JAL-2008 avoid unnecessary repaints; signatures changed from String[] to

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 6b58b51..6ca0769 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -54,6 +54,7 @@ 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;
@@ -164,6 +165,7 @@ public class FeatureSettings extends JPanel implements
 
     table.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent evt)
       {
         selectedRow = table.rowAtPoint(evt.getPoint());
@@ -198,24 +200,19 @@ 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 +234,7 @@ 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 +265,7 @@ public class FeatureSettings extends JPanel implements
 
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     {
+      @Override
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
@@ -289,9 +288,11 @@ 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 }));
       }
 
     });
@@ -300,9 +301,11 @@ 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 }));
       }
 
     });
@@ -337,6 +340,7 @@ public class FeatureSettings extends JPanel implements
         {
           JColorChooser colorChooser;
 
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             if (e.getSource() == mxcol)
@@ -507,6 +511,7 @@ 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());
@@ -969,10 +974,19 @@ 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 +1043,7 @@ 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 +1053,7 @@ 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 +1064,7 @@ 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 +1075,7 @@ 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 +1085,7 @@ 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 +1101,7 @@ 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 +1117,7 @@ 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 +1129,7 @@ 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 +1139,7 @@ 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 +1149,7 @@ 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 +1157,7 @@ public class FeatureSettings extends JPanel implements
     });
     transparency.addChangeListener(new ChangeListener()
     {
+      @Override
       public void stateChanged(ChangeEvent evt)
       {
         fr.setTransparency((100 - transparency.getValue()) / 100f);
@@ -1146,6 +1171,7 @@ 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 +1180,7 @@ 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 +1192,7 @@ 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);
@@ -1304,6 +1332,7 @@ public class FeatureSettings extends JPanel implements
       Runnable fetcher = new Runnable()
       {
 
+        @Override
         public void run()
         {
           doDasFeatureFetch(dassources, true, false);
@@ -1385,6 +1414,7 @@ public class FeatureSettings extends JPanel implements
       this.data = data;
     }
 
+    @Override
     public int getColumnCount()
     {
       return columnNames.length;
@@ -1395,31 +1425,37 @@ 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 +1480,7 @@ 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 +1646,19 @@ 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 +1739,7 @@ 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 +1785,7 @@ class ColorEditor extends AbstractCellEditor implements TableCellEditor,
   }
 
   // Implement the one CellEditor method that AbstractCellEditor doesn't.
+  @Override
   public Object getCellEditorValue()
   {
     if (currentColor == null)
@@ -1754,6 +1796,7 @@ 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)
   {