JAL-591

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

diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java
index e025df6..d7b968d 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSClient.java
+++ b/src/jalview/ws/jws2/MsaWSClient.java
@@ -112,36 +112,46 @@ public class MsaWSClient extends Jws2Client
       return;
     }
     server = sh.service;
-    if (preset!=null) {
-      if (preset instanceof JabaPreset){
-        this.preset = ((JabaPreset)preset).p;
-      }  else
-        if (preset instanceof JabaWsParamSet) {
-          JabaWsParamSet pset = ((JabaWsParamSet)preset);
-          if (arguments!=null && arguments.size()>0)
+    if (preset != null)
+    {
+      if (preset instanceof JabaPreset)
+      {
+        this.preset = ((JabaPreset) preset).p;
+      }
+      else if (preset instanceof JabaWsParamSet)
+      {
+        List<Argument> newargs = new ArrayList<Argument>();
+        JabaWsParamSet pset = ((JabaWsParamSet) preset);
+        for (Option opt : pset.getjabaArguments())
+        {
+          newargs.add(opt);
+        }
+        if (arguments != null && arguments.size() > 0)
+        {
+          // merge arguments with preset's own arguments.
+          for (Argument opt : arguments)
           {
-            // merge arguments with preset's own arguments.
-            List<Argument> oldargs = arguments;
-            arguments = new ArrayList<Argument>();
-            for (Option opt : pset.getjabaArguments()) {
-              arguments.add(opt);
-            }
-            for (Argument opt: oldargs)
-            {
-              arguments.add(opt);
-            }
+            newargs.add(opt);
           }
-        
-      }else{
-        throw new Error("Implementation error: Can only instantiate Jaba parameter sets.");
+        }
+        paramset = newargs;
       }
+      else
+      {
+        throw new Error(
+                "Implementation error: Can only instantiate Jaba parameter sets.");
+      }
+    }
+    else
+    {
+      // just provided with a bunch of arguments
+      this.paramset = arguments;
     }
-    this.paramset = arguments;
     if (editParams)
     {
-      if (sh.paramStore==null)
+      if (sh.paramStore == null)
       {
-        sh.paramStore = new JabaParamStore(sh);
+        sh.paramStore = new JabaParamStore(sh, Desktop.getUserParameterStore());
       }
       WsJobParameters jobParams = new WsJobParameters(sh, preset);
       if (!jobParams.showRunDialog())
@@ -149,11 +159,14 @@ public class MsaWSClient extends Jws2Client
         return;
       }
       WsParamSetI prset = jobParams.getPreset();
-      if (prset==null)
+      if (prset == null)
+      {
+        paramset = JabaParamStore.getJabafromJwsArgs(jobParams
+                .getJobParams());
+      }
+      else
       {
-        paramset = JabaParamStore.getJabafromJwsArgs(jobParams.getJobParams());
-      } else {
-        this.preset = ((JabaPreset)prset).p;
+        this.preset = ((JabaPreset) prset).p;
         paramset = null; // no user supplied parameters.
       }
     }