3 import static org.testng.AssertJUnit.assertEquals;
4 import static org.testng.AssertJUnit.assertFalse;
5 import static org.testng.AssertJUnit.assertNotNull;
6 import static org.testng.AssertJUnit.assertNull;
7 import static org.testng.AssertJUnit.assertTrue;
9 import jalview.datamodel.Alignment;
10 import jalview.datamodel.AlignmentI;
11 import jalview.datamodel.SequenceDummy;
12 import jalview.datamodel.SequenceI;
13 import jalview.gui.AlignFrame;
15 import java.io.IOException;
17 import org.testng.annotations.Test;
19 public class Gff3tests
22 private static String exonerateSeqs = "examples/testdata/exonerateseqs.fa",
23 exonerateOutput = "examples/testdata/exonerateoutput.gff",
24 simpleGff3file = "examples/testdata/simpleGff3.gff";
26 @Test(groups = { "Functional" })
27 public void testExonerateImport()
29 // exonerate does not tag sequences after features, so we have a more
30 // conventional annotation import test here
32 FileLoader loader = new FileLoader(false);
34 AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
37 assertEquals("Unexpected number of DNA protein associations", 0, af
38 .getViewport().getAlignment().getCodonFrames().size());
40 af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
42 assertTrue("Expected at least one DNA protein association", af
43 .getViewport().getAlignment().getDataset().getCodonFrames()
48 @Test(groups = { "Functional" })
49 public void simpleGff3FileIdentify()
51 assertEquals("Didn't recognise file correctly.", IdentifyFile.GFF3File,
52 new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
55 @Test(groups = { "Functional" })
56 public void simpleGff3FileClass() throws IOException
58 AlignmentI dataset = new Alignment(new SequenceI[] {});
59 FeaturesFile ffile = new FeaturesFile(simpleGff3file,
62 boolean parseResult = ffile.parse(dataset, null, null, false, false);
63 assertTrue("return result should be true", parseResult);
64 checkDatasetfromSimpleGff3(dataset);
67 @Test(groups = { "Functional" })
68 public void simpleGff3FileLoader() throws IOException
70 AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
71 simpleGff3file, FormatAdapter.FILE);
73 "Didn't read the alignment into an alignframe from Gff3 File",
75 checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
78 @Test(groups = { "Functional" })
79 public void simpleGff3RelaxedIdMatching() throws IOException
81 AlignmentI dataset = new Alignment(new SequenceI[] {});
82 FeaturesFile ffile = new FeaturesFile(simpleGff3file,
85 boolean parseResult = ffile.parse(dataset, null, null, false, true);
86 assertTrue("return result (relaxedID matching) should be true",
88 checkDatasetfromSimpleGff3(dataset);
91 @Test(groups = { "Functional" })
92 public void readGff3File() throws IOException
94 Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
95 Alignment dataset = new Alignment(gff3reader.getSeqsAsArray());
96 gff3reader.addProperties(dataset);
97 checkDatasetfromSimpleGff3(dataset);
101 private void checkDatasetfromSimpleGff3(AlignmentI dataset)
103 assertEquals("no sequences extracted from GFF3 file", 2,
104 dataset.getHeight());
106 SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
111 "Failed to replace dummy seq1 with real sequence",
112 seq1 instanceof SequenceDummy
113 && ((SequenceDummy) seq1).isDummy());
115 "Failed to replace dummy seq2 with real sequence",
116 seq2 instanceof SequenceDummy
117 && ((SequenceDummy) seq2).isDummy());
118 String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
119 assertFalse("dummy replacement buggy for seq1",
120 placeholderseq.equals(seq1.getSequenceAsString()));
121 assertFalse("dummy replacement buggy for seq2",
122 placeholderseq.equals(seq2.getSequenceAsString()));
123 assertNotNull("No features added to seq1", seq1.getSequenceFeatures());// !=
125 assertEquals("Wrong number of features", 3,
126 seq1.getSequenceFeatures().length);
127 assertNull(seq2.getSequenceFeatures());
129 "Wrong number of features",
131 seq2.getSequenceFeatures() == null ? 0 : seq2
132 .getSequenceFeatures().length);
134 "Expected at least one CDNA/Protein mapping for seq1",
135 dataset.getCodonFrame(seq1) != null
136 && dataset.getCodonFrame(seq1).size() > 0);
139 // @Test(groups ={ "Functional" })
140 // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
142 // fail("Not yet implemented");
145 // @Test(groups ={ "Functional" })
146 // public final void testAlignFileBooleanStringString()
148 // fail("Not yet implemented");