fix aligned DNA codon translation bug(s) and generate AlignedCodonFrame mappings...

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

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 001b232..133dcaf 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -45,7 +45,7 @@ public class UserDefinedColours
   Vector selectedButtons;\r
   ColourSchemeI oldColourScheme;\r
   JInternalFrame frame;\r
-  MCview.PDBCanvas pdbcanvas;\r
+  AppJmol jmol;\r
   Vector upperCaseButtons;\r
   Vector lowerCaseButtons;\r
 \r
@@ -95,10 +95,10 @@ public class UserDefinedColours
     showFrame();\r
   }\r
 \r
-  public UserDefinedColours(MCview.PDBCanvas pdb, ColourSchemeI oldcs)\r
+  public UserDefinedColours(AppJmol jmol, ColourSchemeI oldcs)\r
   {\r
     super();\r
-    pdbcanvas = pdb;\r
+    this.jmol = jmol;\r
 \r
     colorChooser.getSelectionModel().addChangeListener(this);\r
 \r
@@ -418,16 +418,15 @@ public class UserDefinedColours
     if (seqGroup != null)\r
     {\r
       seqGroup.cs = ucs;\r
-      ap.repaint();\r
+      ap.paintAlignment(true);\r
     }\r
     else if (ap != null)\r
     {\r
       ap.alignFrame.changeColour(ucs);\r
     }\r
-    else if (pdbcanvas != null)\r
+    else if (jmol != null)\r
     {\r
-      pdbcanvas.pdb.setColours(ucs);\r
-      pdbcanvas.updateSeqColours();\r
+      jmol.setJalviewColourScheme(ucs);\r
     }\r
   }\r
 \r
@@ -789,12 +788,12 @@ public class UserDefinedColours
       {\r
         ap.av.setGlobalColourScheme(oldColourScheme);\r
       }\r
-      ap.repaint();\r
+      ap.paintAlignment(true);\r
     }\r
 \r
-    if (pdbcanvas != null)\r
+    if (jmol != null)\r
     {\r
-      pdbcanvas.pdb.setColours(oldColourScheme);\r
+      jmol.setJalviewColourScheme(oldColourScheme);\r
     }\r
 \r
     try\r