JAL-1759 merge from develop

[jalview.git] / test / jalview / io / Gff3tests.java

diff --git a/test/jalview/io/Gff3tests.java b/test/jalview/io/Gff3tests.java
index 8df44df..c8cf638 100644 (file)
--- a/test/jalview/io/Gff3tests.java
+++ b/test/jalview/io/Gff3tests.java
@@ -1,5 +1,11 @@
 package jalview.io;
 
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertTrue;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceDummy;
@@ -8,8 +14,7 @@ import jalview.gui.AlignFrame;
 
 import java.io.IOException;
 
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.annotations.Test;
 
 public class Gff3tests
 {
@@ -18,7 +23,7 @@ public class Gff3tests
           exonerateOutput = "examples/testdata/exonerateoutput.gff",
           simpleGff3file = "examples/testdata/simpleGff3.gff";
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void testExonerateImport()
   {
     // exonerate does not tag sequences after features, so we have a more
@@ -29,26 +34,26 @@ public class Gff3tests
     AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
             FormatAdapter.FILE);
 
-    Assert.assertEquals("Unexpected number of DNA protein associations", 0,
+    assertEquals("Unexpected number of DNA protein associations", 0,
             af.getViewport().getAlignment().getCodonFrames().size());
 
     af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
 
-    Assert.assertNotEquals("Expected at least one DNA protein association",
-            0, af.getViewport().getAlignment().getDataset()
-                    .getCodonFrames().size());
+    assertTrue("Expected at least one DNA protein association", af
+            .getViewport().getAlignment().getDataset().getCodonFrames()
+            .size() > 0);
 
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void simpleGff3FileIdentify()
   {
-    Assert.assertEquals("Didn't recognise file correctly.",
+    assertEquals("Didn't recognise file correctly.",
             IdentifyFile.GFF3File,
             new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void simpleGff3FileClass() throws IOException
   {
     AlignmentI dataset = new Alignment(new SequenceI[]
@@ -57,22 +62,22 @@ public class Gff3tests
             FormatAdapter.FILE);
 
     boolean parseResult = ffile.parse(dataset, null, null, false, false);
-    Assert.assertTrue("return result should be true", parseResult);
+    assertTrue("return result should be true", parseResult);
     checkDatasetfromSimpleGff3(dataset);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void simpleGff3FileLoader() throws IOException
   {
     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
             simpleGff3file, FormatAdapter.FILE);
-    Assert.assertTrue(
+    assertTrue(
             "Didn't read the alignment into an alignframe from Gff3 File",
             af != null);
     checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void simpleGff3RelaxedIdMatching() throws IOException
   {
     AlignmentI dataset = new Alignment(new SequenceI[]
@@ -81,12 +86,12 @@ public class Gff3tests
             FormatAdapter.FILE);
 
     boolean parseResult = ffile.parse(dataset, null, null, false, true);
-    Assert.assertTrue("return result (relaxedID matching) should be true",
+    assertTrue("return result (relaxedID matching) should be true",
             parseResult);
     checkDatasetfromSimpleGff3(dataset);
   }
 
-  @Test
+  @Test(groups ={ "Functional" })
   public void readGff3File() throws IOException
   {
     Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
@@ -98,47 +103,50 @@ public class Gff3tests
 
   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
   {
-    Assert.assertEquals("no sequences extracted from GFF3 file", 2,
+    assertEquals("no sequences extracted from GFF3 file", 2,
             dataset.getHeight());
 
     SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
             .findName("seq2");
-    Assert.assertNotNull(seq1);
-    Assert.assertNotNull(seq2);
-    Assert.assertFalse(
+    assertNotNull(seq1);
+    assertNotNull(seq2);
+    assertFalse(
             "Failed to replace dummy seq1 with real sequence",
             seq1 instanceof SequenceDummy
                     && ((SequenceDummy) seq1).isDummy());
-    Assert.assertFalse(
+    assertFalse(
             "Failed to replace dummy seq2 with real sequence",
             seq2 instanceof SequenceDummy
                     && ((SequenceDummy) seq2).isDummy());
     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
-    Assert.assertFalse("dummy replacement buggy for seq1",
+    assertFalse("dummy replacement buggy for seq1",
             placeholderseq.equals(seq1.getSequenceAsString()));
-    Assert.assertNotEquals("dummy replacement buggy for seq2",
+    assertFalse("dummy replacement buggy for seq2",
             placeholderseq.equals(seq2.getSequenceAsString()));
-    Assert.assertNotNull("No features added to seq1",
+    assertNotNull("No features added to seq1",
             seq1.getSequenceFeatures());// != null);
-    Assert.assertEquals("Wrong number of features", 3,
+    assertEquals("Wrong number of features", 3,
             seq1.getSequenceFeatures().length);
-    Assert.assertNull(seq2.getSequenceFeatures());
-    Assert.assertEquals("Wrong number of features", 0, seq2
+    assertNull(seq2.getSequenceFeatures());
+    assertEquals(
+            "Wrong number of features",
+            0,
+            seq2
             .getSequenceFeatures() == null ? 0
             : seq2.getSequenceFeatures().length);
-    Assert.assertTrue(
+    assertTrue(
             "Expected at least one CDNA/Protein mapping for seq1",
             dataset.getCodonFrame(seq1) != null
                     && dataset.getCodonFrame(seq1).size() > 0);
 
   }
-  // @Test
+  // @Test(groups ={ "Functional" })
   // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
   // {
   // fail("Not yet implemented");
   // }
   //
-  // @Test
+  // @Test(groups ={ "Functional" })
   // public final void testAlignFileBooleanStringString()
   // {
   // fail("Not yet implemented");