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.junit.Assert;
  12 import org.junit.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("Unexpected number of DNA protein associations", 0,
  33             af.getViewport().getAlignment().getCodonFrames().size());
  34
  35     af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
  36
  37     Assert.assertNotEquals("Expected at least one DNA protein association",
  38             0, af.getViewport().getAlignment().getDataset()
  39                     .getCodonFrames().size());
  40
  41   }
  42
  43   @Test
  44   public void simpleGff3() throws IOException
  45   {
  46     AlignmentI dataset = new Alignment(new SequenceI[]
  47     {});
  48     FeaturesFile ffile = new FeaturesFile(simpleGff3file,
  49             FormatAdapter.FILE);
  50
  51     boolean parseResult = ffile.parse(dataset, null, null, false, false);
  52     Assert.assertTrue("return result should be true", parseResult);
  53     checkDatasetfromSimpleGff3(dataset);
  54   }
  55
  56   @Test
  57   public void simpleGff3RelaxedIdMatching() throws IOException
  58   {
  59     AlignmentI dataset = new Alignment(new SequenceI[]
  60     {});
  61     FeaturesFile ffile = new FeaturesFile(simpleGff3file,
  62             FormatAdapter.FILE);
  63
  64     boolean parseResult = ffile.parse(dataset, null, null, false, true);
  65     Assert.assertTrue("return result (relaxedID matching) should be true",
  66             parseResult);
  67     checkDatasetfromSimpleGff3(dataset);
  68   }
  69
  70   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
  71   {
  72     Assert.assertEquals("no sequences extracted from GFF3 file", 2,
  73             dataset.getHeight());
  74
  75     SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
  76             .findName("seq2");
  77     Assert.assertNotNull(seq1);
  78     Assert.assertNotNull(seq2);
  79     Assert.assertFalse(
  80             "Failed to replace dummy seq1 with real sequence",
  81             seq1 instanceof SequenceDummy
  82                     && ((SequenceDummy) seq1).isDummy());
  83     Assert.assertFalse(
  84             "Failed to replace dummy seq2 with real sequence",
  85             seq2 instanceof SequenceDummy
  86                     && ((SequenceDummy) seq2).isDummy());
  87     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
  88     Assert.assertFalse("dummy replacement buggy for seq1",
  89             placeholderseq.equals(seq1.getSequenceAsString()));
  90     Assert.assertNotEquals("dummy replacement buggy for seq2",
  91             placeholderseq.equals(seq2.getSequenceAsString()));
  92     Assert.assertNotNull("No features added to seq1",
  93             seq1.getSequenceFeatures());// != null);
  94     Assert.assertEquals("Wrong number of features", 3,
  95             seq1.getSequenceFeatures().length);
  96     Assert.assertNull(seq2.getSequenceFeatures());
  97     Assert.assertEquals("Wrong number of features", 0, seq2
  98             .getSequenceFeatures() == null ? 0
  99             : seq2.getSequenceFeatures().length);
 100
 101   }
 102   // @Test
 103   // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
 104   // {
 105   // fail("Not yet implemented");
 106   // }
 107   //
 108   // @Test
 109   // public final void testAlignFileBooleanStringString()
 110   // {
 111   // fail("Not yet implemented");
 112   // }
 113
 114 }