fix: javadoc warnings

since they've started polluting CI run summaries...

Author: c-dilks

common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicityGenerator.java

@@ -145,7 +145,7 @@ public void addState(HelicityBit bit) {
      * Let the user add a state to initialize the sequence.
      * 
      * This just calls {@link #addState(HelicityBit)} with the raw
-     * {@link #HelicityBit} from the given {@link #HelicityState}.
+     * {@link HelicityBit} from the given {@link HelicityState}.
      *
      * This must be the first helicity state in the next pattern.  States
      * must be added serially and without skipped patterns.  Requires

common-tools/clas-detector/src/main/java/org/jlab/detector/helicity/HelicitySequence.java

@@ -297,7 +297,7 @@ public HelicityBit predictGenerated(long timestamp) {
      * Get whether the pseudo-random generator is initialized.  This must be
      * true before calling the predict methods, because they require a working
      * generator.  The number of valid states required to intialize the generator
-     * is {@link HelicityGenerator.REGISTER_SIZE}.
+     * is {@link HelicityGenerator#REGISTER_SIZE}.
      * 
      * @return whether initialized 
      */

common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/alert/AHDC/AlertDCWireIdentifier.java

@@ -171,7 +171,7 @@ else if (digit == 51) {
     /**
      * Convert layer number (from 0 to 7) to the superlayer-layer id (11,21,...,51)
      * 
-     * @param digit between 0 and 7
+     * @param num between 0 and 7
      * @return layer number between (11,21,...,51)
      */
     public static int number2layer(int num) {

common-tools/clas-geometry/src/main/java/org/jlab/geom/detector/fmt/FMTSuperlayer.java

@@ -7,13 +7,13 @@
 /**
  * A Forward Micromegas Tracker  (FMT) {@link org.jlab.geom.base.Superlayer Superlayer}.
  * <p>
- * Factory: {@link org.jlab.geom.detector.cnd.FMTFactory FMTFactory}<br> 
+ * Factory: {@link org.jlab.geom.detector.fmt.FMTFactory FMTFactory}<br> 
  * Hierarchy: 
  * <code>
- * {@link org.jlab.geom.detector.cnd.FMTDetector FMTDetector} → 
- * {@link org.jlab.geom.detector.cnd.FMTSector FMTSector} → 
- * <b>{@link org.jlab.geom.detector.cnd.FMTSuperlayer FMTSuperlayer}</b> → 
- * {@link org.jlab.geom.detector.cnd.FMTLayer FMTLayer} → 
+ * {@link org.jlab.geom.detector.fmt.FMTDetector FMTDetector} → 
+ * {@link org.jlab.geom.detector.fmt.FMTSector FMTSector} → 
+ * <b>{@link org.jlab.geom.detector.fmt.FMTSuperlayer FMTSuperlayer}</b> → 
+ * {@link org.jlab.geom.detector.fmt.FMTLayer FMTLayer} → 
  * {@link org.jlab.geom.component.TrackerStrip TrackerStrip}
  * </code>
  * 

common-tools/clas-io/src/main/java/org/jlab/io/base/BasicDataBank.java

@@ -565,13 +565,13 @@ public TableModel getTableModel(String mask) {
             if(entryMask.contains(columns[loop])==true||entryMask.size()<2){
                 for(int row = 0; row < nrows; row++){                    
                     if(this.byteContainer.containsKey(columns[loop])==true){
-                        objects[row][loop] = new Byte(this.getByte(columns[loop], row));
+                        objects[row][loop] = this.getByte(columns[loop], row);
                     }
                     if(this.shortContainer.containsKey(columns[loop])==true){
-                        objects[row][loop] = new Short(this.getShort(columns[loop], row));
+                        objects[row][loop] = this.getShort(columns[loop], row);
                     }
                     if(this.intContainer.containsKey(columns[loop])==true){
-                        objects[row][loop] = new Integer(this.getInt(columns[loop], row));
+                        objects[row][loop] = this.getInt(columns[loop], row);
                     }
                     if(this.floatContainer.containsKey(columns[loop])==true){
                         //objects[row][loop] = new Float(this.getFloat(columns[loop], row));
@@ -581,7 +581,7 @@ public TableModel getTableModel(String mask) {
                         objects[row][loop] = String.format("%12.5f",this.getDouble(columns[loop], row));
                     }
                     if(this.longContainer.containsKey(columns[loop])==true){
-                        objects[row][loop] = new Long(this.getLong(columns[loop], row));
+                        objects[row][loop] = this.getLong(columns[loop], row);
                     }
                 }
             }

common-tools/clas-jcsg/src/main/java/eu/mihosoft/vrl/v3d/ext/openjfx/importers/obj/FloatArrayList.java

@@ -94,7 +94,7 @@
  * @see Collection
  * @see List
  * @see LinkedList
- * @see Vector
+ * @see cnuphys.adaptiveSwim.geometry.Vector
  *
  * TODO replace with ObservableFloatArray
  */
@@ -358,7 +358,6 @@ public float[] toFloatArray() {
      *
      * @param index index of the element to return
      * @return the element at the specified position in this list
-     * @throws IndexOutOfBoundsException {@inheritDoc}
      */
     @Override public Float get(int index) {
         rangeCheck(index);
@@ -372,7 +371,6 @@ public float[] toFloatArray() {
      * @param index   index of the element to replace
      * @param element element to be stored at the specified position
      * @return the element previously at the specified position
-     * @throws IndexOutOfBoundsException {@inheritDoc}
      */
     @Override public Float set(int index, Float element) {
         rangeCheck(index);
@@ -400,7 +398,7 @@ public float[] toFloatArray() {
      *
      * @param index   index at which the specified element is to be inserted
      * @param element element to be inserted
-     * @throws IndexOutOfBoundsException {@inheritDoc}
+     * @throws IndexOutOfBoundsException
      */
     @Override public void add(int index, Float element) {
         rangeCheckForAdd(index);
@@ -419,7 +417,7 @@ public float[] toFloatArray() {
      *
      * @param index the index of the element to be removed
      * @return the element that was removed from the list
-     * @throws IndexOutOfBoundsException {@inheritDoc}
+     * @throws IndexOutOfBoundsException
      */
     @Override public Float remove(int index) {
         rangeCheck(index);
@@ -511,7 +509,7 @@ private void fastRemove(int index) {
      * @param index index at which to insert the first element from the specified collection
      * @param c     collection containing elements to be added to this list
      * @return <tt>true</tt> if this list changed as a result of the call
-     * @throws IndexOutOfBoundsException {@inheritDoc}
+     * @throws IndexOutOfBoundsException
      * @throws NullPointerException      if the specified collection is null
      */
     @Override public boolean addAll(int index, Collection<? extends Float> c) {
@@ -687,7 +685,7 @@ private void readObject(java.io.ObjectInputStream s)
      * </p>
      * <p>The returned list iterator is <a href="#fail-fast"><i>fail-fast</i></a>.
      *
-     * @throws IndexOutOfBoundsException {@inheritDoc}
+     * @throws IndexOutOfBoundsException
      */
     @Override public ListIterator<Float> listIterator(int index) {
         if (index < 0 || index > size)
@@ -840,8 +838,8 @@ private class ListItr extends Itr implements ListIterator<Float> {
      * that change the size of this list, or otherwise perturb it in such a fashion that iterations in progress may
      * yield incorrect results.)
      *
-     * @throws IndexOutOfBoundsException {@inheritDoc}
-     * @throws IllegalArgumentException  {@inheritDoc}
+     * @throws IndexOutOfBoundsException
+     * @throws IllegalArgumentException
      */
     @Override public List<Float> subList(int fromIndex, int toIndex) {
         subListRangeCheck(fromIndex, toIndex, size);

common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/SVTVolumeFactory.java

@@ -98,6 +98,7 @@ public class SVTVolumeFactory
 	 * Default: false
 	 * @deprecated
 	 */
+        @Deprecated
 	public boolean HALFBOXES = false;
 
 

common-tools/clas-jcsg/src/main/java/org/jlab/detector/geant4/v2/SVT/Util.java

@@ -465,30 +465,6 @@ public static void scalePosition( Geant4Basic aVol, double aFactor )
 	}
 
 
-	/**
-	 * Recursively multiplies each linear dimension of the given volume and its children by the given scale factor.
-	 * 
-	 * @param aVol volume
-	 * @param aFactor scale factor
-	 * @deprecated
-	 */
-        /*
-	public static void scaleDimensions( Geant4Basic aVol, double aFactor, boolean bRecursive )
-	{
-		aVol.scaleDimensions( aFactor );
-		//aVol.scale( aFactor );
-		
-		if( bRecursive )
-		{
-			List<Geant4Basic> children = aVol.getChildren();
-			for( int i = 0; i < children.size(); i++ )
-			{
-				scaleDimensions( children.get(i), aFactor, true ); // tail recursive
-			}
-		}
-	}
-	*/
-	
 	/**
 	 * Translates the given volume's position by the given shifts. 
 	 * 

common-tools/clas-jcsg/src/main/java/org/jlab/detector/volume/Geant4Basic.java

@@ -347,16 +347,12 @@ public Line3d getLineZ() {
         //return new Line3d(new Vector3d(0, 0, 0), new Vector3d(0, 0, 0));
     }
 
-    /**
-     * @author pdavies
-     */
+    // written by pdavies
     public void setPosition(double x, double y, double z) {
         setPosition(new Vector3d(x, y, z));
     }
 
-    /**
-     * @author pdavies
-     */
+    // written by pdavies
     public void setPosition(Vector3d position) {
         this.translate(position.minus(this.getLocalPosition()));
     }

common-tools/clas-reco/src/main/java/org/jlab/clas/detector/DetectorParticle.java

@@ -239,6 +239,7 @@ public int getSector(DetectorType type) {
      * @deprecated
      * Just for backward compatibility for any external usage
      */
+    @Deprecated
     public int getSector(){
         return this.getSector(DetectorType.ECAL,1);
     }
@@ -313,6 +314,7 @@ public DetectorResponse getHit(DetectorType type, int layer) {
      * @deprecated
      * Just for backward compatibility for any external usage
      */
+    @Deprecated
     public DetectorResponse  getResponse(DetectorType type, int layer){
         return this.getHit(type,layer);
     }