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 ce08077..2cb5953 100644 (file)
--- a/runner/compbio/runner/disorder/GlobPlot.java
+++ b/runner/compbio/runner/disorder/GlobPlot.java
@@ -25,13 +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.Limit;\r
-import compbio.metadata.LimitsManager;\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
@@ -49,17 +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
-       // Cache for Limits information\r
-       private static LimitsManager<GlobPlot> limits;\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
@@ -67,6 +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
@@ -103,41 +94,10 @@ public class GlobPlot extends SkeletalExecutable<GlobPlot>
                return this;\r
        }\r
 \r
+       @SuppressWarnings("unchecked")\r
        @Override\r
-       public Limit<GlobPlot> getLimit(String presetName) {\r
-               if (limits == null) {\r
-                       limits = getLimits();\r
-               }\r
-\r
-               Limit<GlobPlot> limit = null;\r
-               if (limits != null) {\r
-                       // this returns default limit if preset is undefined!\r
-                       limit = limits.getLimitByName(presetName);\r
-               }\r
-               // If limit is not defined for a particular preset, then return default\r
-               // limit\r
-               if (limit == null) {\r
-                       log.debug("Limit for the preset " + presetName\r
-                                       + " is not found. Using default");\r
-                       limit = limits.getDefaultLimit();\r
-               }\r
-               return limit;\r
-       }\r
-\r
-       @Override\r
-       public LimitsManager<GlobPlot> getLimits() {\r
-               // synchronise on static field\r
-               synchronized (log) {\r
-                       if (limits == null) {\r
-                               limits = Util.getLimits(this.getClass());\r
-                       }\r
-               }\r
-               return limits;\r
-       }\r
-\r
-       @Override\r
-       public Class<? extends Executable<?>> getType() {\r
-               return this.getClass();\r
+       public Class<GlobPlot> getType() {\r
+               return (Class<GlobPlot>) this.getClass();\r
        }\r
 \r
 }\r