X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=7d09f1bd4f68c9b6abacc193be131e7af0db7bcd;hb=7c612cf2073df1d290399042a7ecec55adc0e7e7;hp=e4842ee9cf633e1142b03ffaf49afb86a2ccbb3a;hpb=c3ded07cf4a7708564e9878bf1763fe837e03ddc;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index e4842ee..7d09f1b 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,7 +23,6 @@ import java.awt.event.*;
 import javax.swing.*;
 import javax.swing.event.*;
 
-import jalview.gui.*;
 import jalview.schemes.*;
 
 public class GAlignFrame
@@ -115,10 +114,88 @@ public class GAlignFrame
   JMenu jMenu2 = new JMenu();
   JMenuItem padGapsMenuitem = new JMenuItem();
   JMenuItem ClustalRealign = new JMenuItem();
+  protected ButtonGroup colours = new ButtonGroup();
 
   public GAlignFrame()
   {
-    ButtonGroup colours = new ButtonGroup();
+
+
+    try
+    {
+      jbInit();
+      setJMenuBar(alignFrameMenuBar);
+
+      // dynamically fill save as menu with available formats
+      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
+      {
+        JMenuItem item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
+                             elementAt(
+                                 i));
+        item.addActionListener(new java.awt.event.ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            outputText_actionPerformed(e);
+          }
+        });
+
+        outputTextboxMenu.add(item);
+      }
+    }
+    catch (Exception e)
+    {
+    }
+
+
+    if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+    {
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+          getUserColourSchemes().keys();
+
+      while (userColours.hasMoreElements())
+      {
+        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+            nextElement().toString());
+        radioItem.setName("USER_DEFINED");
+        radioItem.addMouseListener(new MouseAdapter()
+            {
+              public void mousePressed(MouseEvent evt)
+              {
+                if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+                {
+                  radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+                  int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+                      "Remove from default list?",
+                      "Remove user defined colour",
+                      JOptionPane.YES_NO_OPTION);
+                  if(option == JOptionPane.YES_OPTION)
+                  {
+                    jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+                    colourMenu.remove(radioItem);
+                  }
+                  else
+                    radioItem.addActionListener(new ActionListener()
+                    {
+                      public void actionPerformed(ActionEvent evt)
+                      {
+                        userDefinedColour_actionPerformed(evt);
+                      }
+                    });
+                }
+              }
+            });
+        radioItem.addActionListener(new ActionListener()
+        {
+          public void actionPerformed(ActionEvent evt)
+          {
+            userDefinedColour_actionPerformed(evt);
+          }
+        });
+        colourMenu.insert(radioItem, 15);
+        colours.add(radioItem);
+      }
+    }
     colours.add(noColourmenuItem);
     colours.add(clustalColour);
     colours.add(zappoColour);
@@ -133,9 +210,13 @@ public class GAlignFrame
     colours.add(BLOSUM62Colour);
     colours.add(nucleotideColour);
 
-    noColourmenuItem.setSelected(true);
+    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
+
 
-    String defaultColour = Preferences.defaultColour;
+  }
+
+  public void setColourSelected(String defaultColour)
+  {
 
     if (defaultColour != null)
     {
@@ -143,6 +224,9 @@ public class GAlignFrame
 
       switch (index)
       {
+        case ColourSchemeProperty.NONE:
+              noColourmenuItem.setSelected(true);
+              break;
         case ColourSchemeProperty.CLUSTAL:
           clustalColour.setSelected(true);
 
@@ -163,6 +247,10 @@ public class GAlignFrame
 
           break;
 
+        case ColourSchemeProperty.TAYLOR:
+          taylorColour.setSelected(true);
+          break;
+
         case ColourSchemeProperty.HYDROPHOBIC:
           hydrophobicityColour.setSelected(true);
 
@@ -200,34 +288,6 @@ public class GAlignFrame
       }
     }
 
-    try
-    {
-      jbInit();
-      setJMenuBar(alignFrameMenuBar);
-
-      JMenuItem item;
-
-      // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
-      {
-        item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
-                             elementAt(
-                                 i));
-        item.addActionListener(new java.awt.event.ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            outputText_actionPerformed(e);
-          }
-        });
-
-        outputTextboxMenu.add(item);
-      }
-    }
-    catch (Exception e)
-    {
-    }
-
   }
 
   private void jbInit()
@@ -237,6 +297,8 @@ public class GAlignFrame
     fileMenu.setText("File");
     saveAlignmentMenu.setMnemonic('L');
     saveAlignmentMenu.setText("Save As");
+    saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+        awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
     saveAlignmentMenu.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -549,7 +611,7 @@ public class GAlignFrame
     });
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem.setText("Show Annotations");
-    annotationPanelMenuItem.setState(jalview.gui.Preferences.showAnnotation);
+    annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));
     annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)