+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import org.junit.Assert;
-import org.junit.Test;
+import java.io.IOException;
+
+import org.testng.annotations.Test;
public class Gff3tests
{
private static String exonerateSeqs = "examples/testdata/exonerateseqs.fa",
- exonerateOutput = "examples/testdata/exonerateoutput.gff";
+ 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("Unexpected number of DNA protein associations", 0,
- af.getViewport().getAlignment().getCodonFrames().size());
+ 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().getCodonFrames().size());
+ assertTrue("Expected at least one DNA protein association", af
+ .getViewport().getAlignment().getDataset().getCodonFrames()
+ .size() > 0);
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void simpleGff3FileIdentify()
+ {
+ assertEquals("Didn't recognise file correctly.", IdentifyFile.GFF3File,
+ new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
+ }
+
+ @Test(groups = { "Functional" })
+ public void simpleGff3FileClass() throws IOException
+ {
+ AlignmentI dataset = new Alignment(new SequenceI[] {});
+ FeaturesFile ffile = new FeaturesFile(simpleGff3file,
+ FormatAdapter.FILE);
+
+ boolean parseResult = ffile.parse(dataset, null, null, false, false);
+ assertTrue("return result should be true", parseResult);
+ checkDatasetfromSimpleGff3(dataset);
+ }
+
+ @Test(groups = { "Functional" })
+ public void simpleGff3FileLoader() throws IOException
+ {
+ AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+ simpleGff3file, FormatAdapter.FILE);
+ assertTrue(
+ "Didn't read the alignment into an alignframe from Gff3 File",
+ af != null);
+ checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
+ }
+
+ @Test(groups = { "Functional" })
+ public void simpleGff3RelaxedIdMatching() throws IOException
+ {
+ AlignmentI dataset = new Alignment(new SequenceI[] {});
+ FeaturesFile ffile = new FeaturesFile(simpleGff3file,
+ FormatAdapter.FILE);
+
+ boolean parseResult = ffile.parse(dataset, null, null, false, true);
+ assertTrue("return result (relaxedID matching) should be true",
+ parseResult);
+ checkDatasetfromSimpleGff3(dataset);
+ }
+
+ @Test(groups = { "Functional" })
+ public void readGff3File() throws IOException
+ {
+ Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
+ Alignment dataset = new Alignment(gff3reader.getSeqsAsArray());
+ gff3reader.addProperties(dataset);
+ checkDatasetfromSimpleGff3(dataset);
+
+ }
+
+ private void checkDatasetfromSimpleGff3(AlignmentI dataset)
+ {
+ assertEquals("no sequences extracted from GFF3 file", 2,
+ dataset.getHeight());
+ SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
+ .findName("seq2");
+ assertNotNull(seq1);
+ assertNotNull(seq2);
+ assertFalse(
+ "Failed to replace dummy seq1 with real sequence",
+ seq1 instanceof SequenceDummy
+ && ((SequenceDummy) seq1).isDummy());
+ assertFalse(
+ "Failed to replace dummy seq2 with real sequence",
+ seq2 instanceof SequenceDummy
+ && ((SequenceDummy) seq2).isDummy());
+ String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
+ assertFalse("dummy replacement buggy for seq1",
+ placeholderseq.equals(seq1.getSequenceAsString()));
+ assertFalse("dummy replacement buggy for seq2",
+ placeholderseq.equals(seq2.getSequenceAsString()));
+ assertNotNull("No features added to seq1", seq1.getSequenceFeatures());// !=
+ // null);
+ 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);
}
- // @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