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diff --git a/test/jalview/gui/AnnotationRowFilterTest.java b/test/jalview/gui/AnnotationRowFilterTest.java
new file mode 100644
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+++ b/test/jalview/gui/AnnotationRowFilterTest.java
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+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+
+import java.util.Vector;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+/**
+ * Tests for methods of base class of annotation column or colour chooser
+ */
+public class AnnotationRowFilterTest
+{
+  AlignFrame af;
+
+  private AnnotationRowFilter testee;
+
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty(
+            Preferences.SHOW_AUTOCALC_ABOVE, Boolean.TRUE.toString());
+    af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
+            DataSourceType.FILE);
+    testee = new AnnotationRowFilter(af.viewport, af.alignPanel)
+    {
+      @Override
+      public void valueChanged(boolean updateAllAnnotation)
+      {
+      }
+
+      @Override
+      public void updateView()
+      {
+      }
+
+      @Override
+      public void reset()
+      {
+      }
+    };
+  }
+
+  /**
+   * Test the method that builds the drop-down list of annotations to choose
+   * from for colour by annotation or select columns by annotation
+   */
+  @Test(groups = "Functional")
+  public void testGetAnnotationItems()
+  {
+    AlignmentI al = af.getViewport().getAlignment();
+    SequenceI seq1 = al.findSequenceMatch("FER_CAPAA")[0];
+    SequenceI seq2 = al.findSequenceMatch("FER_BRANA")[0];
+
+    AlignmentAnnotation ann1 = new AlignmentAnnotation("ann1Label", "ann1",
+            null);
+    al.addAnnotation(ann1);
+    AlignmentAnnotation ann2 = new AlignmentAnnotation("Significance",
+            "ann2", null);
+    al.addAnnotation(ann2);
+    /*
+     * a second Significance alignment annotation
+     */
+    AlignmentAnnotation ann2a = new AlignmentAnnotation("Significance",
+            "ann2", null);
+    al.addAnnotation(ann2a);
+
+    AlignmentAnnotation ann3 = new AlignmentAnnotation("Jronn", "Jronn",
+            null);
+    ann3.setSequenceRef(seq1);
+    al.addAnnotation(ann3);
+    AlignmentAnnotation ann4 = new AlignmentAnnotation("Jronn", "Jronn",
+            null);
+    ann4.setSequenceRef(seq2);
+    al.addAnnotation(ann4);
+    AlignmentAnnotation ann5 = new AlignmentAnnotation("Jnet", "Jnet", null);
+    ann5.setSequenceRef(seq2);
+    al.addAnnotation(ann5);
+    /*
+     * a second Jnet annotation for FER_BRANA
+     */
+    AlignmentAnnotation ann6 = new AlignmentAnnotation("Jnet", "Jnet", null);
+    ann6.setSequenceRef(seq2);
+    al.addAnnotation(ann6);
+
+    /*
+     * drop-down items with 'Per-sequence only' not checked
+     */
+    Vector<String> items = testee.getAnnotationItems(false);
+    assertEquals(
+            items.toString(),
+            "[Conservation, Quality, Consensus, Occupancy, ann1Label, Significance, Significance_1, Jronn_FER_CAPAA, Jronn_FER_BRANA, Jnet_FER_BRANA, Jnet_FER_BRANA_2]");
+    assertEquals(testee.getAnnotationMenuLabel(ann1), "ann1Label");
+    assertEquals(testee.getAnnotationMenuLabel(ann2), "Significance");
+    assertEquals(testee.getAnnotationMenuLabel(ann2a), "Significance_1");
+    assertEquals(testee.getAnnotationMenuLabel(ann3), "Jronn_FER_CAPAA");
+    assertEquals(testee.getAnnotationMenuLabel(ann4), "Jronn_FER_BRANA");
+    assertEquals(testee.getAnnotationMenuLabel(ann5), "Jnet_FER_BRANA");
+    assertEquals(testee.getAnnotationMenuLabel(ann6), "Jnet_FER_BRANA_2");
+
+    /*
+     * drop-down items with 'Per-sequence only' checked
+     */
+    items = testee.getAnnotationItems(true);
+    assertEquals(items.toString(), "[Jronn, Jnet]");
+    // the first annotation of the type is associated with the menu item
+    assertEquals(testee.getAnnotationMenuLabel(ann3), "Jronn");
+    assertEquals(testee.getAnnotationMenuLabel(ann5), "Jnet");
+  }
+}