JAL-2629 hmmsearch # of new sequences now only displayed when specified

diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index d2b469f..bf58a27 100644 (file)
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -387,9 +387,12 @@ public class HMMSearch extends HmmerCommand
         Desktop.addInternalFrame(alignFrame, ttl, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);
 
-        int nNew = checkForNewSequences();
-        JvOptionPane.showMessageDialog(af.alignPanel, nNew + " "
-                + MessageManager.getString("label.new_returned"));
+        if (returnNoOfNewSeqs)
+        {
+          int nNew = checkForNewSequences();
+          JvOptionPane.showMessageDialog(af.alignPanel, nNew + " "
+                  + MessageManager.getString("label.new_returned"));
+        }
 
       }
 
@@ -417,6 +420,7 @@ public class HMMSearch extends HmmerCommand
         if (resultSeq.getName().equals(aliSeq.getName()))
         {
           nNew--;
+          break;
         }
       }
     }
@@ -454,9 +458,12 @@ public class HMMSearch extends HmmerCommand
     HmmerCommand hmmalign = new HMMAlign(frame, alignArgs);
     hmmalign.run();
 
-    int nNew = checkForNewSequences();
-    JvOptionPane.showMessageDialog(frame.alignPanel,
-            nNew + " " + MessageManager.getString("label.new_returned"));
+    if (returnNoOfNewSeqs)
+    {
+      int nNew = checkForNewSequences();
+      JvOptionPane.showMessageDialog(frame.alignPanel,
+              nNew + " " + MessageManager.getString("label.new_returned"));
+    }
   }
 
   /**