Completed TM NuPIC identity test through RunLayer; TM re-write complete

Author: cogmission

Diff for: .classpath

@@ -17,6 +17,9 @@
 	<classpathentry kind="lib" path="libs/java-util-1.19.3.jar" sourcepath="/Users/cogmission/.m2/repository/com/cedarsoftware/java-util/1.19.3/java-util-1.19.3-sources.jar"/>
 	<classpathentry kind="lib" path="libs/objenesis-2.1.jar"/>
 	<classpathentry kind="lib" path="libs/algorithmfoundry-shade-culled-1.3.jar"/>
-	<classpathentry kind="lib" path="libs/fst-2.45.jar"/>
+	<classpathentry kind="lib" path="libs/fst-2.45.jar" sourcepath="/Users/cogmission/git/fast-serialization/src/main/java"/>
+	<classpathentry kind="lib" path="libs/jackson-annotations-2.4.0.jar"/>
+	<classpathentry kind="lib" path="libs/jackson-core-2.4.4.jar"/>
+	<classpathentry kind="lib" path="libs/jackson-databind-2.4.4.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

Diff for: src/jmh/java/org/numenta/nupic/benchmarks/AbstractAlgorithmBenchmark.java

@@ -25,7 +25,7 @@
 import org.numenta.nupic.Parameters;
 import org.numenta.nupic.Parameters.KEY;
 import org.numenta.nupic.algorithms.SpatialPooler;
-import org.numenta.nupic.algorithms.OldTemporalMemory;
+import org.numenta.nupic.algorithms.TemporalMemory;
 import org.numenta.nupic.encoders.ScalarEncoder;
 import org.numenta.nupic.model.Connections;
 import org.openjdk.jmh.annotations.Scope;
@@ -38,7 +38,7 @@ public abstract class AbstractAlgorithmBenchmark {
     protected int[] SDR;
     protected ScalarEncoder encoder;
     protected SpatialPooler pooler;
-    protected OldTemporalMemory temporalMemory;
+    protected TemporalMemory temporalMemory;
     protected Connections memory;
 
     @Setup
@@ -65,8 +65,8 @@ public void init() {
         pooler = new SpatialPooler();
         pooler.init(memory);
 
-        temporalMemory = new OldTemporalMemory();
-        OldTemporalMemory.init(memory);
+        temporalMemory = new TemporalMemory();
+        TemporalMemory.init(memory);
     }
 
     /**

Diff for: src/main/java/org/numenta/nupic/Parameters.java

@@ -33,7 +33,7 @@
 import java.util.Set;
 
 import org.numenta.nupic.algorithms.SpatialPooler;
-import org.numenta.nupic.algorithms.OldTemporalMemory;
+import org.numenta.nupic.algorithms.TemporalMemory;
 import org.numenta.nupic.model.Cell;
 import org.numenta.nupic.model.Column;
 import org.numenta.nupic.model.ComputeCycle;
@@ -50,13 +50,13 @@
 import com.cedarsoftware.util.DeepEquals;
 
 /**
- * Specifies parameters to be used as a configuration for a given {@link OldTemporalMemory}
+ * Specifies parameters to be used as a configuration for a given {@link TemporalMemory}
  * or {@link SpatialPooler}
  *
  * @author David Ray
  * @author Kirill Solovyev
  * @see SpatialPooler
- * @see OldTemporalMemory
+ * @see TemporalMemory
  * @see Connections
  * @see ComputeCycle
  */
@@ -144,7 +144,7 @@ public class Parameters implements Persistable {
     }
 
     /**
-     * Constant values representing configuration parameters for the {@link OldTemporalMemory}
+     * Constant values representing configuration parameters for the {@link TemporalMemory}
      */
     public static enum KEY {
         /////////// Universal Parameters ///////////