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diff --git a/test/jalview/renderer/ResidueColourFinderTest.java b/test/jalview/renderer/ResidueColourFinderTest.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.renderer;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.gui.JvOptionPane;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+
+import java.awt.Color;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class ResidueColourFinderTest
+{
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetResidueColour_zappo()
+  {
+    SequenceI seq = new Sequence("name", "MATVLGSPRAPAFF"); // FER1_MAIZE...
+    AlignmentI al = new Alignment(new SequenceI[] { seq });
+    final AlignViewport av = new AlignViewport(al);
+    ResidueColourFinder rcf = new ResidueColourFinder();
+    av.setGlobalColourScheme(new ZappoColourScheme());
+
+    // @see ResidueProperties.zappo
+    assertEquals(Color.pink,
+            rcf.getResidueColour(true, av.getResidueShading(), null, seq, 0,
+                    null)); // M
+    assertEquals(Color.green,
+            rcf.getResidueColour(true, av.getResidueShading(), null, seq, 2,
+                    null)); // T
+    assertEquals(Color.magenta,
+            rcf.getResidueColour(true, av.getResidueShading(), null, seq, 5,
+                    null)); // G
+    assertEquals(Color.orange,
+            rcf.getResidueColour(true, av.getResidueShading(), null, seq,
+                    12,
+                    null)); // F
+
+    // everything is white if showBoxes is false
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 0, null)); // M
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 2, null)); // T
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 5, null)); // G
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 12, null)); // F
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetResidueColour_none()
+  {
+    SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
+    AlignmentI al = new Alignment(new SequenceI[] { seq });
+    final AlignViewport av = new AlignViewport(al);
+    ResidueColourFinder rcf = new ResidueColourFinder();
+
+    assertEquals(Color.white,
+            rcf.getResidueColour(true, av.getResidueShading(),
+            null, seq, 0, null));
+    assertEquals(Color.white,
+            rcf.getResidueColour(true, av.getResidueShading(),
+            null, seq, 2, null));
+
+    // no change if showBoxes is false
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 0, null));
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 2, null));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetResidueColour_userdef()
+  {
+    SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
+                                                            // gap
+    AlignmentI al = new Alignment(new SequenceI[] { seq });
+    final AlignViewport av = new AlignViewport(al);
+    ResidueColourFinder rcf = new ResidueColourFinder();
+
+    Color[] newColours = new Color[24];
+    for (int i = 0; i < 24; i++)
+    {
+      newColours[i] = null;
+    }
+
+    av.setGlobalColourScheme(new UserColourScheme(newColours));
+
+    // gap colour not specified so gap colour is null
+    // this is consistent with previous behaviour, but may not be correct?
+    assertEquals(null, rcf.getResidueColour(true, av.getResidueShading(),
+            null, seq, 3, null));
+
+    newColours[23] = Color.pink;
+    av.setGlobalColourScheme(new UserColourScheme(newColours));
+
+    // gap colour specified as pink
+    assertEquals(Color.pink, rcf.getResidueColour(true,
+            av.getResidueShading(),
+            null, seq, 3, null));
+
+    // everything is white if showBoxes is false
+    newColours[23] = null;
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(),
+            null, seq, 3, null));
+
+    newColours[23] = Color.pink;
+    av.setGlobalColourScheme(new UserColourScheme(newColours));
+
+    // gap colour specified as pink
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 3, null));
+  }
+
+  // TODO more tests for getResidueColour covering groups, feature rendering...
+}