Merge branch 'develop' into features/JAL-3187_uitweaks

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f3a8ab5..7c0c55c 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -33,6 +33,7 @@ import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsControllerI;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.SimilarityParamsI;
@@ -1478,9 +1479,13 @@ 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
@@ -3186,9 +3191,15 @@ 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())
@@ -3198,6 +3209,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       showSeqFeatures_actionPerformed(null);
     }
     featureSettings = new FeatureSettings(this);
+    return featureSettings;
   }
 
   /**
@@ -4683,6 +4695,11 @@ 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
@@ -4738,6 +4755,21 @@ 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();
+        }
+      }
+
     }
 
     /*
@@ -4935,6 +4967,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               @Override
               public void finished()
               {
+
+                for (FeatureSettingsModelI srcSettings : dbRefFetcher
+                        .getFeatureSettingsModels())
+                {
+
+                  alignPanel.av.mergeFeaturesStyle(srcSettings);
+                }
                 AlignFrame.this.setMenusForViewport();
               }
             });
@@ -5020,6 +5059,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                   @Override
                                   public void finished()
                                   {
+                                    FeatureSettingsModelI srcSettings = dassource[0]
+                                            .getFeatureColourScheme();
+                                    alignPanel.av.mergeFeaturesStyle(
+                                            srcSettings);
                                     AlignFrame.this.setMenusForViewport();
                                   }
                                 });
@@ -5646,6 +5689,19 @@ 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