CARCADE refactor into v3

src/arcade/patch/agent/action/PatchActionKill.java

@@ -0,0 +1,100 @@
+package arcade.patch.agent.action;
+
+import sim.engine.Schedule;
+import sim.engine.SimState;
+import ec.util.MersenneTwisterFast;
+import arcade.core.agent.action.Action;
+import arcade.core.sim.Series;
+import arcade.core.sim.Simulation;
+import arcade.core.util.Parameters;
+import arcade.patch.agent.cell.PatchCellCART;
+import arcade.patch.agent.cell.PatchCellTissue;
+import arcade.patch.agent.process.PatchProcessInflammation;
+import arcade.patch.util.PatchEnums.AntigenFlag;
+import arcade.patch.util.PatchEnums.Domain;
+import arcade.patch.util.PatchEnums.Ordering;
+import arcade.patch.util.PatchEnums.State;
+
+/**
+ * Implementation of {@link Action} for killing tissue agents.
+ *
+ * <p>{@code PatchActionKill} is stepped once after a CD8 CAR T-cell binds to a target tissue cell.
+ * The {@code PatchActionKill} determines if cell has enough granzyme to kill. If so, it kills cell
+ * and calls the reset to neutral helper to return to neutral state. If not, it waits until it has
+ * enough granzyme to kill cell.
+ */
+public class PatchActionKill implements Action {
+
+    /** Target cell cytotoxic CAR T-cell is bound to */
+    PatchCellTissue target;
+
+    /** CAR T-cell inflammation module */
+    PatchProcessInflammation inflammation;
+
+    /** Amount of granzyme inside CAR T-cell */
+    double granzyme;
+
+    /** CAR T-cell that the module is linked to */
+    PatchCellCART c;
+
+    /** Time delay before calling the action [min]. */
+    private final int timeDelay;
+
+    /**
+     * Creates a {@code PatchActionKill} for the given {@link PatchCellCART}.
+     *
+     * @param c the {@link PatchCellCART} the helper is associated with
+     * @param target the {@link PatchCellTissue} the CAR T-cell is bound to
+     */
+    public PatchActionKill(
+            PatchCellCART c,
+            PatchCellTissue target,
+            MersenneTwisterFast random,
+            Series series,
+            Parameters parameters) {
+        this.c = c;
+        this.target = target;
+        this.inflammation = (PatchProcessInflammation) c.getProcess(Domain.INFLAMMATION);
+        this.granzyme = inflammation.getInternal("granzyme");
+        timeDelay = 0;
+    }
+
+    @Override
+    public void schedule(Schedule schedule) {
+        schedule.scheduleOnce(schedule.getTime() + timeDelay, Ordering.ACTIONS.ordinal(), this);
+    }
+
+    @Override
+    public void register(Simulation sim, String population) {}
+
+    @Override
+    public void step(SimState state) {
+        Simulation sim = (Simulation) state;
+
+        // If current CAR T-cell is stopped, stop helper.
+        if (c.isStopped()) {
+            return;
+        }
+
+        // If bound target cell is stopped, stop helper.
+        if (target.isStopped()) {
+            if (c.getBindingFlag() == AntigenFlag.BOUND_ANTIGEN) {
+                c.setBindingFlag(AntigenFlag.UNBOUND);
+            } else {
+                c.setBindingFlag(AntigenFlag.BOUND_CELL_RECEPTOR);
+            }
+            return;
+        }
+
+        if (granzyme >= 1) {
+
+            // Kill bound target cell.
+            PatchCellTissue tissueCell = (PatchCellTissue) target;
+            tissueCell.setState(State.APOPTOTIC);
+
+            // Use up some granzyme in the process.
+            granzyme--;
+            inflammation.setInternal("granzyme", granzyme);
+        }
+    }
+}

src/arcade/patch/agent/action/PatchActionReset.java

@@ -0,0 +1,67 @@
+package arcade.patch.agent.action;
+
+import sim.engine.Schedule;
+import sim.engine.SimState;
+import ec.util.MersenneTwisterFast;
+import arcade.core.agent.action.Action;
+import arcade.core.sim.Series;
+import arcade.core.sim.Simulation;
+import arcade.core.util.Parameters;
+import arcade.patch.agent.cell.PatchCellCART;
+import arcade.patch.agent.process.PatchProcessInflammation;
+import arcade.patch.util.PatchEnums.AntigenFlag;
+import arcade.patch.util.PatchEnums.Ordering;
+import arcade.patch.util.PatchEnums.State;
+
+/**
+ * Implementation of {@link Action} for resetting T cell agents.
+ *
+ * <p>{@code PatchActionReset} is stepped once after a CD8 CAR T-cell binds to a target tissue cell,
+ * or after a CD4 CAR T-cell gets stimulated. The {@code PatchReset} unbinds to any target cell that
+ * the T cell is bound to, and sets the cell state back to undefined.
+ */
+public class PatchActionReset implements Action {
+
+    /** CAR T-cell inflammation module */
+    PatchProcessInflammation inflammation;
+
+    /** CAR T-cell that the module is linked to */
+    PatchCellCART c;
+
+    /** Time delay before calling the action [min]. */
+    private final int timeDelay;
+
+    /**
+     * Creates a {@code PatchActionReset} for the given {@link PatchCellCART}.
+     *
+     * @param c the {@link PatchCellCART} the helper is associated with
+     */
+    public PatchActionReset(
+            PatchCellCART c, MersenneTwisterFast random, Series series, Parameters parameters) {
+        this.c = c;
+        double boundTime = parameters.getInt("BOUND_TIME");
+        double boundRange = parameters.getInt("BOUND_RANGE");
+        timeDelay = (int) (boundTime + Math.round((boundRange * (2 * random.nextInt() - 1))));
+    }
+
+    @Override
+    public void schedule(Schedule schedule) {
+        schedule.scheduleOnce(schedule.getTime() + timeDelay, Ordering.ACTIONS.ordinal(), this);
+    }
+
+    @Override
+    public void register(Simulation sim, String population) {}
+
+    @Override
+    public void step(SimState state) {
+        // If current CAR T-cell is stopped, stop helper.
+        if (c.isStopped()) {
+            return;
+        }
+
+        if (c.getState() == State.CYTOTOXIC || c.getState() == State.STIMULATORY) {
+            c.setBindingFlag(AntigenFlag.UNBOUND);
+            c.setState(State.UNDEFINED);
+        }
+    }
+}