finished test, solved one bug and updated javadoc

src/main/java/teetime/framework/Analysis.java

@@ -210,9 +210,6 @@ public final class Analysis<T extends AnalysisConfiguration> implements Uncaught
 			colorAndConnectStages(i, colors, threadableStage);
 		}
 		if (configuration.getConnections().size() != createdConnections) {
-			for (Connection<?> conn : configuration.getConnections()) {
-				System.out.println(conn.getSourcePort().getOwningStage().getId() + " connects with " + conn.getTargetPort().getOwningStage().getId());
-			}
 			throw new IllegalStateException("Remaining " + (configuration.getConnections().size() - createdConnections) + " connection(s)");
 		}
 	}
@@ -235,7 +232,7 @@ public final class Analysis<T extends AnalysisConfiguration> implements Uncaught
 					}
 				} else {
 					if (colors.containsKey(targetStage)) {
-						if (colors.get(targetStage).equals(i)) {
+						if (!colors.get(targetStage).equals(i)) {
 							throw new IllegalStateException("Crossing threads"); // One stage is connected to a stage of another thread (but not its "headstage")
 						}
 					}

src/main/java/teetime/framework/AnalysisConfiguration.java

@@ -86,7 +86,7 @@ public abstract class AnalysisConfiguration {
 	 * @return
 	 *         the pipe instance which connects the two given stages
 	 *
-	 * @deprecated since 1.2
+	 * @deprecated since 1.2. Use {@link #connectPorts(OutputPort, InputPort)} instead.
 	 */
 	@Deprecated
 	protected static <T> IPipe connectIntraThreads(final OutputPort<? extends T> sourcePort, final InputPort<T> targetPort) {
@@ -101,7 +101,7 @@ public abstract class AnalysisConfiguration {
 	 * @return
 	 *         the pipe instance which connects the two given stages
 	 *
-	 * @deprecated since 1.2
+	 * @deprecated since 1.2. Use {@link #connectPorts(OutputPort, InputPort)} instead.
 	 */
 	@Deprecated
 	protected static <T> IPipe connectBoundedInterThreads(final OutputPort<? extends T> sourcePort, final InputPort<T> targetPort) {
@@ -116,7 +116,7 @@ public abstract class AnalysisConfiguration {
 	 * @return
 	 *         the pipe instance which connects the two given stages
 	 *
-	 * @deprecated since 1.2
+	 * @deprecated since 1.2. Use {@link #connectPorts(OutputPort, InputPort)} instead.
 	 */
 	@Deprecated
 	protected static <T> IPipe connectUnboundedInterThreads(final OutputPort<? extends T> sourcePort, final InputPort<T> targetPort) {
@@ -132,7 +132,7 @@ public abstract class AnalysisConfiguration {
 	 *            capacity of the underlying queue
 	 * @return
 	 *
-	 * @deprecated since 1.2
+	 * @deprecated since 1.2. Use {@link #connectPorts(OutputPort, InputPort)} instead.
 	 */
 	@Deprecated
 	protected static <T> IPipe connectBoundedInterThreads(final OutputPort<? extends T> sourcePort, final InputPort<T> targetPort, final int capacity) {
@@ -148,7 +148,7 @@ public abstract class AnalysisConfiguration {
 	 *            capacity of the underlying queue
 	 * @return
 	 *
-	 * @deprecated since 1.2
+	 * @deprecated since 1.2. Use {@link #connectPorts(OutputPort, InputPort)} instead.
 	 */
 	@Deprecated
 	protected static <T> IPipe connectUnboundedInterThreads(final OutputPort<? extends T> sourcePort, final InputPort<T> targetPort, final int capacity) {

src/test/java/teetime/framework/AnalysisTest.java

@@ -29,6 +29,7 @@ import org.junit.Test;
 import org.junit.rules.ExpectedException;
 
 import teetime.stage.InitialElementProducer;
+import teetime.stage.InstanceOfFilter;
 import teetime.stage.basic.Sink;
 import teetime.util.StopWatch;
 
@@ -131,6 +132,22 @@ public class AnalysisTest {
 	public void testInstantiatePipesIncorrectConfiguration() {
 		thrown.expect(IllegalStateException.class);
 		thrown.expectMessage("Crossing threads");
+		InvalidTestConfig configuration = new InvalidTestConfig();
+		new Analysis<InvalidTestConfig>(configuration);
+	}
+
+	private class InvalidTestConfig extends AnalysisConfiguration {
+		public InitialElementProducer<Object> init = new InitialElementProducer<Object>();
+		public InstanceOfFilter<Object, Object> iof = new InstanceOfFilter<Object, Object>(Object.class);
+		public Sink<Object> sink = new Sink<Object>();
+
+		public InvalidTestConfig() {
+			connectPorts(init.getOutputPort(), iof.getInputPort());
+			connectPorts(iof.getMatchedOutputPort(), sink.getInputPort());
+			connectPorts(init.createOutputPort(), sink.createInputPort());
+			addThreadableStage(init);
+			addThreadableStage(iof);
+		}
 	}
 
 }