JAL-2481 JAL-2593 JAL-2526 further optimisation of feature/index finding

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

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index e40d1a5..d1f4290 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1606,4 +1606,59 @@ public class SequenceTest
     assertEquals(".K..BCD.EF..", sq.getSequenceAsString());
     assertEquals(2, PA.getValue(sq, "changeCount"));
   }
+
+  @Test(groups = { "Functional" })
+  public void testFindPositions()
+  {
+    SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
+
+    /*
+     * invalid inputs
+     */
+    assertNull(sq.findPositions(6, 5));
+    assertNull(sq.findPositions(0, 5));
+    assertNull(sq.findPositions(-1, 5));
+
+    /*
+     * all gapped ranges
+     */
+    assertNull(sq.findPositions(1, 1)); // 1-based columns
+    assertNull(sq.findPositions(5, 5));
+    assertNull(sq.findPositions(5, 6));
+    assertNull(sq.findPositions(5, 7));
+
+    /*
+     * all ungapped ranges
+     */
+    assertEquals(new Range(8, 8), sq.findPositions(2, 2)); // A
+    assertEquals(new Range(8, 9), sq.findPositions(2, 3)); // AB
+    assertEquals(new Range(8, 10), sq.findPositions(2, 4)); // ABC
+    assertEquals(new Range(9, 10), sq.findPositions(3, 4)); // BC
+
+    /*
+     * gap to ungapped range
+     */
+    assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC
+    assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE
+
+    /*
+     * ungapped to gapped range
+     */
+    assertEquals(new Range(10, 10), sq.findPositions(4, 5)); // C
+    assertEquals(new Range(9, 13), sq.findPositions(3, 11)); // BCDEF
+
+    /*
+     * ungapped to ungapped enclosing gaps
+     */
+    assertEquals(new Range(10, 11), sq.findPositions(4, 8)); // CD
+    assertEquals(new Range(8, 13), sq.findPositions(2, 11)); // ABCDEF
+
+    /*
+     * gapped to gapped enclosing ungapped
+     */
+    assertEquals(new Range(8, 10), sq.findPositions(1, 5)); // ABC
+    assertEquals(new Range(11, 12), sq.findPositions(5, 10)); // DE
+    assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot
+    assertEquals(new Range(8, 13), sq.findPositions(1, 99));
+  }
 }