From e7840012a5e8b781766efec1c975400c6469343c Mon Sep 17 00:00:00 2001
From: Jeffrey Phillips Freeman <jeffrey.freeman@syncleus.com>
Date: Fri, 31 Oct 2014 10:01:13 -0400
Subject: [PATCH] Qualified all possible calls with "this".

Issue: DANN-23
Change-Id: I933f7e0786e6bd178513fdd39dac0751f391868d
---
 .../dann/examples/colormap/AboutDialog.java   |  66 ++--
 .../examples/colormap/ColorMap1dCallable.java |  16 +-
 .../examples/colormap/ColorMap2dCallable.java |  20 +-
 .../dann/examples/colormap/ColorMapDemo.java  | 126 ++++----
 .../syncleus/dann/examples/fft/FftDemo.java   | 290 +++++++++---------
 .../visualization/SimpleGraph.java            |  20 +-
 .../visualization/ViewMap.java                |  66 ++--
 .../dann/examples/nci/BrainRunner.java        |  20 +-
 .../syncleus/dann/examples/nci/NciBrain.java  |  28 +-
 .../syncleus/dann/examples/nci/SampleRun.java |   2 +-
 .../syncleus/dann/examples/nci/TrainRun.java  |   2 +-
 .../dann/examples/nci/ui/AboutDialog.java     |  64 ++--
 .../dann/examples/nci/ui/ImagePanel.java      |   2 +-
 .../dann/examples/nci/ui/NciDemo.java         | 250 +++++++--------
 .../dann/examples/nci/ui/ViewBrain.java       |  10 +-
 .../examples/pathfind/AbstractGridCanvas.java | 130 ++++----
 .../examples/pathfind/PathFindDemoPanel.java  |  96 +++---
 .../dann/examples/pathfind/WeightedGrid.java  |  50 +--
 .../syncleus/dann/examples/test/Test3d.java   |   4 +-
 .../examples/tsp/TravellingSalesmanDemo.java  | 162 +++++-----
 .../tsp/TravellingSalesmanPopulation.java     |   4 +-
 .../examples/colormap/TestAboutDialog.java    |  12 +-
 .../examples/colormap/TestColorMapDemo.java   | 154 +++++-----
 .../dann/examples/fft/TestFftDemo.java        |  16 +-
 .../dann/examples/nci/ui/TestAboutDialog.java |  12 +-
 25 files changed, 811 insertions(+), 811 deletions(-)

diff --git a/src/main/java/com/syncleus/dann/examples/colormap/AboutDialog.java b/src/main/java/com/syncleus/dann/examples/colormap/AboutDialog.java
index 439d122..7456bba 100644
--- a/src/main/java/com/syncleus/dann/examples/colormap/AboutDialog.java
+++ b/src/main/java/com/syncleus/dann/examples/colormap/AboutDialog.java
@@ -30,79 +30,79 @@ public class AboutDialog extends JDialog {
     private javax.swing.JTextArea jTextArea1;
     public AboutDialog(final Frame parent, final boolean modal) {
         super(parent, modal);
-        initComponents();
+        this.initComponents();
     }
 
     @SuppressWarnings("unchecked")
     // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
     private void initComponents() {
 
-        jButton1 = new javax.swing.JButton();
-        jLabel1 = new javax.swing.JLabel();
-        jLabel2 = new javax.swing.JLabel();
-        jScrollPane1 = new javax.swing.JScrollPane();
-        jTextArea1 = new javax.swing.JTextArea();
+        this.jButton1 = new javax.swing.JButton();
+        this.jLabel1 = new javax.swing.JLabel();
+        this.jLabel2 = new javax.swing.JLabel();
+        this.jScrollPane1 = new javax.swing.JScrollPane();
+        this.jTextArea1 = new javax.swing.JTextArea();
 
-        setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
-        setTitle("About");
+        this.setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+        this.setTitle("About");
 
-        jButton1.setText("OK");
-        jButton1.setName("ok button"); // NOI18N
-        jButton1.addActionListener(new java.awt.event.ActionListener() {
+        this.jButton1.setText("OK");
+        this.jButton1.setName("ok button"); // NOI18N
+        this.jButton1.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
-                jButton1ActionPerformed(evt);
+                AboutDialog.this.jButton1ActionPerformed(evt);
             }
         });
 
-        jLabel1.setText("Syncleus, Inc.");
+        this.jLabel1.setText("Syncleus, Inc.");
 
-        jLabel2.setText("SOM Color Map Demo");
+        this.jLabel2.setText("SOM Color Map Demo");
 
-        jScrollPane1.setHorizontalScrollBarPolicy(javax.swing.ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
-        jScrollPane1.setHorizontalScrollBar(null);
+        this.jScrollPane1.setHorizontalScrollBarPolicy(javax.swing.ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
+        this.jScrollPane1.setHorizontalScrollBar(null);
 
-        jTextArea1.setColumns(20);
-        jTextArea1.setEditable(false);
-        jTextArea1.setRows(5);
-        jTextArea1.setText("Instructions:\n\nFirst select the number of iterations to train train the som. Next select the\ninitial learning rate for training. Finally choose 1D or 2D output lattice.\n\nNow when you click \"Train & Display\" it will train a new SOM and render the\noutput lattice colors. If the SOM was successful colors should be displayed as\nsmoothly blended colors in 1D or 2D. If the colors do not render properly\nexperiment with different values.");
-        jTextArea1.setWrapStyleWord(true);
-        jScrollPane1.setViewportView(jTextArea1);
+        this.jTextArea1.setColumns(20);
+        this.jTextArea1.setEditable(false);
+        this.jTextArea1.setRows(5);
+        this.jTextArea1.setText("Instructions:\n\nFirst select the number of iterations to train train the som. Next select the\ninitial learning rate for training. Finally choose 1D or 2D output lattice.\n\nNow when you click \"Train & Display\" it will train a new SOM and render the\noutput lattice colors. If the SOM was successful colors should be displayed as\nsmoothly blended colors in 1D or 2D. If the colors do not render properly\nexperiment with different values.");
+        this.jTextArea1.setWrapStyleWord(true);
+        this.jScrollPane1.setViewportView(this.jTextArea1);
 
-        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
-        getContentPane().setLayout(layout);
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this.getContentPane());
+        this.getContentPane().setLayout(layout);
         layout.setHorizontalGroup(
                                          layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                  .addGroup(layout.createSequentialGroup()
                                                                    .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                                                      .addGroup(layout.createSequentialGroup()
                                                                                                        .addContainerGap()
-                                                                                                       .addComponent(jScrollPane1, javax.swing.GroupLayout.DEFAULT_SIZE, 434, Short.MAX_VALUE))
+                                                                                                       .addComponent(this.jScrollPane1, javax.swing.GroupLayout.DEFAULT_SIZE, 434, Short.MAX_VALUE))
                                                                                      .addGroup(layout.createSequentialGroup()
                                                                                                        .addGap(170, 170, 170)
-                                                                                                       .addComponent(jLabel2))
+                                                                                                       .addComponent(this.jLabel2))
                                                                                      .addGroup(layout.createSequentialGroup()
                                                                                                        .addGap(203, 203, 203)
-                                                                                                       .addComponent(jButton1))
+                                                                                                       .addComponent(this.jButton1))
                                                                                      .addGroup(layout.createSequentialGroup()
                                                                                                        .addGap(190, 190, 190)
-                                                                                                       .addComponent(jLabel1)))
+                                                                                                       .addComponent(this.jLabel1)))
                                                                    .addContainerGap())
         );
         layout.setVerticalGroup(
                                        layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                .addGroup(layout.createSequentialGroup()
                                                                  .addContainerGap()
-                                                                 .addComponent(jLabel1)
+                                                                 .addComponent(this.jLabel1)
                                                                  .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                 .addComponent(jLabel2)
+                                                                 .addComponent(this.jLabel2)
                                                                  .addGap(11, 11, 11)
-                                                                 .addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 170, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                 .addComponent(this.jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, 170, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                  .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                 .addComponent(jButton1)
+                                                                 .addComponent(this.jButton1)
                                                                  .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
         );
 
-        pack();
+        this.pack();
     }// </editor-fold>//GEN-END:initComponents
 
     private void jButton1ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButton1ActionPerformed
diff --git a/src/main/java/com/syncleus/dann/examples/colormap/ColorMap1dCallable.java b/src/main/java/com/syncleus/dann/examples/colormap/ColorMap1dCallable.java
index 1755ec2..43fe136 100644
--- a/src/main/java/com/syncleus/dann/examples/colormap/ColorMap1dCallable.java
+++ b/src/main/java/com/syncleus/dann/examples/colormap/ColorMap1dCallable.java
@@ -49,14 +49,14 @@ public final class ColorMap1dCallable implements Callable<Color[]> {
         try {
             //initialize brain
             final ExponentialDecaySomBrain<SomInputNeuron, SomOutputNeuron, SomNeuron, Synapse<SomNeuron>> brain
-                    = new ExponentialDecaySomBrain<SomInputNeuron, SomOutputNeuron, SomNeuron, Synapse<SomNeuron>>(COLOR_CHANNELS, 1, getIterations(), getLearningRate());
+                    = new ExponentialDecaySomBrain<SomInputNeuron, SomOutputNeuron, SomNeuron, Synapse<SomNeuron>>(COLOR_CHANNELS, 1, this.getIterations(), this.getLearningRate());
 
             //create the output latice
-            for (double x = 0; x < getWidth(); x++)
+            for (double x = 0; x < this.getWidth(); x++)
                 brain.createOutput(new Vector(new double[]{x}));
 
             //run through random training data for all iterations
-            for (int iteration = 0; iteration < getIterations(); iteration++) {
+            for (int iteration = 0; iteration < this.getIterations(); iteration++) {
                 this.progress++;
 
                 for (int ci = 0; ci < COLOR_CHANNELS; ci++)
@@ -69,7 +69,7 @@ public final class ColorMap1dCallable implements Callable<Color[]> {
             final Map<Vector, double[]> outputWeightVectors = brain.getOutputWeightVectors();
 
             //construct the color array
-            Color[] colorPositions = new Color[getWidth()];
+            Color[] colorPositions = new Color[this.getWidth()];
             for (Entry<Vector, double[]> weightVector : outputWeightVectors.entrySet()) {
                 final Vector currentPoint = weightVector.getKey();
                 final double[] currentVector = weightVector.getValue();
@@ -98,27 +98,27 @@ public final class ColorMap1dCallable implements Callable<Color[]> {
      * @return the iterations
      */
     public int getIterations() {
-        return iterations;
+        return this.iterations;
     }
 
     /**
      * @return the learningRate
      */
     public double getLearningRate() {
-        return learningRate;
+        return this.learningRate;
     }
 
     /**
      * @return the width
      */
     public int getWidth() {
-        return width;
+        return this.width;
     }
 
     /**
      * @return the progress
      */
     public int getProgress() {
-        return progress;
+        return this.progress;
     }
 }
diff --git a/src/main/java/com/syncleus/dann/examples/colormap/ColorMap2dCallable.java b/src/main/java/com/syncleus/dann/examples/colormap/ColorMap2dCallable.java
index 9b4d999..5c51b16 100644
--- a/src/main/java/com/syncleus/dann/examples/colormap/ColorMap2dCallable.java
+++ b/src/main/java/com/syncleus/dann/examples/colormap/ColorMap2dCallable.java
@@ -50,11 +50,11 @@ public class ColorMap2dCallable implements Callable<Color[][]> {
         try {
             //initialize brain
             final ExponentialDecaySomBrain<SomInputNeuron, SomOutputNeuron, SomNeuron, Synapse<SomNeuron>> brain
-                    = new ExponentialDecaySomBrain<SomInputNeuron, SomOutputNeuron, SomNeuron, Synapse<SomNeuron>>(ColorMap1dCallable.COLOR_CHANNELS, 2, getIterations(), getLearningRate());
+                    = new ExponentialDecaySomBrain<SomInputNeuron, SomOutputNeuron, SomNeuron, Synapse<SomNeuron>>(ColorMap1dCallable.COLOR_CHANNELS, 2, this.getIterations(), this.getLearningRate());
 
             //create the output latice
-            for (double x = 0; x < getWidth(); x++)
-                for (double y = 0; y < getHeight(); y++)
+            for (double x = 0; x < this.getWidth(); x++)
+                for (double y = 0; y < this.getHeight(); y++)
                     brain.createOutput(new Vector(new double[]{x, y}));
 
             //makes sure all the weights are randomly distributed within the
@@ -63,7 +63,7 @@ public class ColorMap2dCallable implements Callable<Color[][]> {
                 synapse.setWeight(RANDOM.nextDouble());
 
             //run through random training data
-            for (int iteration = 0; iteration < getIterations(); iteration++) {
+            for (int iteration = 0; iteration < this.getIterations(); iteration++) {
                 this.progress++;
 
                 for (int ci = 0; ci < ColorMap1dCallable.COLOR_CHANNELS; ci++)
@@ -76,7 +76,7 @@ public class ColorMap2dCallable implements Callable<Color[][]> {
             final Map<Vector, double[]> outputWeightVectors = brain.getOutputWeightVectors();
 
             //construct the color array
-            Color[][] colorPositions = new Color[getWidth()][getHeight()];
+            Color[][] colorPositions = new Color[this.getWidth()][this.getHeight()];
             for (Entry<Vector, double[]> weightVector : outputWeightVectors.entrySet()) {
                 final Vector currentPoint = weightVector.getKey();
                 final double[] currentVector = weightVector.getValue();
@@ -118,34 +118,34 @@ public class ColorMap2dCallable implements Callable<Color[][]> {
      * @return the iterations
      */
     public int getIterations() {
-        return iterations;
+        return this.iterations;
     }
 
     /**
      * @return the learningRate
      */
     public double getLearningRate() {
-        return learningRate;
+        return this.learningRate;
     }
 
     /**
      * @return the width
      */
     public int getWidth() {
-        return width;
+        return this.width;
     }
 
     /**
      * @return the height
      */
     public int getHeight() {
-        return height;
+        return this.height;
     }
 
     /**
      * @return the progress
      */
     public int getProgress() {
-        return progress;
+        return this.progress;
     }
 }
diff --git a/src/main/java/com/syncleus/dann/examples/colormap/ColorMapDemo.java b/src/main/java/com/syncleus/dann/examples/colormap/ColorMapDemo.java
index 48b521e..7750a81 100644
--- a/src/main/java/com/syncleus/dann/examples/colormap/ColorMapDemo.java
+++ b/src/main/java/com/syncleus/dann/examples/colormap/ColorMapDemo.java
@@ -62,7 +62,7 @@ public class ColorMapDemo extends JFrame implements ActionListener {
             LOGGER.warn("Could not set the UI to native look and feel", caught);
         }
 
-        initComponents();
+        this.initComponents();
 
         this.iterationsSpinner.setValue(INITIAL_ITERATIONS);
         this.iterationsSpinner.setModel(this.iterationsModel);
@@ -75,7 +75,7 @@ public class ColorMapDemo extends JFrame implements ActionListener {
         this.addWindowListener(new WindowAdapter() {
             @Override
             public void windowClosing(WindowEvent event) {
-                executor.shutdown();
+                ColorMapDemo.this.executor.shutdown();
             }
         });
     }
@@ -205,95 +205,95 @@ public class ColorMapDemo extends JFrame implements ActionListener {
     // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
     private void initComponents() {
 
-        iterationsSpinner = new javax.swing.JSpinner();
-        jLabel1 = new javax.swing.JLabel();
-        jLabel2 = new javax.swing.JLabel();
-        learningRateSpinner = new javax.swing.JSpinner();
-        jLabel3 = new javax.swing.JLabel();
-        dimentionalityComboBox = new javax.swing.JComboBox();
-        trainDisplayButton = new javax.swing.JButton();
-        progressBar = new javax.swing.JProgressBar();
-        jMenuBar1 = new javax.swing.JMenuBar();
-        jMenu1 = new javax.swing.JMenu();
-        exitMenuItem = new javax.swing.JMenuItem();
-        jMenu2 = new javax.swing.JMenu();
-        aboutMenuItem = new javax.swing.JMenuItem();
+        this.iterationsSpinner = new javax.swing.JSpinner();
+        this.jLabel1 = new javax.swing.JLabel();
+        this.jLabel2 = new javax.swing.JLabel();
+        this.learningRateSpinner = new javax.swing.JSpinner();
+        this.jLabel3 = new javax.swing.JLabel();
+        this.dimentionalityComboBox = new javax.swing.JComboBox();
+        this.trainDisplayButton = new javax.swing.JButton();
+        this.progressBar = new javax.swing.JProgressBar();
+        this.jMenuBar1 = new javax.swing.JMenuBar();
+        this.jMenu1 = new javax.swing.JMenu();
+        this.exitMenuItem = new javax.swing.JMenuItem();
+        this.jMenu2 = new javax.swing.JMenu();
+        this.aboutMenuItem = new javax.swing.JMenuItem();
 
-        setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
-        setTitle("SOM Color Map Demo");
+        this.setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
+        this.setTitle("SOM Color Map Demo");
 
-        iterationsSpinner.setName("iterationsSpinner"); // NOI18N
+        this.iterationsSpinner.setName("iterationsSpinner"); // NOI18N
 
-        jLabel1.setText("Training Iterations:");
+        this.jLabel1.setText("Training Iterations:");
 
-        jLabel2.setText("Learning Rate:");
+        this.jLabel2.setText("Learning Rate:");
 
-        learningRateSpinner.setName("learningRateSpinner"); // NOI18N
+        this.learningRateSpinner.setName("learningRateSpinner"); // NOI18N
 
-        jLabel3.setText("Dimentionality:");
+        this.jLabel3.setText("Dimentionality:");
 
-        dimentionalityComboBox.setModel(new javax.swing.DefaultComboBoxModel(new String[]{"1D", "2D"}));
-        dimentionalityComboBox.setName("dimentionalityComboBox"); // NOI18N
+        this.dimentionalityComboBox.setModel(new javax.swing.DefaultComboBoxModel(new String[]{"1D", "2D"}));
+        this.dimentionalityComboBox.setName("dimentionalityComboBox"); // NOI18N
 
-        trainDisplayButton.setText("Train & Display");
-        trainDisplayButton.setName("trainDisplayButton"); // NOI18N
-        trainDisplayButton.addActionListener(new java.awt.event.ActionListener() {
+        this.trainDisplayButton.setText("Train & Display");
+        this.trainDisplayButton.setName("trainDisplayButton"); // NOI18N
+        this.trainDisplayButton.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
-                trainDisplayButtonActionPerformed(evt);
+                ColorMapDemo.this.trainDisplayButtonActionPerformed(evt);
             }
         });
 
-        progressBar.setStringPainted(true);
+        this.progressBar.setStringPainted(true);
 
-        jMenu1.setText("File");
+        this.jMenu1.setText("File");
 
-        exitMenuItem.setText("Exit");
-        exitMenuItem.addMouseListener(new java.awt.event.MouseAdapter() {
+        this.exitMenuItem.setText("Exit");
+        this.exitMenuItem.addMouseListener(new java.awt.event.MouseAdapter() {
             public void mouseReleased(java.awt.event.MouseEvent evt) {
-                exitMenuItemMouseReleased(evt);
+                ColorMapDemo.this.exitMenuItemMouseReleased(evt);
             }
         });
-        jMenu1.add(exitMenuItem);
+        this.jMenu1.add(this.exitMenuItem);
 
-        jMenuBar1.add(jMenu1);
+        this.jMenuBar1.add(this.jMenu1);
 
-        jMenu2.setText("Help");
+        this.jMenu2.setText("Help");
 
-        aboutMenuItem.setText("About");
-        aboutMenuItem.addMouseListener(new java.awt.event.MouseAdapter() {
+        this.aboutMenuItem.setText("About");
+        this.aboutMenuItem.addMouseListener(new java.awt.event.MouseAdapter() {
             public void mouseReleased(java.awt.event.MouseEvent evt) {
-                aboutMenuItemMouseReleased(evt);
+                ColorMapDemo.this.aboutMenuItemMouseReleased(evt);
             }
         });
-        jMenu2.add(aboutMenuItem);
+        this.jMenu2.add(this.aboutMenuItem);
 
-        jMenuBar1.add(jMenu2);
+        this.jMenuBar1.add(this.jMenu2);
 
-        setJMenuBar(jMenuBar1);
+        this.setJMenuBar(this.jMenuBar1);
 
-        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
-        getContentPane().setLayout(layout);
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this.getContentPane());
+        this.getContentPane().setLayout(layout);
         layout.setHorizontalGroup(
                                          layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                  .addGroup(layout.createSequentialGroup()
                                                                    .addContainerGap()
                                                                    .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                                                      .addGroup(layout.createSequentialGroup()
-                                                                                                       .addComponent(jLabel1)
+                                                                                                       .addComponent(this.jLabel1)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(iterationsSpinner, javax.swing.GroupLayout.DEFAULT_SIZE, 106, Short.MAX_VALUE)
+                                                                                                       .addComponent(this.iterationsSpinner, javax.swing.GroupLayout.DEFAULT_SIZE, 106, Short.MAX_VALUE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(jLabel2)
+                                                                                                       .addComponent(this.jLabel2)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(learningRateSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 43, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.learningRateSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 43, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(jLabel3)
+                                                                                                       .addComponent(this.jLabel3)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(dimentionalityComboBox, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                                                                                                       .addComponent(this.dimentionalityComboBox, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                                                                                      .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
-                                                                                                                                                   .addComponent(progressBar, javax.swing.GroupLayout.DEFAULT_SIZE, 332, Short.MAX_VALUE)
+                                                                                                                                                   .addComponent(this.progressBar, javax.swing.GroupLayout.DEFAULT_SIZE, 332, Short.MAX_VALUE)
                                                                                                                                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                                                                   .addComponent(trainDisplayButton)))
+                                                                                                                                                   .addComponent(this.trainDisplayButton)))
                                                                    .addContainerGap())
         );
         layout.setVerticalGroup(
@@ -301,20 +301,20 @@ public class ColorMapDemo extends JFrame implements ActionListener {
                                                .addGroup(layout.createSequentialGroup()
                                                                  .addContainerGap()
                                                                  .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
-                                                                                   .addComponent(jLabel3)
-                                                                                   .addComponent(dimentionalityComboBox, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                   .addComponent(jLabel1)
-                                                                                   .addComponent(iterationsSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                   .addComponent(learningRateSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                   .addComponent(jLabel2))
+                                                                                   .addComponent(this.jLabel3)
+                                                                                   .addComponent(this.dimentionalityComboBox, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                   .addComponent(this.jLabel1)
+                                                                                   .addComponent(this.iterationsSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                   .addComponent(this.learningRateSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                   .addComponent(this.jLabel2))
                                                                  .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                                                  .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
-                                                                                   .addComponent(progressBar, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
-                                                                                   .addComponent(trainDisplayButton, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+                                                                                   .addComponent(this.progressBar, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                                                                                   .addComponent(this.trainDisplayButton, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
                                                                  .addContainerGap(219, Short.MAX_VALUE))
         );
 
-        pack();
+        this.pack();
     }// </editor-fold>//GEN-END:initComponents
 
     private void exitMenuItemMouseReleased(java.awt.event.MouseEvent evt)//GEN-FIRST:event_exitMenuItemMouseReleased
@@ -337,7 +337,7 @@ public class ColorMapDemo extends JFrame implements ActionListener {
             this.future2d = null;
 
             this.callable1d = new ColorMap1dCallable(iterations, learningRate, 500);
-            this.future1d = executor.submit(this.callable1d);
+            this.future1d = this.executor.submit(this.callable1d);
         }
         else {
             if (this.future1d != null)
@@ -349,7 +349,7 @@ public class ColorMapDemo extends JFrame implements ActionListener {
             this.future1d = null;
 
             this.callable2d = new ColorMap2dCallable(iterations, learningRate, 50, 50);
-            this.future2d = executor.submit(this.callable2d);
+            this.future2d = this.executor.submit(this.callable2d);
         }
 
         this.progressTimer.start();
diff --git a/src/main/java/com/syncleus/dann/examples/fft/FftDemo.java b/src/main/java/com/syncleus/dann/examples/fft/FftDemo.java
index 5aec1dd..ecf1425 100644
--- a/src/main/java/com/syncleus/dann/examples/fft/FftDemo.java
+++ b/src/main/java/com/syncleus/dann/examples/fft/FftDemo.java
@@ -76,22 +76,22 @@ public class FftDemo extends JFrame implements ActionListener {
     private javax.swing.JMenuBar jMenuBar1;
     private javax.swing.JButton listenButton;
     public FftDemo() {
-        initComponents();
+        this.initComponents();
 
         this.setResizable(false);
 
-        this.frequencyBars = new JProgressBar[]{frequencyBar1, frequencyBar2,
-                                                       frequencyBar3, frequencyBar4,
-                                                       frequencyBar5, frequencyBar6,
-                                                       frequencyBar7, frequencyBar8,
-                                                       frequencyBar9, frequencyBar10,
-                                                       frequencyBar11, frequencyBar12,
-                                                       frequencyBar13, frequencyBar14,
-                                                       frequencyBar15, frequencyBar16,
-                                                       frequencyBar17, frequencyBar18,
-                                                       frequencyBar19, frequencyBar20,
-                                                       frequencyBar21, frequencyBar22,
-                                                       frequencyBar23, frequencyBar24};
+        this.frequencyBars = new JProgressBar[]{this.frequencyBar1, this.frequencyBar2,
+                                                       this.frequencyBar3, this.frequencyBar4,
+                                                       this.frequencyBar5, this.frequencyBar6,
+                                                       this.frequencyBar7, this.frequencyBar8,
+                                                       this.frequencyBar9, this.frequencyBar10,
+                                                       this.frequencyBar11, this.frequencyBar12,
+                                                       this.frequencyBar13, this.frequencyBar14,
+                                                       this.frequencyBar15, this.frequencyBar16,
+                                                       this.frequencyBar17, this.frequencyBar18,
+                                                       this.frequencyBar19, this.frequencyBar20,
+                                                       this.frequencyBar21, this.frequencyBar22,
+                                                       this.frequencyBar23, this.frequencyBar24};
 
         //set the colors as a fradient from blue to red
         for (int index = 0; index < this.frequencyBars.length; index++) {
@@ -101,7 +101,7 @@ public class FftDemo extends JFrame implements ActionListener {
         }
 
         this.audioFormat = createAudioFormat();
-        final DataLine.Info dataLineInfo = new DataLine.Info(TargetDataLine.class, audioFormat);
+        final DataLine.Info dataLineInfo = new DataLine.Info(TargetDataLine.class, this.audioFormat);
         TargetDataLine myTargetDataLine = null;
         try {
             myTargetDataLine = (TargetDataLine) AudioSystem.getLine(dataLineInfo);
@@ -133,175 +133,175 @@ public class FftDemo extends JFrame implements ActionListener {
     // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
     private void initComponents() {
 
-        frequencyBar1 = new javax.swing.JProgressBar();
-        listenButton = new javax.swing.JButton();
-        frequencyBar10 = new javax.swing.JProgressBar();
-        frequencyBar2 = new javax.swing.JProgressBar();
-        frequencyBar4 = new javax.swing.JProgressBar();
-        frequencyBar5 = new javax.swing.JProgressBar();
-        frequencyBar9 = new javax.swing.JProgressBar();
-        frequencyBar3 = new javax.swing.JProgressBar();
-        frequencyBar6 = new javax.swing.JProgressBar();
-        frequencyBar7 = new javax.swing.JProgressBar();
-        frequencyBar8 = new javax.swing.JProgressBar();
-        frequencyBar11 = new javax.swing.JProgressBar();
-        frequencyBar12 = new javax.swing.JProgressBar();
-        frequencyBar13 = new javax.swing.JProgressBar();
-        frequencyBar14 = new javax.swing.JProgressBar();
-        frequencyBar15 = new javax.swing.JProgressBar();
-        frequencyBar16 = new javax.swing.JProgressBar();
-        frequencyBar17 = new javax.swing.JProgressBar();
-        frequencyBar18 = new javax.swing.JProgressBar();
-        frequencyBar19 = new javax.swing.JProgressBar();
-        frequencyBar20 = new javax.swing.JProgressBar();
-        frequencyBar21 = new javax.swing.JProgressBar();
-        frequencyBar22 = new javax.swing.JProgressBar();
-        frequencyBar23 = new javax.swing.JProgressBar();
-        frequencyBar24 = new javax.swing.JProgressBar();
-        jMenuBar1 = new javax.swing.JMenuBar();
-        fileMenuItem = new javax.swing.JMenu();
-        exitMenuItem = new javax.swing.JMenuItem();
-        helpMenuItem = new javax.swing.JMenu();
-        aboutMenuItem = new javax.swing.JMenuItem();
-
-        setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
-        setTitle("Fast Fourier Transform Demo");
-
-        frequencyBar1.setForeground(new java.awt.Color(0, 0, 255));
-        frequencyBar1.setOrientation(1);
-
-        listenButton.setText("Listen");
-        listenButton.setName("listenButton"); // NOI18N
-        listenButton.addActionListener(new java.awt.event.ActionListener() {
+        this.frequencyBar1 = new javax.swing.JProgressBar();
+        this.listenButton = new javax.swing.JButton();
+        this.frequencyBar10 = new javax.swing.JProgressBar();
+        this.frequencyBar2 = new javax.swing.JProgressBar();
+        this.frequencyBar4 = new javax.swing.JProgressBar();
+        this.frequencyBar5 = new javax.swing.JProgressBar();
+        this.frequencyBar9 = new javax.swing.JProgressBar();
+        this.frequencyBar3 = new javax.swing.JProgressBar();
+        this.frequencyBar6 = new javax.swing.JProgressBar();
+        this.frequencyBar7 = new javax.swing.JProgressBar();
+        this.frequencyBar8 = new javax.swing.JProgressBar();
+        this.frequencyBar11 = new javax.swing.JProgressBar();
+        this.frequencyBar12 = new javax.swing.JProgressBar();
+        this.frequencyBar13 = new javax.swing.JProgressBar();
+        this.frequencyBar14 = new javax.swing.JProgressBar();
+        this.frequencyBar15 = new javax.swing.JProgressBar();
+        this.frequencyBar16 = new javax.swing.JProgressBar();
+        this.frequencyBar17 = new javax.swing.JProgressBar();
+        this.frequencyBar18 = new javax.swing.JProgressBar();
+        this.frequencyBar19 = new javax.swing.JProgressBar();
+        this.frequencyBar20 = new javax.swing.JProgressBar();
+        this.frequencyBar21 = new javax.swing.JProgressBar();
+        this.frequencyBar22 = new javax.swing.JProgressBar();
+        this.frequencyBar23 = new javax.swing.JProgressBar();
+        this.frequencyBar24 = new javax.swing.JProgressBar();
+        this.jMenuBar1 = new javax.swing.JMenuBar();
+        this.fileMenuItem = new javax.swing.JMenu();
+        this.exitMenuItem = new javax.swing.JMenuItem();
+        this.helpMenuItem = new javax.swing.JMenu();
+        this.aboutMenuItem = new javax.swing.JMenuItem();
+
+        this.setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
+        this.setTitle("Fast Fourier Transform Demo");
+
+        this.frequencyBar1.setForeground(new java.awt.Color(0, 0, 255));
+        this.frequencyBar1.setOrientation(1);
+
+        this.listenButton.setText("Listen");
+        this.listenButton.setName("listenButton"); // NOI18N
+        this.listenButton.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
-                listenButtonActionPerformed(evt);
+                FftDemo.this.listenButtonActionPerformed(evt);
             }
         });
 
-        frequencyBar10.setOrientation(1);
+        this.frequencyBar10.setOrientation(1);
 
-        frequencyBar2.setOrientation(1);
+        this.frequencyBar2.setOrientation(1);
 
-        frequencyBar4.setOrientation(1);
+        this.frequencyBar4.setOrientation(1);
 
-        frequencyBar5.setOrientation(1);
+        this.frequencyBar5.setOrientation(1);
 
-        frequencyBar9.setOrientation(1);
+        this.frequencyBar9.setOrientation(1);
 
-        frequencyBar3.setOrientation(1);
+        this.frequencyBar3.setOrientation(1);
 
-        frequencyBar6.setOrientation(1);
+        this.frequencyBar6.setOrientation(1);
 
-        frequencyBar7.setOrientation(1);
+        this.frequencyBar7.setOrientation(1);
 
-        frequencyBar8.setOrientation(1);
+        this.frequencyBar8.setOrientation(1);
 
-        frequencyBar11.setOrientation(1);
+        this.frequencyBar11.setOrientation(1);
 
-        frequencyBar12.setOrientation(1);
+        this.frequencyBar12.setOrientation(1);
 
-        frequencyBar13.setOrientation(1);
+        this.frequencyBar13.setOrientation(1);
 
-        frequencyBar14.setOrientation(1);
+        this.frequencyBar14.setOrientation(1);
 
-        frequencyBar15.setOrientation(1);
+        this.frequencyBar15.setOrientation(1);
 
-        frequencyBar16.setOrientation(1);
+        this.frequencyBar16.setOrientation(1);
 
-        frequencyBar17.setOrientation(1);
+        this.frequencyBar17.setOrientation(1);
 
-        frequencyBar18.setOrientation(1);
+        this.frequencyBar18.setOrientation(1);
 
-        frequencyBar19.setOrientation(1);
+        this.frequencyBar19.setOrientation(1);
 
-        frequencyBar20.setOrientation(1);
+        this.frequencyBar20.setOrientation(1);
 
-        frequencyBar21.setOrientation(1);
+        this.frequencyBar21.setOrientation(1);
 
-        frequencyBar22.setOrientation(1);
+        this.frequencyBar22.setOrientation(1);
 
-        frequencyBar23.setOrientation(1);
+        this.frequencyBar23.setOrientation(1);
 
-        frequencyBar24.setForeground(new java.awt.Color(255, 0, 0));
-        frequencyBar24.setOrientation(1);
+        this.frequencyBar24.setForeground(new java.awt.Color(255, 0, 0));
+        this.frequencyBar24.setOrientation(1);
 
-        fileMenuItem.setText("File");
+        this.fileMenuItem.setText("File");
 
-        exitMenuItem.setText("Exit");
-        exitMenuItem.addMouseListener(new java.awt.event.MouseAdapter() {
+        this.exitMenuItem.setText("Exit");
+        this.exitMenuItem.addMouseListener(new java.awt.event.MouseAdapter() {
             public void mouseReleased(java.awt.event.MouseEvent evt) {
-                exitMenuItemMouseReleased(evt);
+                FftDemo.this.exitMenuItemMouseReleased(evt);
             }
         });
-        fileMenuItem.add(exitMenuItem);
+        this.fileMenuItem.add(this.exitMenuItem);
 
-        jMenuBar1.add(fileMenuItem);
+        this.jMenuBar1.add(this.fileMenuItem);
 
-        helpMenuItem.setText("Help");
+        this.helpMenuItem.setText("Help");
 
-        aboutMenuItem.setText("About");
-        helpMenuItem.add(aboutMenuItem);
+        this.aboutMenuItem.setText("About");
+        this.helpMenuItem.add(this.aboutMenuItem);
 
-        jMenuBar1.add(helpMenuItem);
+        this.jMenuBar1.add(this.helpMenuItem);
 
-        setJMenuBar(jMenuBar1);
+        this.setJMenuBar(this.jMenuBar1);
 
-        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
-        getContentPane().setLayout(layout);
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this.getContentPane());
+        this.getContentPane().setLayout(layout);
         layout.setHorizontalGroup(
                                          layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                  .addGroup(layout.createSequentialGroup()
                                                                    .addContainerGap()
-                                                                   .addComponent(frequencyBar1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                   .addComponent(this.frequencyBar1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                   .addComponent(frequencyBar2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                   .addComponent(this.frequencyBar2, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                   .addComponent(frequencyBar3, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                   .addComponent(this.frequencyBar3, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                   .addComponent(frequencyBar4, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                   .addComponent(this.frequencyBar4, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                   .addComponent(frequencyBar5, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                   .addComponent(this.frequencyBar5, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                   .addComponent(frequencyBar6, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                   .addComponent(this.frequencyBar6, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                   .addComponent(frequencyBar7, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                   .addComponent(this.frequencyBar7, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                   .addComponent(frequencyBar8, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                   .addComponent(this.frequencyBar8, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                   .addComponent(frequencyBar9, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                   .addComponent(this.frequencyBar9, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                   .addComponent(frequencyBar10, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                   .addComponent(this.frequencyBar10, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
-                                                                   .addComponent(frequencyBar11, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                   .addComponent(this.frequencyBar11, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                                                    .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                                                                                     .addComponent(listenButton)
+                                                                                     .addComponent(this.listenButton)
                                                                                      .addGroup(layout.createSequentialGroup()
-                                                                                                       .addComponent(frequencyBar12, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.frequencyBar12, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(frequencyBar13, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.frequencyBar13, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(frequencyBar14, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.frequencyBar14, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(frequencyBar15, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.frequencyBar15, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(frequencyBar16, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.frequencyBar16, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(frequencyBar17, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.frequencyBar17, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(frequencyBar18, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.frequencyBar18, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(frequencyBar19, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.frequencyBar19, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(frequencyBar20, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.frequencyBar20, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(frequencyBar21, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.frequencyBar21, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(frequencyBar22, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.frequencyBar22, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(frequencyBar23, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.frequencyBar23, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(frequencyBar24, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
+                                                                                                       .addComponent(this.frequencyBar24, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
                                                                    .addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
         );
         layout.setVerticalGroup(
@@ -309,36 +309,36 @@ public class FftDemo extends JFrame implements ActionListener {
                                                .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
                                                                                                              .addContainerGap()
                                                                                                              .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
-                                                                                                                               .addComponent(frequencyBar24, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar23, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar22, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar21, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar20, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar19, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar18, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar17, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar16, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar15, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar14, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar8, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar7, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar6, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar5, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar4, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar3, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar2, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar1, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar9, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar10, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar11, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar12, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
-                                                                                                                               .addComponent(frequencyBar13, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE))
+                                                                                                                               .addComponent(this.frequencyBar24, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar23, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar22, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar21, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar20, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar19, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar18, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar17, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar16, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar15, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar14, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar8, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar7, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar6, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar5, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar4, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar3, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar2, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar1, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar9, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar10, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar11, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar12, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.frequencyBar13, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 235, Short.MAX_VALUE))
                                                                                                              .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                             .addComponent(listenButton)
+                                                                                                             .addComponent(this.listenButton)
                                                                                                              .addContainerGap())
         );
 
-        pack();
+        this.pack();
     }// </editor-fold>//GEN-END:initComponents
 
     private void exitMenuItemMouseReleased(java.awt.event.MouseEvent evt)//GEN-FIRST:event_exitMenuItemMouseReleased
@@ -358,7 +358,7 @@ public class FftDemo extends JFrame implements ActionListener {
                 this.listenButton.setText("Listen");
             }
             else {
-                this.targetDataLine.open(audioFormat);
+                this.targetDataLine.open(this.audioFormat);
                 this.targetDataLine.start();
 
                 this.sampleTimer.start();
@@ -381,7 +381,7 @@ public class FftDemo extends JFrame implements ActionListener {
             final double[] signal = new double[this.transformer.getBlockSize()];
             for (int signalIndex = 0; signalIndex < signal.length; signalIndex++) {
                 final int signalBytesIndex = signalIndex * 2;
-                signal[signalIndex] = bytesToDouble(signalBytes[signalBytesIndex], signalBytes[signalBytesIndex + 1]);
+                signal[signalIndex] = this.bytesToDouble(signalBytes[signalBytesIndex], signalBytes[signalBytesIndex + 1]);
             }
 
             final DiscreteFourierTransform transform = this.transformer.transform(signal);
diff --git a/src/main/java/com/syncleus/dann/examples/hyperassociativemap/visualization/SimpleGraph.java b/src/main/java/com/syncleus/dann/examples/hyperassociativemap/visualization/SimpleGraph.java
index 6cb58b9..c5618c0 100644
--- a/src/main/java/com/syncleus/dann/examples/hyperassociativemap/visualization/SimpleGraph.java
+++ b/src/main/java/com/syncleus/dann/examples/hyperassociativemap/visualization/SimpleGraph.java
@@ -35,10 +35,10 @@ public class SimpleGraph extends AbstractBidirectedAdjacencyGraph<SimpleNode, Bi
         //construct nodes
         for (int layerIndex = 0; layerIndex < layers; layerIndex++) {
             for (int nodeIndex = 0; nodeIndex < nodesPerLayer; nodeIndex++) {
-                nodes[layerIndex][nodeIndex] = new SimpleNode(layerIndex);
-                this.nodeSet.add(nodes[layerIndex][nodeIndex]);
-                this.neighborEdges.put(nodes[layerIndex][nodeIndex], new HashSet<BidirectedEdge<SimpleNode>>());
-                this.neighborNodes.put(nodes[layerIndex][nodeIndex], new HashSet<SimpleNode>());
+                this.nodes[layerIndex][nodeIndex] = new SimpleNode(layerIndex);
+                this.nodeSet.add(this.nodes[layerIndex][nodeIndex]);
+                this.neighborEdges.put(this.nodes[layerIndex][nodeIndex], new HashSet<BidirectedEdge<SimpleNode>>());
+                this.neighborNodes.put(this.nodes[layerIndex][nodeIndex], new HashSet<SimpleNode>());
             }
         }
 
@@ -46,12 +46,12 @@ public class SimpleGraph extends AbstractBidirectedAdjacencyGraph<SimpleNode, Bi
         for (int layerIndex = 0; layerIndex < (layers - 1); layerIndex++)
             for (int nodeIndex = 0; nodeIndex < nodesPerLayer; nodeIndex++) {
                 for (int nodeIndex2 = 0; nodeIndex2 < nodesPerLayer; nodeIndex2++) {
-                    final ImmutableUndirectedEdge<SimpleNode> newEdge = new ImmutableUndirectedEdge<SimpleNode>(nodes[layerIndex][nodeIndex], nodes[layerIndex + 1][nodeIndex2]);
+                    final ImmutableUndirectedEdge<SimpleNode> newEdge = new ImmutableUndirectedEdge<SimpleNode>(this.nodes[layerIndex][nodeIndex], this.nodes[layerIndex + 1][nodeIndex2]);
                     this.edges.add(newEdge);
-                    this.neighborEdges.get(nodes[layerIndex][nodeIndex]).add(newEdge);
-                    this.neighborNodes.get(nodes[layerIndex][nodeIndex]).add(nodes[layerIndex + 1][nodeIndex2]);
-                    this.neighborEdges.get(nodes[layerIndex + 1][nodeIndex2]).add(newEdge);
-                    this.neighborNodes.get(nodes[layerIndex + 1][nodeIndex2]).add(nodes[layerIndex][nodeIndex]);
+                    this.neighborEdges.get(this.nodes[layerIndex][nodeIndex]).add(newEdge);
+                    this.neighborNodes.get(this.nodes[layerIndex][nodeIndex]).add(this.nodes[layerIndex + 1][nodeIndex2]);
+                    this.neighborEdges.get(this.nodes[layerIndex + 1][nodeIndex2]).add(newEdge);
+                    this.neighborNodes.get(this.nodes[layerIndex + 1][nodeIndex2]).add(this.nodes[layerIndex][nodeIndex]);
                 }
             }
     }
@@ -61,7 +61,7 @@ public class SimpleGraph extends AbstractBidirectedAdjacencyGraph<SimpleNode, Bi
     }
 
     public SimpleNode getNode(final int layer, final int index) {
-        if ((index >= nodes[0].length) || (layer >= nodes.length))
+        if ((index >= this.nodes[0].length) || (layer >= this.nodes.length))
             throw new IllegalArgumentException("coordinates are out of bounds");
         return this.nodes[layer][index];
     }
diff --git a/src/main/java/com/syncleus/dann/examples/hyperassociativemap/visualization/ViewMap.java b/src/main/java/com/syncleus/dann/examples/hyperassociativemap/visualization/ViewMap.java
index 03fd5ab..fd49796 100644
--- a/src/main/java/com/syncleus/dann/examples/hyperassociativemap/visualization/ViewMap.java
+++ b/src/main/java/com/syncleus/dann/examples/hyperassociativemap/visualization/ViewMap.java
@@ -35,22 +35,22 @@ public class ViewMap extends JFrame implements ActionListener {
     public ViewMap() {
         // With only 1 thread, we would get a dead-lock when
         // the view-update-thread is waiting for the alignment.
-        executor = Executors.newFixedThreadPool(Math.max(2, Runtime.getRuntime().availableProcessors()));
-        associativeMap = new LayeredHyperassociativeMap(8, executor);
+        this.executor = Executors.newFixedThreadPool(Math.max(2, Runtime.getRuntime().availableProcessors()));
+        this.associativeMap = new LayeredHyperassociativeMap(8, this.executor);
 
         HyperassociativeMapCanvas myMapVisual = null;
         try {
-            myMapVisual = new HyperassociativeMapCanvas(associativeMap, NODE_RADIUS);
-            initComponents();
+            myMapVisual = new HyperassociativeMapCanvas(this.associativeMap, NODE_RADIUS);
+            this.initComponents();
 
-            lastRun = new FutureTask<Void>(new UpdateViewRun(myMapVisual, associativeMap), null);
-            executor.execute(lastRun);
+            this.lastRun = new FutureTask<Void>(new UpdateViewRun(myMapVisual, this.associativeMap), null);
+            this.executor.execute(this.lastRun);
 
             myMapVisual.setFocusTraversalKeysEnabled(false);
-            AssociativeMapKeyAdapter keyAdapter = new AssociativeMapKeyAdapter(associativeMap);
+            AssociativeMapKeyAdapter keyAdapter = new AssociativeMapKeyAdapter(this.associativeMap);
             myMapVisual.addKeyListener(keyAdapter);
             myMapVisual.getCanvas3D().addKeyListener(keyAdapter);
-            addKeyListener(keyAdapter);
+            this.addKeyListener(keyAdapter);
 
             new Timer(100, this).start();
 
@@ -61,22 +61,22 @@ public class ViewMap extends JFrame implements ActionListener {
         }
         catch (ComponentUnavailableException exc) {
             myMapVisual = null;
-            add(exc.newPanel());
+            this.add(exc.newPanel());
         }
-        mapVisual = myMapVisual;
-        if (mapVisual != null) {
-            add(mapVisual);
+        this.mapVisual = myMapVisual;
+        if (this.mapVisual != null) {
+            this.add(this.mapVisual);
         }
 
-        addWindowListener(new WindowAdapter() {
+        this.addWindowListener(new WindowAdapter() {
             @Override
             public void windowClosing(WindowEvent event) {
-                executor.shutdown();
+                ViewMap.this.executor.shutdown();
             }
         });
-        setFocusTraversalKeysEnabled(false);
+        this.setFocusTraversalKeysEnabled(false);
 
-        setSize(800, 600);
+        this.setSize(800, 600);
     }
 
     private static boolean checkClasses() {
@@ -120,26 +120,26 @@ public class ViewMap extends JFrame implements ActionListener {
 
     @Override
     public void actionPerformed(final ActionEvent evt) {
-        if ((lastRun != null) && !lastRun.isDone()) {
+        if ((this.lastRun != null) && !this.lastRun.isDone()) {
             return;
         }
 
-        if (!isVisible()) {
+        if (!this.isVisible()) {
             return;
         }
 
-        lastRun = new FutureTask<Void>(new UpdateViewRun(mapVisual, associativeMap), null);
-        executor.execute(lastRun);
+        this.lastRun = new FutureTask<Void>(new UpdateViewRun(this.mapVisual, this.associativeMap), null);
+        this.executor.execute(this.lastRun);
     }
 
     // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
     private void initComponents() {
 
-        setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
-        setResizable(false);
+        this.setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
+        this.setResizable(false);
 
-        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
-        getContentPane().setLayout(layout);
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this.getContentPane());
+        this.getContentPane().setLayout(layout);
         layout.setHorizontalGroup(
                                          layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                  .addGap(0, 400, Short.MAX_VALUE)
@@ -149,7 +149,7 @@ public class ViewMap extends JFrame implements ActionListener {
                                                .addGap(0, 300, Short.MAX_VALUE)
         );
 
-        pack();
+        this.pack();
     }//GEN-END:initComponents
 
     private static class AssociativeMapKeyAdapter extends KeyAdapter {
@@ -162,32 +162,32 @@ public class ViewMap extends JFrame implements ActionListener {
         @Override
         public void keyPressed(final KeyEvent evt) {
             if (evt.getKeyCode() == KeyEvent.VK_R) {
-                associativeMap.reset();
+                this.associativeMap.reset();
             }
             if (evt.getKeyCode() == KeyEvent.VK_L) {
-                associativeMap.resetLearning();
+                this.associativeMap.resetLearning();
             }
             else if (evt.getKeyCode() == KeyEvent.VK_UP) {
-                double equilibDist = associativeMap.getEquilibriumDistance();
+                double equilibDist = this.associativeMap.getEquilibriumDistance();
                 if (equilibDist < 1.0) {
                     equilibDist *= 1.1;
                 }
                 else {
                     equilibDist += 1.0;
                 }
-                associativeMap.setEquilibriumDistance(equilibDist);
-                associativeMap.resetLearning();
+                this.associativeMap.setEquilibriumDistance(equilibDist);
+                this.associativeMap.resetLearning();
             }
             else if (evt.getKeyCode() == KeyEvent.VK_DOWN) {
-                double equilibDist = associativeMap.getEquilibriumDistance();
+                double equilibDist = this.associativeMap.getEquilibriumDistance();
                 if (equilibDist < 2.0) {
                     equilibDist *= 0.9;
                 }
                 else {
                     equilibDist -= 1.0;
                 }
-                associativeMap.setEquilibriumDistance(equilibDist);
-                associativeMap.resetLearning();
+                this.associativeMap.setEquilibriumDistance(equilibDist);
+                this.associativeMap.resetLearning();
             }
         }
     }
diff --git a/src/main/java/com/syncleus/dann/examples/nci/BrainRunner.java b/src/main/java/com/syncleus/dann/examples/nci/BrainRunner.java
index 7dbc8e7..b9632ca 100644
--- a/src/main/java/com/syncleus/dann/examples/nci/BrainRunner.java
+++ b/src/main/java/com/syncleus/dann/examples/nci/BrainRunner.java
@@ -68,10 +68,10 @@ public class BrainRunner implements Runnable {
     }
 
     public int getSampleProgress() {
-        if (sampleTotal == 0) {
+        if (this.sampleTotal == 0) {
             return 100;
         }
-        return ((sampleTotal - sampleRemaining) * 100) / sampleTotal;
+        return ((this.sampleTotal - this.sampleRemaining) * 100) / this.sampleTotal;
     }
 
     public void setSampleImage(final File sampleFile) {
@@ -116,8 +116,8 @@ public class BrainRunner implements Runnable {
             executor = Executors.newFixedThreadPool(1);
 
             this.brain = new NciBrain(this.compression, this.xSize, this.ySize, this.extraConnectivity);
-            this.brainMap = new LayeredBrainHyperassociativeMap(brain, 3);
-            this.setTrainingImages(trainingFiles);
+            this.brainMap = new LayeredBrainHyperassociativeMap(this.brain, 3);
+            this.setTrainingImages(this.trainingFiles);
 
             this.listener.brainFinishedBuffering();
             while (this.keepRunning) {
@@ -125,16 +125,16 @@ public class BrainRunner implements Runnable {
                 if (this.sampleFile != null) {
                     this.brain.setLearning(false);
 
-                    this.sampleImage = ImageIO.read(sampleFile);
+                    this.sampleImage = ImageIO.read(this.sampleFile);
 
                     final ArrayBlockingQueue<FutureTask<BufferedImage>> processingSampleSegments = new ArrayBlockingQueue<FutureTask<BufferedImage>>(12000, true);
 
                     this.sampleTotal = 0;
                     stopProcessing:
-                    for (int currentY = 0; currentY < this.sampleImage.getHeight(); currentY += ySize) {
-                        for (int currentX = 0; currentX < this.sampleImage.getWidth(); currentX += xSize) {
-                            final int blockWidth = this.sampleImage.getWidth() - currentX < xSize ? this.sampleImage.getWidth() - currentX : xSize;
-                            final int blockHeight = this.sampleImage.getHeight() - currentY < ySize ? this.sampleImage.getHeight() - currentY : ySize;
+                    for (int currentY = 0; currentY < this.sampleImage.getHeight(); currentY += this.ySize) {
+                        for (int currentX = 0; currentX < this.sampleImage.getWidth(); currentX += this.xSize) {
+                            final int blockWidth = this.sampleImage.getWidth() - currentX < this.xSize ? this.sampleImage.getWidth() - currentX : this.xSize;
+                            final int blockHeight = this.sampleImage.getHeight() - currentY < this.ySize ? this.sampleImage.getHeight() - currentY : this.ySize;
                             final BufferedImage currentSegment = this.sampleImage.getSubimage(currentX, currentY, blockWidth, blockHeight);
 
                             final SampleRun sampleRun = new SampleRun(this.brain, currentSegment);
@@ -204,7 +204,7 @@ public class BrainRunner implements Runnable {
                                 this.trainingRemaining = 0;
                             }
                         }
-                        final TrainRun trainRun = new TrainRun(this.brain, this.getRandomTrainingBlock(xSize, ySize));
+                        final TrainRun trainRun = new TrainRun(this.brain, this.getRandomTrainingBlock(this.xSize, this.ySize));
                         final FutureTask<Void> trainTask = new FutureTask<Void>(trainRun, null);
 
                         trainingSegments.add(trainTask);
diff --git a/src/main/java/com/syncleus/dann/examples/nci/NciBrain.java b/src/main/java/com/syncleus/dann/examples/nci/NciBrain.java
index b806049..eaa56d9 100644
--- a/src/main/java/com/syncleus/dann/examples/nci/NciBrain.java
+++ b/src/main/java/com/syncleus/dann/examples/nci/NciBrain.java
@@ -162,7 +162,7 @@ public class NciBrain extends AbstractFullyConnectedFeedforwardBrain<InputBackpr
     }
 
     public BufferedImage test(final BufferedImage originalImage) {
-        setImageOnto(originalImage, true);
+        this.setImageOnto(originalImage, true);
 
         if (this.compressionInputsSet) {
             for (CompressionNeuron compressionNeuron : this.compressedNeurons)
@@ -174,7 +174,7 @@ public class NciBrain extends AbstractFullyConnectedFeedforwardBrain<InputBackpr
         this.propagate();
 
         if (!this.learning) {
-            return createBufferedImage();
+            return this.createBufferedImage();
         }
 
         //now back propogate
@@ -188,7 +188,7 @@ public class NciBrain extends AbstractFullyConnectedFeedforwardBrain<InputBackpr
      * @since 1.0
      */
     public byte[] compress(final BufferedImage originalImage) {
-        setImageOnto(originalImage, false);
+        this.setImageOnto(originalImage, false);
 
         if (this.compressionInputsSet) {
             for (CompressionNeuron compressionNeuron : this.compressedNeurons)
@@ -208,13 +208,13 @@ public class NciBrain extends AbstractFullyConnectedFeedforwardBrain<InputBackpr
     }
 
     private void setImageOnto(final BufferedImage originalImage, final boolean setDesired) {
-        final int[] originalRgbArray = new int[xSize * ySize];
-        originalImage.getRGB(0, 0, (originalImage.getWidth() < xSize ? originalImage.getWidth() : xSize), (originalImage.getHeight() < ySize ? originalImage.getHeight() : ySize), originalRgbArray, 0, xSize);
+        final int[] originalRgbArray = new int[this.xSize * this.ySize];
+        originalImage.getRGB(0, 0, (originalImage.getWidth() < this.xSize ? originalImage.getWidth() : this.xSize), (originalImage.getHeight() < this.ySize ? originalImage.getHeight() : this.ySize), originalRgbArray, 0, this.xSize);
 
         //set the image onto the inputs
-        for (int yIndex = 0; (yIndex < ySize) && (yIndex < originalImage.getHeight()); yIndex++) {
-            for (int xIndex = 0; (xIndex < xSize) && (xIndex < originalImage.getWidth()); xIndex++) {
-                final int rgbCurrent = originalRgbArray[yIndex * xSize + xIndex];
+        for (int yIndex = 0; (yIndex < this.ySize) && (yIndex < originalImage.getHeight()); yIndex++) {
+            for (int xIndex = 0; (xIndex < this.xSize) && (xIndex < originalImage.getWidth()); xIndex++) {
+                final int rgbCurrent = originalRgbArray[yIndex * this.xSize + xIndex];
                 for (int rgbIndex = 0; rgbIndex < CHANNELS; rgbIndex++) {
                     final int channel = (((rgbCurrent >> (rgbIndex * 8)) & 0x000000FF));
                     final double input = (((double) channel) / 127.5) - 1.0;
@@ -240,14 +240,14 @@ public class NciBrain extends AbstractFullyConnectedFeedforwardBrain<InputBackpr
 
         this.propagate();
 
-        return createBufferedImage();
+        return this.createBufferedImage();
     }
 
     private BufferedImage createBufferedImage() {
-        final int[] finalRgbArray = new int[xSize * ySize];
+        final int[] finalRgbArray = new int[this.xSize * this.ySize];
         final BufferedImage uncompressedImage = new BufferedImage(this.xSize, this.ySize, BufferedImage.TYPE_INT_RGB);
-        for (int yIndex = 0; (yIndex < ySize) && (yIndex < uncompressedImage.getHeight()); yIndex++) {
-            for (int xIndex = 0; (xIndex < xSize) && (xIndex < uncompressedImage.getWidth()); xIndex++) {
+        for (int yIndex = 0; (yIndex < this.ySize) && (yIndex < uncompressedImage.getHeight()); yIndex++) {
+            for (int xIndex = 0; (xIndex < this.xSize) && (xIndex < uncompressedImage.getWidth()); xIndex++) {
                 //int rgbCurrent = imageToCompress.getRGB(xIndex, yIndex);
                 int rgbCurrent = 0;
                 for (int rgbIndex = 0; rgbIndex < 4; rgbIndex++) {
@@ -262,10 +262,10 @@ public class NciBrain extends AbstractFullyConnectedFeedforwardBrain<InputBackpr
 
                     rgbCurrent |= (channel & 0x000000FF) << (rgbIndex * 8);
                 }
-                finalRgbArray[xSize * yIndex + (xIndex)] = rgbCurrent;
+                finalRgbArray[this.xSize * yIndex + (xIndex)] = rgbCurrent;
             }
         }
-        uncompressedImage.setRGB(0, 0, xSize, ySize, finalRgbArray, 0, xSize);
+        uncompressedImage.setRGB(0, 0, this.xSize, this.ySize, finalRgbArray, 0, this.xSize);
 
         return uncompressedImage;
     }
diff --git a/src/main/java/com/syncleus/dann/examples/nci/SampleRun.java b/src/main/java/com/syncleus/dann/examples/nci/SampleRun.java
index 3f6d418..df6e835 100644
--- a/src/main/java/com/syncleus/dann/examples/nci/SampleRun.java
+++ b/src/main/java/com/syncleus/dann/examples/nci/SampleRun.java
@@ -37,7 +37,7 @@ public class SampleRun implements Callable<BufferedImage> {
     public BufferedImage call() {
         try {
             this.brain.setLearning(false);
-            return this.brain.uncompress(this.brain.compress(sampleImage));
+            return this.brain.uncompress(this.brain.compress(this.sampleImage));
         }
         catch (Exception caught) {
             LOGGER.error("Exception was caught", caught);
diff --git a/src/main/java/com/syncleus/dann/examples/nci/TrainRun.java b/src/main/java/com/syncleus/dann/examples/nci/TrainRun.java
index 06e5278..4d5297f 100644
--- a/src/main/java/com/syncleus/dann/examples/nci/TrainRun.java
+++ b/src/main/java/com/syncleus/dann/examples/nci/TrainRun.java
@@ -36,7 +36,7 @@ public class TrainRun implements Runnable {
     public void run() {
         try {
             this.brain.setLearning(true);
-            this.brain.test(trainImage);
+            this.brain.test(this.trainImage);
         }
         catch (Exception caught) {
             LOGGER.error("Exception was caught", caught);
diff --git a/src/main/java/com/syncleus/dann/examples/nci/ui/AboutDialog.java b/src/main/java/com/syncleus/dann/examples/nci/ui/AboutDialog.java
index 50020ff..b43dcf3 100644
--- a/src/main/java/com/syncleus/dann/examples/nci/ui/AboutDialog.java
+++ b/src/main/java/com/syncleus/dann/examples/nci/ui/AboutDialog.java
@@ -30,7 +30,7 @@ public class AboutDialog extends JDialog {
     private javax.swing.JTextArea jTextArea1;
     public AboutDialog(final Frame parent, final boolean modal) {
         super(parent, modal);
-        initComponents();
+        this.initComponents();
     }
 
     /**
@@ -43,73 +43,73 @@ public class AboutDialog extends JDialog {
     // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
     private void initComponents() {
 
-        jButton1 = new javax.swing.JButton();
-        jLabel1 = new javax.swing.JLabel();
-        jLabel2 = new javax.swing.JLabel();
-        jScrollPane1 = new javax.swing.JScrollPane();
-        jTextArea1 = new javax.swing.JTextArea();
+        this.jButton1 = new javax.swing.JButton();
+        this.jLabel1 = new javax.swing.JLabel();
+        this.jLabel2 = new javax.swing.JLabel();
+        this.jScrollPane1 = new javax.swing.JScrollPane();
+        this.jTextArea1 = new javax.swing.JTextArea();
 
-        setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
+        this.setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
 
-        jButton1.setText("OK");
-        jButton1.setName("ok button"); // NOI18N
-        jButton1.addActionListener(new java.awt.event.ActionListener() {
+        this.jButton1.setText("OK");
+        this.jButton1.setName("ok button"); // NOI18N
+        this.jButton1.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
-                jButton1ActionPerformed(evt);
+                AboutDialog.this.jButton1ActionPerformed(evt);
             }
         });
 
-        jLabel1.setText("Syncleus, Inc.");
+        this.jLabel1.setText("Syncleus, Inc.");
 
-        jLabel2.setText("Neural Compressed Image Demo");
+        this.jLabel2.setText("Neural Compressed Image Demo");
 
-        jScrollPane1.setHorizontalScrollBarPolicy(javax.swing.ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
-        jScrollPane1.setHorizontalScrollBar(null);
+        this.jScrollPane1.setHorizontalScrollBarPolicy(javax.swing.ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
+        this.jScrollPane1.setHorizontalScrollBar(null);
 
-        jTextArea1.setColumns(20);
-        jTextArea1.setEditable(false);
-        jTextArea1.setRows(5);
-        jTextArea1.setText("Instructions:\n\nFirst press the \"...\" button under training\ndirectory. This will open up a dialog box where\nyou should pick the training directory you wish\nto use with one or more png images. More images\nwill provide better results.\n\nNext press the \"...\" button under original\nimage. This should be any single png file on\nyour system. This will be used when processing\nto show the current results.\n\nNow the buttons at the bottom should be\nenabled, use the \"train\" button to teach the\nneural network how to compress images. Use the\n\"process\" button to process the current image\nthrough the compression algorithm and display\nthe output. Use the \"stop\" button to stop\ntraining premturely.");
-        jTextArea1.setWrapStyleWord(true);
-        jScrollPane1.setViewportView(jTextArea1);
+        this.jTextArea1.setColumns(20);
+        this.jTextArea1.setEditable(false);
+        this.jTextArea1.setRows(5);
+        this.jTextArea1.setText("Instructions:\n\nFirst press the \"...\" button under training\ndirectory. This will open up a dialog box where\nyou should pick the training directory you wish\nto use with one or more png images. More images\nwill provide better results.\n\nNext press the \"...\" button under original\nimage. This should be any single png file on\nyour system. This will be used when processing\nto show the current results.\n\nNow the buttons at the bottom should be\nenabled, use the \"train\" button to teach the\nneural network how to compress images. Use the\n\"process\" button to process the current image\nthrough the compression algorithm and display\nthe output. Use the \"stop\" button to stop\ntraining premturely.");
+        this.jTextArea1.setWrapStyleWord(true);
+        this.jScrollPane1.setViewportView(this.jTextArea1);
 
-        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
-        getContentPane().setLayout(layout);
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this.getContentPane());
+        this.getContentPane().setLayout(layout);
         layout.setHorizontalGroup(
                                          layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                  .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
                                                                                                                .addContainerGap(195, Short.MAX_VALUE)
-                                                                                                               .addComponent(jButton1)
+                                                                                                               .addComponent(this.jButton1)
                                                                                                                .addGap(182, 182, 182))
                                                  .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
                                                                                                                .addGap(141, 141, 141)
                                                                                                                .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                                                                                                  .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
                                                                                                                                                                                                .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 39, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                                                                                                                               .addComponent(jLabel1)
+                                                                                                                                                                                               .addComponent(this.jLabel1)
                                                                                                                                                                                                .addGap(166, 166, 166))
-                                                                                                                                 .addComponent(jLabel2, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 273, Short.MAX_VALUE))
+                                                                                                                                 .addComponent(this.jLabel2, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 273, Short.MAX_VALUE))
                                                                                                                .addContainerGap())
                                                  .addGroup(layout.createSequentialGroup()
                                                                    .addContainerGap()
-                                                                   .addComponent(jScrollPane1, javax.swing.GroupLayout.DEFAULT_SIZE, 404, Short.MAX_VALUE)
+                                                                   .addComponent(this.jScrollPane1, javax.swing.GroupLayout.DEFAULT_SIZE, 404, Short.MAX_VALUE)
                                                                    .addContainerGap())
         );
         layout.setVerticalGroup(
                                        layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                .addGroup(layout.createSequentialGroup()
                                                                  .addContainerGap()
-                                                                 .addComponent(jLabel1)
+                                                                 .addComponent(this.jLabel1)
                                                                  .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                 .addComponent(jLabel2)
+                                                                 .addComponent(this.jLabel2)
                                                                  .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
-                                                                 .addComponent(jScrollPane1, javax.swing.GroupLayout.DEFAULT_SIZE, 391, Short.MAX_VALUE)
+                                                                 .addComponent(this.jScrollPane1, javax.swing.GroupLayout.DEFAULT_SIZE, 391, Short.MAX_VALUE)
                                                                  .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
-                                                                 .addComponent(jButton1)
+                                                                 .addComponent(this.jButton1)
                                                                  .addContainerGap())
         );
 
-        pack();
+        this.pack();
     }// </editor-fold>//GEN-END:initComponents
 
     private void jButton1ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_jButton1ActionPerformed
diff --git a/src/main/java/com/syncleus/dann/examples/nci/ui/ImagePanel.java b/src/main/java/com/syncleus/dann/examples/nci/ui/ImagePanel.java
index 3338b41..73d2882 100644
--- a/src/main/java/com/syncleus/dann/examples/nci/ui/ImagePanel.java
+++ b/src/main/java/com/syncleus/dann/examples/nci/ui/ImagePanel.java
@@ -24,7 +24,7 @@ public class ImagePanel extends javax.swing.JPanel {
     private Image image = null;
 
     public ImagePanel() {
-        initComponents();
+        this.initComponents();
     }
 
     public void setImage(final Image newImage) {
diff --git a/src/main/java/com/syncleus/dann/examples/nci/ui/NciDemo.java b/src/main/java/com/syncleus/dann/examples/nci/ui/NciDemo.java
index 96dcb95..3c3d398 100644
--- a/src/main/java/com/syncleus/dann/examples/nci/ui/NciDemo.java
+++ b/src/main/java/com/syncleus/dann/examples/nci/ui/NciDemo.java
@@ -81,7 +81,7 @@ public class NciDemo extends JFrame implements ActionListener, BrainListener {
             LOGGER.warn("Could not set the UI to native look and feel", caught);
         }
 
-        initComponents();
+        this.initComponents();
 
         this.add(this.originalImagePanel);
         final int currentX = this.separator.getX() + 5;
@@ -146,104 +146,104 @@ public class NciDemo extends JFrame implements ActionListener, BrainListener {
     // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
     private void initComponents() {
 
-        trainingDirectoryText = new javax.swing.JTextField();
-        trainingDirectorySelect = new javax.swing.JButton();
-        jLabel1 = new javax.swing.JLabel();
-        jLabel2 = new javax.swing.JLabel();
-        originalImageSelect = new javax.swing.JButton();
-        originalImageText = new javax.swing.JTextField();
-        trainButton = new javax.swing.JButton();
-        trainingCylcesInput = new javax.swing.JSpinner();
-        processButton = new javax.swing.JButton();
-        jLabel5 = new javax.swing.JLabel();
-        separator = new javax.swing.JSeparator();
-        statusLabel = new javax.swing.JLabel();
-        progress = new javax.swing.JProgressBar();
-        stopButton = new javax.swing.JButton();
-        jMenuBar2 = new javax.swing.JMenuBar();
-        fileMenu1 = new javax.swing.JMenu();
-        quitMenuItem1 = new javax.swing.JMenuItem();
-        toolsMenu = new javax.swing.JMenu();
-        brainViewMenu = new javax.swing.JMenuItem();
-        helpMenu1 = new javax.swing.JMenu();
-        aboutMenuItem1 = new javax.swing.JMenuItem();
-
-        setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
-        setTitle("NCI Demo");
-        setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
-
-        trainingDirectoryText.setEditable(false);
-
-        trainingDirectorySelect.setText("...");
-        trainingDirectorySelect.addActionListener(new java.awt.event.ActionListener() {
+        this.trainingDirectoryText = new javax.swing.JTextField();
+        this.trainingDirectorySelect = new javax.swing.JButton();
+        this.jLabel1 = new javax.swing.JLabel();
+        this.jLabel2 = new javax.swing.JLabel();
+        this.originalImageSelect = new javax.swing.JButton();
+        this.originalImageText = new javax.swing.JTextField();
+        this.trainButton = new javax.swing.JButton();
+        this.trainingCylcesInput = new javax.swing.JSpinner();
+        this.processButton = new javax.swing.JButton();
+        this.jLabel5 = new javax.swing.JLabel();
+        this.separator = new javax.swing.JSeparator();
+        this.statusLabel = new javax.swing.JLabel();
+        this.progress = new javax.swing.JProgressBar();
+        this.stopButton = new javax.swing.JButton();
+        this.jMenuBar2 = new javax.swing.JMenuBar();
+        this.fileMenu1 = new javax.swing.JMenu();
+        this.quitMenuItem1 = new javax.swing.JMenuItem();
+        this.toolsMenu = new javax.swing.JMenu();
+        this.brainViewMenu = new javax.swing.JMenuItem();
+        this.helpMenu1 = new javax.swing.JMenu();
+        this.aboutMenuItem1 = new javax.swing.JMenuItem();
+
+        this.setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
+        this.setTitle("NCI Demo");
+        this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
+
+        this.trainingDirectoryText.setEditable(false);
+
+        this.trainingDirectorySelect.setText("...");
+        this.trainingDirectorySelect.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
-                trainingDirectorySelectActionPerformed(evt);
+                NciDemo.this.trainingDirectorySelectActionPerformed(evt);
             }
         });
 
-        jLabel1.setText("Training Images");
+        this.jLabel1.setText("Training Images");
 
-        jLabel2.setText("Original Image(s)");
+        this.jLabel2.setText("Original Image(s)");
 
-        originalImageSelect.setText("...");
-        originalImageSelect.addActionListener(new java.awt.event.ActionListener() {
+        this.originalImageSelect.setText("...");
+        this.originalImageSelect.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
-                originalImageSelectActionPerformed(evt);
+                NciDemo.this.originalImageSelectActionPerformed(evt);
             }
         });
 
-        originalImageText.setEditable(false);
+        this.originalImageText.setEditable(false);
 
-        trainButton.setText("Train");
-        trainButton.setEnabled(false);
-        trainButton.addActionListener(new java.awt.event.ActionListener() {
+        this.trainButton.setText("Train");
+        this.trainButton.setEnabled(false);
+        this.trainButton.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
-                trainButtonActionPerformed(evt);
+                NciDemo.this.trainButtonActionPerformed(evt);
             }
         });
 
-        trainingCylcesInput.setModel(new javax.swing.SpinnerNumberModel(Integer.valueOf(10000), Integer.valueOf(1), null, Integer.valueOf(1000)));
+        this.trainingCylcesInput.setModel(new javax.swing.SpinnerNumberModel(Integer.valueOf(10000), Integer.valueOf(1), null, Integer.valueOf(1000)));
 
-        processButton.setText("Process");
-        processButton.setEnabled(false);
-        processButton.addActionListener(new java.awt.event.ActionListener() {
+        this.processButton.setText("Process");
+        this.processButton.setEnabled(false);
+        this.processButton.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
-                processButtonActionPerformed(evt);
+                NciDemo.this.processButtonActionPerformed(evt);
             }
         });
 
-        jLabel5.setText("Training Cycles");
+        this.jLabel5.setText("Training Cycles");
 
-        separator.setOrientation(javax.swing.SwingConstants.VERTICAL);
+        this.separator.setOrientation(javax.swing.SwingConstants.VERTICAL);
 
-        statusLabel.setText("Please make selections!");
+        this.statusLabel.setText("Please make selections!");
 
-        progress.setStringPainted(true);
+        this.progress.setStringPainted(true);
 
-        stopButton.setText("Stop");
-        stopButton.setEnabled(false);
-        stopButton.addActionListener(new java.awt.event.ActionListener() {
+        this.stopButton.setText("Stop");
+        this.stopButton.setEnabled(false);
+        this.stopButton.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
-                stopButtonActionPerformed(evt);
+                NciDemo.this.stopButtonActionPerformed(evt);
             }
         });
 
-        fileMenu1.setText("File");
+        this.fileMenu1.setText("File");
 
-        quitMenuItem1.setText("Quit");
-        quitMenuItem1.addMouseListener(new java.awt.event.MouseAdapter() {
+        this.quitMenuItem1.setText("Quit");
+        this.quitMenuItem1.addMouseListener(new java.awt.event.MouseAdapter() {
             public void mouseReleased(java.awt.event.MouseEvent evt) {
-                quitMenuItemMouseReleased(evt);
+                NciDemo.this.quitMenuItemMouseReleased(evt);
             }
         });
-        quitMenuItem1.addActionListener(new java.awt.event.ActionListener() {
+        this.quitMenuItem1.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
-                quitMenuItem1ActionPerformed(evt);
+                NciDemo.this.quitMenuItem1ActionPerformed(evt);
             }
         });
-        quitMenuItem1.addMenuKeyListener(new javax.swing.event.MenuKeyListener() {
+        this.quitMenuItem1.addMenuKeyListener(new javax.swing.event.MenuKeyListener() {
             public void menuKeyPressed(javax.swing.event.MenuKeyEvent evt) {
-                quitMenuItemMenuKeyPressed(evt);
+                NciDemo.this.quitMenuItemMenuKeyPressed(evt);
             }
 
             public void menuKeyReleased(javax.swing.event.MenuKeyEvent evt) {
@@ -252,22 +252,22 @@ public class NciDemo extends JFrame implements ActionListener, BrainListener {
             public void menuKeyTyped(javax.swing.event.MenuKeyEvent evt) {
             }
         });
-        fileMenu1.add(quitMenuItem1);
+        this.fileMenu1.add(this.quitMenuItem1);
 
-        jMenuBar2.add(fileMenu1);
+        this.jMenuBar2.add(this.fileMenu1);
 
-        toolsMenu.setText("Tools");
+        this.toolsMenu.setText("Tools");
 
-        brainViewMenu.setText("3D Brain View");
-        brainViewMenu.setEnabled(false);
-        brainViewMenu.addMouseListener(new java.awt.event.MouseAdapter() {
+        this.brainViewMenu.setText("3D Brain View");
+        this.brainViewMenu.setEnabled(false);
+        this.brainViewMenu.addMouseListener(new java.awt.event.MouseAdapter() {
             public void mouseReleased(java.awt.event.MouseEvent evt) {
-                brainViewMenuMouseReleased(evt);
+                NciDemo.this.brainViewMenuMouseReleased(evt);
             }
         });
-        brainViewMenu.addMenuKeyListener(new javax.swing.event.MenuKeyListener() {
+        this.brainViewMenu.addMenuKeyListener(new javax.swing.event.MenuKeyListener() {
             public void menuKeyPressed(javax.swing.event.MenuKeyEvent evt) {
-                brainViewMenuMenuKeyPressed(evt);
+                NciDemo.this.brainViewMenuMenuKeyPressed(evt);
             }
 
             public void menuKeyReleased(javax.swing.event.MenuKeyEvent evt) {
@@ -276,21 +276,21 @@ public class NciDemo extends JFrame implements ActionListener, BrainListener {
             public void menuKeyTyped(javax.swing.event.MenuKeyEvent evt) {
             }
         });
-        toolsMenu.add(brainViewMenu);
+        this.toolsMenu.add(this.brainViewMenu);
 
-        jMenuBar2.add(toolsMenu);
+        this.jMenuBar2.add(this.toolsMenu);
 
-        helpMenu1.setText("Help");
+        this.helpMenu1.setText("Help");
 
-        aboutMenuItem1.setText("About");
-        aboutMenuItem1.addMouseListener(new java.awt.event.MouseAdapter() {
+        this.aboutMenuItem1.setText("About");
+        this.aboutMenuItem1.addMouseListener(new java.awt.event.MouseAdapter() {
             public void mouseReleased(java.awt.event.MouseEvent evt) {
-                aboutMenuItemMouseReleased(evt);
+                NciDemo.this.aboutMenuItemMouseReleased(evt);
             }
         });
-        aboutMenuItem1.addMenuKeyListener(new javax.swing.event.MenuKeyListener() {
+        this.aboutMenuItem1.addMenuKeyListener(new javax.swing.event.MenuKeyListener() {
             public void menuKeyPressed(javax.swing.event.MenuKeyEvent evt) {
-                aboutMenuItemMenuKeyPressed(evt);
+                NciDemo.this.aboutMenuItemMenuKeyPressed(evt);
             }
 
             public void menuKeyReleased(javax.swing.event.MenuKeyEvent evt) {
@@ -299,47 +299,47 @@ public class NciDemo extends JFrame implements ActionListener, BrainListener {
             public void menuKeyTyped(javax.swing.event.MenuKeyEvent evt) {
             }
         });
-        helpMenu1.add(aboutMenuItem1);
+        this.helpMenu1.add(this.aboutMenuItem1);
 
-        jMenuBar2.add(helpMenu1);
+        this.jMenuBar2.add(this.helpMenu1);
 
-        setJMenuBar(jMenuBar2);
+        this.setJMenuBar(this.jMenuBar2);
 
-        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
-        getContentPane().setLayout(layout);
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this.getContentPane());
+        this.getContentPane().setLayout(layout);
         layout.setHorizontalGroup(
                                          layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                  .addGroup(layout.createSequentialGroup()
                                                                    .addContainerGap()
                                                                    .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                                                                                     .addComponent(jLabel2)
-                                                                                     .addComponent(jLabel1)
-                                                                                     .addComponent(statusLabel, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 244, Short.MAX_VALUE)
+                                                                                     .addComponent(this.jLabel2)
+                                                                                     .addComponent(this.jLabel1)
+                                                                                     .addComponent(this.statusLabel, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 244, Short.MAX_VALUE)
                                                                                      .addGroup(layout.createSequentialGroup()
                                                                                                        .addGap(27, 27, 27)
-                                                                                                       .addComponent(jLabel5)
+                                                                                                       .addComponent(this.jLabel5)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(trainingCylcesInput, javax.swing.GroupLayout.PREFERRED_SIZE, 70, javax.swing.GroupLayout.PREFERRED_SIZE))
+                                                                                                       .addComponent(this.trainingCylcesInput, javax.swing.GroupLayout.PREFERRED_SIZE, 70, javax.swing.GroupLayout.PREFERRED_SIZE))
                                                                                      .addGroup(layout.createSequentialGroup()
                                                                                                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING, false)
-                                                                                                                         .addComponent(trainingDirectoryText, javax.swing.GroupLayout.PREFERRED_SIZE, 215, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                                                         .addComponent(originalImageText, javax.swing.GroupLayout.DEFAULT_SIZE, 215, Short.MAX_VALUE))
+                                                                                                                         .addComponent(this.trainingDirectoryText, javax.swing.GroupLayout.PREFERRED_SIZE, 215, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                                         .addComponent(this.originalImageText, javax.swing.GroupLayout.DEFAULT_SIZE, 215, Short.MAX_VALUE))
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                                                                                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
-                                                                                                                         .addComponent(originalImageSelect, javax.swing.GroupLayout.PREFERRED_SIZE, 22, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                                                         .addComponent(trainingDirectorySelect, javax.swing.GroupLayout.PREFERRED_SIZE, 23, javax.swing.GroupLayout.PREFERRED_SIZE)))
+                                                                                                                         .addComponent(this.originalImageSelect, javax.swing.GroupLayout.PREFERRED_SIZE, 22, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                                         .addComponent(this.trainingDirectorySelect, javax.swing.GroupLayout.PREFERRED_SIZE, 23, javax.swing.GroupLayout.PREFERRED_SIZE)))
                                                                                      .addGroup(layout.createSequentialGroup()
                                                                                                        .addGap(12, 12, 12)
                                                                                                        .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
-                                                                                                                         .addComponent(progress, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
+                                                                                                                         .addComponent(this.progress, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
                                                                                                                          .addGroup(layout.createSequentialGroup()
-                                                                                                                                           .addComponent(trainButton)
+                                                                                                                                           .addComponent(this.trainButton)
                                                                                                                                            .addGap(18, 18, 18)
-                                                                                                                                           .addComponent(processButton)
+                                                                                                                                           .addComponent(this.processButton)
                                                                                                                                            .addGap(18, 18, 18)
-                                                                                                                                           .addComponent(stopButton)))))
+                                                                                                                                           .addComponent(this.stopButton)))))
                                                                    .addGap(18, 18, 18)
-                                                                   .addComponent(separator, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                   .addComponent(this.separator, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                    .addGap(10000, 10000, 10000))
         );
         layout.setVerticalGroup(
@@ -347,36 +347,36 @@ public class NciDemo extends JFrame implements ActionListener, BrainListener {
                                                .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
                                                                                                              .addContainerGap()
                                                                                                              .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
-                                                                                                                               .addComponent(separator, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 715, Short.MAX_VALUE)
+                                                                                                                               .addComponent(this.separator, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 715, Short.MAX_VALUE)
                                                                                                                                .addGroup(layout.createSequentialGroup()
-                                                                                                                                                 .addComponent(jLabel1)
+                                                                                                                                                 .addComponent(this.jLabel1)
                                                                                                                                                  .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                                                                                                                                  .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
-                                                                                                                                                                   .addComponent(trainingDirectoryText, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                                                                                                   .addComponent(trainingDirectorySelect))
+                                                                                                                                                                   .addComponent(this.trainingDirectoryText, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                                                                                   .addComponent(this.trainingDirectorySelect))
                                                                                                                                                  .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                                                                 .addComponent(jLabel2)
+                                                                                                                                                 .addComponent(this.jLabel2)
                                                                                                                                                  .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                                                                                                                                  .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
-                                                                                                                                                                   .addComponent(originalImageText, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                                                                                                   .addComponent(originalImageSelect))
+                                                                                                                                                                   .addComponent(this.originalImageText, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                                                                                   .addComponent(this.originalImageSelect))
                                                                                                                                                  .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 470, Short.MAX_VALUE)
-                                                                                                                                                 .addComponent(statusLabel)
+                                                                                                                                                 .addComponent(this.statusLabel)
                                                                                                                                                  .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                                                                 .addComponent(progress, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                                                                 .addComponent(this.progress, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                                                                  .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                                                                                                                                                  .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
-                                                                                                                                                                   .addComponent(jLabel5)
-                                                                                                                                                                   .addComponent(trainingCylcesInput, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                                                                                                                                                                   .addComponent(this.jLabel5)
+                                                                                                                                                                   .addComponent(this.trainingCylcesInput, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                                                                                                                                                  .addGap(26, 26, 26)
                                                                                                                                                  .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
-                                                                                                                                                                   .addComponent(processButton)
-                                                                                                                                                                   .addComponent(stopButton)
-                                                                                                                                                                   .addComponent(trainButton))))
+                                                                                                                                                                   .addComponent(this.processButton)
+                                                                                                                                                                   .addComponent(this.stopButton)
+                                                                                                                                                                   .addComponent(this.trainButton))))
                                                                                                              .addContainerGap())
         );
 
-        pack();
+        this.pack();
     }// </editor-fold>//GEN-END:initComponents
 
     private void quitMenuItemMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_quitMenuItemMouseReleased
@@ -394,11 +394,11 @@ public class NciDemo extends JFrame implements ActionListener, BrainListener {
     }//GEN-LAST:event_quitMenuItemMenuKeyPressed
 
     private void aboutMenuItemMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_aboutMenuItemMouseReleased
-        displayAbout();
+        this.displayAbout();
     }//GEN-LAST:event_aboutMenuItemMouseReleased
 
     private void aboutMenuItemMenuKeyPressed(javax.swing.event.MenuKeyEvent evt) {//GEN-FIRST:event_aboutMenuItemMenuKeyPressed
-        displayAbout();
+        this.displayAbout();
     }//GEN-LAST:event_aboutMenuItemMenuKeyPressed
 
     private void originalImageSelectActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_originalImageSelectActionPerformed
@@ -432,7 +432,7 @@ public class NciDemo extends JFrame implements ActionListener, BrainListener {
             this.trainingDirectoryText.setText(chooser.getSelectedFile().getAbsolutePath());
             this.trainingDirectory = chooser.getSelectedFile();
 
-            final File[] trainingFiles = trainingDirectory.listFiles(new PngFileFilter());
+            final File[] trainingFiles = this.trainingDirectory.listFiles(new PngFileFilter());
             if (trainingFiles.length <= 0) {
                 this.trainingDirectory = null;
                 this.trainingDirectoryText.setText("");
@@ -469,7 +469,7 @@ public class NciDemo extends JFrame implements ActionListener, BrainListener {
     }//GEN-LAST:event_trainButtonActionPerformed
 
     private void processButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_processButtonActionPerformed
-        if (this.processing || (finalImage == null) || (originalImage == null)) {
+        if (this.processing || (this.finalImage == null) || (this.originalImage == null)) {
             return;
         }
 
@@ -489,16 +489,16 @@ public class NciDemo extends JFrame implements ActionListener, BrainListener {
     }//GEN-LAST:event_stopButtonActionPerformed
 
     public void showBrainView() {
-        if (brainVisual == null) {
+        if (this.brainVisual == null) {
             final JDialog errorDialog = new JDialog();
-            errorDialog.add(errorPanel);
+            errorDialog.add(this.errorPanel);
             errorDialog.setVisible(true);
         }
         else {
             this.brainVisual.refresh();
 
             if (this.viewBrain == null) {
-                this.viewBrain = new ViewBrain(this, brainVisual);
+                this.viewBrain = new ViewBrain(this, this.brainVisual);
             }
 
             this.viewBrain.setVisible(true);
@@ -506,11 +506,11 @@ public class NciDemo extends JFrame implements ActionListener, BrainListener {
     }
 
     private void brainViewMenuMenuKeyPressed(javax.swing.event.MenuKeyEvent evt) {//GEN-FIRST:event_brainViewMenuMenuKeyPressed
-        showBrainView();
+        this.showBrainView();
     }//GEN-LAST:event_brainViewMenuMenuKeyPressed
 
     private void brainViewMenuMouseReleased(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_brainViewMenuMouseReleased
-        showBrainView();
+        this.showBrainView();
     }//GEN-LAST:event_brainViewMenuMouseReleased
 
     private void quitMenuItem1ActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_quitMenuItem1ActionPerformed
@@ -526,14 +526,14 @@ public class NciDemo extends JFrame implements ActionListener, BrainListener {
         }
 
         try {
-            originalImage = ImageIO.read(this.originalImageLocation);
+            this.originalImage = ImageIO.read(this.originalImageLocation);
         }
         catch (IOException caught) {
             LOGGER.warn("IO Exception when reading image", caught);
             return;
         }
         this.originalImagePanel.setImage(this.originalImage);
-        this.finalImage = new BufferedImage(originalImage.getWidth(), originalImage.getHeight(), BufferedImage.TYPE_INT_RGB);
+        this.finalImage = new BufferedImage(this.originalImage.getWidth(), this.originalImage.getHeight(), BufferedImage.TYPE_INT_RGB);
     }
 
     private void displayAbout() {
diff --git a/src/main/java/com/syncleus/dann/examples/nci/ui/ViewBrain.java b/src/main/java/com/syncleus/dann/examples/nci/ui/ViewBrain.java
index 29b6eb9..ae20fc9 100644
--- a/src/main/java/com/syncleus/dann/examples/nci/ui/ViewBrain.java
+++ b/src/main/java/com/syncleus/dann/examples/nci/ui/ViewBrain.java
@@ -33,7 +33,7 @@ public class ViewBrain extends JDialog implements ActionListener, KeyListener {
     public ViewBrain(final Frame parent, final HyperassociativeMapCanvas brainVisual) {
         super(parent, false);
 
-        initComponents();
+        this.initComponents();
 
         this.brainVisual = brainVisual;
 
@@ -92,10 +92,10 @@ public class ViewBrain extends JDialog implements ActionListener, KeyListener {
     // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
     private void initComponents() {
 
-        setResizable(false);
+        this.setResizable(false);
 
-        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
-        getContentPane().setLayout(layout);
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this.getContentPane());
+        this.getContentPane().setLayout(layout);
         layout.setHorizontalGroup(
                                          layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                  .addGap(0, 400, Short.MAX_VALUE)
@@ -105,7 +105,7 @@ public class ViewBrain extends JDialog implements ActionListener, KeyListener {
                                                .addGap(0, 300, Short.MAX_VALUE)
         );
 
-        pack();
+        this.pack();
     }// </editor-fold>//GEN-END:initComponents
     // Variables declaration - do not modify//GEN-BEGIN:variables
     // End of variables declaration//GEN-END:variables
diff --git a/src/main/java/com/syncleus/dann/examples/pathfind/AbstractGridCanvas.java b/src/main/java/com/syncleus/dann/examples/pathfind/AbstractGridCanvas.java
index e0417b8..7efc4dd 100644
--- a/src/main/java/com/syncleus/dann/examples/pathfind/AbstractGridCanvas.java
+++ b/src/main/java/com/syncleus/dann/examples/pathfind/AbstractGridCanvas.java
@@ -71,15 +71,15 @@ public abstract class AbstractGridCanvas extends JPanel implements MouseListener
         this.nodeSize = initialNodeSize;
         this.edgeSize = initialEdgeSize;
         this.path = initialPath;
-        this.pathThickness = Math.max(1, nodeSize / PATH_FRACTION);
-        this.selectedThickness = Math.max(1, Math.min(edgeSize, nodeSize) / BORDER_FRACTION);
+        this.pathThickness = Math.max(1, this.nodeSize / PATH_FRACTION);
+        this.selectedThickness = Math.max(1, Math.min(this.edgeSize, this.nodeSize) / BORDER_FRACTION);
 
-        final int preferredWidth = grid.getWidth() * nodeSize + (grid.getWidth() + 1) * edgeSize;
-        final int preferredHeight = grid.getHeight() * nodeSize + (grid.getHeight() + 1) * edgeSize;
-        setPreferredSize(new Dimension(preferredWidth, preferredHeight));
+        final int preferredWidth = this.grid.getWidth() * this.nodeSize + (this.grid.getWidth() + 1) * this.edgeSize;
+        final int preferredHeight = this.grid.getHeight() * this.nodeSize + (this.grid.getHeight() + 1) * this.edgeSize;
+        this.setPreferredSize(new Dimension(preferredWidth, preferredHeight));
 
-        addMouseListener(this);
-        addMouseMotionListener(this);
+        this.addMouseListener(this);
+        this.addMouseMotionListener(this);
     }
 
     @Override
@@ -90,76 +90,76 @@ public abstract class AbstractGridCanvas extends JPanel implements MouseListener
 
         int px = 0;
         int py = 0;
-        for (int y = 0; y < grid.getHeight(); y++) {
+        for (int y = 0; y < this.grid.getHeight(); y++) {
             px = 0;
-            for (int x = 0; x < grid.getWidth(); x++) {
-                final GridNode gridNode = grid.getNode(x, y);
+            for (int x = 0; x < this.grid.getWidth(); x++) {
+                final GridNode gridNode = this.grid.getNode(x, y);
 
                 if (y != 0) {
-                    final GridNode toNode = grid.getNode(x, y - 1);
+                    final GridNode toNode = this.grid.getNode(x, y - 1);
 
                     //draw filled rect for edge
-                    final WeightedBidirectedEdge<GridNode> upEdge = grid.getEdgeBetween(x, y, x, y - 1);
-                    graphics2D.setColor(getEdgeColor(upEdge));
-                    graphics2D.fillRect(px + edgeSize, py, nodeSize, edgeSize);
+                    final WeightedBidirectedEdge<GridNode> upEdge = this.grid.getEdgeBetween(x, y, x, y - 1);
+                    graphics2D.setColor(this.getEdgeColor(upEdge));
+                    graphics2D.fillRect(px + this.edgeSize, py, this.nodeSize, this.edgeSize);
 
-                    if ((touchedEdge != null) && (touchedEdge.getRightNode() == gridNode) && (touchedEdge.getLeftNode() == toNode)) {
+                    if ((this.touchedEdge != null) && (this.touchedEdge.getRightNode() == gridNode) && (this.touchedEdge.getLeftNode() == toNode)) {
                         //draw border of selected edge
-                        graphics2D.setStroke(new BasicStroke(selectedThickness));
+                        graphics2D.setStroke(new BasicStroke(this.selectedThickness));
                         graphics2D.setColor(/*getTouchedNodeBorderColor()*/Color.ORANGE);
-                        graphics2D.drawRect(px + edgeSize, py, nodeSize, edgeSize);
+                        graphics2D.drawRect(px + this.edgeSize, py, this.nodeSize, this.edgeSize);
                     }
                 }
 
                 if (x != 0) {
-                    final GridNode toNode = grid.getNode(x - 1, y);
+                    final GridNode toNode = this.grid.getNode(x - 1, y);
 
                     //draw filled rect for edge
-                    final WeightedBidirectedEdge<GridNode> rightEdge = grid.getEdgeBetween(x, y, x - 1, y);
-                    graphics2D.setColor(getEdgeColor(rightEdge));
-                    graphics2D.fillRect(px, py + edgeSize, edgeSize, nodeSize);
+                    final WeightedBidirectedEdge<GridNode> rightEdge = this.grid.getEdgeBetween(x, y, x - 1, y);
+                    graphics2D.setColor(this.getEdgeColor(rightEdge));
+                    graphics2D.fillRect(px, py + this.edgeSize, this.edgeSize, this.nodeSize);
 
-                    if ((touchedEdge != null) && (touchedEdge.getRightNode() == gridNode) && (touchedEdge.getLeftNode() == toNode)) {
+                    if ((this.touchedEdge != null) && (this.touchedEdge.getRightNode() == gridNode) && (this.touchedEdge.getLeftNode() == toNode)) {
                         //draw border of selected edge
-                        graphics2D.setStroke(new BasicStroke(selectedThickness));
+                        graphics2D.setStroke(new BasicStroke(this.selectedThickness));
                         graphics2D.setColor(/*getTouchedNodeBorderColor()*/Color.ORANGE);
-                        graphics2D.drawRect(px, py + edgeSize, edgeSize, nodeSize);
+                        graphics2D.drawRect(px, py + this.edgeSize, this.edgeSize, this.nodeSize);
                     }
                 }
 
-                graphics2D.setColor(getNodeColor(gridNode));
-                graphics2D.fillRect(px + edgeSize, py + edgeSize, nodeSize, nodeSize);
+                graphics2D.setColor(this.getNodeColor(gridNode));
+                graphics2D.fillRect(px + this.edgeSize, py + this.edgeSize, this.nodeSize, this.nodeSize);
 
-                if (gridNode == touchedNode) {
-                    graphics2D.setStroke(new BasicStroke(selectedThickness));
+                if (gridNode == this.touchedNode) {
+                    graphics2D.setStroke(new BasicStroke(this.selectedThickness));
                     graphics2D.setColor(/*getTouchedNodeBorderColor()*/Color.ORANGE);
-                    graphics2D.drawRect(px + edgeSize, py + edgeSize, nodeSize, nodeSize);
+                    graphics2D.drawRect(px + this.edgeSize, py + this.edgeSize, this.nodeSize, this.nodeSize);
                 }
 
-                px += nodeSize + edgeSize;
+                px += this.nodeSize + this.edgeSize;
             }
-            py += nodeSize + edgeSize;
+            py += this.nodeSize + this.edgeSize;
         }
 
-        if (path != null) {
+        if (this.path != null) {
             graphics2D.setColor(PATH_COLOR);
 
-            graphics2D.setStroke(new BasicStroke(pathThickness, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND));
+            graphics2D.setStroke(new BasicStroke(this.pathThickness, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND));
 
-            final int centerOffset = (edgeSize + nodeSize / 2);
+            final int centerOffset = (this.edgeSize + this.nodeSize / 2);
 
-            for (BidirectedEdge<GridNode> edge : path) {
+            for (BidirectedEdge<GridNode> edge : this.path) {
                 final int lastX = edge.getLeftNode().getX();
                 final int lastY = edge.getLeftNode().getY();
 
                 final int curX = edge.getRightNode().getX();
                 final int curY = edge.getRightNode().getY();
 
-                final int curPX = getNodePosition(curX) + centerOffset;
-                final int curPY = getNodePosition(curY) + centerOffset;
+                final int curPX = this.getNodePosition(curX) + centerOffset;
+                final int curPY = this.getNodePosition(curY) + centerOffset;
 
-                final int lastPX = getNodePosition(lastX) + centerOffset;
-                final int lastPY = getNodePosition(lastY) + centerOffset;
+                final int lastPX = this.getNodePosition(lastX) + centerOffset;
+                final int lastPY = this.getNodePosition(lastY) + centerOffset;
 
                 graphics2D.drawLine(lastPX, lastPY, curPX, curPY);
             }
@@ -189,7 +189,7 @@ public abstract class AbstractGridCanvas extends JPanel implements MouseListener
      * @return pixel coordinate of a given grid position, which may be outside of the grid's bounds
      */
     private int getNodePosition(final int coordinate) {
-        return coordinate * (nodeSize + edgeSize);
+        return coordinate * (this.nodeSize + this.edgeSize);
     }
 
     /**
@@ -199,7 +199,7 @@ public abstract class AbstractGridCanvas extends JPanel implements MouseListener
      * @return grid coordinate of a given pixel position, which may be outside of the grid's bounds
      */
     protected int getNodePositionPixel(final int x) {
-        return (int) Math.floor(((float) x) / ((float) (nodeSize + edgeSize)));
+        return (int) Math.floor(((float) x) / ((float) (this.nodeSize + this.edgeSize)));
     }
 
     /**
@@ -210,38 +210,38 @@ public abstract class AbstractGridCanvas extends JPanel implements MouseListener
      * @return the edge corresponding to pixel (px, py), or null if no edge was drawn there
      */
     public SimpleWeightedUndirectedEdge<GridNode> getTouchedEdge(final int px, final int py) {
-        final int nx = getNodePositionPixel(px);
-        final int ny = getNodePositionPixel(py);
+        final int nx = this.getNodePositionPixel(px);
+        final int ny = this.getNodePositionPixel(py);
 
-        if (nx * (nodeSize + edgeSize) > px + edgeSize) {
+        if (nx * (this.nodeSize + this.edgeSize) > px + this.edgeSize) {
             return null;
         }
 
-        if (ny * (nodeSize + edgeSize) > py + edgeSize) {
+        if (ny * (this.nodeSize + this.edgeSize) > py + this.edgeSize) {
             return null;
         }
 
-        if (Math.abs((px - nx * (nodeSize + edgeSize)) - (py - ny * (nodeSize + edgeSize))) < edgeSize) {
+        if (Math.abs((px - nx * (this.nodeSize + this.edgeSize)) - (py - ny * (this.nodeSize + this.edgeSize))) < this.edgeSize) {
             return null;
         }
 
-        final boolean upOrLeft = (px - nx * (nodeSize + edgeSize) > py - ny * (nodeSize + edgeSize)) ? true : false;
+        final boolean upOrLeft = (px - nx * (this.nodeSize + this.edgeSize) > py - ny * (this.nodeSize + this.edgeSize)) ? true : false;
 
         if ((nx >= (upOrLeft ? 0 : 1)) && (ny >= (!upOrLeft ? 0 : 1))
-                    && (nx < grid.getWidth()) && (ny < grid.getHeight())) {
+                    && (nx < this.grid.getWidth()) && (ny < this.grid.getHeight())) {
             final List<SimpleWeightedUndirectedEdge<GridNode>> thisEdges;
             final List<SimpleWeightedUndirectedEdge<GridNode>> otherEdges;
-            thisEdges = new LinkedList(grid.getAdjacentEdges(grid.getNode(nx, ny)));
+            thisEdges = new LinkedList(this.grid.getAdjacentEdges(this.grid.getNode(nx, ny)));
             //System.err.println(nx + " " + ny + " : " + thisEdges);
 
             if (upOrLeft) {
                 //up
-                otherEdges = new LinkedList(grid.getAdjacentEdges(grid.getNode(nx, ny - 1)));
+                otherEdges = new LinkedList(this.grid.getAdjacentEdges(this.grid.getNode(nx, ny - 1)));
                 //System.err.println(nx + " " + (ny-1) + " : " + otherEdges);
             }
             else {
                 //left
-                otherEdges = new LinkedList(grid.getAdjacentEdges(grid.getNode(nx - 1, ny)));
+                otherEdges = new LinkedList(this.grid.getAdjacentEdges(this.grid.getNode(nx - 1, ny)));
                 //System.err.println((nx-1) + " " + ny + " : " + otherEdges);
             }
 
@@ -272,18 +272,18 @@ public abstract class AbstractGridCanvas extends JPanel implements MouseListener
      * @return the node corresponding to pixel (px, py), or null if no node was drawn there
      */
     public GridNode getTouchedNode(final int px, final int py) {
-        final int nx = getNodePositionPixel(px);
-        final int ny = getNodePositionPixel(py);
+        final int nx = this.getNodePositionPixel(px);
+        final int ny = this.getNodePositionPixel(py);
 
-        if (nx * (nodeSize + edgeSize) + edgeSize > px) {
+        if (nx * (this.nodeSize + this.edgeSize) + this.edgeSize > px) {
             return null;
         }
-        if (ny * (nodeSize + edgeSize) + edgeSize > py) {
+        if (ny * (this.nodeSize + this.edgeSize) + this.edgeSize > py) {
             return null;
         }
 
-        if ((nx >= 0) && (ny >= 0) && (nx < grid.getWidth()) && (ny < grid.getHeight())) {
-            return grid.getNode(nx, ny);
+        if ((nx >= 0) && (ny >= 0) && (nx < this.grid.getWidth()) && (ny < this.grid.getHeight())) {
+            return this.grid.getNode(nx, ny);
         }
 
         return null;
@@ -316,7 +316,7 @@ public abstract class AbstractGridCanvas extends JPanel implements MouseListener
 
     @Override
     public void mouseDragged(final MouseEvent evt) {
-        updateMouseMoved(evt);
+        this.updateMouseMoved(evt);
     }
 
     /**
@@ -326,9 +326,9 @@ public abstract class AbstractGridCanvas extends JPanel implements MouseListener
      * @param evt mouse event to update according to
      */
     protected void updateMouseMoved(final MouseEvent evt) {
-        final GridNode tNode = getTouchedNode(evt.getX(), evt.getY());
+        final GridNode tNode = this.getTouchedNode(evt.getX(), evt.getY());
 
-        final SimpleWeightedUndirectedEdge<GridNode> tEdge = getTouchedEdge(evt.getX(), evt.getY());
+        final SimpleWeightedUndirectedEdge<GridNode> tEdge = this.getTouchedEdge(evt.getX(), evt.getY());
 
         this.touchedNode = null;
         this.touchedEdge = null;
@@ -342,12 +342,12 @@ public abstract class AbstractGridCanvas extends JPanel implements MouseListener
 
         //System.out.println("touchedNode: " + touchedNode + " , touchedEdge: " + touchedEdge);
 
-        repaint();
+        this.repaint();
     }
 
     @Override
     public void mouseMoved(final MouseEvent evt) {
-        updateMouseMoved(evt);
+        this.updateMouseMoved(evt);
     }
 
     /**
@@ -358,7 +358,7 @@ public abstract class AbstractGridCanvas extends JPanel implements MouseListener
      */
     void setPath(final List<SimpleWeightedUndirectedEdge<GridNode>> nextPath) {
         this.path = nextPath;
-        repaint();
+        this.repaint();
     }
 
     /**
@@ -367,7 +367,7 @@ public abstract class AbstractGridCanvas extends JPanel implements MouseListener
      * @return currently touched edge, or null if none is touched
      */
     public SimpleWeightedUndirectedEdge<GridNode> getTouchedEdge() {
-        return touchedEdge;
+        return this.touchedEdge;
     }
 
     /**
@@ -376,6 +376,6 @@ public abstract class AbstractGridCanvas extends JPanel implements MouseListener
      * @return currently touched GridNode, or null if none is touched
      */
     public GridNode getTouchedNode() {
-        return touchedNode;
+        return this.touchedNode;
     }
 }
diff --git a/src/main/java/com/syncleus/dann/examples/pathfind/PathFindDemoPanel.java b/src/main/java/com/syncleus/dann/examples/pathfind/PathFindDemoPanel.java
index 6b98608..64d4be4 100644
--- a/src/main/java/com/syncleus/dann/examples/pathfind/PathFindDemoPanel.java
+++ b/src/main/java/com/syncleus/dann/examples/pathfind/PathFindDemoPanel.java
@@ -63,7 +63,7 @@ public class PathFindDemoPanel extends JPanel {
     public PathFindDemoPanel(final int width) {
         super(new BorderLayout());
 
-        reinit(width);
+        this.reinit(width);
     }
 
     /**
@@ -134,24 +134,24 @@ public class PathFindDemoPanel extends JPanel {
      *                  (re-)initialize.
      */
     protected void reinit(final int nextWidth) {
-        removeAll();
+        this.removeAll();
 
         final int width = nextWidth;
         final int height = nextWidth;
 
         final double[][] gridWeights = new double[height][width];
-        grid = new WeightedGrid(gridWeights);
-        grid.setAll(INITIAL_GRID_WEIGHT);
+        this.grid = new WeightedGrid(gridWeights);
+        this.grid.setAll(INITIAL_GRID_WEIGHT);
 
-        startNode = grid.getNode(0, 0);
-        endNode = grid.getNode(width - 1, height - 1);
+        this.startNode = this.grid.getNode(0, 0);
+        this.endNode = this.grid.getNode(width - 1, height - 1);
 
-        updatePath();
+        this.updatePath();
 
-        controlPanel = new PathFindControlPanel(this);
-        add(controlPanel, BorderLayout.NORTH);
+        this.controlPanel = new PathFindControlPanel(this);
+        this.add(this.controlPanel, BorderLayout.NORTH);
 
-        gridCanvas = new AbstractGridCanvas(grid, path, DEFAULT_NODE_SIZE, DEFAULT_EDGE_SIZE) {
+        this.gridCanvas = new AbstractGridCanvas(PathFindDemoPanel.this.grid, PathFindDemoPanel.this.path, DEFAULT_NODE_SIZE, DEFAULT_EDGE_SIZE) {
             private boolean mouseDown = false;
 
             @Override
@@ -165,16 +165,16 @@ public class PathFindDemoPanel extends JPanel {
             }
 
             protected void paintCells() {
-                final int selectedIndex = controlPanel.getSelectedIndex();
+                final int selectedIndex = PathFindDemoPanel.this.controlPanel.getSelectedIndex();
 
-                if (mouseDown && (selectedIndex == 0)) {
-                    if (getTouchedNode() != null) {
-                        getTouchedNode().setWeight(paintWeight);
-                        updatePath();
+                if (this.mouseDown && (selectedIndex == 0)) {
+                    if (this.getTouchedNode() != null) {
+                        this.getTouchedNode().setWeight(PathFindDemoPanel.this.paintWeight);
+                        PathFindDemoPanel.this.updatePath();
                     }
-                    else if (getTouchedEdge() != null) {
-                        getTouchedEdge().setWeight(paintWeight);
-                        updatePath();
+                    else if (this.getTouchedEdge() != null) {
+                        this.getTouchedEdge().setWeight(PathFindDemoPanel.this.paintWeight);
+                        PathFindDemoPanel.this.updatePath();
                     }
                 }
 
@@ -195,44 +195,44 @@ public class PathFindDemoPanel extends JPanel {
             @Override
             public void mousePressed(final MouseEvent evt) {
                 super.mousePressed(evt);
-                mouseDown = true;
+                this.mouseDown = true;
             }
 
             @Override
             public void mouseReleased(final MouseEvent evt) {
                 super.mouseReleased(evt);
-                mouseDown = false;
+                this.mouseDown = false;
             }
 
             @Override
             public void mouseClicked(final MouseEvent evt) {
-                final int selectedIndex = controlPanel.getSelectedIndex();
+                final int selectedIndex = PathFindDemoPanel.this.controlPanel.getSelectedIndex();
 
-                final GridNode touchedNode = getTouchedNode();
+                final GridNode touchedNode = this.getTouchedNode();
 
                 //starting position
                 if ((selectedIndex == 1) && (touchedNode != null)) {
-                    if (getTouchedNode() != endNode) {
-                        startNode = touchedNode;
-                        updatePath();
+                    if (this.getTouchedNode() != PathFindDemoPanel.this.endNode) {
+                        PathFindDemoPanel.this.startNode = touchedNode;
+                        PathFindDemoPanel.this.updatePath();
                     }
                     else {
                         warnDifferentLocations();
                     }
                 } //ending position
                 else if ((selectedIndex == 2) && (touchedNode != null)) {
-                    if (touchedNode != startNode) {
-                        endNode = touchedNode;
-                        updatePath();
+                    if (touchedNode != PathFindDemoPanel.this.startNode) {
+                        PathFindDemoPanel.this.endNode = touchedNode;
+                        PathFindDemoPanel.this.updatePath();
                     }
                     else {
                         warnDifferentLocations();
                     }
                 } //paint the map
 
-                mouseDown = true;
+                this.mouseDown = true;
                 paintCells();
-                mouseDown = false;
+                this.mouseDown = false;
             }
 
             private void warnDifferentLocations() {
@@ -240,7 +240,7 @@ public class PathFindDemoPanel extends JPanel {
             }
         };
 
-        add(new JScrollPane(gridCanvas), BorderLayout.CENTER);
+        this.add(new JScrollPane(this.gridCanvas), BorderLayout.CENTER);
     }
 
     /**
@@ -248,10 +248,10 @@ public class PathFindDemoPanel extends JPanel {
      * AStarPathFinder parameters are changed.
      */
     protected void updatePath() {
-        final AstarPathFinder<GridNode, SimpleWeightedUndirectedEdge<GridNode>> pathFinder = new AstarPathFinder<GridNode, SimpleWeightedUndirectedEdge<GridNode>>(grid, new DistanceHeuristic());
-        path = pathFinder.getBestPath(startNode, endNode);
-        if (gridCanvas != null) {
-            gridCanvas.setPath(path);
+        final AstarPathFinder<GridNode, SimpleWeightedUndirectedEdge<GridNode>> pathFinder = new AstarPathFinder<GridNode, SimpleWeightedUndirectedEdge<GridNode>>(this.grid, new DistanceHeuristic());
+        this.path = pathFinder.getBestPath(this.startNode, this.endNode);
+        if (this.gridCanvas != null) {
+            this.gridCanvas.setPath(this.path);
         }
     }
 
@@ -286,7 +286,7 @@ public class PathFindDemoPanel extends JPanel {
         public void actionPerformed(final ActionEvent evt) {
             if (evt.getSource() instanceof PaintButton) {
                 final PaintButton button = (PaintButton) evt.getSource();
-                pathFindDemoPanel.paintWeight = button.getWeight();
+                this.pathFindDemoPanel.paintWeight = button.getWeight();
             }
         }
     }
@@ -298,21 +298,21 @@ public class PathFindDemoPanel extends JPanel {
         public PaintButton(final double drawWeight) {
             super("  ");
             this.weight = drawWeight;
-            setForeground(getColor(weight));
+            this.setForeground(getColor(this.weight));
         }
 
         @Override
         public void paint(final Graphics graphics) {
             super.paint(graphics);
             final Graphics2D graphics2D = (Graphics2D) graphics;
-            graphics2D.setColor(getColor(weight));
+            graphics2D.setColor(getColor(this.weight));
             graphics2D.fillRect(BUTTON_BORDER_SIZE, BUTTON_BORDER_SIZE,
-                                       getWidth() - BUTTON_BORDER_SIZE * 2,
-                                       getHeight() - BUTTON_BORDER_SIZE * 2);
+                                       this.getWidth() - BUTTON_BORDER_SIZE * 2,
+                                       this.getHeight() - BUTTON_BORDER_SIZE * 2);
         }
 
         public double getWeight() {
-            return weight;
+            return this.weight;
         }
     }
 
@@ -330,22 +330,22 @@ public class PathFindDemoPanel extends JPanel {
             for (double d : paintWeights) {
                 final PaintButton button = new PaintButton(d);
                 button.addActionListener(paintButtonActionListener);
-                paintButtonsGroup.add(button);
-                paintButtons.add(button);
-                add(button);
+                this.paintButtonsGroup.add(button);
+                this.paintButtons.add(button);
+                this.add(button);
             }
         }
 
         public List<PaintButton> getPaintButtons() {
-            return paintButtons;
+            return this.paintButtons;
         }
     }
 
     private static class PathFindControlPanel extends JTabbedPane {
         public PathFindControlPanel(final PathFindDemoPanel pathFindDemoPanel) {
-            addTab("Edit", new DrawingPanel(PAINT_WEIGHTS, pathFindDemoPanel));
-            addTab("Start Position", new JLabel("Click a start position"));
-            addTab("Stop Position", new JLabel("Click a stop position"));
+            this.addTab("Edit", new DrawingPanel(PAINT_WEIGHTS, pathFindDemoPanel));
+            this.addTab("Start Position", new JLabel("Click a start position"));
+            this.addTab("Stop Position", new JLabel("Click a stop position"));
             //addTab("Settings", new SettingsPanel());
         }
     }
diff --git a/src/main/java/com/syncleus/dann/examples/pathfind/WeightedGrid.java b/src/main/java/com/syncleus/dann/examples/pathfind/WeightedGrid.java
index 6c3e4d7..a7aff95 100644
--- a/src/main/java/com/syncleus/dann/examples/pathfind/WeightedGrid.java
+++ b/src/main/java/com/syncleus/dann/examples/pathfind/WeightedGrid.java
@@ -48,33 +48,33 @@ public class WeightedGrid extends AbstractBidirectedAdjacencyGraph<GridNode, Sim
         //construct nodes
         for (int y = 0; y < nodeWeights.length; y++) {
             for (int x = 0; x < nodeWeights[0].length; x++) {
-                nodes[y][x] = new GridNode(x, y, nodeWeights[y][x]);
-                this.nodeSet.add(nodes[y][x]);
-                this.neighborEdges.put(nodes[y][x], new HashSet<SimpleWeightedUndirectedEdge<GridNode>>());
-                this.neighborNodes.put(nodes[y][x], new HashSet<GridNode>());
+                this.nodes[y][x] = new GridNode(x, y, nodeWeights[y][x]);
+                this.nodeSet.add(this.nodes[y][x]);
+                this.neighborEdges.put(this.nodes[y][x], new HashSet<SimpleWeightedUndirectedEdge<GridNode>>());
+                this.neighborNodes.put(this.nodes[y][x], new HashSet<GridNode>());
             }
         }
 
         //connect nodes
-        for (int y = 0; y < nodes.length; y++) {
-            for (int x = 0; x < nodes[0].length; x++) {
+        for (int y = 0; y < this.nodes.length; y++) {
+            for (int x = 0; x < this.nodes[0].length; x++) {
                 //connect to the right
-                if (x < nodes[0].length - 1) {
-                    final SimpleWeightedUndirectedEdge<GridNode> newEdge = new SimpleWeightedUndirectedEdge<GridNode>(nodes[y][x], nodes[y][x + 1], 0);
+                if (x < this.nodes[0].length - 1) {
+                    final SimpleWeightedUndirectedEdge<GridNode> newEdge = new SimpleWeightedUndirectedEdge<GridNode>(this.nodes[y][x], this.nodes[y][x + 1], 0);
                     this.edges.add(newEdge);
-                    this.neighborEdges.get(nodes[y][x]).add(newEdge);
-                    this.neighborEdges.get(nodes[y][x + 1]).add(newEdge);
-                    this.neighborNodes.get(nodes[y][x]).add(nodes[y][x + 1]);
-                    this.neighborNodes.get(nodes[y][x + 1]).add(nodes[y][x]);
+                    this.neighborEdges.get(this.nodes[y][x]).add(newEdge);
+                    this.neighborEdges.get(this.nodes[y][x + 1]).add(newEdge);
+                    this.neighborNodes.get(this.nodes[y][x]).add(this.nodes[y][x + 1]);
+                    this.neighborNodes.get(this.nodes[y][x + 1]).add(this.nodes[y][x]);
                 }
                 //connect to the bottom
-                if (y < nodes.length - 1) {
-                    final SimpleWeightedUndirectedEdge<GridNode> newEdge = new SimpleWeightedUndirectedEdge<GridNode>(nodes[y][x], nodes[y + 1][x], 0);
+                if (y < this.nodes.length - 1) {
+                    final SimpleWeightedUndirectedEdge<GridNode> newEdge = new SimpleWeightedUndirectedEdge<GridNode>(this.nodes[y][x], this.nodes[y + 1][x], 0);
                     this.edges.add(newEdge);
-                    this.neighborEdges.get(nodes[y][x]).add(newEdge);
-                    this.neighborEdges.get(nodes[y + 1][x]).add(newEdge);
-                    this.neighborNodes.get(nodes[y][x]).add(nodes[y + 1][x]);
-                    this.neighborNodes.get(nodes[y + 1][x]).add(nodes[y][x]);
+                    this.neighborEdges.get(this.nodes[y][x]).add(newEdge);
+                    this.neighborEdges.get(this.nodes[y + 1][x]).add(newEdge);
+                    this.neighborNodes.get(this.nodes[y][x]).add(this.nodes[y + 1][x]);
+                    this.neighborNodes.get(this.nodes[y + 1][x]).add(this.nodes[y][x]);
                 }
             }
         }
@@ -86,7 +86,7 @@ public class WeightedGrid extends AbstractBidirectedAdjacencyGraph<GridNode, Sim
      * @return the width of the grid (number of nodes horizontal)
      */
     public int getWidth() {
-        return nodes[0].length;
+        return this.nodes[0].length;
     }
 
     /**
@@ -95,7 +95,7 @@ public class WeightedGrid extends AbstractBidirectedAdjacencyGraph<GridNode, Sim
      * @return the height of the grid (number of nodes vertical)
      */
     public int getHeight() {
-        return nodes.length;
+        return this.nodes.length;
     }
 
     /**
@@ -106,7 +106,7 @@ public class WeightedGrid extends AbstractBidirectedAdjacencyGraph<GridNode, Sim
      * @return the node at (x,y) or null if non-existent
      */
     public GridNode getNode(final int x, final int y) {
-        if ((x >= nodes[0].length) || (y >= nodes.length)) {
+        if ((x >= this.nodes[0].length) || (y >= this.nodes.length)) {
             throw new IllegalArgumentException("coordinates are out of bounds");
         }
         return this.nodes[y][x];
@@ -235,10 +235,10 @@ public class WeightedGrid extends AbstractBidirectedAdjacencyGraph<GridNode, Sim
      * @param weight the weight value to set
      */
     public void setAll(final double weight) {
-        for (GridNode gn : getNodes()) {
+        for (GridNode gn : this.getNodes()) {
             gn.setWeight(weight);
         }
-        for (SimpleWeightedUndirectedEdge wbe : getEdges()) {
+        for (SimpleWeightedUndirectedEdge wbe : this.getEdges()) {
             wbe.setWeight(weight);
         }
     }
@@ -259,8 +259,8 @@ public class WeightedGrid extends AbstractBidirectedAdjacencyGraph<GridNode, Sim
             return null;
         }
 
-        final GridNode gridNode = getNode(firstX, firstY);
-        for (SimpleWeightedUndirectedEdge<GridNode> edge : getAdjacentEdges(gridNode)) {
+        final GridNode gridNode = this.getNode(firstX, firstY);
+        for (SimpleWeightedUndirectedEdge<GridNode> edge : this.getAdjacentEdges(gridNode)) {
             final GridNode left = edge.getLeftNode();
             final GridNode right = edge.getRightNode();
             if ((left.getX() == secondX) && (left.getY() == secondY)) {
diff --git a/src/main/java/com/syncleus/dann/examples/test/Test3d.java b/src/main/java/com/syncleus/dann/examples/test/Test3d.java
index 8bec23a..57fff19 100644
--- a/src/main/java/com/syncleus/dann/examples/test/Test3d.java
+++ b/src/main/java/com/syncleus/dann/examples/test/Test3d.java
@@ -85,8 +85,8 @@ public class Test3d extends JFrame {
     private void initComponents() {
         this.drawingPanel = new javax.swing.JPanel();
 
-        setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
-        setTitle("Hello Universe");
+        this.setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
+        this.setTitle("Hello Universe");
         this.drawingPanel.setLayout(new java.awt.BorderLayout());
 
         this.drawingPanel.setPreferredSize(new java.awt.Dimension(250, 250));
diff --git a/src/main/java/com/syncleus/dann/examples/tsp/TravellingSalesmanDemo.java b/src/main/java/com/syncleus/dann/examples/tsp/TravellingSalesmanDemo.java
index f7d7507..a9cfe8f 100644
--- a/src/main/java/com/syncleus/dann/examples/tsp/TravellingSalesmanDemo.java
+++ b/src/main/java/com/syncleus/dann/examples/tsp/TravellingSalesmanDemo.java
@@ -79,7 +79,7 @@ public class TravellingSalesmanDemo extends JFrame implements ActionListener {
             LOGGER.warn("Could not set the UI to native look and feel", caught);
         }
 
-        initComponents();
+        this.initComponents();
 
         this.citiesSpinner.setModel(this.citiesModel);
         this.mutabilitySpinner.setModel(this.mutabilityModel);
@@ -200,106 +200,106 @@ public class TravellingSalesmanDemo extends JFrame implements ActionListener {
     // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
     private void initComponents() {
 
-        citiesLabel = new javax.swing.JLabel();
-        citiesSpinner = new javax.swing.JSpinner();
-        populationLabel = new javax.swing.JLabel();
-        populationSpinner = new javax.swing.JSpinner();
-        mutabilityLabel = new javax.swing.JLabel();
-        mutabilitySpinner = new javax.swing.JSpinner();
-        crossoverLabel = new javax.swing.JLabel();
-        crossoverSpinner = new javax.swing.JSpinner();
-        dieOffLabel = new javax.swing.JLabel();
-        dieOffSpinner = new javax.swing.JSpinner();
-        evolveDisplayButton = new javax.swing.JButton();
-        progressBar = new javax.swing.JProgressBar();
-        generationsLabel = new javax.swing.JLabel();
-        generationsSpinner = new javax.swing.JSpinner();
-        menuBar = new javax.swing.JMenuBar();
-        fileMenuItem = new javax.swing.JMenu();
-        quitMenuItem = new javax.swing.JMenuItem();
-        helpMenuItem = new javax.swing.JMenu();
-        aboutMenuItem = new javax.swing.JMenuItem();
-
-        setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
-        setTitle("Travelling Salesman Demo");
-
-        citiesLabel.setText("Cities:");
-
-        populationLabel.setText("Population:");
-
-        mutabilityLabel.setText("Mutability:");
-
-        crossoverLabel.setText("Crossover:");
-
-        dieOffLabel.setText("Die Off:");
-
-        evolveDisplayButton.setText("Evolve & Display");
-        evolveDisplayButton.addActionListener(new java.awt.event.ActionListener() {
+        this.citiesLabel = new javax.swing.JLabel();
+        this.citiesSpinner = new javax.swing.JSpinner();
+        this.populationLabel = new javax.swing.JLabel();
+        this.populationSpinner = new javax.swing.JSpinner();
+        this.mutabilityLabel = new javax.swing.JLabel();
+        this.mutabilitySpinner = new javax.swing.JSpinner();
+        this.crossoverLabel = new javax.swing.JLabel();
+        this.crossoverSpinner = new javax.swing.JSpinner();
+        this.dieOffLabel = new javax.swing.JLabel();
+        this.dieOffSpinner = new javax.swing.JSpinner();
+        this.evolveDisplayButton = new javax.swing.JButton();
+        this.progressBar = new javax.swing.JProgressBar();
+        this.generationsLabel = new javax.swing.JLabel();
+        this.generationsSpinner = new javax.swing.JSpinner();
+        this.menuBar = new javax.swing.JMenuBar();
+        this.fileMenuItem = new javax.swing.JMenu();
+        this.quitMenuItem = new javax.swing.JMenuItem();
+        this.helpMenuItem = new javax.swing.JMenu();
+        this.aboutMenuItem = new javax.swing.JMenuItem();
+
+        this.setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
+        this.setTitle("Travelling Salesman Demo");
+
+        this.citiesLabel.setText("Cities:");
+
+        this.populationLabel.setText("Population:");
+
+        this.mutabilityLabel.setText("Mutability:");
+
+        this.crossoverLabel.setText("Crossover:");
+
+        this.dieOffLabel.setText("Die Off:");
+
+        this.evolveDisplayButton.setText("Evolve & Display");
+        this.evolveDisplayButton.addActionListener(new java.awt.event.ActionListener() {
             public void actionPerformed(java.awt.event.ActionEvent evt) {
-                evolveDisplayButtonActionPerformed(evt);
+                TravellingSalesmanDemo.this.evolveDisplayButtonActionPerformed(evt);
             }
         });
 
-        progressBar.setStringPainted(true);
+        this.progressBar.setStringPainted(true);
 
-        generationsLabel.setText("Generations:");
+        this.generationsLabel.setText("Generations:");
 
-        fileMenuItem.setText("File");
+        this.fileMenuItem.setText("File");
 
-        quitMenuItem.setText("Quit");
-        quitMenuItem.addMouseListener(new java.awt.event.MouseAdapter() {
+        this.quitMenuItem.setText("Quit");
+        this.quitMenuItem.addMouseListener(new java.awt.event.MouseAdapter() {
             public void mouseReleased(java.awt.event.MouseEvent evt) {
-                quitMenuItemMouseReleased(evt);
+                TravellingSalesmanDemo.this.quitMenuItemMouseReleased(evt);
             }
         });
-        fileMenuItem.add(quitMenuItem);
+        this.fileMenuItem.add(this.quitMenuItem);
 
-        menuBar.add(fileMenuItem);
+        this.menuBar.add(this.fileMenuItem);
 
-        helpMenuItem.setText("Help");
+        this.helpMenuItem.setText("Help");
 
-        aboutMenuItem.setText("About");
-        helpMenuItem.add(aboutMenuItem);
+        this.aboutMenuItem.setText("About");
+        this.helpMenuItem.add(this.aboutMenuItem);
 
-        menuBar.add(helpMenuItem);
+        this.menuBar.add(this.helpMenuItem);
 
-        setJMenuBar(menuBar);
+        this.setJMenuBar(this.menuBar);
 
-        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
-        getContentPane().setLayout(layout);
+        javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this.getContentPane());
+        this.getContentPane().setLayout(layout);
         layout.setHorizontalGroup(
                                          layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                  .addGroup(layout.createSequentialGroup()
                                                                    .addContainerGap()
                                                                    .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                                                                                      .addGroup(layout.createSequentialGroup()
-                                                                                                       .addComponent(citiesLabel)
+                                                                                                       .addComponent(this.citiesLabel)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(citiesSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 40, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.citiesSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 40, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(populationLabel)
+                                                                                                       .addComponent(this.populationLabel)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(populationSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 51, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.populationSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 51, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(mutabilityLabel)
+                                                                                                       .addComponent(this.mutabilityLabel)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(mutabilitySpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 45, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.mutabilitySpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 45, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(crossoverLabel)
+                                                                                                       .addComponent(this.crossoverLabel)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(crossoverSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 47, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.crossoverSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 47, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(dieOffLabel)
+                                                                                                       .addComponent(this.dieOffLabel)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(dieOffSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 46, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                                       .addComponent(this.dieOffSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, 46, javax.swing.GroupLayout.PREFERRED_SIZE)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(generationsLabel)
+                                                                                                       .addComponent(this.generationsLabel)
                                                                                                        .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
-                                                                                                       .addComponent(generationsSpinner, javax.swing.GroupLayout.DEFAULT_SIZE, 62, Short.MAX_VALUE))
+                                                                                                       .addComponent(this.generationsSpinner, javax.swing.GroupLayout.DEFAULT_SIZE, 62, Short.MAX_VALUE))
                                                                                      .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
-                                                                                                                                                   .addComponent(progressBar, javax.swing.GroupLayout.DEFAULT_SIZE, 501, Short.MAX_VALUE)
+                                                                                                                                                   .addComponent(this.progressBar, javax.swing.GroupLayout.DEFAULT_SIZE, 501, Short.MAX_VALUE)
                                                                                                                                                    .addGap(10, 10, 10)
-                                                                                                                                                   .addComponent(evolveDisplayButton)))
+                                                                                                                                                   .addComponent(this.evolveDisplayButton)))
                                                                    .addContainerGap())
         );
         layout.setVerticalGroup(
@@ -307,26 +307,26 @@ public class TravellingSalesmanDemo extends JFrame implements ActionListener {
                                                .addGroup(layout.createSequentialGroup()
                                                                  .addContainerGap()
                                                                  .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
-                                                                                   .addComponent(citiesLabel)
-                                                                                   .addComponent(citiesSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                   .addComponent(populationLabel)
-                                                                                   .addComponent(populationSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                   .addComponent(mutabilityLabel)
-                                                                                   .addComponent(mutabilitySpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                   .addComponent(crossoverLabel)
-                                                                                   .addComponent(crossoverSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                   .addComponent(dieOffLabel)
-                                                                                   .addComponent(dieOffSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                   .addComponent(generationsLabel)
-                                                                                   .addComponent(generationsSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
+                                                                                   .addComponent(this.citiesLabel)
+                                                                                   .addComponent(this.citiesSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                   .addComponent(this.populationLabel)
+                                                                                   .addComponent(this.populationSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                   .addComponent(this.mutabilityLabel)
+                                                                                   .addComponent(this.mutabilitySpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                   .addComponent(this.crossoverLabel)
+                                                                                   .addComponent(this.crossoverSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                   .addComponent(this.dieOffLabel)
+                                                                                   .addComponent(this.dieOffSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                   .addComponent(this.generationsLabel)
+                                                                                   .addComponent(this.generationsSpinner, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
                                                                  .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
                                                                  .addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
-                                                                                   .addComponent(progressBar, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
-                                                                                   .addComponent(evolveDisplayButton, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
+                                                                                   .addComponent(this.progressBar, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
+                                                                                   .addComponent(this.evolveDisplayButton, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
                                                                  .addContainerGap(520, Short.MAX_VALUE))
         );
 
-        pack();
+        this.pack();
     }// </editor-fold>//GEN-END:initComponents
 
     private void quitMenuItemMouseReleased(java.awt.event.MouseEvent evt)//GEN-FIRST:event_quitMenuItemMouseReleased
diff --git a/src/main/java/com/syncleus/dann/examples/tsp/TravellingSalesmanPopulation.java b/src/main/java/com/syncleus/dann/examples/tsp/TravellingSalesmanPopulation.java
index f757a21..cafaf61 100644
--- a/src/main/java/com/syncleus/dann/examples/tsp/TravellingSalesmanPopulation.java
+++ b/src/main/java/com/syncleus/dann/examples/tsp/TravellingSalesmanPopulation.java
@@ -65,7 +65,7 @@ public class TravellingSalesmanPopulation extends AbstractGeneticAlgorithmPopula
         if (populationSize < TravellingSalesmanFitnessFunction.MINIMUM_CITIES)
             throw new IllegalArgumentException("populationSize must have atleast " + TravellingSalesmanFitnessFunction.MINIMUM_CITIES + " elements");
 
-        this.addAll(initialChromosomes(cities.length, populationSize));
+        this.addAll(initialChromosomes(this.cities.length, populationSize));
     }
 
     @Override
@@ -84,6 +84,6 @@ public class TravellingSalesmanPopulation extends AbstractGeneticAlgorithmPopula
     }
 
     public Vector[] getCities() {
-        return cities.clone();
+        return this.cities.clone();
     }
 }
diff --git a/src/test/java/com/syncleus/dann/examples/colormap/TestAboutDialog.java b/src/test/java/com/syncleus/dann/examples/colormap/TestAboutDialog.java
index 5fa031d..ab94dbd 100644
--- a/src/test/java/com/syncleus/dann/examples/colormap/TestAboutDialog.java
+++ b/src/test/java/com/syncleus/dann/examples/colormap/TestAboutDialog.java
@@ -40,19 +40,19 @@ public class TestAboutDialog {
             }
         });
 
-        aboutFixture = new DialogFixture(aboutDialog);
-        aboutFixture.show();
+        this.aboutFixture = new DialogFixture(aboutDialog);
+        this.aboutFixture.show();
     }
 
     @After
     public void tearDown() {
-        aboutFixture.cleanUp();
+        this.aboutFixture.cleanUp();
     }
 
     @Test
     public void testDisplays() {
-        aboutFixture.requireVisible();
-        aboutFixture.button("ok button").click();
-        aboutFixture.requireNotVisible();
+        this.aboutFixture.requireVisible();
+        this.aboutFixture.button("ok button").click();
+        this.aboutFixture.requireNotVisible();
     }
 }
diff --git a/src/test/java/com/syncleus/dann/examples/colormap/TestColorMapDemo.java b/src/test/java/com/syncleus/dann/examples/colormap/TestColorMapDemo.java
index 9d83dd1..9fb0909 100644
--- a/src/test/java/com/syncleus/dann/examples/colormap/TestColorMapDemo.java
+++ b/src/test/java/com/syncleus/dann/examples/colormap/TestColorMapDemo.java
@@ -42,121 +42,121 @@ public class TestColorMapDemo {
             }
         });
 
-        colorMapDemoFixture = new FrameFixture(colorMapDemo);
-        colorMapDemoFixture.show();
+        this.colorMapDemoFixture = new FrameFixture(colorMapDemo);
+        this.colorMapDemoFixture.show();
     }
 
     @After
     public void tearDown() {
-        colorMapDemoFixture.cleanUp();
+        this.colorMapDemoFixture.cleanUp();
     }
 
     @Test
     public void testComponents() {
-        colorMapDemoFixture.requireVisible();
+        this.colorMapDemoFixture.requireVisible();
 
         //test the spinner
         //spinners should take values of arbitrary granularity
-        colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("257");
-        colorMapDemoFixture.spinner("iterationsSpinner").requireValue(257);
-        colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("0.16492");
-        colorMapDemoFixture.spinner("learningRateSpinner").requireValue(0.16492);
+        this.colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("257");
+        this.colorMapDemoFixture.spinner("iterationsSpinner").requireValue(257);
+        this.colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("0.16492");
+        this.colorMapDemoFixture.spinner("learningRateSpinner").requireValue(0.16492);
         //lets try incrementing
-        colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("100");
-        colorMapDemoFixture.spinner("iterationsSpinner").requireValue(100);
-        colorMapDemoFixture.spinner("iterationsSpinner").increment(9);
-        colorMapDemoFixture.spinner("iterationsSpinner").requireValue(1000);
-        colorMapDemoFixture.spinner("iterationsSpinner").increment(100);
-        colorMapDemoFixture.spinner("iterationsSpinner").requireValue(10000);
-        colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("0.01");
-        colorMapDemoFixture.spinner("learningRateSpinner").increment(9);
-        double currentValue = Double.valueOf(colorMapDemoFixture.spinner("learningRateSpinner").text());
+        this.colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("100");
+        this.colorMapDemoFixture.spinner("iterationsSpinner").requireValue(100);
+        this.colorMapDemoFixture.spinner("iterationsSpinner").increment(9);
+        this.colorMapDemoFixture.spinner("iterationsSpinner").requireValue(1000);
+        this.colorMapDemoFixture.spinner("iterationsSpinner").increment(100);
+        this.colorMapDemoFixture.spinner("iterationsSpinner").requireValue(10000);
+        this.colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("0.01");
+        this.colorMapDemoFixture.spinner("learningRateSpinner").increment(9);
+        double currentValue = Double.valueOf(this.colorMapDemoFixture.spinner("learningRateSpinner").text());
         Assert.assertTrue("learning rate spinner did not increment properly", (currentValue - 0.1) < 0.00001);
-        colorMapDemoFixture.spinner("learningRateSpinner").increment(100);
-        currentValue = Double.valueOf(colorMapDemoFixture.spinner("learningRateSpinner").text());
+        this.colorMapDemoFixture.spinner("learningRateSpinner").increment(100);
+        currentValue = Double.valueOf(this.colorMapDemoFixture.spinner("learningRateSpinner").text());
         Assert.assertTrue("learning rate spinner did not increment properly", (currentValue - 1.0) < 0.001);
         //lets try decrementing
-        colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("10000");
-        colorMapDemoFixture.spinner("iterationsSpinner").requireValue(10000);
-        colorMapDemoFixture.spinner("iterationsSpinner").decrement(10);
-        colorMapDemoFixture.spinner("iterationsSpinner").requireValue(9000);
-        colorMapDemoFixture.spinner("iterationsSpinner").decrement(100);
-        colorMapDemoFixture.spinner("iterationsSpinner").requireValue(100);
-        colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("1.0");
-        colorMapDemoFixture.spinner("learningRateSpinner").decrement(10);
-        currentValue = Double.valueOf(colorMapDemoFixture.spinner("learningRateSpinner").text());
+        this.colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("10000");
+        this.colorMapDemoFixture.spinner("iterationsSpinner").requireValue(10000);
+        this.colorMapDemoFixture.spinner("iterationsSpinner").decrement(10);
+        this.colorMapDemoFixture.spinner("iterationsSpinner").requireValue(9000);
+        this.colorMapDemoFixture.spinner("iterationsSpinner").decrement(100);
+        this.colorMapDemoFixture.spinner("iterationsSpinner").requireValue(100);
+        this.colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("1.0");
+        this.colorMapDemoFixture.spinner("learningRateSpinner").decrement(10);
+        currentValue = Double.valueOf(this.colorMapDemoFixture.spinner("learningRateSpinner").text());
         Assert.assertTrue("learning rate spinner did not increment properly", (currentValue - 0.9) < 0.00001);
-        colorMapDemoFixture.spinner("learningRateSpinner").decrement(100);
-        currentValue = Double.valueOf(colorMapDemoFixture.spinner("learningRateSpinner").text());
+        this.colorMapDemoFixture.spinner("learningRateSpinner").decrement(100);
+        currentValue = Double.valueOf(this.colorMapDemoFixture.spinner("learningRateSpinner").text());
         Assert.assertTrue("learning rate spinner did not increment properly", (currentValue - 0.01) < 0.00001);
     }
 
     @Test(expected = UnexpectedException.class)
     public void testIterationsMinimum() {
-        colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("1000");
-        colorMapDemoFixture.spinner("iterationsSpinner").requireValue(1000);
-        colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("0");
+        this.colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("1000");
+        this.colorMapDemoFixture.spinner("iterationsSpinner").requireValue(1000);
+        this.colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("0");
     }
 
     @Test(expected = UnexpectedException.class)
     public void testIterationsMaximum() {
-        colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("1000");
-        colorMapDemoFixture.spinner("iterationsSpinner").requireValue(1000);
-        colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("100000");
+        this.colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("1000");
+        this.colorMapDemoFixture.spinner("iterationsSpinner").requireValue(1000);
+        this.colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("100000");
     }
 
     @Test(expected = UnexpectedException.class)
     public void testLearningRateMinimum() {
-        colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("0.5");
-        colorMapDemoFixture.spinner("learningRateSpinner").requireValue(0.5);
-        colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("0");
+        this.colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("0.5");
+        this.colorMapDemoFixture.spinner("learningRateSpinner").requireValue(0.5);
+        this.colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("0");
     }
 
     @Test(expected = UnexpectedException.class)
     public void testLearningRateMaximum() {
-        colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("0.5");
-        colorMapDemoFixture.spinner("learningRateSpinner").requireValue(0.5);
-        colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("1.001");
+        this.colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("0.5");
+        this.colorMapDemoFixture.spinner("learningRateSpinner").requireValue(0.5);
+        this.colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("1.001");
     }
 
     @Test
     public void testTrainingDisplay() {
-        colorMapDemoFixture.requireVisible();
+        this.colorMapDemoFixture.requireVisible();
 
         //train and display for various parameters
-        colorMapDemoFixture.button("trainDisplayButton").requireEnabled();
-
-        colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("10000");
-        colorMapDemoFixture.button("trainDisplayButton").click();
-        colorMapDemoFixture.button("trainDisplayButton").requireDisabled();
-        colorMapDemoFixture.button("trainDisplayButton").requireEnabled(Timeout.timeout(30000));
-
-        colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("5000");
-        colorMapDemoFixture.spinner("iterationsSpinner").requireValue(5000);
-        colorMapDemoFixture.button("trainDisplayButton").click();
-        colorMapDemoFixture.button("trainDisplayButton").requireDisabled();
-        colorMapDemoFixture.button("trainDisplayButton").requireEnabled(Timeout.timeout(30000));
-
-        colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("100");
-        colorMapDemoFixture.spinner("iterationsSpinner").requireValue(100);
-        colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("5000");
-        colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("0.1");
-        colorMapDemoFixture.spinner("learningRateSpinner").requireValue(0.1);
-        colorMapDemoFixture.comboBox("dimentionalityComboBox").selectItem("2D");
-        colorMapDemoFixture.comboBox("dimentionalityComboBox").requireSelection(1);
-        colorMapDemoFixture.button("trainDisplayButton").click();
-        colorMapDemoFixture.button("trainDisplayButton").requireDisabled();
-        colorMapDemoFixture.button("trainDisplayButton").requireEnabled(Timeout.timeout(30000));
-
-        colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("250");
-        colorMapDemoFixture.spinner("iterationsSpinner").requireValue(250);
-        colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("5000");
-        colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("1.0");
-        colorMapDemoFixture.spinner("learningRateSpinner").requireValue(1.0);
-        colorMapDemoFixture.comboBox("dimentionalityComboBox").selectItem("1D");
-        colorMapDemoFixture.comboBox("dimentionalityComboBox").requireSelection(0);
-        colorMapDemoFixture.button("trainDisplayButton").click();
-        colorMapDemoFixture.button("trainDisplayButton").requireDisabled();
-        colorMapDemoFixture.button("trainDisplayButton").requireEnabled(Timeout.timeout(30000));
+        this.colorMapDemoFixture.button("trainDisplayButton").requireEnabled();
+
+        this.colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("10000");
+        this.colorMapDemoFixture.button("trainDisplayButton").click();
+        this.colorMapDemoFixture.button("trainDisplayButton").requireDisabled();
+        this.colorMapDemoFixture.button("trainDisplayButton").requireEnabled(Timeout.timeout(30000));
+
+        this.colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("5000");
+        this.colorMapDemoFixture.spinner("iterationsSpinner").requireValue(5000);
+        this.colorMapDemoFixture.button("trainDisplayButton").click();
+        this.colorMapDemoFixture.button("trainDisplayButton").requireDisabled();
+        this.colorMapDemoFixture.button("trainDisplayButton").requireEnabled(Timeout.timeout(30000));
+
+        this.colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("100");
+        this.colorMapDemoFixture.spinner("iterationsSpinner").requireValue(100);
+        this.colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("5000");
+        this.colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("0.1");
+        this.colorMapDemoFixture.spinner("learningRateSpinner").requireValue(0.1);
+        this.colorMapDemoFixture.comboBox("dimentionalityComboBox").selectItem("2D");
+        this.colorMapDemoFixture.comboBox("dimentionalityComboBox").requireSelection(1);
+        this.colorMapDemoFixture.button("trainDisplayButton").click();
+        this.colorMapDemoFixture.button("trainDisplayButton").requireDisabled();
+        this.colorMapDemoFixture.button("trainDisplayButton").requireEnabled(Timeout.timeout(30000));
+
+        this.colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("250");
+        this.colorMapDemoFixture.spinner("iterationsSpinner").requireValue(250);
+        this.colorMapDemoFixture.spinner("iterationsSpinner").enterTextAndCommit("5000");
+        this.colorMapDemoFixture.spinner("learningRateSpinner").enterTextAndCommit("1.0");
+        this.colorMapDemoFixture.spinner("learningRateSpinner").requireValue(1.0);
+        this.colorMapDemoFixture.comboBox("dimentionalityComboBox").selectItem("1D");
+        this.colorMapDemoFixture.comboBox("dimentionalityComboBox").requireSelection(0);
+        this.colorMapDemoFixture.button("trainDisplayButton").click();
+        this.colorMapDemoFixture.button("trainDisplayButton").requireDisabled();
+        this.colorMapDemoFixture.button("trainDisplayButton").requireEnabled(Timeout.timeout(30000));
     }
 }
diff --git a/src/test/java/com/syncleus/dann/examples/fft/TestFftDemo.java b/src/test/java/com/syncleus/dann/examples/fft/TestFftDemo.java
index e04461e..9b154ad 100644
--- a/src/test/java/com/syncleus/dann/examples/fft/TestFftDemo.java
+++ b/src/test/java/com/syncleus/dann/examples/fft/TestFftDemo.java
@@ -40,29 +40,29 @@ public class TestFftDemo {
             }
         });
 
-        fftDemoFixture = new FrameFixture(fftDemo);
-        fftDemoFixture.show();
+        this.fftDemoFixture = new FrameFixture(fftDemo);
+        this.fftDemoFixture.show();
     }
 
     @After
     public void tearDown() {
-        fftDemoFixture.cleanUp();
+        this.fftDemoFixture.cleanUp();
     }
 
     @Test
     public void testComponents() {
-        fftDemoFixture.requireVisible();
+        this.fftDemoFixture.requireVisible();
 
         //start listening
-        fftDemoFixture.button("listenButton").click();
+        this.fftDemoFixture.button("listenButton").click();
 
         //check that its listening
-        fftDemoFixture.button("listenButton").requireText("Stop");
+        this.fftDemoFixture.button("listenButton").requireText("Stop");
 
         //stop listening
-        fftDemoFixture.button("listenButton").click();
+        this.fftDemoFixture.button("listenButton").click();
 
         //check if stopped
-        fftDemoFixture.button("listenButton").requireText("Listen");
+        this.fftDemoFixture.button("listenButton").requireText("Listen");
     }
 }
diff --git a/src/test/java/com/syncleus/dann/examples/nci/ui/TestAboutDialog.java b/src/test/java/com/syncleus/dann/examples/nci/ui/TestAboutDialog.java
index 0596116..9160086 100644
--- a/src/test/java/com/syncleus/dann/examples/nci/ui/TestAboutDialog.java
+++ b/src/test/java/com/syncleus/dann/examples/nci/ui/TestAboutDialog.java
@@ -41,19 +41,19 @@ public class TestAboutDialog {
             }
         });
 
-        aboutFixture = new DialogFixture(aboutDialog);
-        aboutFixture.show();
+        this.aboutFixture = new DialogFixture(aboutDialog);
+        this.aboutFixture.show();
     }
 
     @After
     public void tearDown() {
-        aboutFixture.cleanUp();
+        this.aboutFixture.cleanUp();
     }
 
     @Test
     public void testDisplays() {
-        aboutFixture.requireVisible();
-        aboutFixture.button("ok button").click();
-        aboutFixture.requireNotVisible();
+        this.aboutFixture.requireVisible();
+        this.aboutFixture.button("ok button").click();
+        this.aboutFixture.requireNotVisible();
     }
 }
-- 
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