JAL-2759 Updated test

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

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index f470d45..72bfd86 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -41,13 +41,13 @@ import java.util.BitSet;
 import java.util.List;
 import java.util.Vector;
 
-import junit.extensions.PA;
-
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class SequenceTest
 {
 
@@ -799,7 +799,7 @@ public class SequenceTest
     Assert.assertEquals(pdbe1a,
             sq.getDatasetSequence().getPDBEntry("1PDB"),
             "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
-    ArrayList<Annotation> annotsList = new ArrayList<Annotation>();
+    ArrayList<Annotation> annotsList = new ArrayList<>();
     System.out.println(">>>>>> " + sq.getSequenceAsString().length());
     annotsList.add(new Annotation("A", "A", 'X', 0.1f));
     annotsList.add(new Annotation("A", "A", 'X', 0.1f));
@@ -1674,6 +1674,20 @@ public class SequenceTest
   }
 
   @Test(groups = { "Functional" })
+  public void testGapBitset()
+  {
+    SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
+    BitSet bs = sq.gapBitset();
+    BitSet expected = new BitSet();
+    expected.set(0);
+    expected.set(4, 7);
+    expected.set(9);
+    expected.set(11, 13);
+
+    assertTrue(bs.equals(expected));
+
+  }
+
   public void testFindFeatures_largeEndPos()
   {
     /*
@@ -1843,6 +1857,7 @@ public class SequenceTest
 
     /*
      * delete gaps and residues internally (new dataset sequence)
+     * first delete from gap to residue
      */
     sq = new Sequence("test/8-10", "A-B-C");
     sq.createDatasetSequence();
@@ -1850,7 +1865,34 @@ public class SequenceTest
     assertEquals("A-C", sq.getSequenceAsString());
     assertEquals(8, sq.getStart());
     assertEquals(9, sq.getEnd());
-    assertEquals("ACDEF", sq.getDatasetSequence().getSequenceAsString());
+    assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
+    assertEquals(8, sq.getDatasetSequence().getStart());
+    assertEquals(9, sq.getDatasetSequence().getEnd());
+
+    /*
+     * internal delete from gap to gap
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(1, 4); // delete -B-
+    assertEquals("AC", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(9, sq.getEnd());
+    assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
+    assertEquals(8, sq.getDatasetSequence().getStart());
+    assertEquals(9, sq.getDatasetSequence().getEnd());
+
+    /*
+     * internal delete from residue to residue
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(2, 3); // delete B
+    assertEquals("A--C", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(9, sq.getEnd());
+    assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
     assertEquals(8, sq.getDatasetSequence().getStart());
+    assertEquals(9, sq.getDatasetSequence().getEnd());
   }
 }