Clean up logging system

[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..996e7d8 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
@@ -14,13 +13,12 @@ import compbio.runner.Util;
 \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
@@ -51,7 +49,6 @@ public class RNAalifold extends SkeletalExecutable<RNAalifold>
                        throws ResultNotAvailableException {\r
                try {\r
                        return Util.readRNAStruct(workDirectory, getOutput());\r
-                       \r
                } catch (FileNotFoundException e) {\r
                        log.error(e.getMessage(), e.getCause());\r
                        throw new ResultNotAvailableException(e);\r