JAL-2759 unit tests for VisibleContigsIterator

diff --git a/src/jalview/datamodel/VisibleContigsIterator.java b/src/jalview/datamodel/VisibleContigsIterator.java
index d98121a..6d3f43d 100644 (file)
--- a/src/jalview/datamodel/VisibleContigsIterator.java
+++ b/src/jalview/datamodel/VisibleContigsIterator.java
@@ -39,9 +39,17 @@ public class VisibleContigsIterator implements Iterator<int[]>
         }
         if (hideStart > vstart)
         {
-          int[] contig = new int[] { vstart, hideStart - 1 };
-          vcontigs.add(contig);
-          endsAtHidden = true;
+          if (end - 1 > hideStart - 1)
+          {
+            int[] contig = new int[] { vstart, hideStart - 1 };
+            vcontigs.add(contig);
+            endsAtHidden = true;
+          }
+          else
+          {
+            int[] contig = new int[] { vstart, end - 1 };
+            vcontigs.add(contig);
+          }
         }
         vstart = hideEnd + 1;
 

diff --git a/test/jalview/datamodel/VisibleContigsIteratorTest.java b/test/jalview/datamodel/VisibleContigsIteratorTest.java
new file mode 100644 (file)
index 0000000..8f31dae
--- /dev/null
+++ b/test/jalview/datamodel/VisibleContigsIteratorTest.java
@@ -0,0 +1,223 @@
+/*
+ * 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.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+public class VisibleContigsIteratorTest
+{
+  /**
+   * Test the iterator with single visible regions
+   */
+  @Test(groups = { "Functional" })
+  public void testSimpleVisibleRegions()
+  {
+    List<int[]> hiddenColumns = null;
+
+    // null hidden columns
+    VisibleContigsIterator it = new VisibleContigsIterator(3, 10,
+            hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    int[] result = it.next();
+    assertEquals(3, result[0]);
+    assertEquals(9, result[1]);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+
+    hiddenColumns = new ArrayList<>();
+
+    // no hidden columns
+    it = new VisibleContigsIterator(3, 10,
+            hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(3, result[0]);
+    assertEquals(9, result[1]);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+
+    // hidden columns, but not where we are looking
+    hiddenColumns.add(new int[] { 5, 10 });
+    hiddenColumns.add(new int[] { 25, 40 });
+
+    it = new VisibleContigsIterator(2, 3, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(2, result[0]);
+    assertEquals(2, result[1]);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+
+    it = new VisibleContigsIterator(5, 7, hiddenColumns);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+
+    it = new VisibleContigsIterator(11, 15, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(11, result[0]);
+    assertEquals(14, result[1]);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+
+    it = new VisibleContigsIterator(50, 60, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(50, result[0]);
+    assertEquals(59, result[1]);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+  }
+
+  /**
+   * Test the iterator with multiple visible regions
+   */
+  @Test(groups = { "Functional" })
+  public void testMultipleVisibleRegions()
+  {
+    List<int[]> hiddenColumns = new ArrayList<>();
+    hiddenColumns.add(new int[] { 5, 10 });
+    hiddenColumns.add(new int[] { 25, 40 });
+
+    // all hidden columns covered
+    VisibleContigsIterator it = new VisibleContigsIterator(3, 50,
+            hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    int[] result = it.next();
+    assertEquals(3, result[0]);
+    assertEquals(4, result[1]);
+
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(11, result[0]);
+    assertEquals(24, result[1]);
+
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(41, result[0]);
+    assertEquals(49, result[1]);
+
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+  }
+
+  /**
+   * Test the iterator with regions which start/end at hidden region edges
+   */
+  @Test(groups = { "Functional" })
+  public void testVisibleRegionsAtHiddenEdges()
+  {
+    List<int[]> hiddenColumns = new ArrayList<>();
+    hiddenColumns.add(new int[] { 5, 10 });
+    hiddenColumns.add(new int[] { 25, 40 });
+
+    VisibleContigsIterator it = new VisibleContigsIterator(0, 10,
+            hiddenColumns);
+    assertTrue(it.hasNext());
+    assertTrue(it.endsAtHidden());
+    int[] result = it.next();
+    assertEquals(0, result[0]);
+    assertEquals(4, result[1]);
+    assertFalse(it.hasNext());
+    assertTrue(it.endsAtHidden());
+
+    it = new VisibleContigsIterator(2, 11, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertTrue(it.endsAtHidden());
+    result = it.next();
+    assertEquals(2, result[0]);
+    assertEquals(4, result[1]);
+    assertFalse(it.hasNext());
+    assertTrue(it.endsAtHidden());
+
+    it = new VisibleContigsIterator(2, 12, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(2, result[0]);
+    assertEquals(4, result[1]);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(11, result[0]);
+    assertEquals(11, result[1]);
+    assertFalse(it.hasNext());
+    assertFalse(it.endsAtHidden());
+
+    it = new VisibleContigsIterator(13, 25, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(13, result[0]);
+    assertEquals(24, result[1]);
+    assertFalse(it.hasNext());
+
+    it = new VisibleContigsIterator(13, 26, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertTrue(it.endsAtHidden());
+    result = it.next();
+    assertEquals(13, result[0]);
+    assertEquals(24, result[1]);
+    assertFalse(it.hasNext());
+
+    it = new VisibleContigsIterator(13, 27, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertTrue(it.endsAtHidden());
+    result = it.next();
+    assertEquals(13, result[0]);
+    assertEquals(24, result[1]);
+    assertFalse(it.hasNext());
+
+    it = new VisibleContigsIterator(13, 41, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertTrue(it.endsAtHidden());
+    result = it.next();
+    assertEquals(13, result[0]);
+    assertEquals(24, result[1]);
+    assertFalse(it.hasNext());
+
+    it = new VisibleContigsIterator(13, 42, hiddenColumns);
+    assertTrue(it.hasNext());
+    assertFalse(it.endsAtHidden());
+    result = it.next();
+    assertEquals(13, result[0]);
+    assertEquals(24, result[1]);
+    assertTrue(it.hasNext());
+    result = it.next();
+    assertEquals(41, result[0]);
+    assertEquals(41, result[1]);
+  }
+}