Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

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

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 45e4b95..5366913 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -24,6 +24,7 @@ import jalview.analysis.AnnotationSorter;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
@@ -806,7 +807,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           // could not be validated and it is not clear if it is now being
           // called. Log warning here in case it is called and unforeseen
           // problems occur
-          Cache.log.warn(
+          Console.warn(
                   "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
 
           // scroll to start of panel
@@ -1464,9 +1465,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      if (Cache.log.isDebugEnabled())
+      if (Console.isDebugEnabled())
       {
-        Cache.log.warn("Closing alignment panel which is already closed.");
+        Console.warn("Closing alignment panel which is already closed.");
       }
     }
   }
@@ -1541,13 +1542,16 @@ public class AlignmentPanel extends GAlignmentPanel implements
     } catch (Exception ex)
     {
     }
-
     if (b)
     {
-      alignFrame.setDisplayedView(this);
+      setAlignFrameView();
     }
   }
-
+  public void setAlignFrameView()
+  {
+    alignFrame.setDisplayedView(this);
+  }
+  
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {