Fix wrong error message

[jabaws.git] / runner / compbio / runner / structure / RNAalifold.java

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