X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FUserDefinedColours.java;h=86e1f5d17dc29caf884d2642c7b9fcd60a0ebb98;hb=9fff97021c2c637e426f6971d54dcf3fd4191985;hp=80d91efdfcdbac60c4c1e7148c21b2c6f138fb1a;hpb=309f2ebc93eb5aab5478279a3c40914f216f01a4;p=jalview.git

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 80d91ef..86e1f5d 100755
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -214,7 +214,7 @@ public class UserDefinedColours
     }
 
     UserColourScheme ucs = new UserColourScheme(newColours);
-    ucs.setThreshold(0);
+    ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
 
     if (seqGroup != null)
     {
@@ -228,27 +228,6 @@ public class UserDefinedColours
     ap.repaint();
   }
 
-  public static UserColourScheme loadDefaultColours(String file)
-  {
-    UserColourScheme ucs = null;
-    try
-    {
-      BufferedReader in = new BufferedReader(new FileReader(file));
-      Color[] newColours = new Color[24];
-      for (int i = 0; i < 24; i++)
-      {
-        newColours[i] = new Color(Integer.parseInt(in.readLine()));
-      }
-
-      ucs = new UserColourScheme(newColours);
-      ucs.setThreshold(0);
-
-    }
-    catch (Exception ex)
-    {}
-
-    return ucs;
-  }
 
   protected void cancelButton_actionPerformed(ActionEvent e)
   {