Javadoc (in progress) and cleaning examples in distro

examples/3_Haptics/EnclosedMarbles/EnclosedMarbles.pde

@@ -1,3 +1,8 @@
+/* 
+  WARNING : Haptic models haven't been ported to the new API yet
+  this model won't currently build 
+  */
+
 /*  LIB imports */
 import miPhysics.*;
 

examples/3_Haptics/HapticAudioTemplate/HapticAudioTemplate.pde

@@ -1,3 +1,9 @@
+/* 
+  WARNING : Haptic models haven't been ported to the new API yet
+  this model won't currently build 
+  */
+
+
 /**
  **********************************************************************************************************************
  */

examples/3_Haptics/HapticBeam/HapticBeam.pde

@@ -1,3 +1,9 @@
+/* 
+  WARNING : Haptic models haven't been ported to the new API yet
+  this model won't currently build 
+  */
+
+
 /**
  **********************************************************************************************************************
  */

examples/3_Haptics/HapticsOnlyTemplate/HapticsOnlyTemplate.pde

@@ -1,3 +1,9 @@
+/* 
+  WARNING : Haptic models haven't been ported to the new API yet
+  this model won't currently build 
+  */
+
+
 /**
  **********************************************************************************************************************
  */

examples/3_Haptics/HeavyMassChain/HeavyMassChain.pde

@@ -1,3 +1,9 @@
+/* 
+  WARNING : Haptic models haven't been ported to the new API yet
+  this model won't currently build 
+  */
+
+
 /**
  **********************************************************************************************************************
  */

examples/3_Haptics/MultipleStrings/MultipleStrings.pde

@@ -1,3 +1,10 @@
+/* 
+  WARNING : Haptic models haven't been ported to the new API yet
+  this model won't currently build 
+  */
+
+
+
 /**
  **********************************************************************************************************************
  */

examples/3_Haptics/PluckedString/PluckedString.pde

@@ -1,3 +1,10 @@
+/* 
+  WARNING : Haptic models haven't been ported to the new API yet
+  this model won't currently build 
+  */
+
+
+
 /**
  **********************************************************************************************************************
  */

examples/3_Haptics/RecoilString/RecoilString.pde

@@ -1,3 +1,9 @@
+/* 
+  WARNING : Haptic models haven't been ported to the new API yet
+  this model won't currently build 
+  */
+
+
 /**
  **********************************************************************************************************************
  */

examples/3_Haptics/SixResonnantStrings/SixResonnantStrings.pde

@@ -1,3 +1,10 @@
+/* 
+  WARNING : Haptic models haven't been ported to the new API yet
+  this model won't currently build 
+  */
+
+
+
 /**
  **********************************************************************************************************************
  */

resources/build.xml

@@ -155,6 +155,7 @@ ${line}
 				<path refid="classpath" />
 			</classpath>
 			<compilerarg value="-Xlint" />
+
 		</javac>
 		<copy todir="${project.bin.data}">
 			<fileset dir="${project.data}" excludes="README" />
@@ -181,6 +182,12 @@ ${line}
 				<exclude name="**/*README*" />
 				<!-- not including the ModelLoader examples for now -->
 				<exclude name="**/5_ModelLoader/**" />
+				<exclude name="**/2_Audio/control/**" />
+				<exclude name="**/2_Audio/BeamBender/**" />
+				<exclude name="**/4_TopoGenerator/**" />
+				<exclude name="**/TestExample/**" />
+				<exclude name="**/collisionEngineTester/**" />
+				<exclude name="**/TopoCreatorTest**/**" />
 			</fileset>
 		</copy>
 		<copy todir="${project.tmp}/${project.name}/src">

src/miPhysics/Engine/Attractor3D.java

@@ -10,6 +10,11 @@
  */
 public class Attractor3D extends Interaction {
 
+    /**
+     * Attractor module
+     * @param limitDist threshold distance below which the attraction force is null.
+     * @param attrFactor the attraction force factor.
+     */
     public Attractor3D(double limitDist, double attrFactor) {
         super(limitDist, null, null);
         m_attrFactor = attrFactor;

src/miPhysics/Engine/AutoCollider.java

@@ -10,6 +10,9 @@
 
 //TODO : If you change the underlying physical model during simulation, it will break! Make safer
 
+/**
+ * Autocollision handling mechanism for a physical model
+ */
 public class AutoCollider {
 
     PhyModel m_model;
@@ -118,6 +121,16 @@ private class Pair {
         }
     }
 
+    /**
+     * Setup an auto-collider system for a given physical model.
+     * @param mdl the model.
+     * @param size the size of individual voxels
+     * @param nbX voxels along X dimension
+     * @param nbY voxels along Y dimension
+     * @param nbZ voxels along Z dimension
+     * @param K stiffness of autocollision interactions
+     * @param Z damping of autocollision interactions
+     */
     public AutoCollider(PhyModel mdl, double size, int nbX, int nbY, int nbZ, double K, double Z){
         // save the model reference
         this.m_model = mdl;

src/miPhysics/Engine/Bubble3D.java

@@ -14,8 +14,6 @@ public class Bubble3D extends Interaction {
      * @param distance distance (radius) between both Mats.
      * @param K_param stiffness parameter.
      * @param Z_param damping parameter.
-     * @param m1 first (enclosed) Mass module.
-     * @param m2 second (enclosing) Mass module.
      */
     public Bubble3D(double distance, double K_param, double Z_param) {
         super(distance, null, null);

src/miPhysics/Engine/CollisionEngine.java

@@ -2,6 +2,10 @@
 
 import java.util.ArrayList;
 
+/**
+ * The global collision engine for the physics context. It can handle both collisions between
+ * two sub-models (physical models) and auto-collision of the masses inside a physical model.
+ */
 public class CollisionEngine {
 
     ArrayList<MassCollider> m_colliders = new ArrayList<>();
@@ -11,6 +15,13 @@ public CollisionEngine(){
 
     }
 
+    /**
+     * Register a collision between two sub-models.
+     * @param m1 the first physical model.
+     * @param m2 the second physical model.
+     * @param stiffness stiffness of the collisions.
+     * @param damping damping of the collisions.
+     */
     public void addCollision(PhyModel m1, PhyModel m2, double stiffness, double damping){
 
         recursiveColliders(m1, m2, stiffness, damping,  m_colliders);
@@ -21,6 +32,14 @@ public void addCollision(PhyModel m1, PhyModel m2, double stiffness, double damp
     }
 
 
+    /**
+     * Register auto-collision between the masses of a physical model.
+     * @param mdl the physical model.
+     * @param size size of the auto-collision voxels.
+     * @param dim gid size (number of voxels).
+     * @param stiffness stiffness of collisions.
+     * @param damping damping of collisions.
+     */
     public void addAutoCollision(PhyModel mdl, double size, int dim, double stiffness, double damping){
         m_autoColliders.add(new AutoCollider(mdl, size, dim, dim, dim, stiffness, damping));
     }
@@ -42,6 +61,9 @@ private void recursiveColliders(PhyModel m1, PhyModel m2, double K, double Z,  A
         }
     }
 
+    /**
+     * Compute all collusions and auto-collisions.
+     */
     public void runCollisions(){
         for(MassCollider mc : m_colliders){
             mc.detectCollisions();

src/miPhysics/Engine/Contact3D.java

@@ -17,11 +17,9 @@ public class Contact3D extends Interaction {
 
     private double interSize;
     /**
-     * @param distance
-     * @param K_param
-     * @param Z_param
-     * @param m1
-     * @param m2
+     * A conctact interaction defined between two points
+     * @param K_param the stiffness of the collision interaction.
+     * @param Z_param the damping of the collision interaction.
      */
     public Contact3D(double K_param, double Z_param) {
         super(0, null, null);

src/miPhysics/Engine/Driver3D.java

@@ -9,6 +9,10 @@
 
 public class Driver3D extends InOut {
 
+    /**
+     * Create the driver and attach it to a mass module
+     * @param m the to drive.
+     */
     public Driver3D(Mass m) {
         super(m);
         setType(inOutType.DRIVER3D);
@@ -30,7 +34,7 @@ public void compute() {
     }
 
     /**
-     * Apply position to connected Mass element
+     * Apply an input position to the mass element controlled by the driver.
      * @param pos the position to apply
      */
     public void applyPos(Vect3D pos){
@@ -43,7 +47,7 @@ public void applyPos(double x, double y, double z){
     }
 
     /**
-     * Apply force to connected Mass module
+     * Apply an input force to the mass controlled by the driver.
      * @param frc the Vec3D containing the force to apply
      */
     public void applyFrc(Vect3D frc){
@@ -64,7 +68,13 @@ public void moveDriver(Mass m){
     }
 
 
-
+    /**
+     * Trigger a force ramp applied to the controlled mass.
+     * @param x force amount along X.
+     * @param y force amount along Y.
+     * @param z force amount along Z.
+     * @param timeSteps steps in samples over which the force ramp is applied.
+     */
     public void triggerForceRamp(double x, double y, double z, int timeSteps){
         m_rampSteps = timeSteps;
         m_targetForce.x = x;
@@ -75,6 +85,11 @@ public void triggerForceRamp(double x, double y, double z, int timeSteps){
         m_rampActive = true;
     }
 
+    /**
+     * Trigger a force ramp applied to the controlled mass.
+     * @param frc 3D vector containing the force to apply.
+     * @param timeSteps steps in samples over which the force ramp is applied.
+     */
     public void triggerForceRamp(Vect3D frc, int timeSteps){
         this.triggerForceRamp(frc.x, frc.y, frc.z, timeSteps);
     }

src/miPhysics/Engine/Ground1D.java

@@ -1,7 +1,14 @@
 package miPhysics.Engine;
 
+/**
+ * One dimensional fixed point module.
+ */
 public class Ground1D extends Mass {
 
+	/**
+	 * @param size radius of the module.
+	 * @param initPos initial position.
+	 */
 	public Ground1D(double size, Vect3D initPos) {
 		super(1., size, initPos, initPos); // the mass parameter is unused.
 		setType(massType.GROUND1D);

src/miPhysics/Engine/Ground3D.java

@@ -1,11 +1,16 @@
 package miPhysics.Engine;
 
 /**
- * Fixed point Mass module.
+ * 3D Fixed point Mass module.
  * @author James Leonard / [email protected]
  *
  */
 public class Ground3D extends Mass {
+
+	/**
+	 * @param size radius of the module.
+	 * @param initPos initial position.
+	 */
 	public Ground3D(double size, Vect3D initPos) {
 		super(1., size,  initPos, initPos); // the mass parameter is unused.
 		setType(massType.GROUND3D);

src/miPhysics/Engine/InOut.java

@@ -11,25 +11,23 @@
 public abstract class InOut extends Module {
 
     /**
-     * Constructor method.
-     * @param distance resting distance of the Interaction.
-     * @param m1 connected Mass at one end.
-     * @param m2 connected Mass at other end.
+     * Generic in/out module constructor
+     * @param m
      */
     public InOut(Mass m) {
         m_mat = m;
         m_type = inOutType.UNDEFINED;
     }
 
     /**
-     * Compute behavior of the Interaction (depends on the concrete implementation of concerned module).
+     * Compute behavior of the In/Out (depends on the concrete implementation of concerned module).
      *
      */
     public abstract void compute();
 
     /**
      * Connect the InOut module to one Mass module.
-     * @param m connected Mass.
+     * @param m1 connected Mass.
      */
     public void connect (Mass m1) {
         m_mat = m1;

src/miPhysics/Engine/Mass.java

@@ -12,6 +12,7 @@ public abstract class Mass extends PhyObject {
      * Constructor method.
      *
      * @param M mass value.
+     * @param size radius of the mass.
      * @param initPos initial position.
      * @param initPosR delayed initial position.
      */

src/miPhysics/Engine/MassCollider.java

@@ -4,6 +4,9 @@
 import miPhysics.Utility.SpacePrint;
 import java.util.ArrayList;
 
+/**
+ * Collider class handling collision between two physical models.
+ */
 public class MassCollider {
 
     private Pair<PhyModel, PhyModel> m_colMdls;

src/miPhysics/Engine/Module.java

@@ -1,7 +1,7 @@
 package miPhysics.Engine;
 
 /**
- * Abstract class defining modules
+ * Abstract class defining modules (any type of physical element).
  *
  * @author James Leonard / [email protected]
  *

src/miPhysics/Engine/Observer3D.java

@@ -10,7 +10,11 @@
 
 public class Observer3D extends InOut {
 
-
+    /**
+     * Create an observer
+     * @param f a possible filter type on the observed output.
+     * @param m the mass to observe.
+     */
     public Observer3D(filterType f, Mass m) {
         super(m);
         setType(inOutType.OBSERVER3D);