X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;h=4d08b15c29e98642a6a6954987fc4ebd8769132e;hb=cce9e4df53a94d9e7f841d25a6063c597f7a2ab9;hp=37d39b673b33977006f73af0ae6b4d285c147f73;hpb=3412b273e964fb1a9d22564b04a5f0c827ec2461;p=jalview.git

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 37d39b6..4d08b15 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1,24 +1,26 @@
 package jalview.datamodel;
 
-import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.assertNull;
-import org.testng.annotations.Test;
-import org.testng.annotations.BeforeMethod;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
 import java.util.Arrays;
 import java.util.List;
 
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 public class SequenceTest
 {
   SequenceI seq;
 
-  @BeforeMethod
+ @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
     seq = new Sequence("FER1", "AKPNGVL");
   }
-  @Test
+  @Test(groups ={ "Functional" })
   public void testInsertGapsAndGapmaps()
   {
     SequenceI aseq = seq.deriveSequence();
@@ -33,7 +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
@@ -49,7 +51,7 @@ public class SequenceTest
     assertNull(seq.getAnnotation());
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetAnnotation_forLabel()
   {
     AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1", 1f);
@@ -72,7 +74,7 @@ public class SequenceTest
     return annotation;
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetAlignmentAnnotations_forCalcIdAndLabel()
   {
     AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
@@ -105,7 +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());
@@ -135,7 +137,7 @@ public class SequenceTest
 
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetStartGetEnd()
   {
     SequenceI seq = new Sequence("test", "ABCDEF");
@@ -155,7 +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");
@@ -183,7 +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");
@@ -218,7 +220,7 @@ public class SequenceTest
     assertEquals(7, seq.findPosition(11));
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testDeleteChars()
   {
     SequenceI seq = new Sequence("test", "ABCDEF");
@@ -236,7 +238,7 @@ public class SequenceTest
     assertEquals(6, seq.getEnd());
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testInsertCharAt()
   {
     // non-static methods:
@@ -253,7 +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-");
@@ -265,7 +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");
@@ -314,7 +316,7 @@ public class SequenceTest
    * entries are the residue positions at the sequence position (or to the right
    * if a gap)
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testFindPositionMap()
   {
     /*
@@ -332,7 +334,7 @@ public class SequenceTest
   /**
    * Test for getSubsequence
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testGetSubsequence()
   {
     SequenceI seq = new Sequence("TestSeq", "ABCDEFG");
@@ -352,7 +354,7 @@ public class SequenceTest
   /**
    * Test for deriveSequence applied to a sequence with a dataset
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testDeriveSequence_existingDataset()
   {
     SequenceI seq = new Sequence("Seq1", "CD");
@@ -367,7 +369,7 @@ public class SequenceTest
   /**
    * Test for deriveSequence applied to an ungapped sequence with no dataset
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testDeriveSequence_noDatasetUngapped()
   {
     SequenceI seq = new Sequence("Seq1", "ABCDEF");
@@ -382,7 +384,7 @@ public class SequenceTest
   /**
    * Test for deriveSequence applied to a gapped sequence with no dataset
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testDeriveSequence_noDatasetGapped()
   {
     SequenceI seq = new Sequence("Seq1", "AB-C.D EF");