X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;fp=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=5aa9499c209c59089820124a63ad09bb02811498;hb=0b573ed90b14079f7326281f50c0c9cffdace586;hp=9fe2e92dc4afab8845901049cd1f1dd031165cea;hpb=85f6e96380285dfda463cd36317c55c4f5184ad8;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 9fe2e92..5aa9499 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -20,8 +20,10 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
+import jalview.api.ViewStyleI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.FeatureMatcher;
@@ -36,6 +38,7 @@ import jalview.schemes.FeatureColour;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
+import jalview.viewmodel.styles.ViewStyle;
 import jalview.xml.binding.jalview.JalviewUserColours;
 import jalview.xml.binding.jalview.JalviewUserColours.Colour;
 import jalview.xml.binding.jalview.JalviewUserColours.Filter;
@@ -45,6 +48,7 @@ import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
 import java.awt.Dimension;
+import java.awt.FlowLayout;
 import java.awt.Font;
 import java.awt.Graphics;
 import java.awt.GridLayout;
@@ -145,7 +149,9 @@ public class FeatureSettings extends JPanel
 
   float originalTransparency;
 
-  Map<String, FeatureMatcherSetI> originalFilters;
+  private ViewStyleI originalViewStyle;
+
+  private Map<String, FeatureMatcherSetI> originalFilters;
 
   final JInternalFrame frame;
 
@@ -192,6 +198,7 @@ public class FeatureSettings extends JPanel
     transparency.setMaximum(100 - originalTransparencyAsPercent);
 
     originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
+    originalViewStyle = new ViewStyle(af.viewport.getViewStyle());
 
     try
     {
@@ -277,20 +284,23 @@ public class FeatureSettings extends JPanel
       @Override
       public void mousePressed(MouseEvent evt)
       {
-        selectedRow = table.rowAtPoint(evt.getPoint());
+        Point pt = evt.getPoint();
+        selectedRow = table.rowAtPoint(pt);
         String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
         if (evt.isPopupTrigger())
         {
           Object colour = table.getValueAt(selectedRow, COLOUR_COLUMN);
           showPopupMenu(selectedRow, type, colour, evt.getPoint());
         }
-        else if (evt.getClickCount() == 2)
+        else if (evt.getClickCount() == 2
+                && table.columnAtPoint(pt) == TYPE_COLUMN)
         {
           boolean invertSelection = evt.isAltDown();
           boolean toggleSelection = Platform.isControlDown(evt);
           boolean extendSelection = evt.isShiftDown();
           fr.ap.alignFrame.avc.markColumnsContainingFeatures(
                   invertSelection, extendSelection, toggleSelection, type);
+          fr.ap.av.sendSelection();
         }
       }
 
@@ -379,7 +389,7 @@ public class FeatureSettings extends JPanel
                       javax.swing.event.InternalFrameEvent evt)
               {
                 fr.removePropertyChangeListener(change);
-              };
+              }
             });
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     inConstruction = false;
@@ -513,6 +523,7 @@ public class FeatureSettings extends JPanel
       {
         fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
                 false, type);
+        fr.ap.av.sendSelection();
       }
     });
     JMenuItem clearCols = new JMenuItem(MessageManager
@@ -524,6 +535,7 @@ public class FeatureSettings extends JPanel
       {
         fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
                 false, type);
+        fr.ap.av.sendSelection();
       }
     });
     JMenuItem hideCols = new JMenuItem(
@@ -534,6 +546,7 @@ public class FeatureSettings extends JPanel
       public void actionPerformed(ActionEvent arg0)
       {
         fr.ap.alignFrame.hideFeatureColumns(type, true);
+        fr.ap.av.sendSelection();
       }
     });
     JMenuItem hideOtherCols = new JMenuItem(
@@ -544,6 +557,7 @@ public class FeatureSettings extends JPanel
       public void actionPerformed(ActionEvent arg0)
       {
         fr.ap.alignFrame.hideFeatureColumns(type, false);
+        fr.ap.av.sendSelection();
       }
     });
     men.add(selCols);
@@ -607,7 +621,7 @@ public class FeatureSettings extends JPanel
       {
         fr.setGroupVisibility(check.getText(), check.isSelected());
         resetTable(new String[] { grp });
-        af.alignPanel.paintAlignment(true, true);
+        refreshDisplay();
       }
     });
     groupPanel.add(check);
@@ -1166,7 +1180,7 @@ public class FeatureSettings extends JPanel
 
     if (fr.setFeaturePriority(rowData, visibleNew))
     {
-      af.alignPanel.paintAlignment(true, true);
+      refreshDisplay();
     }
   }
 
@@ -1275,6 +1289,7 @@ public class FeatureSettings extends JPanel
         fr.setTransparency(originalTransparency);
         fr.setFeatureFilters(originalFilters);
         updateFeatureRenderer(originalData);
+        af.getViewport().setViewStyle(originalViewStyle);
         close();
       }
     });
@@ -1325,7 +1340,7 @@ public class FeatureSettings extends JPanel
         if (!inConstruction)
         {
           fr.setTransparency((100 - transparency.getValue()) / 100f);
-          af.alignPanel.paintAlignment(true, true);
+          refreshDisplay();
         }
       }
     });
@@ -1334,8 +1349,42 @@ public class FeatureSettings extends JPanel
     transparency.setToolTipText(
             MessageManager.getString("label.transparency_tip"));
 
-    JPanel transPanel = new JPanel(new GridLayout(1, 2));
-    bigPanel.add(transPanel, BorderLayout.SOUTH);
+    boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+    String text = MessageManager.formatMessage("label.show_linked_features",
+            nucleotide
+                    ? MessageManager.getString("label.protein")
+                            .toLowerCase()
+                    : "CDS");
+    JCheckBox showComplement = new JCheckBox(text);
+    showComplement.setSelected(af.getViewport().isShowComplementFeatures());
+    showComplement.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        af.getViewport()
+                .setShowComplementFeatures(showComplement.isSelected());
+        refreshDisplay();
+      }
+    });
+
+    JCheckBox showComplementOnTop = new JCheckBox(
+            MessageManager.getString("label.on_top"));
+    showComplementOnTop
+            .setSelected(af.getViewport().isShowComplementFeaturesOnTop());
+    showComplementOnTop.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        af.getViewport().setShowComplementFeaturesOnTop(
+                showComplementOnTop.isSelected());
+        refreshDisplay();
+      }
+    });
+
+    JPanel lowerPanel = new JPanel(new GridLayout(1, 2));
+    bigPanel.add(lowerPanel, BorderLayout.SOUTH);
 
     JPanel transbuttons = new JPanel(new GridLayout(5, 1));
     transbuttons.add(optimizeOrder);
@@ -1343,8 +1392,21 @@ public class FeatureSettings extends JPanel
     transbuttons.add(sortByScore);
     transbuttons.add(sortByDens);
     transbuttons.add(help);
-    transPanel.add(transparency);
-    transPanel.add(transbuttons);
+
+    boolean hasComplement = af.getViewport().getCodingComplement() != null;
+    JPanel transPanelLeft = new JPanel(
+            new GridLayout(hasComplement ? 3 : 2, 1));
+    transPanelLeft.add(new JLabel(" Colour transparency" + ":"));
+    transPanelLeft.add(transparency);
+    if (hasComplement)
+    {
+      JPanel cp = new JPanel(new FlowLayout(FlowLayout.LEFT));
+      cp.add(showComplement);
+      cp.add(showComplementOnTop);
+      transPanelLeft.add(cp);
+    }
+    lowerPanel.add(transPanelLeft);
+    lowerPanel.add(transbuttons);
 
     JPanel buttonPanel = new JPanel();
     buttonPanel.add(ok);
@@ -1358,11 +1420,27 @@ public class FeatureSettings extends JPanel
   }
 
   /**
+   * Repaints alignment, structure and overview (if shown). If there is a
+   * complementary view which is showing this view's features, then also
+   * repaints that.
+   */
+  void refreshDisplay()
+  {
+    af.alignPanel.paintAlignment(true, true);
+    AlignViewportI complement = af.getViewport().getCodingComplement();
+    if (complement != null && complement.isShowComplementFeatures())
+    {
+      AlignFrame af2 = Desktop.getAlignFrameFor(complement);
+      af2.alignPanel.paintAlignment(true, true);
+    }
+  }
+
+  /**
    * Answers a suitable tooltip to show on the colour cell of the table
    * 
    * @param fcol
    * @param withHint
-   *          if true include 'click to edit' and similar text
+   *                   if true include 'click to edit' and similar text
    * @return
    */
   public static String getColorTooltip(FeatureColourI fcol,
@@ -1499,13 +1577,22 @@ public class FeatureSettings extends JPanel
     }
 
     /**
-     * Answers the class of the object in column c of the first row of the table
+     * Answers the class of column c of the table
      */
     @Override
     public Class<?> getColumnClass(int c)
     {
-      Object v = getValueAt(0, c);
-      return v == null ? null : v.getClass();
+      switch (c)
+      {
+      case TYPE_COLUMN:
+        return String.class;
+      case COLOUR_COLUMN:
+        return FeatureColour.class;
+      case FILTER_COLUMN:
+        return FeatureMatcherSet.class;
+      default:
+        return Boolean.class;
+      }
     }
 
     @Override