X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;h=4d08b15c29e98642a6a6954987fc4ebd8769132e;hb=refs%2Fheads%2Ffeatures%2FJAL-857_dynamic-example-files;hp=fa4d7172e14ce37b917c069161016d2941c2ef29;hpb=b13f521553582ef2fbfd7815ae25e23284babdea;p=jalview.git

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index fa4d717..4d08b15 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1,26 +1,26 @@
 package jalview.datamodel;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
 
 import java.util.Arrays;
 import java.util.List;
 
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
 public class SequenceTest
 {
   SequenceI seq;
 
-  @Before
+ @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
     seq = new Sequence("FER1", "AKPNGVL");
   }
-  @Test
+  @Test(groups ={ "Functional" })
   public void testInsertGapsAndGapmaps()
   {
     SequenceI aseq = seq.deriveSequence();
@@ -35,7 +35,7 @@ public class SequenceTest
     assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetAnnotation()
   {
     // initial state returns null not an empty array
@@ -51,7 +51,7 @@ public class SequenceTest
     assertNull(seq.getAnnotation());
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetAnnotation_forLabel()
   {
     AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1", 1f);
@@ -74,7 +74,7 @@ public class SequenceTest
     return annotation;
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetAlignmentAnnotations_forCalcIdAndLabel()
   {
     AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
@@ -107,7 +107,7 @@ public class SequenceTest
    * setting the sequenceRef on the annotation. Adding the same annotation twice
    * should be ignored.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testAddAlignmentAnnotation()
   {
     assertNull(seq.getAnnotation());
@@ -137,7 +137,7 @@ public class SequenceTest
 
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetStartGetEnd()
   {
     SequenceI seq = new Sequence("test", "ABCDEF");
@@ -157,7 +157,7 @@ public class SequenceTest
    * Tests for the method that returns an alignment column position (base 1) for
    * a given sequence position (base 1).
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testFindIndex()
   {
     SequenceI seq = new Sequence("test", "ABCDEF");
@@ -185,7 +185,7 @@ public class SequenceTest
    * Tests for the method that returns a dataset sequence position (base 1) for
    * an aligned column position (base 0).
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testFindPosition()
   {
     SequenceI seq = new Sequence("test", "ABCDEF");
@@ -220,7 +220,7 @@ public class SequenceTest
     assertEquals(7, seq.findPosition(11));
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testDeleteChars()
   {
     SequenceI seq = new Sequence("test", "ABCDEF");
@@ -238,7 +238,7 @@ public class SequenceTest
     assertEquals(6, seq.getEnd());
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testInsertCharAt()
   {
     // non-static methods:
@@ -255,7 +255,7 @@ public class SequenceTest
    * Test the method that returns an array of aligned sequence positions where
    * the array index is the data sequence position (both base 0).
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGapMap()
   {
     SequenceI seq = new Sequence("test", "-A--B-CD-E--F-");
@@ -267,7 +267,7 @@ public class SequenceTest
    * Test the method that gets sequence features, either from the sequence or
    * its dataset.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetSequenceFeatures()
   {
     SequenceI seq = new Sequence("test", "GATCAT");
@@ -310,4 +310,90 @@ public class SequenceTest
     seq.getDatasetSequence().setDatasetSequence(seq); // loop!
     assertNull(seq.getSequenceFeatures());
   }
-}
\ No newline at end of file
+
+  /**
+   * Test the method that returns an array, indexed by sequence position, whose
+   * entries are the residue positions at the sequence position (or to the right
+   * if a gap)
+   */
+  @Test(groups ={ "Functional" })
+  public void testFindPositionMap()
+  {
+    /*
+     * Note: Javadoc for findPosition says it returns the residue position to
+     * the left of a gapped position; in fact it returns the position to the
+     * right. Also it returns a non-existent residue position for a gap beyond
+     * the sequence.
+     */
+    Sequence seq = new Sequence("TestSeq", "AB.C-D E.");
+    int[] map = seq.findPositionMap();
+    assertEquals(Arrays.toString(new int[]
+    { 1, 2, 3, 3, 4, 4, 5, 5, 6 }), Arrays.toString(map));
+  }
+
+  /**
+   * Test for getSubsequence
+   */
+  @Test(groups ={ "Functional" })
+  public void testGetSubsequence()
+  {
+    SequenceI seq = new Sequence("TestSeq", "ABCDEFG");
+    seq.createDatasetSequence();
+
+    // positions are base 0, end position is exclusive
+    SequenceI subseq = seq.getSubSequence(2, 4);
+
+    assertEquals("CD", subseq.getSequenceAsString());
+    // start/end are base 1 positions
+    assertEquals(3, subseq.getStart());
+    assertEquals(4, subseq.getEnd());
+    // subsequence shares the full dataset sequence
+    assertSame(seq.getDatasetSequence(), subseq.getDatasetSequence());
+  }
+
+  /**
+   * Test for deriveSequence applied to a sequence with a dataset
+   */
+  @Test(groups ={ "Functional" })
+  public void testDeriveSequence_existingDataset()
+  {
+    SequenceI seq = new Sequence("Seq1", "CD");
+    seq.setDatasetSequence(new Sequence("Seq1", "ABCDEF"));
+    seq.setStart(3);
+    seq.setEnd(4);
+    SequenceI derived = seq.deriveSequence();
+    assertEquals("CD", derived.getSequenceAsString());
+    assertSame(seq.getDatasetSequence(), derived.getDatasetSequence());
+  }
+
+  /**
+   * Test for deriveSequence applied to an ungapped sequence with no dataset
+   */
+  @Test(groups ={ "Functional" })
+  public void testDeriveSequence_noDatasetUngapped()
+  {
+    SequenceI seq = new Sequence("Seq1", "ABCDEF");
+    assertEquals(1, seq.getStart());
+    assertEquals(6, seq.getEnd());
+    SequenceI derived = seq.deriveSequence();
+    assertEquals("ABCDEF", derived.getSequenceAsString());
+    assertEquals("ABCDEF", derived.getDatasetSequence()
+            .getSequenceAsString());
+  }
+
+  /**
+   * Test for deriveSequence applied to a gapped sequence with no dataset
+   */
+  @Test(groups ={ "Functional" })
+  public void testDeriveSequence_noDatasetGapped()
+  {
+    SequenceI seq = new Sequence("Seq1", "AB-C.D EF");
+    assertEquals(1, seq.getStart());
+    assertEquals(6, seq.getEnd());
+    assertNull(seq.getDatasetSequence());
+    SequenceI derived = seq.deriveSequence();
+    assertEquals("AB-C.D EF", derived.getSequenceAsString());
+    assertEquals("ABCDEF", derived.getDatasetSequence()
+            .getSequenceAsString());
+  }
+}