From: kiramt <k.mourao@dundee.ac.uk>
Date: Thu, 21 Sep 2017 16:00:56 +0000 (+0100)
Subject: JAL-2674 unit test for gapBitSet
X-Git-Tag: Release_2_10_4~55^2~1^2~115
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3b3e2d07b59fdce55435f360003a1a1904643640;p=jalview.git

JAL-2674 unit test for gapBitSet
---

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 6844072..b9f93c3 100644
--- 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));
@@ -1672,4 +1672,19 @@ public class SequenceTest
     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--");
+    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));
+
+  }
 }