X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Frunner%2Fstructure%2FRNAalifold.java;h=c0a50fe73fc1d6ae334cca147bd1f91a511a4bc5;hb=e6227b3fc0bb5abdf275bb24a87607b0555bce10;hp=918918e007fbd078c88c2fc4d316193d8fedfba4;hpb=c84ec6492607920b938cfa3645e1a92e15727dd1;p=jabaws.git

diff --git a/runner/compbio/runner/structure/RNAalifold.java b/runner/compbio/runner/structure/RNAalifold.java
index 918918e..c0a50fe 100644
--- a/runner/compbio/runner/structure/RNAalifold.java
+++ b/runner/compbio/runner/structure/RNAalifold.java
@@ -1,6 +1,5 @@
 package compbio.runner.structure;
 
-
 import java.io.FileNotFoundException;
 import java.io.IOException;
 
@@ -10,17 +9,16 @@ import compbio.data.sequence.RNAStructScoreManager;
 import compbio.engine.client.PipedExecutable;
 import compbio.engine.client.SkeletalExecutable;
 import compbio.metadata.ResultNotAvailableException;
-import compbio.runner.Util;
+import compbio.runner.RunnerUtil;
 
 public class RNAalifold extends SkeletalExecutable<RNAalifold> 
 		implements PipedExecutable<RNAalifold> {
-	
-	
+
 	private static Logger log = Logger.getLogger(RNAalifold.class);
 
 	// May not be necessary as defult is "<space>" but still dont know
 	// How to deal with different key value separators for different params
-	public static final String KEY_VALUE_SEPARATOR = Util.SPACE;
+	public static final String KEY_VALUE_SEPARATOR = " ";
 	
 	public RNAalifold() {
 		super(KEY_VALUE_SEPARATOR);
@@ -50,8 +48,7 @@ public class RNAalifold extends SkeletalExecutable<RNAalifold>
 	public RNAStructScoreManager getResults(String workDirectory)
 			throws ResultNotAvailableException {
 		try {
-			return Util.readRNAStruct(workDirectory, getOutput());
-			
+			return RunnerUtil.readRNAStruct(workDirectory, getOutput());
 		} catch (FileNotFoundException e) {
 			log.error(e.getMessage(), e.getCause());
 			throw new ResultNotAvailableException(e);