import java.io.IOException;
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.Test;
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");
}
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);
}
{
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());
}
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);
}
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