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

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

diff --git a/runner/compbio/runner/disorder/GlobPlot.java b/runner/compbio/runner/disorder/GlobPlot.java
index a5b887a..2cb5953 100644 (file)
--- a/runner/compbio/runner/disorder/GlobPlot.java
+++ b/runner/compbio/runner/disorder/GlobPlot.java
@@ -25,11 +25,10 @@ import org.apache.log4j.Logger;
 import compbio.data.sequence.ScoreManager;\r
 import compbio.data.sequence.SequenceUtil;\r
 import compbio.data.sequence.UnknownFileFormatException;\r
-import compbio.engine.client.Executable;\r
 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
 /**\r
  * ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame\r
@@ -47,14 +46,10 @@ import compbio.runner.Util;
  * This is not a standard GlobPlot! The script has been modified!\r
  * \r
  */\r
-public class GlobPlot extends SkeletalExecutable<GlobPlot>\r
-               implements\r
-                       PipedExecutable<GlobPlot> {\r
+public class GlobPlot extends SkeletalExecutable<GlobPlot> implements PipedExecutable<GlobPlot> {\r
 \r
        private static Logger log = Logger.getLogger(GlobPlot.class);\r
 \r
-       public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
-\r
        /* The parameter list there must not contain same values! */\r
        public GlobPlot() {\r
                // remove default input to prevent it to appear in the parameters list\r
@@ -62,6 +57,7 @@ public class GlobPlot extends SkeletalExecutable<GlobPlot>
                // super.setInput("");\r
        }\r
 \r
+       @Override\r
        @SuppressWarnings("unchecked")\r
        public ScoreManager getResults(String workDirectory)\r
                        throws ResultNotAvailableException {\r
@@ -100,8 +96,8 @@ public class GlobPlot extends SkeletalExecutable<GlobPlot>
 \r
        @SuppressWarnings("unchecked")\r
        @Override\r
-       public Class<Executable<GlobPlot>> getType() {\r
-               return (Class<Executable<GlobPlot>>) this.getClass();\r
+       public Class<GlobPlot> getType() {\r
+               return (Class<GlobPlot>) this.getClass();\r
        }\r
 \r
 }\r