Index: /trunk/autoquest-plugin-alignment/.classpath
===================================================================
--- /trunk/autoquest-plugin-alignment/.classpath	(revision 1542)
+++ /trunk/autoquest-plugin-alignment/.classpath	(revision 1543)
@@ -14,10 +14,10 @@
 	</classpathentry>
 	<classpathentry including="**/*.java" kind="src" path="src/main/resources"/>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
 		</attributes>
 	</classpathentry>
-	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.7">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
Index: /trunk/autoquest-plugin-alignment/.settings/org.eclipse.jdt.core.prefs
===================================================================
--- /trunk/autoquest-plugin-alignment/.settings/org.eclipse.jdt.core.prefs	(revision 1542)
+++ /trunk/autoquest-plugin-alignment/.settings/org.eclipse.jdt.core.prefs	(revision 1543)
@@ -1,5 +1,12 @@
 eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
 org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.7
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
 org.eclipse.jdt.core.compiler.compliance=1.7
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
 org.eclipse.jdt.core.compiler.source=1.7
Index: /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java
===================================================================
--- /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java	(revision 1542)
+++ /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/commands/CMDbinaryAlignment.java	(revision 1543)
@@ -62,5 +62,5 @@
 		Object obj = GlobalDataContainer.getInstance().getData(sequencesName);
 		if (obj != null) {
-			if (obj.getClass().equals(SimpleSequenceGenerator.class)) {
+			if (obj instanceof SimpleSequenceGenerator) {
 				gen = (SimpleSequenceGenerator) obj;
 				Console.println("Number of sequences: " + gen.sequenceCount());
Index: /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java
===================================================================
--- /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java	(revision 1542)
+++ /trunk/autoquest-plugin-alignment/src/main/java/de/ugoe/cs/autoquest/plugin/alignment/seqgen/SimpleSequenceGenerator.java	(revision 1543)
@@ -66,4 +66,5 @@
 						uniqueTasks.addSymbol(taskInstance,
 								taskInstance.getTask());
+				
 								templist.getSequence()[i]=taskInstance.getTask().getId();
 								
@@ -75,5 +76,5 @@
 					
 				}
-
+				
 				comparator.clearBuffers();
 				numberseqs.add(templist);