IgnoreGapsConsensus

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

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