Reworked serialization api

Author: cogmission

.classpath

@@ -18,10 +18,7 @@
 	<classpathentry kind="lib" path="libs/slf4j-api-1.7.10.jar"/>
 	<classpathentry kind="lib" path="libs/trove-3.1a1.jar" sourcepath="/Users/cogmission/Resources/trove/3.1a1/trove-3.1a1-src.jar"/>
 	<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/kryo-shaded-3.0.3.jar" sourcepath="/Users/cogmission/.m2/repository/com/esotericsoftware/kryo-shaded/3.0.3/kryo-shaded-3.0.3-sources.jar"/>
-	<classpathentry kind="lib" path="libs/kryo-serializers-0.37.jar" sourcepath="/Users/cogmission/.m2/repository/de/javakaffee/kryo-serializers/0.37/kryo-serializers-0.37-sources.jar"/>
 	<classpathentry kind="lib" path="libs/objenesis-2.1.jar"/>
-	<classpathentry kind="lib" path="libs/minlog-1.3-SNAPHOT.jar"/>
 	<classpathentry combineaccessrules="false" kind="src" path="/fast-serialization"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

Changelog.txt

@@ -19,5 +19,3 @@ Changes for Serialization branch (notes for CHANGELOG.md)
 11. Added NetworkSerializer interface (and NetworkSerializerImpl) which executes FST serialization
     and simultaneously implements the Kryo interface also.
 12. Added the SerialConfig class which contains config information for the NetworkSerializer.
-13. Added Network.Scheme enum which has two values { FST, KRYO }, to designate underlying 
-    serialization scheme (Kryo still delegates to FST but implements Kryo Serializer interface)

build.gradle

@@ -49,9 +49,6 @@ dependencies {
     compile group: 'org.slf4j', name: 'slf4j-api', version:'1.7.10'
 	compile group: 'io.reactivex', name: 'rxjava', version: '1.0.10'
 	compile group: 'de.ruedigermoeller', name: 'fst', version: '2.45'
-	compile group: 'com.esotericsoftware', name: 'kryo-shaded', version: '3.0.3'
-	compile group: 'com.esotericsoftware', name: 'minlog', version: '1.3-SNAPSHOT'
-	compile group: 'de.javakaffee', name: 'kryo-serializers', version: '0.37'
 	compile group: 'com.cedarsoftware', name: 'java-util', version: '1.19.3'
 	testCompile group: 'junit', name: 'junit', version:'4.11'
     testCompile group: 'ch.qos.logback', name: 'logback-classic', version:'1.1.2'

libs/kryo-serializers-0.37.jar

@@ -49,8 +49,8 @@
 			<groupId>com.chaschev</groupId>
 			<artifactId>chutils</artifactId>
 			<version>1.4</version>
-			<!--We're only interested in ASCIITable from this library, so exclude all 
-				transitive dependencies -->
+			<!--We're only interested in ASCIITable from this library, so exclude 
+				all transitive dependencies -->
 			<exclusions>
 				<exclusion>
 					<groupId>org.mockito</groupId>
@@ -128,21 +128,6 @@
 			<version>2.45</version>
 		</dependency>
 		<dependency>
-			<groupId>com.esotericsoftware</groupId>
-			<artifactId>kryo-shaded</artifactId>
-			<version>3.0.3</version>
-		</dependency>
-		<dependency>
-			<groupId>com.esotericsoftware</groupId>
-			<artifactId>minlog</artifactId>
-			<version>1.3-SNAPHOT</version>
-		</dependency>
-		<dependency>
-			<groupId>de.javakaffee</groupId>
-			<artifactId>kryo-serializers</artifactId>
-			<version>0.37</version>
-        </dependency>
-        <dependency>
 			<groupId>org.openjdk.jmh</groupId>
 			<artifactId>jmh-core</artifactId>
 			<version>1.11.3</version>

libs/kryo-shaded-3.0.3.jar

@@ -204,6 +204,9 @@ public void burstColumns(Connections c, ComputeCycle cycle,
         activeColumns.removeAll(predictedColumns);
 
         for(Column column : activeColumns) {
+            if(column == null || column.getCells() == null) {
+                System.out.println("here");
+            }
             List<Cell> cells = column.getCells();
             cycle.activeCells.addAll(cells);
 

libs/minlog-1.3-SNAPHOT.jar

@@ -28,32 +28,33 @@
  * <p>
  * Executes check point behavior through the {@link #checkPoint(Observer)} method. The
  * checkPoint() method adds the specified {@link rx.Observer} to the list of those
- * observers notified following a check point operation. The notification consists of
+ * observers notified following a check point operation. This "subscribe" action invokes
+ * the underlying check point operation and returns a notification. The notification consists of
  * a byte[] containing the serialized {@link Network}.
  * </p><p>
  * <b>Typical usage is as follows:</b>
  * <pre>
- *  {@link Network} network = ...
+ *  {@link Persistence} p = Persistence.get();
  *  
- *  network.checkPointer().checkPoint(new Observer<byte[]>() { 
+ *  p.checkPointOp().checkPoint(new Observer<byte[]>() { 
  *      public void onCompleted() {}
  *      public void onError(Throwable e) { e.printStackTrace(); }
  *      public void onNext(byte[] bytes) {
  *          // Do work here, use serialized Network byte[] here if desired...
  *      }
  *  });
  * 
- * Merely by adding this Observer, the Network knows to check point after completion of 
+ * Again, by subscribing to this CheckPointOp, the Network knows to check point after completion of 
  * the current compute cycle (it checks the List of Observers to see if it's non-empty).
  * Then after it notifies all current observers, it clears the list prior to the next 
- * following compute cycle. see {@link PersistenceAPI} for a more detailed discussion...
+ * following compute cycle. see {@link PAPI} for a more detailed discussion...
  * 
  * @author cogmission
  *
- * @param <T>  a {@link Network} 
+ * @param <T>  the notification return type
  */
 @FunctionalInterface
-public interface CheckPointer<T> {
+public interface CheckPointOp<T> {
     /**
      * Registers the Observer for a single notification following the checkPoint
      * operation. The user will be notified with the byte[] of the {@link Network}