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 5314c5c..7a5c1f1 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -110,7 +110,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (seqGroup != null)
     {
-      oldColourScheme = seqGroup.cs;
+      oldColourScheme = seqGroup.getColourScheme();
     }
     else
     {
@@ -437,7 +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);
       }
     }
 
@@ -523,7 +524,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (seqGroup != null)
     {
-      seqGroup.cs = ucs;
+      seqGroup.setColourScheme(ucs);
       ap.paintAlignment(true);
     }
     else if (ap != null)
@@ -587,10 +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;
   }
@@ -822,7 +823,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = oldColourScheme;
+        seqGroup.setColourScheme(oldColourScheme);
       }
       else
       {