X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FHiddenColumnsTest.java;fp=test%2Fjalview%2Fdatamodel%2FHiddenColumnsTest.java;h=7c88d7109a988583d6e9b713ba8ddba4a6a59a91;hb=f063821ed0be9c1581af74643a1aa5798731af65;hp=0000000000000000000000000000000000000000;hpb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;p=jalview.git

diff --git a/test/jalview/datamodel/HiddenColumnsTest.java b/test/jalview/datamodel/HiddenColumnsTest.java
new file mode 100644
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+++ b/test/jalview/datamodel/HiddenColumnsTest.java
@@ -0,0 +1,734 @@
+/*
+ * 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.Assert.assertNull;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.analysis.AlignmentGenerator;
+import jalview.gui.JvOptionPane;
+
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.List;
+import java.util.Random;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class HiddenColumnsTest
+{
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  /**
+   * Test the method which counts the number of hidden columns
+   */
+  @Test(groups = { "Functional" })
+  public void testGetSize()
+  {
+    HiddenColumns hidden = new HiddenColumns();
+    assertEquals(0, hidden.getSize());
+
+    hidden.hideColumns(3, 5);
+    assertEquals(3, hidden.getSize());
+
+    hidden.hideColumns(8, 8);
+    assertEquals(4, hidden.getSize());
+
+    hidden.hideColumns(9, 14);
+    assertEquals(10, hidden.getSize());
+
+    ColumnSelection cs = new ColumnSelection();
+    hidden.revealAllHiddenColumns(cs);
+    assertEquals(0, hidden.getSize());
+  }
+
+  /**
+   * Test the method that finds the visible column position of an alignment
+   * column, allowing for hidden columns.
+   */
+  @Test(groups = { "Functional" })
+  public void testFindColumnPosition()
+  {
+    HiddenColumns cs = new HiddenColumns();
+    assertEquals(5, cs.findColumnPosition(5));
+
+    // hiding column 6 makes no difference
+    cs.hideColumns(6, 6);
+    assertEquals(5, cs.findColumnPosition(5));
+
+    // hiding column 4 moves column 5 to column 4
+    cs.hideColumns(4, 4);
+    assertEquals(4, cs.findColumnPosition(5));
+
+    // hiding column 4 moves column 4 to position 3
+    assertEquals(3, cs.findColumnPosition(4));
+
+    // hiding columns 1 and 2 moves column 5 to column 2
+    cs.hideColumns(1, 2);
+    assertEquals(2, cs.findColumnPosition(5));
+
+    // check with > 1 hidden column regions
+    // where some columns are in the hidden regions
+    HiddenColumns cs2 = new HiddenColumns();
+    cs2.hideColumns(5, 10);
+    cs2.hideColumns(20, 27);
+    cs2.hideColumns(40, 44);
+
+    // hiding columns 5-10 and 20-27 moves column 8 to column 4
+    assertEquals(4, cs2.findColumnPosition(8));
+
+    // and moves column 24 to 13
+    assertEquals(13, cs2.findColumnPosition(24));
+
+    // and moves column 28 to 14
+    assertEquals(14, cs2.findColumnPosition(28));
+
+    // and moves column 40 to 25
+    assertEquals(25, cs2.findColumnPosition(40));
+
+    // check when hidden columns start at 0 that the visible column
+    // is returned as 0
+    HiddenColumns cs3 = new HiddenColumns();
+    cs3.hideColumns(0, 4);
+    assertEquals(0, cs3.findColumnPosition(2));
+
+  }
+
+  /**
+   * Test the method that finds the visible column position a given distance
+   * before another column
+   */
+  @Test(groups = { "Functional" })
+  public void testFindColumnNToLeft()
+  {
+    HiddenColumns cs = new HiddenColumns();
+
+    // test that without hidden columns, findColumnNToLeft returns
+    // position n to left of provided position
+    int pos = cs.subtractVisibleColumns(3, 10);
+    assertEquals(7, pos);
+
+    // 0 returns same position
+    pos = cs.subtractVisibleColumns(0, 10);
+    assertEquals(10, pos);
+
+    // overflow to left returns negative number
+    pos = cs.subtractVisibleColumns(3, 0);
+    assertEquals(-3, pos);
+
+    // test that with hidden columns to left of result column
+    // behaviour is the same as above
+    cs.hideColumns(1, 3);
+
+    // position n to left of provided position
+    pos = cs.subtractVisibleColumns(3, 10);
+    assertEquals(7, pos);
+
+    // 0 returns same position
+    pos = cs.subtractVisibleColumns(0, 10);
+    assertEquals(10, pos);
+
+    // test with one set of hidden columns between start and required position
+    cs.hideColumns(12, 15);
+    pos = cs.subtractVisibleColumns(8, 17);
+    assertEquals(5, pos);
+
+    // test with two sets of hidden columns between start and required position
+    cs.hideColumns(20, 21);
+    pos = cs.subtractVisibleColumns(8, 23);
+    assertEquals(9, pos);
+
+    // repeat last 2 tests with no hidden columns to left of required position
+    ColumnSelection colsel = new ColumnSelection();
+    cs.revealAllHiddenColumns(colsel);
+
+    // test with one set of hidden columns between start and required position
+    cs.hideColumns(12, 15);
+    pos = cs.subtractVisibleColumns(8, 17);
+    assertEquals(5, pos);
+
+    // test with two sets of hidden columns between start and required position
+    cs.hideColumns(20, 21);
+    pos = cs.subtractVisibleColumns(8, 23);
+    assertEquals(9, pos);
+
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetVisibleContigs()
+  {
+    HiddenColumns cs = new HiddenColumns();
+    cs.hideColumns(3, 6);
+    cs.hideColumns(8, 9);
+    cs.hideColumns(12, 12);
+
+    // start position is inclusive, end position exclusive:
+    int[] visible = cs.getVisibleContigs(1, 13);
+    assertEquals("[1, 2, 7, 7, 10, 11]", Arrays.toString(visible));
+
+    visible = cs.getVisibleContigs(4, 14);
+    assertEquals("[7, 7, 10, 11, 13, 13]", Arrays.toString(visible));
+
+    visible = cs.getVisibleContigs(3, 10);
+    assertEquals("[7, 7]", Arrays.toString(visible));
+
+    visible = cs.getVisibleContigs(4, 6);
+    assertEquals("[]", Arrays.toString(visible));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testEquals()
+  {
+    HiddenColumns cs = new HiddenColumns();
+    cs.hideColumns(5, 9);
+
+    // a different set of hidden columns
+    HiddenColumns cs2 = new HiddenColumns();
+
+    // with no hidden columns
+    assertFalse(cs.equals(cs2));
+    assertFalse(cs2.equals(cs));
+
+    // with hidden columns added in a different order
+    cs2.hideColumns(6, 9);
+    cs2.hideColumns(5, 8);
+
+    assertTrue(cs.equals(cs2));
+    assertTrue(cs.equals(cs));
+    assertTrue(cs2.equals(cs));
+    assertTrue(cs2.equals(cs2));
+  }
+
+  @Test(groups = "Functional")
+  public void testCopyConstructor()
+  {
+    HiddenColumns cs = new HiddenColumns();
+    cs.hideColumns(10, 11);
+    cs.hideColumns(5, 7);
+    assertEquals("[5, 7]",
+            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+
+    HiddenColumns cs2 = new HiddenColumns(cs);
+    assertTrue(cs2.hasHiddenColumns());
+    assertEquals(2, cs2.getHiddenColumnsCopy().size());
+    // hidden columns are held in column order
+    assertEquals("[5, 7]",
+            Arrays.toString(cs2.getHiddenColumnsCopy().get(0)));
+    assertEquals("[10, 11]",
+            Arrays.toString(cs2.getHiddenColumnsCopy().get(1)));
+  }
+
+  /**
+   * Test the code used to locate the reference sequence ruler origin
+   */
+  @Test(groups = { "Functional" })
+  public void testLocateVisibleBoundsofSequence()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+    HiddenColumns cs = al.getHiddenColumns();
+    ColumnSelection colsel = new ColumnSelection();
+
+    SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
+    assertEquals(2, seq.findIndex(seq.getStart()));
+
+    // no hidden columns
+    assertEquals(
+            Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
+                seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
+                seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
+                seq.findIndex(seq.getEnd()) - 1 }),
+            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+
+    // hidden column on gap after end of sequence - should not affect bounds
+    colsel.hideSelectedColumns(13, al.getHiddenColumns());
+    assertEquals(
+            Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
+                seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
+                seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
+                seq.findIndex(seq.getEnd()) - 1 }),
+            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+
+    cs.revealAllHiddenColumns(colsel);
+    // hidden column on gap before beginning of sequence - should vis bounds by
+    // one
+    colsel.hideSelectedColumns(0, al.getHiddenColumns());
+    assertEquals(
+            Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 2,
+                seq.findIndex(seq.getEnd()) - 2, seq.getStart(),
+                seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
+                seq.findIndex(seq.getEnd()) - 1 }),
+            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+
+    cs.revealAllHiddenColumns(colsel);
+    // hide columns around most of sequence - leave one residue remaining
+    cs.hideColumns(1, 3);
+    cs.hideColumns(6, 11);
+    assertEquals("-D",
+            cs.getVisibleSequenceStrings(0, 5, new SequenceI[] { seq })[0]);
+    assertEquals(
+            Arrays.toString(new int[] { 1, 1, 3, 3,
+                seq.findIndex(seq.getStart()) - 1,
+                seq.findIndex(seq.getEnd()) - 1 }),
+            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+    cs.revealAllHiddenColumns(colsel);
+
+    // hide whole sequence - should just get location of hidden region
+    // containing sequence
+    cs.hideColumns(1, 11);
+    assertEquals(
+            Arrays.toString(new int[] { 0, 1, 0, 0,
+                seq.findIndex(seq.getStart()) - 1,
+                seq.findIndex(seq.getEnd()) - 1 }),
+            Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
+
+  }
+
+  @Test(groups = { "Functional" })
+  public void testLocateVisibleBoundsPathologicals()
+  {
+    // test some pathological cases we missed
+    AlignmentI al = new Alignment(new SequenceI[] { new Sequence(
+            "refseqGaptest", "KTDVTI----------NFI-----G----L") });
+    HiddenColumns cs = new HiddenColumns();
+    cs.hideInsertionsFor(al.getSequenceAt(0));
+    assertEquals(
+            "G",
+            ""
+                    + al.getSequenceAt(0).getCharAt(
+                            cs.adjustForHiddenColumns(9)));
+
+  }
+
+  @Test(groups = { "Functional" })
+  public void testHideColumns()
+  {
+    // create random alignment
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+    ColumnSelection colsel = new ColumnSelection();
+    HiddenColumns cs = al.getHiddenColumns();
+    colsel.hideSelectedColumns(5, al.getHiddenColumns());
+    List<int[]> hidden = cs.getHiddenColumnsCopy();
+    assertEquals(1, hidden.size());
+    assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
+
+    colsel.hideSelectedColumns(3, al.getHiddenColumns());
+    hidden = cs.getHiddenColumnsCopy();
+    assertEquals(2, hidden.size());
+    // two hidden ranges, in order:
+    assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
+    assertEquals("[3, 3]", Arrays.toString(hidden.get(0)));
+    assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
+
+    // hiding column 4 expands [3, 3] to [3, 4]
+    // and merges to [5, 5] to make [3, 5]
+    colsel.hideSelectedColumns(4, al.getHiddenColumns());
+    hidden = cs.getHiddenColumnsCopy();
+    assertEquals(1, hidden.size());
+    assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));
+
+    // clear hidden columns (note they are added to selected)
+    cs.revealAllHiddenColumns(colsel);
+    // it is now actually null but getter returns an empty list
+    assertTrue(cs.getHiddenColumnsCopy().isEmpty());
+
+    cs.hideColumns(3, 6);
+    hidden = cs.getHiddenColumnsCopy();
+    int[] firstHiddenRange = hidden.get(0);
+    assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
+
+    // adding a subrange of already hidden should do nothing
+    cs.hideColumns(4, 5);
+    hidden = cs.getHiddenColumnsCopy();
+    assertEquals(1, hidden.size());
+    assertEquals("[3, 6]",
+            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+    cs.hideColumns(3, 5);
+    hidden = cs.getHiddenColumnsCopy();
+    assertEquals(1, hidden.size());
+    assertEquals("[3, 6]",
+            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+    cs.hideColumns(4, 6);
+    hidden = cs.getHiddenColumnsCopy();
+    assertEquals(1, hidden.size());
+    assertEquals("[3, 6]",
+            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+    cs.hideColumns(3, 6);
+    hidden = cs.getHiddenColumnsCopy();
+    assertEquals(1, hidden.size());
+    assertEquals("[3, 6]",
+            Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+
+    cs.revealAllHiddenColumns(colsel);
+    cs.hideColumns(2, 4);
+    hidden = cs.getHiddenColumnsCopy();
+    assertEquals(1, hidden.size());
+    assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
+
+    // extend contiguous with 2 positions overlap
+    cs.hideColumns(3, 5);
+    hidden = cs.getHiddenColumnsCopy();
+    assertEquals(1, hidden.size());
+    assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
+
+    // extend contiguous with 1 position overlap
+    cs.hideColumns(5, 6);
+    hidden = cs.getHiddenColumnsCopy();
+    assertEquals(1, hidden.size());
+    assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
+
+    // extend contiguous with overlap both ends:
+    cs.hideColumns(1, 7);
+    hidden = cs.getHiddenColumnsCopy();
+    assertEquals(1, hidden.size());
+    assertEquals("[1, 7]", Arrays.toString(hidden.get(0)));
+  }
+
+  /**
+   * Test the method that reveals a range of hidden columns given the start
+   * column of the range
+   */
+  @Test(groups = { "Functional" })
+  public void testRevealHiddenColumns()
+  {
+    ColumnSelection colsel = new ColumnSelection();
+    HiddenColumns cs = new HiddenColumns();
+    cs.hideColumns(5, 8);
+    colsel.addElement(10);
+    cs.revealHiddenColumns(5, colsel);
+    // hidden columns list now null but getter returns empty list:
+    assertTrue(cs.getHiddenColumnsCopy().isEmpty());
+    // revealed columns are marked as selected (added to selection):
+    assertEquals("[10, 5, 6, 7, 8]", colsel.getSelected().toString());
+
+    // calling with a column other than the range start does nothing:
+    colsel = new ColumnSelection();
+    cs = new HiddenColumns();
+    cs.hideColumns(5, 8);
+    List<int[]> hidden = cs.getHiddenColumnsCopy();
+    cs.revealHiddenColumns(6, colsel);
+    assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
+    assertTrue(colsel.getSelected().isEmpty());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testRevealAllHiddenColumns()
+  {
+    HiddenColumns cs = new HiddenColumns();
+    ColumnSelection colsel = new ColumnSelection();
+    cs.hideColumns(5, 8);
+    cs.hideColumns(2, 3);
+    colsel.addElement(11);
+    colsel.addElement(1);
+    cs.revealAllHiddenColumns(colsel);
+
+    /*
+     * revealing hidden columns adds them (in order) to the (unordered)
+     * selection list
+     */
+    assertTrue(cs.getHiddenColumnsCopy().isEmpty());
+    assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]", colsel.getSelected()
+            .toString());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testIsVisible()
+  {
+    HiddenColumns cs = new HiddenColumns();
+    cs.hideColumns(2, 4);
+    cs.hideColumns(6, 7);
+    assertTrue(cs.isVisible(0));
+    assertTrue(cs.isVisible(-99));
+    assertTrue(cs.isVisible(1));
+    assertFalse(cs.isVisible(2));
+    assertFalse(cs.isVisible(3));
+    assertFalse(cs.isVisible(4));
+    assertTrue(cs.isVisible(5));
+    assertFalse(cs.isVisible(6));
+    assertFalse(cs.isVisible(7));
+  }
+
+  /**
+   * Test for the case when a hidden range encloses more one already hidden
+   * range
+   */
+  @Test(groups = { "Functional" })
+  public void testHideColumns_subsumingHidden()
+  {
+    /*
+     * JAL-2370 bug scenario:
+     * two hidden ranges subsumed by a third
+     */
+    HiddenColumns cs = new HiddenColumns();
+    cs.hideColumns(49, 59);
+    cs.hideColumns(69, 79);
+    List<int[]> hidden = cs.getHiddenColumnsCopy();
+    assertEquals(2, hidden.size());
+    assertEquals("[49, 59]", Arrays.toString(hidden.get(0)));
+    assertEquals("[69, 79]", Arrays.toString(hidden.get(1)));
+
+    cs.hideColumns(48, 80);
+    hidden = cs.getHiddenColumnsCopy();
+    assertEquals(1, hidden.size());
+    assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));
+
+    /*
+     * another...joining hidden ranges
+     */
+    cs = new HiddenColumns();
+    cs.hideColumns(10, 20);
+    cs.hideColumns(30, 40);
+    cs.hideColumns(50, 60);
+    // hiding 21-49 should merge to one range
+    cs.hideColumns(21, 49);
+    hidden = cs.getHiddenColumnsCopy();
+    assertEquals(1, hidden.size());
+    assertEquals("[10, 60]", Arrays.toString(hidden.get(0)));
+
+    /*
+     * another...left overlap, subsumption, right overlap,
+     * no overlap of existing hidden ranges
+     */
+    cs = new HiddenColumns();
+    cs.hideColumns(10, 20);
+    cs.hideColumns(10, 20);
+    cs.hideColumns(30, 35);
+    cs.hideColumns(40, 50);
+    cs.hideColumns(60, 70);
+
+    cs.hideColumns(15, 45);
+    hidden = cs.getHiddenColumnsCopy();
+    assertEquals(2, hidden.size());
+    assertEquals("[10, 50]", Arrays.toString(hidden.get(0)));
+    assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testHideBitset()
+  {
+    HiddenColumns cs;
+
+    BitSet one = new BitSet();
+
+    // one hidden range
+    one.set(1);
+    cs = new HiddenColumns();
+    cs.hideMarkedBits(one);
+    assertEquals(1, cs.getHiddenColumnsCopy().size());
+
+    one.set(2);
+    cs = new HiddenColumns();
+    cs.hideMarkedBits(one);
+    assertEquals(1, cs.getHiddenColumnsCopy().size());
+
+    one.set(3);
+    cs = new HiddenColumns();
+    cs.hideMarkedBits(one);
+    assertEquals(1, cs.getHiddenColumnsCopy().size());
+
+    // split
+    one.clear(2);
+    cs = new HiddenColumns();
+    cs.hideMarkedBits(one);
+    assertEquals(2, cs.getHiddenColumnsCopy().size());
+
+    assertEquals(0, cs.adjustForHiddenColumns(0));
+    assertEquals(2, cs.adjustForHiddenColumns(1));
+    assertEquals(4, cs.adjustForHiddenColumns(2));
+
+    // one again
+    one.clear(1);
+    cs = new HiddenColumns();
+    cs.hideMarkedBits(one);
+
+    assertEquals(1, cs.getHiddenColumnsCopy().size());
+
+    assertEquals(0, cs.adjustForHiddenColumns(0));
+    assertEquals(1, cs.adjustForHiddenColumns(1));
+    assertEquals(2, cs.adjustForHiddenColumns(2));
+    assertEquals(4, cs.adjustForHiddenColumns(3));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetBitset()
+  {
+    BitSet toMark, fromMark;
+    long seed = -3241532;
+    Random number = new Random(seed);
+    for (int n = 0; n < 1000; n++)
+    {
+      // create a random bitfield
+      toMark = BitSet.valueOf(new long[] { number.nextLong(),
+          number.nextLong(), number.nextLong() });
+      toMark.set(n * number.nextInt(10), n * (25 + number.nextInt(25)));
+      HiddenColumns hc = new HiddenColumns();
+      hc.hideMarkedBits(toMark);
+
+      // see if we can recover bitfield
+      hc.markHiddenRegions(fromMark = new BitSet());
+      assertEquals(toMark, fromMark);
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testFindHiddenRegionPositions()
+  {
+    HiddenColumns hc = new HiddenColumns();
+
+    List<Integer> positions = hc.findHiddenRegionPositions();
+    assertTrue(positions.isEmpty());
+
+    hc.hideColumns(3, 7);
+    hc.hideColumns(10, 10);
+    hc.hideColumns(14, 15);
+
+    positions = hc.findHiddenRegionPositions();
+    assertEquals(3, positions.size());
+    assertEquals(3, positions.get(0).intValue());
+    assertEquals(5, positions.get(1).intValue());
+    assertEquals(8, positions.get(2).intValue());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testRegionsToString()
+  {
+    HiddenColumns hc = new HiddenColumns();
+
+    String result = hc.regionsToString(",", "--");
+    assertEquals("", result);
+
+    hc.hideColumns(3, 7);
+    hc.hideColumns(10, 10);
+    hc.hideColumns(14, 15);
+
+    result = hc.regionsToString(",", "--");
+    assertEquals("3--7,10--10,14--15", result);
+  }
+
+  @Test(groups = "Functional")
+  public void getVisibleStartAndEndIndexTest()
+  {
+    Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
+    AlignmentI align = new Alignment(new SequenceI[] { seq });
+    HiddenColumns hc = new HiddenColumns();
+
+    int[] startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+    assertEquals(0, startEnd[0]);
+    assertEquals(25, startEnd[1]);
+
+    hc.hideColumns(0, 0);
+    startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+    assertEquals(1, startEnd[0]);
+    assertEquals(25, startEnd[1]);
+
+    hc.hideColumns(6, 9);
+    hc.hideColumns(11, 12);
+    startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+    assertEquals(1, startEnd[0]);
+    assertEquals(25, startEnd[1]);
+
+    hc.hideColumns(24, 25);
+    startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+    System.out.println(startEnd[0] + " : " + startEnd[1]);
+    assertEquals(1, startEnd[0]);
+    assertEquals(23, startEnd[1]);
+  }
+
+  @Test(groups = "Functional")
+  public void testGetRegionWithEdgeAtRes()
+  {
+    HiddenColumns hc = new HiddenColumns();
+
+    int[] result = hc.getRegionWithEdgeAtRes(5);
+    assertNull(result);
+
+    hc.hideColumns(3, 7);
+    hc.hideColumns(10, 10);
+    hc.hideColumns(14, 15);
+
+    result = hc.getRegionWithEdgeAtRes(3);
+    assertEquals(3, result[0]);
+    assertEquals(7, result[1]);
+
+    result = hc.getRegionWithEdgeAtRes(5);
+    assertEquals(10, result[0]);
+    assertEquals(10, result[1]);
+
+    result = hc.getRegionWithEdgeAtRes(6);
+    assertNull(result);
+  }
+
+  @Test(groups = "Functional")
+  public void testPropagateInsertions()
+  {
+    // create an alignment with no gaps - this will be the profile seq and other
+    // JPRED seqs
+    AlignmentGenerator gen = new AlignmentGenerator(false);
+    AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
+
+    // get the profileseq
+    SequenceI profileseq = al.getSequenceAt(0);
+    SequenceI gappedseq = new Sequence(profileseq);
+    gappedseq.insertCharAt(5, al.getGapCharacter());
+    gappedseq.insertCharAt(6, al.getGapCharacter());
+    gappedseq.insertCharAt(7, al.getGapCharacter());
+    gappedseq.insertCharAt(8, al.getGapCharacter());
+    
+    // create an alignment view with the gapped sequence
+    SequenceI[] seqs = new SequenceI[1];
+    seqs[0] = gappedseq;
+    AlignmentI newal = new Alignment(seqs);
+    HiddenColumns hidden = new HiddenColumns();
+    hidden.hideColumns(15, 17);
+
+    AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
+            false);
+
+    // confirm that original contigs are as expected
+    int[] oldcontigs = hidden.getVisibleContigs(0, 20);
+    int[] testcontigs = { 0, 14, 18, 19 };
+    assertTrue(Arrays.equals(oldcontigs, testcontigs));
+            
+    // propagate insertions
+    HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
+            view);
+
+    // confirm that the contigs have changed to account for the gaps
+    int[] newcontigs = result.getVisibleContigs(0, 20);
+    testcontigs[1] = 10;
+    testcontigs[2] = 14;
+    assertTrue(Arrays.equals(newcontigs, testcontigs));
+    
+  }
+}