JAL-1365 refactored core methods from RNAAliFold and AACon service clients to a commo...

[jalview.git] / src / jalview / ws / jws2 / RNAalifoldClient.java

diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
index d86f15a..b8b30c5 100644 (file)
--- a/src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/src/jalview/ws/jws2/RNAalifoldClient.java
@@ -21,6 +21,12 @@ import compbio.data.sequence.Range;
 import compbio.data.sequence.Score;
 import compbio.metadata.Argument;
 
+/**
+ * Client for the JABA RNA Alifold Service
+ * @author daluke - Daniel Barton
+ *
+ */
+
 public class RNAalifoldClient extends JabawsAlignCalcWorker implements
         AlignCalcWorkerI
 {
@@ -38,24 +44,25 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
   {
     super(sh, alignFrame, preset, paramset);
 
-    if (arguments == null)
-      arguments = new ArrayList<Argument>();
+    //if (arguments == null)
+    //  arguments = new ArrayList<Argument>();
 
     af = alignFrame;
     methodName = sh.serviceType;
-
+    alignedSeqs=true;
+    submitGaps=true;
     nucleotidesAllowed = true;
     proteinAllowed = false;
     initViewportParams();
   }
+  
+  public String getCalcId()
+  {
+    return CALC_ID;
+  }
+  private static String CALC_ID="jalview.ws.jws2.RNAalifoldClient";
 
-  protected void initViewportParams()
   {
-    ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
-            getCalcId(),
-            new AAConSettings(true, service, this.preset,
-                    (arguments != null) ? JabaParamStore
-                            .getJwsArgsfromJaba(arguments) : null), true);
   }
 
   @Override
@@ -332,10 +339,4 @@ public class RNAalifoldClient extends JabawsAlignCalcWorker implements
     char ss = (Pattern.matches(regex, Character.toString(chr))) ? 'S' : ' ';
     return ss;
   }
-
-  public String getCalcId()
-  {
-    return SequenceAnnotationWSClient.AAConCalcId;
-  }
-
 }