Index: mttroot/mtt/bin/trans/m/makedef.m
==================================================================
--- mttroot/mtt/bin/trans/m/makedef.m
+++ mttroot/mtt/bin/trans/m/makedef.m
@@ -1,95 +1,129 @@
 function makedef(structure,deffilenum);
 
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %% Version control history
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% %% $Id$
-% %% $Log$
-% %% Revision 1.5  1996/11/09 21:05:44  peterg
-% %% Only generates MTTIm when at least 2 states!
-% %%
-% %% Revision 1.4  1996/08/30  19:42:36  peter
-% %% Added newline at end of file.
-% %%
-% %% Revision 1.3  1996/08/24 15:06:22  peter
-% %% Write `END;' at end to please reduce.
-% %%
-% %% Revision 1.2  1996/08/18 20:05:20  peter
-% %% Put unded version control
-% %%
-% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-
-
-states = structure(1);
-nonstates=structure(2);
-inputs=structure(3);
-outputs=structure(4);
-zero_outputs = structure(5);
-
-pc = '%';
-% Declare reduce constants;
-fprintf(deffilenum, 'MTTNx := %1.0f;\n', states);
-fprintf(deffilenum, 'MTTNz := %1.0f;\n', nonstates);
-fprintf(deffilenum, 'MTTNu := %1.0f;\n', inputs);
-fprintf(deffilenum, 'MTTNy := %1.0f;\n', outputs);
-fprintf(deffilenum, 'MTTNyz := %1.0f;\n', zero_outputs);
-
-% Declare reduce matrices
-fprintf(deffilenum, '%s Declare reduce matrices\n', pc);
-if states>0
-  fprintf(deffilenum, 'matrix MTTx(%1.0f,1);\n', states);
-  fprintf(deffilenum, 'matrix MTTdx(%1.0f,1);\n', states);
-end;
-if nonstates>0
-  fprintf(deffilenum, 'matrix MTTz(%1.0f,1);\n', nonstates);
-  fprintf(deffilenum, 'matrix MTTdz(%1.0f,1);\n', nonstates);
-end;
-if inputs>0
-  fprintf(deffilenum, 'matrix MTTu(%1.0f,1);\n', inputs);
-end;
-if outputs>0
-  fprintf(deffilenum, 'matrix MTTy(%1.0f,1);\n', outputs);
-end;
-if zero_outputs>0
-  fprintf(deffilenum, 'matrix MTTyz(%1.0f,1);\n', zero_outputs);
-  fprintf(deffilenum, 'matrix MTTui(%1.0f,1);\n', zero_outputs);
-end;
-
-% Make an Nx x Nx unit matrix
-if states>0
-  fprintf(deffilenum, 'matrix MTTI(%1.0f,%1.0f);\n', states,states);
-  for i = 1:states
-    fprintf(deffilenum, 'MTTI(%1.0f,%1.0f) := 1;\n', i, i);
-  end
-end;
-
-% Make an Nx/2 x Nx/2 unit matrix
-if states>1
-  fprintf(deffilenum, 'matrix MTTIm(%1.0f,%1.0f);\n', states/2,states/2);
-  for i = 1:states/2
-    fprintf(deffilenum, 'MTTIM(%1.0f,%1.0f) := 1;\n', i, i);
-  end
-end;
-
-% Set the y, yz, u, x and dx matrices
-fprintf(deffilenum, '%s Set the y, yz, u and x matrices\n', pc);
-for i=1:outputs
-  fprintf(deffilenum, 'MTTy(%1.0f,1) := MTTy%1.0f;\n', i, i);
-end;
-for i=1:zero_outputs
-  fprintf(deffilenum, 'MTTyz(%1.0f,1) := MTTyz%1.0f;\n', i, i);
-  fprintf(deffilenum, 'MTTui(%1.0f,1) := MTTui%1.0f;\n', i, i);
-end;
-for i=1:inputs
-  fprintf(deffilenum, 'MTTu(%1.0f,1) := MTTu%1.0f;\n', i, i);
-end;
-for i=1:states
-  fprintf(deffilenum, 'MTTx(%1.0f,1) := MTTx%1.0f;\n', i, i);
-end;
-for i=1:nonstates
-  fprintf(deffilenum, 'MTTdz(%1.0f,1) := MTTdz%1.0f;\n', i, i);
-end;
-
-fprintf(deffilenum, 'END;\n');
-  
+  ## %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+  ## %% Version control history
+  ## %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+  ## %% $Id$
+  ## %% $Log$
+  ## %% Revision 1.6  1996/12/07 18:21:57  peterg
+  ## %% Now uses fopen + file number
+  ## %%
+  ## %% Revision 1.5  1996/11/09 21:05:44  peterg
+  ## %% Only generates MTTIm when at least 2 states!
+  ## %%
+  ## %% Revision 1.4  1996/08/30  19:42:36  peter
+  ## %% Added newline at end of file.
+  ## %%
+  ## %% Revision 1.3  1996/08/24 15:06:22  peter
+  ## %% Write `END;' at end to please reduce.
+  ## %%
+  ## %% Revision 1.2  1996/08/18 20:05:20  peter
+  ## %% Put unded version control
+  ## %%
+  ## %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+
+
+  states = structure(1);
+  nonstates=structure(2);
+  inputs=structure(3);
+  outputs=structure(4);
+  zero_outputs = structure(5);
+  internal_inputs = structure(6);
+  connecting_inputs = structure(7);
+
+  pc = '%';
+  ## Declare reduce constants;
+  fprintf(deffilenum, 'MTTNx := %1.0f;\n', states);
+  fprintf(deffilenum, 'MTTNz := %1.0f;\n', nonstates);
+  fprintf(deffilenum, 'MTTNu := %1.0f;\n', inputs);
+  fprintf(deffilenum, 'MTTNy := %1.0f;\n', outputs);
+  fprintf(deffilenum, 'MTTNyz := %1.0f;\n', zero_outputs);
+  fprintf(deffilenum, 'MTTNui := %1.0f;\n', internal_inputs);
+  fprintf(deffilenum, 'MTTNuc := %1.0f;\n', connecting_inputs);
+
+  ## Declare reduce matrices
+  fprintf(deffilenum, '%s Declare reduce matrices\n', pc);
+  if states>0
+    fprintf(deffilenum, 'matrix MTTx(%1.0f,1);\n', states);
+    fprintf(deffilenum, 'matrix MTTdx(%1.0f,1);\n', states);
+  endif
+
+  if nonstates>0
+    fprintf(deffilenum, 'matrix MTTz(%1.0f,1);\n', nonstates);
+    fprintf(deffilenum, 'matrix MTTdz(%1.0f,1);\n', nonstates);
+  endif
+
+  if inputs>0
+    fprintf(deffilenum, 'matrix MTTu(%1.0f,1);\n', inputs);
+    fprintf(deffilenum, 'matrix MTTdu(%1.0f,1);\n', inputs);
+  endif
+
+  if outputs>0
+    fprintf(deffilenum, 'matrix MTTy(%1.0f,1);\n', outputs);
+  endif
+
+  if zero_outputs>0
+    fprintf(deffilenum, 'matrix MTTyz(%1.0f,1);\n', zero_outputs);
+    fprintf(deffilenum, 'matrix MTTui(%1.0f,1);\n', zero_outputs);
+  endif
+
+  if internal_inputs>0
+    fprintf(deffilenum, 'matrix MTTui(%1.0f,1);\n', inputs);
+  endif
+
+  if connecting_inputs>0
+    fprintf(deffilenum, 'matrix MTTuc(%1.0f,1);\n', connecting_inputs);
+  endif
+
+
+  ## Make an Nx x Nx unit matrix
+  if states>0
+    fprintf(deffilenum, 'matrix MTTI(%1.0f,%1.0f);\n', states,states);
+    for i = 1:states
+      fprintf(deffilenum, 'MTTI(%1.0f,%1.0f) := 1;\n', i, i);
+    end
+  endif
+
+
+  ## Make an Nx/2 x Nx/2 unit matrix
+  if states>1
+    fprintf(deffilenum, 'matrix MTTIm(%1.0f,%1.0f);\n', states/2,states/2);
+    for i = 1:states/2
+      fprintf(deffilenum, 'MTTIM(%1.0f,%1.0f) := 1;\n', i, i);
+    end
+  endif
+
+
+  ## Set the y, yz, du, u, x and dx matrices
+  fprintf(deffilenum, '%s Set the y, yz, u and x matrices\n', pc);
+  for i=1:outputs
+    fprintf(deffilenum, 'MTTy(%1.0f,1) := MTTy%1.0f;\n', i, i);
+  endfor
+
+  for i=1:zero_outputs
+    fprintf(deffilenum, 'MTTyz(%1.0f,1) := MTTyz%1.0f;\n', i, i);
+    fprintf(deffilenum, 'MTTui(%1.0f,1) := MTTui%1.0f;\n', i, i);
+  endfor
+
+  for i=1:inputs
+    fprintf(deffilenum, 'MTTu(%1.0f,1) := MTTu%1.0f;\n', i, i);
+  endfor
+
+  for i=1:inputs
+    fprintf(deffilenum, 'MTTdu(%1.0f,1) := MTTdu%1.0f;\n', i, i);
+  endfor
+
+  for i=1:states
+    fprintf(deffilenum, 'MTTx(%1.0f,1) := MTTx%1.0f;\n', i, i);
+  endfor
+
+  for i=1:nonstates
+    fprintf(deffilenum, 'MTTdz(%1.0f,1) := MTTdz%1.0f;\n', i, i);
+  endfor
+
+endfunction
+  
+
+
+