X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=1152a6e089f2252d0ba666f42696921ff20ea8a9;hb=3609d4b908fa64cab35f2348401baab3347188fc;hp=e66b8d18525cc4e5dc8881165318d6dd92221d40;hpb=2eea4e73351d902cd88923d863e9780fa57a0ee7;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e66b8d1..1152a6e 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1750,9 +1750,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           closeView(alignPanel);
         }
       }
-
       if (closeAllTabs)
       {
+        if (featureSettings != null && featureSettings.isOpen())
+        {
+          featureSettings.close();
+          featureSettings = null;
+        }
         /*
          * this will raise an INTERNAL_FRAME_CLOSED event and this method will
          * be called recursively, with the frame now in 'closed' state
@@ -3465,9 +3469,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void featureSettings_actionPerformed(ActionEvent e)
   {
+    showFeatureSettingsUI();
+  }
+
+  @Override
+  public FeatureSettingsControllerI showFeatureSettingsUI()
+  {
     if (featureSettings != null)
     {
-      featureSettings.close();
+      featureSettings.closeOldSettings();
       featureSettings = null;
     }
     if (!showSeqFeatures.isSelected())
@@ -3477,6 +3487,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       showSeqFeatures_actionPerformed(null);
     }
     featureSettings = new FeatureSettings(this);
+    return featureSettings;
   }
 
   /**
@@ -5006,7 +5017,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             if (parseFeaturesFile(file, sourceType))
             {
-              alignPanel.paintAlignment(true, true);
+              SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
+              if (splitFrame != null)
+              {
+                splitFrame.repaint();
+              }
+              else
+              {
+                alignPanel.paintAlignment(true, true);
+              }
             }
           }
           else
@@ -5061,6 +5080,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       viewport = alignPanel.av;
       avc.setViewportAndAlignmentPanel(viewport, alignPanel);
       setMenusFromViewport(viewport);
+      if (featureSettings != null && featureSettings.isOpen()
+              && featureSettings.fr.getViewport() != viewport)
+      {
+        if (viewport.isShowSequenceFeatures())
+        {
+          // refresh the featureSettings to reflect UI change
+          showFeatureSettingsUI();
+        }
+        else
+        {
+          // close feature settings for this view.
+          featureSettings.close();
+        }
+      }
+
     }
 
     /*
@@ -5988,6 +6022,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
   }
+
+  private Rectangle lastFeatureSettingsBounds = null;
+  @Override
+  public void setFeatureSettingsGeometry(Rectangle bounds)
+  {
+    lastFeatureSettingsBounds = bounds;
+  }
+
+  @Override
+  public Rectangle getFeatureSettingsGeometry()
+  {
+    return lastFeatureSettingsBounds;
+  }
 }
 
 class PrintThread extends Thread