From 0d972c388b6e0f25e0725531000fbf72eb032f53 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Fri, 28 Nov 2014 14:01:15 +0000
Subject: [PATCH] JAL-1583 new validInput flag set according to validity of
 all MSA jobs prepared for submission

---
 src/jalview/ws/jws2/MsaWSThread.java |   17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index 635f92b..c4f3d2d 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -485,7 +485,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     SequenceI[][] conmsa = _msa.getVisibleContigs('-');
     if (conmsa != null)
     {
-      int njobs = conmsa.length;
+      int nvalid = 0, njobs = conmsa.length;
       jobs = new MsaWSJob[njobs];
       for (int j = 0; j < njobs; j++)
       {
@@ -497,6 +497,10 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         {
           jobs[j] = new MsaWSJob(0, conmsa[j]);
         }
+        if (((MsaWSJob) jobs[j]).hasValidInput())
+        {
+          nvalid++;
+        }
         ((MsaWSJob) jobs[j]).preset = preset;
         ((MsaWSJob) jobs[j]).arguments = paramset;
         ((MsaWSJob) jobs[j]).alignmentProgram = wsname;
@@ -507,9 +511,20 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         }
         wsinfo.setProgressText(jobs[j].getJobnum(), OutputHeader);
       }
+      validInput = nvalid > 0;
     }
   }
 
+  boolean validInput = false;
+
+  /**
+   * 
+   * @return true if the thread will perform a calculation
+   */
+  public boolean hasValidInput()
+  {
+    return validInput;
+  }
   public boolean isCancellable()
   {
     return true;
-- 
1.7.10.2