+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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;
import java.io.IOException;
-import org.testng.Assert;
import org.testng.annotations.Test;
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
AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
FormatAdapter.FILE);
- Assert.assertEquals(0, af.getViewport().getAlignment().getCodonFrames()
- .size(), "Unexpected number of DNA protein associations");
+ assertEquals("Unexpected number of DNA protein associations", 0, af
+ .getViewport().getAlignment().getCodonFrames().size());
af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
- Assert.assertNotEquals(
+ assertNotEquals("Expected at least one DNA protein association",
0, af.getViewport().getAlignment().getDataset()
.getCodonFrames().size(),
- "Expected at least one DNA protein association");
+ );
}
- @Test
+ @Test(groups = { "Functional" })
public void simpleGff3FileIdentify()
{
- Assert.assertEquals("Didn't recognise file correctly.",
- IdentifyFile.GFF3File,
+ 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[]
- {});
+ AlignmentI dataset = new Alignment(new SequenceI[] {});
FeaturesFile ffile = new FeaturesFile(simpleGff3file,
FormatAdapter.FILE);
boolean parseResult = ffile.parse(dataset, null, null, false, false);
- Assert.assertTrue(parseResult, "return result should be true");
+ 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(af != null,
- "Didn't read the alignment into an alignframe from Gff3 File");
+ 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[]
- {});
+ AlignmentI dataset = new Alignment(new SequenceI[] {});
FeaturesFile ffile = new FeaturesFile(simpleGff3file,
FormatAdapter.FILE);
boolean parseResult = ffile.parse(dataset, null, null, false, true);
- Assert.assertTrue(parseResult,
- "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);
private void checkDatasetfromSimpleGff3(AlignmentI dataset)
{
- Assert.assertEquals(2, dataset.getHeight(),
- "no sequences extracted from GFF3 file");
+ 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(),
- "Failed to replace dummy seq1 with real sequence");
- Assert.assertFalse(
+ && ((SequenceDummy) seq1).isDummy());
+ assertFalse(
+ "Failed to replace dummy seq2 with real sequence",
seq2 instanceof SequenceDummy
&& ((SequenceDummy) seq2).isDummy(),
"Failed to replace dummy seq2 with real sequence");
String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
- Assert.assertFalse(placeholderseq.equals(seq1.getSequenceAsString()),
- "dummy replacement buggy for seq1");
- Assert.assertNotEquals("dummy replacement buggy for seq2",
+ assertFalse("dummy replacement buggy for seq1",
+ placeholderseq.equals(seq1.getSequenceAsString()));
+ assertFalse("dummy replacement buggy for seq2",
placeholderseq.equals(seq2.getSequenceAsString()));
- 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(
- seq2
- .getSequenceFeatures() == null ? 0
- : seq2
- .getSequenceFeatures().length, 0,
- "Wrong number of features");
- Assert.assertTrue(
+ assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
+ assertEquals("Wrong number of features", 3,
+ seq1.getSequenceFeatures().length);
+ assertNull(seq2.getSequenceFeatures());
+ assertEquals(
+ "Wrong number of features",
+ 0,
+ seq2.getSequenceFeatures() == null ? 0 : seq2
+ .getSequenceFeatures().length);
+ assertTrue(
+ "Expected at least one CDNA/Protein mapping for seq1",
dataset.getCodonFrame(seq1) != null
&& dataset.getCodonFrame(seq1).size() > 0,
"Expected at least one CDNA/Protein mapping for seq1");
}
- // @Test
+ // @Test(groups ={ "Functional" })
// public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
// {
// fail("Not yet implemented");
// }
//
- // @Test
+ // @Test(groups ={ "Functional" })
// public final void testAlignFileBooleanStringString()
// {
// fail("Not yet implemented");
git://source.jalview.org / jalview.git / blobdiff