Merge branch 'develop' into features/JAL-2110_crossRefDuplications

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 6b58b51..09204d1 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -28,7 +28,9 @@ import jalview.gui.Help.HelpId;
 import jalview.io.JalviewFileChooser;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.GraduatedColor;
+import jalview.util.Format;
 import jalview.util.MessageManager;
+import jalview.util.QuickSort;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
 
@@ -54,9 +56,11 @@ 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;
+import java.util.Map;
 import java.util.Set;
 import java.util.Vector;
 
@@ -164,10 +168,11 @@ public class FeatureSettings extends JPanel implements
 
     table.addMouseListener(new MouseAdapter()
     {
+      @Override
       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(),
@@ -198,24 +203,19 @@ public class FeatureSettings extends JPanel implements
 
     table.addMouseMotionListener(new MouseMotionAdapter()
     {
+      @Override
       public void mouseDragged(MouseEvent evt)
       {
         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);
-
+          Object[][] data = ((FeatureTableModel) table.getModel())
+                  .getData();
+          Object[] temp = data[selectedRow];
+          data[selectedRow] = data[newRow];
+          data[newRow] = temp;
+          updateFeatureRenderer(data);
+          table.repaint();
           selectedRow = newRow;
         }
       }
@@ -237,6 +237,7 @@ public class FeatureSettings extends JPanel implements
     final FeatureSettings fs = this;
     fr.addPropertyChangeListener(change = new PropertyChangeListener()
     {
+      @Override
       public void propertyChange(PropertyChangeEvent evt)
       {
         if (!fs.resettingTable && !fs.handlingUpdate)
@@ -267,6 +268,7 @@ public class FeatureSettings extends JPanel implements
 
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     {
+      @Override
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
@@ -278,7 +280,8 @@ public class FeatureSettings extends JPanel implements
   }
 
   protected void popupSort(final int selectedRow, final String type,
-          final Object typeCol, final Hashtable minmax, int x, int y)
+          final Object typeCol, final Map<String, float[][]> minmax, int x,
+          int y)
   {
     JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
             "label.settings_for_param", new String[] { type }));
@@ -289,9 +292,11 @@ public class FeatureSettings extends JPanel implements
     scr.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.af.avc.sortAlignmentByFeatureScore(new String[] { type });
+        me.af.avc.sortAlignmentByFeatureScore(Arrays
+                .asList(new String[] { type }));
       }
 
     });
@@ -300,16 +305,18 @@ public class FeatureSettings extends JPanel implements
     dens.addActionListener(new ActionListener()
     {
 
+      @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.af.avc.sortAlignmentByFeatureDensity(new String[] { type });
+        me.af.avc.sortAlignmentByFeatureDensity(Arrays
+                .asList(new String[] { type }));
       }
 
     });
     men.add(dens);
     if (minmax != null)
     {
-      final Object typeMinMax = minmax.get(type);
+      final float[][] typeMinMax = minmax.get(type);
       /*
        * final JCheckBoxMenuItem chb = new JCheckBoxMenuItem("Vary Height"); //
        * this is broken at the moment and isn't that useful anyway!
@@ -324,7 +331,7 @@ public class FeatureSettings extends JPanel implements
        * 
        * men.add(chb);
        */
-      if (typeMinMax != null && ((float[][]) typeMinMax)[0] != null)
+      if (typeMinMax != null && typeMinMax[0] != null)
       {
         // if (table.getValueAt(row, column));
         // graduated colourschemes for those where minmax exists for the
@@ -337,6 +344,7 @@ public class FeatureSettings extends JPanel implements
         {
           JColorChooser colorChooser;
 
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             if (e.getSource() == mxcol)
@@ -388,7 +396,6 @@ public class FeatureSettings extends JPanel implements
             MessageManager.getString("label.select_columns_containing"));
     selCols.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
@@ -400,7 +407,6 @@ public class FeatureSettings extends JPanel implements
             MessageManager.getString("label.select_columns_not_containing"));
     clearCols.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
@@ -408,8 +414,30 @@ 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);
   }
 
@@ -507,6 +535,7 @@ public class FeatureSettings extends JPanel implements
     check.setFont(new Font("Serif", Font.BOLD, 12));
     check.addItemListener(new ItemListener()
     {
+      @Override
       public void itemStateChanged(ItemEvent evt)
       {
         fr.setGroupVisibility(check.getText(), check.isSelected());
@@ -803,7 +832,7 @@ public class FeatureSettings extends JPanel implements
   void save()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            Cache.getProperty("LAST_DIRECTORY"),
             new String[] { "fc" },
             new String[] { "Sequence Feature Colours" },
             "Sequence Feature Colours");
@@ -824,34 +853,35 @@ public class FeatureSettings extends JPanel implements
         PrintWriter out = new PrintWriter(new OutputStreamWriter(
                 new FileOutputStream(choice), "UTF-8"));
 
-        Set fr_colours = fr.getAllFeatureColours();
-        Iterator e = fr_colours.iterator();
+        Set<String> fr_colours = fr.getAllFeatureColours();
+        Iterator<String> e = fr_colours.iterator();
         float[] sortOrder = new float[fr_colours.size()];
         String[] sortTypes = new String[fr_colours.size()];
         int i = 0;
         while (e.hasNext())
         {
-          sortTypes[i] = e.next().toString();
+          sortTypes[i] = e.next();
           sortOrder[i] = fr.getOrder(sortTypes[i]);
           i++;
         }
-        jalview.util.QuickSort.sort(sortOrder, sortTypes);
+        QuickSort.sort(sortOrder, sortTypes);
         sortOrder = null;
         Object fcol;
         GraduatedColor gcol;
-        for (i = 0; i < sortTypes.length; i++)
+        for (String featureType : sortTypes)
         {
           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
-          col.setName(sortTypes[i]);
-          col.setRGB(jalview.util.Format.getHexString(fr.getColour(col
-                  .getName())));
-          fcol = fr.getFeatureStyle(sortTypes[i]);
+          col.setName(featureType);
+          fcol = fr.getFeatureStyle(featureType);
+          Color colour = fcol instanceof Color ? (Color) fcol
+                  : ((GraduatedColor) fcol).getMaxColor();
+          col.setRGB(Format.getHexString(colour));
           if (fcol instanceof GraduatedColor)
           {
             gcol = (GraduatedColor) fcol;
             col.setMin(gcol.getMin());
             col.setMax(gcol.getMax());
-            col.setMinRGB(jalview.util.Format.getHexString(gcol
+            col.setMinRGB(Format.getHexString(gcol
                     .getMinColor()));
             col.setAutoScale(gcol.isAutoScale());
             col.setThreshold(gcol.getThresh());
@@ -969,10 +999,19 @@ 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;
@@ -1029,6 +1068,7 @@ public class FeatureSettings extends JPanel implements
     invert.setText(MessageManager.getString("label.invert_selection"));
     invert.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         invertSelection();
@@ -1038,6 +1078,7 @@ public class FeatureSettings extends JPanel implements
     optimizeOrder.setText(MessageManager.getString("label.optimise_order"));
     optimizeOrder.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         orderByAvWidth();
@@ -1048,6 +1089,7 @@ public class FeatureSettings extends JPanel implements
             .setText(MessageManager.getString("label.seq_sort_by_score"));
     sortByScore.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         af.avc.sortAlignmentByFeatureScore(null);
@@ -1058,6 +1100,7 @@ public class FeatureSettings extends JPanel implements
             .getString("label.sequence_sort_by_density"));
     sortByDens.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         af.avc.sortAlignmentByFeatureDensity(null);
@@ -1067,6 +1110,7 @@ public class FeatureSettings extends JPanel implements
     help.setText(MessageManager.getString("action.help"));
     help.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         try
@@ -1082,6 +1126,7 @@ public class FeatureSettings extends JPanel implements
     help.setText(MessageManager.getString("action.help"));
     help.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         try
@@ -1097,6 +1142,7 @@ public class FeatureSettings extends JPanel implements
     cancel.setText(MessageManager.getString("action.cancel"));
     cancel.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         fr.setTransparency(originalTransparency);
@@ -1108,6 +1154,7 @@ public class FeatureSettings extends JPanel implements
     ok.setText(MessageManager.getString("action.ok"));
     ok.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         close();
@@ -1117,6 +1164,7 @@ public class FeatureSettings extends JPanel implements
     loadColours.setText(MessageManager.getString("label.load_colours"));
     loadColours.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         load();
@@ -1126,6 +1174,7 @@ public class FeatureSettings extends JPanel implements
     saveColours.setText(MessageManager.getString("label.save_colours"));
     saveColours.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         save();
@@ -1133,6 +1182,7 @@ public class FeatureSettings extends JPanel implements
     });
     transparency.addChangeListener(new ChangeListener()
     {
+      @Override
       public void stateChanged(ChangeEvent evt)
       {
         fr.setTransparency((100 - transparency.getValue()) / 100f);
@@ -1146,6 +1196,7 @@ public class FeatureSettings extends JPanel implements
     fetchDAS.setText(MessageManager.getString("label.fetch_das_features"));
     fetchDAS.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         fetchDAS_actionPerformed(e);
@@ -1154,6 +1205,7 @@ public class FeatureSettings extends JPanel implements
     saveDAS.setText(MessageManager.getString("action.save_as_default"));
     saveDAS.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         saveDAS_actionPerformed(e);
@@ -1165,6 +1217,7 @@ public class FeatureSettings extends JPanel implements
     cancelDAS.setText(MessageManager.getString("action.cancel_fetch"));
     cancelDAS.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         cancelDAS_actionPerformed(e);
@@ -1273,7 +1326,7 @@ public class FeatureSettings extends JPanel implements
    * 
    * @return vector of selected das source nicknames
    */
-  public Vector getSelectedSources()
+  public Vector<jalviewSourceI> getSelectedSources()
   {
     return dassourceBrowser.getSelectedSources();
   }
@@ -1304,6 +1357,7 @@ public class FeatureSettings extends JPanel implements
       Runnable fetcher = new Runnable()
       {
 
+        @Override
         public void run()
         {
           doDasFeatureFetch(dassources, true, false);
@@ -1385,6 +1439,7 @@ public class FeatureSettings extends JPanel implements
       this.data = data;
     }
 
+    @Override
     public int getColumnCount()
     {
       return columnNames.length;
@@ -1395,31 +1450,37 @@ public class FeatureSettings extends JPanel implements
       return data[row];
     }
 
+    @Override
     public int getRowCount()
     {
       return data.length;
     }
 
+    @Override
     public String getColumnName(int col)
     {
       return columnNames[col];
     }
 
+    @Override
     public Object getValueAt(int row, int col)
     {
       return data[row][col];
     }
 
+    @Override
     public Class getColumnClass(int c)
     {
       return getValueAt(0, c).getClass();
     }
 
+    @Override
     public boolean isCellEditable(int row, int col)
     {
       return col == 0 ? false : true;
     }
 
+    @Override
     public void setValueAt(Object value, int row, int col)
     {
       data[row][col] = value;
@@ -1444,6 +1505,7 @@ public class FeatureSettings extends JPanel implements
       setVerticalTextPosition(SwingConstants.CENTER);
     }
 
+    @Override
     public Component getTableCellRendererComponent(JTable table,
             Object color, boolean isSelected, boolean hasFocus, int row,
             int column)
@@ -1609,16 +1671,19 @@ class FeatureIcon implements Icon
     }
   }
 
+  @Override
   public int getIconWidth()
   {
     return width;
   }
 
+  @Override
   public int getIconHeight()
   {
     return height;
   }
 
+  @Override
   public void paintIcon(Component c, Graphics g, int x, int y)
   {
 
@@ -1699,6 +1764,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
   /**
    * Handles events from the editor button and from the dialog's OK button.
    */
+  @Override
   public void actionPerformed(ActionEvent e)
   {
 
@@ -1744,6 +1810,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
   }
 
   // Implement the one CellEditor method that AbstractCellEditor doesn't.
+  @Override
   public Object getCellEditorValue()
   {
     if (currentColor == null)
@@ -1754,6 +1821,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
   }
 
   // Implement the one method defined by TableCellEditor.
+  @Override
   public Component getTableCellEditorComponent(JTable table, Object value,
           boolean isSelected, int row, int column)
   {