JAL-975 JAL-1002 ensure custom parameters are actually passed to service

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

diff --git a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
index d84f365..9a1557c 100644 (file)
--- a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
@@ -162,7 +162,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
         guiProgress.setProgressBar("JABA " + getServiceActionText(),
                 progressId = System.currentTimeMillis());
       }
-      if (preset == null)
+      if (preset == null && arguments==null)
       {
         rslt = aaservice.analize(seqs);
       }
@@ -300,7 +300,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
       if (ap != null)
       {
         calcMan.workerComplete(this);
-        if (guiProgress != null)
+        if (guiProgress != null && progressId!=-1)
         {
           guiProgress.setProgressBar("", progressId);
         }