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 simpleGff3FileIdentify()
  45   {
  46     Assert.assertEquals("Didn't recognise file correctly.",
  47             IdentifyFile.GFF3File,
  48             new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
  49   }
  50
  51   @Test
  52   public void simpleGff3FileClass() throws IOException
  53   {
  54     AlignmentI dataset = new Alignment(new SequenceI[]
  55     {});
  56     FeaturesFile ffile = new FeaturesFile(simpleGff3file,
  57             FormatAdapter.FILE);
  58
  59     boolean parseResult = ffile.parse(dataset, null, null, false, false);
  60     Assert.assertTrue("return result should be true", parseResult);
  61     checkDatasetfromSimpleGff3(dataset);
  62   }
  63
  64   @Test
  65   public void simpleGff3FileLoader() throws IOException
  66   {
  67     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
  68             simpleGff3file, null);
  69     Assert.assertTrue(
  70             "Didn't read the alignment into an alignframe from Gff3 File",
  71             af != null);
  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("return result (relaxedID matching) should be true",
  85             parseResult);
  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("no sequences extracted from GFF3 file", 2,
 102             dataset.getHeight());
 103
 104     SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
 105             .findName("seq2");
 106     Assert.assertNotNull(seq1);
 107     Assert.assertNotNull(seq2);
 108     Assert.assertFalse(
 109             "Failed to replace dummy seq1 with real sequence",
 110             seq1 instanceof SequenceDummy
 111                     && ((SequenceDummy) seq1).isDummy());
 112     Assert.assertFalse(
 113             "Failed to replace dummy seq2 with real sequence",
 114             seq2 instanceof SequenceDummy
 115                     && ((SequenceDummy) seq2).isDummy());
 116     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 117     Assert.assertFalse("dummy replacement buggy for seq1",
 118             placeholderseq.equals(seq1.getSequenceAsString()));
 119     Assert.assertNotEquals("dummy replacement buggy for seq2",
 120             placeholderseq.equals(seq2.getSequenceAsString()));
 121     Assert.assertNotNull("No features added to seq1",
 122             seq1.getSequenceFeatures());// != null);
 123     Assert.assertEquals("Wrong number of features", 3,
 124             seq1.getSequenceFeatures().length);
 125     Assert.assertNull(seq2.getSequenceFeatures());
 126     Assert.assertEquals("Wrong number of features", 0, seq2
 127             .getSequenceFeatures() == null ? 0
 128             : seq2.getSequenceFeatures().length);
 129     Assert.assertTrue(
 130             "Expected at least one CDNA/Protein mapping for seq1",
 131             dataset.getCodonFrame(seq1) != null
 132                     && dataset.getCodonFrame(seq1).size() > 0);
 133
 134   }
 135   // @Test
 136   // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
 137   // {
 138   // fail("Not yet implemented");
 139   // }
 140   //
 141   // @Test
 142   // public final void testAlignFileBooleanStringString()
 143   // {
 144   // fail("Not yet implemented");
 145   // }
 146
 147 }