package jalview.io;

import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;

import java.io.IOException;

import org.junit.Assert;
import org.junit.Test;

public class Gff3tests
{

  private static String exonerateSeqs = "examples/testdata/exonerateseqs.fa",
          exonerateOutput = "examples/testdata/exonerateoutput.gff",
          simpleGff3file = "examples/testdata/simpleGff3.gff";

  @Test
  public void testExonerateImport()
  {
    // exonerate does not tag sequences after features, so we have a more
    // conventional annotation import test here

    FileLoader loader = new FileLoader(false);

    AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
            FormatAdapter.FILE);

    Assert.assertEquals("Unexpected number of DNA protein associations", 0,
            af.getViewport().getAlignment().getCodonFrames().size());

    af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);

    Assert.assertNotEquals("Expected at least one DNA protein association",
            0, af.getViewport().getAlignment().getDataset()
                    .getCodonFrames().size());

  }

  @Test
  public void simpleGff3() throws IOException
  {
    AlignmentI dataset = new Alignment(new SequenceI[]
    {});
    FeaturesFile ffile = new FeaturesFile(simpleGff3file,
            FormatAdapter.FILE);

    boolean parseResult = ffile.parse(dataset, null, null, false, false);
    Assert.assertTrue("return result should be true", parseResult);
    checkDatasetfromSimpleGff3(dataset);
  }

  @Test
  public void simpleGff3RelaxedIdMatching() throws IOException
  {
    AlignmentI dataset = new Alignment(new SequenceI[]
    {});
    FeaturesFile ffile = new FeaturesFile(simpleGff3file,
            FormatAdapter.FILE);

    boolean parseResult = ffile.parse(dataset, null, null, false, true);
    Assert.assertTrue("return result (relaxedID matching) should be true",
            parseResult);
    checkDatasetfromSimpleGff3(dataset);
  }

  private void checkDatasetfromSimpleGff3(AlignmentI dataset)
  {
    Assert.assertEquals("no sequences extracted from GFF3 file", 2,
            dataset.getHeight());

    SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
            .findName("seq2");
    Assert.assertNotNull(seq1);
    Assert.assertNotNull(seq2);
    Assert.assertFalse(
            "Failed to replace dummy seq1 with real sequence",
            seq1 instanceof SequenceDummy
                    && ((SequenceDummy) seq1).isDummy());
    Assert.assertFalse(
            "Failed to replace dummy seq2 with real sequence",
            seq2 instanceof SequenceDummy
                    && ((SequenceDummy) seq2).isDummy());
    String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
    Assert.assertFalse("dummy replacement buggy for seq1",
            placeholderseq.equals(seq1.getSequenceAsString()));
    Assert.assertNotEquals("dummy replacement buggy for seq2",
            placeholderseq.equals(seq2.getSequenceAsString()));
    Assert.assertNotNull("No features added to seq1",
            seq1.getSequenceFeatures());// != null);
    Assert.assertEquals("Wrong number of features", 3,
            seq1.getSequenceFeatures().length);
    Assert.assertNull(seq2.getSequenceFeatures());
    Assert.assertEquals("Wrong number of features", 0, seq2
            .getSequenceFeatures() == null ? 0
            : seq2.getSequenceFeatures().length);

  }
  // @Test
  // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
  // {
  // fail("Not yet implemented");
  // }
  //
  // @Test
  // public final void testAlignFileBooleanStringString()
  // {
  // fail("Not yet implemented");
  // }

}