+++ /dev/null
-/*
- * 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 jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-
-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",
- simpleGff3file = "examples/testdata/simpleGff3.gff";
-
- @Test(groups = { "Functional" })
- public void testExonerateImport()
- {
- // exonerate does not tag sequences after features, so we have a more
- // conventional annotation import test here
-
- FileLoader loader = new FileLoader(false);
-
- AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
- FormatAdapter.FILE);
-
- assertEquals("Unexpected number of DNA protein associations", 0, af
- .getViewport().getAlignment().getCodonFrames().size());
-
- af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
-
- 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(groups ={ "Functional" })
- // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
- // {
- // fail("Not yet implemented");
- // }
- //
- // @Test(groups ={ "Functional" })
- // public final void testAlignFileBooleanStringString()
- // {
- // fail("Not yet implemented");
- // }
-
-}
git://source.jalview.org / jalview.git / blobdiff