JWS-86 made few changes to text, plus couple of links were faulty so changed ClustalW...

[jabaws.git] / runner / compbio / runner / disorder / Jronn.java

diff --git a/runner/compbio/runner/disorder/Jronn.java b/runner/compbio/runner/disorder/Jronn.java
index d9d388f..b123996 100644 (file)
--- a/runner/compbio/runner/disorder/Jronn.java
+++ b/runner/compbio/runner/disorder/Jronn.java
@@ -35,7 +35,7 @@ import compbio.engine.client.CommandBuilder;
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r
 import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.Util;\r
+import compbio.engine.client.EngineUtil;\r
 \r
 /**\r
  * Command line\r
@@ -57,7 +57,6 @@ public class Jronn extends SkeletalExecutable<Jronn> {
 \r
        private final String ncorePrm = "-n=";\r
 \r
-       public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
        public static final String STAT_FILE = "stat.txt";\r
 \r
        public Jronn() {\r
@@ -93,15 +92,14 @@ public class Jronn extends SkeletalExecutable<Jronn> {
                String settings = ph.getProperty("jronn.jar.file");\r
                if (compbio.util.Util.isEmpty(settings)) {\r
                        throw new NullPointerException(\r
-                                       "Please define jronn.jar.file property in Executable.properties file"\r
-                                                       + "and initialize it with the location of jronn jar file");\r
+                       "Please define jronn.jar.file property in Executable.properties file and initialize it with the location of jronn jar file");\r
                }\r
                if (new File(settings).isAbsolute()) {\r
                        // Jronn jar can be found so no actions necessary\r
                        // no further actions is necessary\r
                        return settings;\r
                }\r
-               return compbio.engine.client.Util.convertToAbsolute(settings);\r
+               return EngineUtil.convertToAbsolute(settings);\r
        }\r
 \r
        @Override\r