JAL-1782 refactored JAL-1766 JAL-653 tests to TestNG

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

diff --git a/test/jalview/io/Gff3tests.java b/test/jalview/io/Gff3tests.java
index 8df44df..56b57af 100644 (file)
--- a/test/jalview/io/Gff3tests.java
+++ b/test/jalview/io/Gff3tests.java
@@ -8,8 +8,8 @@ import jalview.gui.AlignFrame;
 
 import java.io.IOException;
 
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.Test;
 
 public class Gff3tests
 {
@@ -29,14 +29,15 @@ public class Gff3tests
     AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
             FormatAdapter.FILE);
 
-    Assert.assertEquals("Unexpected number of DNA protein associations", 0,
-            af.getViewport().getAlignment().getCodonFrames().size());
+    Assert.assertEquals(0, af.getViewport().getAlignment().getCodonFrames()
+            .size(), "Unexpected number of DNA protein associations");
 
     af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
 
-    Assert.assertNotEquals("Expected at least one DNA protein association",
+    Assert.assertNotEquals(
             0, af.getViewport().getAlignment().getDataset()
-                    .getCodonFrames().size());
+            .getCodonFrames().size(),
+            "Expected at least one DNA protein association");
 
   }
 
@@ -57,7 +58,7 @@ public class Gff3tests
             FormatAdapter.FILE);
 
     boolean parseResult = ffile.parse(dataset, null, null, false, false);
-    Assert.assertTrue("return result should be true", parseResult);
+    Assert.assertTrue(parseResult, "return result should be true");
     checkDatasetfromSimpleGff3(dataset);
   }
 
@@ -66,9 +67,8 @@ public class Gff3tests
   {
     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
             simpleGff3file, FormatAdapter.FILE);
-    Assert.assertTrue(
-            "Didn't read the alignment into an alignframe from Gff3 File",
-            af != null);
+    Assert.assertTrue(af != null,
+            "Didn't read the alignment into an alignframe from Gff3 File");
     checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
   }
 
@@ -81,8 +81,8 @@ public class Gff3tests
             FormatAdapter.FILE);
 
     boolean parseResult = ffile.parse(dataset, null, null, false, true);
-    Assert.assertTrue("return result (relaxedID matching) should be true",
-            parseResult);
+    Assert.assertTrue(parseResult,
+            "return result (relaxedID matching) should be true");
     checkDatasetfromSimpleGff3(dataset);
   }
 
@@ -98,38 +98,41 @@ public class Gff3tests
 
   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
   {
-    Assert.assertEquals("no sequences extracted from GFF3 file", 2,
-            dataset.getHeight());
+    Assert.assertEquals(2, dataset.getHeight(),
+            "no sequences extracted from GFF3 file");
 
     SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
             .findName("seq2");
     Assert.assertNotNull(seq1);
     Assert.assertNotNull(seq2);
     Assert.assertFalse(
-            "Failed to replace dummy seq1 with real sequence",
             seq1 instanceof SequenceDummy
-                    && ((SequenceDummy) seq1).isDummy());
+            && ((SequenceDummy) seq1).isDummy(),
+            "Failed to replace dummy seq1 with real sequence");
     Assert.assertFalse(
-            "Failed to replace dummy seq2 with real sequence",
             seq2 instanceof SequenceDummy
-                    && ((SequenceDummy) seq2).isDummy());
+            && ((SequenceDummy) seq2).isDummy(),
+            "Failed to replace dummy seq2 with real sequence");
     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
-    Assert.assertFalse("dummy replacement buggy for seq1",
-            placeholderseq.equals(seq1.getSequenceAsString()));
+    Assert.assertFalse(placeholderseq.equals(seq1.getSequenceAsString()),
+            "dummy replacement buggy for seq1");
     Assert.assertNotEquals("dummy replacement buggy for seq2",
             placeholderseq.equals(seq2.getSequenceAsString()));
-    Assert.assertNotNull("No features added to seq1",
-            seq1.getSequenceFeatures());// != null);
-    Assert.assertEquals("Wrong number of features", 3,
-            seq1.getSequenceFeatures().length);
+    Assert.assertNotNull(seq1.getSequenceFeatures(),
+            "No features added to seq1");
+    Assert.assertEquals(seq1.getSequenceFeatures().length, 3,
+            "Wrong number of features");
     Assert.assertNull(seq2.getSequenceFeatures());
-    Assert.assertEquals("Wrong number of features", 0, seq2
+    Assert.assertEquals(
+            seq2
             .getSequenceFeatures() == null ? 0
-            : seq2.getSequenceFeatures().length);
+ : seq2
+                    .getSequenceFeatures().length, 0,
+            "Wrong number of features");
     Assert.assertTrue(
-            "Expected at least one CDNA/Protein mapping for seq1",
             dataset.getCodonFrame(seq1) != null
-                    && dataset.getCodonFrame(seq1).size() > 0);
+            && dataset.getCodonFrame(seq1).size() > 0,
+            "Expected at least one CDNA/Protein mapping for seq1");
 
   }
   // @Test