Update dependencies and fix javadoc issues

modules/AppearanceAPI/src/main/java/org/gephi/appearance/api/Interpolator.java

@@ -211,15 +211,12 @@ public abstract class Interpolator {
          * use Bernstein basis to evaluate 1D cubic Bezier curve (quicker and
          * more numerically stable than power basis) -- 1D control coordinates
          * are (0, p1, p2, 1), where p1 and p2 are in range [0,1], and there is
-         * no ordering constraint on p1 and p2, i.e., p1 <= p2 does not have to
-         * be true @param t is the pa
-         *
-         * ramaterized value in range [0,1] @param p1 is 1st control point
-         * coordinate in range [0,1] @param p2 is 2nd control point coor
-         *
-         * d
-         * inate in range [0,1] @return the value of the Bezier curve at
-         * parameter t
+         * no ordering constraint on p1 and p2, i.e., p1 &lt;= p2 does not have to
+         * be true 
+         * @param t is the paramaterized value in range [0,1]
+         * @param p1 is 1st control point coordinate in range [0,1]
+         * @param p2 is 2nd control point coordinate in range [0,1]
+         * @return the value of the Bezier curve at parameter t
          */
         private float eval(float t, float p1, float p2) {
             // Use optimzied version of the normal Bernstein basis form of Bezier:
@@ -233,15 +230,12 @@ public abstract class Interpolator {
         /**
          * evaluate Bernstein basis derivative of 1D cubic Bezier curve, where
          * 1D control points are (0, p1, p2, 1), where p1 and p2 are in range
-         * [0,1], and there is no ordering constraint on p1 and p2, i.e., p1 <=
-         * p2 does not have to be true @param t is the paramaterized
-         *
-         * value in range [0,1] @param p1 is 1st control point coordinate in
-         * range [0,1] @param p2 is 2nd control point coo
-         *
-         * r
-         * dinate in range [0,1] @return the value of the Bezier curve at
-         * parameter t
+         * [0,1], and there is no ordering constraint on p1 and p2, i.e., p1 &lt;=
+         * p2 does not have to be true 
+         * @param t is the paramaterized value in range [0,1]
+         * @param p1 is 1st control point coordinate in range [0,1]
+         * @param p2 is 2nd control point coordinate in range [0,1]
+         * @return the value of the Bezier curve at parameter t
          */
         private float evalDerivative(float t, float p1, float p2) {
             // use optimzed version of Berstein basis Bezier derivative:
@@ -258,8 +252,7 @@ public abstract class Interpolator {
          * x-value sample array that was created on construction
          *
          * @param x is x-value of cubic bezier curve, in range [0,1]
-         * @return a good initial guess for parameter t (in range [0,1]) that
-         * gives x
+         * @return a good initial guess for parameter t (in range [0,1]) that gives x
          */
         private float getInitialGuessForT(float x) {
             // find which places in the array that x would be sandwiched between,

modules/DataLaboratoryAPI/src/main/java/org/gephi/datalab/api/AttributeColumnsController.java

@@ -362,7 +362,7 @@ public interface AttributeColumnsController {
 
     /**
      * <p>Calculates all statistics at once from a number/number list column using <code>MathUtils</code> class.</p>
-     * <p>Returns an array of <b>length=8</b> of <code>BigDecimal</code> numbers with the results in the following order: 
+     * Returns an array of <b>length=8</b> of <code>BigDecimal</code> numbers with the results in the following order: 
      * <ol>
      * <li>average</li>
      * <li>first quartile (Q1)</li>
@@ -373,7 +373,6 @@ public interface AttributeColumnsController {
      * <li>minimumValue</li>
      * <li>maximumValue</li>
      * </ol>
-     * </p>
      * <p>The column can only be a number/number list column.</p>
      * <p>Otherwise, a IllegalArgumentException will be thrown.</p>
      * @param table Table of the column

modules/DataLaboratoryAPI/src/main/java/org/gephi/datalab/api/AttributeColumnsMergeStrategiesController.java

@@ -80,12 +80,11 @@ public interface AttributeColumnsMergeStrategiesController {
      * <p>Only one of the 2 column could be null, and its corresponding start/end default will be used.</p>
      * <p>Columns can be of any type. If not numeric, their values will be parsed.</p>
      * <p>Default start and end values will be used when the columns don't have a value or it can't be parsed to a double.</p>
-     * <p>When start > end for any reason:
+     * When start &gt; end for any reason:
      * <ul>
      * <li>If both columns were provided: A infinite time interval will be set</li>
      * <li>If only one column was provided: The value for the provided column will be kept and the other will be infinite</li>
      * </ul>
-     * </p>
      * @param table Table of the columns, can't be null or wrong
      * @param startColumn Column to use as start value
      * @param endColumn Column to use as end value
@@ -101,12 +100,11 @@ public interface AttributeColumnsMergeStrategiesController {
      * <p>Columns can be of any type.</p>
      * <p>Default start and end values will be used when the columns don't have a value or it can't be parsed to a date.
      * If a default value can't be parsed to a date, infinity will be used as default instead.</p>
-     * <p>When start > end for any reason:
+     * When start &gt; end for any reason:
      * <ul>
      * <li>If both columns were provided: A infinite time interval will be set</li>
      * <li>If only one column was provided: The value for the provided column will be kept and the other will be infinite</li>
      * </ul>
-     * </p>
      * @param table Table of the columns, can't be null or wrong
      * @param startColumn Column to use as start value
      * @param endColumn Column to use as end value

modules/Gleem/src/main/java/org/gephi/lib/gleem/linalg/Rotf.java

@@ -239,7 +239,7 @@ public class Rotf {
   /** Turns the upper left 3x3 of the passed matrix into a rotation.
       Implementation from Watt and Watt, <u>Advanced Animation and
       Rendering Techniques</u>.
-      @see gleem.linalg.Mat4f#getRotation */
+      @see org.gephi.lib.gleem.linalg.Mat4f#getRotation */
   public void fromMatrix(Mat4f mat) {
     // FIXME: Should reimplement to follow Horn's advice of using
     // eigenvector decomposition to handle roundoff error in given

modules/Gleem/src/main/java/org/gephi/lib/gleem/linalg/Vec2f.java

@@ -68,7 +68,7 @@ public class Vec2f {
     this.y = y;
   }
 
-  /** Sets the ith component, 0 <= i < 2 */
+  /** Sets the ith component, 0 &lt;= i &lt; 2 */
   public void set(int i, float val) {
     switch (i) {
     case 0: x = val; break;
@@ -77,7 +77,7 @@ public class Vec2f {
     }
   }
 
-  /** Gets the ith component, 0 <= i < 2 */
+  /** Gets the ith component, 0 &lt;= i &lt; 2 */
   public float get(int i) {
     switch (i) {
     case 0: return x;

modules/Gleem/src/main/java/org/gephi/lib/gleem/linalg/Vec3d.java

@@ -42,7 +42,7 @@ public class Vec3d {
     this.z = z;
   }
 
-  /** Sets the ith component, 0 <= i < 3 */
+  /** Sets the ith component, 0 &lt;= i &lt; 3 */
   public void set(int i, double val) {
     switch (i) {
     case 0: x = val; break;
@@ -52,7 +52,7 @@ public class Vec3d {
     }
   }
 
-  /** Gets the ith component, 0 <= i < 3 */
+  /** Gets the ith component, 0 &lt;= i &lt; 3 */
   public double get(int i) {
     switch (i) {
     case 0: return x;

modules/Gleem/src/main/java/org/gephi/lib/gleem/linalg/Vec3f.java

@@ -82,7 +82,7 @@ public class Vec3f {
     this.z = z;
   }
 
-  /** Sets the ith component, 0 <= i < 3 */
+  /** Sets the ith component, 0 &lt;= i &lt; 3 */
   public void set(int i, float val) {
     switch (i) {
     case 0: x = val; break;
@@ -92,7 +92,7 @@ public class Vec3f {
     }
   }
 
-  /** Gets the ith component, 0 <= i < 3 */
+  /** Gets the ith component, 0 &lt;= i &lt; 3 */
   public float get(int i) {
     switch (i) {
     case 0: return x;

modules/Gleem/src/main/java/org/gephi/lib/gleem/linalg/Vec4f.java

@@ -72,7 +72,7 @@ public class Vec4f {
     this.w = w;
   }
 
-  /** Sets the ith component, 0 <= i < 4 */
+  /** Sets the ith component, 0 &lt;= i &lt; 4 */
   public void set(int i, float val) {
     switch (i) {
     case 0: x = val; break;
@@ -83,7 +83,7 @@ public class Vec4f {
     }
   }
 
-  /** Gets the ith component, 0 <= i < 4 */
+  /** Gets the ith component, 0 &lt;= i &lt; 4 */
   public float get(int i) {
     switch (i) {
     case 0: return x;

modules/StatisticsPlugin/src/main/java/org/gephi/statistics/plugin/ClusteringCoefficient.java

@@ -141,7 +141,7 @@ class ArrayWrapper implements Comparable {
 
     /**
      *
-     * @param pArray
+     * @param array
      */
     ArrayWrapper(int ID, EdgeWrapper[] array) {
         this.array = array;
@@ -154,7 +154,7 @@ class ArrayWrapper implements Comparable {
 
     /**
      *
-     * @param pIndex
+     * @param index
      * @return
      */
     public int get(int index) {

modules/TimelineAPI/src/main/java/org/gephi/timeline/api/TimelineChart.java

@@ -41,19 +41,19 @@ Portions Copyrighted 2011 Gephi Consortium.
  */
 package org.gephi.timeline.api;
 
-import org.gephi.graph.api.Graph;
+import org.gephi.graph.api.GraphModel;
 
 /**
  * Sparkline type chart visible in the timeline, for instance the number of
  * nodes over time.
  * <p>
  * Charts are usually created from the Statistics module and data are saved
- * within {@link Graph#getAttributes()}. Columns can be accessed from the graph
- * table in the {@link AttributeModel#getGraphTable() }.
+ * within {@link GraphModel}. Columns can be accessed from the graph
+ * table in the {@link GraphModel}.
+ * </p>
  *
  * @author Mathieu Bastian
- * @see
- * TimelineController#selectColumn(org.gephi.data.attributes.api.AttributeColumn)
+ * @see TimelineController#selectColumn(java.lang.String)
  */
 public interface TimelineChart {
 

modules/TimelineAPI/src/main/java/org/gephi/timeline/api/TimelineController.java

@@ -49,15 +49,18 @@ import org.gephi.project.api.Workspace;
  * <p>
  * By default the timeline is disabled and can be enabled with the
  * <code>setEnabled()</code> method. Once enabled, the controller is setting its
- * interval value to the {@link DynamicModel}.
+ * interval value to the DynamicModel.
+ * </p>
  * <p>
  * The interval can be animated using the <code>startPlay()</code> and
  * <code>stopPlay()</code> methods. Configuration parameters are also available.
+ * </p>
  * <p>
  * This controller also allows to lookup graph attribute columns that can be
  * used as sparklines (e.g. node count, average degree...). Use the
  * <code>selectColumn()</code> to create a {@link TimelineChart} accessible from
  * the <code>TimelineModel</code>.
+ * </p>
  *
  * @author Julian Bilcke, Mathieu Bastian
  * @see TimelineModel
@@ -86,7 +89,7 @@ public interface TimelineController {
      *
      * @param min the lower bound
      * @param max the upper bound
-     * @throws IllegalArgumentException if <code>min<code> is superior or equal than
+     * @throws IllegalArgumentException if <code>min</code> is superior or equal than
      * <code>max</code> or out of bounds
      */
     public void setCustomBounds(double min, double max);
@@ -105,7 +108,7 @@ public interface TimelineController {
      *
      * @param from the lower bound
      * @param to the upper bound
-     * @throws IllegalArgumentException if <code>min<code> is superior or equal than
+     * @throws IllegalArgumentException if <code>min</code> is superior or equal than
      * <code>max</code> or out of bounds
      */
     public void setInterval(double from, double to);

modules/UIComponents/src/main/java/org/gephi/ui/components/JRangeSlider.java

@@ -186,7 +186,7 @@ public class JRangeSlider extends JSlider {
 
         /**
          * Constructs a RangeSliderUI for the specified slider component.
-         * @param b RangeSlider
+         * @param slider RangeSlider
          */
         public JRangeSliderWindowsUI(JSlider slider) {
             super(slider);
@@ -754,7 +754,7 @@ public class JRangeSlider extends JSlider {
 
         /**
          * Constructs a RangeSliderUI for the specified slider component.
-         * @param b RangeSlider
+         * @param slider RangeSlider
          */
         public JRangeSliderBasicUI(JSlider slider) {
             super(slider);

modules/UIComponents/src/main/java/org/gephi/ui/components/richtooltip/JRichTooltipPanel.java

@@ -71,7 +71,7 @@ class JRichTooltipPanel extends JPanel {
     }
 
     /**
-     * Sets the look and feel (L&F) object that renders this component.
+     * Sets the look and feel (L&F) object that renders this component.
      *
      * @param ui
      *            The UI delegate.

modules/UIComponents/src/main/java/org/gephi/ui/components/splineeditor/SplineEditor.java

@@ -52,9 +52,7 @@ import org.openide.util.NbBundle;
 import org.openide.windows.WindowManager;
 
 /**
- * Adaptation of the SwingX demo SplineEditor. Used to get a
- * {@link Interpolator} for computing.
- * <p>
+ * Adaptation of the SwingX demo SplineEditor. Used to get a Interpolator for computing.
  * <a href="http://www.jroller.com/gfx/entry/swing_demos_animations_and_swing">Romain Guy's article</a>
  *
  * @author Mathieu Bastian

modules/UIUtils/src/main/java/org/gephi/ui/utils/IntervalBoundValidator.java

@@ -55,7 +55,7 @@ import org.openide.util.NbBundle;
 public class IntervalBoundValidator implements Validator<String> {
 
     /**
-     * If not null, interval start <= end is also validated.
+     * If not null, interval start &lt;= end is also validated.
      */
     private JTextComponent intervalStartTextField = null;
 

modules/Utils/src/main/java/org/gephi/utils/CharsetToolkit.java

@@ -141,7 +141,7 @@ public class CharsetToolkit {
 
     /**
      * <p>Guess the encoding of the provided buffer.</p>
-     * If Byte Order Markers are encountered at the beginning of the buffer, we immidiately
+     * <p>If Byte Order Markers are encountered at the beginning of the buffer, we immidiately
      * return the charset implied by this BOM. Otherwise, the file would not be a human
      * readable text file.</p>
      *

pom.xml

@@ -220,15 +220,15 @@
 
         <gephi.maven-jar-plugin.version>3.1.0</gephi.maven-jar-plugin.version>
 
-        <gephi.maven-jarsigner-plugin.version>1.4</gephi.maven-jarsigner-plugin.version>
+        <gephi.maven-jarsigner-plugin.version>3.0.0</gephi.maven-jarsigner-plugin.version>
 
-        <gephi.maven-javadoc-plugin.version>2.10.4</gephi.maven-javadoc-plugin.version> 
+        <gephi.maven-javadoc-plugin.version>3.0.1</gephi.maven-javadoc-plugin.version> 
 
         <gephi.maven-license-plugin.version>1.9.0</gephi.maven-license-plugin.version>
 
         <gephi.maven-release-plugin.version>2.5.3</gephi.maven-release-plugin.version>
 
-        <gephi.maven-resources-plugin.version>3.0.2</gephi.maven-resources-plugin.version>
+        <gephi.maven-resources-plugin.version>3.1.0</gephi.maven-resources-plugin.version>
 
         <gephi.maven-site-plugin.version>3.7.1</gephi.maven-site-plugin.version>