Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures

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

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 79bb2bb..9629b6f 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -290,6 +290,61 @@ public class SequenceTest
     assertEquals(0, sq.findIndex(2));
   }
 
+  @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));
+  }
+
   /**
    * Tests for the method that returns a dataset sequence position (start..) for
    * an aligned column position (base 0).
@@ -465,8 +520,7 @@ public class SequenceTest
     assertEquals("test:Pos13:Col10:startCol3:endCol10:tok0",
             PA.getValue(sq, "cursor").toString());
     sq.sequenceChanged();
-    assertEquals(12, sq.findPosition(8));
-    cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(12, sq.findPosition(8)); // E12
     // sequenceChanged() invalidates cursor.lastResidueColumn
     cursor = (SequenceCursor) PA.getValue(sq, "cursor");
     assertEquals("test:Pos12:Col9:startCol3:endCol0:tok1",
@@ -505,6 +559,13 @@ public class SequenceTest
     assertEquals(6, sq.getEnd());
     assertNull(PA.getValue(sq, "datasetSequence"));
 
+    sq = new Sequence("test", "ABCDE");
+    sq.deleteChars(0, 3);
+    assertEquals("DE", sq.getSequenceAsString());
+    assertEquals(4, sq.getStart());
+    assertEquals(5, sq.getEnd());
+    assertNull(PA.getValue(sq, "datasetSequence"));
+
     /*
      * delete at end
      */
@@ -514,6 +575,21 @@ public class SequenceTest
     assertEquals(1, sq.getStart());
     assertEquals(4, sq.getEnd());
     assertNull(PA.getValue(sq, "datasetSequence"));
+
+    /*
+     * delete more positions than there are
+     */
+    sq = new Sequence("test/8-11", "ABCD");
+    sq.deleteChars(0, 99);
+    assertEquals("", sq.getSequenceAsString());
+    assertEquals(12, sq.getStart()); // = findPosition(99) ?!?
+    assertEquals(11, sq.getEnd());
+
+    sq = new Sequence("test/8-11", "----");
+    sq.deleteChars(0, 99); // ArrayIndexOutOfBoundsException <= 2.10.2
+    assertEquals("", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(11, sq.getEnd());
   }
 
   @Test(groups = { "Functional" })
@@ -1614,6 +1690,10 @@ public class SequenceTest
     // cursor should now be at [D 6]
     cursor = (SequenceCursor) PA.getValue(sq, "cursor");
     assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
+    assertEquals(0, cursor.lastColumnPosition); // not yet found
+    assertEquals(13, sq.findPosition(8)); // E13
+    cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(9, cursor.lastColumnPosition); // found
 
     /*
      * deleteChars should invalidate the cached cursor
@@ -1693,61 +1773,6 @@ public class SequenceTest
   }
 
   @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));
-  }
-
-  @Test(groups = { "Functional" })
   public void testGapBitset()
   {
     SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");