package jalview.ext.ensembl;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;

import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyLite;
import jalview.util.MapList;

import java.util.List;

import org.testng.annotations.Test;

public class EnsemblCdnaTest
{
  /**
   * Test that the cdna part of genomic sequence is correctly identified by
   * 'exon' features (or subtypes) - reverse strand case.
   */
  @Test(groups = "Functional")
  public void getGenomicRangesFromFeatures_reverseStrand()
  {
    EnsemblCdna testee = new EnsemblCdna();
    SequenceI genomic = new SequenceDummy("chr7");
    genomic.setStart(10000);
    genomic.setEnd(50000);
    String transcriptId = "ABC123";

    // exon at (start+10000) length 501
    SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
            null);
    sf.setValue("Parent", "transcript:" + transcriptId);
    sf.setStrand("-");
    genomic.addSequenceFeature(sf);

    // exon (sub-type) at (start + exon_variant) length 101
    sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
    sf.setValue("Parent", "transcript:" + transcriptId);
    sf.setStrand("-");
    genomic.addSequenceFeature(sf);

    // exon belonging to a different transcript doesn't count
    sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
    sf.setValue("Parent", "transcript:anotherOne");
    genomic.addSequenceFeature(sf);

    // transcript feature doesn't count
    sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
    genomic.addSequenceFeature(sf);

    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());

    MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
            transcriptId, 23);
    List<int[]> fromRanges = ranges.getFromRanges();
    assertEquals(2, fromRanges.size());

    /*
     * from ranges should be sorted by start order descending
     * and hold mappings from reverse strand sense
     */
    assertEquals(20500, fromRanges.get(0)[0]);
    assertEquals(20000, fromRanges.get(0)[1]);
    assertEquals(10600, fromRanges.get(1)[0]);
    assertEquals(10500, fromRanges.get(1)[1]);
    // to range should start from given start numbering
    List<int[]> toRanges = ranges.getToRanges();
    assertEquals(1, toRanges.size());
    assertEquals(23, toRanges.get(0)[0]);
    assertEquals(624, toRanges.get(0)[1]);
  }

  /**
   * Test that the cdna part of genomic sequence is correctly identified by
   * 'exon' features (or subtypes).
   */
  @Test(groups = "Functional")
  public void getGenomicRangesFromFeatures()
  {
    EnsemblCdna testee = new EnsemblCdna();
    SequenceI genomic = new SequenceDummy("chr7");
    genomic.setStart(10000);
    genomic.setEnd(50000);
    String transcriptId = "ABC123";
  
    // exon at (start+10000) length 501
    SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
            null);
    sf.setValue("Parent", "transcript:" + transcriptId);
    sf.setStrand("+");
    genomic.addSequenceFeature(sf);
  
    // exon (sub-type) at (start + exon_variant) length 101
    sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
    sf.setValue("Parent", "transcript:" + transcriptId);
    sf.setStrand("+");
    genomic.addSequenceFeature(sf);
  
    // exon belonging to a different transcript doesn't count
    sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
    sf.setValue("Parent", "transcript:anotherOne");
    genomic.addSequenceFeature(sf);
  
    // transcript feature doesn't count
    sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
    sf.setStrand("-"); // weird but ignored
    genomic.addSequenceFeature(sf);
  
    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
  
    MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
            transcriptId, 23);
    List<int[]> fromRanges = ranges.getFromRanges();
    assertEquals(2, fromRanges.size());
    // from ranges should be sorted by start order
    assertEquals(10500, fromRanges.get(0)[0]);
    assertEquals(10600, fromRanges.get(0)[1]);
    assertEquals(20000, fromRanges.get(1)[0]);
    assertEquals(20500, fromRanges.get(1)[1]);
    // to range should start from given start numbering
    List<int[]> toRanges = ranges.getToRanges();
    assertEquals(1, toRanges.size());
    assertEquals(23, toRanges.get(0)[0]);
    assertEquals(624, toRanges.get(0)[1]);
  }

  /**
   * The method under test should give up and return null if both forward and
   * reverse strands are present in the features of interest
   */
  @Test(groups = "Functional")
  public void getGenomicRangesFromFeatures_mixedStrand()
  {
    EnsemblCdna testee = new EnsemblCdna();
    SequenceI genomic = new SequenceDummy("chr7");
    genomic.setStart(10000);
    genomic.setEnd(50000);
    String transcriptId = "ABC123";
  
    SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
            null);
    sf.setValue("Parent", "transcript:" + transcriptId);
    sf.setStrand("-");
    genomic.addSequenceFeature(sf);
  
    sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
    sf.setValue("Parent", "transcript:" + transcriptId);
    sf.setStrand("+");
    genomic.addSequenceFeature(sf);
  
    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
  
    MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
            transcriptId, 23);
    assertNull(ranges);
  }
}