package jalview.ext.ensembl;

import jalview.datamodel.Alignment;
import jalview.datamodel.SequenceI;
import jalview.ext.ensembl.SeqFetcher;
import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
import jalview.io.AppletFormatAdapter;
import jalview.io.FastaFile;
import jalview.io.FileParse;

import java.lang.reflect.Method;
import java.util.Arrays;

import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

public class SeqFetcherTest
{
  @Test
  public void testCheckEnsembl()
  {
    SeqFetcher sf = new SeqFetcher();
    sf.setTestEnsemblStatus(true);
    sf.setTesting(true);
    Assert.assertTrue(sf.isEnsemblAvailable());
    sf.setTestEnsemblStatus(false);
    Assert.assertFalse(sf.isEnsemblAvailable());
  }

  @Test(suiteName = "live")
  public void testLiveCheckEnsembl()
  {
    SeqFetcher sf = new SeqFetcher();
    boolean isAvailable = sf.isEnsemblAvailable();
    System.out.println("Ensembl is "
            + (isAvailable ? "UP!" : "DOWN ******************* BAD!"));
  }

  @DataProvider(name = "ens_seqs")
  public Object[][] createData(Method m)
  {
    System.out.println(m.getName());
    return allSeqs;
  }

  public static Object[][] allSeqs = new Object[][]
  {
  {
      EnsemblSeqType.CDS,
      "CCDS5863.1",
      ">CCDS5863.1\n"
              + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
              + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
              + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
              + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
              + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
              + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
              + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
              + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
              + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
              + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
              + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
              + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
              + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
              + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
              + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
              + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
              + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
              + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
              + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
              + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
              + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
              + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
              + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
              + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
              + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
              + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
              + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
              + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
              + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
              + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
              + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
              + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
              + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
              + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
              + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
              + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
              + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
              + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
              + "GGTGCGTTTCCTGTCCACTGA" } };

  @Test(dataProvider = "ens_seqs", suiteName = "live")
  public void testGetOneSeqs(EnsemblSeqType type, String sq, String fastasq)
          throws Exception
  {
    SeqFetcher sf = new SeqFetcher();
    FileParse fp = sf.getSequenceReader(type, Arrays.asList(new String[]
    { sq }));
    SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
    FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
    SequenceI[] trueSqs = trueRes.getSeqsAsArray();
    Assert.assertEquals(sqs.length, trueSqs.length,
            "Different number of sequences retrieved for query " + sq);
    Alignment ral = new Alignment(sqs);
    for (SequenceI tr : trueSqs)
    {
      SequenceI[] rseq;
      Assert.assertNotNull(
              rseq = ral.findSequenceMatch(tr.getName()),
              "Couldn't find sequences matching expected sequence "
                      + tr.getName());
      Assert.assertEquals(rseq.length, 1,
              "Expected only one sequence for sequence ID " + tr.getName());
      Assert.assertEquals(
              rseq[0].getSequenceAsString(),
              tr.getSequenceAsString(),
              "Sequences differ for " + tr.getName() + "\n" + "Exp:"
                      + tr.getSequenceAsString() + "\n" + "Got:"
                      + rseq[0].getSequenceAsString());
    }
  }
}