JAL-2172 unit test added

[jalview.git] / test / jalview / datamodel / ColumnSelectionTest.java

diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index 0e7678b..04af3ce 100644 (file)
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -100,19 +100,76 @@ public class ColumnSelectionTest
   public void testLocateVisibleBoundsofSequence()
   {
     ColumnSelection cs = new ColumnSelection();
-    SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E");
+    SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
     assertEquals(2, seq.findIndex(seq.getStart()));
-    assertEquals(Arrays.toString(new int[] { seq.findIndex(seq.getStart()),
-        seq.findIndex(seq.getEnd()), seq.getStart(), seq.getEnd() }),
+
+    // 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
+    cs.hideColumns(13);
+    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();
+    // hidden column on gap before beginning of sequence - should vis bounds by
+    // one
+    cs.hideColumns(0);
+    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();
+    // 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 }),
+    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();
+
+    // 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")});
+    ColumnSelection cs = new ColumnSelection();
+    cs.hideInsertionsFor(al.getSequenceAt(0));
+    assertEquals(
+            "G",
+            ""
+                    + al.getSequenceAt(0).getCharAt(
+                            cs.adjustForHiddenColumns(9)));
+
+
+  }
   @Test(groups = { "Functional" })
   public void testHideColumns()
   {
@@ -268,10 +325,14 @@ public class ColumnSelectionTest
    * this fails, HideSelectedColumns may also fail
    */
   @Test(groups = { "Functional" })
-  public void testgetSelectedRanges()
+  public void testGetSelectedRanges()
   {
+    /*
+     * getSelectedRanges returns ordered columns regardless
+     * of the order in which they are added
+     */
     ColumnSelection cs = new ColumnSelection();
-    int[] sel = { 2, 3, 4, 7, 8, 9, 20, 21, 22 };
+    int[] sel = { 4, 3, 7, 21, 9, 20, 8, 22, 2 };
     for (int col : sel)
     {
       cs.addElement(col);
@@ -421,4 +482,84 @@ public class ColumnSelectionTest
     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);
+    cs.hideColumns(3);
+    cs.hideColumns(7);
+    cs.hideColumns(5,9);
+
+    // same selections added in a different order
+    ColumnSelection cs2 = new ColumnSelection();
+    cs2.addElement(1);
+    cs2.addElement(513);
+    cs2.addElement(0);
+
+    // 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);
+    cs2.hideColumns(3);
+    
+    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.hideColumns(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 returns selected columns, in the order in which they
+   * were added
+   */
+  @Test(groups = { "Functional" })
+  public void testGetSelection()
+  {
+    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());
+    int i = 0;
+    for (int col : sel)
+    {
+      assertEquals(col, selected.get(i++).intValue());
+    }
+
+    cs.removeElement(7);
+    cs.addElement(1);
+    cs.removeElement(4);
+    selected = cs.getSelected();
+    assertEquals(3, selected.size());
+    assertEquals(3, selected.get(0).intValue());
+    assertEquals(21, selected.get(1).intValue());
+    assertEquals(1, selected.get(2).intValue());
+  }
 }