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

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

diff --git a/runner/compbio/runner/disorder/Disembl.java b/runner/compbio/runner/disorder/Disembl.java
index 6b014ba..b6453a7 100644 (file)
--- a/runner/compbio/runner/disorder/Disembl.java
+++ b/runner/compbio/runner/disorder/Disembl.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
  * DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops\r
@@ -56,17 +53,10 @@ import compbio.runner.Util;
  * This is not a standard DisEMBL! The script has been modified!\r
  * \r
  */\r
-public class Disembl extends SkeletalExecutable<Disembl>\r
-               implements\r
-                       PipedExecutable<Disembl> {\r
+public class Disembl extends SkeletalExecutable<Disembl> implements PipedExecutable<Disembl> {\r
 \r
        private static Logger log = Logger.getLogger(Disembl.class);\r
 \r
-       // Cache for Limits information\r
-       private static LimitsManager<Disembl> limits;\r
-\r
-       public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
-\r
        /**\r
         * For the region to be considered disordered the values must exceed these\r
         */\r
@@ -110,6 +100,7 @@ public class Disembl extends SkeletalExecutable<Disembl>
                log.trace("DRESULTS: " + results);\r
                return results;\r
        }\r
+\r
        @Override\r
        public Disembl setInput(String inFile) {\r
                super.setInput(inFile);\r
@@ -117,41 +108,10 @@ public class Disembl extends SkeletalExecutable<Disembl>
                return this;\r
        }\r
 \r
+       @SuppressWarnings("unchecked")\r
        @Override\r
-       public Limit<Disembl> getLimit(String presetName) {\r
-               if (limits == null) {\r
-                       limits = getLimits();\r
-               }\r
-\r
-               Limit<Disembl> 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<Disembl> 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<Disembl> getType() {\r
+               return (Class<Disembl>) this.getClass();\r
        }\r
 \r
 }\r