Merge branch 'develop' into bug/JAL-2314

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

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 83a8d24..9ab4327 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -29,6 +29,7 @@ import jalview.jbgui.GUserDefinedColours;
 import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.JalviewUserColours;
 import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeLoader;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
@@ -71,7 +72,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
   private static final String LAST_DIRECTORY = "LAST_DIRECTORY";
 
-  private static final int MY_FRAME_HEIGHT = 420;
+  private static final int MY_FRAME_HEIGHT = 440;
 
   private static final int MY_FRAME_WIDTH = 810;
 
@@ -276,14 +277,9 @@ public class UserDefinedColours extends GUserDefinedColours implements
   {
     JButton button = null;
     final Color newColour = colorChooser.getColor();
-    for (int i = 0; i < selectedButtons.size(); i++)
-    {
-      button = selectedButtons.get(i);
-      button.setBackground(newColour);
-      button.setForeground(ColorUtils.brighterThan(newColour));
-    }
     if (lcaseColour.isSelected())
     {
+      selectedButtons.clear();
       for (int i = 0; i < lowerCaseButtons.size(); i++)
       {
         button = lowerCaseButtons.get(i);
@@ -291,6 +287,12 @@ public class UserDefinedColours extends GUserDefinedColours implements
         button.setForeground(ColorUtils.brighterThan(button.getBackground()));
       }
     }
+    for (int i = 0; i < selectedButtons.size(); i++)
+    {
+      button = selectedButtons.get(i);
+      button.setBackground(newColour);
+      button.setForeground(ColorUtils.brighterThan(newColour));
+    }
   }
 
   /**
@@ -589,11 +591,6 @@ public class UserDefinedColours extends GUserDefinedColours implements
       ucs.setLowerCaseColours(newColours);
     }
 
-    // if (ap != null)
-    // {
-    // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
-    // }
-
     return ucs;
   }
 
@@ -625,7 +622,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     File choice = chooser.getSelectedFile();
     Cache.setProperty(LAST_DIRECTORY, choice.getParent());
 
-    UserColourScheme ucs = ColourSchemes.loadColourScheme(choice
+    UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(choice
             .getAbsolutePath());
     Color[] colors = ucs.getColours();
     schemeName.setText(ucs.getSchemeName());
@@ -674,7 +671,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
       {
         colours = colours.substring(0, colours.indexOf("|"));
       }
-      ret = ColourSchemes.loadColourScheme(colours);
+      ret = ColourSchemeLoader.loadColourScheme(colours);
     }
 
     if (ret == null)