JAL-1355
[jalview.git] / src / jalview / gui / FeatureSettings.java
index 963209c..08c4ef2 100644 (file)
@@ -1,26 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
 import java.io.*;
 import java.util.*;
 import java.util.List;
-
 import java.awt.*;
 import java.awt.event.*;
 import java.beans.PropertyChangeEvent;
@@ -99,12 +101,19 @@ public class FeatureSettings extends JPanel
       public void mousePressed(MouseEvent evt)
       {
         selectedRow = table.rowAtPoint(evt.getPoint());
-        if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+        if (evt.isPopupTrigger())
         {
           popupSort(selectedRow, (String) table.getValueAt(selectedRow, 0),
                   table.getValueAt(selectedRow, 1), fr.minmax, evt.getX(),
                   evt.getY());
         }
+        else if (evt.getClickCount() == 2)
+        {
+          fr.ap.alignFrame.avc.markColumnsContainingFeatures(
+                  evt.isAltDown(), evt.isShiftDown() || evt.isMetaDown(),
+                  evt.isMetaDown(),
+                  (String) table.getValueAt(selectedRow, 0));
+        }
       }
     });
 
@@ -132,7 +141,8 @@ public class FeatureSettings extends JPanel
         }
       }
     });
-
+    table.setToolTipText(JvSwingUtils
+                    .wrapTooltip(MessageManager.getString("label.feature_settings_click_drag")));
     scrollPane.setViewportView(table);
 
     dassourceBrowser = new DasSourceBrowser(this);
@@ -166,11 +176,15 @@ public class FeatureSettings extends JPanel
     frame.setContentPane(this);
     if (new jalview.util.Platform().isAMac())
     {
-      Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), 475, 480);
+      Desktop.addInternalFrame(frame,
+              MessageManager.getString("label.sequence_feature_settings"),
+              475, 480);
     }
     else
     {
-      Desktop.addInternalFrame(frame, MessageManager.getString("label.sequence_feature_settings"), 400, 450);
+      Desktop.addInternalFrame(frame,
+              MessageManager.getString("label.sequence_feature_settings"),
+              400, 450);
     }
 
     frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
@@ -188,8 +202,11 @@ public class FeatureSettings extends JPanel
   protected void popupSort(final int selectedRow, final String type,
           final Object typeCol, final Hashtable minmax, int x, int y)
   {
-    JPopupMenu men = new JPopupMenu(MessageManager.formatMessage("label.settings_for_param", new String[]{type}));
-    JMenuItem scr = new JMenuItem(MessageManager.getString("label.sort_by_score"));
+    JPopupMenu men = new JPopupMenu(MessageManager.formatMessage(
+            "label.settings_for_param", new String[]
+            { type }));
+    JMenuItem scr = new JMenuItem(
+            MessageManager.getString("label.sort_by_score"));
     men.add(scr);
     final FeatureSettings me = this;
     scr.addActionListener(new ActionListener()
@@ -202,7 +219,8 @@ public class FeatureSettings extends JPanel
       }
 
     });
-    JMenuItem dens = new JMenuItem(MessageManager.getString("label.sort_by_density"));
+    JMenuItem dens = new JMenuItem(
+            MessageManager.getString("label.sort_by_density"));
     dens.addActionListener(new ActionListener()
     {
 
@@ -291,6 +309,32 @@ public class FeatureSettings extends JPanel
         });
       }
     }
+    JMenuItem selCols = new JMenuItem(
+            MessageManager.getString("label.select_columns_containing"));
+    selCols.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
+                false, type);
+      }
+    });
+    JMenuItem clearCols = new JMenuItem(
+            MessageManager.getString("label.select_columns_not_containing"));
+    clearCols.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
+                false, type);
+      }
+    });
+    men.add(selCols);
+    men.add(clearCols);
     men.show(table, x, y);
   }
 
@@ -924,7 +968,8 @@ public class FeatureSettings extends JPanel
       }
     });
     sortByScore.setFont(JvSwingUtils.getLabelFont());
-    sortByScore.setText(MessageManager.getString("label.seq_sort_by_score"));
+    sortByScore
+            .setText(MessageManager.getString("label.seq_sort_by_score"));
     sortByScore.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -933,7 +978,8 @@ public class FeatureSettings extends JPanel
       }
     });
     sortByDens.setFont(JvSwingUtils.getLabelFont());
-    sortByDens.setText(MessageManager.getString("label.sequence_sort_by_density"));
+    sortByDens.setText(MessageManager
+            .getString("label.sequence_sort_by_density"));
     sortByDens.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -1130,13 +1176,13 @@ public class FeatureSettings extends JPanel
   private String[] getDisplayedFeatureGroups()
   {
     String[] gps = null;
+    ArrayList<String> _gps = new ArrayList<String>();
     if (fr != null)
     {
 
       if (fr.featureGroups != null)
       {
         Iterator en = fr.featureGroups.keySet().iterator();
-        gps = new String[fr.featureColours.size()];
         int g = 0;
         boolean valid = false;
         while (en.hasNext())
@@ -1146,17 +1192,18 @@ public class FeatureSettings extends JPanel
           if (on != null && on.booleanValue())
           {
             valid = true;
-            gps[g++] = gp;
+            _gps.add(gp);
           }
         }
-        while (g < gps.length)
-        {
-          gps[g++] = null;
-        }
         if (!valid)
         {
           return null;
         }
+        else
+        {
+          gps = new String[_gps.size()];
+          _gps.toArray(gps);
+        }
       }
     }
     return gps;
@@ -1311,10 +1358,15 @@ public class FeatureSettings extends JPanel
   public void noDasSourceActive()
   {
     complete();
-    JOptionPane.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);
+    JOptionPane
+            .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);
   }
 
   // ///////////////////////////////////////////////////////////////////////