Disembl further implementation

[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 716859f..8f4256f 100644 (file)
--- a/runner/compbio/runner/disorder/Disembl.java
+++ b/runner/compbio/runner/disorder/Disembl.java
@@ -20,6 +20,7 @@ import java.util.Map;
 import org.apache.log4j.Logger;\r
 \r
 import compbio.data.sequence.Score;\r
+import compbio.engine.client.CommandBuilder;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.PipedExecutable;\r
 import compbio.engine.client.SkeletalExecutable;\r
@@ -43,6 +44,12 @@ import compbio.runner.Util;
  *      'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 < fasta_file'\r
  *      print 'Mode: "default"(nothing) or "scores" which will give scores per\r
  *      residue in TAB separated format'\r
+ * \r
+ *      Internal parameters names are: sj\r
+ * \r
+ *      //TODO? pw jd ct rt lt\r
+ * \r
+ *      the order is preserved\r
  */\r
 public class Disembl extends SkeletalExecutable<Disembl>\r
                implements\r
@@ -53,6 +60,7 @@ public class Disembl extends SkeletalExecutable<Disembl>
        // Cache for Limits information\r
        private static LimitsManager<Disembl> limits;\r
 \r
+       // CHECK THIS !!!\r
        public static final String KEY_VALUE_SEPARATOR = Util.SPACE;\r
 \r
        public Disembl() {\r
@@ -114,4 +122,15 @@ public class Disembl extends SkeletalExecutable<Disembl>
                return this.getClass();\r
        }\r
 \r
+       @Override\r
+       public CommandBuilder<Disembl> getParameters(ExecProvider provider) {\r
+               // If Savitzky-Golay smoothing parameter is specified then set it\r
+               String val = cbuilder.getParamValue("sg");\r
+               log.info("DisEMBL sav-gol value: " + val);\r
+               if (val != null) {\r
+                       cbuilder.removeParam("sg");\r
+                       cbuilder.setFirst(val);\r
+               }\r
+               return super.getParameters(provider);\r
+       }\r
 }\r