edit jws2 job parameters before running job

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

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 3ecce57..d9f92f9 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -347,6 +347,12 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     {
       this.lastChunk = lastChunk;
     }
+
+    String alignmentProgram=null;
+    public String getAlignmentProgram()
+    {
+      return alignmentProgram;
+    }
     
   }
 
@@ -419,6 +425,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         }
         ((MsaWSJob) jobs[j]).preset = preset;
         ((MsaWSJob) jobs[j]).arguments = paramset;
+        ((MsaWSJob) jobs[j]).alignmentProgram = wsname;
         if (njobs > 0)
         {
           wsinfo
@@ -546,6 +553,11 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       // TODO: get the parameters (if any) for this job and submit the job
       if (j.arguments!=null && j.arguments.size()>0)
       {
+        StringBuffer pset = new StringBuffer();
+        for (Argument arg: j.arguments) {
+          pset.append(arg.getName()+" "+arg.getDefaultValue()+"\n");
+        }
+        j.setStatus("Custom Parameters:\n"+pset.toString()+"\nJob Output:\n");
         j.setJobId(server.customAlign(j.seqs, j.arguments));
       } else
         if (j.preset!=null)
@@ -690,7 +702,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       {
         msjob = (MsaWSJob)jobs[j];
         Object[] res = msjob.getAlignment();
-        lastProgram = msjob.alignment.getMetadata().getProgram().name();
+        lastProgram = msjob.getAlignmentProgram();
         alorders.add(res[1]);
         results[j] = (SequenceI[]) res[0];
         orders[j] = (AlignmentOrder) res[1];