JavaDoc improvements

addons/batikvis/src/main/java/elki/visualization/batikutil/ThumbnailRegistryEntry.java

@@ -181,6 +181,8 @@ public static Filter handleURL(ParsedURL url) {
   private static class InternalParsedURLData extends ParsedURLData {
     /**
      * Constructor.
+     * 
+     * @param id ID string
      */
     public InternalParsedURLData(String id) {
       super();

addons/batikvis/src/main/java/elki/visualization/gui/ResultWindow.java

@@ -223,6 +223,14 @@ protected synchronized void updateVisualizerMenus() {
       menubar.repaint();
     }
 
+    /**
+     * Build the menu bar
+     * 
+     * @param items Menu items collection
+     * @param r Root object
+     * @param vistree Visualization tree
+     * @param proj Projection
+     */
     private void recursiveBuildMenu(Collection<JMenuItem> items, Object r, Hierarchy<Object> vistree, Projection proj) {
       // Make a submenu for this element
       final String nam;
@@ -289,6 +297,12 @@ private void recursiveBuildMenu(Collection<JMenuItem> items, Object r, Hierarchy
       items.add(submenu);
     }
 
+    /**
+     * Make a menu item for a visualizer.
+     *
+     * @param r Visualizer
+     * @return Menu item
+     */
     private JMenuItem makeMenuItemForVisualizer(Object r) {
       if(r instanceof VisualizationMenuAction) {
         final VisualizationMenuAction action = (VisualizationMenuAction) r;
@@ -365,6 +379,9 @@ public void enableWriter(boolean b) {
     }
   }
 
+  /**
+   * Menu bar
+   */
   private DynamicMenu menubar;
 
   /**
@@ -517,7 +534,7 @@ public void showOverview() {
   /**
    * Navigate to a subplot.
    *
-   * @param e
+   * @param e Event
    */
   protected void showSubplot(DetailViewSelectedEvent e) {
     if(!single) {

addons/batikvis/src/main/java/elki/visualization/gui/overview/OverviewPlot.java

@@ -396,6 +396,7 @@ private void initializePlot() {
    * @param it Plot item
    * @param task Task
    * @param parent Parent element to draw to
+   * @return Visualization
    */
   private Visualization embedOrThumbnail(final int thumbsize, PlotItem it, VisualizationTask task, Element parent) {
     final Visualization vis;

addons/batikvis/src/main/java/elki/visualization/gui/overview/PlotItem.java

@@ -174,14 +174,19 @@ public String toString() {
    * @author Erich Schubert
    */
   private static class ItmItr implements Iterator<PlotItem> {
+    /** Next item to return */
     PlotItem next;
 
+    /** Current iterator */
     Iterator<PlotItem> cur;
 
+    /** Subitem iterator */
     Iterator<PlotItem> sub;
 
     /**
      * Constructor.
+     * 
+     * @param start Start item
      */
     public ItmItr(PlotItem start) {
       super();

addons/batikvis/src/main/java/elki/visualization/gui/overview/RectangleArranger.java

@@ -85,7 +85,7 @@ public class RectangleArranger<T> {
   /**
    * Constructor.
    *
-   * @param ratio
+   * @param ratio Window ratio
    */
   public RectangleArranger(double ratio) {
     this(ratio, 1.0);
@@ -289,11 +289,24 @@ public void put(double w, double h, T data) {
     }
   }
 
+  /**
+   * Compute the area increase of a change.
+   * 
+   * @param winc Width increase
+   * @param hinc Height increase
+   * @return Area increase
+   */
   protected double computeIncreaseArea(double winc, double hinc) {
     double inc = Math.max(winc, hinc * ratio);
     return inc * (hinc + inc / ratio + winc / ratio);
   }
 
+  /**
+   * Split a row.
+   * 
+   * @param bestey Row index
+   * @param besthi Row height to split off
+   */
   protected void splitRow(int bestey, double besthi) {
     assert (bestey < heights.size());
     if(heights.get(bestey) - besthi <= Double.MIN_NORMAL) {
@@ -308,6 +321,12 @@ protected void splitRow(int bestey, double besthi) {
     usage.add(bestey + 1, new ArrayList<>(usage.get(bestey)));
   }
 
+  /**
+   * Split a column.
+   * 
+   * @param bestex Column id
+   * @param bestwi Width to split off
+   */
   protected void splitCol(int bestex, double bestwi) {
     assert (bestex < widths.size());
     if(widths.get(bestex) - bestwi <= Double.MIN_NORMAL) {
@@ -326,6 +345,11 @@ protected void splitCol(int bestex, double bestwi) {
     assert assertConsistent();
   }
 
+  /**
+   * Resize the canvas by an increment.
+   * 
+   * @param inc Increment to add to the x axis
+   */
   private void resize(double inc) {
     final int cols = widths.size(), rows = heights.size();
     if(LOG.isDebuggingFine()) {

addons/batikvis/src/main/java/elki/visualization/projections/SimpleParallel.java

@@ -136,6 +136,12 @@ public LinearScale getAxisScale(int axis) {
     return scales[dimOrder[axis]];
   }
 
+  /**
+   * Check if a dimension is hidden
+   * 
+   * @param truedim Original dimension (not display offset)
+   * @return {@code true} if hidden
+   */
   protected boolean isDimHidden(int truedim) {
     return (flags[truedim] & FLAG_HIDDEN) == FLAG_HIDDEN;
   }

addons/batikvis/src/main/java/elki/visualization/projector/ParallelPlotFactory.java

@@ -70,6 +70,12 @@ public void processNewResult(VisualizerContext context, Object start) {
     });
   }
 
+  /**
+   * Get the dimensionality of a relation.
+   * 
+   * @param rel Relation
+   * @return Dimensionality
+   */
   private int dimensionality(Relation<?> rel) {
     if(TypeUtil.NUMBER_VECTOR_FIELD.isAssignableFromType(rel.getDataTypeInformation())) {
       @SuppressWarnings("unchecked")

addons/batikvis/src/main/java/elki/visualization/style/marker/PrettyMarkers.java

@@ -104,6 +104,7 @@ public PrettyMarkers(StyleLibrary style) {
    * @param y position
    * @param style marker style (enumerated)
    * @param size size
+   * @param intensity intensity
    * @return container element
    */
   public Element plotMarker(SVGPlot plot, double x, double y, int style, double size, double intensity) {
@@ -264,6 +265,7 @@ public Element plotMarker(SVGPlot plot, double x, double y, int style, double si
    * @param y Y position
    * @param size Size
    * @param color Color string
+   * @return SVG element
    */
   protected Element plotSimple(SVGPlot plot, double x, double y, double size, String color) {
     Element marker = plot.svgCircle(x, y, size * .5);

addons/batikvis/src/main/java/elki/visualization/visualizers/pairsegments/CircleSegmentsVisualizer.java

@@ -249,6 +249,11 @@ public Instance(VisualizerContext context, VisualizationTask task, Visualization
       addListeners();
     }
 
+    /**
+     * Toggle showing the unclustered pairs
+     * 
+     * @param show Show unclusered pairs
+     */
     public void toggleUnclusteredPairs(boolean show) {
       noIncrementalRedraw = true;
       showUnclusteredPairs = show;
@@ -313,6 +318,8 @@ public void fullRedraw() {
 
     /**
      * Define and add required CSS classes
+     * 
+     * @param maxClusterSize Maximum number of clusters
      */
     protected void addCSSClasses(int maxClusterSize) {
       StyleLibrary style = context.getStyleLibrary();
@@ -477,6 +484,9 @@ private void drawSegments() {
       }
     }
 
+    /**
+     * Redraw the current selection
+     */
     private void redrawSelection() {
       final StyleLibrary style = context.getStyleLibrary();
       LOG.debug("Updating selection only.");
@@ -551,6 +561,11 @@ protected String[] makeGradient(int shades, String[] colors) {
       return colorShades;
     }
 
+    /**
+     * Draw the clustering information
+     * 
+     * @return SVG element
+     */
     protected Element drawClusteringInfo() {
       Element thumbnail = SVGUtil.svgElement(svgp.getDocument(), SVGConstants.SVG_G_TAG);
 
@@ -577,6 +592,13 @@ protected Element drawClusteringInfo() {
       return thumbnail;
     }
 
+    /**
+     * Hover handling for segments.
+     * 
+     * @param segment Segment
+     * @param ringid Ring ID (depth)
+     * @param active Activate or deactivate hover
+     */
     protected void segmentHover(Segment segment, int ringid, boolean active) {
       if(active) {
         // abort if this are the unclustered pairs
@@ -627,6 +649,13 @@ protected void segmentHover(Segment segment, int ringid, boolean active) {
       }
     }
 
+    /**
+     * Click handler for a segment.
+     * 
+     * @param segment Segment clicked
+     * @param evt Click event
+     * @param dblClick Double click?
+     */
     protected void segmentClick(Segment segment, Event evt, boolean dblClick) {
       MouseEvent mouse = (MouseEvent) evt;
 

addons/batikvis/src/main/java/elki/visualization/visualizers/parallel/index/RTreeParallelVisualization.java

@@ -139,7 +139,7 @@ public void fullRedraw() {
       super.fullRedraw();
       addCSSClasses(svgp);
       E root = tree.getRootEntry();
-      visualizeRTreeEntry(svgp, layer, proj, tree, root, 0, 0);
+      visualizeRTreeEntry(svgp, layer, proj, tree, root, 0);
     }
 
     /**
@@ -186,7 +186,7 @@ private void addCSSClasses(SVGPlot svgp) {
      * @param entry Current entry
      * @param depth Current depth
      */
-    private void visualizeRTreeEntry(SVGPlot svgp, Element layer, ProjectionParallel proj, AbstractRStarTree<? extends N, E, ?> rtree, E entry, int depth, int step) {
+    private void visualizeRTreeEntry(SVGPlot svgp, Element layer, ProjectionParallel proj, AbstractRStarTree<? extends N, E, ?> rtree, E entry, int depth) {
       final int dim = proj.getVisibleDimensions();
       double[] min = proj.fastProjectDataToRenderSpace(SpatialUtil.getMin(entry));
       double[] max = proj.fastProjectDataToRenderSpace(SpatialUtil.getMax(entry));
@@ -207,7 +207,7 @@ private void visualizeRTreeEntry(SVGPlot svgp, Element layer, ProjectionParallel
         for(int i = 0; i < node.getNumEntries(); i++) {
           E child = node.getEntry(i);
           if(!(child instanceof LeafEntry)) {
-            visualizeRTreeEntry(svgp, layer, proj, rtree, child, depth + 1, ++step);
+            visualizeRTreeEntry(svgp, layer, proj, rtree, child, depth + 1);
           }
         }
       }
@@ -221,6 +221,7 @@ private void visualizeRTreeEntry(SVGPlot svgp, Element layer, ProjectionParallel
    * @author Erich Schubert
    */
   public static class Par implements Parameterizer {
+    /** Fill areas */
     protected boolean fill = true;
 
     @Override

addons/batikvis/src/main/java/elki/visualization/visualizers/parallel/selection/SelectionToolAxisRangeVisualization.java

@@ -164,6 +164,7 @@ private void deleteChildren(Element container) {
      * @param x2 max x-value
      * @param y1 min y-value
      * @param y2 max y-value
+     * @param ranges HyperBoundingBox for the selected ranges
      */
     private void updateSelectionRectKoordinates(double x1, double x2, double y1, double y2, ModifiableHyperBoundingBox ranges) {
       final int dims = proj.getVisibleDimensions();

addons/batikvis/src/main/java/elki/visualization/visualizers/visunproj/KeyVisualization.java

@@ -88,6 +88,7 @@ public void processNewResult(VisualizerContext context, Object start) {
   /**
    * Compute the size of the clustering.
    *
+   * @param <M> Model type
    * @param c Clustering
    * @return Array storing the depth and the number of leaf nodes.
    */
@@ -103,6 +104,7 @@ protected static <M extends Model> int[] findDepth(Clustering<M> c) {
   /**
    * Recursive depth computation.
    *
+   * @param <M> Model type
    * @param hier Hierarchy
    * @param cluster Current cluster
    * @param size Counting array.

addons/uncertain/src/main/java/elki/clustering/uncertain/FDBSCANNeighborPredicate.java

@@ -232,6 +232,13 @@ public DBIDs getNeighbors(DBIDRef reference) {
       return resultList;
     }
 
+    /**
+     * Check a pair of samples.
+     * 
+     * @param o1 First object
+     * @param o2 Second object
+     * @return {@code true} if close
+     */
     private boolean checkSamples(UncertainObject o1, UncertainObject o2) {
       final SquaredEuclideanDistance distance = SquaredEuclideanDistance.STATIC;
       // Optimization for discrete objects:

elki-classification/src/main/java/elki/classification/KNNClassifier.java

@@ -125,6 +125,13 @@ public ClassLabel classify(O instance) {
     return bestl;
   }
 
+  /**
+   * Class probabilities
+   * 
+   * @param instance Object to classify
+   * @param labels Labels to classify into
+   * @return Class probabilities
+   */
   public double[] classProbabilities(O instance, ArrayList<ClassLabel> labels) {
     int[] occurences = new int[labels.size()];
 

elki-classification/src/main/java/elki/classification/PriorProbabilityClassifier.java

@@ -66,9 +66,6 @@ public PriorProbabilityClassifier() {
     super();
   }
 
-  /**
-   * Learns the prior probability for all classes.
-   */
   @Override
   public void buildClassifier(Database database, Relation<? extends ClassLabel> labelrep) {
     Object2IntOpenHashMap<ClassLabel> count = new Object2IntOpenHashMap<>();
@@ -92,6 +89,13 @@ public void buildClassifier(Database database, Relation<? extends ClassLabel> la
     }
   }
 
+  /**
+   * Class probabilities.
+   * 
+   * @param instance Instance to classify
+   * @param labels Labels to classify into
+   * @return Probabilities
+   */
   public double[] classProbabilities(Object instance, ArrayList<ClassLabel> labels) {
     return alignLabels(this.labels, distribution, labels);
   }

elki-classification/src/main/java/elki/evaluation/classification/holdout/StratifiedCrossValidation.java

@@ -44,9 +44,14 @@
  */
 public class StratifiedCrossValidation extends AbstractHoldout {
   /**
-   * Holds the number of folds, current fold.
+   * Holds the number of folds
    */
-  protected int nfold, fold;
+  protected int nfold;
+
+  /**
+   * Current fold
+   */
+  protected int fold;
 
   /**
    * Partition assignment, sizes

elki-classification/src/main/java/elki/evaluation/classification/holdout/TrainingAndTestSet.java

@@ -51,6 +51,10 @@ public class TrainingAndTestSet {
   /**
    * Provides a pair of training and test data sets out of the given two
    * databases.
+   * 
+   * @param training the training data set
+   * @param test the test data set
+   * @param labels union of all labels present in training and test
    */
   public TrainingAndTestSet(MultipleObjectsBundle training, MultipleObjectsBundle test, ArrayList<ClassLabel> labels) {
     this.training = training;