JAL-2361 Blosum is enabled for peptide

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

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 90ad51d..048f441 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -28,7 +28,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
 import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.StructureFile;
@@ -40,12 +40,14 @@ import jalview.schemes.PurinePyrimidineColourScheme;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.dbsources.Pdb;
 
+import java.awt.Color;
 import java.awt.event.ActionEvent;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
@@ -66,7 +68,6 @@ import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
 import javax.swing.JInternalFrame;
 import javax.swing.JMenu;
-import javax.swing.JOptionPane;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 import javax.swing.event.MenuEvent;
@@ -575,12 +576,12 @@ public class ChimeraViewFrame extends StructureViewerBase
             jmb.openFile(pe);
             jmb.addSequence(pos, jmb.getSequence()[pos]);
             File fl = new File(pe.getFile());
-            String protocol = AppletFormatAdapter.URL;
+            DataSourceType protocol = DataSourceType.URL;
             try
             {
               if (fl.exists())
               {
-                protocol = AppletFormatAdapter.FILE;
+                protocol = DataSourceType.FILE;
               }
             } catch (Throwable e)
             {
@@ -925,18 +926,27 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   @Override
-  public void userColour_actionPerformed(ActionEvent actionEvent)
+  public void userColour_actionPerformed(ActionEvent e)
   {
-    userColour.setSelected(true);
-    new UserDefinedColours(this, null);
+    if (e.getActionCommand().equals(
+            MessageManager.getString("action.user_defined")))
+    {
+      new UserDefinedColours(this, null);
+    }
+    else
+    {
+      UserColourScheme udc = UserDefinedColours.getUserColourSchemes().get(
+              e.getActionCommand());
+      jmb.setJalviewColourScheme(udc);
+    }
   }
 
   @Override
   public void backGround_actionPerformed(ActionEvent actionEvent)
   {
-    java.awt.Color col = JColorChooser
-            .showDialog(this, MessageManager
-                    .getString("label.select_backgroud_colour"), null);
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_background_colour"),
+            null);
     if (col != null)
     {
       jmb.setBackgroundColour(col);