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JAL-3603 load annotation file from RELATIVE_URL in JS, small code tidies
[jalview.git] / src / jalview / gui / AlignFrame.java
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 77b8552..7818748 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -20,6 +20,58 @@
  */
 package jalview.gui;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComponent;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
+import ext.vamsas.ServiceHandle;
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.CrossRef;
@@ -33,6 +85,7 @@ 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;
@@ -102,59 +155,6 @@ import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusAdapter;
-import java.awt.event.FocusEvent;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.PrintWriter;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JComponent;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLabel;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
-import ext.vamsas.ServiceHandle;
-
 /**
  * DOCUMENT ME!
  * 
@@ -1489,10 +1489,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     final JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(
-            MessageManager.getString("label.load_jalview_annotations"));
-    chooser.setToolTipText(
-            MessageManager.getString("label.load_jalview_annotations"));
+    String tooltip = MessageManager.getString("label.load_jalview_annotations");
+    chooser.setDialogTitle(tooltip);
+    chooser.setToolTipText(tooltip);
     chooser.setResponseHandler(0, new Runnable()
     {
       @Override
@@ -1543,9 +1542,13 @@ 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
@@ -2158,7 +2161,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();
@@ -2205,7 +2208,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();
@@ -2224,7 +2227,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
 
         // propagate alignment changed.
-        viewport.getRanges().setEndSeq(alignment.getHeight());
+        viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
         if (annotationAdded)
         {
           // Duplicate sequence annotation in all views.
@@ -3250,9 +3253,15 @@ 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())
@@ -3262,6 +3271,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       showSeqFeatures_actionPerformed(null);
     }
     featureSettings = new FeatureSettings(this);
+    return featureSettings;
   }
 
   /**
@@ -4791,7 +4801,15 @@ 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
@@ -4847,6 +4865,21 @@ 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();
+        }
+      }
+
     }
 
     /*
@@ -5044,6 +5077,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               @Override
               public void finished()
               {
+
+                for (FeatureSettingsModelI srcSettings : dbRefFetcher
+                        .getFeatureSettingsModels())
+                {
+
+                  alignPanel.av.mergeFeaturesStyle(srcSettings);
+                }
                 AlignFrame.this.setMenusForViewport();
               }
             });
@@ -5120,6 +5160,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                   @Override
                                   public void finished()
                                   {
+                                    FeatureSettingsModelI srcSettings = dassource[0]
+                                            .getFeatureColourScheme();
+                                    alignPanel.av.mergeFeaturesStyle(
+                                            srcSettings);
                                     AlignFrame.this.setMenusForViewport();
                                   }
                                 });
@@ -5750,6 +5794,18 @@ 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