Clean-up, refactoring, commenting. Parameters file containts only options since Jalvi...

[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 c6c79ec..918918e 100644 (file)
--- a/runner/compbio/runner/structure/RNAalifold.java
+++ b/runner/compbio/runner/structure/RNAalifold.java
@@ -3,26 +3,15 @@ package compbio.runner.structure;
 \r
 import java.io.FileNotFoundException;\r
 import java.io.IOException;\r
-import java.util.Arrays;\r
-import java.util.List;\r
-\r
-\r
-\r
-\r
 \r
 import org.apache.log4j.Logger;\r
 \r
-import compbio.data.sequence.ScoreManager;\r
 import compbio.data.sequence.RNAStructScoreManager;\r
-import compbio.data.sequence.UnknownFileFormatException;\r
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.runner.Util;\r
 \r
-\r
-import compbio.engine.client.CommandBuilder;\r
-\r
 public class RNAalifold extends SkeletalExecutable<RNAalifold> \r
                implements PipedExecutable<RNAalifold> {\r
        \r
@@ -31,7 +20,7 @@ public class RNAalifold extends SkeletalExecutable<RNAalifold>
 \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 = " ";\r
+       public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
        \r
        public RNAalifold() {\r
                super(KEY_VALUE_SEPARATOR);\r