properly deprecated everything

ihmc-common-walking-control-modules/src/main/java/us/ihmc/commonWalkingControlModules/controllerCore/WholeBodyControllerCore.java

@@ -176,6 +176,7 @@ public void reset()
     * @deprecated Use {@link #compute(ControllerCoreCommandInterface)} instead, note that it also makes
     *       {@link #compute()} obsolete.
     */
+   @Deprecated
    public void submitControllerCoreCommand(ControllerCoreCommandInterface controllerCoreCommand)
    {
       reset();
@@ -213,6 +214,7 @@ private void checkControlModeHandled()
     * @deprecated Use {@link #compute(ControllerCoreCommandInterface)} instead, note that it also makes
     *       {@link #submitControllerCoreCommand(ControllerCoreCommandInterface)} obsolete.
     */
+   @Deprecated
    public void compute()
    {
       controllerCoreComputeTimer.startMeasurement();

ihmc-common-walking-control-modules/src/main/java/us/ihmc/commonWalkingControlModules/controllerCore/command/feedbackController/FeedbackControlCommandList.java

@@ -144,6 +144,7 @@ public void removeCommand(int commandIndex)
     * @return the last command.
     * @deprecated this method should be removed and it is not really useful anyway.
     */
+   @Deprecated
    public FeedbackControlCommand<?> pollCommand()
    {
       if (commandList.isEmpty())

ihmc-common-walking-control-modules/src/main/java/us/ihmc/commonWalkingControlModules/controllerCore/command/inverseDynamics/InverseDynamicsCommandList.java

@@ -98,6 +98,7 @@ public InverseDynamicsCommand<?> getCommand(int commandIndex)
     * @return the last command.
     * @deprecated this method should be removed and it is not really useful anyway.
     */
+   @Deprecated
    public InverseDynamicsCommand<?> pollCommand()
    {
       if (commandList.isEmpty())

ihmc-common-walking-control-modules/src/main/java/us/ihmc/commonWalkingControlModules/controllerCore/command/inverseKinematics/InverseKinematicsCommandList.java

@@ -98,6 +98,7 @@ public InverseKinematicsCommand<?> getCommand(int commandIndex)
     * @return the last command.
     * @deprecated this method should be removed and it is not really useful anyway.
     */
+   @Deprecated
    public InverseKinematicsCommand<?> pollCommand()
    {
       if (commandList.isEmpty())

ihmc-common-walking-control-modules/src/main/java/us/ihmc/commonWalkingControlModules/controllerCore/command/virtualModelControl/VirtualModelControlCommandList.java

@@ -99,6 +99,7 @@ public VirtualModelControlCommand<?> getCommand(int commandIndex)
     * @return the last command.
     * @deprecated this method should be removed and it is not really useful anyway.
     */
+   @Deprecated
    public VirtualModelControlCommand<?> pollCommand()
    {
       if (commandList.isEmpty())

ihmc-common-walking-control-modules/src/test/java/us/ihmc/commonWalkingControlModules/controlModules/legConfiguration/TriangleToolsTest.java

@@ -465,7 +465,7 @@ public void testComputeSideLengthFromSideSideAngle()
       sideBLength = 1.0;
       angleB = 0.8;
       isAngleAObtuse = false;
-      assertTrue("Case 3 failed.", new Double(TriangleTools.computeSideLengthFromSideSideAngle(sideALength, sideBLength, angleB, isAngleAObtuse)).isNaN());
+      assertTrue("Case 3 failed.", Double.valueOf(TriangleTools.computeSideLengthFromSideSideAngle(sideALength, sideBLength, angleB, isAngleAObtuse)).isNaN());
 
       // Case 4: Known angle < Pi/2 and adjacent side > opposite side and opposite side > height and angleA is acute
       sideALength = 1.5;
@@ -496,14 +496,14 @@ public void testComputeSideLengthFromSideSideAngle()
       sideBLength = 1.0;
       angleB = 1.75;
       isAngleAObtuse = false;
-      assertTrue("Case 7 failed.", new Double(TriangleTools.computeSideLengthFromSideSideAngle(sideALength, sideBLength, angleB, isAngleAObtuse)).isNaN());
+      assertTrue("Case 7 failed.", Double.valueOf(TriangleTools.computeSideLengthFromSideSideAngle(sideALength, sideBLength, angleB, isAngleAObtuse)).isNaN());
 
       // Case 8: Known angle > Pi/2 and adjacent side > opposite side
       sideALength = 1.5;
       sideBLength = 1.0;
       angleB = 1.75;
       isAngleAObtuse = false;
-      assertTrue("Case 8 failed.", new Double(TriangleTools.computeSideLengthFromSideSideAngle(sideALength, sideBLength, angleB, isAngleAObtuse)).isNaN());
+      assertTrue("Case 8 failed.", Double.valueOf(TriangleTools.computeSideLengthFromSideSideAngle(sideALength, sideBLength, angleB, isAngleAObtuse)).isNaN());
 
       // Random Testing
       Random random = new Random(34534L);

ihmc-communication/src/test/java/us/ihmc/communication/remote/DataObjectTransponderTest.java

@@ -97,7 +97,7 @@ public void testDoubleBidirectionalCommunication() throws InterruptedException
    @Test
    public void testSerializabilityOfInteger() throws IOException
    {
-      Integer integer = new Integer(2);
+      Integer integer = Integer.valueOf(2);
       Assertions.assertSerializable(integer);
    }
 

ihmc-high-level-behaviors/src/main/java/us/ihmc/behaviors/BehaviorModule.java

@@ -18,6 +18,7 @@
  *
  * @deprecated Replaced by ROS2BehaviorTreeExecutor
  */
+@Deprecated
 public class BehaviorModule
 {
    private final BehaviorTreeMessage behaviorTreeMessage = new BehaviorTreeMessage();

ihmc-high-level-behaviors/src/main/java/us/ihmc/behaviors/buildingExploration/old/BuildingExplorationBehavior.java

@@ -25,6 +25,7 @@
  * This was intended to be an upgrade for the 2019 Atlas building exploration demo but never got used.
  * @deprecated Not supported right now. Being kept for reference or revival.
  */
+@Deprecated
 public class BuildingExplorationBehavior extends ResettingNode implements Destroyable
 {
    private final BehaviorHelper helper;

ihmc-high-level-behaviors/src/main/java/us/ihmc/behaviors/buildingExploration/old/BuildingExplorationBehaviorOld.java

@@ -46,6 +46,7 @@
  * an upgrade was planned but never finished.
  * @deprecated Not supported right now. Being kept for reference or revival.
  */
+@Deprecated
 public class BuildingExplorationBehaviorOld extends ResettingNode implements Destroyable
 {
    private static final int UPDATE_RATE_MILLIS = 50;

ihmc-high-level-behaviors/src/main/java/us/ihmc/behaviors/door/DoorBehavior.java

@@ -27,6 +27,7 @@
  * A behavior tree layer on top of the door behavior that John wrote for Atlas.
  * @deprecated Not supported right now. Being kept for reference or revival.
  */
+@Deprecated
 public class DoorBehavior extends ResettingNode implements Destroyable
 {
    private BehaviorHelper helper;

ihmc-high-level-behaviors/src/main/java/us/ihmc/behaviors/exploreArea/ExploreAreaBehavior.java

@@ -24,6 +24,7 @@
  * An attempt mostly in simulation to explore a building.
  * @deprecated Not supported right now. Being kept for reference or revival.
  */
+@Deprecated
 public class ExploreAreaBehavior extends FallbackNode implements Destroyable
 {
    public static final double TICK_PERIOD = UnitConversions.hertzToSeconds(2);

ihmc-high-level-behaviors/src/main/java/us/ihmc/behaviors/fancyPoses/FancyPosesBehavior.java

@@ -32,6 +32,7 @@
 /**
  * @deprecated Not supported right now. Being kept for reference or revival.
  */
+@Deprecated
 public class FancyPosesBehavior extends LocalOnlyBehaviorTreeNodeExecutor implements Destroyable
 {
    private final BehaviorHelper helper;

ihmc-high-level-behaviors/src/main/java/us/ihmc/behaviors/lookAndStep/LookAndStepSupportRegionsPublisher.java

@@ -33,6 +33,7 @@
 /**
  * @deprecated This class isn't currently used.
  */
+@Deprecated
 public class LookAndStepSupportRegionsPublisher
 {
    private ResettableExceptionHandlingExecutorService executor;

ihmc-high-level-behaviors/src/main/java/us/ihmc/behaviors/navigation/NavigationBehavior.java

@@ -54,6 +54,7 @@
  * Used visibility graphs to walk through a maze.
  * @deprecated Not supported right now. Being kept for reference or revival.
  */
+@Deprecated
 public class NavigationBehavior extends LocalOnlyBehaviorTreeNodeExecutor implements Destroyable
 {
    private static final Point3D goal = new Point3D(MAZE_CORRIDOR_SQUARE_SIZE * 4.0, MAZE_CORRIDOR_SQUARE_SIZE, 0.0);

ihmc-high-level-behaviors/src/main/java/us/ihmc/behaviors/patrol/PatrolBehavior.java

@@ -40,6 +40,7 @@
  * This also was used to walk to high and low big planar regions autonomously.
  * @deprecated Not supported right now. Being kept for reference or revival.
  */
+@Deprecated
 public class PatrolBehavior extends LocalOnlyBehaviorTreeNodeExecutor
 {
    public enum PatrolBehaviorState

ihmc-high-level-behaviors/src/main/java/us/ihmc/behaviors/stairs/TraverseStairsBehavior.java

@@ -34,6 +34,7 @@
  * stairs autonomously, I think we might be able to simplify it on Nadia.
  * @deprecated Not supported right now. Being kept for reference or revival.
  */
+@Deprecated
 public class TraverseStairsBehavior extends ResettingNode
 {
    private static final int UPDATE_RATE_MILLIS = 100;

ihmc-high-level-behaviors/src/main/java/us/ihmc/behaviors/targetFollowing/TargetFollowingBehavior.java

@@ -24,6 +24,7 @@
  * are good videos of it following Bhavyansh.
  * @deprecated Not supported right now. Being kept for reference or revival.
  */
+@Deprecated
 public class TargetFollowingBehavior extends ResettingNode implements Destroyable
 {
    private final BehaviorHelper helper;

ihmc-high-level-behaviors/src/main/java/us/ihmc/behaviors/tools/BehaviorMessageTools.java

@@ -9,6 +9,7 @@
  * @deprecated This class is kept only so that other code can stay compiling as
  *               we use it for reference in rewriting the behavior tree implementation.
  */
+@Deprecated
 public class BehaviorMessageTools
 {
    /**

ihmc-high-level-behaviors/src/main/java/us/ihmc/behaviors/tools/perception/AlternateHeightMapUpdater.java

@@ -21,6 +21,7 @@
  *
  * @deprecated Needs work
  */
+@Deprecated
 public class AlternateHeightMapUpdater
 {
    private final HeightMapParameters parameters;

ihmc-humanoid-behaviors/src/main/java/us/ihmc/humanoidBehaviors/behaviors/primitives/ClearLidarBehavior.java

@@ -7,6 +7,7 @@
 /**
  * @deprecated The lidar stuff is broken. What about implement a centralized LidarBufferBehavior that records lidar in an internal buffer.
  */
+@Deprecated
 public class ClearLidarBehavior extends AbstractBehavior
 {
    private final YoBoolean packetHasBeenSent = new YoBoolean("packetHasBeenSent" + behaviorName, registry);

ihmc-humanoid-behaviors/src/main/java/us/ihmc/humanoidBehaviors/behaviors/primitives/EnableLidarBehavior.java

@@ -7,6 +7,7 @@
 /**
  * @deprecated Broken. See {@link ClearLidarBehavior}.
  */
+@Deprecated
 public class EnableLidarBehavior extends AbstractBehavior
 {
    private final YoBoolean packetHasBeenSent = new YoBoolean("packetHasBeenSent" + behaviorName, registry);

ihmc-humanoid-behaviors/src/main/java/us/ihmc/humanoidBehaviors/behaviors/primitives/SetLidarParametersBehavior.java

@@ -9,6 +9,7 @@
  * @deprecated This is not working anymore. See {@link ClearLidarBehavior}.
  *
  */
+@Deprecated
 public class SetLidarParametersBehavior extends AbstractBehavior
 {
    private final YoBoolean packetHasBeenSent = new YoBoolean("packetHasBeenSent" + behaviorName, registry);

ihmc-humanoid-behaviors/src/main/java/us/ihmc/humanoidBehaviors/behaviors/scripts/engine/ScriptFileSaver.java

@@ -46,6 +46,7 @@ public ScriptFileSaver(File file, boolean overwriteExistingScript) throws IOExce
     * @deprecated This method is highly inefficient. The whole scripting needs to be redone to better
     *             implement the transform.
     */
+   @Deprecated
    public void recordObject(long timestamp, Object object, RigidBodyTransform objectTransform) throws IOException
    {
 

ihmc-humanoid-robotics/src/main/java/us/ihmc/humanoidRobotics/communication/packets/dataobjects/HandConfiguration.java

@@ -8,6 +8,7 @@
  * @author twan
 *         Date: 6/8/13
 */
+@Deprecated
 public enum HandConfiguration
 {
    @RosEnumValueDocumentation(documentation = "stops the fingers at their current position")

ihmc-humanoid-robotics/src/main/java/us/ihmc/humanoidRobotics/footstep/FootstepUtils.java

@@ -126,7 +126,7 @@ public static RobotSide getFrontFootRobotSideFromFootsteps(SideDependentList<Foo
          FramePoint3D footstepPosition = new FramePoint3D();
          footSteps.get(side).getPosition(footstepPosition);
          footstepPosition.changeFrame(worldFrame);
-         distances.set(side, new Double(footstepPosition.distanceSquared(destinationInWorld)));
+         distances.set(side, Double.valueOf(footstepPosition.distanceSquared(destinationInWorld)));
       }
 
       RobotSide frontSide = (distances.get(RobotSide.LEFT) <= distances.get(RobotSide.RIGHT)) ? RobotSide.LEFT : RobotSide.RIGHT;

ihmc-interfaces/src/main/generated-java/perception_msgs/msg/dds/RequestPlanarRegionsListMessage.java

@@ -12,6 +12,7 @@
        * Use this message to request new planar regions
        * @deprecated REA always publishes planar regions when running. To request REA to clear its internal state, see REAStateRequestMessage.
        */
+@Deprecated
 public class RequestPlanarRegionsListMessage extends Packet<RequestPlanarRegionsListMessage> implements Settable<RequestPlanarRegionsListMessage>, EpsilonComparable<RequestPlanarRegionsListMessage>
 {
    public static final byte SINGLE_UPDATE = (byte) 0;

ihmc-java-toolkit/src/main/java/us/ihmc/tools/ArrayTools.java

@@ -32,7 +32,7 @@ public static double[] parseDoubleArray(String stringSource) throws IOException
       StringTokenizer tokenizer = new StringTokenizer(line.replace("{", "").replace("}", "").replace(" ", "").replace(";", ""), ",");
       while (tokenizer.hasMoreElements())
       {
-         retArray.add(new Double(Double.parseDouble((String) tokenizer.nextElement())));
+         retArray.add(Double.valueOf(Double.parseDouble((String) tokenizer.nextElement())));
 
          // retArray.add(new
          // Double(Double.parseDouble(tokenizer.nextToken())));
@@ -79,7 +79,7 @@ public static double[] parseDoubleArrayFromMATLAB(String stringSource) throws IO
       StringTokenizer tokenizer = new StringTokenizer(line.replace("[", "").replace("]", "").replace(" ", ""), ",");
       while (tokenizer.hasMoreElements())
       {
-         retArray.add(new Double(Double.parseDouble((String) tokenizer.nextElement())));
+         retArray.add(Double.valueOf(Double.parseDouble((String) tokenizer.nextElement())));
 
          // retArray.add(new
          // Double(Double.parseDouble(tokenizer.nextToken())));
@@ -135,7 +135,7 @@ public static int[] parseIntegerArray(String stringSource) throws IOException
                                                       ",");
       while (tokenizer.hasMoreElements())
       {
-         retArray.add(new Integer(Integer.parseInt((String) tokenizer.nextElement())));
+         retArray.add(Integer.valueOf(Integer.parseInt((String) tokenizer.nextElement())));
       }
 
       int[] ret = new int[retArray.size()];

ihmc-java-toolkit/src/main/java/us/ihmc/tools/inputDevices/joystick/mapping/MadCatzFLY5StickMapping.java

@@ -19,10 +19,12 @@ public enum MadCatzFLY5StickMapping implements JoystickMapping
    THROTTLE_LEFT,
    THROTTLE_RIGHT,
    /** @deprecated Not supported on Windows */
+   @Deprecated
    THROTTLE_LOCK,
    HAT,
    THUMB_SCOLL_UP,
    /** @deprecated Not identified on Linux */
+   @Deprecated
    THUMB_SCOLL_DOWN,
    STICK_ROLL,
    STICK_PITCH,
@@ -38,6 +40,7 @@ public enum MadCatzFLY5StickMapping implements JoystickMapping
    BUTTON_10,
    BUTTON_11,
    /** @deprecated Not identified on Linux */
+   @Deprecated
    BASE_MODE_BUTTON;
 
    public static final MadCatzFLY5StickMapping[] values = values();

ihmc-java-toolkit/src/main/java/us/ihmc/tools/inputDevices/joystick/mapping/SaitekX52Mapping.java

@@ -18,6 +18,7 @@ public enum SaitekX52Mapping implements JoystickMapping
    /** Mappings for Windows, Mac, Linux */
    TRIGGER_PARITIAL,
    /** @deprecated Only works on Windows and Mac */
+   @Deprecated
    TRIGGER_FULL,
    PINKY_TRIGGER,
    SAFE_FIRE,
@@ -42,8 +43,10 @@ public enum SaitekX52Mapping implements JoystickMapping
    BASE_SWITCH_CENTER_UP,
    BASE_SWITCH_CENTER_DOWN,
    /** @deprecated Only works on Windows and Mac */
+   @Deprecated
    BASE_SWITCH_RIGHT_UP,
    /** @deprecated Only works on Windows and Mac */
+   @Deprecated
    BASE_SWITCH_RIGHT_DOWN,
    STICK_PITCH,
    STICK_ROLL,
@@ -53,18 +56,25 @@ public enum SaitekX52Mapping implements JoystickMapping
    BIG_ROTARY_KNOB,
    LITTLE_ROTARY_KNOB,
    /** @deprecated Only works on Windows and Mac */
+   @Deprecated
    FUNCTION,
    /** @deprecated Only works on Linux */
+   @Deprecated
    START_STOP,
    /** @deprecated Only works on Linux */
+   @Deprecated
    RESET,
    /** @deprecated Only works on Linux */
+   @Deprecated
    INFO,
    /** @deprecated Only works on Linux */
+   @Deprecated
    MOUSE_TOGGLE,
    /** @deprecated Only works on Windows and Linux */
+   @Deprecated
    NIPPLE_LEFT_RIGHT,
    /** @deprecated Only works on Windows and Linux */
+   @Deprecated
    NIPPLE_UP_DOWN,
    ;
 

ihmc-java-toolkit/src/main/java/us/ihmc/tools/inputDevices/joystick/mapping/Thrustmaster16000M.java

@@ -31,12 +31,15 @@ public enum Thrustmaster16000M implements JoystickMapping
    BASE_BUTTON_LEFT_SIDE_LOWER_CENTER,
    BASE_BUTTON_LEFT_SIDE_LOWER_RIGHT,
    /** @deprecated Only works on Windows and Mac */
+   @Deprecated
    BASE_BUTTON_RIGHT_SIDE_UPPER_LEFT,
    BASE_BUTTON_RIGHT_SIDE_UPPER_CENTER,
    BASE_BUTTON_RIGHT_SIDE_UPPER_RIGHT,
    /** @deprecated Only works on Windows and Mac */
+   @Deprecated
    BASE_BUTTON_RIGHT_SIDE_LOWER_LEFT,
    /** @deprecated Only works on Windows and Mac */
+   @Deprecated
    BASE_BUTTON_RIGHT_SIDE_LOWER_CENTER,
    BASE_BUTTON_RIGHT_SIDE_LOWER_RIGHT,
    ;

ihmc-java-toolkit/src/main/java/us/ihmc/tools/inputDevices/joystick/mapping/XBoxOneMapping.java

@@ -37,14 +37,19 @@ public enum XBoxOneMapping implements JoystickMapping
    LEFT_STICK_BUTTON,
    RIGHT_STICK_BUTTON,
    /** @deprecated Only works on Windows and Linux */
+   @Deprecated
    DPAD,
    /** @deprecated Only works on Mac */
+   @Deprecated
    DPAD_UP,
    /** @deprecated Only works on Mac */
+   @Deprecated
    DPAD_DOWN,
    /** @deprecated Only works on Mac */
+   @Deprecated
    DPAD_LEFT,
    /** @deprecated Only works on Mac */
+   @Deprecated
    DPAD_RIGHT,
    SLIDER;
 

ihmc-java-toolkit/src/main/java/us/ihmc/tools/property/StoredPropertySet.java

@@ -83,7 +83,7 @@ public class StoredPropertySet implements StoredPropertySetBasics
    private final String capitalizedClassName;
    private WorkspaceResourceFile workspaceJSONFile;
 
-   private final Map<StoredPropertyKey, List<Runnable>> propertyChangedListeners = new HashMap<>();
+   private final Map<StoredPropertyKey<?>, List<Runnable>> propertyChangedListeners = new HashMap<>();
    private final List<Notification> anyPropertyChangedListeners = new ArrayList<>();
 
    public StoredPropertySet(StoredPropertyKeyList keys, Class<?> classForLoading)