X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2Fdisorder%2FJronn.java;h=55200c204d1b383fc2795df9fc2f0fe43b3f44bc;hb=HEAD;hp=617d3bb232588c0303a3fb1bf014e61572603d34;hpb=9ba9d7fd62b1f98b09ed4097c4b38ae94e25a72a;p=jabaws.git

diff --git a/runner/compbio/runner/disorder/Jronn.java b/runner/compbio/runner/disorder/Jronn.java
index 617d3bb..55200c2 100644
--- a/runner/compbio/runner/disorder/Jronn.java
+++ b/runner/compbio/runner/disorder/Jronn.java
@@ -1,6 +1,6 @@
-/* Copyright (c) 2009 Peter Troshin
+/* Copyright (c) 2011 Peter Troshin
  *  
- *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0     
+ *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     
  * 
  *  This library is free software; you can redistribute it and/or modify it under the terms of the
  *  Apache License version 2 as published by the Apache Software Foundation
@@ -34,8 +34,6 @@ import compbio.data.sequence.UnknownFileFormatException;
 import compbio.engine.client.CommandBuilder;
 import compbio.engine.client.Executable;
 import compbio.engine.client.SkeletalExecutable;
-import compbio.metadata.Limit;
-import compbio.metadata.LimitsManager;
 import compbio.metadata.ResultNotAvailableException;
 import compbio.runner.Util;
 
@@ -59,9 +57,6 @@ public class Jronn extends SkeletalExecutable<Jronn> {
 
 	private final String ncorePrm = "-n=";
 
-	// Cache for Limits information
-	private static LimitsManager<Jronn> limits;
-
 	public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
 	public static final String STAT_FILE = "stat.txt";
 
@@ -98,7 +93,6 @@ public class Jronn extends SkeletalExecutable<Jronn> {
 	}
 
 	private static String getLibPath() {
-
 		String settings = ph.getProperty("jronn.jar.file");
 		if (compbio.util.Util.isEmpty(settings)) {
 			throw new NullPointerException(
@@ -132,40 +126,10 @@ public class Jronn extends SkeletalExecutable<Jronn> {
 		return this;
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
-	public Limit<Jronn> getLimit(String presetName) {
-		if (limits == null) {
-			limits = getLimits();
-		}
-		Limit<Jronn> limit = null;
-		if (limits != null) {
-			// this returns default limit if preset is undefined!
-			limit = limits.getLimitByName(presetName);
-		}
-		// If limit is not defined for a particular preset, then return default
-		// limit
-		if (limit == null) {
-			log.debug("Limit for the preset " + presetName
-					+ " is not found. Using default");
-			limit = limits.getDefaultLimit();
-		}
-		return limit;
-	}
-
-	@Override
-	public LimitsManager<Jronn> getLimits() {
-		// synchronise on static field
-		synchronized (log) {
-			if (limits == null) {
-				limits = Util.getLimits(this.getClass());
-			}
-		}
-		return limits;
-	}
-
-	@Override
-	public Class<? extends Executable<?>> getType() {
-		return this.getClass();
+	public Class<Jronn> getType() {
+		return (Class<Jronn>) this.getClass();
 	}
 
 	public static String getStatFile() {