package jalview.io;

import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;

import java.util.ArrayList;

import org.junit.After;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;

public class JSONFileTest
{
  private JSONFile jsonFile;

  private int TEST_SEQ_HEIGHT = 0;

  private int TEST_GRP_HEIGHT = 0;

  private int TEST_ANOT_HEIGHT = 0;

  @Before
  public void setUp() throws Exception
  {
    jsonFile = new JSONFile();

    // create and add sequences
    Sequence[] seqs = new Sequence[5];
    seqs[0] = new Sequence("FER_CAPAN",
            "SVSATMISTSFMPRKPAVTSL-KPIPNVGE--ALF", 3, 34);
    seqs[1] = new Sequence("FER1_SOLLC",
            "SISGTMISTSFLPRKPAVTSL-KAISNVGE--ALF", 3, 34);
    seqs[2] = new Sequence("Q93XJ9_SOLTU",
            "SISGTMISTSFLPRKPVVTSL-KAISNVGE--ALF", 3, 34);
    seqs[3] = new Sequence("FER1_PEA",
            "ALYGTAVSTSFLRTQPMPMSV-TTTKAFSN--GFL", 6, 37);
    seqs[4] = new Sequence("Q7XA98_TRIPR",
            "ALYGTAVSTSFMRRQPVPMSV-ATTTTTKAFPSGF", 6, 39);

    // create and add sequence features
    SequenceFeature seqFeature2 = new SequenceFeature("feature_x",
            "desciption", "status", 22, 29, "jalview");
    SequenceFeature seqFeature3 = new SequenceFeature("feature_x",
            "desciption", "status", 25, 32, "jalview");
    SequenceFeature seqFeature4 = new SequenceFeature("feature_x",
            "desciption", "status", 25, 32, "jalview");
    seqs[2].addSequenceFeature(seqFeature2);
    seqs[3].addSequenceFeature(seqFeature3);
    seqs[4].addSequenceFeature(seqFeature4);

    // add created features to features displayed
    FeaturesDisplayed fDis = new FeaturesDisplayed();
    fDis.setVisible("feature_x");
    jsonFile.setDisplayedFeatures(fDis);
    JSONFile.setSeqFeaturesEnabled(true);

    for (Sequence seq : seqs)
    {
      seq.setDatasetSequence(seq);
      jsonFile.seqs.add(seq);
    }

    // create and add sequence groups
    ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
    grpSeqs.add(seqs[0]);
    grpSeqs.add(seqs[1]);
    grpSeqs.add(seqs[2]);
    ColourSchemeI scheme = jsonFile.getJalviewColorScheme("zappo");
    SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1114606272",
            scheme, true, true, false, 2, 9);
    seqGrp.setShowNonconserved(false);
    seqGrp.setDescription(null);
    jsonFile.seqGroups.add(seqGrp);

    // create and add annotation
    Annotation[] annot = new Annotation[35];
    annot[0] = new Annotation("", "", '\u0000', 0);
    annot[1] = new Annotation("", "", '\u0000', 0);
    annot[2] = new Annotation("α", "", 'H', 0);
    annot[3] = new Annotation("α", "", 'H', 0);
    annot[4] = new Annotation("α", "", 'H', 0);
    annot[5] = new Annotation("α", "", 'H', 0);
    annot[6] = new Annotation("", "", '\u0000', 0);
    annot[7] = new Annotation("", "", '\u0000', 0);
    annot[8] = new Annotation("", "", '\u0000', 0);
    annot[9] = new Annotation("", "", '\u0000', 0);
    annot[10] = new Annotation("β", "", 'E', 0);
    annot[11] = new Annotation("β", "", 'E', 0);
    annot[12] = new Annotation("", "", '\u0000', 0);
    annot[13] = new Annotation("", "", '\u0000', 0);
    annot[14] = new Annotation("", "", '\u0000', 0);
    annot[15] = new Annotation("", "", '\u0000', 0);
    annot[16] = new Annotation("α", "", 'H', 0);
    annot[17] = new Annotation("α", "", 'H', 0);
    annot[18] = new Annotation("α", "", 'H', 0);
    annot[19] = new Annotation("α", "", 'H', 0);
    annot[20] = new Annotation("α", "", 'H', 0);

    annot[21] = new Annotation("", "", '\u0000', 0);
    annot[22] = new Annotation("", "", '\u0000', 0);
    annot[23] = new Annotation("", "", '\u0000', 0);
    annot[24] = new Annotation("", "", '\u0000', 0);
    annot[25] = new Annotation("", "", '\u0000', 0);
    annot[26] = new Annotation("", "", '\u0000', 0);
    annot[27] = new Annotation("", "", '\u0000', 0);
    annot[28] = new Annotation("", "", '\u0000', 0);
    annot[29] = new Annotation("", "", '\u0000', 0);
    annot[30] = new Annotation("", "", '\u0000', 0);
    annot[31] = new Annotation("", "", '\u0000', 0);
    annot[32] = new Annotation("β", "", 'E', 0);
    annot[33] = new Annotation("β", "", 'E', 0);
    annot[34] = new Annotation("β", "", 'E', 0);

    AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
            "Secondary Structure", "New description", annot);
    jsonFile.annotations.add(alignAnnot);

    // Alignment al = new Alignment(seqs);
    TEST_SEQ_HEIGHT = jsonFile.seqs.size();
    TEST_GRP_HEIGHT = jsonFile.seqGroups.size();
    TEST_ANOT_HEIGHT = jsonFile.annotations.size();
  }

  @After
  public void tearDown() throws Exception
  {
  }

  @Test
  public void test()
  {
    String jsonOuput = jsonFile.print();
    // System.out.println(">>>>>>>>>>>>>> " + jsonOuput);
    JSONFile output = new JSONFile().parse(jsonOuput);

    int matchedCounter = 0;
    for (SequenceI in : jsonFile.getSeqs())
    {
      for (SequenceI out : output.getSeqs())
      {
        if (in.getName().equals(out.getName())
                && in.getSequenceAsString().equals(
                        out.getSequenceAsString())
                && in.getStart() == out.getStart()
                && in.getEnd() == out.getEnd() && featuresMatched(in, out))
        {
          // System.out.println(">>>> Seq Match Detected");
          ++matchedCounter;
        }
      }
    }
    Assert.assertTrue(matchedCounter == TEST_SEQ_HEIGHT);

    matchedCounter = 0;
    for (SequenceGroup in : jsonFile.getSeqGroups())
    {
      for (SequenceGroup out : output.getSeqGroups())
      {
        if (in.getName().equals(out.getName())
                && in.getColourText() == out.getColourText()
                && in.getDisplayBoxes() == out.getDisplayBoxes()
                && in.getIgnoreGapsConsensus() == out
                        .getIgnoreGapsConsensus() && in.cs.equals(out.cs)
                && in.getSequences().size() == out.getSequences().size())
        {
          // System.out.println(">>>> Grp Match Detected");
          ++matchedCounter;
        }
      }
    }
    Assert.assertTrue(matchedCounter == TEST_GRP_HEIGHT);

    matchedCounter = 0;
    for (AlignmentAnnotation in : jsonFile.annotations)
    {
      for (AlignmentAnnotation out : output.annotations)
      {
        try
        {
          // System.out.println("label >>>>> " + in.label + " | " + out.label);
          // System.out.println("label >>>>> " + in.description + " | "
          // + out.description);
          // System.out.println("label >>>>> " + in.annotations.length + " | "
          // + out.annotations.length);
          if (in.label.equals(out.label)
                  && in.description.equals(out.description)
                && in.annotations.length == out.annotations.length)
        {
          ++matchedCounter;
        }
        } catch (Exception e)
        {
          e.printStackTrace();
        }
      }
    }
    // System.out.println("matched >>>>> " + matchedCounter + " | "
    // + TEST_ANOT_HEIGHT);
    Assert.assertTrue(matchedCounter == TEST_ANOT_HEIGHT);

  }

  private boolean featuresMatched(SequenceI seq1, SequenceI seq2)
  {
    boolean matched = false;
    try
    {
      if (seq1 == null && seq2 == null)
      {
        return true;
      }

      SequenceFeature[] inFeature = seq1.getSequenceFeatures();
      SequenceFeature[] outFeature = seq2.getSequenceFeatures();

      if (inFeature == null && outFeature == null)
      {
        return true;
      }
      else if ((inFeature == null && outFeature != null)
              || (inFeature != null && outFeature == null))
      {
        return false;
      }

      int testSize = inFeature.length;
      int matchedCount = 0;
      // System.out.println(">>>>>>>>>>>>> 1");
      for (SequenceFeature in : inFeature)
      {
        for (SequenceFeature out : inFeature)
        {
          if (inFeature.length == outFeature.length
                  && in.getBegin() == out.getBegin()
                  && in.getEnd() == out.getEnd()
                  && in.getScore() == out.getScore()
                  && in.getFeatureGroup().equals(out.getFeatureGroup()))
          {

            ++matchedCount;
          }
        }
      }
      if (testSize == matchedCount)
      {
        matched = true;
      }
    } catch (Exception e)
    {
      e.printStackTrace();
    }
    // System.out.println(">>>>>>>>>>>>>> features matched : " + matched);
    return matched;
  }
}