test/jalview/io/Gff3tests.java

   1 package jalview.io;
   2
   3 import jalview.datamodel.Alignment;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.SequenceDummy;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.gui.AlignFrame;
   8
   9 import java.io.IOException;
  10
  11 import org.testng.Assert;
  12 import org.testng.annotations.Test;
  13
  14 public class Gff3tests
  15 {
  16
  17   private static String exonerateSeqs = "examples/testdata/exonerateseqs.fa",
  18           exonerateOutput = "examples/testdata/exonerateoutput.gff",
  19           simpleGff3file = "examples/testdata/simpleGff3.gff";
  20
  21   @Test
  22   public void testExonerateImport()
  23   {
  24     // exonerate does not tag sequences after features, so we have a more
  25     // conventional annotation import test here
  26
  27     FileLoader loader = new FileLoader(false);
  28
  29     AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
  30             FormatAdapter.FILE);
  31
  32     Assert.assertEquals(0, af.getViewport().getAlignment().getCodonFrames()
  33             .size(), "Unexpected number of DNA protein associations");
  34
  35     af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
  36
  37     Assert.assertNotEquals(
  38             0, af.getViewport().getAlignment().getDataset()
  39             .getCodonFrames().size(),
  40             "Expected at least one DNA protein association");
  41
  42   }
  43
  44   @Test
  45   public void simpleGff3FileIdentify()
  46   {
  47     Assert.assertEquals("Didn't recognise file correctly.",
  48             IdentifyFile.GFF3File,
  49             new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
  50   }
  51
  52   @Test
  53   public void simpleGff3FileClass() throws IOException
  54   {
  55     AlignmentI dataset = new Alignment(new SequenceI[]
  56     {});
  57     FeaturesFile ffile = new FeaturesFile(simpleGff3file,
  58             FormatAdapter.FILE);
  59
  60     boolean parseResult = ffile.parse(dataset, null, null, false, false);
  61     Assert.assertTrue(parseResult, "return result should be true");
  62     checkDatasetfromSimpleGff3(dataset);
  63   }
  64
  65   @Test
  66   public void simpleGff3FileLoader() throws IOException
  67   {
  68     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
  69             simpleGff3file, FormatAdapter.FILE);
  70     Assert.assertTrue(af != null,
  71             "Didn't read the alignment into an alignframe from Gff3 File");
  72     checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
  73   }
  74
  75   @Test
  76   public void simpleGff3RelaxedIdMatching() throws IOException
  77   {
  78     AlignmentI dataset = new Alignment(new SequenceI[]
  79     {});
  80     FeaturesFile ffile = new FeaturesFile(simpleGff3file,
  81             FormatAdapter.FILE);
  82
  83     boolean parseResult = ffile.parse(dataset, null, null, false, true);
  84     Assert.assertTrue(parseResult,
  85             "return result (relaxedID matching) should be true");
  86     checkDatasetfromSimpleGff3(dataset);
  87   }
  88
  89   @Test
  90   public void readGff3File() throws IOException
  91   {
  92     Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
  93     Alignment dataset = new Alignment(gff3reader.getSeqsAsArray());
  94     gff3reader.addProperties(dataset);
  95     checkDatasetfromSimpleGff3(dataset);
  96
  97   }
  98
  99   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 100   {
 101     Assert.assertEquals(2, dataset.getHeight(),
 102             "no sequences extracted from GFF3 file");
 103
 104     SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
 105             .findName("seq2");
 106     Assert.assertNotNull(seq1);
 107     Assert.assertNotNull(seq2);
 108     Assert.assertFalse(
 109             seq1 instanceof SequenceDummy
 110             && ((SequenceDummy) seq1).isDummy(),
 111             "Failed to replace dummy seq1 with real sequence");
 112     Assert.assertFalse(
 113             seq2 instanceof SequenceDummy
 114             && ((SequenceDummy) seq2).isDummy(),
 115             "Failed to replace dummy seq2 with real sequence");
 116     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 117     Assert.assertFalse(placeholderseq.equals(seq1.getSequenceAsString()),
 118             "dummy replacement buggy for seq1");
 119     Assert.assertNotEquals("dummy replacement buggy for seq2",
 120             placeholderseq.equals(seq2.getSequenceAsString()));
 121     Assert.assertNotNull(seq1.getSequenceFeatures(),
 122             "No features added to seq1");
 123     Assert.assertEquals(seq1.getSequenceFeatures().length, 3,
 124             "Wrong number of features");
 125     Assert.assertNull(seq2.getSequenceFeatures());
 126     Assert.assertEquals(
 127             seq2
 128             .getSequenceFeatures() == null ? 0
 129  : seq2
 130                     .getSequenceFeatures().length, 0,
 131             "Wrong number of features");
 132     Assert.assertTrue(
 133             dataset.getCodonFrame(seq1) != null
 134             && dataset.getCodonFrame(seq1).size() > 0,
 135             "Expected at least one CDNA/Protein mapping for seq1");
 136
 137   }
 138   // @Test
 139   // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
 140   // {
 141   // fail("Not yet implemented");
 142   // }
 143   //
 144   // @Test
 145   // public final void testAlignFileBooleanStringString()
 146   // {
 147   // fail("Not yet implemented");
 148   // }
 149
 150 }