Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index cf7bdb3..d65016e 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -58,6 +58,7 @@ import java.io.FileOutputStream;
 import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
+import java.util.Arrays;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
@@ -173,7 +174,7 @@ public class FeatureSettings extends JPanel implements
       public void mousePressed(MouseEvent evt)
       {
         selectedRow = table.rowAtPoint(evt.getPoint());
-        if (SwingUtilities.isRightMouseButton(evt))
+        if (evt.isPopupTrigger())
         {
           popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
                   table.getValueAt(selectedRow, 1), fr.getMinMax(),
@@ -181,14 +182,16 @@ public class FeatureSettings extends JPanel implements
         }
         else if (evt.getClickCount() == 2)
         {
+          boolean invertSelection = evt.isAltDown();
+          boolean toggleSelection = Platform.isControlDown(evt);
+          boolean extendSelection = evt.isShiftDown();
           fr.ap.alignFrame.avc.markColumnsContainingFeatures(
-                  evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(),
-                  evt.isMetaDown(),
+                  invertSelection, extendSelection, toggleSelection,
                   (String) table.getValueAt(selectedRow, 0));
         }
       }
 
-      // isPopupTrigger fires on mouseReleased on Mac
+      // isPopupTrigger fires on mouseReleased on Windows
       @Override
       public void mouseReleased(MouseEvent evt)
       {
@@ -210,19 +213,22 @@ public class FeatureSettings extends JPanel implements
         int newRow = table.rowAtPoint(evt.getPoint());
         if (newRow != selectedRow && selectedRow != -1 && newRow != -1)
         {
-          Object[] temp = new Object[3];
-          temp[0] = table.getValueAt(selectedRow, 0);
-          temp[1] = table.getValueAt(selectedRow, 1);
-          temp[2] = table.getValueAt(selectedRow, 2);
-
-          table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);
-          table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);
-          table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);
-
-          table.setValueAt(temp[0], newRow, 0);
-          table.setValueAt(temp[1], newRow, 1);
-          table.setValueAt(temp[2], newRow, 2);
-
+          /*
+           * reposition 'selectedRow' to 'newRow' (the dragged to location)
+           * this could be more than one row away for a very fast drag action
+           * so just swap it with adjacent rows until we get it there
+           */
+          Object[][] data = ((FeatureTableModel) table.getModel())
+                  .getData();
+          int direction = newRow < selectedRow ? -1 : 1;
+          for (int i = selectedRow; i != newRow; i += direction)
+          {
+            Object[] temp = data[i];
+            data[i] = data[i + direction];
+            data[i + direction] = temp;
+          }
+          updateFeatureRenderer(data);
+          table.repaint();
           selectedRow = newRow;
         }
       }
@@ -286,7 +292,7 @@ public class FeatureSettings extends JPanel implements
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 
-  protected void popupSort(final int row, final String type,
+  protected void popupSort(final int selectedRow, final String type,
           final Object typeCol, final Map<String, float[][]> minmax, int x,
           int y)
   {
@@ -304,7 +310,8 @@ public class FeatureSettings extends JPanel implements
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.af.avc.sortAlignmentByFeatureScore(new String[] { type });
+        me.af.avc.sortAlignmentByFeatureScore(Arrays
+                .asList(new String[] { type }));
       }
 
     });
@@ -316,7 +323,8 @@ public class FeatureSettings extends JPanel implements
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.af.avc.sortAlignmentByFeatureDensity(new String[] { type });
+        me.af.avc.sortAlignmentByFeatureDensity(Arrays
+                .asList(new String[] { type }));
       }
 
     });
@@ -380,13 +388,15 @@ public class FeatureSettings extends JPanel implements
               {
                 FeatureColourChooser fc = (FeatureColourChooser) e
                         .getSource();
-                table.setValueAt(fc.getLastColour(), row, 1);
+                table.setValueAt(fc.getLastColour(), selectedRow, 1);
                 table.validate();
               }
               else
               {
                 // probably the color chooser!
-                table.setValueAt(colorChooser.getColor(), row, 1);
+                table.setValueAt(
+                        new FeatureColour(colorChooser.getColor()),
+                        selectedRow, 1);
                 table.validate();
                 me.updateFeatureRenderer(
                         ((FeatureTableModel) table.getModel()).getData(),
@@ -402,7 +412,6 @@ public class FeatureSettings extends JPanel implements
             MessageManager.getString("label.select_columns_containing"));
     selCols.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
@@ -414,7 +423,6 @@ public class FeatureSettings extends JPanel implements
             MessageManager.getString("label.select_columns_not_containing"));
     clearCols.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
@@ -422,8 +430,30 @@ public class FeatureSettings extends JPanel implements
                 false, type);
       }
     });
+    JMenuItem hideCols = new JMenuItem(
+            MessageManager.getString("label.hide_columns_containing"));
+    hideCols.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        fr.ap.alignFrame.hideFeatureColumns(type, true);
+      }
+    });
+    JMenuItem hideOtherCols = new JMenuItem(
+            MessageManager.getString("label.hide_columns_not_containing"));
+    hideOtherCols.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        fr.ap.alignFrame.hideFeatureColumns(type, false);
+      }
+    });
     men.add(selCols);
     men.add(clearCols);
+    men.add(hideCols);
+    men.add(hideOtherCols);
     men.show(table, x, y);
   }
 
@@ -719,10 +749,8 @@ public class FeatureSettings extends JPanel implements
   void load()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            new String[] { "fc" },
-            new String[] { "Sequence Feature Colours" },
-            "Sequence Feature Colours");
+            Cache.getProperty("LAST_DIRECTORY"), "fc",
+            "Sequence Feature Colours", "Sequence Feature Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle(MessageManager
             .getString("label.load_feature_colours"));
@@ -814,10 +842,8 @@ public class FeatureSettings extends JPanel implements
   void save()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            new String[] { "fc" },
-            new String[] { "Sequence Feature Colours" },
-            "Sequence Feature Colours");
+            Cache.getProperty("LAST_DIRECTORY"), "fc",
+            "Sequence Feature Colours", "Sequence Feature Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle(MessageManager
             .getString("label.save_feature_colours"));
@@ -970,10 +996,19 @@ public class FeatureSettings extends JPanel implements
     updateFeatureRenderer(data, true);
   }
 
+  /**
+   * Update the priority order of features; only repaint if this changed the
+   * order of visible features
+   * 
+   * @param data
+   * @param visibleNew
+   */
   private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
   {
-    fr.setFeaturePriority(data, visibleNew);
-    af.alignPanel.paintAlignment(true);
+    if (fr.setFeaturePriority(data, visibleNew))
+    {
+      af.alignPanel.paintAlignment(true);
+    }
   }
 
   int selectedRow = -1;
@@ -1364,15 +1399,15 @@ public class FeatureSettings extends JPanel implements
   public void noDasSourceActive()
   {
     complete();
-    JOptionPane
+    JvOptionPane
             .showInternalConfirmDialog(
                     Desktop.desktop,
                     MessageManager
                             .getString("label.no_das_sources_selected_warn"),
                     MessageManager
                             .getString("label.no_das_sources_selected_title"),
-                    JOptionPane.DEFAULT_OPTION,
-                    JOptionPane.INFORMATION_MESSAGE);
+                    JvOptionPane.DEFAULT_OPTION,
+                    JvOptionPane.INFORMATION_MESSAGE);
   }
 
   // ///////////////////////////////////////////////////////////////////////