs:
+%   object:GUI - current GUI object
+%   src:double - source of the callback calling
+%   event:eventdata - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = resize_fig(object,src,event)
+if(object.initialized == 1)
+    object.draw_allgrids(0);
+    object.set_command_pos;
+end
+end
+
diff --git a/@GUI/save_call.m b/@GUI/save_call.m
index 50f83fdd1192974267ffd1c4662878e13eee649c..61f344f88b356dc50948c093606361fb65b57cea 100644
--- a/@GUI/save_call.m
+++ b/@GUI/save_call.m
@@ -1,74 +1,76 @@
-    %% save_call
-        %    callback function that is called whenever the save button is
-        %    pressed. This function will generate code and store it in the
-        %    embedded matlab block, it will then generate the corresponding
-        %    input and output ports and connect them to the embedded matlab
-        %    block.
-        % inputs:
-        %   object:GUI - current GUI object
-        %   src:double - source of the callback calling
-        %   event:eventdata - event that triggered the callback
-        % outputs:
-        %   none
-        function eml_handle = save_call(object,src,event)
-             if(object.check_call([],[]) == 1)
-                 return;
-             end
-             
-             function_names = EMLGenerator.parse_inputs(get(object.function_name_control,'String'));
-             function_name = char(function_names{1}(1));
-            object.save_data;
-            if object.mode == 0
-                model = gcs;
-                %make sure we are not looking at the library model
-                %if (strcmp(model,'eml_lib') || strcmp(model,'simulink'))
-                    %create a new model
-                    found = any(ismember(find_system('type', 'block_diagram'),'Table'))
-                    if found == 0
-                       
-                   
-                        new_system('Table','Model')
+%% save_call
+%    callback function that is called whenever the save button is
+%    pressed. This function will generate code and store it in the
+%    embedded matlab block, it will then generate the corresponding
+%    input and output ports and connect them to the embedded matlab
+%    block.
+% inputs:
+%   object:GUI - current GUI object
+%   src:double - source of the callback calling
+%   event:eventdata - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function eml_handle = save_call(object,src,event)
+if(object.check_call([],[]) == 1)
+    return;
+end
 
-                    end
-                    model = 'Table'
-                %end
-                open_system(model);
-                load_system('TableLibrary');
-                new_block = add_block('TableLibrary/Tabular Expression',[model '/' function_name]);
-                set_param(new_block,'UserData',object.Data)
-                set_param(new_block, 'UserDataPersistent', 'on');
-                object.mode = 1;
-                object.block_handle = new_block;
-                object.save_call([],[]);
-            elseif object.mode == 1
-                
-                load_system('simulink')
-                % generate the code
-                redo = object.check_output_consistent;
-                if redo
-                    object.EMLGen.set_datatype(object.output_data_type);
-                else
-                    object.EMLGen.set_datatype([]);
-                end
-                code = object.EMLGen.generate_eml_code;
-                
-                %code = [code object.generate_code(object.Grid1,object.Grid2,0)];
-                %fprintf('%s',code);
+function_names = EMLGenerator.parse_inputs(get(object.function_name_control,'String'));
+function_name = char(function_names{1}(1));
+object.save_data;
+if object.mode == 0
+    model = gcs;
+    %make sure we are not looking at the library model
+    %if (strcmp(model,'eml_lib') || strcmp(model,'simulink'))
+    %create a new model
+    found = any(ismember(find_system('type', 'block_diagram'),'Table'))
+    if found == 0
+        
+        
+        new_system('Table','Model')
+        
+    end
+    model = 'Table'
+    %end
+    open_system(model);
+    load_system('TableLibrary');
+    new_block = add_block('TableLibrary/Tabular Expression',[model '/' function_name]);
+    set_param(new_block,'UserData',object.Data)
+    set_param(new_block, 'UserDataPersistent', 'on');
+    object.mode = 1;
+    object.block_handle = new_block;
+    object.save_call([],[]);
+elseif object.mode == 1
+    
+    load_system('simulink')
+    % generate the code
+    redo = object.check_output_consistent;
+    if redo
+        object.EMLGen.set_datatype(object.output_data_type);
+    else
+        object.EMLGen.set_datatype([]);
+    end
+    code = object.EMLGen.generate_eml_code;
+    
+    %code = [code object.generate_code(object.Grid1,object.Grid2,0)];
+    %fprintf('%s',code);
+    
+    eml_handle = TableBlock.set_code(object.block_handle,code,function_name);
+    
+    
+    
+    if (object.mode == 1)
+        
+        TableBlock.set_block_display(object.block_handle,object.pvs_checked);
+    end
+    
+    if ~redo
+        object.save_call([],[]);
+    end
+end
+end
 
-               eml_handle = TableBlock.set_code(object.block_handle,code,function_name);
 
-                
-                
-                if (object.mode == 1)
 
-                    TableBlock.set_block_display(object.block_handle,object.pvs_checked);
-                end
-                
-                if ~redo
-                    object.save_call([],[]);
-                end
-            end
-        end
-        
-       
-        
diff --git a/@GUI/save_conditions.m b/@GUI/save_conditions.m
index 6dc2f4117dccb5b07703b49b7dc61b0519161bba..ffc704f5c05b7dab6818a5fe6af72018c24f5da0 100644
--- a/@GUI/save_conditions.m
+++ b/@GUI/save_conditions.m
@@ -1,21 +1,23 @@
-        %% save_conditions
-        % this function is used to save the strings that are in each of the
-        % condition edit boxes string field. We do this because when we
-        % want to reopen the gui we want to repopulate these fields but the
-        % handles to the edit boxes will disappear when we close the gui,
-        % so we need to save the strings into variables in each of the Cell
-        % objects. function is recursive.
-        % inputs:
-        %   obj:GUI - current GUI object
-        %   grid:Grid - grid to be saved.
-        % outputs:
-        %   none
-        function [] = save_conditions(object,grid)
-            for i=1:size(grid.cells,2)
-                if ~isempty(grid.cells(i).subgrid)
-                    object.save_conditions(grid.cells(i).subgrid);
-                end
-                grid.cells(i).cond_text = get(grid.cells(i).cond,'String');
-            end
-        end
-        
+%% save_conditions
+% this function is used to save the strings that are in each of the
+% condition edit boxes string field. We do this because when we
+% want to reopen the gui we want to repopulate these fields but the
+% handles to the edit boxes will disappear when we close the gui,
+% so we need to save the strings into variables in each of the Cell
+% objects. function is recursive.
+% inputs:
+%   obj:GUI - current GUI object
+%   grid:Grid - grid to be saved.
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = save_conditions(object,grid)
+for i=1:size(grid.cells,2)
+    if ~isempty(grid.cells(i).subgrid)
+        object.save_conditions(grid.cells(i).subgrid);
+    end
+    grid.cells(i).cond_text = get(grid.cells(i).cond,'String');
+end
+end
+
diff --git a/@GUI/save_data.m b/@GUI/save_data.m
index c1a99cba9e96e7313506b0ae1096b63ab4aa84c6..d05a6936286be521982ea0270d5805411a1487b0 100644
--- a/@GUI/save_data.m
+++ b/@GUI/save_data.m
@@ -1,29 +1,31 @@
-        %% save_data
-        %    save the current state of the table to the data object so that
-        %    it can be saved either in a block or in a binary file
-        % inputs:
-        %   object:GUI - current GUI object
-        % outputs:
-        %   none
-        function [] = save_data(object)
-            save_conditions(object,object.Grid2);
-            save_conditions(object,object.Grid1);
-            save_results(object,object.Grid0);
-            % depricated
-            object.function_name_text = get(object.function_name_control,'String');
-            object.function_inputs_text = get(object.function_inputs_control,'String');
-            % new storage
-            object.Data.function_name = get(object.function_name_control,'String');
-            object.Data.function_inputs = get(object.function_inputs_control,'String');
-            object.Data.checked = object.pvs_checked;
-            object.Data.multi_mode = object.multi_mode;
-            %object.Data.open = 0;
-            %object.Data.fig = [];
-           
-            set.set = 1;
-            set.inputs = object.settings.pvs_includes;
-            set.count = object.settings.counter_trials;
-            set.range = object.settings.counter_range;
-            object.Data.settings = set;
-        end
-        
+%% save_data
+%    save the current state of the table to the data object so that
+%    it can be saved either in a block or in a binary file
+% inputs:
+%   object:GUI - current GUI object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = save_data(object)
+save_conditions(object,object.Grid2);
+save_conditions(object,object.Grid1);
+save_results(object,object.Grid0);
+% depricated
+object.function_name_text = get(object.function_name_control,'String');
+object.function_inputs_text = get(object.function_inputs_control,'String');
+% new storage
+object.Data.function_name = get(object.function_name_control,'String');
+object.Data.function_inputs = get(object.function_inputs_control,'String');
+object.Data.checked = object.pvs_checked;
+object.Data.multi_mode = object.multi_mode;
+%object.Data.open = 0;
+%object.Data.fig = [];
+
+set.set = 1;
+set.inputs = object.settings.pvs_includes;
+set.count = object.settings.counter_trials;
+set.range = object.settings.counter_range;
+object.Data.settings = set;
+end
+
diff --git a/@GUI/save_ext_call.m b/@GUI/save_ext_call.m
index 7ab3e188fca7669c08eefd6cc8a5d3f38bd55b14..b9103cbbcd373604ee3071ccd0b5ce620c292e7d 100644
--- a/@GUI/save_ext_call.m
+++ b/@GUI/save_ext_call.m
@@ -1,35 +1,36 @@
- %% save_ext_call
-        %    callback function that is called whenever the save ext button
-        %    is pressed. This function will generate the code for the table
-        %    and output it to an external embedded matlab file which can
-        %    then be used in other functions. Filename of new file will be
-        %    the same as the expression name, currently this function will
-        %    overwrite an existing file of the same name.
-        % inputs:
-        %   object:GUI - current GUI object
-        %   src:double - source of the callback calling
-        %   event:eventdata - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = save_ext_call(object,src,event)
-            object.save_data;
-            % file name will be expression_name.m
-            fileid = fopen([get(object.function_name_control,'String') '.m'],'w');
-            %code = [];
-            %code = sprintf('function output = %s(%s)\n%s\noutput=0;\n',get(object.function_name_control,'String'),get(object.function_inputs_control,'String'),'%%#eml');
-            %code = [code object.generate_code(object.Grid1,object.Grid2,0)];
-            code = object.EMLGen.generate_eml_code;
-            
-            fprintf(fileid,code);
-            % save an extra file called expression_name.data which
-            % contains a binary representation of the current gui object.
-            filename = [get(object.function_name_control,'String') '.table'];
-            %save(filename,'object');
-            object.save_data;
+%% save_ext_call
+%    callback function that is called whenever the save ext button
+%    is pressed. This function will generate the code for the table
+%    and output it to an external embedded matlab file which can
+%    then be used in other functions. Filename of new file will be
+%    the same as the expression name, currently this function will
+%    overwrite an existing file of the same name.
+% inputs:
+%   object:GUI - current GUI object
+%   src:double - source of the callback calling
+%   event:eventdata - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = save_ext_call(object,src,event)
+object.save_data;
+% file name will be expression_name.m
+fileid = fopen([get(object.function_name_control,'String') '.m'],'w');
+%code = [];
+%code = sprintf('function output = %s(%s)\n%s\noutput=0;\n',get(object.function_name_control,'String'),get(object.function_inputs_control,'String'),'%%#eml');
+%code = [code object.generate_code(object.Grid1,object.Grid2,0)];
+code = object.EMLGen.generate_eml_code;
+
+fprintf(fileid,code);
+% save an extra file called expression_name.data which
+% contains a binary representation of the current gui object.
+filename = [get(object.function_name_control,'String') '.table'];
+%save(filename,'object');
+object.save_data;
+
+object.save_settings;
+object.Data.save;
+fclose(fileid);
+end
 
-            object.save_settings;
-            object.Data.save;
-            fclose(fileid);
-        end
-        
-  
\ No newline at end of file
diff --git a/@GUI/save_results.m b/@GUI/save_results.m
index ae44757605267a81cbce66b9fad09bf1c4e1e13c..5644c2bc745a9231ff8570c3ca641194139e8358 100644
--- a/@GUI/save_results.m
+++ b/@GUI/save_results.m
@@ -1,14 +1,16 @@
-        %% save_results
-        %   Save as save_conditions but for the results grid, since not a
-        %   recursive datatype we do not need to recurse.
-        % inputs:
-        %   obj:GUI - current GUI object
-        %   grid:RGrid - results grid to be saved.
-        % outputs:
-        %   none
-        function [] = save_results(object,grid)
-            for i=1:size(grid.Cells,2)
-                grid.Cells(i).result_text = get(grid.Cells(i).result,'String');
-            end
-        end
-        
+%% save_results
+%   Save as save_conditions but for the results grid, since not a
+%   recursive datatype we do not need to recurse.
+% inputs:
+%   obj:GUI - current GUI object
+%   grid:RGrid - results grid to be saved.
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = save_results(object,grid)
+for i=1:size(grid.Cells,2)
+    grid.Cells(i).result_text = get(grid.Cells(i).result,'String');
+end
+end
+
diff --git a/@GUI/save_settings.m b/@GUI/save_settings.m
index e5d5f21d7f329bd3477e32e963789e5f6ca2d5c9..ff588cd80af8c795ae0c6fb43821e31a82d5b9bc 100644
--- a/@GUI/save_settings.m
+++ b/@GUI/save_settings.m
@@ -1,16 +1,18 @@
-        %% save_settings
-        %    save just the settings to the data object
-        % inputs:
-        %   object:GUI - current GUI object
-        % outputs:
-        %   none
-        function [] = save_settings(object)
-            set.set = 1;
-            set.inputs = object.settings.pvs_includes;
-            set.count = object.settings.counter_trials;
-            set.range = object.settings.counter_range;
-            object.Data.settings = set;
-            object.Data.function_name = get(object.function_name_control,'String');
-            object.Data.function_inputs = get(object.function_inputs_control,'String');
-        end
-        
+%% save_settings
+%    save just the settings to the data object
+% inputs:
+%   object:GUI - current GUI object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = save_settings(object)
+set.set = 1;
+set.inputs = object.settings.pvs_includes;
+set.count = object.settings.counter_trials;
+set.range = object.settings.counter_range;
+object.Data.settings = set;
+object.Data.function_name = get(object.function_name_control,'String');
+object.Data.function_inputs = get(object.function_inputs_control,'String');
+end
+
diff --git a/@GUI/setData.m b/@GUI/setData.m
index 2041d56ea502b9c50c6b3309845a4f5b4127eaf1..f86079ca2c010c736901615fc8e9c478ef0fb740 100644
--- a/@GUI/setData.m
+++ b/@GUI/setData.m
@@ -1,22 +1,23 @@
 %% setData
-        %   set the gui data object based on inputed data structure
-        % inputs:
-        %   obj:GUI - GUI object
-        %   Data:Data - Data object
-        % outputs:
-        %   object:GUI - object that is created
-        function [] = setData(object,Data)
-            object.Data = Data;
-            object.Grid0 = Data.Grid0;
-            object.Grid1 = Data.Grid1;
-            object.Grid2 = Data.Grid2;
-            object.pvs_checked = Data.checked;
-            object.function_name_text = Data.function_name;
-            object.function_inputs_text = Data.function_inputs;
-            object.multi_mode = Data.multi_mode;
-            if isempty(object.multi_mode)
-                object.multi_mode = 0;
-            end
-        end
-        
-        
\ No newline at end of file
+%   set the gui data object based on inputed data structure
+% inputs:
+%   obj:GUI - GUI object
+%   Data:Data - Data object
+% outputs:
+%   object:GUI - object that is created
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = setData(object,Data)
+object.Data = Data;
+object.Grid0 = Data.Grid0;
+object.Grid1 = Data.Grid1;
+object.Grid2 = Data.Grid2;
+object.pvs_checked = Data.checked;
+object.function_name_text = Data.function_name;
+object.function_inputs_text = Data.function_inputs;
+object.multi_mode = Data.multi_mode;
+if isempty(object.multi_mode)
+    object.multi_mode = 0;
+end
+end
+
diff --git a/@GUI/setPBenable.m b/@GUI/setPBenable.m
index 8d1828d8af3a6698ac2112de7a0479f99cd4e6e7..6453143fd57b08e06fb9321e8b54f1170eabf803 100644
--- a/@GUI/setPBenable.m
+++ b/@GUI/setPBenable.m
@@ -1,22 +1,24 @@
-        
-        %% setBPenable
-        %    enable or diable the delete cell buttons based on the size of
-        %    a grid, so that you can't delete below one cell.
-        % inputs:
-        %   object:GUI - current GUI object
-        % outputs:
-        %   none
-        function [] = setPBenable(object)
-           if size(object.Grid1.cells,2) > 1
-                set(object.Grid1.delete_cell_pb,'Enable','on');
-           else
-                set(object.Grid1.delete_cell_pb,'Enable','off');
-           end
-           
-           if size(object.Grid2.cells,2) > 1
-                set(object.Grid2.delete_cell_pb,'Enable','on');
-           else
-                set(object.Grid2.delete_cell_pb,'Enable','off');
-           end
-            
-        end
\ No newline at end of file
+
+%% setBPenable
+%    enable or diable the delete cell buttons based on the size of
+%    a grid, so that you can't delete below one cell.
+% inputs:
+%   object:GUI - current GUI object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = setPBenable(object)
+if size(object.Grid1.cells,2) > 1
+    set(object.Grid1.delete_cell_pb,'Enable','on');
+else
+    set(object.Grid1.delete_cell_pb,'Enable','off');
+end
+
+if size(object.Grid2.cells,2) > 1
+    set(object.Grid2.delete_cell_pb,'Enable','on');
+else
+    set(object.Grid2.delete_cell_pb,'Enable','off');
+end
+
+end
\ No newline at end of file
diff --git a/@GUI/set_command_pos.m b/@GUI/set_command_pos.m
index bcbdf1874efefe44affe0585aa755d06ea365683..ca1eec8fe5264578d43161167fb84c8659955c6a 100644
--- a/@GUI/set_command_pos.m
+++ b/@GUI/set_command_pos.m
@@ -1,29 +1,30 @@
- %% set_command_pos
-        %    sets the location of all the command buttons, labels and edit
-        %    boxes, places objects at the top of the figure which it
-        %    determines by looking at the height of the figure handle
-        % inputs:
-        %   obj:GUI - current GUI object
-        % outputs:
-        %   none
-        function [] = set_command_pos(object)
-            figpos = get(object.fig,'Position');
-            % figure out the height of the figure
-            l_fig_height = figpos(4);
-            set(object.edit_tog,'Position',[object.pb_offset l_fig_height-object.pb_offset-object.pb_height object.pb_width object.pb_height])
-            set(object.save_pb,'Position',[object.pb_offset*2+object.pb_width,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
-            set(object.close_pb,'Position',[object.pb_offset*3+object.pb_width*2,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
-            set(object.save_ext_pb,'Position',[object.pb_offset*4+object.pb_width*3,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
-            set(object.check_pb,'Position',[object.pb_offset*5+object.pb_width*4,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
-            set(object.pvs_pb,'Position',[object.pb_offset*6+object.pb_width*5,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
-            set(object.input_pb,'Position',[object.pb_offset*7+object.pb_width*6,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
-            set(object.settings_pb,'Position',[object.pb_offset*8+object.pb_width*7,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
+%% set_command_pos
+%    sets the location of all the command buttons, labels and edit
+%    boxes, places objects at the top of the figure which it
+%    determines by looking at the height of the figure handle
+% inputs:
+%   obj:GUI - current GUI object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = set_command_pos(object)
+figpos = get(object.fig,'Position');
+% figure out the height of the figure
+l_fig_height = figpos(4);
+set(object.edit_tog,'Position',[object.pb_offset l_fig_height-object.pb_offset-object.pb_height object.pb_width object.pb_height])
+set(object.save_pb,'Position',[object.pb_offset*2+object.pb_width,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
+set(object.close_pb,'Position',[object.pb_offset*3+object.pb_width*2,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
+set(object.save_ext_pb,'Position',[object.pb_offset*4+object.pb_width*3,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
+set(object.check_pb,'Position',[object.pb_offset*5+object.pb_width*4,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
+set(object.pvs_pb,'Position',[object.pb_offset*6+object.pb_width*5,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
+set(object.input_pb,'Position',[object.pb_offset*7+object.pb_width*6,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
+set(object.settings_pb,'Position',[object.pb_offset*8+object.pb_width*7,l_fig_height-object.pb_offset-object.pb_height,object.pb_width,object.pb_height])
+
+set(object.input_label,'Position',[object.pb_offset l_fig_height-object.pb_offset*3-object.pb_height-object.htx_height object.pb_width object.htx_height]);
+set(object.function_inputs_control,'Position',[object.pb_offset*2+object.pb_width l_fig_height-object.pb_offset*3-object.htx_height-object.pb_height object.text_width object.htx_height]);
+set(object.name_label,'Position',[object.pb_offset*2+object.pb_width+object.text_width l_fig_height-object.pb_offset*3-object.pb_height-object.htx_height object.pb_width object.htx_height]);
+set(object.function_name_control,'Position',[object.pb_offset*3+object.pb_width*2+object.text_width l_fig_height-object.pb_offset*3-object.pb_height-object.htx_height object.text_width object.htx_height]);
+%set(object.multi_grp,'Position',[object.pb_offset*3+object.pb_width*2+object.text_width l_fig_height-object.pb_offset*3-object.pb_height-object.htx_height*2 object.text_width object.htx_height]);
+end
 
-            set(object.input_label,'Position',[object.pb_offset l_fig_height-object.pb_offset*3-object.pb_height-object.htx_height object.pb_width object.htx_height]);
-            set(object.function_inputs_control,'Position',[object.pb_offset*2+object.pb_width l_fig_height-object.pb_offset*3-object.htx_height-object.pb_height object.text_width object.htx_height]);
-            set(object.name_label,'Position',[object.pb_offset*2+object.pb_width+object.text_width l_fig_height-object.pb_offset*3-object.pb_height-object.htx_height object.pb_width object.htx_height]);
-            set(object.function_name_control,'Position',[object.pb_offset*3+object.pb_width*2+object.text_width l_fig_height-object.pb_offset*3-object.pb_height-object.htx_height object.text_width object.htx_height]);
-            %set(object.multi_grp,'Position',[object.pb_offset*3+object.pb_width*2+object.text_width l_fig_height-object.pb_offset*3-object.pb_height-object.htx_height*2 object.text_width object.htx_height]);
-        end
-        
-     
\ No newline at end of file
diff --git a/@GUI/set_grid.m b/@GUI/set_grid.m
index 803a10975f98ebdd1e4b80e9b2e1fadeacbfd370..c6eb70086a7453f39fc2257156dce71ebd4ce8b1 100644
--- a/@GUI/set_grid.m
+++ b/@GUI/set_grid.m
@@ -1,16 +1,18 @@
-        %% set_grid
-        %    allows accessing objects to set the grid variables to the
-        %    inputed objects
-        % inputs:
-        %   obj:GUI - current GUI object
-        %   grid2:Grid - Grid on the left
-        %   grid1:Grid - Grid on the top
-        %   grid0:RGrid - Results grid
-        % outputs:
-        %   none
-        function [] = set_grid(object,grid2,grid1,grid0)
-            object.Grid2 = grid2;
-            object.Grid1 = grid1;
-            object.Grid0 = grid0;
-        end
-        
+%% set_grid
+%    allows accessing objects to set the grid variables to the
+%    inputed objects
+% inputs:
+%   obj:GUI - current GUI object
+%   grid2:Grid - Grid on the left
+%   grid1:Grid - Grid on the top
+%   grid0:RGrid - Results grid
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = set_grid(object,grid2,grid1,grid0)
+object.Grid2 = grid2;
+object.Grid1 = grid1;
+object.Grid0 = grid0;
+end
+
diff --git a/@GUI/settings_call.m b/@GUI/settings_call.m
index 1a32f7026c3b433f36b914a8313827d0bc9d9058..ccbb260010654a0b34cc5e5ba3eecc64af96c693 100644
--- a/@GUI/settings_call.m
+++ b/@GUI/settings_call.m
@@ -1,14 +1,15 @@
-      %% settings_call
-        %   open up the settings window
-        % inputs:
-        %   obj:GUI - GUI objecto
-        %   src:double - source of the callback calling
-        %   event:eventdata - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = settings_call(object,src,event)
-            object.settings.show;
-            
-        end
-        
-    
\ No newline at end of file
+%% settings_call
+%   open up the settings window
+% inputs:
+%   obj:GUI - GUI objecto
+%   src:double - source of the callback calling
+%   event:eventdata - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = settings_call(object,src,event)
+object.settings.show;
+
+end
+
diff --git a/@GUI/textbox_callback.m b/@GUI/textbox_callback.m
index afec9062ead363e816b9545a4304daa5657b28f0..879f822bb8b74137e94e758fdde2de103326736b 100644
--- a/@GUI/textbox_callback.m
+++ b/@GUI/textbox_callback.m
@@ -1,57 +1,59 @@
 %% textbox_callback
-        %    callback for when the text of a callback is changed.
-        % inputs:
-        %   object - current GUI object
-        %   src - source of the callback calling
-        %   event - event that triggered the callback
-        % outputs:
-        %   none   
-        function [] = textbox_callback(object,src,event)
-            % make sure the character pressed isn't empty
-            
-            if((strcmp(event.Character,'z')) && (strcmp(char(event.Modifier),'command') || strcmp(char(event.Modifier),'control')))
-                return
-            end
-            if((strcmp(event.Character,'r')) && (strcmp(char(event.Modifier),'command') || strcmp(char(event.Modifier),'control')))
-                return
-            end
-             if(~isempty(unicode2native(event.Character)))
-                 % make sure the character is a printable character
-                 if event.Character > 33 || event.Character == 8
-                     if object.pvs_checked == 1
-                     object.pvs_checked = 0;
-                     object.update_Statusbar
-                         if (object.mode == 1)
-                             TableBlock.set_block_display(object.block_handle,object.pvs_checked);
-                         end
-                     end
-                 end
-                %if time > 0.2
-                
-                %uicontrol(object.function_name_control);
-                
-                % hack because api does not update the string field of
-                % textbox until after it loses focus. temporarily focus on
-                % label, read string, refocus on textbox.
-                uicontrol(object.name_label);
-                   
-                
-                undo_data.action = 1;
-                undo_data.grid = [];
-                undo_data.cell = src;
-                undo_data.text = get(src,'String');
-               undo_data.subgrid = []
-                
-                object.undo_man.new_state(undo_data);
-                %end
-                tic;
-                uicontrol(src);
-                figure(object.fig);
-                
-            %end
-           
-            object.update_undoredo
+%    callback for when the text of a callback is changed.
+% inputs:
+%   object - current GUI object
+%   src - source of the callback calling
+%   event - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = textbox_callback(object,src,event)
+% make sure the character pressed isn't empty
 
-
-            
-        end
\ No newline at end of file
+if((strcmp(event.Character,'z')) && (strcmp(char(event.Modifier),'command') || strcmp(char(event.Modifier),'control')))
+    return
+end
+if((strcmp(event.Character,'r')) && (strcmp(char(event.Modifier),'command') || strcmp(char(event.Modifier),'control')))
+    return
+end
+if(~isempty(unicode2native(event.Character)))
+    % make sure the character is a printable character
+    if event.Character > 33 || event.Character == 8
+        if object.pvs_checked == 1
+            object.pvs_checked = 0;
+            object.update_Statusbar
+            if (object.mode == 1)
+                TableBlock.set_block_display(object.block_handle,object.pvs_checked);
+            end
+        end
+    end
+    %if time > 0.2
+    
+    %uicontrol(object.function_name_control);
+    
+    % hack because api does not update the string field of
+    % textbox until after it loses focus. temporarily focus on
+    % label, read string, refocus on textbox.
+    uicontrol(object.name_label);
+    
+    
+    undo_data.action = 1;
+    undo_data.grid = [];
+    undo_data.cell = src;
+    undo_data.text = get(src,'String');
+    undo_data.subgrid = []
+    
+    object.undo_man.new_state(undo_data);
+    %end
+    tic;
+    uicontrol(src);
+    figure(object.fig);
+    
+    %end
+    
+    object.update_undoredo
+    
+    
+    
+end
\ No newline at end of file
diff --git a/@GUI/undo_call.m b/@GUI/undo_call.m
index 3568ee8b6fa19778f3dfefa356b7734e1094367d..fbb4680686a3946dd42430606f9be6465493f62e 100644
--- a/@GUI/undo_call.m
+++ b/@GUI/undo_call.m
@@ -1,44 +1,46 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [] = undo_call(object,src,event)
 %UNTITLED Summary of this function goes here
 %   Detailed explanation goes here
 object.undo_man
- recalled_data = object.undo_man.undo;
- if isempty(recalled_data);
-     return;
- else
-     switch recalled_data.action
-         case 1 % changed cell contents
-             try
-             set(recalled_data.cell,'String',recalled_data.text);
-             catch exception
-             end
-         case 2 % created new cell in grid
-             recalled_data.grid.pb_delete_call(recalled_data.grid.delete_cell_pb,1);
-         case 3 % deleted cell in grid (not the last)
-             recalled_data.grid.cells = [recalled_data.grid.cells recalled_data.cell];
-             recalled_data.grid.num_cells = recalled_data.grid.num_cells + 1;
+recalled_data = object.undo_man.undo;
+if isempty(recalled_data);
+    return;
+else
+    switch recalled_data.action
+        case 1 % changed cell contents
+            try
+                set(recalled_data.cell,'String',recalled_data.text);
+            catch exception
+            end
+        case 2 % created new cell in grid
+            recalled_data.grid.pb_delete_call(recalled_data.grid.delete_cell_pb,1);
+        case 3 % deleted cell in grid (not the last)
+            recalled_data.grid.cells = [recalled_data.grid.cells recalled_data.cell];
+            recalled_data.grid.num_cells = recalled_data.grid.num_cells + 1;
             % refresh the rGrid so that a new results cell is created
             if(~isempty(recalled_data.grid.rGrid))
                 recalled_data.grid.rGrid.refresh;
             end
-             object.reset_wh();
+            object.reset_wh();
             %gui.draw_grid2(gui.Grid2);
             object.draw_allgrids(1);
             object.undo_man.search_replace(1,recalled_data.subgrid,recalled_data.cell.cond);
             set(recalled_data.grid.delete_cell_pb,'Enable','on');
-        
-         case 4 % new grid
-             recalled_data.grid.deep_delete;
-             recalled_data.cell.subgrid = [];
-             recalled_data.cell.pb_flag = 1;
-             object.reset_wh();
+            
+        case 4 % new grid
+            recalled_data.grid.deep_delete;
+            recalled_data.cell.subgrid = [];
+            recalled_data.cell.pb_flag = 1;
+            object.reset_wh();
             %gui.draw_grid2(gui.Grid2);
             object.draw_allgrids(1);
             
-         case 5 % deleting last cell in grid
+        case 5 % deleting last cell in grid
             recalled_data.cell.subgrid = recalled_data.grid;
             recalled_data.cell.pb_flag = 0;
-             if(~isempty(recalled_data.cell.parent_grid.rGrid))
+            if(~isempty(recalled_data.cell.parent_grid.rGrid))
                 recalled_data.cell.parent_grid.rGrid.delete_g2s(recalled_data.cell);
             end
             if(~isempty(recalled_data.grid.rGrid))
@@ -47,20 +49,20 @@ object.undo_man
             object.reset_wh();
             %gui.draw_grid2(gui.Grid2);
             object.draw_allgrids(1);
-%             object.undo_call([],[]);
+            %             object.undo_call([],[]);
             
             recalled_data.grid.cells = [recalled_data.grid.cells recalled_data.subgrid];
-             recalled_data.grid.num_cells = recalled_data.grid.num_cells + 1;
+            recalled_data.grid.num_cells = recalled_data.grid.num_cells + 1;
             % refresh the rGrid so that a new results cell is created
             if(~isempty(recalled_data.grid.rGrid))
                 recalled_data.grid.rGrid.refresh;
             end
-             object.reset_wh();
+            object.reset_wh();
             %gui.draw_grid2(gui.Grid2);
             object.draw_allgrids(1);
             set(recalled_data.grid.delete_cell_pb,'Enable','on');
-     end
- end
+    end
+end
 % object.setData(recalled_data);
 % object.set_command_pos;
 %             object.reset_wh();
diff --git a/@GUI/update_Statusbar.m b/@GUI/update_Statusbar.m
index 2628999195193382a64a6da4f32c27429780f22b..d09d93c8a5ea1a655b257383e1d2c6401f7a7668 100644
--- a/@GUI/update_Statusbar.m
+++ b/@GUI/update_Statusbar.m
@@ -1,27 +1,28 @@
 %% update_Statusbar
-        %   update the statusbar located at bottom of window based on
-        %   current state of typecheckness
-        % inputs:
-        %   obj:GUI - GUI object
-        % outputs:
-        %   none
-        function [] = update_Statusbar(object)
-            
-        warning off MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame
-            % statusbar depends on JavaFrame which may be obsolete in
-            % future versions of Matlab, can still use in old versions
-            try
-                if (object.pvs_checked == 0)
-                   sb = statusbar(object.fig, 'Status: Not Typechecked');
-                   set(sb.TextPanel,'Foreground',[1,0,0]);
-                elseif (object.pvs_checked == 1)
-                  sb = statusbar(object.fig, 'Status: Typechecked');
-                   set(sb.TextPanel,'Foreground',[0,1,0]);
+%   update the statusbar located at bottom of window based on
+%   current state of typecheckness
+% inputs:
+%   obj:GUI - GUI object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = update_Statusbar(object)
 
-                end
-            catch exception
-                % do nothing if exception found, may change in future.
-                
-            end
-        end
- 
\ No newline at end of file
+warning off MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame
+% statusbar depends on JavaFrame which may be obsolete in
+% future versions of Matlab, can still use in old versions
+try
+    if (object.pvs_checked == 0)
+        sb = statusbar(object.fig, 'Status: Not Typechecked');
+        set(sb.TextPanel,'Foreground',[1,0,0]);
+    elseif (object.pvs_checked == 1)
+        sb = statusbar(object.fig, 'Status: Typechecked');
+        set(sb.TextPanel,'Foreground',[0,1,0]);
+        
+    end
+catch exception
+    % do nothing if exception found, may change in future.
+    
+end
+end
diff --git a/@GUI/update_multi_check_status.m b/@GUI/update_multi_check_status.m
index c566299e866db5ea4f15ef2fed36bc4e7fe4f181..4a0229ed5791d82f97202aa871402621a6e659af 100644
--- a/@GUI/update_multi_check_status.m
+++ b/@GUI/update_multi_check_status.m
@@ -1,7 +1,9 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function update_multi_check_status( object )
 
 
-if object.multi_mode == 0 
+if object.multi_mode == 0
     set(object.multi_opt_reg,'Checked','on');
     set(object.multi_opt_out,'Checked','off');
 else
diff --git a/@GUI/update_undoredo.m b/@GUI/update_undoredo.m
index 48d1d43b49c1a753cd36b85e8157508e965a53e1..7aa78341e66c9ccfa6da1a3e147f8bcf0019daf0 100644
--- a/@GUI/update_undoredo.m
+++ b/@GUI/update_undoredo.m
@@ -1,3 +1,5 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [ ] = update_undoredo( object )
 % updates the menu options so that they are either enabled or disabled
 
@@ -10,10 +12,10 @@ end
 if (object.undo_man.current_depth == 0)
     set(object.undo_opt,'Enable','off');
 else
-        set(object.undo_opt,'Enable','on');
+    set(object.undo_opt,'Enable','on');
 end
 
-    
+
 
 
 end
diff --git a/@Grid/Grid.m b/@Grid/Grid.m
index 8d91625ee8065aa60d18273f4c47d39e7b91bb69..9b4425c6c1cb2775450b370c917f70fa5eb07b10 100644
--- a/@Grid/Grid.m
+++ b/@Grid/Grid.m
@@ -1,5 +1,7 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 classdef Grid < handle
-
+    
     properties
         parent_cell = [];
         parent_grid = [];
diff --git a/@Grid/clone.m b/@Grid/clone.m
index c0ed182e31a0c7faf8bcd2c822b3b628f4d779c4..842e29efc65d33ee3d0245051aab84d5b2ff904f 100644
--- a/@Grid/clone.m
+++ b/@Grid/clone.m
@@ -1,25 +1,27 @@
-    %% clone
-         %    function will create a copy of the current grid and store it
-         %    in dest_grid, since grid is a recursive datatype this is a
-         %    recursive function in order to do a deep clone.
-         % inputs:
-         %   object:Grid - current Grid object
-         %   dest_grid:Grid - grid to copy contents to
-         %   index:int - index of the current grid
-         %   p_cell:Cell - parent cell of the current grid.
-         % outputs:
-         %   none
-         function [] = clone(object,dest_grid,index,p_cell)
-            for i=1:size(object.cells,2)
-                dest_grid.new_Cell();
-                dest_grid.cells(i).cond_text = object.cells(i).cond_text;
-                if (~isempty(object.cells(i).subgrid))
-                    dest_grid.cells(i).subgrid = Grid(dest_grid.cells(i).cell_index,dest_grid.cells(i));
-                    dest_grid.cells(i).subgrid.set_rGrid(dest_grid.cells(i).parent_grid.rGrid);
-                   object.cells(i).subgrid.clone(dest_grid.cells(i).subgrid,object.cells(i).subgrid.grid_index,dest_grid.cells(i))
-                else
-                    
-                end
-                
-            end
-         end
\ No newline at end of file
+%% clone
+%    function will create a copy of the current grid and store it
+%    in dest_grid, since grid is a recursive datatype this is a
+%    recursive function in order to do a deep clone.
+% inputs:
+%   object:Grid - current Grid object
+%   dest_grid:Grid - grid to copy contents to
+%   index:int - index of the current grid
+%   p_cell:Cell - parent cell of the current grid.
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = clone(object,dest_grid,index,p_cell)
+for i=1:size(object.cells,2)
+    dest_grid.new_Cell();
+    dest_grid.cells(i).cond_text = object.cells(i).cond_text;
+    if (~isempty(object.cells(i).subgrid))
+        dest_grid.cells(i).subgrid = Grid(dest_grid.cells(i).cell_index,dest_grid.cells(i));
+        dest_grid.cells(i).subgrid.set_rGrid(dest_grid.cells(i).parent_grid.rGrid);
+        object.cells(i).subgrid.clone(dest_grid.cells(i).subgrid,object.cells(i).subgrid.grid_index,dest_grid.cells(i))
+    else
+        
+    end
+    
+end
+end
\ No newline at end of file
diff --git a/@Grid/deep_delete.m b/@Grid/deep_delete.m
index 4ee31856df78d788308048c7cdf95c619a935e66..2034a3aba2c177f8307e272ceb8bede3004ea111 100644
--- a/@Grid/deep_delete.m
+++ b/@Grid/deep_delete.m
@@ -1,24 +1,25 @@
 %% deep_delete
-         %    deletes an entire grid as well as all the subgrids associated
-         %    with it.
-         % inputs:
-         %   object:Grid - current Grid object
-         % outputs:
-         %   none
-         function [] = deep_delete(object)
-             % loop through each cell and delete the associated result
-             % cells and call delete_Cell on each of the cells, which will
-             % then call deep_delete on its subgrids.
-             for i=size(object.cells,2):-1:1
-                 object.rGrid.delete_g2s(object.cells(i));
-                 object.cells(i).delete_Cell;
-                 %object.cells(i) = [];
-             end
-             delete(object.new_cell_pb)
-             delete(object.delete_cell_pb)
-             object.new_cell_pb = [];
-             object.delete_cell_pb = [];
-             
-         end
-         
-     
\ No newline at end of file
+%    deletes an entire grid as well as all the subgrids associated
+%    with it.
+% inputs:
+%   object:Grid - current Grid object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = deep_delete(object)
+% loop through each cell and delete the associated result
+% cells and call delete_Cell on each of the cells, which will
+% then call deep_delete on its subgrids.
+for i=size(object.cells,2):-1:1
+    object.rGrid.delete_g2s(object.cells(i));
+    object.cells(i).delete_Cell;
+    %object.cells(i) = [];
+end
+delete(object.new_cell_pb)
+delete(object.delete_cell_pb)
+object.new_cell_pb = [];
+object.delete_cell_pb = [];
+
+end
+
diff --git a/@Grid/delete_Cell.m b/@Grid/delete_Cell.m
index d4d1f8de22baad38982d34d79d200bfd4141e0e6..2d9fe0c21292a6b9141f9571fabf33df960246c8 100644
--- a/@Grid/delete_Cell.m
+++ b/@Grid/delete_Cell.m
@@ -1,25 +1,26 @@
 %% delete_Cell
-        %    deletes the last cell in the grid, also deletes an associated
-        %    new grid push button,
-        %    TODO, need to implement the case where last cell is deleted.
-        % inputs:
-        %   object:Grid - current Grid object
-        % outputs
-        %   none
-        function [] = delete_Cell(object)
-            
-           
-           last_cell = object.num_cells;
-           object.rGrid.delete_g2s(object.cells(end));
-           %delete(object.cells(end).cond)
-           object.cells(end).cond = [];
-           %delete(object.cells(end).grid_pb);
-           object.cells(end).grid_pb = [];
-           %delete(object.cells(end))
-           object.cells(end) = [];
-           if(~isempty(object.rGrid))
-                object.rGrid.refresh;
-            end
-        end
-    
-        
\ No newline at end of file
+%    deletes the last cell in the grid, also deletes an associated
+%    new grid push button,
+%    TODO, need to implement the case where last cell is deleted.
+% inputs:
+%   object:Grid - current Grid object
+% outputs
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = delete_Cell(object)
+
+
+last_cell = object.num_cells;
+object.rGrid.delete_g2s(object.cells(end));
+%delete(object.cells(end).cond)
+object.cells(end).cond = [];
+%delete(object.cells(end).grid_pb);
+object.cells(end).grid_pb = [];
+%delete(object.cells(end))
+object.cells(end) = [];
+if(~isempty(object.rGrid))
+    object.rGrid.refresh;
+end
+end
+
diff --git a/@Grid/max_width.m b/@Grid/max_width.m
index e4ee6165bd18f6d73808a65fb1b586fad6b48d0c..69610a043c3dbb734e5be13ce0751c69f1fe2cda 100644
--- a/@Grid/max_width.m
+++ b/@Grid/max_width.m
@@ -1,24 +1,25 @@
 
-        %% max_width
-        %    determines the maximum width from a current grid, the maximum
-        %    widht represents the number of levels of subgrids from a given
-        %    grid.
-        % inputs:
-        %   object:Grid - current Grid object
-        % outputs:
-        %   m:integer - value representing the maximum width from the
-        %   current grid.
-        function m = max_width(object,width)
-            temp = [];
-            for i=1:size(object.cells,2)
-                if (~isempty(object.cells(i).subgrid))
-                    temp = [temp object.cells(i).subgrid.max_width(width+1)];
-                else
-                    temp = [temp width];
-                end
-                
-            end
-            m = max(temp);
-        end
-        
-        
\ No newline at end of file
+%% max_width
+%    determines the maximum width from a current grid, the maximum
+%    widht represents the number of levels of subgrids from a given
+%    grid.
+% inputs:
+%   object:Grid - current Grid object
+% outputs:
+%   m:integer - value representing the maximum width from the
+%   current grid.
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function m = max_width(object,width)
+temp = [];
+for i=1:size(object.cells,2)
+    if (~isempty(object.cells(i).subgrid))
+        temp = [temp object.cells(i).subgrid.max_width(width+1)];
+    else
+        temp = [temp width];
+    end
+    
+end
+m = max(temp);
+end
+
diff --git a/@Grid/new_Cell.m b/@Grid/new_Cell.m
index 24a5b9be4654cf6fe016ebfa900956f153e0e324..8f1e325e1def4636c450ce797bbbc1f30d43309d 100644
--- a/@Grid/new_Cell.m
+++ b/@Grid/new_Cell.m
@@ -1,17 +1,18 @@
- %% new_Cell
-        %    creates a new cell in the current grid.
-        % inputs:
-        %   object:Grid - current Grid object
-        % outputs:
-        %   none
-        function [] = new_Cell(object)
-           cell = Cell(object.num_cells+1,object);
-            object.num_cells = object.num_cells + 1;
-            object.cells = [object.cells cell];
-            % refresh the rGrid so that a new results cell is created
-            if(~isempty(object.rGrid))
-                object.rGrid.refresh;
-            end
-        end
-        
-        
\ No newline at end of file
+%% new_Cell
+%    creates a new cell in the current grid.
+% inputs:
+%   object:Grid - current Grid object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = new_Cell(object)
+cell = Cell(object.num_cells+1,object);
+object.num_cells = object.num_cells + 1;
+object.cells = [object.cells cell];
+% refresh the rGrid so that a new results cell is created
+if(~isempty(object.rGrid))
+    object.rGrid.refresh;
+end
+end
+
diff --git a/@Grid/pb_delete_call.m b/@Grid/pb_delete_call.m
index e0719897fde308effbfcc598ee6e5568a5f156a5..af316c79cc8c25e2940456a0b963b2e2d3039d69 100644
--- a/@Grid/pb_delete_call.m
+++ b/@Grid/pb_delete_call.m
@@ -7,6 +7,8 @@
 %   event:eventdata - event that triggered the callback
 % outputs:
 %   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [] = pb_delete_call(object,src,event)
 gui = get(src,'userdata');
 gui.save_data;
@@ -20,22 +22,22 @@ if size(object.cells,2) == 1
         
         
         if isempty(event) || event ~= 1
-        
+            
             undo_data.action = 5;
             undo_data.grid = object;
             undo_data.cell = object.parent_cell;
             undo_data.text = deleted_cell.cond;
             undo_data.subgrid = deleted_cell;
-
+            
             gui.undo_man.new_state(undo_data);
-        
-         end
+            
+        end
         
     end
     
     
 else
-     if isempty(event) || event ~= 1
+    if isempty(event) || event ~= 1
         
         undo_data.action = 3;
         undo_data.grid = object;
@@ -46,7 +48,7 @@ else
         gui.undo_man.new_state(undo_data);
         
     end
-   
+    
 end
 
 % button could be pressed in the left or top grid so we need to
@@ -73,7 +75,7 @@ if size(object.cells,2) == 0
     end
     
     
-
+    
 end
 
 
diff --git a/@Grid/pb_new_call.m b/@Grid/pb_new_call.m
index 2a9c4d78df5d2f8b8333e7dcc713956081ea14c4..e18a39a0d15d7f01bfd10bfd513e128766638fae 100644
--- a/@Grid/pb_new_call.m
+++ b/@Grid/pb_new_call.m
@@ -1,38 +1,39 @@
 %% pb_new_call
-        %    call back function for the new cell push button. When button
-        %    is pressed a new cell object is created in the current grid 
-        %    and the table is redrawn
-        % inputs:
-        %   object:Grid - current Grid object
-        %   src:double - source of the callback calling
-        %   event:eventdata - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = pb_new_call(object,src,event)
-           gui = get(src,'userdata');
-            object.new_Cell;
-            gui.reset_wh();
-            %gui.draw_grid2(gui.Grid2);
-            gui.draw_allgrids(0);
-            if size(object.cells,2) > 1
-                set(object.delete_cell_pb,'Enable','on');
-            else
-                set(object.delete_cell_pb,'Enable','off');
-            end
-            
-            if isempty(event) || event ~= 1
-            undo_data.action = 2;
-            undo_data.grid = object;
-            undo_data.cell = [];
-            undo_data.text = [];
-            undo_data.subgrid = []
-            
-            
-            gui.undo_man.new_state(undo_data);
-            end
-            gui.update_undoredo
+%    call back function for the new cell push button. When button
+%    is pressed a new cell object is created in the current grid
+%    and the table is redrawn
+% inputs:
+%   object:Grid - current Grid object
+%   src:double - source of the callback calling
+%   event:eventdata - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = pb_new_call(object,src,event)
+gui = get(src,'userdata');
+object.new_Cell;
+gui.reset_wh();
+%gui.draw_grid2(gui.Grid2);
+gui.draw_allgrids(0);
+if size(object.cells,2) > 1
+    set(object.delete_cell_pb,'Enable','on');
+else
+    set(object.delete_cell_pb,'Enable','off');
+end
+
+if isempty(event) || event ~= 1
+    undo_data.action = 2;
+    undo_data.grid = object;
+    undo_data.cell = [];
+    undo_data.text = [];
+    undo_data.subgrid = []
+    
+    
+    gui.undo_man.new_state(undo_data);
+end
+gui.update_undoredo
+
+
+end
 
-            
-        end
-        
-       
\ No newline at end of file
diff --git a/@Grid/set_delete_pb.m b/@Grid/set_delete_pb.m
index 2a52f208b230e8f6276f6ccc04c263d1f950ad7b..3f817d4506699bc3b330132c945c68be94749fed 100644
--- a/@Grid/set_delete_pb.m
+++ b/@Grid/set_delete_pb.m
@@ -1,21 +1,22 @@
 %% set_delete_pb
-        %    create the delete cell push button
-        % inputs:
-        %   object:Grid - current Grid object
-        % outputs:
-        %   none
-        function [] = set_delete_pb(object,fig,pos)
-            if(isempty(object.delete_cell_pb) || ~ishghandle(object.delete_cell_pb))
-            object.delete_cell_pb = uicontrol('style','push',...
-                'units','pix',...
-                'string','delete',...
-                'HorizontalAlign','left',...
-                'Parent',fig,...
-                'position',pos,...
-                'callback',@(src,event)pb_delete_call(object,src,event));
-            else
-                set(object.delete_cell_pb,'position',pos);
-            end
-        end
-        
-        
\ No newline at end of file
+%    create the delete cell push button
+% inputs:
+%   object:Grid - current Grid object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = set_delete_pb(object,fig,pos)
+if(isempty(object.delete_cell_pb) || ~ishghandle(object.delete_cell_pb))
+    object.delete_cell_pb = uicontrol('style','push',...
+        'units','pix',...
+        'string','delete',...
+        'HorizontalAlign','left',...
+        'Parent',fig,...
+        'position',pos,...
+        'callback',@(src,event)pb_delete_call(object,src,event));
+else
+    set(object.delete_cell_pb,'position',pos);
+end
+end
+
diff --git a/@Grid/set_heights.m b/@Grid/set_heights.m
index 1d4532a9d55e7d4269fe3eb1aa2ce3cb5e2e5ae3..a34b4b801f53ae643cd7eb35efd7f676d1b1cd17 100644
--- a/@Grid/set_heights.m
+++ b/@Grid/set_heights.m
@@ -1,20 +1,21 @@
-   %% set_heights
-        %    sets the heights for each of the cells and subcells of a grid,
-        %    uses the cells cal_height method to determine what the heights
-        %    should be.
-        % inputs:
-        %   object:Grid - current Grid object
-        %   edit:boolean - current value of the edit toggle.
-        % outputs:
-        %   none
-        function [] = set_heights(object,edit)
-            for i = 1:size(object.cells,2)
-                if (~isempty(object.cells(i).subgrid))
-                    object.cells(i).subgrid.set_heights(edit);
-                end
-                object.cells(i).height = object.cells(i).cal_height(edit);
-            end
-        
-        end
-        
-       
\ No newline at end of file
+%% set_heights
+%    sets the heights for each of the cells and subcells of a grid,
+%    uses the cells cal_height method to determine what the heights
+%    should be.
+% inputs:
+%   object:Grid - current Grid object
+%   edit:boolean - current value of the edit toggle.
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = set_heights(object,edit)
+for i = 1:size(object.cells,2)
+    if (~isempty(object.cells(i).subgrid))
+        object.cells(i).subgrid.set_heights(edit);
+    end
+    object.cells(i).height = object.cells(i).cal_height(edit);
+end
+
+end
+
diff --git a/@Grid/set_pb.m b/@Grid/set_pb.m
index 70a43a95c50b07e6f3f31a8db35d22ae2a6d4def..e3f91033b59618c966d36ff6b947c44c3222cebb 100644
--- a/@Grid/set_pb.m
+++ b/@Grid/set_pb.m
@@ -1,21 +1,22 @@
- %% set_pb
-        %    create the new cell push button
-        % inputs:
-        %   object:Grid - current Grid object
-        % outputs:
-        %   none
-        function [] = set_pb(object,fig,pos)
-            if(isempty(object.new_cell_pb) || ~ishghandle(object.new_cell_pb))
-            object.new_cell_pb = uicontrol('style','push',...
-                'units','pix',...
-                'string','new',...
-                'HorizontalAlign','left',...
-                'Parent',fig,...
-                'position',pos,...
-                'callback',@(src,event)pb_new_call(object,src,event));
-            else
-                set(object.new_cell_pb,'position',pos);
-            end
-        end
-        
-        
\ No newline at end of file
+%% set_pb
+%    create the new cell push button
+% inputs:
+%   object:Grid - current Grid object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = set_pb(object,fig,pos)
+if(isempty(object.new_cell_pb) || ~ishghandle(object.new_cell_pb))
+    object.new_cell_pb = uicontrol('style','push',...
+        'units','pix',...
+        'string','new',...
+        'HorizontalAlign','left',...
+        'Parent',fig,...
+        'position',pos,...
+        'callback',@(src,event)pb_new_call(object,src,event));
+else
+    set(object.new_cell_pb,'position',pos);
+end
+end
+
diff --git a/@Grid/set_rGrid.m b/@Grid/set_rGrid.m
index 833b9836bc3898559d97c9ba3e37deba61824ed4..6db6dadeb606cdee032b7ed86477e8e1e3209932 100644
--- a/@Grid/set_rGrid.m
+++ b/@Grid/set_rGrid.m
@@ -1,12 +1,13 @@
 %% set_rGrid
-        %    set the reference to the Results grid
-        % inputs:
-        %   object:Grid - current Grid objectect
-        %   r:RGrid - result Grid
-        % outputs:
-        %   none
-        function [] = set_rGrid(object,r)
-            object.rGrid = r;
-        end
-        
-       
\ No newline at end of file
+%    set the reference to the Results grid
+% inputs:
+%   object:Grid - current Grid objectect
+%   r:RGrid - result Grid
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = set_rGrid(object,r)
+object.rGrid = r;
+end
+
diff --git a/@Grid/set_widths.m b/@Grid/set_widths.m
index 7e8ffa15ca392c1cc68a6af291483bacb8f0f76c..c067c8dd42408ba4c892ee62f607ff1e900fabfc 100644
--- a/@Grid/set_widths.m
+++ b/@Grid/set_widths.m
@@ -1,21 +1,22 @@
 %% set_widths
-        %    sets the widths for each of the cells and subcells in a grid.
-        %    the width of a cell is equal to the max width of the previous
-        %    level - 1 if the cell has no subgrids, or 1 if the cell has a
-        %    subgrid.
-        % inputs:
-        %   object:Grid - current Grid object
-        % outputs:
-        %   none
-        function [] = set_widths(object,max_width)
-            for i=1:size(object.cells,2)
-                if (~isempty(object.cells(i).subgrid))
-                    object.cells(i).subgrid.set_widths(max_width-1);
-                    object.cells(i).width = 1;   
-                else
-                    object.cells(i).width = max_width;
-                end                
-            end
-        end
-        
-     
\ No newline at end of file
+%    sets the widths for each of the cells and subcells in a grid.
+%    the width of a cell is equal to the max width of the previous
+%    level - 1 if the cell has no subgrids, or 1 if the cell has a
+%    subgrid.
+% inputs:
+%   object:Grid - current Grid object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = set_widths(object,max_width)
+for i=1:size(object.cells,2)
+    if (~isempty(object.cells(i).subgrid))
+        object.cells(i).subgrid.set_widths(max_width-1);
+        object.cells(i).width = 1;
+    else
+        object.cells(i).width = max_width;
+    end
+end
+end
+
diff --git a/@PVS_checker/PVS_checker.m b/@PVS_checker/PVS_checker.m
index 47a90eb6ce31ee204542a194cc738201218e0af4..49a5f8414ab6e83ebfabe31f01ca182133eac243 100644
--- a/@PVS_checker/PVS_checker.m
+++ b/@PVS_checker/PVS_checker.m
@@ -1,3 +1,5 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 classdef PVS_checker < handle
     % class contains all the functionality specific to the PVS theorem
     % prover
@@ -28,7 +30,7 @@ classdef PVS_checker < handle
         [paren_string, new_pos] = parse_paren(string,pos)
         
         matlab_type = matlab_type_to_pvs_type( pvs_type )
-
+        
         
         version = get_pvs_version
         
diff --git a/@PVS_checker/check_status.m b/@PVS_checker/check_status.m
index d905d7c76ed45b12794b073daf554a721ed11ffd..0d1c059b42b9984e5b34928a59379fe054ff0744 100644
--- a/@PVS_checker/check_status.m
+++ b/@PVS_checker/check_status.m
@@ -1,28 +1,30 @@
-        %% check_status
-        %   checks the status of a pvs_checker object by generating a
-        %   status script running it a checking the results to ensure that
-        %   all the theories are proved.
-        % inputs:
-        %   object:PVS_checker - PVS_checker object
-        % outputs:
-        %   status:boolean - 0 if pvs file has been checked, 1 if it has
-        %   not
-        function status = check_status(object)
-            script_name = object.generate_pvs_status_script(object.data.function_name);
-            [status, result] = system(['pvs -batch -v 3 -l ' script_name]);
-            parsed = object.parse_status(result);
-            pass = 1;
-            if (size(parsed,2) == 0)
-                pass = 0;
-            end
-            for i=1:2:size(parsed,2)-1
-                if ~strncmp(parsed(i+1),'proved',6)
-                    pass = 0;
-                end
-            end
-            
-            status = pass;
-            delete(script_name);
-            
-        end
-        
+%% check_status
+%   checks the status of a pvs_checker object by generating a
+%   status script running it a checking the results to ensure that
+%   all the theories are proved.
+% inputs:
+%   object:PVS_checker - PVS_checker object
+% outputs:
+%   status:boolean - 0 if pvs file has been checked, 1 if it has
+%   not
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function status = check_status(object)
+script_name = object.generate_pvs_status_script(object.data.function_name);
+[status, result] = system(['pvs -batch -v 3 -l ' script_name]);
+parsed = object.parse_status(result);
+pass = 1;
+if (size(parsed,2) == 0)
+    pass = 0;
+end
+for i=1:2:size(parsed,2)-1
+    if ~strncmp(parsed(i+1),'proved',6)
+        pass = 0;
+    end
+end
+
+status = pass;
+delete(script_name);
+
+end
+
diff --git a/@PVS_checker/generate_pvs.m b/@PVS_checker/generate_pvs.m
index 343eb72dd9f8c1ce322c957722bc38188040f7d2..4c12c1a98a31c03f4e14e70c3fefe215ae31b7bf 100644
--- a/@PVS_checker/generate_pvs.m
+++ b/@PVS_checker/generate_pvs.m
@@ -1,99 +1,100 @@
-        %% genereate_pvs
-        %   function will generate the pvs conditional code for a given
-        %   table
-        % inputs:
-        %   object:PVS_checker - PVS_checker object
-        %   g1:Grid - left grid
-        %   g2:Grid - top grid
-        %   depth:int - number representing depth inside the table
-        % outputs:
-        %   code:string - pvs code
-        %
-        function code = generate_pvs(object,g1,g2,depth)
-          g1cond1 = g1.cells(1).cond_text;
-          g2cond1 = g2.cells(1).cond_text;
-          code = [];
-          %1D horizontal
-          if(~isempty(g1cond1) && isempty(g2cond1))
-            code = [code object.generate_pvs_horizontal(g1,g2.cells(1),depth)];
-          % something in vertical column
-          else
-
-            code = [code sprintf('COND\n')];
-            elsecell = [];
-            for i=1:size(g2.cells,2)
-                g2cond = g2.cells(i).cond_text;
-                % condition string of otherwise corresponds to an else
-                % statement, we allow this statement to be in any order
-                % in the cells of the grid, so we need to find where it
-                % is, if it exists.
-                if (strcmp(g2cond,'otherwise'))
-                    elsecell = g2.cells(i);
-                    found = 1;
-                    continue
+%% genereate_pvs
+%   function will generate the pvs conditional code for a given
+%   table
+% inputs:
+%   object:PVS_checker - PVS_checker object
+%   g1:Grid - left grid
+%   g2:Grid - top grid
+%   depth:int - number representing depth inside the table
+% outputs:
+%   code:string - pvs code
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function code = generate_pvs(object,g1,g2,depth)
+g1cond1 = g1.cells(1).cond_text;
+g2cond1 = g2.cells(1).cond_text;
+code = [];
+%1D horizontal
+if(~isempty(g1cond1) && isempty(g2cond1))
+    code = [code object.generate_pvs_horizontal(g1,g2.cells(1),depth)];
+    % something in vertical column
+else
+    
+    code = [code sprintf('COND\n')];
+    elsecell = [];
+    for i=1:size(g2.cells,2)
+        g2cond = g2.cells(i).cond_text;
+        % condition string of otherwise corresponds to an else
+        % statement, we allow this statement to be in any order
+        % in the cells of the grid, so we need to find where it
+        % is, if it exists.
+        if (strcmp(g2cond,'otherwise'))
+            elsecell = g2.cells(i);
+            found = 1;
+            continue
+        end
+        code = [code sprintf('%s->',object.matlab_to_pvs_syntax_translation(strtrim(char(g2.cells(i).cond_text))))];
+        
+        if(~isempty(g2.cells(i).subgrid))
+            code = [code object.generate_pvs(g1,g2.cells(i).subgrid,depth)];
+        else
+            if (~isempty(g1cond1))
+                if (object.data.multi_mode == 0)
+                    code = [code object.generate_pvs_horizontal(g1,g2.cells(i),depth)];
+                else
+                    code = [code object.generate_pvs_multi_output(g1,g2.cells(i),depth)];
                 end
-                code = [code sprintf('%s->',object.matlab_to_pvs_syntax_translation(strtrim(char(g2.cells(i).cond_text))))];
+            else
                 
-                if(~isempty(g2.cells(i).subgrid))
-                    code = [code object.generate_pvs(g1,g2.cells(i).subgrid,depth)];
+                resultcell = object.data.Grid0.search_return(g1.cells(1),g2.cells(i));
+                if(~isempty(resultcell))
+                    code = [code object.matlab_to_pvs_syntax_translation(strtrim(char(resultcell.result_text)))];
+                    
+                    
                 else
-                    if (~isempty(g1cond1))
-                        if (object.data.multi_mode == 0)
-                         code = [code object.generate_pvs_horizontal(g1,g2.cells(i),depth)];
-                        else
-                            code = [code object.generate_pvs_multi_output(g1,g2.cells(i),depth)];
-                        end
-                    else    
-                
-                        resultcell = object.data.Grid0.search_return(g1.cells(1),g2.cells(i));
-                        if(~isempty(resultcell))
-                            code = [code object.matlab_to_pvs_syntax_translation(strtrim(char(resultcell.result_text)))];
-
-                            
-                        else
-                        end
-                    end
                 end
-                if(isempty(elsecell))
-                    if(i~= size(g2.cells,2))
-                        code = [code sprintf(',\n')];
-                    else
-                        code = [code sprintf('\n')];
-                    end
-                else
-                    code = [code sprintf(',\n')];
-                end      
-              
             end
-           if(~isempty(elsecell))
-                 %resultcell = object.Grid0.search_return(elsecell,elsecell);
-                code = [code sprintf('ELSE->')];
-
-                if(~isempty(elsecell.subgrid))
-                    code = [code object.generate_pvs(g1,elsecell.subgrid,depth) sprintf('\n')];
+        end
+        if(isempty(elsecell))
+            if(i~= size(g2.cells,2))
+                code = [code sprintf(',\n')];
+            else
+                code = [code sprintf('\n')];
+            end
+        else
+            code = [code sprintf(',\n')];
+        end
+        
+    end
+    if(~isempty(elsecell))
+        %resultcell = object.Grid0.search_return(elsecell,elsecell);
+        code = [code sprintf('ELSE->')];
+        
+        if(~isempty(elsecell.subgrid))
+            code = [code object.generate_pvs(g1,elsecell.subgrid,depth) sprintf('\n')];
+        else
+            if (~isempty(g1cond1))
+                if (object.data.multi_mode == 0)
+                    code = [code object.generate_pvs_horizontal(g1,elsecell,depth) sprintf('\n')];
                 else
-                    if (~isempty(g1cond1))
-                        if (object.data.multi_mode == 0)
-                         code = [code object.generate_pvs_horizontal(g1,elsecell,depth) sprintf('\n')];
-                        else
-                          code = [code object.generate_pvs_multi_output(g1,elsecell,depth) sprintf('\n')];
-
-                        end
-                    else    
-                
-                        resultcell = object.data.Grid0.search_return(g1.cells(1),elsecell);
-                        if(~isempty(resultcell))
-                            code = [code object.matlab_to_pvs_syntax_translation(strtrim(char(resultcell.result_text))) sprintf('\n')];
-
-                        end
-                    end
+                    code = [code object.generate_pvs_multi_output(g1,elsecell,depth) sprintf('\n')];
+                    
                 end
+            else
                 
-           end
-
-         code = [code sprintf('ENDCOND')];
- 
-          end
+                resultcell = object.data.Grid0.search_return(g1.cells(1),elsecell);
+                if(~isempty(resultcell))
+                    code = [code object.matlab_to_pvs_syntax_translation(strtrim(char(resultcell.result_text))) sprintf('\n')];
+                    
+                end
+            end
         end
         
-        
+    end
+    
+    code = [code sprintf('ENDCOND')];
+    
+end
+end
+
+
diff --git a/@PVS_checker/generate_pvs_file.m b/@PVS_checker/generate_pvs_file.m
index a6dbf7f33f75f2aba8ab7ba7b626709b136d45c4..92830ef4f9844a71661bdcd978d1a0a4c93fc613 100644
--- a/@PVS_checker/generate_pvs_file.m
+++ b/@PVS_checker/generate_pvs_file.m
@@ -8,6 +8,8 @@
 %   extension
 % outputs;
 %   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [] = generate_pvs_file(object,filename)
 % type_mode = 0 -> use pvs types
 % type_mode = 1 -> use simulink typing information
diff --git a/@PVS_checker/generate_pvs_horizontal.m b/@PVS_checker/generate_pvs_horizontal.m
index 6aff7a110187175bc9c0f41439de90af8a9d6d7f..f49cc3dd104266c5597912024a01d628ee42d47b 100644
--- a/@PVS_checker/generate_pvs_horizontal.m
+++ b/@PVS_checker/generate_pvs_horizontal.m
@@ -10,6 +10,8 @@
 % outputs:
 %   code:string - pvs code
 %
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function code = generate_pvs_horizontal(object,g1,g2_cell,depth)
 
 code = [];
diff --git a/@PVS_checker/generate_pvs_multi_output.m b/@PVS_checker/generate_pvs_multi_output.m
index cc7a3c5bf944609b90aef74f5192365ecaf13585..1a45e46b9295a06a0b0bc3d45eb40b3f0545eca1 100644
--- a/@PVS_checker/generate_pvs_multi_output.m
+++ b/@PVS_checker/generate_pvs_multi_output.m
@@ -10,6 +10,8 @@
 %   use
 % outputs:
 %   code:string - string of eml code
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function code = generate_eml_multi(object,g1,g2_cell,depth)
 
 
@@ -28,14 +30,14 @@ for i=1:size(g1.cells,2)
     output = char(output_parsed{1}(1))
     
     %if (i == 1)
-        code = [code sprintf('%s := ',output)];
+    code = [code sprintf('%s := ',output)];
     %else
     %    code1 = [code1 sprintf(',%s',output)];
     %end
     resultcell = object.data.Grid0.search_return(g1.cells(i),g2_cell);
     if(~isempty(resultcell))
         %if (i == 1)
-            code = [code sprintf('%s',strtrim(char(resultcell.result_text)))];
+        code = [code sprintf('%s',strtrim(char(resultcell.result_text)))];
         %else
         %    code2 = [code2 sprintf(',%s',strtrim(char(resultcell.result_text)))];
         %end
@@ -44,8 +46,8 @@ for i=1:size(g1.cells,2)
     else
     end
     if i ~= size(object.data.Grid1.cells,2)
-            code = [code ',']
-        end
+        code = [code ',']
+    end
 end
 code = ['(#' code '#)']
 %code1 = [code1 ']'];
diff --git a/@PVS_checker/generate_pvs_script.m b/@PVS_checker/generate_pvs_script.m
index 48c7a331b77b75b65b01eb33430d225e1b20f0d9..83d277aac84109d6ca4708648684cb5345e09c22 100644
--- a/@PVS_checker/generate_pvs_script.m
+++ b/@PVS_checker/generate_pvs_script.m
@@ -1,18 +1,19 @@
-        %% generate_pvs_script
-        %  generate the pvs script used to prove and look for counter
-        %  examples for a theory. script will have name filename.el
-        % inputs:
-        %   object:PVS_checker - PVS_checker object
-        %   filename:string - filename to save the script as, exclude
-        %       extension.
-        % outputs:
-        %    none
-        %
-        function [] = generate_pvs_script(object,filename)
-            fileid = fopen([filename '.el'],'w');
-            code = ['(prove-tccs-pvs-file "' filename '" "(try (try (tcc) (try (assert) (skip) (fail) ) (fail))(skip) (random-test :count ' sprintf('%ld',object.data.settings.count) ' :size ' sprintf('%d',object.data.settings.range) '))"  )' sprintf('\n')];
+%% generate_pvs_script
+%  generate the pvs script used to prove and look for counter
+%  examples for a theory. script will have name filename.el
+% inputs:
+%   object:PVS_checker - PVS_checker object
+%   filename:string - filename to save the script as, exclude
+%       extension.
+% outputs:
+%    none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = generate_pvs_script(object,filename)
+fileid = fopen([filename '.el'],'w');
+code = ['(prove-tccs-pvs-file "' filename '" "(try (try (tcc) (try (assert) (skip) (fail) ) (fail))(skip) (random-test :count ' sprintf('%ld',object.data.settings.count) ' :size ' sprintf('%d',object.data.settings.range) '))"  )' sprintf('\n')];
+
+fprintf(fileid,code);
+fclose(fileid);
+end
 
-            fprintf(fileid,code);
-            fclose(fileid);
-        end
-        
diff --git a/@PVS_checker/generate_pvs_status_script.m b/@PVS_checker/generate_pvs_status_script.m
index 013416a092b548637b3cd2536668a6fa806a8079..b89e82015c1286d7e9868bae86f7f7c3c54f752b 100644
--- a/@PVS_checker/generate_pvs_status_script.m
+++ b/@PVS_checker/generate_pvs_status_script.m
@@ -1,17 +1,19 @@
-        %% generate_pvs_status_script
-        %   generate the script used for checking the status of a pvs file
-        % inputs:
-        %   object:PVS_checker - PVS_checker object
-        %   filename:string - filename of the pvs file to checkstatus of,
-        %   excluding extension
-        % outputs:
-        %   script_name:string - filename of the script of format name.el
-        function [script_name] = generate_pvs_status_script(object,filename)
-            script_name = [filename '_status' '.el'];
-            fileid = fopen(script_name,'w');
-            code = ['(status-proof-pvs-file "' filename '")'];
+%% generate_pvs_status_script
+%   generate the script used for checking the status of a pvs file
+% inputs:
+%   object:PVS_checker - PVS_checker object
+%   filename:string - filename of the pvs file to checkstatus of,
+%   excluding extension
+% outputs:
+%   script_name:string - filename of the script of format name.el
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [script_name] = generate_pvs_status_script(object,filename)
+script_name = [filename '_status' '.el'];
+fileid = fopen(script_name,'w');
+code = ['(status-proof-pvs-file "' filename '")'];
+
+fprintf(fileid,code);
+fclose(fileid);
+end
 
-            fprintf(fileid,code);
-            fclose(fileid);
-        end
-        
diff --git a/@PVS_checker/get_pvs_version.m b/@PVS_checker/get_pvs_version.m
index 8d6c8e1467480d58d048b9936633af07cb3fbbef..b9330eff4e5847314ccaa58ebebe20376e1e566e 100644
--- a/@PVS_checker/get_pvs_version.m
+++ b/@PVS_checker/get_pvs_version.m
@@ -1,4 +1,6 @@
- function version = get_pvs_version
-                [status, result] = system('pvs --version');
-                version = result;
-        end
\ No newline at end of file
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function version = get_pvs_version
+[status, result] = system('pvs --version');
+version = result;
+end
\ No newline at end of file
diff --git a/@PVS_checker/matlab_to_pvs_syntax_translation.m b/@PVS_checker/matlab_to_pvs_syntax_translation.m
index c9bbd642d174bf33eb5f020d842f220795a6d8a2..3ebb69a22733852f36327f7a26428f80129f637b 100644
--- a/@PVS_checker/matlab_to_pvs_syntax_translation.m
+++ b/@PVS_checker/matlab_to_pvs_syntax_translation.m
@@ -1,23 +1,25 @@
-        %% matlab_to_pvs_syntax_translation
-        %translate matlab syntax to pvs syntax,
-        % will be added to in the future
-        % will only work for functions in the prelude
-        %   
-        % inputs:
-        %   object:PVS_checker - PVS_checker object
-        %   matlab_string:string - string to be converted from matlab
-        %       syntax to pvs
-        % outputs;
-        %   pvs_string:string - string converted to pvs syntax.
-        function pvs_string = matlab_to_pvs_syntax_translation(object,matlab_string)
-            pvs_string = regexprep(matlab_string,'&&',' AND ');
-            pvs_string = regexprep(pvs_string,'~(?!=)',' NOT ');
-            pvs_string = regexprep(pvs_string,'~=',' /= ');
-            pvs_string = regexprep(pvs_string,'==',' = ');
-            pvs_string = regexprep(pvs_string,'\|\|',' OR ');
-            pvs_string = regexprep(pvs_string,'ceil','ceiling');
-        end
-        
-        
-       
-        
+%% matlab_to_pvs_syntax_translation
+%translate matlab syntax to pvs syntax,
+% will be added to in the future
+% will only work for functions in the prelude
+%
+% inputs:
+%   object:PVS_checker - PVS_checker object
+%   matlab_string:string - string to be converted from matlab
+%       syntax to pvs
+% outputs;
+%   pvs_string:string - string converted to pvs syntax.
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function pvs_string = matlab_to_pvs_syntax_translation(object,matlab_string)
+pvs_string = regexprep(matlab_string,'&&',' AND ');
+pvs_string = regexprep(pvs_string,'~(?!=)',' NOT ');
+pvs_string = regexprep(pvs_string,'~=',' /= ');
+pvs_string = regexprep(pvs_string,'==',' = ');
+pvs_string = regexprep(pvs_string,'\|\|',' OR ');
+pvs_string = regexprep(pvs_string,'ceil','ceiling');
+end
+
+
+
+
diff --git a/@PVS_checker/matlab_type_to_pvs_type.m b/@PVS_checker/matlab_type_to_pvs_type.m
index 70f198b07b644735ff303624c8c6e1ae4e636169..093ba9b3832e43f3f0d3d705fc6da7cf41c8e271 100644
--- a/@PVS_checker/matlab_type_to_pvs_type.m
+++ b/@PVS_checker/matlab_type_to_pvs_type.m
@@ -1,21 +1,23 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function matlab_type = matlab_type_to_pvs_type( pvs_type )
-    if(strcmp(pvs_type,'logical'))
-        matlab_type = 'bool';
-    elseif (strncmp(pvs_type, 'int',3))
-        matlab_type = pvs_type;
-    elseif (strncmp(pvs_type, 'uint', 4))
-        matlab_type = pvs_type;
-    elseif (strcmp(pvs_type,'single') || strcmp(pvs_type,'double'))
-        matlab_type = 'real';
-    elseif (strncmp(pvs_type,'Inherit',7))
-        matlab_type = 'real';
-    elseif (strncmp(pvs_type,'fixdt',5))
-        params = regexp(pvs_type,'(?<=\().*(?=\))','match');
-        split_params = regexp(params,',','split');
-        matlab_type = sprintf('fp2[%d,%d,%d]',eval(char(split_params{1}(2))),eval(char(split_params{1}(2)))-eval(char(split_params{1}(3)))-eval(char(split_params{1}(1))),eval(char(split_params{1}(1))));
-    else
-        matlab_type = 'error';
-    end   
+if(strcmp(pvs_type,'logical'))
+    matlab_type = 'bool';
+elseif (strncmp(pvs_type, 'int',3))
+    matlab_type = pvs_type;
+elseif (strncmp(pvs_type, 'uint', 4))
+    matlab_type = pvs_type;
+elseif (strcmp(pvs_type,'single') || strcmp(pvs_type,'double'))
+    matlab_type = 'real';
+elseif (strncmp(pvs_type,'Inherit',7))
+    matlab_type = 'real';
+elseif (strncmp(pvs_type,'fixdt',5))
+    params = regexp(pvs_type,'(?<=\().*(?=\))','match');
+    split_params = regexp(params,',','split');
+    matlab_type = sprintf('fp2[%d,%d,%d]',eval(char(split_params{1}(2))),eval(char(split_params{1}(2)))-eval(char(split_params{1}(3)))-eval(char(split_params{1}(1))),eval(char(split_params{1}(1))));
+else
+    matlab_type = 'error';
+end
 
 
 
diff --git a/@PVS_checker/parse_decl_id.m b/@PVS_checker/parse_decl_id.m
index edf2be5f546897d83d6ce8a8025f4603dc4642b3..5d4234997a4e66b8ac10a716fcfa10586cb8de36 100644
--- a/@PVS_checker/parse_decl_id.m
+++ b/@PVS_checker/parse_decl_id.m
@@ -7,6 +7,8 @@
 % outputs;
 %   decl_id:string - the declaration id name
 %   new_pos:int - the position where the ending char was found.
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [decl_id,new_pos] = parse_decl_id(string,pos)
 i = pos + 1;
 decl_id.id = [];
diff --git a/@PVS_checker/parse_id.m b/@PVS_checker/parse_id.m
index ac2ad9ab93d92d0e710f1eecd66e81aa37bfba19..21f3c6a7ff205b3e8571abc68c35e4f4dc31c663 100644
--- a/@PVS_checker/parse_id.m
+++ b/@PVS_checker/parse_id.m
@@ -6,6 +6,8 @@
 % outputs;
 %   id:structure - structure containing the parsed prf id section
 %   new_pos:int - the position where the ending char was found.
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [id,new_pos] = parse_id(string,pos)
 i = pos + 1;
 id.id = [];
diff --git a/@PVS_checker/parse_paren.m b/@PVS_checker/parse_paren.m
index b500ca961053fd874561f07accb76e013d6ce815..83111d23046266f783092d1a576fb827ea759e27 100644
--- a/@PVS_checker/parse_paren.m
+++ b/@PVS_checker/parse_paren.m
@@ -9,6 +9,8 @@
 %   paren_string:string - the string contained within the
 %       parenthesis
 %   new_pos:int - the position where the ending parenthesis was found.
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [paren_string, new_pos] = parse_paren(string,pos)
 % pos points to opening (
 paren_string = string(pos);
diff --git a/@PVS_checker/parse_prf_file.m b/@PVS_checker/parse_prf_file.m
index 16049af18661f0538f6047fae2192a77c166ac89..a5f53fab6c426e5ade5dbf747fc2f93ae64b18d3 100644
--- a/@PVS_checker/parse_prf_file.m
+++ b/@PVS_checker/parse_prf_file.m
@@ -7,6 +7,8 @@
 % outputs;
 %   theory_id:string - Theory name
 %   decls:structure - structure of the declarations for the theory
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [theory_id, decls] = parse_prf_file(string)
 decls = [];
 
diff --git a/@PVS_checker/parse_pvs_result.m b/@PVS_checker/parse_pvs_result.m
index 802e05180133e8d8fbcb66b5af5cef8cff6af6d6..2ef3994e3eefe1f78b5f348ae4297a3a49fe7724 100644
--- a/@PVS_checker/parse_pvs_result.m
+++ b/@PVS_checker/parse_pvs_result.m
@@ -1,48 +1,50 @@
-        %% parse_pvs_result
-        %   parse the stuff that comes back from pvs batch mode, extract
-        %   the counter examples and theorems.
-        % inputs:
-        %   object:PVS_checker - PVS_checker object
-        %   result:string - string containing text that comes back from pvs
-        % outputs:
-        %   output:structure - results paresed into structure for easier
-        %       manipulatings
-        %   error:boolean - 0 if no error, 1 if error found during parsing.
-        function [output error] = parse_pvs_result(object,result)
-            found = regexp(result,'\w+(?=[\.]{4,})|(?<=[\.]{4,})\w+','match');
-            if (isempty(found))
-                error = 1;
-                output = [];
-            else
-                seqs = [];
-                for i = 1:2:size(found,2)-1
-                    if(~strcmp(char(found(i+1)),'proved'))
-                        
-                        found4 = [];
-                        % These parsing depend on the version of PVS used,
-                        % which may be a bad idea, although pvs is not
-                        
-                        if strncmp(object.pvs_version,'PVS Version 4.0',15)
-                        % find the TCC that was unprovable
-                            search_str = sprintf('(?<=Proving formula %s[\\n]*)%s.*?(?=[ \\n]*Rerunning step)',char(found(i)),char(found(i)));
-                        elseif strncmp(object.pvs_version,'PVS Version 4.2',15)
-                            search_str =  sprintf('(?<=Installing rewrite rule singleton_rew\\s\\s)%s.*?(?=[ \\n]*Rerunning step)',char(found(i)));
-                        end
-                        found2 = regexp(result,char(search_str),'match','once');
-
-
-                        % find the counter examples
-                        search_str = sprintf('(?<=%s.*?substitutions:).*?(?=This will undo the proof to: \\n%s)|(?<=%s.*?)No counter-examples(?=.*?%s)',char(found(i)),char(found(i)),char(found(i)),char(found(i)));
-                        found3 = regexp(result,char(search_str),'match','once');
-                        if (~strcmp(found3,'No counter-examples'))
-                            found4 = regexp(found3,'[^\n]*(?===>)|(?<===>)[^\n]*','match');
-                        end
-                        seqs = [seqs struct('id', '1234a', 'TCC', found(i), 'seq', found2, 'ce', {found4})];
-                    end
-
-                end
-                output = seqs;
-                error = 0;
+%% parse_pvs_result
+%   parse the stuff that comes back from pvs batch mode, extract
+%   the counter examples and theorems.
+% inputs:
+%   object:PVS_checker - PVS_checker object
+%   result:string - string containing text that comes back from pvs
+% outputs:
+%   output:structure - results paresed into structure for easier
+%       manipulatings
+%   error:boolean - 0 if no error, 1 if error found during parsing.
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [output error] = parse_pvs_result(object,result)
+found = regexp(result,'\w+(?=[\.]{4,})|(?<=[\.]{4,})\w+','match');
+if (isempty(found))
+    error = 1;
+    output = [];
+else
+    seqs = [];
+    for i = 1:2:size(found,2)-1
+        if(~strcmp(char(found(i+1)),'proved'))
+            
+            found4 = [];
+            % These parsing depend on the version of PVS used,
+            % which may be a bad idea, although pvs is not
+            
+            if strncmp(object.pvs_version,'PVS Version 4.0',15)
+                % find the TCC that was unprovable
+                search_str = sprintf('(?<=Proving formula %s[\\n]*)%s.*?(?=[ \\n]*Rerunning step)',char(found(i)),char(found(i)));
+            elseif strncmp(object.pvs_version,'PVS Version 4.2',15)
+                search_str =  sprintf('(?<=Installing rewrite rule singleton_rew\\s\\s)%s.*?(?=[ \\n]*Rerunning step)',char(found(i)));
             end
+            found2 = regexp(result,char(search_str),'match','once');
+            
+            
+            % find the counter examples
+            search_str = sprintf('(?<=%s.*?substitutions:).*?(?=This will undo the proof to: \\n%s)|(?<=%s.*?)No counter-examples(?=.*?%s)',char(found(i)),char(found(i)),char(found(i)),char(found(i)));
+            found3 = regexp(result,char(search_str),'match','once');
+            if (~strcmp(found3,'No counter-examples'))
+                found4 = regexp(found3,'[^\n]*(?===>)|(?<===>)[^\n]*','match');
+            end
+            seqs = [seqs struct('id', '1234a', 'TCC', found(i), 'seq', found2, 'ce', {found4})];
         end
         
+    end
+    output = seqs;
+    error = 0;
+end
+end
+
diff --git a/@PVS_checker/parse_status.m b/@PVS_checker/parse_status.m
index 0f470cd05eed324d209a3a1c2dacdb6c485058e3..768fd27e84d42f4eec7e50e5bfbb0e43ddbdfc50 100644
--- a/@PVS_checker/parse_status.m
+++ b/@PVS_checker/parse_status.m
@@ -1,16 +1,18 @@
-        %% parse_status
-        %   parse the result of running the pvs status script. look for a
-        %   list of theorems and associated status return that in parsed
-        %   list.
-        % inputs:
-        %   object:PVS_checker - PVS_checker object
-        %   string:string - string containing output of runnign pvs script
-        % outputs:
-        %   parsed:array - array containing each of the theorems of the pvs
-        %   file followed by its status so will look something like 
-        %   ['TCC1' 'proved' 'TCC2' 'unfinished']... etc
-        function [parsed] = parse_status(object,string)
-              thrms_status = regexp(string,'\w+(?=[\.]{4,})|(?<=[\.]{4,})\w+','match');
-              parsed = thrms_status;
-                
-        end
\ No newline at end of file
+%% parse_status
+%   parse the result of running the pvs status script. look for a
+%   list of theorems and associated status return that in parsed
+%   list.
+% inputs:
+%   object:PVS_checker - PVS_checker object
+%   string:string - string containing output of runnign pvs script
+% outputs:
+%   parsed:array - array containing each of the theorems of the pvs
+%   file followed by its status so will look something like
+%   ['TCC1' 'proved' 'TCC2' 'unfinished']... etc
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [parsed] = parse_status(object,string)
+thrms_status = regexp(string,'\w+(?=[\.]{4,})|(?<=[\.]{4,})\w+','match');
+parsed = thrms_status;
+
+end
\ No newline at end of file
diff --git a/@PVS_checker/pvs_check.m b/@PVS_checker/pvs_check.m
index ff865eba50469aa47e2a2d6646bdf06232f144fa..25347d357b2d0bc23544294c0804ac9654e7a15e 100644
--- a/@PVS_checker/pvs_check.m
+++ b/@PVS_checker/pvs_check.m
@@ -1,80 +1,82 @@
-        %% pvs_check
-        %   function will generate a pvs file for table, and depending on
-        %   user input 
-        % inputs:
-        %   object:PVS_checker - PVS_checker object
-        % outputs;
-        %   check:boolean - 0 if typecheck fails, 1 if succeds
-        %   output:structure - if typecheck succeds then output contains
-        %       parsed output from pvs 
-        function [check,output] = pvs_check(object)
-            check = 0;
-            output = [];
-            % file name will be expression_name.m
-            
-             function_names = EMLGenerator.parse_inputs(object.data.function_name);
-             function_name = char(function_names{1}(1));
-            object.generate_pvs_file(function_name);
-            
-            object.pvs_version = PVS_checker.get_pvs_version;
-            
-            
-            % THIS SECTION NEEDS SOME WORK
-            %-------------
-            % delete the existing proof
-            % update (22/07/10):
-            % has been fixed up now checks if prf file exists and prompts
-            % user to overwrite it.
-            
-            exists = 0;
-            button = '';
-            if (exist([function_name '.prf'],'file'))
-                exists = 1;
-                button = questdlg(['A proof file already exists for function ' function_name sprintf('\n') ' What would you like to do' sprintf('\n') 'Note: Attempting to prove will delete existing prf file'],'prf exists','Attempt to prove','Open PVS','Cancel','Cancel') 
-            end
-            
-            if (exists == 1 && (isempty(button) || strcmp(button,'Cancel')))
-                output = 'canceled';
-                return;
-            elseif (exists == 1 && (strcmp(button,'Open PVS')));
-                [status, result] = system(['pvs ' function_name '.pvs']);
-                output = 'canceled';
-            elseif (exists == 0 || strcmp(button,'Attempt to prove'))
-                box = waitbar(0,'Generating Proof Script') 
+%% pvs_check
+%   function will generate a pvs file for table, and depending on
+%   user input
+% inputs:
+%   object:PVS_checker - PVS_checker object
+% outputs;
+%   check:boolean - 0 if typecheck fails, 1 if succeds
+%   output:structure - if typecheck succeds then output contains
+%       parsed output from pvs
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [check,output] = pvs_check(object)
+check = 0;
+output = [];
+% file name will be expression_name.m
 
+function_names = EMLGenerator.parse_inputs(object.data.function_name);
+function_name = char(function_names{1}(1));
+object.generate_pvs_file(function_name);
 
-                    delete([function_name '.prf'])
+object.pvs_version = PVS_checker.get_pvs_version;
 
 
-                % generate the proof script
-                object.generate_pvs_script(function_name)
-                waitbar(.10,box,'Running Proof') 
-                %---------
-                % call pvs in batch mode with script
-                % ADD check that pvs actually exists in system
-                [status, result] = system(['pvs -batch -v 3 -l ' function_name '.el'])
-                %objectect.msgbox_scroll(result);
-                waitbar(.70,box,'Parsing Results') 
-                [parsed error] = object.parse_pvs_result(result);
-                
-                if (error == 1)
-                    err_str = ['There was an error proving tabular expression ' sprintf('\n\n') 'Error string below:' sprintf('\n\n') result];
-                    GUI.msgbox_scroll(err_str);
-                else
+% THIS SECTION NEEDS SOME WORK
+%-------------
+% delete the existing proof
+% update (22/07/10):
+% has been fixed up now checks if prf file exists and prompts
+% user to overwrite it.
 
-                    if (isempty(parsed))
-                        check = 1;
-                        output = [];
-                    else
-                        output = parsed;
-                    end
-                end
-                waitbar(.100,box,'Deleting Proof Script') 
+exists = 0;
+button = '';
+if (exist([function_name '.prf'],'file'))
+    exists = 1;
+    button = questdlg(['A proof file already exists for function ' function_name sprintf('\n') ' What would you like to do' sprintf('\n') 'Note: Attempting to prove will delete existing prf file'],'prf exists','Attempt to prove','Open PVS','Cancel','Cancel')
+end
 
-                delete([function_name '.el']);
-                
-                delete(box);
-            end
-        end
-        
+if (exists == 1 && (isempty(button) || strcmp(button,'Cancel')))
+    output = 'canceled';
+    return;
+elseif (exists == 1 && (strcmp(button,'Open PVS')));
+    [status, result] = system(['pvs ' function_name '.pvs']);
+    output = 'canceled';
+elseif (exists == 0 || strcmp(button,'Attempt to prove'))
+    box = waitbar(0,'Generating Proof Script')
+    
+    
+    delete([function_name '.prf'])
+    
+    
+    % generate the proof script
+    object.generate_pvs_script(function_name)
+    waitbar(.10,box,'Running Proof')
+    %---------
+    % call pvs in batch mode with script
+    % ADD check that pvs actually exists in system
+    [status, result] = system(['pvs -batch -v 3 -l ' function_name '.el'])
+    %objectect.msgbox_scroll(result);
+    waitbar(.70,box,'Parsing Results')
+    [parsed error] = object.parse_pvs_result(result);
+    
+    if (error == 1)
+        err_str = ['There was an error proving tabular expression ' sprintf('\n\n') 'Error string below:' sprintf('\n\n') result];
+        GUI.msgbox_scroll(err_str);
+    else
         
+        if (isempty(parsed))
+            check = 1;
+            output = [];
+        else
+            output = parsed;
+        end
+    end
+    waitbar(.100,box,'Deleting Proof Script')
+    
+    delete([function_name '.el']);
+    
+    delete(box);
+end
+end
+
+
diff --git a/@PVS_checker/pvs_check_for_imports.m b/@PVS_checker/pvs_check_for_imports.m
index 6d9a3bc7f2524c284937ccc0202120ba5364ce52..e917b8d3c398879773de53daa7665613adca162e 100644
--- a/@PVS_checker/pvs_check_for_imports.m
+++ b/@PVS_checker/pvs_check_for_imports.m
@@ -1,15 +1,17 @@
-        %% pvs_check_for_imports
-        %   checks both horizontal and vertical grids for functions for
-        %   which there is a file on the path of the same name, in which
-        %   case create pvs code to import the pvs file for that function
-        % inputs:
-        %   object:PVS_checker - PVS_checker object
-        % outputs:
-        %   string:string - pvs code of imports
-        %
-        function string = pvs_check_for_imports(object)
-            [string,found] = object.pvs_check_for_imports_g(object.data.Grid2,{});
-            [string2,found2] = object.pvs_check_for_imports_g(object.data.Grid1,found);
-            string = [string string2];
-        end
-        
+%% pvs_check_for_imports
+%   checks both horizontal and vertical grids for functions for
+%   which there is a file on the path of the same name, in which
+%   case create pvs code to import the pvs file for that function
+% inputs:
+%   object:PVS_checker - PVS_checker object
+% outputs:
+%   string:string - pvs code of imports
+%
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function string = pvs_check_for_imports(object)
+[string,found] = object.pvs_check_for_imports_g(object.data.Grid2,{});
+[string2,found2] = object.pvs_check_for_imports_g(object.data.Grid1,found);
+string = [string string2];
+end
+
diff --git a/@PVS_checker/pvs_check_for_imports_g.m b/@PVS_checker/pvs_check_for_imports_g.m
index 983f2736333d7fef4998566c97130a0195e58e84..7084be4a432191f3fd4275c6e5c0a9cda5658c7a 100644
--- a/@PVS_checker/pvs_check_for_imports_g.m
+++ b/@PVS_checker/pvs_check_for_imports_g.m
@@ -1,37 +1,39 @@
-        %% pvs_check_for_imports_g
-        %   recursively check a grid for an imported functions, see comment
-        %   for pvs_check_for_imports
-        % inputs:
-        %   object:PVS_checker - PVS_checker object
-        %   grid:Grid - grid to check
-        %   found:array - list of functions already imported so we dont
-        %       import the same thing twice.
-        % outputs:
-        %   string:string - pvs code
-        %   found:array - updated list of found functions to import
-        %
-        function [string,found] = pvs_check_for_imports_g(object,grid,found)
-            string = [];
-            for i=1:size(grid.cells,2)
-                % recurse through
-                if (~isempty(grid.cells(i).subgrid))
-                    string = [string object.pvs_check_for_imports_g(grid.cells(i).subgrid)];
-                end
-                text = char(grid.cells(i).cond_text);
-                
-                vars = regexp(text,'([a-zA-Z][a-zA-Z0-9_]*)','match');
-                
-                for j=1:size(vars,2)
-                   if(exist(vars{j},'file')==2 && ~strcmp(vars{j},'otherwise'))
-                       %check if already imported file
-                       if (~any(ismember(found,vars{j})))
-                            string = [string 'IMPORTING ' vars{j} sprintf('\n')];
-                            found = [found vars{j}];
-                       end
-                   end
-                end
+%% pvs_check_for_imports_g
+%   recursively check a grid for an imported functions, see comment
+%   for pvs_check_for_imports
+% inputs:
+%   object:PVS_checker - PVS_checker object
+%   grid:Grid - grid to check
+%   found:array - list of functions already imported so we dont
+%       import the same thing twice.
+% outputs:
+%   string:string - pvs code
+%   found:array - updated list of found functions to import
+%
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [string,found] = pvs_check_for_imports_g(object,grid,found)
+string = [];
+for i=1:size(grid.cells,2)
+    % recurse through
+    if (~isempty(grid.cells(i).subgrid))
+        string = [string object.pvs_check_for_imports_g(grid.cells(i).subgrid)];
+    end
+    text = char(grid.cells(i).cond_text);
+    
+    vars = regexp(text,'([a-zA-Z][a-zA-Z0-9_]*)','match');
+    
+    for j=1:size(vars,2)
+        if(exist(vars{j},'file')==2 && ~strcmp(vars{j},'otherwise'))
+            %check if already imported file
+            if (~any(ismember(found,vars{j})))
+                string = [string 'IMPORTING ' vars{j} sprintf('\n')];
+                found = [found vars{j}];
             end
         end
-        
-        
-        
+    end
+end
+end
+
+
+
diff --git a/@PVS_checker/user_imports.m b/@PVS_checker/user_imports.m
index c30770fb21ebd4c1edca59734e83cf64b1013bb8..225f7ea663c6999cfa5968cecaa33ae8987b3f6a 100644
--- a/@PVS_checker/user_imports.m
+++ b/@PVS_checker/user_imports.m
@@ -1,18 +1,20 @@
-        %% user_imports
-        %   returns the string importing a user selected pvs file to import
-        % inputs:
-        %   object:PVS_checker - PVS_checker object
-        % outputs;
-        %   string:string - string of pvs code to add to generated file
-        function [string] = user_imports(object)
-            string = [];
-            if ~isempty(object.data.settings.inputs)
-                files = regexp(object.data.settings.inputs,',','split');
-                
-                for i=1:size(files,2)
-                   file_no_ext = regexp(files{i},'\w*(?=\.\w*)','match');
-                   string = [string sprintf('IMPORTING %s\n', char(file_no_ext)) ];
-                end
-            end
-        end
-        
+%% user_imports
+%   returns the string importing a user selected pvs file to import
+% inputs:
+%   object:PVS_checker - PVS_checker object
+% outputs;
+%   string:string - string of pvs code to add to generated file
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [string] = user_imports(object)
+string = [];
+if ~isempty(object.data.settings.inputs)
+    files = regexp(object.data.settings.inputs,',','split');
+    
+    for i=1:size(files,2)
+        file_no_ext = regexp(files{i},'\w*(?=\.\w*)','match');
+        string = [string sprintf('IMPORTING %s\n', char(file_no_ext)) ];
+    end
+end
+end
+
diff --git a/@RCell/RCell.m b/@RCell/RCell.m
index 04af5759603852b268b2d29b9a954a0e69b2d783..24ea3debffa034ce1bcd358979cab471fa4e5759 100644
--- a/@RCell/RCell.m
+++ b/@RCell/RCell.m
@@ -1,3 +1,5 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 classdef RCell < handle
     %UNTITLED2 Summary of this class goes here
     %   Detailed explanation goes here
@@ -23,7 +25,7 @@ classdef RCell < handle
             n.Cell2 = cell2;
         end
         
-       
+        
     end
     
 end
diff --git a/@RCell/flag_cell.m b/@RCell/flag_cell.m
index 9dcf342c923cc1dc4d12acf3384094845feb6d5d..0ceff27cf760e72c5761d548296632a3d261dc67 100644
--- a/@RCell/flag_cell.m
+++ b/@RCell/flag_cell.m
@@ -1,27 +1,29 @@
- %% flag_cell
-        %   allows changing the background color of a cell based on an
-        %   inputed mode
-        % inputs
-        %   object:RCell - current object
-        %   mode:int - 
-        %       0 - normal
-        %       1 - red (error/false)
-        %       2 - green (ok/true)
-        % outputs:
-        %   none
-        function [] = flag_cell(object,mode)
-        
-            if (isempty(object.color))
-                object.color = get(object.result,'BackgroundColor');
-            end
-            if ishandle(object.result)
-                if (mode == 0)
-                    set(object.result,'BackgroundColor',object.color);
-                elseif (mode == 1)
-                    set(object.result,'BackgroundColor',[0.92 0.65 0.65])
-                elseif (mode == 2)
-                    set(object.result,'BackgroundColor',[0.03 1.0 0.32]);
-                end
-            end
-        
-        end
\ No newline at end of file
+%% flag_cell
+%   allows changing the background color of a cell based on an
+%   inputed mode
+% inputs
+%   object:RCell - current object
+%   mode:int -
+%       0 - normal
+%       1 - red (error/false)
+%       2 - green (ok/true)
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = flag_cell(object,mode)
+
+if (isempty(object.color))
+    object.color = get(object.result,'BackgroundColor');
+end
+if ishandle(object.result)
+    if (mode == 0)
+        set(object.result,'BackgroundColor',object.color);
+    elseif (mode == 1)
+        set(object.result,'BackgroundColor',[0.92 0.65 0.65])
+    elseif (mode == 2)
+        set(object.result,'BackgroundColor',[0.03 1.0 0.32]);
+    end
+end
+
+end
\ No newline at end of file
diff --git a/@RGrid/RGrid.m b/@RGrid/RGrid.m
index 8eeae15fd28cf66e9252a13ec64620d71cfe3122..b3437de71a04d29761ee747b0da9de80c5ed5228 100644
--- a/@RGrid/RGrid.m
+++ b/@RGrid/RGrid.m
@@ -1,3 +1,5 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 classdef RGrid < handle
 
     
diff --git a/@RGrid/delete_g1s.m b/@RGrid/delete_g1s.m
index 4f15a7b359e0fb8d8ff654f1ebc619e65265924e..2c5258b1578a6fd3ec9f24baf9026cd6430d9f49 100644
--- a/@RGrid/delete_g1s.m
+++ b/@RGrid/delete_g1s.m
@@ -1,22 +1,24 @@
-        %% delete_g1s
-        %    Same as delete_g2s but we are now deleting RCell with a
-        %    reference to the inputed cell in their Cell1
-        % inputs:
-        %   object:RGrid - reference to current RGrid
-        %   cell:Cell - reference to cell being deleted
-        % outputs;
-        %   none
-        function [] = delete_g1s(object,cell)
-            deleted = [];
-            for i=1:size(object.Cells,2)
-                if (object.Cells(i).Cell1 == cell)
-                    deleted = [deleted i];
-                    
-                end
-            end
-            if(~isempty(deleted))
-                delete(object.Cells(deleted).result);
-                object.Cells(deleted) = [];
-            end
-        end
+%% delete_g1s
+%    Same as delete_g2s but we are now deleting RCell with a
+%    reference to the inputed cell in their Cell1
+% inputs:
+%   object:RGrid - reference to current RGrid
+%   cell:Cell - reference to cell being deleted
+% outputs;
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = delete_g1s(object,cell)
+deleted = [];
+for i=1:size(object.Cells,2)
+    if (object.Cells(i).Cell1 == cell)
+        deleted = [deleted i];
         
+    end
+end
+if(~isempty(deleted))
+    delete(object.Cells(deleted).result);
+    object.Cells(deleted) = [];
+end
+end
+
diff --git a/@RGrid/delete_g2s.m b/@RGrid/delete_g2s.m
index b4c14271220c614344f5f487b5d42c39cc211e6c..cf356c529b4ee6309b79109ad4c0dc8bef7157af 100644
--- a/@RGrid/delete_g2s.m
+++ b/@RGrid/delete_g2s.m
@@ -1,25 +1,27 @@
-        %% delete_g2s
-        %    function will delete all the cells that reference an inputed
-        %    condition cell as their Cell2.
-        % inputs:
-        %   object:RGrid - reference to current RGrid 
-        %   cell:Cell - reference to cell being deleted
-        % outputs;
-        %   none
-        function [] = delete_g2s(object,cell)
-            deleted = [];
-            % loop through all the cells, if we find any Rcell with cell as
-            % its Cell2 then add the index to the array, if we were to
-            % delete the cell right away the array size would decrease and
-            % we would get out of bounds issues.
-            for i=1:size(object.Cells,2)
-                if (object.Cells(i).Cell2 == cell)
-                    deleted = [deleted i];          
-                end
-            end
-            if(~isempty(deleted))
-                delete(object.Cells(deleted).result);
-                object.Cells(deleted) = [];
-            end
-        end
-        
+%% delete_g2s
+%    function will delete all the cells that reference an inputed
+%    condition cell as their Cell2.
+% inputs:
+%   object:RGrid - reference to current RGrid
+%   cell:Cell - reference to cell being deleted
+% outputs;
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = delete_g2s(object,cell)
+deleted = [];
+% loop through all the cells, if we find any Rcell with cell as
+% its Cell2 then add the index to the array, if we were to
+% delete the cell right away the array size would decrease and
+% we would get out of bounds issues.
+for i=1:size(object.Cells,2)
+    if (object.Cells(i).Cell2 == cell)
+        deleted = [deleted i];
+    end
+end
+if(~isempty(deleted))
+    delete(object.Cells(deleted).result);
+    object.Cells(deleted) = [];
+end
+end
+
diff --git a/@RGrid/new_RCell.m b/@RGrid/new_RCell.m
index 5fa77f38a0dd170f2372cb85963d4f58604f0a27..7aab7a3f45567883351def57d29c6719e030da2a 100644
--- a/@RGrid/new_RCell.m
+++ b/@RGrid/new_RCell.m
@@ -1,16 +1,17 @@
-  %% new_RCell
-        %   creates a new Cell in the current RGrid 
-        % inputs:
-        %   object:RGrid - current RGrid object
-        %   cell1:Cell - reference to condition cell in top grid
-        %   cell2:Cell - reference to condition cell in left grid
-        % outputs;
-        %   none
-        function [] = new_RCell(object,cell1,cell2)
-            cell = RCell;
-            cell.Cell1 = cell1;
-            cell.Cell2 = cell2;
-            object.Cells = [object.Cells cell];
-        end
-        
-      
\ No newline at end of file
+%% new_RCell
+%   creates a new Cell in the current RGrid
+% inputs:
+%   object:RGrid - current RGrid object
+%   cell1:Cell - reference to condition cell in top grid
+%   cell2:Cell - reference to condition cell in left grid
+% outputs;
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = new_RCell(object,cell1,cell2)
+cell = RCell;
+cell.Cell1 = cell1;
+cell.Cell2 = cell2;
+object.Cells = [object.Cells cell];
+end
+
diff --git a/@RGrid/refresh.m b/@RGrid/refresh.m
index da8370720e039440c11da154132fea42162ab2ed..6a003dcf991986055189e36a7ccadd09b608fbbf 100644
--- a/@RGrid/refresh.m
+++ b/@RGrid/refresh.m
@@ -1,11 +1,13 @@
-        %% refresh
-        %    calls the setup function, might add furthur functionality in
-        %    the future to this function
-        % inputs:
-        %   object:RGrid - reference to current RGrid
-        % outputs;
-        %   none
-        function [] = refresh(object)    
-            object.setup(object.Grid1,object.Grid2);
-        end
-        
+%% refresh
+%    calls the setup function, might add furthur functionality in
+%    the future to this function
+% inputs:
+%   object:RGrid - reference to current RGrid
+% outputs;
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = refresh(object)
+object.setup(object.Grid1,object.Grid2);
+end
+
diff --git a/@RGrid/search.m b/@RGrid/search.m
index 7a155ebb5e9f92ca8ae93f75295d351d00f7934e..649ded7ae4a68bc9a692b3bbde76073ca129961e 100644
--- a/@RGrid/search.m
+++ b/@RGrid/search.m
@@ -1,19 +1,20 @@
-  %% search
-        %    determine wheter a results cell exists for a pair of condition
-        %    cells.
-        % inputs:
-        %   object:RGrid - reference to current RGrid
-        %   cell1:Cell - reference to condition cell in top grid.
-        %   cell2:Cell - reference to condition cell in left grid.
-        % outputs;
-        %   cell:boolean - 1 if cell is found, 0 if cell is not found
-        function cell = search(object,cell1,cell2)
-            cell = 0;
-            for i=1:size(object.Cells,2)
-                if (object.Cells(i).Cell1 == cell1 && object.Cells(i).Cell2 == cell2);
-                    cell = 1;
-                end 
-            end
-        end
-        
-        
\ No newline at end of file
+%% search
+%    determine wheter a results cell exists for a pair of condition
+%    cells.
+% inputs:
+%   object:RGrid - reference to current RGrid
+%   cell1:Cell - reference to condition cell in top grid.
+%   cell2:Cell - reference to condition cell in left grid.
+% outputs;
+%   cell:boolean - 1 if cell is found, 0 if cell is not found
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function cell = search(object,cell1,cell2)
+cell = 0;
+for i=1:size(object.Cells,2)
+    if (object.Cells(i).Cell1 == cell1 && object.Cells(i).Cell2 == cell2);
+        cell = 1;
+    end
+end
+end
+
diff --git a/@RGrid/search_return.m b/@RGrid/search_return.m
index aae6668555a10f864599ce25161f9a14fe6661a5..592c575bc5ff4bab927499f36baf8af6b16bf98d 100644
--- a/@RGrid/search_return.m
+++ b/@RGrid/search_return.m
@@ -1,19 +1,21 @@
 %% search_return
-        %    determine where a results cell exists for a pair of condition
-        %    cells and returns the cell itself.
-        % inputs:
-        %   object:RGrid - reference to current RGrid
-        %   cell1:Cell - reference to condition cell in top grid.
-        %   cell2:Cell - reference to condition cell in left grid.
-        % outputs;
-        %   cell:RCell - if found returns reference to cell, if not returns
-        %   empty
-        function cell = search_return(object,cell1,cell2)
-            cell = [];
-             for i=1:size(object.Cells,2)
-                if (object.Cells(i).Cell1 == cell1 && object.Cells(i).Cell2 == cell2);
-                    cell = object.Cells(i);
-                end 
-             end
-        end
-            
+%    determine where a results cell exists for a pair of condition
+%    cells and returns the cell itself.
+% inputs:
+%   object:rgrid - reference to current rgrid
+%   cell1:cell - reference to condition cell in top grid.
+%   cell2:cell - reference to condition cell in left grid.
+% outputs;
+%   cell:rcell - if found returns reference to cell, if not returns
+%   empty
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function cell = search_return(object,cell1,cell2)
+cell = [];
+for i=1:size(object.cells,2)
+    if (object.cells(i).cell1 == cell1 && object.cells(i).cell2 == cell2);
+        cell = object.cells(i);
+    end
+end
+end
+
diff --git a/@RGrid/setup.m b/@RGrid/setup.m
index 34c85a375a8d8cf442a0a87644c7793ca0cabb0b..9dabc3ba29eb0eed5438e1f4d672ed0c5dc0d9aa 100644
--- a/@RGrid/setup.m
+++ b/@RGrid/setup.m
@@ -1,29 +1,31 @@
-        %% setup
-        %    this function will loop through all the cells in both the left
-        %    grid and the top grid, once we reach a leaf cell for both
-        %    grids, if there does not exist an RCell in the RGrid for both
-        %    these leaf cells then we need to create one.
-        % inputs:
-        %   object:RGrid - reference to current RGrid
-        %   g1:Grid - reference to the top grid
-        %   g2:Grid - reference to the left grid.
-        % outputs;
-        %   
-        function [] = setup(object,g1,g2)
-            for i=1:size(g2.cells,2)
-                if (~isempty(g2.cells(i).subgrid))
-                    object.setup(g1,g2.cells(i).subgrid);
-                else
-                    for j=1:size(g1.cells,2)
-                        if(~isempty(g1.cells(j).subgrid))
-                            object.setup(g1.cells(j).subgrid,g2);
-                        else
-                            if (object.search(g1.cells(j),g2.cells(i)) == 0)
-                                rcell = RCell(g1.cells(j),g2.cells(i));
-                                object.Cells = [object.Cells rcell];
-                            end
-                        end
-                    end
+%% setup
+%    this function will loop through all the cells in both the left
+%    grid and the top grid, once we reach a leaf cell for both
+%    grids, if there does not exist an RCell in the RGrid for both
+%    these leaf cells then we need to create one.
+% inputs:
+%   object:RGrid - reference to current RGrid
+%   g1:Grid - reference to the top grid
+%   g2:Grid - reference to the left grid.
+% outputs;
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = setup(object,g1,g2)
+for i=1:size(g2.cells,2)
+    if (~isempty(g2.cells(i).subgrid))
+        object.setup(g1,g2.cells(i).subgrid);
+    else
+        for j=1:size(g1.cells,2)
+            if(~isempty(g1.cells(j).subgrid))
+                object.setup(g1.cells(j).subgrid,g2);
+            else
+                if (object.search(g1.cells(j),g2.cells(i)) == 0)
+                    rcell = RCell(g1.cells(j),g2.cells(i));
+                    object.Cells = [object.Cells rcell];
                 end
             end
-        end
\ No newline at end of file
+        end
+    end
+end
+end
\ No newline at end of file
diff --git a/@Settings/Settings.m b/@Settings/Settings.m
index 02f62d4d308c78f512027f80e150e878e2c5f5d0..00c0da904146dc4c78a851e7f4f20e165387757f 100644
--- a/@Settings/Settings.m
+++ b/@Settings/Settings.m
@@ -1,3 +1,5 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 classdef Settings < handle
     %UNTITLED Summary of this class goes here
     %   Detailed explanation goes here
@@ -38,7 +40,7 @@ classdef Settings < handle
         end
         
         
-       
+        
     end
     
 end
diff --git a/@Settings/apply_call.m b/@Settings/apply_call.m
index bc15bdb90bde314b2b5125ae391cbd30eae3a99d..ce61188d04c900ff34c4e464f9828f6b046cfc2b 100644
--- a/@Settings/apply_call.m
+++ b/@Settings/apply_call.m
@@ -1,13 +1,15 @@
-        %% apply_call
-        %    callback for apply button, save the settings but do not close
-        %    figure.
-        % inputs:
-        %   object:Settings - current object
-        %   src - source of the callback calling
-        %   event - event that triggered the callback
-        % outputs:
-        %   none
-        function err = apply_call(object,src,event)
-           object.save
-        end
-        
+%% apply_call
+%    callback for apply button, save the settings but do not close
+%    figure.
+% inputs:
+%   object:Settings - current object
+%   src - source of the callback calling
+%   event - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function err = apply_call(object,src,event)
+object.save
+end
+
diff --git a/@Settings/cancel_call.m b/@Settings/cancel_call.m
index 0b9deaf2334ec38bebe01083894ad625d4778973..ea47f52bea779dbf0adfa066dfe1a55721312667 100644
--- a/@Settings/cancel_call.m
+++ b/@Settings/cancel_call.m
@@ -1,11 +1,13 @@
-        %% cancel_call
-        %    callback for cancel button, cose figure don't save settings
-        % inputs:
-        %   object:Settings - current object
-        %   src - source of the callback calling
-        %   event - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = cancel_call(object,src,event)
-            object.close_fig([],[]);
-        end
+%% cancel_call
+%    callback for cancel button, cose figure don't save settings
+% inputs:
+%   object:Settings - current object
+%   src - source of the callback calling
+%   event - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = cancel_call(object,src,event)
+object.close_fig([],[]);
+end
diff --git a/@Settings/close_fig.m b/@Settings/close_fig.m
index 416d324c5e4ae5bd2299273566d194fd53f0739e..d764de05b3d4e967dc429cc201b20faa4da5ff76 100644
--- a/@Settings/close_fig.m
+++ b/@Settings/close_fig.m
@@ -1,14 +1,16 @@
-        %% close_fig
-        %    when close button is pressed delete the figure, allow a new
-        %    one to be opened
-        % inputs:
-        %   object:Settings - current object
-        %   src - source of the callback calling
-        %   event - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = close_fig(object,src,event)
-            delete(object.fig);
-            object.open = 0;
-        end
-        
+%% close_fig
+%    when close button is pressed delete the figure, allow a new
+%    one to be opened
+% inputs:
+%   object:Settings - current object
+%   src - source of the callback calling
+%   event - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = close_fig(object,src,event)
+delete(object.fig);
+object.open = 0;
+end
+
diff --git a/@Settings/elipse_call.m b/@Settings/elipse_call.m
index d4705459e06eb0d3d212c0e2774b4b7b00483593..7166e1c9868f0114167752659be8d3c59408fe72 100644
--- a/@Settings/elipse_call.m
+++ b/@Settings/elipse_call.m
@@ -1,28 +1,30 @@
-        %% elipse_call
-        %    callback for when the elipses button is pressed, show file
-        %    picker, update the textbox of selected files.
-        % inputs:
-        %   object:Settings - current object
-        %   src - source of the callback calling
-        %   event - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = elipse_call(object,src,event)
-            files = uigetfile('*.pvs','Select pvs files','MultiSelect','on');
-            string = [];
-            if iscell(files)
-                for i = 1:size(files,2)
-                    string = strcat(string,files(i));
-                    %string = [string, files(i)];
-                    if i ~= size(files,2)
-                        string = strcat(string,', ');
-                        %string = [string, ',']
-                    end
-                end
-                
-            else
-                string = files;
-            end
-            set(object.include_text,'String',char(string));
+%% elipse_call
+%    callback for when the elipses button is pressed, show file
+%    picker, update the textbox of selected files.
+% inputs:
+%   object:Settings - current object
+%   src - source of the callback calling
+%   event - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = elipse_call(object,src,event)
+files = uigetfile('*.pvs','Select pvs files','MultiSelect','on');
+string = [];
+if iscell(files)
+    for i = 1:size(files,2)
+        string = strcat(string,files(i));
+        %string = [string, files(i)];
+        if i ~= size(files,2)
+            string = strcat(string,', ');
+            %string = [string, ',']
         end
-        
+    end
+    
+else
+    string = files;
+end
+set(object.include_text,'String',char(string));
+end
+
diff --git a/@Settings/init.m b/@Settings/init.m
index 9929ec50e3d8f229d1124a9c0fc38034e700004d..83b83c949354dac93e470f73dbcc86fe02baca1b 100644
--- a/@Settings/init.m
+++ b/@Settings/init.m
@@ -1,15 +1,16 @@
 %% init
-        %    
-        % inputs:
-        %   object:Settings - current object
-        % outputs:
-        %   none
-        function [] = init(object)
-            % initialize the default values of the properties
-            object.pvs_includes = [];
-            object.counter_trials = 1000;
-            object.counter_range = 100;
-            
-        end
-        
-    
\ No newline at end of file
+%
+% inputs:
+%   object:Settings - current object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = init(object)
+% initialize the default values of the properties
+object.pvs_includes = [];
+object.counter_trials = 1000;
+object.counter_range = 100;
+
+end
+
diff --git a/@Settings/ok_call.m b/@Settings/ok_call.m
index a03bb567dc17b370b812134049a65bd21449e7b2..5b295452e9d3087497272f0cf28e77a120bdf214 100644
--- a/@Settings/ok_call.m
+++ b/@Settings/ok_call.m
@@ -1,15 +1,17 @@
-        
-        %% ok_call
-        %    save settings and close figure
-        % inputs:
-        %   object:Settings - current object
-        %   src - source of the callback calling
-        %   event - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = ok_call(object,src,event)
-            if ~(object.save);
-                object.close_fig([],[]);
-            end
-            
-        end
\ No newline at end of file
+
+%% ok_call
+%    save settings and close figure
+% inputs:
+%   object:Settings - current object
+%   src - source of the callback calling
+%   event - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = ok_call(object,src,event)
+if ~(object.save);
+    object.close_fig([],[]);
+end
+
+end
\ No newline at end of file
diff --git a/@Settings/save.m b/@Settings/save.m
index 60be5dfd3884cee07a76849b103518717671b535..b0b52b3e160a957934ec24467d99f97335ee6fcb 100644
--- a/@Settings/save.m
+++ b/@Settings/save.m
@@ -1,30 +1,32 @@
-        %% save
-        %    save the settigns to the object properties, check to ensure
-        %    that user input validates.
-        % inputs:
-        %   object:Settings - current object
-        % outputs:
-        %   none
-        function err = save(object)
-            msg = []    ;
-            err = 0;
-            if isempty(str2num(get(object.count_text,'String')))
-                msg = [msg get(object.count_text,'String') ' is not a valid number'];
-                err = 1;
-            else
-                object.counter_trials = str2num(get(object.count_text,'String'));
-            end
-            
-            if isempty(str2num(get(object.range_text,'String')))
-                msg = [msg sprintf('\n') get(object.count_text,'String') ' is not a valid number'];
-                err = 1;
-            else
-                object.counter_range = str2num(get(object.range_text,'String'));
-            end
-            object.pvs_includes = get(object.include_text,'String');
-           
-            if err
-                msgbox(msg);
-            end
-        end
-        
+%% save
+%    save the settigns to the object properties, check to ensure
+%    that user input validates.
+% inputs:
+%   object:Settings - current object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function err = save(object)
+msg = []    ;
+err = 0;
+if isempty(str2num(get(object.count_text,'String')))
+    msg = [msg get(object.count_text,'String') ' is not a valid number'];
+    err = 1;
+else
+    object.counter_trials = str2num(get(object.count_text,'String'));
+end
+
+if isempty(str2num(get(object.range_text,'String')))
+    msg = [msg sprintf('\n') get(object.count_text,'String') ' is not a valid number'];
+    err = 1;
+else
+    object.counter_range = str2num(get(object.range_text,'String'));
+end
+object.pvs_includes = get(object.include_text,'String');
+
+if err
+    msgbox(msg);
+end
+end
+
diff --git a/@Settings/setvalues.m b/@Settings/setvalues.m
index dc26fbc3d32432d49eb719516bd513edc672c275..9d98617251458352f5d29c2e479f673b1cd5c934 100644
--- a/@Settings/setvalues.m
+++ b/@Settings/setvalues.m
@@ -1,15 +1,16 @@
-    %% setvalues
-        %    update the object settings based on an inputed structure
-        %    containing these desired values
-        % inputs:
-        %   object:Settings - current object
-        % outputs:
-        %   none
-        function [] = setvalues(object,settings)
-           
-            object.pvs_includes = settings.inputs;
-            object.counter_trials = settings.count;
-            object.counter_range = settings.range;
-        end
-        
-     
\ No newline at end of file
+%% setvalues
+%    update the object settings based on an inputed structure
+%    containing these desired values
+% inputs:
+%   object:Settings - current object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = setvalues(object,settings)
+
+object.pvs_includes = settings.inputs;
+object.counter_trials = settings.count;
+object.counter_range = settings.range;
+end
+
diff --git a/@Settings/show.m b/@Settings/show.m
index d2ae0be8394fa4893a74f645a3291cda4a6506a1..f498ce37c37c0a4cde72e8eaac111ebda29ef1b9 100644
--- a/@Settings/show.m
+++ b/@Settings/show.m
@@ -1,135 +1,137 @@
-   %% show
-        %    create the figure to show the gui used to change the settings
-        % inputs:
-        %   object:Settings - current object
-        % outputs:
-        %   none
-        function [] = show(object)
-            if (object.open)
-                figure(object.fig)
-            else
-                
-            object.fig = figure('units','pixels',...
-                'position',[0 0 object.fig_width object.fig_height],...
-                'menubar','none',...
-                'name','Settings',...
-                'numbertitle','off',...
-                'resize','off',...
-                'CloseRequestFcn',@(src,event)close_fig(object,src,event));
-            end
-            
-            % Ok Button
-             uicontrol('style','push',...
-                'units','pix',...
-                'string','Ok',...
-                'HorizontalAlign','left',...
-                'Parent',object.fig,... 
-                'Position',[object.fig_width - object.button_width*3 - object.button_offset*3, object.button_offset, object.button_width, object.button_height],...
-                'callback',@(src,event)ok_call(object,src,event));
-            
-            % Cancel Button
-             uicontrol('style','push',...
-                'units','pix',...
-                'string','Cancel',...
-                'HorizontalAlign','left',...
-                'Parent',object.fig,...
-                'Position',[object.fig_width - object.button_width*2 - object.button_offset*2, object.button_offset, object.button_width, object.button_height],...
-                'callback',@(src,event)cancel_call(object,src,event));
-            
-            
-            % Apply Button
-            uicontrol('style','push',...
-                'units','pix',...
-                'string','Apply',...
-                'HorizontalAlign','left',...
-                'Parent',object.fig,...
-                'Position',[object.fig_width - object.button_width - object.button_offset, object.button_offset, object.button_width, object.button_height],...
-                'callback',@(src,event)apply_call(object,src,event));
-            
-            % main label
-            uicontrol('style','text',...
-                'string','Table Tool Settings',...
-                'HorizontalAlign','center',...
-                'FontWeight','bold',...
-                'Parent',object.fig,...
-                'Position',[0, object.fig_height-object.text_offset-object.title_height, object.fig_width, object.title_height],...
-                'BackgroundColor',get(object.fig,'Color'));
-            
-            panel_height = object.text_offset*6+object.label_height*3;
-            panel_width = object.fig_width-object.text_offset*2;
-            panel = uipanel('Title','PVS',...
-                'visible','on',...
-                'units','pix',...
-                'BackgroundColor',get(object.fig,'Color'),...
-                'Position',[object.text_offset,object.fig_height-object.text_offset-object.title_height-panel_height,panel_width,panel_height]);
-            
-            
-            % imports label
-            uicontrol('style','text',...
-                'string','Imports:',...
-                'HorizontalAlign','left',...
-                'parent',panel,...
-                'Position',[object.text_offset, panel_height-object.text_offset*3-object.label_height, object.label_width, object.label_height],...
-                'BackgroundColor',get(object.fig,'Color'));
-            
-            elipse_width = 20;
-            % import text box
-            object.include_text = uicontrol('style','edit',...
-                'units','pix',...
-                'Parent',panel,...
-                'String',object.pvs_includes,...
-                'HorizontalAlign','center',...
-                'BackgroundColor',get(object.fig,'Color'),...
-                'Position',[object.text_offset+object.label_width, panel_height-object.text_offset*2-object.label_height, panel_width - (object.text_offset*3+object.label_width+elipse_width), object.label_height]);
-            
-            % elipsis button
-            uicontrol('style','push',...
-                'units','pix',...
-                'string','...',...
-                'HorizontalAlign','left',...
-                'Parent',panel,...
-                'Position',[panel_width-elipse_width-object.text_offset, panel_height-object.text_offset*2-object.label_height, elipse_width, object.label_height],...
-                'callback',@(src,event)elipse_call(object,src,event));
-            
-            
-            
-            % count label
-            uicontrol('style','text',...
-                'string','Test Count:',...
-                'HorizontalAlign','left',...
-                'parent',panel,...
-                'Position',[object.text_offset, panel_height-object.text_offset*4-object.label_height*2, object.label_width, object.label_height],...
-                'BackgroundColor',get(object.fig,'Color'));
-            
-            % count text box
-            object.count_text = uicontrol('style','edit',...
-                'units','pix',...
-                'Parent',panel,...
-                'String',object.counter_trials,...
-                'HorizontalAlign','center',...
-                'BackgroundColor',get(object.fig,'Color'),...
-                'Position',[object.text_offset+object.label_width, panel_height-object.text_offset*3-object.label_height*2, panel_width - (object.text_offset*2+object.label_width), object.label_height]);
-            
-            
-            % range label
-            uicontrol('style','text',...
-                'string','Test Range:',...
-                'HorizontalAlign','left',...
-                'parent',panel,...
-                'Position',[object.text_offset, panel_height-object.text_offset*5-object.label_height*3, object.label_width, object.label_height],...
-                'BackgroundColor',get(object.fig,'Color'));
-            
-            % range text box
-            object.range_text = uicontrol('style','edit',...
-                'units','pix',...
-                'Parent',panel,...
-                'String',object.counter_range,...
-                'HorizontalAlign','center',...
-                'BackgroundColor',get(object.fig,'Color'),...
-                'Position',[object.text_offset+object.label_width, panel_height-object.text_offset*4-object.label_height*3, panel_width - (object.text_offset*2+object.label_width), object.label_height]);
-            
-            
-            object.open = 1;
-        end
-
-        
+%% show
+%    create the figure to show the gui used to change the settings
+% inputs:
+%   object:Settings - current object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = show(object)
+if (object.open)
+    figure(object.fig)
+else
+    
+    object.fig = figure('units','pixels',...
+        'position',[0 0 object.fig_width object.fig_height],...
+        'menubar','none',...
+        'name','Settings',...
+        'numbertitle','off',...
+        'resize','off',...
+        'CloseRequestFcn',@(src,event)close_fig(object,src,event));
+end
+
+% Ok Button
+uicontrol('style','push',...
+    'units','pix',...
+    'string','Ok',...
+    'HorizontalAlign','left',...
+    'Parent',object.fig,...
+    'Position',[object.fig_width - object.button_width*3 - object.button_offset*3, object.button_offset, object.button_width, object.button_height],...
+    'callback',@(src,event)ok_call(object,src,event));
+
+% Cancel Button
+uicontrol('style','push',...
+    'units','pix',...
+    'string','Cancel',...
+    'HorizontalAlign','left',...
+    'Parent',object.fig,...
+    'Position',[object.fig_width - object.button_width*2 - object.button_offset*2, object.button_offset, object.button_width, object.button_height],...
+    'callback',@(src,event)cancel_call(object,src,event));
+
+
+% Apply Button
+uicontrol('style','push',...
+    'units','pix',...
+    'string','Apply',...
+    'HorizontalAlign','left',...
+    'Parent',object.fig,...
+    'Position',[object.fig_width - object.button_width - object.button_offset, object.button_offset, object.button_width, object.button_height],...
+    'callback',@(src,event)apply_call(object,src,event));
+
+% main label
+uicontrol('style','text',...
+    'string','Table Tool Settings',...
+    'HorizontalAlign','center',...
+    'FontWeight','bold',...
+    'Parent',object.fig,...
+    'Position',[0, object.fig_height-object.text_offset-object.title_height, object.fig_width, object.title_height],...
+    'BackgroundColor',get(object.fig,'Color'));
+
+panel_height = object.text_offset*6+object.label_height*3;
+panel_width = object.fig_width-object.text_offset*2;
+panel = uipanel('Title','PVS',...
+    'visible','on',...
+    'units','pix',...
+    'BackgroundColor',get(object.fig,'Color'),...
+    'Position',[object.text_offset,object.fig_height-object.text_offset-object.title_height-panel_height,panel_width,panel_height]);
+
+
+% imports label
+uicontrol('style','text',...
+    'string','Imports:',...
+    'HorizontalAlign','left',...
+    'parent',panel,...
+    'Position',[object.text_offset, panel_height-object.text_offset*3-object.label_height, object.label_width, object.label_height],...
+    'BackgroundColor',get(object.fig,'Color'));
+
+elipse_width = 20;
+% import text box
+object.include_text = uicontrol('style','edit',...
+    'units','pix',...
+    'Parent',panel,...
+    'String',object.pvs_includes,...
+    'HorizontalAlign','center',...
+    'BackgroundColor',get(object.fig,'Color'),...
+    'Position',[object.text_offset+object.label_width, panel_height-object.text_offset*2-object.label_height, panel_width - (object.text_offset*3+object.label_width+elipse_width), object.label_height]);
+
+% elipsis button
+uicontrol('style','push',...
+    'units','pix',...
+    'string','...',...
+    'HorizontalAlign','left',...
+    'Parent',panel,...
+    'Position',[panel_width-elipse_width-object.text_offset, panel_height-object.text_offset*2-object.label_height, elipse_width, object.label_height],...
+    'callback',@(src,event)elipse_call(object,src,event));
+
+
+
+% count label
+uicontrol('style','text',...
+    'string','Test Count:',...
+    'HorizontalAlign','left',...
+    'parent',panel,...
+    'Position',[object.text_offset, panel_height-object.text_offset*4-object.label_height*2, object.label_width, object.label_height],...
+    'BackgroundColor',get(object.fig,'Color'));
+
+% count text box
+object.count_text = uicontrol('style','edit',...
+    'units','pix',...
+    'Parent',panel,...
+    'String',object.counter_trials,...
+    'HorizontalAlign','center',...
+    'BackgroundColor',get(object.fig,'Color'),...
+    'Position',[object.text_offset+object.label_width, panel_height-object.text_offset*3-object.label_height*2, panel_width - (object.text_offset*2+object.label_width), object.label_height]);
+
+
+% range label
+uicontrol('style','text',...
+    'string','Test Range:',...
+    'HorizontalAlign','left',...
+    'parent',panel,...
+    'Position',[object.text_offset, panel_height-object.text_offset*5-object.label_height*3, object.label_width, object.label_height],...
+    'BackgroundColor',get(object.fig,'Color'));
+
+% range text box
+object.range_text = uicontrol('style','edit',...
+    'units','pix',...
+    'Parent',panel,...
+    'String',object.counter_range,...
+    'HorizontalAlign','center',...
+    'BackgroundColor',get(object.fig,'Color'),...
+    'Position',[object.text_offset+object.label_width, panel_height-object.text_offset*4-object.label_height*3, panel_width - (object.text_offset*2+object.label_width), object.label_height]);
+
+
+object.open = 1;
+end
+
+
diff --git a/@UndoManager/UndoManager.m b/@UndoManager/UndoManager.m
index 7fd92868917b65fff473abb9eb5097ffce0679bb..44c25d63b6e917b41c8d2f9b74b5965011408416 100644
--- a/@UndoManager/UndoManager.m
+++ b/@UndoManager/UndoManager.m
@@ -1,3 +1,5 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 classdef UndoManager < handle
     %UNDOMANAGER Summary of this class goes here
     %   Detailed explanation goes here
diff --git a/@UndoManager/new_state.m b/@UndoManager/new_state.m
index 6b4358766be3afb8104ecaafaad7bf8e65efb465..27443a7ee1a39df6e9c3dbe4eef4c92ff71c1159 100644
--- a/@UndoManager/new_state.m
+++ b/@UndoManager/new_state.m
@@ -1,3 +1,5 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [] = new_state( object, data )
 %UNTITLED Summary of this function goes here
 %   Detailed explanation goes here
diff --git a/@ValidationReport/ValidationReport.m b/@ValidationReport/ValidationReport.m
index bcee5f7274ce8ae67459ac2b492a6367a93e15b0..0d3b25bed2da537567f92a28590bebc2776e2793 100644
--- a/@ValidationReport/ValidationReport.m
+++ b/@ValidationReport/ValidationReport.m
@@ -1,3 +1,5 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 classdef ValidationReport < handle
     %UNTITLED Summary of this class goes here
     %   Detailed explanation goes here
@@ -29,7 +31,7 @@ classdef ValidationReport < handle
         gui = [];
         pb_nav_width = 60;
         pb_nav_height = 20;
-       
+        
         offset = 10;
         page = 1;
         keyword = '1234a';
@@ -43,13 +45,13 @@ classdef ValidationReport < handle
         %   guinew:GUI - main gui object
         % outputs:
         %   object:ValidationReport - current object
-
+        
         function object = ValidationReport(guinew)
             object.gui = guinew;
         end
         
         
-
+        
     end
     
 end
diff --git a/@ValidationReport/close_req_call.m b/@ValidationReport/close_req_call.m
index e01089d8d0335d9f74c21f784f455e6374fa16bd..4fb16b7f300f070efb9e2161dadc811c37b22908 100644
--- a/@ValidationReport/close_req_call.m
+++ b/@ValidationReport/close_req_call.m
@@ -1,18 +1,20 @@
-        
-        %% close_req_call
-        %    when request to close object comes, update the gui so that it
-        %    doesn't show the colours and close the figure
-        % inputs:
-        %   object:ValidationReport - current object
-        %   src - source of the callback calling
-        %   event - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = close_req_call(object,src,event)
-                    if (object.gui.Data.open)
-                        object.gui.check_call([],[]);
-                    end
-                    object.gui.validation_report_handle = 0;
-                    delete(object.fig);
-        end
-        
+
+%% close_req_call
+%    when request to close object comes, update the gui so that it
+%    doesn't show the colours and close the figure
+% inputs:
+%   object:ValidationReport - current object
+%   src - source of the callback calling
+%   event - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = close_req_call(object,src,event)
+if (object.gui.Data.open)
+    object.gui.check_call([],[]);
+end
+object.gui.validation_report_handle = 0;
+delete(object.fig);
+end
+
diff --git a/@ValidationReport/init.m b/@ValidationReport/init.m
index b4c16cc8782c2e85235e798ae813f3a38d7fa294..ad810cba248d04e1928f3c133619abf799faf4e4 100644
--- a/@ValidationReport/init.m
+++ b/@ValidationReport/init.m
@@ -1,121 +1,123 @@
-        %% init
-        %    initialize the Validation report, set up the gui
-        % inputs:
-        %   object:ValidationReport - current object
-        % outputs:
-        %   none
-        function [] = init(object)
-            
-            if size(object.PVS_results,2) == 0
-            
-            else
-            
-                object.fig_width = object.offset + object.TCC_width + object.offset + object.seq_width + object.offset + object.ce_width + object.offset;
-                object.fig_height = object.offset + object.header_height + object.offset + object.seq_height + object.offset;
-                object.fig = figure('units','pixels',...
-                    'position',[0, 0, object.fig_width, object.fig_height ],...
-                    'menubar','none',...
-                    'name','PVS Report',...       
-                    'numbertitle','off',...
-                    'resize','off',...
-                    'CloseRequestFcn',@(src,event)close_req_call(object,src,event));
+%% init
+%    initialize the Validation report, set up the gui
+% inputs:
+%   object:ValidationReport - current object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = init(object)
 
-                stop = 0;
-                i = 1;
-                count = 0;
+if size(object.PVS_results,2) == 0
+    
+else
+    
+    object.fig_width = object.offset + object.TCC_width + object.offset + object.seq_width + object.offset + object.ce_width + object.offset;
+    object.fig_height = object.offset + object.header_height + object.offset + object.seq_height + object.offset;
+    object.fig = figure('units','pixels',...
+        'position',[0, 0, object.fig_width, object.fig_height ],...
+        'menubar','none',...
+        'name','PVS Report',...
+        'numbertitle','off',...
+        'resize','off',...
+        'CloseRequestFcn',@(src,event)close_req_call(object,src,event));
+    
+    stop = 0;
+    i = 1;
+    count = 0;
+    
+    %first i will be '1234a'
+    
+    
+    object.edit_tcc = uicontrol('style','edit',...
+        'Parent',object.fig,...
+        'units','pix',...
+        'min',0,'max',1,...  % This is the key to multiline edits.
+        'Max',2.0,...
+        'Clipping','on',...
+        'fontweight','bold',...
+        'BackgroundColor',[1 1 1],...
+        'horizontalalign','center',...
+        'fontsize',11);
+    
+    object.edit_seq = uicontrol('style','edit',...
+        'Parent',object.fig,...
+        'units','pix',...
+        'min',0,'max',1,...  % This is the key to multiline edits.
+        'Max',2.0,...
+        'Clipping','on',...
+        'fontweight','bold',...
+        'BackgroundColor',[1 1 1],...
+        'horizontalalign','left',...
+        'fontsize',11);
+    
+    
+    object.edit_ce = uicontrol('style','edit',...
+        'Parent',object.fig,...
+        'units','pix',...
+        'min',0,'max',1,...  % This is the key to multiline edits.
+        'Max',2.0,...
+        'Clipping','on',...
+        'fontweight','bold',...
+        'BackgroundColor',[1 1 1],...
+        'horizontalalign','left',...
+        'fontsize',11);
+    
+    object.pb_next = uicontrol('style','push',...
+        'units','pix',...
+        'string','Next',...
+        'HorizontalAlign','left',...
+        'Parent',object.fig,...
+        'callback',@(src,event)pb_next_call(object,src,event));
+    
+    if(size(object.PVS_results,2)<=1)
+        set(object.pb_next,'enable','off');
+    end
+    
+    
+    object.pb_prev = uicontrol('style','push',...
+        'units','pix',...
+        'string','Prev',...
+        'HorizontalAlign','left',...
+        'Parent',object.fig,...
+        'enable','off',...
+        'callback',@(src,event)pb_prev_call(object,src,event));
+    
+    object.label_tcc = uicontrol('style','text',...
+        'string','TCC Name',...
+        'HorizontalAlign','left',...
+        'BackgroundColor',get(object.fig,'Color'));
+    object.label_seq = uicontrol('style','text',...
+        'string','Sequent',...
+        'HorizontalAlign','left',...
+        'BackgroundColor',get(object.fig,'Color'));
+    object.label_ce = uicontrol('style','text',...
+        'string','Counter Example',...
+        'HorizontalAlign','left',...
+        'BackgroundColor',get(object.fig,'Color'));
+    object.label_page = uicontrol('style','text',...
+        'string','',...
+        'HorizontalAlign','center',...
+        'BackgroundColor',get(object.fig,'Color'));
+    object.label_title = uicontrol('style','text',...
+        'string','Typecheck Summary',...
+        'HorizontalAlign','left',...
+        'FontWeight','bold',...
+        'FontSize',15,...
+        'BackgroundColor',get(object.fig,'Color'));
+    
+    object.pb_open = uicontrol('style','push',...
+        'units','pix',...
+        'string','Open PVS',...
+        'HorizontalAlign','left',...
+        'Parent',object.fig,...
+        'enable','on',...
+        'callback',@(src,event)pb_open_call(object,src,event));
+    
+    object.position;
+    object.populate;
+    object.gui.validation_report_handle = object.fig;
+end
 
-                    %first i will be '1234a'
+end
 
-
-                object.edit_tcc = uicontrol('style','edit',...
-                    'Parent',object.fig,...
-                    'units','pix',...
-                    'min',0,'max',1,...  % This is the key to multiline edits.
-                    'Max',2.0,...
-                    'Clipping','on',...
-                    'fontweight','bold',...
-                    'BackgroundColor',[1 1 1],...
-                    'horizontalalign','center',...
-                    'fontsize',11);
-
-                 object.edit_seq = uicontrol('style','edit',...
-                    'Parent',object.fig,...
-                    'units','pix',...
-                    'min',0,'max',1,...  % This is the key to multiline edits.
-                    'Max',2.0,...
-                    'Clipping','on',...
-                    'fontweight','bold',...
-                    'BackgroundColor',[1 1 1],...
-                    'horizontalalign','left',...
-                    'fontsize',11);
-
-
-                  object.edit_ce = uicontrol('style','edit',...
-                    'Parent',object.fig,...
-                    'units','pix',...
-                    'min',0,'max',1,...  % This is the key to multiline edits.
-                    'Max',2.0,...
-                    'Clipping','on',...
-                    'fontweight','bold',...
-                    'BackgroundColor',[1 1 1],...
-                    'horizontalalign','left',...
-                    'fontsize',11);
-
-                object.pb_next = uicontrol('style','push',...
-                    'units','pix',...
-                    'string','Next',...
-                    'HorizontalAlign','left',...
-                    'Parent',object.fig,...
-                    'callback',@(src,event)pb_next_call(object,src,event));
-
-                if(size(object.PVS_results,2)<=1)
-                    set(object.pb_next,'enable','off');
-                end
-
-
-                object.pb_prev = uicontrol('style','push',...
-                    'units','pix',...
-                    'string','Prev',...
-                    'HorizontalAlign','left',...
-                    'Parent',object.fig,...
-                    'enable','off',...
-                    'callback',@(src,event)pb_prev_call(object,src,event));
-                
-                object.label_tcc = uicontrol('style','text',...
-                'string','TCC Name',...
-                'HorizontalAlign','left',...
-                'BackgroundColor',get(object.fig,'Color'));
-                object.label_seq = uicontrol('style','text',...
-                'string','Sequent',...
-                'HorizontalAlign','left',...
-                'BackgroundColor',get(object.fig,'Color'));
-                object.label_ce = uicontrol('style','text',...
-                'string','Counter Example',...
-                'HorizontalAlign','left',...
-                'BackgroundColor',get(object.fig,'Color'));
-            object.label_page = uicontrol('style','text',...
-                'string','',...
-                'HorizontalAlign','center',...
-                'BackgroundColor',get(object.fig,'Color'));
-            object.label_title = uicontrol('style','text',...
-                'string','Typecheck Summary',...
-                'HorizontalAlign','left',...
-                'FontWeight','bold',...
-                'FontSize',15,...
-                'BackgroundColor',get(object.fig,'Color'));
-            
-            object.pb_open = uicontrol('style','push',...
-                    'units','pix',...
-                    'string','Open PVS',...
-                    'HorizontalAlign','left',...
-                    'Parent',object.fig,...
-                    'enable','on',...
-                    'callback',@(src,event)pb_open_call(object,src,event));
-                
-                object.position;
-                object.populate;
-                object.gui.validation_report_handle = object.fig;
-            end
-            
-        end
-        
diff --git a/@ValidationReport/pb_next_call.m b/@ValidationReport/pb_next_call.m
index 0bd63b1bc22f9be19ccb45bb256dfa3a288537b8..b531f9ffd0ab3cd443e922662254e984c8507e5c 100644
--- a/@ValidationReport/pb_next_call.m
+++ b/@ValidationReport/pb_next_call.m
@@ -1,19 +1,21 @@
-        %% pb_next_call
-        %    callback for the next button, move to the next
-        %    record, update the gui objects.
-        % inputs:
-        %   objectect:Settings - current object
-        %   src - source of the callback calling
-        %   event - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = pb_next_call(object,src,event)
-            object.page = object.page + 1;
-            object.populate;
-            if (object.page == size(object.PVS_results,2))
-                set(src,'enable','off');
-
-           
-            end
-            set(object.pb_prev,'enable','on');
-        end
+%% pb_next_call
+%    callback for the next button, move to the next
+%    record, update the gui objects.
+% inputs:
+%   objectect:Settings - current object
+%   src - source of the callback calling
+%   event - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = pb_next_call(object,src,event)
+object.page = object.page + 1;
+object.populate;
+if (object.page == size(object.PVS_results,2))
+    set(src,'enable','off');
+    
+    
+end
+set(object.pb_prev,'enable','on');
+end
diff --git a/@ValidationReport/pb_open_call.m b/@ValidationReport/pb_open_call.m
index 86f0f9971551c2762aa8ce2c090993c9e24bd26c..12fe10387dd65620ce86a104b8c0666d3c77bcd9 100644
--- a/@ValidationReport/pb_open_call.m
+++ b/@ValidationReport/pb_open_call.m
@@ -1,14 +1,16 @@
-        %% pb_open_call
-        %    callback for the open button, opens pvs to the pvs file being
-        %    used.
-        % inputs:
-        %   object:ValidationReport - current object
-        %   src - source of the callback calling
-        %   event - event that triggered the callback
-        % outputs:
-        %   none
-         function [] = pb_open_call(object,src,event)
-              [status, result] = system(['pvs ' get(object.gui.function_name_control,'String') '.pvs']);
+%% pb_open_call
+%    callback for the open button, opens pvs to the pvs file being
+%    used.
+% inputs:
+%   object:ValidationReport - current object
+%   src - source of the callback calling
+%   event - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = pb_open_call(object,src,event)
+[status, result] = system(['pvs ' get(object.gui.function_name_control,'String') '.pvs']);
+
+end
 
-         end
-        
diff --git a/@ValidationReport/pb_prev_call.m b/@ValidationReport/pb_prev_call.m
index 9f41cf97c9600716d5da6fc8b581f6a05f7fd965..57ebf44538055954879e002a1dca356ade322919 100644
--- a/@ValidationReport/pb_prev_call.m
+++ b/@ValidationReport/pb_prev_call.m
@@ -1,20 +1,22 @@
-        %% pb_prev_call
-        %    callback for the previous button, move to the previous
-        %    record, update the gui objects.
-        % inputs:
-        %   object:ValidationReport - current object
-        %   src - source of the callback calling
-        %   event - event that triggered the callback
-        % outputs:
-        %   none
-        function [] = pb_prev_call(object,src,event)
-            object.page = object.page - 1;
-            object.populate
-            if(object.page == 1)
-                set(src,'enable','off');
-      
-            end
-            set(object.pb_next,'enable','on');
-        end
-        
-        
+%% pb_prev_call
+%    callback for the previous button, move to the previous
+%    record, update the gui objects.
+% inputs:
+%   object:ValidationReport - current object
+%   src - source of the callback calling
+%   event - event that triggered the callback
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = pb_prev_call(object,src,event)
+object.page = object.page - 1;
+object.populate
+if(object.page == 1)
+    set(src,'enable','off');
+    
+end
+set(object.pb_next,'enable','on');
+end
+
+
diff --git a/@ValidationReport/populate.m b/@ValidationReport/populate.m
index b986e5b96a87fe37efa64c8871d6f36b949c1e65..2176c7545bf941ff1713c06cfb1ad2506b9836c6 100644
--- a/@ValidationReport/populate.m
+++ b/@ValidationReport/populate.m
@@ -1,34 +1,36 @@
-        %% populate
-        %    update all the textboxes to the current page of the pvs
-        %    results
-        % inputs:
-        %   object:ValidationReport - current object
-        % outputs:
-        %   none
-        function [] = populate(object)
-            % temporarily used to reset colours
-            object.gui.check_call([],[]);
-            set(object.edit_tcc,'string',char(object.PVS_results(object.page).TCC));
-            set(object.edit_seq,'string',char(object.PVS_results(object.page).seq));
-            set(object.label_page,'string',[num2str(object.page) '  of  ' num2str(size(object.PVS_results,2))]);
-            counter = [];
-            if size(object.PVS_results(object.page).ce,2) == 0
-                counter = ['no counter example generated'];
-           
-            else
-                for i = 1:2:size(object.PVS_results(object.page).ce,2)
-                    
-                    
-                    % need to do some translation back to matlab syntax
-                    new_value = regexprep(char(object.PVS_results(object.page).ce(i+1)),'FALSE',' 0 ');
-                    new_value = regexprep(new_value,'TRUE',' 1 ');
-                    eval(['value = ' char(new_value)])
-
-                    counter = [counter char(object.PVS_results(object.page).ce(i)) ' = ' num2str(value) ';' sprintf('\n')];
-                end
-
-             
-             object.gui.evaluate_counter(counter);
-            end
-                         set(object.edit_ce,'string',counter);
-        end
\ No newline at end of file
+%% populate
+%    update all the textboxes to the current page of the pvs
+%    results
+% inputs:
+%   object:ValidationReport - current object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = populate(object)
+% temporarily used to reset colours
+object.gui.check_call([],[]);
+set(object.edit_tcc,'string',char(object.PVS_results(object.page).TCC));
+set(object.edit_seq,'string',char(object.PVS_results(object.page).seq));
+set(object.label_page,'string',[num2str(object.page) '  of  ' num2str(size(object.PVS_results,2))]);
+counter = [];
+if size(object.PVS_results(object.page).ce,2) == 0
+    counter = ['no counter example generated'];
+    
+else
+    for i = 1:2:size(object.PVS_results(object.page).ce,2)
+        
+        
+        % need to do some translation back to matlab syntax
+        new_value = regexprep(char(object.PVS_results(object.page).ce(i+1)),'FALSE',' 0 ');
+        new_value = regexprep(new_value,'TRUE',' 1 ');
+        eval(['value = ' char(new_value)])
+        
+        counter = [counter char(object.PVS_results(object.page).ce(i)) ' = ' num2str(value) ';' sprintf('\n')];
+    end
+    
+    
+    object.gui.evaluate_counter(counter);
+end
+set(object.edit_ce,'string',counter);
+end
\ No newline at end of file
diff --git a/@ValidationReport/position.m b/@ValidationReport/position.m
index 4adfbd314a0c3e635f00da17f9fbdc3a096268fa..0842253da5a19b6e300a8b6357cbf2863504cb0f 100644
--- a/@ValidationReport/position.m
+++ b/@ValidationReport/position.m
@@ -1,22 +1,24 @@
-        %% position
-        %    set the position of all the gui elements
-        % inputs:
-        %   object:ValidationReport - current object
-        % outputs:
-        %   none
-        function [] = position(object)
-            set(object.edit_tcc,'position',[object.offset, (object.fig_height - object.offset - object.header_height - object.offset - object.seq_height) ,object.TCC_width,object.TCC_height])
-            set(object.edit_seq,'position',[object.offset + object.TCC_width + object.offset, (object.fig_height - object.offset - object.header_height - object.offset - object.seq_height),object.seq_width,object.seq_height])
-            set(object.edit_ce, 'position',[object.offset + object.TCC_width + object.offset + object.seq_width + object.offset, (object.fig_height - object.offset - object.header_height - object.offset - object.seq_height) ,object.ce_width,object.ce_height])
-        
-            set(object.label_tcc,'position',[object.offset, (object.fig_height - object.offset - object.header_height) ,object.TCC_width,object.label_height])
-            set(object.label_seq,'position',[object.offset + object.TCC_width + object.offset, (object.fig_height - object.offset - object.header_height) ,object.TCC_width,object.label_height])
-            set(object.label_ce,'position',[object.offset + object.TCC_width + object.offset + object.seq_width + object.offset, (object.fig_height - object.offset - object.header_height) ,object.TCC_width,object.label_height])
-            
-            set(object.label_title,'position',[object.offset, (object.fig_height - object.offset - object.label_height*2) ,object.TCC_width,object.label_height*2])
-            set(object.label_page,'position',[object.fig_width-object.pb_nav_width*2-object.offset*2, object.fig_height-object.offset-object.header_height+object.label_height+object.pb_nav_height+object.offset/2,object.pb_nav_width*2+object.offset,object.pb_nav_height]);
-            set(object.pb_next,'position',[object.fig_width - object.pb_nav_width - object.offset, object.fig_height - object.offset - object.header_height + object.label_height + object.offset/2, object.pb_nav_width, object.pb_nav_height]);
-            set(object.pb_prev,'position',[object.fig_width - object.pb_nav_width - object.offset - object.offset - object.pb_nav_width, object.fig_height - object.offset - object.header_height + object.label_height+object.offset/2, object.pb_nav_width, object.pb_nav_height]);
-            set(object.pb_open,'position',[object.fig_width - object.pb_nav_width - object.offset - object.offset - object.pb_nav_width - object.offset - object.pb_nav_width, object.fig_height - object.offset - object.header_height + object.label_height+object.offset/2, object.pb_nav_width, object.pb_nav_height]);
-        end
-        
+%% position
+%    set the position of all the gui elements
+% inputs:
+%   object:ValidationReport - current object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = position(object)
+set(object.edit_tcc,'position',[object.offset, (object.fig_height - object.offset - object.header_height - object.offset - object.seq_height) ,object.TCC_width,object.TCC_height])
+set(object.edit_seq,'position',[object.offset + object.TCC_width + object.offset, (object.fig_height - object.offset - object.header_height - object.offset - object.seq_height),object.seq_width,object.seq_height])
+set(object.edit_ce, 'position',[object.offset + object.TCC_width + object.offset + object.seq_width + object.offset, (object.fig_height - object.offset - object.header_height - object.offset - object.seq_height) ,object.ce_width,object.ce_height])
+
+set(object.label_tcc,'position',[object.offset, (object.fig_height - object.offset - object.header_height) ,object.TCC_width,object.label_height])
+set(object.label_seq,'position',[object.offset + object.TCC_width + object.offset, (object.fig_height - object.offset - object.header_height) ,object.TCC_width,object.label_height])
+set(object.label_ce,'position',[object.offset + object.TCC_width + object.offset + object.seq_width + object.offset, (object.fig_height - object.offset - object.header_height) ,object.TCC_width,object.label_height])
+
+set(object.label_title,'position',[object.offset, (object.fig_height - object.offset - object.label_height*2) ,object.TCC_width,object.label_height*2])
+set(object.label_page,'position',[object.fig_width-object.pb_nav_width*2-object.offset*2, object.fig_height-object.offset-object.header_height+object.label_height+object.pb_nav_height+object.offset/2,object.pb_nav_width*2+object.offset,object.pb_nav_height]);
+set(object.pb_next,'position',[object.fig_width - object.pb_nav_width - object.offset, object.fig_height - object.offset - object.header_height + object.label_height + object.offset/2, object.pb_nav_width, object.pb_nav_height]);
+set(object.pb_prev,'position',[object.fig_width - object.pb_nav_width - object.offset - object.offset - object.pb_nav_width, object.fig_height - object.offset - object.header_height + object.label_height+object.offset/2, object.pb_nav_width, object.pb_nav_height]);
+set(object.pb_open,'position',[object.fig_width - object.pb_nav_width - object.offset - object.offset - object.pb_nav_width - object.offset - object.pb_nav_width, object.fig_height - object.offset - object.header_height + object.label_height+object.offset/2, object.pb_nav_width, object.pb_nav_height]);
+end
+
diff --git a/@ValidationReport/set_results.m b/@ValidationReport/set_results.m
index 97ec340c3cfda6dd6f4a89f70b939518a85b006a..a4a3e19619719b6a7f702724ec1ef1f4f12ef87e 100644
--- a/@ValidationReport/set_results.m
+++ b/@ValidationReport/set_results.m
@@ -1,10 +1,12 @@
 %% set_results
-        %    set the results property
-        % inputs:
-        %   object:ValidationReport - current object
-        % outputs:
-        %   none
-        function [] = set_results(object,res)
-            object.PVS_results = res;
-        end
-        
+%    set the results property
+% inputs:
+%   object:ValidationReport - current object
+% outputs:
+%   none
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
+function [] = set_results(object,res)
+object.PVS_results = res;
+end
+
diff --git a/TTdiag.m b/TTdiag.m
index 286f5fe59f04f336630a98a9084152bf22434654..3cef7c9825366f4922e288ace7b4401998f39872 100644
--- a/TTdiag.m
+++ b/TTdiag.m
@@ -1,3 +1,5 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function TTdiag(varargin)
 
 orig_gcbh = gcbh;
@@ -10,7 +12,7 @@ Action = varargin{1};
 switch Action,
     case 'Open',
         Mode = varargin{2};
-
+        
         if 2 ~= nargin
             DAStudio.warning('improper function use')
         end
@@ -18,15 +20,15 @@ switch Action,
         switch Mode,
             
             case 'Simulink'
-                 LocalOpenBlockFcn(blockHandleTTTopMask,1);
+                LocalOpenBlockFcn(blockHandleTTTopMask,1);
             case 'Matlab'
-                 LocalOpenBlockFcn([],0);
+                LocalOpenBlockFcn([],0);
         end
         
     case 'Close',
         blockHandleTTTopMask = orig_gcbh;
         LocalCloseBlockFcn(blockHandleTTTopMask);
-
+        
     case 'Copy',
         blockHandleTTTopMask = orig_gcbh;
         LocalCopyBlockFcn(blockHandleTTTopMask);
@@ -36,7 +38,7 @@ switch Action,
             DAStudio.warning('improper function use')
         end
         file = varargin{2};
-        try 
+        try
             data = importdata(file);
             gui = GUI([],0);
             gui.setData(data)
@@ -45,107 +47,107 @@ switch Action,
             msgbox(exception.identifier)
         end
     case 'Delete'
-       blockHandleTTTopMask = orig_gcbh;
-       data = get_param(blockHandleTTTopMask,'UserData');
-       if isempty(data)
-           return
-       end
+        blockHandleTTTopMask = orig_gcbh;
+        data = get_param(blockHandleTTTopMask,'UserData');
+        if isempty(data)
+            return
+        end
         if ~data.valid
-             errordlg(...
-          DAStudio.message('Block Data has been corputed'),...
-          'Error', 'modal')
+            errordlg(...
+                DAStudio.message('Block Data has been corputed'),...
+                'Error', 'modal')
             return
         end
-       
+        
         if data.open && ishandle(data.fig)
             delete(data.fig)
             data.fig = [];
             data.open = 0;
-            set_param(blockHandleTTTopMask,'UserData',data); 
-
+            set_param(blockHandleTTTopMask,'UserData',data);
+            
         end
         
-    otherwise,  
+    otherwise,
         DAStudio.error('Simulink:dialog:UnknownAction',Action);
-    
         
-
+        
+        
         
         
 end
-    
+
 end
 
 function LocalCopyBlockFcn(blockHandleTTTopMask)
-    data = get(blockHandleTTTopMask,'UserData');
-    if(~isempty(data))
-        data_new = data.clone(blockHandleTTTopMask);  
-  
-        set_param(blockHandleTTTopMask,'UserData',data_new)
-    end
+data = get(blockHandleTTTopMask,'UserData');
+if(~isempty(data))
+    data_new = data.clone(blockHandleTTTopMask);
+    
+    set_param(blockHandleTTTopMask,'UserData',data_new)
+end
 end
 
 function LocalOpenBlockFcn(blockHandleTTTopMask,mode)
-    data = [];
-    if (mode == 1)
-            modelHandle = bdroot(blockHandleTTTopMask);
-
-
-        % check if the user is trying to open the block from the library
-        if strcmp(get_param(modelHandle,'Lock'), 'on') || ...
-         strcmp(get_param(blockHandleTTTopMask,'LinkStatus'),'implicit')
-
-          errordlg(...
-              DAStudio.message('can not open Model Locked, Add to new model to use'),...
-              'Error', 'modal')
-            return
-        end
-
-
-
-        data = get_param(blockHandleTTTopMask,'UserData');
-    end
+data = [];
+if (mode == 1)
+    modelHandle = bdroot(blockHandleTTTopMask);
     
-    if isempty(data)
-        data = Data();
-        data.init();
-
-    else
-        if ~data.valid
-             errordlg(...
-          DAStudio.message('Block Data has been corputed'),...
-          'Error', 'modal')
-            return
-        end
-        if data.open
-            if ishghandle(data.fig)
-             figure(data.fig)
-
-            end
-            return
-        end
+    
+    % check if the user is trying to open the block from the library
+    if strcmp(get_param(modelHandle,'Lock'), 'on') || ...
+            strcmp(get_param(blockHandleTTTopMask,'LinkStatus'),'implicit')
         
+        errordlg(...
+            DAStudio.message('can not open Model Locked, Add to new model to use'),...
+            'Error', 'modal')
+        return
     end
-    if mode == 1
-        gui = GUI(blockHandleTTTopMask,1);   
-    elseif mode == 0
-        gui = GUI([],0);
-    end
+    
+    
+    
+    data = get_param(blockHandleTTTopMask,'UserData');
+end
 
-    gui.setData(data)
-    gui.init();
-        if(mode == 1)
-            set_param(blockHandleTTTopMask,'UserData',data); 
-            set_param(blockHandleTTTopMask, 'UserDataPersistent', 'on');
+if isempty(data)
+    data = Data();
+    data.init();
+    
+else
+    if ~data.valid
+        errordlg(...
+            DAStudio.message('Block Data has been corputed'),...
+            'Error', 'modal')
+        return
+    end
+    if data.open
+        if ishghandle(data.fig)
+            figure(data.fig)
+            
         end
+        return
+    end
     
+end
+if mode == 1
+    gui = GUI(blockHandleTTTopMask,1);
+elseif mode == 0
+    gui = GUI([],0);
+end
+
+gui.setData(data)
+gui.init();
+if(mode == 1)
+    set_param(blockHandleTTTopMask,'UserData',data);
+    set_param(blockHandleTTTopMask, 'UserDataPersistent', 'on');
+end
+
 end
 
 function LocalCloseRequestBlockFcn(blockHandleTTTopMask)
 
-    modelHandle = bdroot(blockHandleTTTopMask);
+modelHandle = bdroot(blockHandleTTTopMask);
 
-    data = get_param(blockHandleTTTopMask,'UserData');
+data = get_param(blockHandleTTTopMask,'UserData');
 
 
 
@@ -154,7 +156,7 @@ if ~isempty(data)
         delete(data.fig)
     end
 end
-        %set_param(gui.fig,'Visible','off')
+%set_param(gui.fig,'Visible','off')
 
 end
 
diff --git a/TableToolMatlab.m b/TableToolMatlab.m
index 3b305588409f515e437edc22cea571ef54def43a..1bbda4a194ceaf4e6a506186ed512bc8153457cd 100644
--- a/TableToolMatlab.m
+++ b/TableToolMatlab.m
@@ -1,3 +1,5 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [ output_args ] = TableToolMatlab( input_args )
 %TABLETOOLMATLAB Summary of this function goes here
 %   Detailed explanation goes here
diff --git a/check_system.m b/check_system.m
index 87636c9835e8cd93d78400730f43a4172ceb6de8..774b2835c12cadcee5cfc2c73099dba2f575ff6b 100644
--- a/check_system.m
+++ b/check_system.m
@@ -1,3 +1,5 @@
+% Author: Colin Eles elesc@mcmaster.ca
+% Organization: McMaster Centre for Software Certification
 function [ output_args ] = check_system(system)
 %UNTITLED Summary of this function goes here
 %   Detailed explanation goes here
@@ -12,12 +14,12 @@ for i = 1:size(blocks,1)
             if (check == 1)
                 msg = [msg char(blocks(i)) ' is valid' sprintf('\n')]
                 
-            else 
+            else
                 msg = [msg char(blocks(i)) ' is not valid' sprintf('\n')]
             end
             block_data.checked = check;
             TableBlock.set_block_display(char(blocks(i)),block_data.checked)
-
+            
         end
     end
 end
diff --git a/html/TT_help.m b/html/TT_help.m
index 2bc6354c78cc34c29aae8a338921feb5296a6892..51ef8dd37ca3a05ce2035da3166fab46baf0292b 100644
--- a/html/TT_help.m
+++ b/html/TT_help.m
@@ -3,6 +3,5 @@
 % *Available Documentation*
 %
 % * <TT_gs_top.html Getting Started>
-% * <TT_ug.html User Guide>
 %
 % Copyright 2010 Colin Eles
diff --git a/html/TT_ug.m b/html/TT_ug.m
index 4ac2e045dd4a6f05b6768d296bc0e7b636225965..c9920f21809cc01ec33ea5ae1d7396f5b6536c36 100644
--- a/html/TT_ug.m
+++ b/html/TT_ug.m
@@ -1,4 +1,6 @@
 %% User Guide
 %
 % * <TT_ug_opening.html Creating a new Table>
-% * <TT_ug_editing.html Editing a Tabular Expression>
\ No newline at end of file
+% * <TT_ug_editing.html Editing a Tabular Expression>
+%
+% Copyright 2010 Colin Eles
\ No newline at end of file
diff --git a/html/html/TT_help.html b/html/html/TT_help.html
index 29ae52d738f7c647f8af9707e8966910fa11071e..14144969e5922fa47e6dbe1d68f78e0247767daa 100644
--- a/html/html/TT_help.html
+++ b/html/html/TT_help.html
@@ -6,7 +6,7 @@
    <!--
 This HTML is auto-generated from an M-file.
 To make changes, update the M-file and republish this document.
-      --><title>Table Toolbox</title><meta name="generator" content="MATLAB 7.10"><meta name="date" content="2010-09-02"><meta name="m-file" content="TT_help"><style type="text/css">
+      --><title>Table Toolbox</title><meta name="generator" content="MATLAB 7.10"><meta name="date" content="2010-09-17"><meta name="m-file" content="TT_help"><style type="text/css">
 
 body {
   background-color: white;
@@ -62,7 +62,7 @@ p.footer {
   color: gray;
 }
 
-  </style></head><body><div class="content"><h1>Table Toolbox</h1><p><b>Available Documentation</b></p><div><ul><li><a href="TT_gs_top.html">Getting Started</a></li></ul></div><p>Copyright 2010 Colin Eles</p><p class="footer"><br>
+  </style></head><body><div class="content"><h1>Table Toolbox</h1><p><b>Available Documentation</b></p><div><ul><li><a href="TT_gs_top.html">Getting Started</a></li></ul></div><p class="footer"><br>
       Published with MATLAB&reg; 7.10<br></p></div><!--
 ##### SOURCE BEGIN #####
 %% Table Toolbox
@@ -71,8 +71,6 @@ p.footer {
 %
 % * <TT_gs_top.html Getting Started>
 %
-%
-% Copyright 2010 Colin Eles
 
 ##### SOURCE END #####
 --></body></html>
\ No newline at end of file