X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=engine%2Fcompbio%2Fengine%2Fclient%2FSkeletalExecutable.java;h=369f8e71adb0eb58155d028151c4352bcad94593;hb=c7c5df620d816bf197c48f059a9ed3300fdf277a;hp=b289f6c32530197cd7598310cde85e6b90d9e0d4;hpb=2a269830633463e5016d5c92ed672d9e312c9776;p=jabaws.git

diff --git a/engine/compbio/engine/client/SkeletalExecutable.java b/engine/compbio/engine/client/SkeletalExecutable.java
index b289f6c..369f8e7 100644
--- a/engine/compbio/engine/client/SkeletalExecutable.java
+++ b/engine/compbio/engine/client/SkeletalExecutable.java
@@ -42,9 +42,13 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
 	// Cache for Limits information
 	private LimitsManager<T> limits;
 
-	protected String inputFile = "input.txt";
-	protected String outputFile = "output.txt";
-	protected String errorFile = "error.txt";
+	public static final String INPUT = "input.txt";
+	public static final String OUTPUT = "result.txt";
+	public static final String ERROR = "error.txt";
+
+	protected String inputFile = INPUT;
+	protected String outputFile = OUTPUT;
+	protected String errorFile = ERROR;
 
 	private boolean isInputSet = false;
 	private boolean isOutputSet = false;
@@ -257,7 +261,8 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
 		return code;
 	}
 
-	public String getClusterSettings() {
+	@Override
+	public String getClusterJobSettings() {
 		String settings = ph.getProperty(getType().getSimpleName()
 				.toLowerCase() + ".cluster.settings");
 		return settings == null ? "" : settings;
@@ -293,11 +298,16 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
 	}
 
 	@Override
-	public Limit<T> getLimit(String presetName) {
-
+	public synchronized Limit<T> getLimit(String presetName) {
+		// Assume this function is called for the first time and thus need
+		// initialization
 		if (limits == null) {
 			limits = getLimits();
 		}
+		// Either the initialization failed or limits were not configured.
+		if (limits == null) {
+			return null;
+		}
 
 		Limit<T> limit = null;
 		if (limits != null) {
@@ -318,7 +328,7 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
 	public LimitsManager<T> getLimits() {
 		synchronized (SkeletalExecutable.class) {
 			if (limits == null) {
-				limits = compbio.runner.Util.getLimits(this.getType());
+				limits = compbio.engine.client.Util.getLimits(this.getType());
 			}
 		}
 		return limits;
@@ -328,6 +338,6 @@ public abstract class SkeletalExecutable<T> implements Executable<T> {
 	 * 
 	 * @return subclasses must return their type
 	 */
-	public abstract Class<Executable<T>> getType();
+	public abstract Class<T> getType();
 
 }