JAL-3070 use ArgumentI in all public constructors, convert to service specific argume...

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

diff --git a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
index dd64e77..1a361c4 100644 (file)
--- a/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
+++ b/src/jalview/ws/jws2/AbstractJabaCalcWorker.java
@@ -36,6 +36,7 @@ import jalview.workers.AlignCalcWorker;
 import jalview.ws.jws2.dm.AAConSettings;
 import jalview.ws.jws2.dm.JabaWsParamSet;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
 import jalview.ws.params.WsParamSetI;
 
 import java.util.ArrayList;
@@ -44,7 +45,6 @@ import java.util.List;
 import java.util.Map;
 
 import compbio.data.sequence.FastaSequence;
-import compbio.metadata.Argument;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
 import compbio.metadata.JobSubmissionException;
@@ -58,7 +58,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
 
   protected WsParamSetI preset;
 
-  protected List<Argument> arguments;
+  protected List<ArgumentI> arguments;
 
   protected IProgressIndicator guiProgress;
 
@@ -78,10 +78,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
     {
       ((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
               getCalcId(),
-              new AAConSettings(true, service, this.preset,
-                      (arguments != null)
-                              ? JabaParamStore.getJwsArgsfromJaba(arguments)
-                              : null),
+              new AAConSettings(true, service, this.preset, arguments),
               true);
     }
   }
@@ -98,7 +95,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
     return preset;
   }
 
-  public List<Argument> getArguments()
+  public List<ArgumentI> getArguments()
   {
     return arguments;
   }
@@ -112,7 +109,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
    * @param newarguments
    */
   public void updateParameters(final WsParamSetI newpreset,
-          final List<Argument> newarguments)
+          final List<ArgumentI> newarguments)
   {
     preset = newpreset;
     arguments = newarguments;
@@ -129,7 +126,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
     }
     if (arguments != null && arguments.size() > 0)
     {
-      for (Argument rg : arguments)
+      for (Object rg : JabaParamStore.getJabafromJwsArgs(arguments))
       {
         if (Option.class.isAssignableFrom(rg.getClass()))
         {
@@ -168,7 +165,7 @@ public abstract class AbstractJabaCalcWorker extends AlignCalcWorker
   }
 
   public AbstractJabaCalcWorker(Jws2Instance service, AlignFrame alignFrame,
-          WsParamSetI preset, List<Argument> paramset)
+          WsParamSetI preset, List<ArgumentI> paramset)
   {
     this(alignFrame.getCurrentView(), alignFrame.alignPanel);
     this.guiProgress = alignFrame;