test/jalview/io/Gff3tests.java

   1 package jalview.io;
   2
   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;
   8
   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;
  14
  15 import java.io.IOException;
  16
  17 import org.testng.annotations.Test;
  18
  19 public class Gff3tests
  20 {
  21
  22   private static String exonerateSeqs = "examples/testdata/exonerateseqs.fa",
  23           exonerateOutput = "examples/testdata/exonerateoutput.gff",
  24           simpleGff3file = "examples/testdata/simpleGff3.gff";
  25
  26   @Test(groups ={ "Functional" })
  27   public void testExonerateImport()
  28   {
  29     // exonerate does not tag sequences after features, so we have a more
  30     // conventional annotation import test here
  31
  32     FileLoader loader = new FileLoader(false);
  33
  34     AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
  35             FormatAdapter.FILE);
  36
  37     assertEquals("Unexpected number of DNA protein associations", 0,
  38             af.getViewport().getAlignment().getCodonFrames().size());
  39
  40     af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
  41
  42     assertTrue("Expected at least one DNA protein association", af
  43             .getViewport().getAlignment().getDataset().getCodonFrames()
  44             .size() > 0);
  45
  46   }
  47
  48   @Test(groups ={ "Functional" })
  49   public void simpleGff3FileIdentify()
  50   {
  51     assertEquals("Didn't recognise file correctly.",
  52             IdentifyFile.GFF3File,
  53             new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
  54   }
  55
  56   @Test(groups ={ "Functional" })
  57   public void simpleGff3FileClass() 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, false);
  65     assertTrue("return result should be true", parseResult);
  66     checkDatasetfromSimpleGff3(dataset);
  67   }
  68
  69   @Test(groups ={ "Functional" })
  70   public void simpleGff3FileLoader() throws IOException
  71   {
  72     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
  73             simpleGff3file, FormatAdapter.FILE);
  74     assertTrue(
  75             "Didn't read the alignment into an alignframe from Gff3 File",
  76             af != null);
  77     checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
  78   }
  79
  80   @Test(groups ={ "Functional" })
  81   public void simpleGff3RelaxedIdMatching() throws IOException
  82   {
  83     AlignmentI dataset = new Alignment(new SequenceI[]
  84     {});
  85     FeaturesFile ffile = new FeaturesFile(simpleGff3file,
  86             FormatAdapter.FILE);
  87
  88     boolean parseResult = ffile.parse(dataset, null, null, false, true);
  89     assertTrue("return result (relaxedID matching) should be true",
  90             parseResult);
  91     checkDatasetfromSimpleGff3(dataset);
  92   }
  93
  94   @Test(groups ={ "Functional" })
  95   public void readGff3File() throws IOException
  96   {
  97     Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
  98     Alignment dataset = new Alignment(gff3reader.getSeqsAsArray());
  99     gff3reader.addProperties(dataset);
 100     checkDatasetfromSimpleGff3(dataset);
 101
 102   }
 103
 104   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 105   {
 106     assertEquals("no sequences extracted from GFF3 file", 2,
 107             dataset.getHeight());
 108
 109     SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
 110             .findName("seq2");
 111     assertNotNull(seq1);
 112     assertNotNull(seq2);
 113     assertFalse(
 114             "Failed to replace dummy seq1 with real sequence",
 115             seq1 instanceof SequenceDummy
 116                     && ((SequenceDummy) seq1).isDummy());
 117     assertFalse(
 118             "Failed to replace dummy seq2 with real sequence",
 119             seq2 instanceof SequenceDummy
 120                     && ((SequenceDummy) seq2).isDummy());
 121     String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
 122     assertFalse("dummy replacement buggy for seq1",
 123             placeholderseq.equals(seq1.getSequenceAsString()));
 124     assertFalse("dummy replacement buggy for seq2",
 125             placeholderseq.equals(seq2.getSequenceAsString()));
 126     assertNotNull("No features added to seq1",
 127             seq1.getSequenceFeatures());// != null);
 128     assertEquals("Wrong number of features", 3,
 129             seq1.getSequenceFeatures().length);
 130     assertNull(seq2.getSequenceFeatures());
 131     assertEquals(
 132             "Wrong number of features",
 133             0,
 134             seq2
 135             .getSequenceFeatures() == null ? 0
 136             : seq2.getSequenceFeatures().length);
 137     assertTrue(
 138             "Expected at least one CDNA/Protein mapping for seq1",
 139             dataset.getCodonFrame(seq1) != null
 140                     && dataset.getCodonFrame(seq1).size() > 0);
 141
 142   }
 143   // @Test(groups ={ "Functional" })
 144   // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
 145   // {
 146   // fail("Not yet implemented");
 147   // }
 148   //
 149   // @Test(groups ={ "Functional" })
 150   // public final void testAlignFileBooleanStringString()
 151   // {
 152   // fail("Not yet implemented");
 153   // }
 154
 155 }