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, af
  38             .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.", IdentifyFile.GFF3File,
  52             new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
  53   }
  54
  55   @Test(groups = { "Functional" })
  56   public void simpleGff3FileClass() throws IOException
  57   {
  58     AlignmentI dataset = new Alignment(new SequenceI[] {});
  59     FeaturesFile ffile = new FeaturesFile(simpleGff3file,
  60             FormatAdapter.FILE);
  61
  62     boolean parseResult = ffile.parse(dataset, null, null, false, false);
  63     assertTrue("return result should be true", parseResult);
  64     checkDatasetfromSimpleGff3(dataset);
  65   }
  66
  67   @Test(groups = { "Functional" })
  68   public void simpleGff3FileLoader() throws IOException
  69   {
  70     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
  71             simpleGff3file, FormatAdapter.FILE);
  72     assertTrue(
  73             "Didn't read the alignment into an alignframe from Gff3 File",
  74             af != null);
  75     checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
  76   }
  77
  78   @Test(groups = { "Functional" })
  79   public void simpleGff3RelaxedIdMatching() throws IOException
  80   {
  81     AlignmentI dataset = new Alignment(new SequenceI[] {});
  82     FeaturesFile ffile = new FeaturesFile(simpleGff3file,
  83             FormatAdapter.FILE);
  84
  85     boolean parseResult = ffile.parse(dataset, null, null, false, true);
  86     assertTrue("return result (relaxedID matching) should be true",
  87             parseResult);
  88     checkDatasetfromSimpleGff3(dataset);
  89   }
  90
  91   @Test(groups = { "Functional" })
  92   public void readGff3File() throws IOException
  93   {
  94     Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
  95     Alignment dataset = new Alignment(gff3reader.getSeqsAsArray());
  96     gff3reader.addProperties(dataset);
  97     checkDatasetfromSimpleGff3(dataset);
  98
  99   }
 100
 101   private void checkDatasetfromSimpleGff3(AlignmentI dataset)
 102   {
 103     assertEquals("no sequences extracted from GFF3 file", 2,
 104             dataset.getHeight());
 105
 106     SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
 107             .findName("seq2");
 108     assertNotNull(seq1);
 109     assertNotNull(seq2);
 110     assertFalse(
 111             "Failed to replace dummy seq1 with real sequence",
 112             seq1 instanceof SequenceDummy
 113                     && ((SequenceDummy) seq1).isDummy());
 114     assertFalse(
 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());// !=
 124                                                                            // null);
 125     assertEquals("Wrong number of features", 3,
 126             seq1.getSequenceFeatures().length);
 127     assertNull(seq2.getSequenceFeatures());
 128     assertEquals(
 129             "Wrong number of features",
 130             0,
 131             seq2.getSequenceFeatures() == null ? 0 : seq2
 132                     .getSequenceFeatures().length);
 133     assertTrue(
 134             "Expected at least one CDNA/Protein mapping for seq1",
 135             dataset.getCodonFrame(seq1) != null
 136                     && dataset.getCodonFrame(seq1).size() > 0);
 137
 138   }
 139   // @Test(groups ={ "Functional" })
 140   // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
 141   // {
 142   // fail("Not yet implemented");
 143   // }
 144   //
 145   // @Test(groups ={ "Functional" })
 146   // public final void testAlignFileBooleanStringString()
 147   // {
 148   // fail("Not yet implemented");
 149   // }
 150
 151 }