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diff --git a/test/jalview/gui/AnnotationColumnChooserTest.java b/test/jalview/gui/AnnotationColumnChooserTest.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.gui;
+
+import static org.testng.Assert.assertFalse;
+import static org.testng.AssertJUnit.assertEquals;
+
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+
+import java.io.IOException;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+/**
+ * Unit tests for AnnotationChooser
+ * 
+ * @author kmourao
+ *
+ */
+public class AnnotationColumnChooserTest
+{
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  // 4 sequences x 13 positions
+  final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n"
+          + "TIETHKEAELVG-\n"
+          + ">FER_CAPAN Ferredoxin, chloroplast precursor\n"
+          + "TIETHKEAELVG-\n"
+          + ">FER1_SOLLC Ferredoxin-1, chloroplast precursor\n"
+          + "TIETHKEEELTA-\n" + ">Q93XJ9_SOLTU Ferredoxin I precursor\n"
+          + "TIETHKEEELTA-\n";
+
+  AnnotationChooser testee;
+
+  AlignmentPanel parentPanel;
+
+  AlignFrame af;
+
+  @BeforeMethod(alwaysRun = true)
+  public void setUp() throws IOException
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    // pin down annotation sort order for test
+    Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
+            SequenceAnnotationOrder.NONE.name());
+    final String TRUE = Boolean.TRUE.toString();
+    Cache.applicationProperties.setProperty(Preferences.SHOW_AUTOCALC_ABOVE,
+            TRUE);
+    Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
+
+    AlignmentI al = new FormatAdapter().readFile(TEST_DATA,
+            DataSourceType.PASTE, FileFormat.Fasta);
+    af = new AlignFrame(al, 700, 500);
+    parentPanel = new AlignmentPanel(af, af.getViewport());
+    addAnnotations();
+  }
+
+  /**
+   * Add 4 annotations, 3 of them sequence-specific.
+   * 
+   * <PRE>
+   * ann1 - for sequence 0 - label 'IUPRED' ann2 - not sequence related - label
+   * 'Beauty' ann3 - for sequence 3 - label 'JMol' ann4 - for sequence 2 - label
+   * 'IUPRED' ann5 - for sequence 1 - label 'JMol'
+   */
+  private void addAnnotations()
+  {
+    Annotation an = new Annotation(2f);
+    Annotation[] anns = new Annotation[] { an, an, an };
+    AlignmentAnnotation ann0 = new AlignmentAnnotation("IUPRED", "", anns);
+    AlignmentAnnotation ann1 = new AlignmentAnnotation("Beauty", "", anns);
+    AlignmentAnnotation ann2 = new AlignmentAnnotation("JMol", "", anns);
+    AlignmentAnnotation ann3 = new AlignmentAnnotation("IUPRED", "", anns);
+    AlignmentAnnotation ann4 = new AlignmentAnnotation("JMol", "", anns);
+    SequenceI[] seqs = parentPanel.getAlignment().getSequencesArray();
+    ann0.setSequenceRef(seqs[0]);
+    ann2.setSequenceRef(seqs[3]);
+    ann3.setSequenceRef(seqs[2]);
+    ann4.setSequenceRef(seqs[1]);
+    parentPanel.getAlignment().addAnnotation(ann0);
+    parentPanel.getAlignment().addAnnotation(ann1);
+    parentPanel.getAlignment().addAnnotation(ann2);
+    parentPanel.getAlignment().addAnnotation(ann3);
+    parentPanel.getAlignment().addAnnotation(ann4);
+  }
+
+  /**
+   * Test reset
+   */
+  @Test(groups = { "Functional" })
+  public void testReset()
+  {
+    AnnotationColumnChooser acc = new AnnotationColumnChooser(
+            af.getViewport(), af.alignPanel);
+
+    HiddenColumns oldhidden = new HiddenColumns();
+    oldhidden.hideColumns(10, 20);
+    acc.setOldHiddenColumns(oldhidden);
+
+    HiddenColumns newHidden = new HiddenColumns();
+    newHidden.hideColumns(0, 3);
+    newHidden.hideColumns(22, 25);
+    af.getViewport().setHiddenColumns(newHidden);
+
+    HiddenColumns currentHidden = af.getViewport().getAlignment()
+            .getHiddenColumns();
+    List<int[]> regions = currentHidden.getHiddenColumnsCopy();
+    assertEquals(regions.get(0)[0], 0);
+    assertEquals(regions.get(0)[1], 3);
+    assertEquals(regions.get(1)[0], 22);
+    assertEquals(regions.get(1)[1], 25);
+
+    // now reset hidden columns
+    acc.reset();
+    currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+    regions = currentHidden.getHiddenColumnsCopy();
+    assertEquals(regions.get(0)[0], 10);
+    assertEquals(regions.get(0)[1], 20);
+
+    // check works with empty hidden columns as old columns
+    oldhidden = new HiddenColumns();
+    acc.setOldHiddenColumns(oldhidden);
+    acc.reset();
+    currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+    assertFalse(currentHidden.hasHiddenColumns());
+
+    // check works with empty hidden columns as new columns
+    oldhidden.hideColumns(10, 20);
+    acc.setOldHiddenColumns(oldhidden);
+    currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+    assertFalse(currentHidden.hasHiddenColumns());
+
+    acc.reset();
+    currentHidden = af.getViewport().getAlignment().getHiddenColumns();
+    regions = currentHidden.getHiddenColumnsCopy();
+    assertEquals(regions.get(0)[0], 10);
+    assertEquals(regions.get(0)[1], 20);
+  }
+}