package jalview.io;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
import static org.testng.Assert.assertNull;

import java.io.File;
import java.io.IOException;
import java.net.MalformedURLException;
import java.util.List;
import java.util.Set;

import org.testng.annotations.Test;

import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.SequenceFeatures;

public class EmblFlatFileTest
{
  /**
   * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
   * one of them reverse strand
   * 
   * @throws MalformedURLException
   * @throws IOException
   */
  @Test(groups = "Functional")
  public void testParse() throws MalformedURLException, IOException
  {
    File dataFile = new File("test/jalview/io/J03321.embl.txt");
    FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
    EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
    parser.parse();
    List<SequenceI> seqs = parser.getSeqs();

    assertEquals(seqs.size(), 1);
    SequenceI seq = seqs.get(0);
    assertEquals(seq.getName(), "EmblTest|J03321");
    assertEquals(seq.getLength(), 7502);

    /*
     * should be 9 CDS features (one is a 'join' of two exons)
     */
    Set<String> featureTypes = seq.getFeatures().getFeatureTypes();
    assertEquals(featureTypes.size(), 1);
    assertTrue(featureTypes.contains("CDS"));
    
    /*
     * inspect some features (sort them for convenience of test assertions)
     */
    List<SequenceFeature> features = seq.getFeatures()
            .getAllFeatures("CDS");
    SequenceFeatures.sortFeatures(features,  true);
    assertEquals(features.size(), 9);
    
    SequenceFeature sf = features.get(0);
    assertEquals(sf.getBegin(), 1);
    assertEquals(sf.getEnd(), 437);
    assertEquals(sf.getDescription(),
            "Exon 2 for protein EMBLCDS:AAA91567.1");
    assertEquals(sf.getFeatureGroup(), "EmblTest");
    assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
    assertEquals(sf.getPhase(), "0");
    assertEquals(sf.getStrand(), 1);
    assertEquals(sf.getValue("note"), "pGP7-D");
    // second exon of circular DNA!
    assertEquals(sf.getValue("exon number"), 2);
    assertEquals(sf.getValue("product"), "hypothetical protein");
    assertEquals(sf.getValue("transl_table"), "11");
    
    sf = features.get(1);
    assertEquals(sf.getBegin(), 488);
    assertEquals(sf.getEnd(), 1480);
    assertEquals(sf.getDescription(),
            "Exon 1 for protein EMBLCDS:AAA91568.1");
    assertEquals(sf.getFeatureGroup(), "EmblTest");
    assertEquals(sf.getEnaLocation(), "complement(488..1480)");
    assertEquals(sf.getPhase(), "0");
    assertEquals(sf.getStrand(), -1); // reverse strand!
    assertEquals(sf.getValue("note"), "pGP8-D");
    assertEquals(sf.getValue("exon number"), 1);
    assertEquals(sf.getValue("product"), "hypothetical protein");
    
    sf = features.get(7);
    assertEquals(sf.getBegin(), 6045);
    assertEquals(sf.getEnd(), 6788);
    assertEquals(sf.getDescription(),
            "Exon 1 for protein EMBLCDS:AAA91574.1");
    assertEquals(sf.getFeatureGroup(), "EmblTest");
    assertEquals(sf.getEnaLocation(), "6045..6788");
    assertEquals(sf.getPhase(), "0");
    assertEquals(sf.getStrand(), 1);
    assertEquals(sf.getValue("note"), "pGP6-D (gtg start codon)");
    assertEquals(sf.getValue("exon number"), 1);
    assertEquals(sf.getValue("product"), "hypothetical protein");
    
    /*
     * CDS at 7022-7502 is the first exon of the circular DNA CDS
     */
    sf = features.get(8);
    assertEquals(sf.getBegin(), 7022);
    assertEquals(sf.getEnd(), 7502);
    assertEquals(sf.getDescription(),
            "Exon 1 for protein EMBLCDS:AAA91567.1");
    assertEquals(sf.getFeatureGroup(), "EmblTest");
    assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
    assertEquals(sf.getPhase(), "0");
    assertEquals(sf.getStrand(), 1);
    assertEquals(sf.getValue("note"), "pGP7-D");
    assertEquals(sf.getValue("exon number"), 1);
    assertEquals(sf.getValue("product"), "hypothetical protein");

    /*
     * there are 4 'direct' (DR) dbrefs, and numerous CDS /db_xref entries,
     * some of them (e.g. INTERPRO) duplicates; sample a few here
     * Note DBRefEntry constructor capitalises source
     */
    List<DBRefEntry> dbrefs = seq.getDBRefs();
    assertEquals(dbrefs.size(), 31);
    // 1st DR line; note trailing period is removed
    assertTrue(dbrefs.contains(new DBRefEntry("MD5", "0",
            "d4c4942a634e3df4995fd5ac75c26a61")));
    // the 4th DR line:
    assertTrue(
            dbrefs.contains(new DBRefEntry("EuropePMC", "0", "PMC87941")));
    // from the first CDS feature; note canonicalisation to "UNIPROT"
    assertTrue(dbrefs.contains(new DBRefEntry("GOA", "0", "P0CE19")));
    assertTrue(dbrefs.contains(new DBRefEntry("UNIPROT", "0", "P0CE19")));
    // from the last CDS feature
    assertTrue(dbrefs.contains(new DBRefEntry("INTERPRO", "0", "IPR005350")));

    // todo: mappings to, and sequences for, UNIPROT proteins
  }
}