Merge develop to Release_2_8_3_Branch

[jalview.git] / src / jalview / jbgui / GPreferences.java

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 8f226ef..1d35477 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -22,6 +22,7 @@ package jalview.jbgui;
 
 import jalview.gui.JvSwingUtils;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.jbgui.PDBDocFieldPreferences.PreferenceSource;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -149,6 +150,7 @@ public class GPreferences extends JPanel
 
   protected JTextField chimeraPath = new JTextField();
 
+
   /*
    * Colours tab components
    */
@@ -156,7 +158,9 @@ public class GPreferences extends JPanel
 
   protected JPanel maxColour = new JPanel();
 
-  protected JComboBox<String> colour = new JComboBox<String>();
+  protected JComboBox<String> protColour = new JComboBox<String>();
+
+  protected JComboBox<String> nucColour = new JComboBox<String>();
 
   /*
    * Connections tab components
@@ -692,16 +696,30 @@ public class GPreferences extends JPanel
         maxColour_actionPerformed(maxColour);
       }
     });
-    colour.setFont(verdana11);
-    colour.setBounds(new Rectangle(172, 225, 155, 21));
-    JLabel colourLabel = new JLabel();
-    colourLabel.setFont(verdana11);
-    colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    colourLabel.setText(MessageManager.getString("label.alignment_colour")
+
+    protColour.setFont(verdana11);
+    protColour.setBounds(new Rectangle(172, 225, 155, 21));
+    JLabel protColourLabel = new JLabel();
+    protColourLabel.setFont(verdana11);
+    protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
+    protColourLabel.setText(MessageManager
+            .getString("label.prot_alignment_colour") + " ");
+    JvSwingUtils.addtoLayout(coloursTab, MessageManager
+            .getString("label.default_colour_scheme_for_alignment"),
+            protColourLabel, protColour);
+
+    nucColour.setFont(verdana11);
+    nucColour.setBounds(new Rectangle(172, 240, 155, 21));
+    JLabel nucColourLabel = new JLabel();
+    nucColourLabel.setFont(verdana11);
+    nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
+    nucColourLabel.setText(MessageManager
+            .getString("label.nuc_alignment_colour")
             + " ");
     JvSwingUtils.addtoLayout(coloursTab, MessageManager
             .getString("label.default_colour_scheme_for_alignment"),
-            colourLabel, colour);
+            nucColourLabel, nucColour);
+
     JPanel annotationShding = new JPanel();
     annotationShding.setBorder(new TitledBorder(MessageManager
             .getString("label.annotation_shading_default")));
@@ -729,8 +747,8 @@ public class GPreferences extends JPanel
             .getString("label.structure_options")));
     structureTab.setLayout(null);
     final int width = 400;
-    final int height = 23;
-    final int lineSpacing = 30;
+    final int height = 22;
+    final int lineSpacing = 25;
     int ypos = 30;
 
     structFromPdb.setFont(verdana11);
@@ -824,9 +842,23 @@ public class GPreferences extends JPanel
     });
     structureTab.add(chimeraPath);
 
+    ypos += lineSpacing;
+    // scrl_pdbDocFieldConfig.setPreferredSize(new Dimension(450, 100));
+    // scrl_pdbDocFieldConfig
+    // .setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+    // scrl_pdbDocFieldConfig.setBounds();
+    PDBDocFieldPreferences docFieldPref = new PDBDocFieldPreferences(
+            PreferenceSource.PREFERENCES);
+    docFieldPref.setBounds(new Rectangle(10, ypos + 5, 450, 120));
+    structureTab.add(docFieldPref);
+
+
+
+
     return structureTab;
   }
 
+
   /**
    * Action on choosing a structure viewer from combobox options.
    *