JAL-2480 tidy generic initialisations, SequenceFeatures.varargToTypes

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

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 90856e8..e40d1a5 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -106,15 +106,6 @@ public class SequenceTest
     // change sequence, should trigger an update of cached result
     sq.setSequence("ASDFASDFADSF");
     assertTrue(sq.isProtein());
-    /*
-     * in situ change of sequence doesn't change hashcode :-O
-     * (sequence should not expose internal implementation)
-     */
-    for (int i = 0; i < sq.getSequence().length; i++)
-    {
-      sq.getSequence()[i] = "acgtu".charAt(i % 5);
-    }
-    assertTrue(sq.isProtein()); // but it isn't
   }
 
   @Test(groups = { "Functional" })
@@ -449,11 +440,14 @@ public class SequenceTest
     sq.sequenceChanged();
     assertEquals(12, sq.findPosition(8));
     cursor = (SequenceCursor) PA.getValue(sq, "cursor");
-    assertEquals("test:Pos12:Col9:startCol3:endCol10:tok1",
+    // sequenceChanged() invalidates cursor.lastResidueColumn
+    cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals("test:Pos12:Col9:startCol3:endCol0:tok1",
             cursor.toString());
     // findPosition with cursor accepts base 1 column values
     assertEquals(13, ((Sequence) sq).findPosition(10, cursor));
-    assertEquals(13, sq.findPosition(9));
+    assertEquals(13, sq.findPosition(9)); // F13
+    // lastResidueColumn has now been found and saved in cursor
     assertEquals("test:Pos13:Col10:startCol3:endCol10:tok1",
             PA.getValue(sq, "cursor").toString());
   }
@@ -1571,4 +1565,45 @@ public class SequenceTest
     cursor = (SequenceCursor) PA.getValue(sq, "cursor");
     assertEquals(new SequenceCursor(sq, 13, 10, ++token), cursor);
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetSequence()
+  {
+    String seqstring = "-A--BCD-EF--";
+    Sequence sq = new Sequence("test/8-13", seqstring);
+    sq.createDatasetSequence();
+    assertTrue(Arrays.equals(sq.getSequence(), seqstring.toCharArray()));
+    assertTrue(Arrays.equals(sq.getDatasetSequence().getSequence(),
+            "ABCDEF".toCharArray()));
+
+    // verify a copy of the sequence array is returned
+    char[] theSeq = (char[]) PA.getValue(sq, "sequence");
+    assertNotSame(theSeq, sq.getSequence());
+    theSeq = (char[]) PA.getValue(sq.getDatasetSequence(), "sequence");
+    assertNotSame(theSeq, sq.getDatasetSequence().getSequence());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testReplace()
+  {
+    String seqstring = "-A--BCD-EF--";
+    SequenceI sq = new Sequence("test/8-13", seqstring);
+    assertEquals(0, PA.getValue(sq, "changeCount"));
+
+    assertEquals(0, sq.replace('A', 'A')); // same char
+    assertEquals(seqstring, sq.getSequenceAsString());
+    assertEquals(0, PA.getValue(sq, "changeCount"));
+
+    assertEquals(0, sq.replace('X', 'Y')); // not there
+    assertEquals(seqstring, sq.getSequenceAsString());
+    assertEquals(0, PA.getValue(sq, "changeCount"));
+
+    assertEquals(1, sq.replace('A', 'K'));
+    assertEquals("-K--BCD-EF--", sq.getSequenceAsString());
+    assertEquals(1, PA.getValue(sq, "changeCount"));
+
+    assertEquals(6, sq.replace('-', '.'));
+    assertEquals(".K..BCD.EF..", sq.getSequenceAsString());
+    assertEquals(2, PA.getValue(sq, "changeCount"));
+  }
 }