X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FColumnSelectionTest.java;h=d581345e5a99303e481d14a45fe32539c7427396;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=38e9c934f702a9c1058c176694f5ec0498294828;hpb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;p=jalview.git

diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index 38e9c93..d581345 100644
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -1,31 +1,97 @@
+/*
+ * 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.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
 
+import jalview.analysis.AlignmentGenerator;
+import jalview.gui.JvOptionPane;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.ThresholdType;
+
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.Collections;
+import java.util.ConcurrentModificationException;
+import java.util.Iterator;
 import java.util.List;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class ColumnSelectionTest
 {
 
-  @Test(groups ={ "Functional" })
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @Test(groups = { "Functional" })
   public void testAddElement()
   {
     ColumnSelection cs = new ColumnSelection();
     cs.addElement(2);
     cs.addElement(5);
+    cs.addElement(3);
+    cs.addElement(5); // ignored
     List<Integer> sel = cs.getSelected();
-    assertEquals(2, sel.size());
-    assertEquals(new Integer(2), sel.get(0));
-    assertEquals(new Integer(5), sel.get(1));
+    assertEquals("[2, 5, 3]", sel.toString());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetElementsFrom()
+  {
+    ColumnSelection fromcs = new ColumnSelection();
+    ColumnSelection tocs = new ColumnSelection();
+    HiddenColumns hidden = new HiddenColumns();
+
+    fromcs.addElement(2);
+    fromcs.addElement(3);
+    fromcs.addElement(5);
+
+    tocs.setElementsFrom(fromcs, hidden);
+    assertTrue(tocs.equals(fromcs));
+
+    hidden.hideColumns(4, 6);
+    tocs.setElementsFrom(fromcs, hidden);
+
+    // expect cols 2 and 3 to be selected but not 5
+    ColumnSelection expectcs = new ColumnSelection();
+    expectcs.addElement(2);
+    expectcs.addElement(3);
+    assertTrue(tocs.equals(expectcs));
   }
 
   /**
    * Test the remove method - in particular to verify that remove(int i) removes
    * the element whose value is i, _NOT_ the i'th element.
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testRemoveElement()
   {
     ColumnSelection cs = new ColumnSelection();
@@ -37,39 +103,626 @@ public class ColumnSelectionTest
     cs.removeElement(1);
     List<Integer> sel = cs.getSelected();
     assertEquals(2, sel.size());
-    assertEquals(new Integer(2), sel.get(0));
-    assertEquals(new Integer(5), sel.get(1));
+    assertEquals(Integer.valueOf(2), sel.get(0));
+    assertEquals(Integer.valueOf(5), sel.get(1));
 
     // removing an element in the list removes it
     cs.removeElement(2);
+    // ...and also from the read-only view
+    assertEquals(1, sel.size());
+    sel = cs.getSelected();
     assertEquals(1, sel.size());
-    assertEquals(new Integer(5), sel.get(0));
+    assertEquals(Integer.valueOf(5), sel.get(0));
+  }
+
+  /**
+   * Test the method that hides a specified column including any adjacent
+   * selected columns. This is a convenience method for the case where multiple
+   * column regions are selected and then hidden using menu option View | Hide |
+   * Selected Columns.
+   */
+  @Test(groups = { "Functional" })
+  public void testHideColumns_withSelection()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+    ColumnSelection cs = new ColumnSelection();
+    // select columns 4-6
+    cs.addElement(4);
+    cs.addElement(5);
+    cs.addElement(6);
+    // hide column 5 (and adjacent):
+    cs.hideSelectedColumns(5, al.getHiddenColumns());
+    // 4,5,6 now hidden:
+    Iterator<int[]> regions = al.getHiddenColumns().iterator();
+    assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+    assertEquals("[4, 6]", Arrays.toString(regions.next()));
+    // none now selected:
+    assertTrue(cs.getSelected().isEmpty());
+
+    // repeat, hiding column 4 (5 and 6)
+    al = gen.generate(50, 20, 123, 5, 5);
+    cs = new ColumnSelection();
+    cs.addElement(4);
+    cs.addElement(5);
+    cs.addElement(6);
+    cs.hideSelectedColumns(4, al.getHiddenColumns());
+    regions = al.getHiddenColumns().iterator();
+    assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+    assertEquals("[4, 6]", Arrays.toString(regions.next()));
+    assertTrue(cs.getSelected().isEmpty());
+
+    // repeat, hiding column (4, 5 and) 6
+    al = gen.generate(50, 20, 123, 5, 5);
+    cs = new ColumnSelection();
+    cs.addElement(4);
+    cs.addElement(5);
+    cs.addElement(6);
+    cs.hideSelectedColumns(6, al.getHiddenColumns());
+    regions = al.getHiddenColumns().iterator();
+    assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+    assertEquals("[4, 6]", Arrays.toString(regions.next()));
+    assertTrue(cs.getSelected().isEmpty());
+
+    // repeat, with _only_ adjacent columns selected
+    al = gen.generate(50, 20, 123, 5, 5);
+    cs = new ColumnSelection();
+    cs.addElement(4);
+    cs.addElement(6);
+    cs.hideSelectedColumns(5, al.getHiddenColumns());
+    regions = al.getHiddenColumns().iterator();
+    assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+    assertEquals("[4, 6]", Arrays.toString(regions.next()));
+    assertTrue(cs.getSelected().isEmpty());
+  }
+
+  /**
+   * Test the method that hides all (possibly disjoint) selected column ranges
+   */
+  @Test(groups = { "Functional" })
+  public void testHideSelectedColumns()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+    ColumnSelection cs = new ColumnSelection();
+    int[] sel = { 2, 3, 4, 7, 8, 9, 20, 21, 22 };
+    for (int col : sel)
+    {
+      cs.addElement(col);
+    }
+
+    HiddenColumns cols = al.getHiddenColumns();
+    cols.hideColumns(15, 18);
+
+    cs.hideSelectedColumns(al);
+    assertTrue(cs.getSelected().isEmpty());
+    Iterator<int[]> regions = cols.iterator();
+    assertEquals(4, cols.getNumberOfRegions());
+    assertEquals("[2, 4]", Arrays.toString(regions.next()));
+    assertEquals("[7, 9]", Arrays.toString(regions.next()));
+    assertEquals("[15, 18]", Arrays.toString(regions.next()));
+    assertEquals("[20, 22]", Arrays.toString(regions.next()));
+  }
+
+  /**
+   * Test the method that gets runs of selected columns ordered by column. If
+   * this fails, HideSelectedColumns may also fail
+   */
+  @Test(groups = { "Functional" })
+  public void testGetSelectedRanges()
+  {
+    /*
+     * getSelectedRanges returns ordered columns regardless
+     * of the order in which they are added
+     */
+    ColumnSelection cs = new ColumnSelection();
+    int[] sel = { 4, 3, 7, 21, 9, 20, 8, 22, 2 };
+    for (int col : sel)
+    {
+      cs.addElement(col);
+    }
+    List<int[]> range;
+    range = cs.getSelectedRanges();
+    assertEquals(3, range.size());
+    assertEquals("[2, 4]", Arrays.toString(range.get(0)));
+    assertEquals("[7, 9]", Arrays.toString(range.get(1)));
+    assertEquals("[20, 22]", Arrays.toString(range.get(2)));
+    cs.addElement(0);
+    cs.addElement(1);
+    range = cs.getSelectedRanges();
+    assertEquals(3, range.size());
+    assertEquals("[0, 4]", Arrays.toString(range.get(0)));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testInvertColumnSelection()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(4);
+    cs.addElement(6);
+    cs.addElement(8);
+
+    HiddenColumns cols = al.getHiddenColumns();
+    cols.hideColumns(3, 3);
+    cols.hideColumns(6, 6);
+
+    // invert selection from start (inclusive) to end (exclusive)
+    cs.invertColumnSelection(2, 9, al);
+    assertEquals("[2, 5, 7]", cs.getSelected().toString());
+
+    cs.invertColumnSelection(1, 9, al);
+    assertEquals("[1, 4, 8]", cs.getSelected().toString());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testMaxColumnSelection()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(0);
+    cs.addElement(513);
+    cs.addElement(1);
+    assertEquals(513, cs.getMax());
+    cs.removeElement(513);
+    assertEquals(1, cs.getMax());
+    cs.removeElement(1);
+    assertEquals(0, cs.getMax());
+    cs.addElement(512);
+    cs.addElement(513);
+    assertEquals(513, cs.getMax());
+
+  }
+
+  @Test(groups = { "Functional" })
+  public void testMinColumnSelection()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(0);
+    cs.addElement(513);
+    cs.addElement(1);
+    assertEquals(0, cs.getMin());
+    cs.removeElement(0);
+    assertEquals(1, cs.getMin());
+    cs.addElement(0);
+    assertEquals(0, cs.getMin());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testEquals()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(0);
+    cs.addElement(513);
+    cs.addElement(1);
+
+    // same selections added in a different order
+    ColumnSelection cs2 = new ColumnSelection();
+    cs2.addElement(1);
+    cs2.addElement(513);
+    cs2.addElement(0);
+
+    assertTrue(cs.equals(cs2));
+    assertTrue(cs.equals(cs));
+    assertTrue(cs2.equals(cs));
+    assertTrue(cs2.equals(cs2));
+
+    cs2.addElement(12);
+    assertFalse(cs.equals(cs2));
+    assertFalse(cs2.equals(cs));
+
+    cs2.removeElement(12);
+    assertTrue(cs.equals(cs2));
   }
 
+  /*
+      cs2.hideSelectedColumns(88);
+      assertFalse(cs.equals(cs2));
+      /*
+       * unhiding a column adds it to selection!
+       */
+  /*    cs2.revealHiddenColumns(88);
+      assertFalse(cs.equals(cs2));
+      cs.addElement(88);
+      assertTrue(cs.equals(cs2));
+    */
+
   /**
-   * Test the method that finds the visible column position of an alignment
-   * column, allowing for hidden columns.
+   * Test the method that returns selected columns, in the order in which they
+   * were added
    */
-  @Test(groups ={ "Functional" })
-  public void testFindColumnPosition()
+  @Test(groups = { "Functional" })
+  public void testGetSelected()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    int[] sel = { 4, 3, 7, 21 };
+    for (int col : sel)
+    {
+      cs.addElement(col);
+    }
+
+    List<Integer> selected = cs.getSelected();
+    assertEquals(4, selected.size());
+    assertEquals("[4, 3, 7, 21]", selected.toString());
+
+    /*
+     * getSelected returns a read-only view of the list
+     * verify the view follows any changes in it
+     */
+    cs.removeElement(7);
+    cs.addElement(1);
+    cs.removeElement(4);
+    assertEquals("[3, 21, 1]", selected.toString());
+  }
+
+  /**
+   * Test to verify that the list returned by getSelection cannot be modified
+   */
+  @Test(groups = { "Functional" })
+  public void testGetSelected_isReadOnly()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(3);
+
+    List<Integer> selected = cs.getSelected();
+    try
+    {
+      selected.clear();
+      fail("expected exception");
+    } catch (UnsupportedOperationException e)
+    {
+      // expected
+    }
+    try
+    {
+      selected.add(1);
+      fail("expected exception");
+    } catch (UnsupportedOperationException e)
+    {
+      // expected
+    }
+    try
+    {
+      selected.remove(3);
+      fail("expected exception");
+    } catch (UnsupportedOperationException e)
+    {
+      // expected
+    }
+    try
+    {
+      Collections.sort(selected);
+      fail("expected exception");
+    } catch (UnsupportedOperationException e)
+    {
+      // expected
+    }
+  }
+
+  /**
+   * Test that demonstrates a ConcurrentModificationException is thrown if you
+   * change the selection while iterating over it
+   */
+  @Test(
+    groups = "Functional",
+    expectedExceptions =
+    { ConcurrentModificationException.class })
+  public void testGetSelected_concurrentModification()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(0);
+    cs.addElement(1);
+    cs.addElement(2);
+
+    /*
+     * simulate changing the list under us (e.g. in a separate
+     * thread) while iterating over it -> ConcurrentModificationException
+     */
+    List<Integer> selected = cs.getSelected();
+    for (Integer col : selected)
+    {
+      if (col.intValue() == 0)
+      {
+        cs.removeElement(1);
+      }
+    }
+  }
+
+  @Test(groups = "Functional")
+  public void testMarkColumns()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(5); // this will be cleared
+    BitSet toMark = new BitSet();
+    toMark.set(1);
+    toMark.set(3);
+    toMark.set(6);
+    toMark.set(9);
+
+    assertTrue(cs.markColumns(toMark, 3, 8, false, false, false));
+    List<Integer> selected = cs.getSelected();
+    assertEquals(2, selected.size());
+    assertTrue(selected.contains(3));
+    assertTrue(selected.contains(6));
+  }
+
+  @Test(groups = "Functional")
+  public void testMarkColumns_extend()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(1);
+    cs.addElement(5);
+    BitSet toMark = new BitSet();
+    toMark.set(1);
+    toMark.set(3);
+    toMark.set(6);
+    toMark.set(9);
+
+    /*
+     * extending selection of {3, 6} should leave {1, 3, 5, 6} selected
+     */
+    assertTrue(cs.markColumns(toMark, 3, 8, false, true, false));
+    List<Integer> selected = cs.getSelected();
+    assertEquals(4, selected.size());
+    assertTrue(selected.contains(1));
+    assertTrue(selected.contains(3));
+    assertTrue(selected.contains(5));
+    assertTrue(selected.contains(6));
+  }
+
+  @Test(groups = "Functional")
+  public void testMarkColumns_invert()
   {
     ColumnSelection cs = new ColumnSelection();
-    assertEquals(5, cs.findColumnPosition(5));
+    cs.addElement(5); // this will be cleared
+    BitSet toMark = new BitSet();
+    toMark.set(1);
+    toMark.set(3);
+    toMark.set(6);
+    toMark.set(9);
+
+    /*
+     * inverted selection of {3, 6} should select {4, 5, 7, 8}
+     */
+    assertTrue(cs.markColumns(toMark, 3, 8, true, false, false));
+    List<Integer> selected = cs.getSelected();
+    assertEquals(4, selected.size());
+    assertTrue(selected.contains(4));
+    assertTrue(selected.contains(5));
+    assertTrue(selected.contains(7));
+    assertTrue(selected.contains(8));
+  }
+
+  @Test(groups = "Functional")
+  public void testMarkColumns_toggle()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(1); // outside change range
+    cs.addElement(3);
+    cs.addElement(4);
+    cs.addElement(10); // outside change range
+    BitSet toMark = new BitSet();
+    toMark.set(1);
+    toMark.set(3);
+    toMark.set(6);
+    toMark.set(9);
+
+    /*
+     * toggling state of {3, 6} should leave {1, 4, 6, 10} selected
+     */
+    assertTrue(cs.markColumns(toMark, 3, 8, false, false, true));
+    List<Integer> selected = cs.getSelected();
+    assertEquals(4, selected.size());
+    assertTrue(selected.contains(1));
+    assertTrue(selected.contains(4));
+    assertTrue(selected.contains(6));
+    assertTrue(selected.contains(10));
+  }
+
+  @Test(groups = "Functional")
+  public void testCopyConstructor()
+  {
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(3);
+    cs.addElement(1);
+
+    ColumnSelection cs2 = new ColumnSelection(cs);
+    assertTrue(cs2.hasSelectedColumns());
+
+    // order of column selection is preserved
+    assertEquals("[3, 1]", cs2.getSelected().toString());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testStretchGroup_expand()
+  {
+    /*
+     * test that emulates clicking column 4 (selected)
+     * and dragging right to column 5 (all base 0)
+     */
+    ColumnSelection cs = new ColumnSelection();
+    cs.addElement(4);
+    SequenceGroup sg = new SequenceGroup();
+    sg.setStartRes(4);
+    sg.setEndRes(4);
+    cs.stretchGroup(5, sg, 4, 4);
+    assertEquals(cs.getSelected().size(), 2);
+    assertTrue(cs.contains(4));
+    assertTrue(cs.contains(5));
+    assertEquals(sg.getStartRes(), 4);
+    assertEquals(sg.getEndRes(), 5);
+
+    /*
+     * emulate drag right with columns 10-20 already selected
+     */
+    cs.clear();
+    for (int i = 10; i <= 20; i++)
+    {
+      cs.addElement(i);
+    }
+    assertEquals(cs.getSelected().size(), 11);
+    sg = new SequenceGroup();
+    sg.setStartRes(10);
+    sg.setEndRes(20);
+    cs.stretchGroup(21, sg, 10, 20);
+    assertEquals(cs.getSelected().size(), 12);
+    assertTrue(cs.contains(10));
+    assertTrue(cs.contains(21));
+    assertEquals(sg.getStartRes(), 10);
+    assertEquals(sg.getEndRes(), 21);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testStretchGroup_shrink()
+  {
+    /*
+     * emulate drag left to 19 with columns 10-20 already selected
+     */
+    ColumnSelection cs = new ColumnSelection();
+    for (int i = 10; i <= 20; i++)
+    {
+      cs.addElement(i);
+    }
+    assertEquals(cs.getSelected().size(), 11);
+    SequenceGroup sg = new SequenceGroup();
+    sg.setStartRes(10);
+    sg.setEndRes(20);
+    cs.stretchGroup(19, sg, 10, 20);
+    assertEquals(cs.getSelected().size(), 10);
+    assertTrue(cs.contains(10));
+    assertTrue(cs.contains(19));
+    assertFalse(cs.contains(20));
+    assertEquals(sg.getStartRes(), 10);
+    assertEquals(sg.getEndRes(), 19);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testFilterAnnotations()
+  {
+    ColumnSelection cs = new ColumnSelection();
+
+    /*
+     * filter with no conditions clears the selection
+     */
+    Annotation[] anns = new Annotation[] { null };
+    AnnotationFilterParameter filter = new AnnotationFilterParameter();
+    cs.addElement(3);
+    int added = cs.filterAnnotations(anns, filter);
+    assertEquals(0, added);
+    assertTrue(cs.isEmpty());
+
+    /*
+     * select on description (regex)
+     */
+    filter.setRegexString("w.rld");
+    filter.addRegexSearchField(SearchableAnnotationField.DESCRIPTION);
+    Annotation helix = new Annotation("(", "hello", '<', 2f);
+    Annotation sheet = new Annotation("(", "world", '<', 2f);
+    added = cs.filterAnnotations(new Annotation[] { null, helix, sheet },
+            filter);
+    assertEquals(1, added);
+    assertTrue(cs.contains(2));
+
+    /*
+     * select on label (invalid regex, exact match)
+     */
+    filter = new AnnotationFilterParameter();
+    filter.setRegexString("(");
+    filter.addRegexSearchField(SearchableAnnotationField.DISPLAY_STRING);
+    added = cs.filterAnnotations(new Annotation[] { null, helix, sheet },
+            filter);
+    assertEquals(2, added);
+    assertTrue(cs.contains(1));
+    assertTrue(cs.contains(2));
+
+    /*
+     * select Helix (secondary structure symbol H)
+     */
+    filter = new AnnotationFilterParameter();
+    filter.setFilterAlphaHelix(true);
+    helix = new Annotation("x", "desc", 'H', 0f);
+    sheet = new Annotation("x", "desc", 'E', 1f);
+    Annotation turn = new Annotation("x", "desc", 'S', 2f);
+    Annotation ann4 = new Annotation("x", "desc", 'Y', 3f);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 }, filter);
+    assertEquals(1, added);
+    assertTrue(cs.contains(1));
+
+    /*
+     * select Helix and Sheet (E)
+     */
+    filter.setFilterBetaSheet(true);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 }, filter);
+    assertEquals(2, added);
+    assertTrue(cs.contains(1));
+    assertTrue(cs.contains(2));
+
+    /*
+     * select Sheet and Turn (S)
+     */
+    filter.setFilterAlphaHelix(false);
+    filter.setFilterTurn(true);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 }, filter);
+    assertEquals(2, added);
+    assertTrue(cs.contains(2));
+    assertTrue(cs.contains(3));
 
-    // hiding column 6 makes no difference
-    cs.hideColumns(6, 6);
-    assertEquals(5, cs.findColumnPosition(5));
+    /*
+     * select value < 2f (ann1, ann2)
+     */
+    filter = new AnnotationFilterParameter();
+    filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
+    filter.setThresholdValue(2f);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 }, filter);
+    assertEquals(2, added);
+    assertTrue(cs.contains(1));
+    assertTrue(cs.contains(2));
 
-    // hiding column 5 makes no difference
-    cs.hideColumns(5, 5);
-    assertEquals(5, cs.findColumnPosition(5));
+    /*
+     * select value > 2f (ann4 only)
+     */
+    filter.setThresholdType(ThresholdType.ABOVE_THRESHOLD);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 }, filter);
+    assertEquals(1, added);
+    assertTrue(cs.contains(4));
 
-    // hiding column 4 moves column 5 to column 4
-    cs.hideColumns(4, 4);
-    assertEquals(4, cs.findColumnPosition(5));
+    /*
+     * select >2f or Helix
+     */
+    filter.setFilterAlphaHelix(true);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 }, filter);
+    assertEquals(2, added);
+    assertTrue(cs.contains(1));
+    assertTrue(cs.contains(4));
 
-    // hiding columns 1 and 2 moves column 5 to column 2
-    cs.hideColumns(1, 2);
-    assertEquals(2, cs.findColumnPosition(5));
+    /*
+     * select < 1f or Helix; one annotation matches both
+     * return value should only count it once
+     */
+    filter.setThresholdType(ThresholdType.BELOW_THRESHOLD);
+    filter.setThresholdValue(1f);
+    added = cs
+            .filterAnnotations(new Annotation[]
+            { null, helix, sheet, turn, ann4 }, filter);
+    assertEquals(1, added);
+    assertTrue(cs.contains(1));
   }
 }