move step() down to TissueCell

src/arcade/patch/agent/cell/PatchCell.java

@@ -3,7 +3,6 @@
 import java.util.HashMap;
 import java.util.Map;
 import sim.engine.Schedule;
-import sim.engine.SimState;
 import sim.engine.Stoppable;
 import sim.util.Bag;
 import ec.util.MersenneTwisterFast;
@@ -85,7 +84,7 @@ public abstract class PatchCell implements Cell {
     int age;
 
     /** Cell energy [fmol ATP]. */
-    private double energy;
+    double energy;
 
     /** Number of divisions. */
     int divisions;
@@ -103,19 +102,19 @@ public abstract class PatchCell implements Cell {
     final double criticalHeight;
 
     /** Cell state change flag. */
-    private Flag flag;
+    Flag flag;
 
     /** Variation in cell agent parameters. */
     private final double heterogeneity;
 
     /** Fraction of necrotic cells that become apoptotic. */
-    private final double necroticFraction;
+    final double necroticFraction;
 
     /** Fraction of senescent cells that become apoptotic. */
-    private final double senescentFraction;
+    final double senescentFraction;
 
     /** Maximum energy deficit before necrosis. */
-    private final double energyThreshold;
+    final double energyThreshold;
 
     /** Cell state module. */
     protected Module module;
@@ -309,56 +308,6 @@ public void schedule(Schedule schedule) {
         stopper = schedule.scheduleRepeating(this, Ordering.CELLS.ordinal(), 1);
     }
 
-    @Override
-    public void step(SimState simstate) {
-        Simulation sim = (Simulation) simstate;
-
-        // Increase age of cell.
-        age++;
-
-        // TODO: check for death due to age
-
-        // Step metabolism process.
-        processes.get(Domain.METABOLISM).step(simstate.random, sim);
-
-        // Check energy status. If cell has less energy than threshold, it will
-        // necrose. If overall energy is negative, then cell enters quiescence.
-        if (state != State.APOPTOTIC && energy < 0) {
-            if (energy < energyThreshold) {
-                if (simstate.random.nextDouble() > necroticFraction) {
-                    setState(State.APOPTOTIC);
-                } else {
-                    setState(State.NECROTIC);
-                }
-            } else if (state != State.QUIESCENT && state != State.SENESCENT) {
-                setState(State.QUIESCENT);
-            }
-        }
-
-        // Step signaling network process.
-        processes.get(Domain.SIGNALING).step(simstate.random, sim);
-
-        // Change state from undefined.
-        if (state == State.UNDEFINED) {
-            if (flag == Flag.MIGRATORY) {
-                setState(State.MIGRATORY);
-            } else if (divisions == 0) {
-                if (simstate.random.nextDouble() > senescentFraction) {
-                    setState(State.APOPTOTIC);
-                } else {
-                    setState(State.SENESCENT);
-                }
-            } else {
-                setState(State.PROLIFERATIVE);
-            }
-        }
-
-        // Step the module for the cell state.
-        if (module != null) {
-            module.step(simstate.random, sim);
-        }
-    }
-
     @Override
     public CellContainer convert() {
         return new PatchCellContainer(id, parent, pop, age, divisions, state,

src/arcade/patch/agent/cell/PatchCellTissue.java

@@ -5,6 +5,11 @@
 import arcade.core.env.location.Location;
 import arcade.core.util.MiniBox;
 
+import sim.engine.SimState;
+import arcade.core.sim.Simulation;
+import static arcade.patch.util.PatchEnums.Domain;
+import static arcade.patch.util.PatchEnums.Flag;
+import static arcade.patch.util.PatchEnums.State;
 /**
  * Extension of {@link PatchCell} for healthy tissue cells.
  */
@@ -40,4 +45,57 @@ public PatchCell make(int newID, CellState newState, Location newLocation,
         return new PatchCellTissue(newID, id, pop, newState, age, divisions, newLocation,
                 parameters, volume, height, criticalVolume, criticalHeight);
     }
+
+    /* consider making PatchCell parameters protected instead of private */
+    /* make step()  method that overrides main that is moved over from PatchCell */
+
+    @Override
+    public void step(SimState simstate) {
+        Simulation sim = (Simulation) simstate;
+
+        // Increase age of cell.
+        super.age++;
+
+        // TODO: check for death due to age
+
+        // Step metabolism process.
+        super.processes.get(Domain.METABOLISM).step(simstate.random, sim);
+
+        // Check energy status. If cell has less energy than threshold, it will
+        // necrose. If overall energy is negative, then cell enters quiescence.
+        if (state != State.APOPTOTIC && energy < 0) {
+            if (super.energy < super.energyThreshold) {
+                if (simstate.random.nextDouble() > super.necroticFraction) {
+                    super.setState(State.APOPTOTIC);
+                } else {
+                    super.setState(State.NECROTIC);
+                }
+            } else if (state != State.QUIESCENT && state != State.SENESCENT) {
+                super.setState(State.QUIESCENT);
+            }
+        }
+
+        // Step signaling network process.
+        super.processes.get(Domain.SIGNALING).step(simstate.random, sim);
+
+        // Change state from undefined.
+        if (super.state == State.UNDEFINED) {
+            if (super.flag == Flag.MIGRATORY) {
+                super.setState(State.MIGRATORY);
+            } else if (super.divisions == 0) {
+                if (simstate.random.nextDouble() > super.senescentFraction) {
+                    super.setState(State.APOPTOTIC);
+                } else {
+                    super.setState(State.SENESCENT);
+                }
+            } else {
+                super.setState(State.PROLIFERATIVE);
+            }
+        }
+
+        // Step the module for the cell state.
+        if (super.module != null) {
+            super.module.step(simstate.random, sim);
+        }
+    }
 }

test/arcade/patch/util/PatchEnumsTest.java

@@ -1,8 +1,15 @@
 package arcade.patch.util;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.EnumSet;
 import org.junit.Test;
+
+import arcade.patch.util.PatchEnums.Category;
+import arcade.patch.util.PatchEnums.Domain;
+import arcade.patch.util.PatchEnums.Flag;
+import arcade.patch.util.PatchEnums.Ordering;
+import arcade.patch.util.PatchEnums.State;
 import ec.util.MersenneTwisterFast;
 import static org.junit.Assert.*;
 import static org.mockito.Mockito.*;
@@ -101,4 +108,20 @@ public void Category_random_returnsCategory() {
         EnumSet<Category> enumSetRandom = EnumSet.copyOf(enumRandom);
         assertEquals(enumSet, enumSetRandom);
     }
+
+    @Test
+    public void Ordering_in_expected_order() {
+        // Create list of all values.
+        ArrayList<Ordering> enumList = new ArrayList<Ordering>(Arrays.asList(Ordering.values()));
+
+        int n = -1;
+        int verify = -2;
+        // Grabbing order of items in enum
+        for (Ordering x: enumList){
+            verify = x.ordinal();
+            n++;
+            // Verify order of enum
+            assertEquals(n, verify);
+        }
+    }
 }