/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.ext.ensembl;

import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;

import jalview.datamodel.Alignment;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FastaFile;
import jalview.io.FileParse;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyLite;

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

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

public class EnsemblSeqProxyTest
{

  @BeforeClass(alwaysRun = true)
  public void setUpJvOptionPane()
  {
    JvOptionPane.setInteractiveMode(false);
    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  }

  private static final Object[][] allSeqs = new Object[][] {
      {
          new EnsemblProtein(),
          "CCDS5863.1",
          ">CCDS5863.1\n"
                  + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
                  + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
                  + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
                  + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
                  + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
                  + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
                  + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
                  + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
                  + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
                  + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
                  + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
                  + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
                  + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
      {
          new EnsemblCdna(),
          "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\n" },
      {
          new EnsemblProtein(),
          "ENSP00000288602",
          ">ENSP00000288602\n"
                  + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
                  + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
                  + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
                  + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
                  + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
                  + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
                  + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
                  + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
                  + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
                  + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
                  + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
                  + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
                  + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };

  @BeforeClass(alwaysRun = true)
  public void setUp()
  {
    SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
  }

  @AfterClass(alwaysRun = true)
  public void tearDown()
  {
    SequenceOntologyFactory.setInstance(null);
  }

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

  @Test(dataProvider = "ens_seqs", suiteName = "live")
  public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
          String fastasq) throws Exception
  {
    FileParse fp = proxy.getSequenceReader(Arrays
            .asList(new String[] { sq }));
    SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
    FastaFile trueRes = new FastaFile(fastasq, DataSourceType.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)
    {
      // 12/05/2017 failing for EnsemblCdna which is returning protein
      // Ensembl helpdesk ticket 187998
      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());

    }
  }

  @Test(groups = "Functional")
  public void getGenomicRangesFromFeatures()
  {

  }

  @Test(groups = "Functional")
  public void testIsTranscriptIdentifier()
  {
    EnsemblSeqProxy testee = new EnsemblGene();
    assertFalse(testee.isTranscriptIdentifier(null));
    assertFalse(testee.isTranscriptIdentifier(""));
    assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
    assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
    assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
    assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
    assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
    assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
  }

  @Test(groups = "Functional")
  public void testIsGeneIdentifier()
  {
    EnsemblSeqProxy testee = new EnsemblGene();
    assertFalse(testee.isGeneIdentifier(null));
    assertFalse(testee.isGeneIdentifier(""));
    assertFalse(testee.isGeneIdentifier("ENST00000012345"));
    assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
    assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
    assertFalse(testee.isGeneIdentifier("ensg00000012345"));
    assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
    assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
  }

  /**
   * Test the method that appends a single allele's reverse complement to a
   * string buffer
   */
  @Test(groups = "Functional")
  public void testReverseComplementAllele()
  {
    StringBuilder sb = new StringBuilder();
    EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
    EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
    EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
    EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
    EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
    assertEquals("C,c,G,A,T", sb.toString());

    sb = new StringBuilder();
    EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
    EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
    EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
    assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
  }

  /**
   * Test the method that computes the reverse complement of the alleles in a
   * sequence_variant feature
   */
  @Test(groups = "Functional")
  public void testReverseComplementAlleles()
  {
    String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
    SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
            1, 2, 0f, null);
    sf.setValue("alleles", alleles);
    sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");

    EnsemblSeqProxy.reverseComplementAlleles(sf);
    String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
    // verify description is updated with reverse complement
    assertEquals(revcomp, sf.getDescription());
    // verify alleles attribute is updated with reverse complement
    assertEquals(revcomp, sf.getValue("alleles"));
    // verify attributes string is updated with reverse complement
    assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
  }

  @Test(groups = "Functional")
  public void testSortFeatures()
  {
    SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
    SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
    SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
    SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
    List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
        sf2, sf3, sf4 });

    // sort by start position ascending (forward strand)
    // sf2 and sf3 tie and should not be reordered by sorting
    SequenceFeatures.sortFeatures(sfs, true);
    assertSame(sfs.get(0), sf2);
    assertSame(sfs.get(1), sf3);
    assertSame(sfs.get(2), sf1);
    assertSame(sfs.get(3), sf4);

    // sort by end position descending (reverse strand)
    SequenceFeatures.sortFeatures(sfs, false);
    assertSame(sfs.get(0), sf1);
    assertSame(sfs.get(1), sf3);
    assertSame(sfs.get(2), sf2);
    assertSame(sfs.get(3), sf4);
  }
}