Merge branch 'develop' into efficiency/JAL-2034_JAL-1421

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

diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index 0245b15..1a7ae32 100644 (file)
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -93,6 +93,83 @@ public class ColumnSelectionTest
     assertEquals(2, cs.findColumnPosition(5));
   }
 
+  /**
+   * Test the code used to locate the reference sequence ruler origin
+   */
+  @Test(groups = { "Functional" })
+  public void testLocateVisibleBoundsofSequence()
+  {
+    ColumnSelection cs = 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
+    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,
+                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()
   {
@@ -401,4 +478,53 @@ 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));
+  }
 }