X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fanalysis%2FAnnotationSorterTest.java;h=1731302357d835e9b3a07cccad6267aef9e64a87;hb=8bbcfb93404decd6d660ca32b69a29f8a1f34e82;hp=239eb4c04974f73e3f13035fe81e0d845526621b;hpb=76139ef711627a3176736af47272ff55be62e720;p=jalview.git

diff --git a/test/jalview/analysis/AnnotationSorterTest.java b/test/jalview/analysis/AnnotationSorterTest.java
index 239eb4c..1731302 100644
--- a/test/jalview/analysis/AnnotationSorterTest.java
+++ b/test/jalview/analysis/AnnotationSorterTest.java
@@ -1,6 +1,7 @@
 package jalview.analysis;
 
-import static org.junit.Assert.assertEquals;
+import static org.testng.AssertJUnit.assertEquals;
+
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -11,8 +12,8 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Random;
 
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
 public class AnnotationSorterTest
 {
@@ -29,7 +30,7 @@ public class AnnotationSorterTest
   /*
    * Set up 6 sequences and 7 annotations.
    */
-  @Before
+ @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
     al = buildAlignment(NUM_SEQS);
@@ -83,7 +84,7 @@ public class AnnotationSorterTest
    * sequence ref</li>
    * </ul>
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSortBySequenceAndType_autocalcLast()
   {
     // @formatter:off
@@ -110,7 +111,7 @@ public class AnnotationSorterTest
   /**
    * Variant with autocalculated annotations sorting to front
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSortBySequenceAndType_autocalcFirst()
   {
     // @formatter:off
@@ -146,7 +147,7 @@ public class AnnotationSorterTest
    * sequence ref</li>
    * </ul>
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSortByTypeAndSequence_autocalcLast()
   {
     // @formatter:off
@@ -173,7 +174,7 @@ public class AnnotationSorterTest
   /**
    * Variant of test with autocalculated annotations sorted to front
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSortByTypeAndSequence_autocalcFirst()
   {
     // @formatter:off
@@ -201,7 +202,7 @@ public class AnnotationSorterTest
    * Variant of test with autocalculated annotations sorted to front but
    * otherwise no change.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testNoSort_autocalcFirst()
   {
     // @formatter:off
@@ -225,7 +226,7 @@ public class AnnotationSorterTest
     assertEquals("Structure", anns[6].label);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSort_timingPresorted()
   {
     testTiming_presorted(50, 100);
@@ -241,23 +242,23 @@ public class AnnotationSorterTest
    */
   private void testTiming_presorted(final int numSeqs, final int numAnns)
   {
-    al = buildAlignment(numSeqs);
-    anns = buildAnnotations(numAnns);
+    Alignment alignment = buildAlignment(numSeqs);
+    AlignmentAnnotation[] annotations = buildAnnotations(numAnns);
 
     /*
      * Set the annotations presorted by label
      */
     Random r = new Random();
-    final SequenceI[] sequences = al.getSequencesArray();
-    for (int i = 0; i < anns.length; i++)
+    final SequenceI[] sequences = alignment.getSequencesArray();
+    for (int i = 0; i < annotations.length; i++)
     {
       SequenceI randomSequenceRef = sequences[r.nextInt(sequences.length)];
-      anns[i].sequenceRef = randomSequenceRef;
-      anns[i].label = "label" + i;
+      annotations[i].sequenceRef = randomSequenceRef;
+      annotations[i].label = "label" + i;
     }
     long startTime = System.currentTimeMillis();
-    AnnotationSorter testee = new AnnotationSorter(al, false);
-    testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+    AnnotationSorter testee = new AnnotationSorter(alignment, false);
+    testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
     long endTime = System.currentTimeMillis();
     final long elapsed = endTime - startTime;
     System.out.println("Timing test for presorted " + numSeqs
@@ -268,7 +269,7 @@ public class AnnotationSorterTest
   /**
    * Timing tests for sorting randomly sorted annotations for various sizes.
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSort_timingUnsorted()
   {
     testTiming_unsorted(50, 100);
@@ -285,23 +286,23 @@ public class AnnotationSorterTest
    */
   private void testTiming_unsorted(final int numSeqs, final int numAnns)
   {
-    al = buildAlignment(numSeqs);
-    anns = buildAnnotations(numAnns);
+    Alignment alignment = buildAlignment(numSeqs);
+    AlignmentAnnotation[] annotations = buildAnnotations(numAnns);
 
     /*
      * Set the annotations in random order with respect to the sequences
      */
     Random r = new Random();
-    final SequenceI[] sequences = al.getSequencesArray();
-    for (int i = 0; i < anns.length; i++)
+    final SequenceI[] sequences = alignment.getSequencesArray();
+    for (int i = 0; i < annotations.length; i++)
     {
       SequenceI randomSequenceRef = sequences[r.nextInt(sequences.length)];
-      anns[i].sequenceRef = randomSequenceRef;
-      anns[i].label = "label" + i;
+      annotations[i].sequenceRef = randomSequenceRef;
+      annotations[i].label = "label" + i;
     }
     long startTime = System.currentTimeMillis();
-    AnnotationSorter testee = new AnnotationSorter(al, false);
-    testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+    AnnotationSorter testee = new AnnotationSorter(alignment, false);
+    testee.sort(annotations, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
     long endTime = System.currentTimeMillis();
     final long elapsed = endTime - startTime;
     System.out.println("Timing test for unsorted " + numSeqs
@@ -312,7 +313,7 @@ public class AnnotationSorterTest
   /**
    * Timing test for sorting annotations with a limited range of types (labels).
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testSort_timingSemisorted()
   {
     testTiming_semiSorted(50, 100);
@@ -335,8 +336,8 @@ public class AnnotationSorterTest
    */
   private void testTiming_semiSorted(final int numSeqs, final int numAnns)
   {
-    al = buildAlignment(numSeqs);
-    anns = buildAnnotations(numAnns);
+    Alignment alignment = buildAlignment(numSeqs);
+    AlignmentAnnotation[] annotations = buildAnnotations(numAnns);
 
     String[] labels = new String[]
     { "label1", "label2", "label3", "label4", "label5", "label6" };
@@ -345,16 +346,16 @@ public class AnnotationSorterTest
      * Set the annotations in sequence order with randomly assigned labels.
      */
     Random r = new Random();
-    final SequenceI[] sequences = al.getSequencesArray();
-    for (int i = 0; i < anns.length; i++)
+    final SequenceI[] sequences = alignment.getSequencesArray();
+    for (int i = 0; i < annotations.length; i++)
     {
       SequenceI sequenceRef = sequences[i % sequences.length];
-      anns[i].sequenceRef = sequenceRef;
-      anns[i].label = labels[r.nextInt(labels.length)];
+      annotations[i].sequenceRef = sequenceRef;
+      annotations[i].label = labels[r.nextInt(labels.length)];
     }
     long startTime = System.currentTimeMillis();
-    AnnotationSorter testee = new AnnotationSorter(al, false);
-    testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+    AnnotationSorter testee = new AnnotationSorter(alignment, false);
+    testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
     long endTime = System.currentTimeMillis();
     long elapsed = endTime - startTime;
     System.out.println("Sort by label for semisorted " + numSeqs
@@ -363,7 +364,7 @@ public class AnnotationSorterTest
 
     // now resort by sequence
     startTime = System.currentTimeMillis();
-    testee.sort(anns, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
+    testee.sort(annotations, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
     endTime = System.currentTimeMillis();
     elapsed = endTime - startTime;
     System.out.println("Resort by sequence for semisorted " + numSeqs
@@ -372,7 +373,7 @@ public class AnnotationSorterTest
 
     // now resort by label
     startTime = System.currentTimeMillis();
-    testee.sort(anns, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
+    testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
     endTime = System.currentTimeMillis();
     elapsed = endTime - startTime;
     System.out.println("Resort by label for semisorted " + numSeqs