JAL-2505 make SequenceFeature type, begin, end, featureGroup final

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

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 586cc5d..e3e39f7 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -23,6 +23,7 @@ package jalview.datamodel;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNotSame;
 import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
@@ -287,19 +288,129 @@ public class SequenceTest
   @Test(groups = { "Functional" })
   public void testDeleteChars()
   {
+    /*
+     * internal delete
+     */
+    SequenceI sq = new Sequence("test", "ABCDEF");
+    assertNull(PA.getValue(sq, "datasetSequence"));
+    assertEquals(1, sq.getStart());
+    assertEquals(6, sq.getEnd());
+    sq.deleteChars(2, 3);
+    assertEquals("ABDEF", sq.getSequenceAsString());
+    assertEquals(1, sq.getStart());
+    assertEquals(5, sq.getEnd());
+    assertNull(PA.getValue(sq, "datasetSequence"));
+
+    /*
+     * delete at start
+     */
+    sq = new Sequence("test", "ABCDEF");
+    sq.deleteChars(0, 2);
+    assertEquals("CDEF", sq.getSequenceAsString());
+    assertEquals(3, sq.getStart());
+    assertEquals(6, sq.getEnd());
+    assertNull(PA.getValue(sq, "datasetSequence"));
+
+    /*
+     * delete at end
+     */
+    sq = new Sequence("test", "ABCDEF");
+    sq.deleteChars(4, 6);
+    assertEquals("ABCD", sq.getSequenceAsString());
+    assertEquals(1, sq.getStart());
+    assertEquals(4, sq.getEnd());
+    assertNull(PA.getValue(sq, "datasetSequence"));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteChars_withDbRefsAndFeatures()
+  {
+    /*
+     * internal delete - new dataset sequence created
+     * gets a copy of any dbrefs
+     */
     SequenceI sq = new Sequence("test", "ABCDEF");
+    sq.createDatasetSequence();
+    DBRefEntry dbr1 = new DBRefEntry("Uniprot", "0", "a123");
+    sq.addDBRef(dbr1);
+    Object ds = PA.getValue(sq, "datasetSequence");
+    assertNotNull(ds);
     assertEquals(1, sq.getStart());
     assertEquals(6, sq.getEnd());
     sq.deleteChars(2, 3);
     assertEquals("ABDEF", sq.getSequenceAsString());
     assertEquals(1, sq.getStart());
     assertEquals(5, sq.getEnd());
+    Object newDs = PA.getValue(sq, "datasetSequence");
+    assertNotNull(newDs);
+    assertNotSame(ds, newDs);
+    assertNotNull(sq.getDBRefs());
+    assertEquals(1, sq.getDBRefs().length);
+    assertNotSame(dbr1, sq.getDBRefs()[0]);
+    assertEquals(dbr1, sq.getDBRefs()[0]);
 
+    /*
+     * internal delete with sequence features
+     * (failure case for JAL-2541)
+     */
     sq = new Sequence("test", "ABCDEF");
+    sq.createDatasetSequence();
+    SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
+            "CathGroup");
+    sq.addSequenceFeature(sf1);
+    ds = PA.getValue(sq, "datasetSequence");
+    assertNotNull(ds);
+    assertEquals(1, sq.getStart());
+    assertEquals(6, sq.getEnd());
+    sq.deleteChars(2, 4);
+    assertEquals("ABEF", sq.getSequenceAsString());
+    assertEquals(1, sq.getStart());
+    assertEquals(4, sq.getEnd());
+    newDs = PA.getValue(sq, "datasetSequence");
+    assertNotNull(newDs);
+    assertNotSame(ds, newDs);
+    SequenceFeature[] sfs = sq.getSequenceFeatures();
+    assertNotNull(sfs);
+    assertEquals(1, sfs.length);
+    assertNotSame(sf1, sfs[0]);
+    assertEquals(sf1, sfs[0]);
+
+    /*
+     * delete at start - no new dataset sequence created
+     * any sequence features remain as before
+     */
+    sq = new Sequence("test", "ABCDEF");
+    sq.createDatasetSequence();
+    ds = PA.getValue(sq, "datasetSequence");
+    sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f, "CathGroup");
+    sq.addSequenceFeature(sf1);
     sq.deleteChars(0, 2);
     assertEquals("CDEF", sq.getSequenceAsString());
     assertEquals(3, sq.getStart());
     assertEquals(6, sq.getEnd());
+    assertSame(ds, PA.getValue(sq, "datasetSequence"));
+    sfs = sq.getSequenceFeatures();
+    assertNotNull(sfs);
+    assertEquals(1, sfs.length);
+    assertSame(sf1, sfs[0]);
+
+    /*
+     * delete at end - no new dataset sequence created
+     * any dbrefs remain as before
+     */
+    sq = new Sequence("test", "ABCDEF");
+    sq.createDatasetSequence();
+    ds = PA.getValue(sq, "datasetSequence");
+    dbr1 = new DBRefEntry("Uniprot", "0", "a123");
+    sq.addDBRef(dbr1);
+    sq.deleteChars(4, 6);
+    assertEquals("ABCD", sq.getSequenceAsString());
+    assertEquals(1, sq.getStart());
+    assertEquals(4, sq.getEnd());
+    assertSame(ds, PA.getValue(sq, "datasetSequence"));
+    assertNotNull(sq.getDBRefs());
+    assertEquals(1, sq.getDBRefs().length);
+    assertSame(dbr1, sq.getDBRefs()[0]);
   }
 
   @Test(groups = { "Functional" })
@@ -355,7 +466,8 @@ public class SequenceTest
      * Note JAL-2046: spurious: we have no use case for this at the moment.
      * This test also buggy - as sf2.equals(sf), no new feature is added
      */
-    SequenceFeature sf2 = new SequenceFeature();
+    SequenceFeature sf2 = new SequenceFeature("Scop", "desc", 2, 5, 1f,
+            null);
     sq.getDatasetSequence().addSequenceFeature(sf2);
     sfs = sq.getSequenceFeatures();
     assertEquals(1, sfs.length);