Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...

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

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 012edb6..7a5c1f1 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -64,7 +64,8 @@ import javax.swing.event.ChangeListener;
 public class UserDefinedColours extends GUserDefinedColours implements
         ChangeListener
 {
-  private static final Font VERDANA_BOLD_10 = new Font("Verdana", Font.BOLD, 10);
+  private static final Font VERDANA_BOLD_10 = new Font("Verdana",
+          Font.BOLD, 10);
 
   public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
 
@@ -109,7 +110,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (seqGroup != null)
     {
-      oldColourScheme = seqGroup.cs;
+      oldColourScheme = seqGroup.getColourScheme();
     }
     else
     {
@@ -150,7 +151,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (oldColourScheme instanceof UserColourScheme)
     {
-      schemeName.setText(((UserColourScheme) oldColourScheme).getSchemeName());
+      schemeName.setText(((UserColourScheme) oldColourScheme)
+              .getSchemeName());
     }
 
     resetButtonPanel(false);
@@ -403,8 +405,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
    * @param buttonIndex
    *          the button's position in the list
    */
-  JButton makeButton(String label, String residue,
-          List<JButton> buttons, int buttonIndex)
+  JButton makeButton(String label, String residue, List<JButton> buttons,
+          int buttonIndex)
   {
     final JButton button;
     Color col;
@@ -435,7 +437,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
       col = Color.white;
       if (oldColourScheme != null && oldColourScheme.isSimple())
       {
-        col = oldColourScheme.findColour(residue.charAt(0));
+        col = oldColourScheme.findColour(residue.charAt(0), 0, null, null,
+                0f);
       }
     }
 
@@ -521,7 +524,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (seqGroup != null)
     {
-      seqGroup.cs = ucs;
+      seqGroup.setColourScheme(ucs);
       ap.paintAlignment(true);
     }
     else if (ap != null)
@@ -585,10 +588,10 @@ public class UserDefinedColours extends GUserDefinedColours implements
       ucs.setLowerCaseColours(newColours);
     }
 
-    if (ap != null)
-    {
-      ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
-    }
+    // if (ap != null)
+    // {
+    // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+    // }
 
     return ucs;
   }
@@ -605,8 +608,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
     upperCaseButtons = new ArrayList<JButton>();
     lowerCaseButtons = new ArrayList<JButton>();
 
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            Cache.getProperty(LAST_DIRECTORY), "jc", "Jalview User Colours");
+    JalviewFileChooser chooser = new JalviewFileChooser("jc",
+            "Jalview User Colours");
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
             .getString("label.load_colour_scheme"));
@@ -621,7 +624,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
     File choice = chooser.getSelectedFile();
     Cache.setProperty(LAST_DIRECTORY, choice.getParent());
 
-    UserColourScheme ucs = ColourSchemes.loadColourScheme(choice.getAbsolutePath());
+    UserColourScheme ucs = ColourSchemes.loadColourScheme(choice
+            .getAbsolutePath());
     Color[] colors = ucs.getColours();
     schemeName.setText(ucs.getSchemeName());
 
@@ -713,8 +717,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
       }
       ColourSchemes.getInstance().removeColourScheme(name);
     }
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            Cache.getProperty(LAST_DIRECTORY), "jc",
+    JalviewFileChooser chooser = new JalviewFileChooser("jc",
             "Jalview User Colours");
 
     JalviewFileView fileView = new JalviewFileView();
@@ -820,7 +823,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = oldColourScheme;
+        seqGroup.setColourScheme(oldColourScheme);
       }
       else
       {