fixed bug preventing compilation. Improved maven buildscript to pull freehep fromt he public repo.

build.xml

@@ -114,7 +114,7 @@
 		</manifestclasspath>
         <jar destfile="build/jar/dann_examples.jar" basedir="build/classes">
             <manifest>
-                <attribute name="Main-Class" value="com.syncleus.core.dann.examples.Main"/>
+                <attribute name="Main-Class" value="com.syncleus.dann.examples.Main"/>
 				<attribute name="Class-Path" value="${manifest.classpath}"/>
 				<attribute name="Product-Name" value="dANN"/>
 				<attribute name="Package-Title" value="com.syncleus.dann"/>
@@ -139,7 +139,7 @@
         <mkdir dir="build/jar"/>
         <jar destfile="build/jar/dann_examples-tests.jar" basedir="build/tests/classes">
             <manifest>
-                <attribute name="Main-Class" value="com.syncleus.core.dann.examples.Main"/>
+                <attribute name="Main-Class" value="com.syncleus.dann.examples.Main"/>
 				<attribute name="Class-Path" value="${manifest.classpath}"/>
 				<attribute name="Product-Name" value="dANN"/>
 				<attribute name="Package-Title" value="com.syncleus.dann"/>
@@ -169,7 +169,7 @@
 		</manifestclasspath>
         <jar destfile="build/jar/dann_examples.jar" basedir="build/classes">
             <manifest>
-                <attribute name="Main-Class" value="com.syncleus.core.dann.examples.Main"/>
+                <attribute name="Main-Class" value="com.syncleus.dann.examples.Main"/>
 				<attribute name="Class-Path" value="${manifest.classpath}"/>
 				<attribute name="Product-Name" value="dANN"/>
 				<attribute name="Package-Title" value="com.syncleus.dann"/>
@@ -193,7 +193,7 @@
         <mkdir dir="build/jar"/>
         <jar destfile="build/jar/dann_examples-tests.jar" basedir="build/tests/classes">
             <manifest>
-                <attribute name="Main-Class" value="com.syncleus.core.dann.examples.Main"/>
+                <attribute name="Main-Class" value="com.syncleus.dann.examples.Main"/>
 				<attribute name="Class-Path" value="${manifest.classpath}"/>
 				<attribute name="Product-Name" value="dANN"/>
 				<attribute name="Package-Title" value="com.syncleus.dann"/>
@@ -216,7 +216,7 @@
     </target>
 
     <target name="run" description="run the application after it has been built">
-        <java fork="true" classname="com.syncleus.core.dann.examples.Main">
+        <java fork="true" classname="com.syncleus.dann.examples.Main">
             <jvmarg value="-Xmx512m" />
             <classpath refid="classpath.run"/>
         </java>
@@ -224,7 +224,7 @@
 
 	<!-- TODO remove this target as well as the code it runs -->
     <target name="run-tests" description="this is a temporary target that will be removed, tests some experimental code">
-        <java fork="true" classname="com.syncleus.core.dann.examples.test.Test3d">
+        <java fork="true" classname="com.syncleus.dann.examples.test.Test3d">
             <jvmarg value="-Xmx512m" />
             <classpath refid="classpath.test"/>
         </java>
@@ -238,7 +238,7 @@
                 <path location="build/jar/dann_examples.jar"/>
             </classpath>
         </nbprofiledirect>
-        <java fork="true" classname="com.syncleus.core.dann.examples.Main">
+        <java fork="true" classname="com.syncleus.dann.examples.Main">
             <jvmarg value="${profiler.info.jvmargs.agent}"/>
             <jvmarg value="-Xmx512m" />
             <classpath refid="classpath.run"/>

pom.xml

@@ -32,10 +32,7 @@
 		<dependency>
 			<groupId>org.freehep</groupId>
 			<artifactId>freehep-java3d</artifactId>
-			<version>1.0</version>
-			<scope>system</scope>
-			<!-- FIXME This is the last jar in the repo we still depend on -->
-			<systemPath>${basedir}/lib/build/java3d/freehep/freehep-j3d.jar</systemPath>
+			<version>2.0-SNAPSHOT</version>
 		</dependency>
 
 		<dependency>
@@ -55,4 +52,12 @@
 
 	</dependencies>
 
+	<repositories>
+	  <repository>
+		<id>freehep-maven</id>
+		<name>Maven FreeHEP</name>
+		<url>http://java.freehep.org/maven2</url>
+	  </repository>
+	</repositories>
+
 </project>

script/run-genetics.bat

-java -Xmx128m -classpath ..\build\jar\dann_examples.jar;..\..\java_dann\build\jar\dann.jar;..\lib\freehep-j3d.jar;../lib/j3dcore.jar;../lib/vecmath.jar;../lib/j3dutils.jar;..\..\java_dann\lib\log4j-1.2.15.jar com.syncleus.core.dann.examples.test.Test3d
+java -Xmx128m -classpath ..\build\jar\dann_examples.jar;..\..\java_dann\build\jar\dann.jar;..\lib\freehep-j3d.jar;../lib/j3dcore.jar;../lib/vecmath.jar;../lib/j3dutils.jar;..\..\java_dann\lib\log4j-1.2.15.jar com.syncleus.dann.examples.test.Test3d
 @PAUSE
\ No newline at end of file

script/run-genetics.sh

 #!/bin/sh
-java -Xmx128m -classpath ../build/jar/dann_examples.jar:../../java_dann/build/jar/dann.jar:../lib/freehep-j3d.jar:../lib/j3dcore.jar:../lib/vecmath.jar:../lib/j3dutils.jar com.syncleus.core.dann.examples.test.Test3d
+java -Xmx128m -classpath ../build/jar/dann_examples.jar:../../java_dann/build/jar/dann.jar:../lib/freehep-j3d.jar:../lib/j3dcore.jar:../lib/vecmath.jar:../lib/j3dutils.jar com.syncleus.dann.examples.test.Test3d

script/run.bat

-java -Xmx320m -classpath ..\build\jar\dann_examples.jar;..\..\java_dann\build\jar\dann.jar;../lib/j3dcore.jar;../lib/vecmath.jar;../lib/j3dutils.jar;..\..\java_dann\lib\log4j-1.2.15.jar com.syncleus.core.dann.examples.Main
+java -Xmx320m -classpath ..\build\jar\dann_examples.jar;..\..\java_dann\build\jar\dann.jar;../lib/j3dcore.jar;../lib/vecmath.jar;../lib/j3dutils.jar;..\..\java_dann\lib\log4j-1.2.15.jar com.syncleus.dann.examples.Main
 @PAUSE
\ No newline at end of file

script/run.sh

 #!/bin/sh
-java -Xmx320m -classpath ../build/jar/dann_examples.jar:../../java_dann/build/jar/dann.jar:../lib/j3dcore.jar:../lib/vecmath.jar:../lib/j3dutils.jar com.syncleus.core.dann.examples.Main
+java -Xmx320m -classpath ../build/jar/dann_examples.jar:../../java_dann/build/jar/dann.jar:../lib/j3dcore.jar:../lib/vecmath.jar:../lib/j3dutils.jar com.syncleus.dann.examples.Main

src/main/java/com/syncleus/core/dann/examples/Main.java → src/main/java/com/syncleus/dann/examples/Main.java

@@ -16,14 +16,12 @@
  *  Philadelphia, PA 19148                                                     *
  *                                                                             *
  ******************************************************************************/
-package com.syncleus.core.dann.examples;
+package com.syncleus.dann.examples;
 
 
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.InputStreamReader;
-import org.apache.log4j.xml.DOMConfigurator;
+import java.io.*;
 import org.apache.log4j.Logger;
+import org.apache.log4j.xml.DOMConfigurator;
 
 
 /** Runs dANN demos from a console menu.
@@ -62,17 +60,17 @@ public class Main
             if (selectorArg != null)
             {
                 if (selectorArg.compareTo("--xor") == 0)
-                    com.syncleus.core.dann.examples.xor.XorDemo.main(newArgs);
+                    com.syncleus.dann.examples.xor.XorDemo.main(newArgs);
                 else if (selectorArg.compareTo("--nci") == 0)
-                    com.syncleus.core.dann.examples.nci.ui.NciDemo.main(newArgs);
+                    com.syncleus.dann.examples.nci.ui.NciDemo.main(newArgs);
                 else if (selectorArg.compareTo("--colormap") == 0)
-                    com.syncleus.core.dann.examples.colormap.ColorMapDemo.main(newArgs);
+                    com.syncleus.dann.examples.colormap.ColorMapDemo.main(newArgs);
                 else if (selectorArg.compareTo("--hyperassociativemap") == 0)
-                    com.syncleus.core.dann.examples.hyperassociativemap.visualization.ViewMap.main(newArgs);
+                    com.syncleus.dann.examples.hyperassociativemap.visualization.ViewMap.main(newArgs);
                 else if (selectorArg.compareTo("--tsp") == 0)
-                    com.syncleus.core.dann.examples.tsp.TravellingSalesmanDemo.main(newArgs);
+                    com.syncleus.dann.examples.tsp.TravellingSalesmanDemo.main(newArgs);
                 else if (selectorArg.compareTo("--fft") == 0)
-                    com.syncleus.core.dann.examples.fft.FftDemo.main(newArgs);
+                    com.syncleus.dann.examples.fft.FftDemo.main(newArgs);
 
                 return;
             }
@@ -115,13 +113,13 @@ public class Main
                 switch (currentCommand)
                 {
 				case 'c':
-					com.syncleus.core.dann.examples.colormap.ColorMapDemo.main(newArgs);
+					com.syncleus.dann.examples.colormap.ColorMapDemo.main(newArgs);
 					break;
                 case 'x':
-                    com.syncleus.core.dann.examples.xor.XorDemo.main(newArgs);
+                    com.syncleus.dann.examples.xor.XorDemo.main(newArgs);
                     break;
                 case 'i':
-                    com.syncleus.core.dann.examples.nci.ui.NciDemo.main(newArgs);
+                    com.syncleus.dann.examples.nci.ui.NciDemo.main(newArgs);
                     break;
                 case 'h':
                     System.out.println("The command line differs for each of the example files.");
@@ -130,16 +128,16 @@ public class Main
                     System.out.println("java -jar bin dANN-examples.jar --xor [save-location]");
                     break;
                 case 'v':
-                    com.syncleus.core.dann.examples.hyperassociativemap.visualization.ViewMap.main(newArgs);
+                    com.syncleus.dann.examples.hyperassociativemap.visualization.ViewMap.main(newArgs);
                     break;
 				case 't':
-					com.syncleus.core.dann.examples.tsp.TravellingSalesmanDemo.main(newArgs);
+					com.syncleus.dann.examples.tsp.TravellingSalesmanDemo.main(newArgs);
 					break;
 				case 'f':
-					com.syncleus.core.dann.examples.fft.FftDemo.main(newArgs);
+					com.syncleus.dann.examples.fft.FftDemo.main(newArgs);
 					break;
 				case 'p':
-					com.syncleus.core.dann.examples.pathfind.PathFindDemoPanel.main(newArgs);
+					com.syncleus.dann.examples.pathfind.PathFindDemoPanel.main(newArgs);
 					break;
                 case 'q':
 					System.out.print("Quiting...");

src/main/java/com/syncleus/core/dann/examples/colormap/AboutDialog.java → src/main/java/com/syncleus/dann/examples/colormap/AboutDialog.java

@@ -16,10 +16,10 @@
  *  Philadelphia, PA 19148                                                     *
  *                                                                             *
  ******************************************************************************/
-package com.syncleus.core.dann.examples.colormap;
+package com.syncleus.dann.examples.colormap;
 
-import java.awt.Frame;
-import javax.swing.JDialog;
+import javax.swing.*;
+import java.awt.*;
 
 public class AboutDialog extends JDialog
 {

src/main/java/com/syncleus/core/dann/examples/colormap/ColorMap1dCallable.java → src/main/java/com/syncleus/dann/examples/colormap/ColorMap1dCallable.java

@@ -16,17 +16,17 @@
  *  Philadelphia, PA 19148                                                     *
  *                                                                             *
  ******************************************************************************/
-package com.syncleus.core.dann.examples.colormap;
+package com.syncleus.dann.examples.colormap;
 
-import java.util.concurrent.Callable;
+import java.awt.*;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Random;
+import java.util.concurrent.Callable;
 import com.syncleus.dann.math.Vector;
 import com.syncleus.dann.neural.Synapse;
 import com.syncleus.dann.neural.som.*;
 import com.syncleus.dann.neural.som.brain.ExponentialDecaySomBrain;
-import java.util.Map.Entry;
-import java.awt.Color;
 import org.apache.log4j.Logger;
 
 public final class ColorMap1dCallable implements Callable<Color[]>

src/main/java/com/syncleus/core/dann/examples/colormap/ColorMap2dCallable.java → src/main/java/com/syncleus/dann/examples/colormap/ColorMap2dCallable.java

@@ -16,17 +16,17 @@
  *  Philadelphia, PA 19148                                                     *
  *                                                                             *
  ******************************************************************************/
-package com.syncleus.core.dann.examples.colormap;
+package com.syncleus.dann.examples.colormap;
 
-import java.util.concurrent.Callable;
+import java.awt.*;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Random;
+import java.util.concurrent.Callable;
 import com.syncleus.dann.math.Vector;
 import com.syncleus.dann.neural.Synapse;
 import com.syncleus.dann.neural.som.*;
 import com.syncleus.dann.neural.som.brain.ExponentialDecaySomBrain;
-import java.util.Map.Entry;
-import java.awt.Color;
 import org.apache.log4j.Logger;
 
 public class ColorMap2dCallable implements Callable<Color[][]>

src/main/java/com/syncleus/core/dann/examples/colormap/ColorMapDemo.java → src/main/java/com/syncleus/dann/examples/colormap/ColorMapDemo.java

@@ -16,12 +16,12 @@
  *  Philadelphia, PA 19148                                                     *
  *                                                                             *
  ******************************************************************************/
-package com.syncleus.core.dann.examples.colormap;
+package com.syncleus.dann.examples.colormap;
 
+import javax.swing.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.util.concurrent.*;
-import javax.swing.*;
 import org.apache.log4j.Logger;
 
 public class ColorMapDemo extends javax.swing.JFrame implements ActionListener, WindowListener

src/main/java/com/syncleus/core/dann/examples/fft/FftDemo.java → src/main/java/com/syncleus/dann/examples/fft/FftDemo.java

@@ -16,19 +16,13 @@
  *  Philadelphia, PA 19148                                                     *
  *                                                                             *
  ******************************************************************************/
-package com.syncleus.core.dann.examples.fft;
-
-import javax.sound.sampled.AudioFormat;
-import javax.sound.sampled.AudioSystem;
-import javax.sound.sampled.DataLine;
-import javax.sound.sampled.LineUnavailableException;
-import javax.sound.sampled.TargetDataLine;
-import java.awt.Color;
-import java.awt.event.ActionListener;
-import javax.swing.JFrame;
-import javax.swing.JProgressBar;
+package com.syncleus.dann.examples.fft;
+
+import javax.sound.sampled.*;
+import javax.swing.*;
+import java.awt.*;
 import java.awt.event.ActionEvent;
-import javax.swing.Timer;
+import java.awt.event.ActionListener;
 import com.syncleus.dann.dataprocessing.signal.transform.*;
 
 public class FftDemo extends JFrame implements ActionListener

src/main/java/com/syncleus/core/dann/examples/hyperassociativemap/visualization/LayeredHyperassociativeMap.java → src/main/java/com/syncleus/dann/examples/hyperassociativemap/visualization/LayeredHyperassociativeMap.java

@@ -16,10 +16,10 @@
  *  Philadelphia, PA 19148                                                     *
  *                                                                             *
  ******************************************************************************/
-package com.syncleus.core.dann.examples.hyperassociativemap.visualization;
+package com.syncleus.dann.examples.hyperassociativemap.visualization;
 
-import com.syncleus.dann.graph.drawing.hyperassociativemap.*;
 import java.util.concurrent.ExecutorService;
+import com.syncleus.dann.graph.drawing.hyperassociativemap.HyperassociativeMap;
 
 public class LayeredHyperassociativeMap extends HyperassociativeMap<SimpleGraph, SimpleNode>
 {

src/main/java/com/syncleus/core/dann/examples/hyperassociativemap/visualization/SimpleGraph.java → src/main/java/com/syncleus/dann/examples/hyperassociativemap/visualization/SimpleGraph.java

@@ -16,10 +16,10 @@
  *  Philadelphia, PA 19148                                                     *
  *                                                                             *
  ******************************************************************************/
-package com.syncleus.core.dann.examples.hyperassociativemap.visualization;
+package com.syncleus.dann.examples.hyperassociativemap.visualization;
 
-import com.syncleus.dann.graph.*;
 import java.util.*;
+import com.syncleus.dann.graph.*;
 
 public class SimpleGraph extends AbstractBidirectedAdjacencyGraph<SimpleNode, BidirectedEdge<SimpleNode>>
 {

src/main/java/com/syncleus/core/dann/examples/hyperassociativemap/visualization/SimpleNode.java → src/main/java/com/syncleus/dann/examples/hyperassociativemap/visualization/SimpleNode.java

@@ -16,7 +16,7 @@
  *  Philadelphia, PA 19148                                                     *
  *                                                                             *
  ******************************************************************************/
-package com.syncleus.core.dann.examples.hyperassociativemap.visualization;
+package com.syncleus.dann.examples.hyperassociativemap.visualization;
 
 
 public class SimpleNode

src/main/java/com/syncleus/core/dann/examples/hyperassociativemap/visualization/UpdateViewRun.java → src/main/java/com/syncleus/dann/examples/hyperassociativemap/visualization/UpdateViewRun.java

@@ -16,11 +16,10 @@
  *  Philadelphia, PA 19148                                                     *
  *                                                                             *
  ******************************************************************************/
-package com.syncleus.core.dann.examples.hyperassociativemap.visualization;
+package com.syncleus.dann.examples.hyperassociativemap.visualization;
 
 import com.syncleus.dann.graph.drawing.hyperassociativemap.HyperassociativeMap;
-import com.syncleus.dann.graph.drawing.hyperassociativemap.visualization.*;
-
+import com.syncleus.dann.graph.drawing.hyperassociativemap.visualization.HyperassociativeMapCanvas;
 
 
 public class UpdateViewRun implements Runnable