jzy3d · hoijui · May 6, 2020 · May 6, 2020 · May 6, 2020 · May 6, 2020
diff --git a/.classpath b/.classpath
diff --git a/.project b/.project
diff --git a/README.md b/README.md
@@ -1,12 +1,13 @@
-jzy3d-graphs
-============
+# jzy3d-graphs
 
-A set of tools to compute and draw 3d graphs layouts based on Gephi Toolkit.
+A set of tools to compute and draw 3D graph layouts,
+based on the Gephi Toolkit.
 
-<img src="doc/graph7.png">
+![](doc/graph7.png)
 
-Example programs in src/main/java
+Example programs in _src/main/java/_:
 
-org.jzy3d.graphs.trials.ImportAndDrawTrial
+[org.jzy3d.graphs.trials.ImportAndDrawTrial](
+src/main/java/org/jzy3d/graphs/trials/ImportAndDrawTrial.java)
 
-More information at http://www.jzy3d.org/plugins-graphs.php
+More information on [the homepage](http://www.jzy3d.org/plugins-graphs.php).
diff --git a/pom.xml b/pom.xml
@@ -9,12 +9,8 @@
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <version.mvn.ftp>1.0-beta-6</version.mvn.ftp>
-
     </properties>
 
-
-
-
     <dependencies>
         <dependency>
             <groupId>org.jzy3d</groupId>
@@ -65,6 +61,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-plugin</artifactId>
+                <version>3.0.0-M4</version>
                 <configuration>
                 </configuration>
             </plugin>

diff --git a/src/main/java/org/gephi/layout/plugin/ForceVectorNodeLayoutData3d.java b/src/main/java/org/gephi/layout/plugin/ForceVectorNodeLayoutData3d.java
@@ -1,5 +1,6 @@
 /*
 Copyright 2008-2010 Gephi
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
 Authors : Mathieu Bastian <[email protected]>
 Website : http://www.gephi.org
 
@@ -59,3 +60,4 @@ public class ForceVectorNodeLayoutData3d implements LayoutData {
     public float old_dz = 0;
     public float freeze = 0f;
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/ForceVectorUtils3d.java b/src/main/java/org/gephi/layout/plugin/ForceVectorUtils3d.java
@@ -1,6 +1,7 @@
 /*
 Copyright 2008-2010 Gephi
-Authors : Mathieu Jacomy
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
+Authors : Mathieu Jacomy <[email protected]>
 Website : http://www.gephi.org
 
 This file is part of Gephi.
@@ -52,7 +53,7 @@ public static void fcBiRepulsor(Node N1, Node N2, double c) {
         double xDist = N1.x() - N2.x();	// distance en x entre les deux noeuds
         double yDist = N1.y() - N2.y();
         double zDist = N1.z() - N2.z();
-        
+
         double dist = (float) Math.sqrt(xDist * xDist + yDist * yDist + zDist * zDist);	// distance tout court
 
         if (dist > 0) {
@@ -75,7 +76,7 @@ public static void fcBiRepulsor(Node N1, Node N2, double c) {
         double xDist = N1.x() - N2.x();	// distance en x entre les deux noeuds
         double yDist = N1.y() - N2.y();
         double zDist = N1.z() - N2.z();
-        
+
         double dist = (float) Math.sqrt(xDist * xDist + yDist * yDist + zDist * zDist); // distance tout court
 
         if (dist > 0) {
@@ -237,3 +238,4 @@ protected static double repulsion(double c, double dist) {
         return 0.001 * c / dist;
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/forceAtlas23d/ForceAtlas23d.java b/src/main/java/org/gephi/layout/plugin/forceAtlas23d/ForceAtlas23d.java
@@ -1,5 +1,6 @@
 /*
 Copyright 2008-2011 Gephi
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
 Authors : Mathieu Jacomy <[email protected]>
 Website : http://www.gephi.org
 
@@ -131,7 +132,7 @@ public void goAlgo() {
             return;
         }
         graph = graphModel.getGraphVisible();
-        
+
         //this.timeInterval = DynamicUtilities.getVisibleInterval(dynamicModel);
 
         graph.readLock();
@@ -551,3 +552,4 @@ private double getWeight(Edge edge) {
         //}
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/forceAtlas23d/ForceAtlas23dLayoutData.java b/src/main/java/org/gephi/layout/plugin/forceAtlas23d/ForceAtlas23dLayoutData.java
@@ -1,5 +1,6 @@
 /*
 Copyright 2008-2011 Gephi
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
 Authors : Mathieu Jacomy <[email protected]>
 Website : http://www.gephi.org
 
@@ -58,3 +59,4 @@ public class ForceAtlas23dLayoutData implements LayoutData {
     public double old_dz = 0;
     public double mass = 1;
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/forceAtlas23d/ForceAtlas2Builder.java b/src/main/java/org/gephi/layout/plugin/forceAtlas23d/ForceAtlas2Builder.java
@@ -1,5 +1,6 @@
 /*
 Copyright 2008-2011 Gephi
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
 Authors : Mathieu Jacomy <[email protected]>
 Website : http://www.gephi.org
 
@@ -102,4 +103,5 @@ public int getSpeedRank() {
             return 4;
         }
     }
-}
+}
+
diff --git a/src/main/java/org/gephi/layout/plugin/forceAtlas23d/ForceFactory.java b/src/main/java/org/gephi/layout/plugin/forceAtlas23d/ForceFactory.java
@@ -1,5 +1,6 @@
 /*
 Copyright 2008-2011 Gephi
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
 Authors : Mathieu Jacomy <[email protected]>
 Website : http://www.gephi.org
 
@@ -618,3 +619,4 @@ public void apply(Node n1, Node n2, double e) {
         }
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/forceAtlas23d/NodesThread.java b/src/main/java/org/gephi/layout/plugin/forceAtlas23d/NodesThread.java
@@ -1,5 +1,6 @@
 /*
 Copyright 2008-2011 Gephi
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
 Authors : Mathieu Jacomy <[email protected]>
 Website : http://www.gephi.org
 
@@ -99,3 +100,4 @@ public void run() {
         }
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/forceAtlas23d/Operation.java b/src/main/java/org/gephi/layout/plugin/forceAtlas23d/Operation.java
@@ -1,5 +1,6 @@
 /*
 Copyright 2008-2011 Gephi
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
 Authors : Mathieu Jacomy <[email protected]>
 Website : http://www.gephi.org
 
@@ -49,3 +50,4 @@ public abstract class Operation {
 
     public abstract void execute();
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/forceAtlas23d/OperationNodeNodeAttract.java b/src/main/java/org/gephi/layout/plugin/forceAtlas23d/OperationNodeNodeAttract.java
@@ -1,5 +1,6 @@
 /*
 Copyright 2008-2011 Gephi
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
 Authors : Mathieu Jacomy <[email protected]>
 Website : http://www.gephi.org
 
@@ -67,3 +68,4 @@ public void execute() {
         f.apply(n1, n2, coefficient);
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/forceAtlas23d/OperationNodeNodeRepulse.java b/src/main/java/org/gephi/layout/plugin/forceAtlas23d/OperationNodeNodeRepulse.java
@@ -1,5 +1,6 @@
 /*
 Copyright 2008-2011 Gephi
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
 Authors : Mathieu Jacomy <[email protected]>
 Website : http://www.gephi.org
 
@@ -65,3 +66,4 @@ public void execute() {
         f.apply(n1, n2);
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/forceAtlas23d/OperationNodeRegionRepulse.java b/src/main/java/org/gephi/layout/plugin/forceAtlas23d/OperationNodeRegionRepulse.java
@@ -1,5 +1,6 @@
 /*
 Copyright 2008-2011 Gephi
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
 Authors : Mathieu Jacomy <[email protected]>
 Website : http://www.gephi.org
 
@@ -67,3 +68,4 @@ public void execute() {
         r.applyForce(n, f, theta);
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/forceAtlas23d/OperationNodeRepulse.java b/src/main/java/org/gephi/layout/plugin/forceAtlas23d/OperationNodeRepulse.java
@@ -1,5 +1,6 @@
 /*
 Copyright 2008-2011 Gephi
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
 Authors : Mathieu Jacomy <[email protected]>
 Website : http://www.gephi.org
 
@@ -65,3 +66,4 @@ public void execute() {
         f.apply(n, coefficient);
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/forceAtlas23d/Region.java b/src/main/java/org/gephi/layout/plugin/forceAtlas23d/Region.java
@@ -1,5 +1,6 @@
 /*
 Copyright 2008-2011 Gephi
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
 Authors : Mathieu Jacomy <[email protected]>
 Website : http://www.gephi.org
 
@@ -221,7 +222,7 @@ public double getMassCenterY() {
     public void setMassCenterY(double massCenterY) {
         this.massCenterY = massCenterY;
     }
-    
+
     public double getMassCenterZ() {
         return massCenterZ;
     }
@@ -230,3 +231,4 @@ public void setMassCenterZ(double massCenterZ) {
         this.massCenterZ = massCenterZ;
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/forceAtlas3d/ForceAtlasLayout3d.java b/src/main/java/org/gephi/layout/plugin/forceAtlas3d/ForceAtlasLayout3d.java
@@ -1,6 +1,7 @@
 /*
 Copyright 2008-2010 Gephi
-Authors : Mathieu Jacomy
+SPDX-License-Identifier: GPL-3.0-only OR CDDL-1.0
+Authors : Mathieu Jacomy <[email protected]>
 Website : http://www.gephi.org
 
 This file is part of Gephi.
@@ -511,3 +512,4 @@ public void setAdjustSizes(Boolean adjustSizes) {
         this.adjustSizes = adjustSizes;
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/openord3d/Combine3d.java b/src/main/java/org/gephi/layout/plugin/openord3d/Combine3d.java
@@ -1,4 +1,5 @@
 /*
+SPDX-License-Identifier: BSD-3-Clause
 Copyright 2007 Sandia Corporation. Under the terms of Contract
 DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
 certain rights in this software.
@@ -172,3 +173,4 @@ public void waitForIteration() {
         }
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/openord3d/Control3d.java b/src/main/java/org/gephi/layout/plugin/openord3d/Control3d.java
@@ -1,4 +1,5 @@
 /*
+SPDX-License-Identifier: BSD-3-Clause
 Copyright 2007 Sandia Corporation. Under the terms of Contract
 DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
 certain rights in this software.
@@ -326,3 +327,4 @@ public void setProgressTicket(ProgressTicket progressTicket) {
         this.progressTicket = progressTicket;
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/openord3d/DensityGrid3d.java b/src/main/java/org/gephi/layout/plugin/openord3d/DensityGrid3d.java
@@ -1,4 +1,5 @@
 /*
+SPDX-License-Identifier: BSD-3-Clause
 Copyright 2007 Sandia Corporation. Under the terms of Contract
 DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
 certain rights in this software.
@@ -249,3 +250,4 @@ public static float getViewSize() {
 	 * = bins[i][j].clone(); } } return densityGrid; }
 	 */
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/openord3d/Node3d.java b/src/main/java/org/gephi/layout/plugin/openord3d/Node3d.java
@@ -1,4 +1,5 @@
 /*
+SPDX-License-Identifier: BSD-3-Clause
 Copyright 2007 Sandia Corporation. Under the terms of Contract
 DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
 certain rights in this software.
@@ -69,3 +70,4 @@ protected Node3d clone() {
         return clone;
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/openord3d/OpenOrd3dLayout.java b/src/main/java/org/gephi/layout/plugin/openord3d/OpenOrd3dLayout.java
@@ -1,4 +1,5 @@
 /*
+SPDX-License-Identifier: BSD-3-Clause
 Copyright 2007 Sandia Corporation. Under the terms of Contract
 DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
 certain rights in this software.
@@ -503,3 +504,4 @@ public void setProgressTicket(ProgressTicket progressTicket) {
         this.progressTicket = progressTicket;
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/openord3d/OpenOrd3dLayoutBuilder.java b/src/main/java/org/gephi/layout/plugin/openord3d/OpenOrd3dLayoutBuilder.java
@@ -1,4 +1,5 @@
 /*
+SPDX-License-Identifier: BSD-3-Clause
 Copyright 2007 Sandia Corporation. Under the terms of Contract
 DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
 certain rights in this software.
@@ -93,3 +94,4 @@ public int getSpeedRank() {
         }
     }
 }
+
diff --git a/src/main/java/org/gephi/layout/plugin/openord3d/Worker3d.java b/src/main/java/org/gephi/layout/plugin/openord3d/Worker3d.java
@@ -1,4 +1,5 @@
 /*
+SPDX-License-Identifier: BSD-3-Clause
 Copyright 2007 Sandia Corporation. Under the terms of Contract
 DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
 certain rights in this software.
@@ -356,3 +357,4 @@ public int getId() {
         return id;
     }
 }
+