case invariant matching of seqeunce feature to sequence id string

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index a714ce6..1c488fe 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -587,10 +587,18 @@ public class AlignFrame
 
     validate();
   }
-
-
-
-
+  /**
+   * 
+   * @return true if any progress bars are still active
+   */
+  public boolean operationInProgress()
+  {
+    if (progressBars!=null && progressBars.size()>0)
+    {
+      return true;
+    }
+    return false;
+  }
   /*
    Added so Castor Mapping file can obtain Jalview Version
   */
@@ -2858,7 +2866,7 @@ public class AlignFrame
   {
     SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByPID(viewport.getAlignment(),
-                              viewport.getAlignment().getSequenceAt(0));
+                              viewport.getAlignment().getSequenceAt(0), null);
     addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
                                     viewport.alignment));
     alignPanel.paintAlignment(true);
@@ -3121,7 +3129,7 @@ public class AlignFrame
       public void actionPerformed(ActionEvent e)
       {
         SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray();
-        AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());
+        AlignmentSorter.sortByAnnotationScore(scoreLabel, viewport.getAlignment());//,viewport.getSelectionGroup());
         addHistoryItem(new OrderCommand("Sort by "+scoreLabel, oldOrder, viewport.alignment));
         alignPanel.paintAlignment(true);
       }