diff --git a/Neocognitron.jar b/Neocognitron.jar
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diff --git a/README b/README
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+++ b/README
@@ -1,7 +1,22 @@
 
-The purpose of this repository is to keep track of my work on recreating the Neocognitron for one of my graduate classes. The Neocognitron is an artificial neural network which can be used to recognize handwritten characters.
+The Neocognitron is a neural network proposed by Fukushima; it is used for character recognition. This repository contains everything you need to experiment with a basic Neocognitron. This code was created for my final project in Pattern Recognition at RIT.
 
-For now, the code is a work in progress and as such, is poorly commented and does not completely work. I make no promises that I will finish this code! If you are interested in implementing a Neocognitron, feel free to email me if you have any questions.
 
+The organization of this project is as follows:
 
-Created by Nicholas J. Conn
\ No newline at end of file
+src     Contains all the source code for the project
+data    Contains all the training files needed to run the Neocognitron. Also contains previously saved Neocognitrons.
+doc     Complete javadoc for the entire project. Start with doc/index.html 
+
+
+To run the project, use the executable jar file, Neocognitron.jar.
+
+Use the following command to verify the saved Neocognitron.
+java -jar Neocognitron.jar verify
+
+Use the following command to generate your own Neocognitrons. To stop the program, press "ctrl-c".
+java -jar Neocognitron.jar
+
+
+
+Created by Nicholas J. Conn on 5-20-2012
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@@ -2,9 +2,9 @@
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+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
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+<meta name="date" content="2012-05-20">
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+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
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+<meta name="date" content="2012-05-20">
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+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
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+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
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+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
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+<meta name="date" content="2012-05-20">
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+<meta name="date" content="2012-05-20">
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@@ -75,11 +75,11 @@ <h2 class="title">V</h2>
 <dd>
 <div class="block">Initialize the vc-cell, with weight d.</div>
 </dd>
-<dt><span class="strong"><a href="../neocognitron/NeocognitronTrainer.html#verifyNeocognitron(neocognitron.Neocognitron)">verifyNeocognitron(Neocognitron)</a></span> - Method in class neocognitron.<a href="../neocognitron/NeocognitronTrainer.html" title="class in neocognitron">NeocognitronTrainer</a></dt>
+<dt><span class="strong"><a href="../neocognitron/NeocognitronTrainer.html#verifyNeocognitron(neocognitron.Neocognitron, boolean)">verifyNeocognitron(Neocognitron, boolean)</a></span> - Method in class neocognitron.<a href="../neocognitron/NeocognitronTrainer.html" title="class in neocognitron">NeocognitronTrainer</a></dt>
 <dd>
 <div class="block">Calculate the error rate of a specific neocognitron.</div>
 </dd>
-<dt><span class="strong"><a href="../neocognitron/NeocognitronTrainer.html#verifyNeocognitron(neocognitron.Neocognitron, java.util.ArrayList)">verifyNeocognitron(Neocognitron, ArrayList&lt;double[][]&gt;)</a></span> - Method in class neocognitron.<a href="../neocognitron/NeocognitronTrainer.html" title="class in neocognitron">NeocognitronTrainer</a></dt>
+<dt><span class="strong"><a href="../neocognitron/NeocognitronTrainer.html#verifyNeocognitron(neocognitron.Neocognitron, java.util.ArrayList, boolean)">verifyNeocognitron(Neocognitron, ArrayList&lt;double[][]&gt;, boolean)</a></span> - Method in class neocognitron.<a href="../neocognitron/NeocognitronTrainer.html" title="class in neocognitron">NeocognitronTrainer</a></dt>
 <dd>
 <div class="block">Calculate the error rate of a specific neocognitron using a specific
  list of inputs.</div>
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+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
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+<meta name="date" content="2012-05-20">
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-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
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-<!-- Generated by javadoc on Sat May 19 22:25:26 EDT 2012 -->
+<!-- Generated by javadoc on Sun May 20 13:42:51 EDT 2012 -->
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+++ b/doc/neocognitron/CCell.html
@@ -2,9 +2,9 @@
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 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>CCell</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
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diff --git a/doc/neocognitron/CLayer.html b/doc/neocognitron/CLayer.html
index 2201538..8058140 100644
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 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
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 <title>CLayer</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
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index 2441396..c09d267 100644
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 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
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 <title>Location</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
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diff --git a/doc/neocognitron/Neocognitron.html b/doc/neocognitron/Neocognitron.html
index 206da00..e346b75 100644
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@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Neocognitron</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
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diff --git a/doc/neocognitron/NeocognitronStructure.html b/doc/neocognitron/NeocognitronStructure.html
index d9980fa..eadc974 100644
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 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>NeocognitronStructure</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
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diff --git a/doc/neocognitron/NeocognitronTrainer.html b/doc/neocognitron/NeocognitronTrainer.html
index ae19736..132be43 100644
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+++ b/doc/neocognitron/NeocognitronTrainer.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>NeocognitronTrainer</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 </head>
 <body>
@@ -156,16 +156,18 @@ <h3>Method Summary</h3>
 </tr>
 <tr class="altColor">
 <td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><strong><a href="../neocognitron/NeocognitronTrainer.html#verifyNeocognitron(neocognitron.Neocognitron)">verifyNeocognitron</a></strong>(<a href="../neocognitron/Neocognitron.html" title="class in neocognitron">Neocognitron</a>&nbsp;n)</code>
-<div class="block">Calculate the error rate of a specific neocognitron.</div>
+<td class="colLast"><code><strong><a href="../neocognitron/NeocognitronTrainer.html#verifyNeocognitron(neocognitron.Neocognitron, java.util.ArrayList, boolean)">verifyNeocognitron</a></strong>(<a href="../neocognitron/Neocognitron.html" title="class in neocognitron">Neocognitron</a>&nbsp;n,
+                  java.util.ArrayList&lt;double[][]&gt;&nbsp;t,
+                  boolean&nbsp;verbose)</code>
+<div class="block">Calculate the error rate of a specific neocognitron using a specific
+ list of inputs.</div>
 </td>
 </tr>
 <tr class="rowColor">
 <td class="colFirst"><code>double</code></td>
-<td class="colLast"><code><strong><a href="../neocognitron/NeocognitronTrainer.html#verifyNeocognitron(neocognitron.Neocognitron, java.util.ArrayList)">verifyNeocognitron</a></strong>(<a href="../neocognitron/Neocognitron.html" title="class in neocognitron">Neocognitron</a>&nbsp;n,
-                  java.util.ArrayList&lt;double[][]&gt;&nbsp;t)</code>
-<div class="block">Calculate the error rate of a specific neocognitron using a specific
- list of inputs.</div>
+<td class="colLast"><code><strong><a href="../neocognitron/NeocognitronTrainer.html#verifyNeocognitron(neocognitron.Neocognitron, boolean)">verifyNeocognitron</a></strong>(<a href="../neocognitron/Neocognitron.html" title="class in neocognitron">Neocognitron</a>&nbsp;n,
+                  boolean&nbsp;verbose)</code>
+<div class="block">Calculate the error rate of a specific neocognitron.</div>
 </td>
 </tr>
 <tr class="altColor">
@@ -257,29 +259,31 @@ <h4>getNeocognitron</h4>
 <dt><span class="strong">Returns:</span></dt><dd>Resulting Neocognitron.</dd></dl>
 </li>
 </ul>
-<a name="verifyNeocognitron(neocognitron.Neocognitron)">
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-<pre>public&nbsp;double&nbsp;verifyNeocognitron(<a href="../neocognitron/Neocognitron.html" title="class in neocognitron">Neocognitron</a>&nbsp;n)</pre>
+<pre>public&nbsp;double&nbsp;verifyNeocognitron(<a href="../neocognitron/Neocognitron.html" title="class in neocognitron">Neocognitron</a>&nbsp;n,
+                        boolean&nbsp;verbose)</pre>
 <div class="block">Calculate the error rate of a specific neocognitron.</div>
-<dl><dt><span class="strong">Parameters:</span></dt><dd><code>n</code> - The neocognitron under test.</dd>
+<dl><dt><span class="strong">Parameters:</span></dt><dd><code>n</code> - The neocognitron under test.</dd><dd><code>verbose</code> - Display each test on the console.</dd>
 <dt><span class="strong">Returns:</span></dt><dd>The resulting error rate.</dd></dl>
 </li>
 </ul>
-<a name="verifyNeocognitron(neocognitron.Neocognitron, java.util.ArrayList)">
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 <pre>public&nbsp;double&nbsp;verifyNeocognitron(<a href="../neocognitron/Neocognitron.html" title="class in neocognitron">Neocognitron</a>&nbsp;n,
-                        java.util.ArrayList&lt;double[][]&gt;&nbsp;t)</pre>
+                        java.util.ArrayList&lt;double[][]&gt;&nbsp;t,
+                        boolean&nbsp;verbose)</pre>
 <div class="block">Calculate the error rate of a specific neocognitron using a specific
  list of inputs.</div>
-<dl><dt><span class="strong">Parameters:</span></dt><dd><code>n</code> - The neocognitron under test</dd><dd><code>t</code> - The list of files used to verify the network</dd>
+<dl><dt><span class="strong">Parameters:</span></dt><dd><code>n</code> - The neocognitron under test</dd><dd><code>t</code> - The list of files used to verify the network</dd><dd><code>verbose</code> - Display each test on the console.</dd>
 <dt><span class="strong">Returns:</span></dt><dd>The resulting error rate</dd></dl>
 </li>
 </ul>
diff --git a/doc/neocognitron/OutputConnections.html b/doc/neocognitron/OutputConnections.html
index eaf9e04..7ee2627 100644
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-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>OutputConnections</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
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 <body>
diff --git a/doc/neocognitron/RunTest.html b/doc/neocognitron/RunTest.html
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 <title>RunTest</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
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diff --git a/doc/neocognitron/SCell.html b/doc/neocognitron/SCell.html
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 <title>SCell</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
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diff --git a/doc/neocognitron/SLayer.html b/doc/neocognitron/SLayer.html
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-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
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-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
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 <body>
diff --git a/doc/neocognitron/VCCell.html b/doc/neocognitron/VCCell.html
index 3cc6b6a..44f003d 100644
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@@ -2,9 +2,9 @@
 <!-- NewPage -->
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-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>VCCell</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
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 </head>
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diff --git a/doc/neocognitron/VSCell.html b/doc/neocognitron/VSCell.html
index 393a31a..7ac5abe 100644
--- a/doc/neocognitron/VSCell.html
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@@ -2,9 +2,9 @@
 <!-- NewPage -->
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 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>VSCell</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
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 <body>
diff --git a/doc/neocognitron/class-use/CCell.html b/doc/neocognitron/class-use/CCell.html
index 151038a..fbc096a 100644
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@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:26 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Uses of Class neocognitron.CCell</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
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 <body>
diff --git a/doc/neocognitron/class-use/CLayer.html b/doc/neocognitron/class-use/CLayer.html
index 559c8e0..6a9e987 100644
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@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:26 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Uses of Class neocognitron.CLayer</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
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@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:26 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Uses of Class neocognitron.Location</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/doc/neocognitron/class-use/Neocognitron.html b/doc/neocognitron/class-use/Neocognitron.html
index acab26b..5f97114 100644
--- a/doc/neocognitron/class-use/Neocognitron.html
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@@ -2,9 +2,9 @@
 <!-- NewPage -->
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-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:26 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Uses of Class neocognitron.Neocognitron</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
 </head>
 <body>
@@ -116,16 +116,18 @@ <h3>Uses of <a href="../../neocognitron/Neocognitron.html" title="class in neoco
 </tr>
 <tr class="rowColor">
 <td class="colFirst"><code>double</code></td>
-<td class="colLast"><span class="strong">NeocognitronTrainer.</span><code><strong><a href="../../neocognitron/NeocognitronTrainer.html#verifyNeocognitron(neocognitron.Neocognitron)">verifyNeocognitron</a></strong>(<a href="../../neocognitron/Neocognitron.html" title="class in neocognitron">Neocognitron</a>&nbsp;n)</code>
-<div class="block">Calculate the error rate of a specific neocognitron.</div>
+<td class="colLast"><span class="strong">NeocognitronTrainer.</span><code><strong><a href="../../neocognitron/NeocognitronTrainer.html#verifyNeocognitron(neocognitron.Neocognitron, java.util.ArrayList, boolean)">verifyNeocognitron</a></strong>(<a href="../../neocognitron/Neocognitron.html" title="class in neocognitron">Neocognitron</a>&nbsp;n,
+                  java.util.ArrayList&lt;double[][]&gt;&nbsp;t,
+                  boolean&nbsp;verbose)</code>
+<div class="block">Calculate the error rate of a specific neocognitron using a specific
+ list of inputs.</div>
 </td>
 </tr>
 <tr class="altColor">
 <td class="colFirst"><code>double</code></td>
-<td class="colLast"><span class="strong">NeocognitronTrainer.</span><code><strong><a href="../../neocognitron/NeocognitronTrainer.html#verifyNeocognitron(neocognitron.Neocognitron, java.util.ArrayList)">verifyNeocognitron</a></strong>(<a href="../../neocognitron/Neocognitron.html" title="class in neocognitron">Neocognitron</a>&nbsp;n,
-                  java.util.ArrayList&lt;double[][]&gt;&nbsp;t)</code>
-<div class="block">Calculate the error rate of a specific neocognitron using a specific
- list of inputs.</div>
+<td class="colLast"><span class="strong">NeocognitronTrainer.</span><code><strong><a href="../../neocognitron/NeocognitronTrainer.html#verifyNeocognitron(neocognitron.Neocognitron, boolean)">verifyNeocognitron</a></strong>(<a href="../../neocognitron/Neocognitron.html" title="class in neocognitron">Neocognitron</a>&nbsp;n,
+                  boolean&nbsp;verbose)</code>
+<div class="block">Calculate the error rate of a specific neocognitron.</div>
 </td>
 </tr>
 <tr class="rowColor">
diff --git a/doc/neocognitron/class-use/NeocognitronStructure.html b/doc/neocognitron/class-use/NeocognitronStructure.html
index 9b808dc..919a897 100644
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@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:26 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Uses of Class neocognitron.NeocognitronStructure</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
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 <body>
diff --git a/doc/neocognitron/class-use/NeocognitronTrainer.html b/doc/neocognitron/class-use/NeocognitronTrainer.html
index 66d3dc9..ecf9919 100644
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@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:26 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Uses of Class neocognitron.NeocognitronTrainer</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/doc/neocognitron/class-use/OutputConnections.html b/doc/neocognitron/class-use/OutputConnections.html
index 860c5a6..8f0f3e8 100644
--- a/doc/neocognitron/class-use/OutputConnections.html
+++ b/doc/neocognitron/class-use/OutputConnections.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:26 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Uses of Class neocognitron.OutputConnections</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/doc/neocognitron/class-use/RunTest.html b/doc/neocognitron/class-use/RunTest.html
index d1020ab..fd1a5c8 100644
--- a/doc/neocognitron/class-use/RunTest.html
+++ b/doc/neocognitron/class-use/RunTest.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:26 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Uses of Class neocognitron.RunTest</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/doc/neocognitron/class-use/SCell.html b/doc/neocognitron/class-use/SCell.html
index d826d00..1f8d711 100644
--- a/doc/neocognitron/class-use/SCell.html
+++ b/doc/neocognitron/class-use/SCell.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:26 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Uses of Class neocognitron.SCell</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/doc/neocognitron/class-use/SLayer.html b/doc/neocognitron/class-use/SLayer.html
index 12419da..e006683 100644
--- a/doc/neocognitron/class-use/SLayer.html
+++ b/doc/neocognitron/class-use/SLayer.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:26 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Uses of Class neocognitron.SLayer</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/doc/neocognitron/class-use/VCCell.html b/doc/neocognitron/class-use/VCCell.html
index e122968..c8d3689 100644
--- a/doc/neocognitron/class-use/VCCell.html
+++ b/doc/neocognitron/class-use/VCCell.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Uses of Class neocognitron.VCCell</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/doc/neocognitron/class-use/VSCell.html b/doc/neocognitron/class-use/VSCell.html
index af223fd..e72a172 100644
--- a/doc/neocognitron/class-use/VSCell.html
+++ b/doc/neocognitron/class-use/VSCell.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Uses of Class neocognitron.VSCell</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../../stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/doc/neocognitron/package-frame.html b/doc/neocognitron/package-frame.html
index 46721ff..f08e9b5 100644
--- a/doc/neocognitron/package-frame.html
+++ b/doc/neocognitron/package-frame.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>neocognitron</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/doc/neocognitron/package-summary.html b/doc/neocognitron/package-summary.html
index c951694..08c3e58 100644
--- a/doc/neocognitron/package-summary.html
+++ b/doc/neocognitron/package-summary.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>neocognitron</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/doc/neocognitron/package-tree.html b/doc/neocognitron/package-tree.html
index 9110064..66cdc98 100644
--- a/doc/neocognitron/package-tree.html
+++ b/doc/neocognitron/package-tree.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>neocognitron Class Hierarchy</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/doc/neocognitron/package-use.html b/doc/neocognitron/package-use.html
index 518c4db..faae68b 100644
--- a/doc/neocognitron/package-use.html
+++ b/doc/neocognitron/package-use.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:26 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Uses of Package neocognitron</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/doc/overview-tree.html b/doc/overview-tree.html
index 6e3cdbd..6311c2a 100644
--- a/doc/overview-tree.html
+++ b/doc/overview-tree.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:26 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Class Hierarchy</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/doc/serialized-form.html b/doc/serialized-form.html
index 3707472..76f0d1f 100644
--- a/doc/serialized-form.html
+++ b/doc/serialized-form.html
@@ -2,9 +2,9 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (version 1.7.0_04) on Sat May 19 22:25:25 EDT 2012 -->
+<!-- Generated by javadoc (version 1.7.0_04) on Sun May 20 13:42:51 EDT 2012 -->
 <title>Serialized Form</title>
-<meta name="date" content="2012-05-19">
+<meta name="date" content="2012-05-20">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 </head>
 <body>
diff --git a/src/neocognitron/NeocognitronStructure.java b/src/neocognitron/NeocognitronStructure.java
index 73d7e3d..39aa7ca 100644
--- a/src/neocognitron/NeocognitronStructure.java
+++ b/src/neocognitron/NeocognitronStructure.java
@@ -46,10 +46,10 @@ public class NeocognitronStructure implements Serializable {
 	public double alpha = Math.random()*.08+.42;
 
 	// Values used to determine c and d
-	double[] gamma = {0.11, 0.42, 0.06};
+//	double[] gamma = {0.11, 0.42, 0.06};
 //	double[] delta = {0.49, 0.87, 0.52};
 //	double[] delta_bar = {.39, .68, .39};
-//	double[] gamma = {Math.random(), Math.random(), Math.random()};
+	double[] gamma = {Math.random(), Math.random(), Math.random()};
 	double[] delta = {Math.random()*.2+.4, Math.random()*.75+.2, Math.random()*.3+.4};
 	double[] delta_bar = {Math.random(), Math.random(), Math.random()};
 	
@@ -74,7 +74,7 @@ public NeocognitronStructure() {
 	public void generateC() {
 		
 		// For first layer, depends on input
-		c[0] = generateMonotonic(Math.random()*.75, sWindowSize[0], 1, true);
+		c[0] = generateMonotonic(gamma[0], sWindowSize[0], 1, true);
 		for (int l = 1; l < numLayers; l++) {
 			c[l] = generateMonotonic(gamma[l], sWindowSize[l], numCPlanes[l-1], true);
 		}
diff --git a/src/neocognitron/NeocognitronTrainer.java b/src/neocognitron/NeocognitronTrainer.java
index 823becc..3f89b4f 100644
--- a/src/neocognitron/NeocognitronTrainer.java
+++ b/src/neocognitron/NeocognitronTrainer.java
@@ -1,6 +1,7 @@
 package neocognitron;
 
 import java.io.File;
+import java.text.DecimalFormat;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -20,6 +21,8 @@ public class NeocognitronTrainer {
 	// File to save the most successful neocognitron during training
 	File neoFile;
 
+	DecimalFormat df = new DecimalFormat("#.##");
+
 	/**
 	 * Initialize the neocognitron trainer with a set of input files, training
 	 * files, and the output file for the best neocognitron
@@ -96,9 +99,9 @@ public Neocognitron getNeocognitron(int trainingLoops) {
 			do {	// and while the training is not successful
 				output = runTrainingSet(trainingLoops);
 				count++;
-				System.out.print("Loop: " + count + "\t\tBest: " + bestError + "\t\tCurrent: " + errorRate + "\r");
+				System.out.print("Loop: " + count + "      Best: " + df.format(bestError) + "      Current: " + df.format(errorRate) + "\r");
 			} while(!verifyTraining(output));
-			errorRate = verifyNeocognitron(output,testInputs);
+			errorRate = verifyNeocognitron(output,testInputs, false);
 			if (errorRate < bestError) {
 				Neocognitron.SaveNeocognitron(output, neoFile);
 				bestError = errorRate;
@@ -112,21 +115,23 @@ public Neocognitron getNeocognitron(int trainingLoops) {
 	 * Calculate the error rate of a specific neocognitron.
 	 * 
 	 * @param n		The neocognitron under test.
+	 * @param verbose	Display each test on the console.
 	 * @return		The resulting error rate.
 	 */
-	public double verifyNeocognitron(Neocognitron n) {
-		return verifyNeocognitron(n, testInputs);
+	public double verifyNeocognitron(Neocognitron n, boolean verbose) {
+		return verifyNeocognitron(n, testInputs, verbose);
 	}
 
 	/**
 	 * Calculate the error rate of a specific neocognitron using a specific
 	 * list of inputs.
 	 * 
-	 * @param n		The neocognitron under test
-	 * @param t		The list of files used to verify the network
-	 * @return		The resulting error rate
+	 * @param n			The neocognitron under test
+	 * @param t			The list of files used to verify the network
+	 * @param verbose	Display each test on the console.
+	 * @return			The resulting error rate
 	 */
-	public double verifyNeocognitron(Neocognitron n, ArrayList<double[][]> t) {
+	public double verifyNeocognitron(Neocognitron n, ArrayList<double[][]> t, boolean verbose) {
 		if (t.size() % inputs.size() != 0) {
 			throw new IllegalArgumentException();
 		}
@@ -134,12 +139,14 @@ public double verifyNeocognitron(Neocognitron n, ArrayList<double[][]> t) {
 		double output = 0;
 		
 		int trainingOutput, testOutput;
-		System.out.println("Training vs Test");
+		if (verbose)
+			System.out.println("Training vs Test");
 		for (int i = 0; i < t.size(); i++) {
 			trainingOutput = n.propagate(inputs.get(i%inputs.size()), false);
 			testOutput = n.propagate(t.get(i), false);
 
-			System.out.println(trainingOutput + "\t" + testOutput);
+			if (verbose)
+				System.out.println(trainingOutput + "\t" + testOutput);
 			
 			if (trainingOutput !=  testOutput)
 				output++;
diff --git a/src/neocognitron/RunTest.java b/src/neocognitron/RunTest.java
index eff1128..240e8d5 100644
--- a/src/neocognitron/RunTest.java
+++ b/src/neocognitron/RunTest.java
@@ -20,7 +20,11 @@ public static void main ( String[] args )
 	{
 		System.out.println("Starting Test!");
 
-		TrainerTest();
+		if (args.length != 0 && args[0].equals("verify")) {
+				TestBestSaved();
+		}
+		else
+			TrainerTest();
 	}
 	
 	/**
@@ -73,7 +77,7 @@ public static void TestBestSaved() {
 		}
 		
 		
-		File[] faFiles = new File("data/Saved Networks/30 Percent").listFiles();
+		File[] faFiles = new File("data/Saved Networks").listFiles();
 		for (File file : faFiles) {
 			int dotPosition = file.toString().lastIndexOf(".");
 			if (dotPosition != -1) {
@@ -83,7 +87,7 @@ public static void TestBestSaved() {
 			    	Neocognitron n = Neocognitron.OpenNeocognitron(file);
 			    	NeocognitronStructure s = n.getStructure();
 			    	NeocognitronTrainer trainer = new NeocognitronTrainer(inputs, testInputs,null);
-			    	double error = trainer.verifyNeocognitron(n);
+			    	double error = trainer.verifyNeocognitron(n,true);
 			    	System.out.println("Eror Rate: " + error);
 			    	System.out.println("Planes: " + s.numCPlanes[0]);
 			    	System.out.println("r values: " + OutputConnections.arrayToString(s.r) );
@@ -119,7 +123,7 @@ public static void TrainerTest() {
 			}
 		}
 		
-		files = new File[10];
+		files = new File[15];
 		files[0] = new File ("data/Training Images/0_01.bmp");
 		files[1] = new File ("data/Training Images/1_01.bmp");
 		files[2] = new File ("data/Training Images/2_01.bmp");
@@ -130,6 +134,11 @@ public static void TrainerTest() {
 		files[7] = new File ("data/Training Images/2_02.bmp");
 		files[8] = new File ("data/Training Images/3_02.bmp");
 		files[9] = new File ("data/Training Images/4_02.bmp");
+		files[10] = new File ("data/Training Images/0_03.bmp");
+		files[11] = new File ("data/Training Images/1_03.bmp");
+		files[12] = new File ("data/Training Images/2_03.bmp");
+		files[13] = new File ("data/Training Images/3_03.bmp");
+		files[14] = new File ("data/Training Images/4_03.bmp");
 		
 		ArrayList<double[][]> testInputs = new ArrayList<double[][]>();
 		for(int i = 0; i < files.length; i++ ) {
@@ -141,11 +150,11 @@ public static void TrainerTest() {
 			}
 		}
 
-		SimpleDateFormat dateFormat = new SimpleDateFormat("-yyyyMMdd-hhmm");		
+		SimpleDateFormat dateFormat = new SimpleDateFormat("-yyyyMMdd-hhmmssSS");		
 		NeocognitronTrainer trainer = new NeocognitronTrainer(inputs, testInputs, new File ("data/Saved Networks/BestNeocognitron" + dateFormat.format(new Date())+ ".neo"));
 		//Neocognitron n = trainer.getNeocognitron(20);
 		Neocognitron n = trainer.getNeocognitron((int)Math.round(Math.random()*15+5));
-		trainer.verifyNeocognitron(n, testInputs);
+		trainer.verifyNeocognitron(n, testInputs,false);
 	}
 	
 	/**
diff --git a/src/neocognitron/SLayer.java b/src/neocognitron/SLayer.java
index 176038e..89a4f15 100644
--- a/src/neocognitron/SLayer.java
+++ b/src/neocognitron/SLayer.java
@@ -89,7 +89,7 @@ public void InitializeA(int previousPlanes) {
 		for (int k = 0; k < planes; k++) {
 			for (int ck = 0; ck < previousPlanes; ck++) {
 				for (int w = 0; w < Math.pow(windowSize, 2); w++ ) {
-						a[k][ck][w] = Math.random()*.5;
+						a[k][ck][w] = Math.random()*.4;
 				}
 			}
 		}