/*
 * 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.io;

import static org.testng.AssertJUnit.assertNotNull;

import jalview.api.AlignExportSettingI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.schemes.ColourSchemeI;

import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;

import org.testng.Assert;
import org.testng.AssertJUnit;
import org.testng.annotations.AfterTest;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;

public class JSONFileTest
{

  private int TEST_SEQ_HEIGHT = 0;

  private int TEST_GRP_HEIGHT = 0;

  private int TEST_ANOT_HEIGHT = 0;

  private int TEST_CS_HEIGHT = 0;

  private String TEST_JSON_FILE = "examples/example.json";

  private Alignment alignment;

  private HashMap<String, SequenceI> expectedSeqs = new HashMap<String, SequenceI>();

  private HashMap<String, AlignmentAnnotation> expectedAnnots = new HashMap<String, AlignmentAnnotation>();

  private HashMap<String, SequenceGroup> expectedGrps = new HashMap<String, SequenceGroup>();

  private ColumnSelection expectedColSel = new ColumnSelection();

  private SequenceI[] expectedHiddenSeqs = new SequenceI[1];

  private AlignmentI testAlignment;

  private int passedCount;

  private JSONFile testJsonFile;

  private JSONFile jf;

  @BeforeTest(alwaysRun = true)
  public void setup() throws Exception
  {
    // 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);

    SequenceI hiddenSeq = new Sequence("FER_TOCH",
            "FILGTMISKSFLFRKPAVTSL-KAISNVGE--ALF", 3, 34);
    expectedHiddenSeqs[0] = hiddenSeq;

    // create and add sequence features
    SequenceFeature seqFeature2 = new SequenceFeature("feature_x",
            "desciption", "status", 6, 15, "Jalview");
    SequenceFeature seqFeature3 = new SequenceFeature("feature_x",
            "desciption", "status", 9, 18, "Jalview");
    SequenceFeature seqFeature4 = new SequenceFeature("feature_x",
            "desciption", "status", 9, 18, "Jalview");
    seqs[2].addSequenceFeature(seqFeature2);
    seqs[3].addSequenceFeature(seqFeature3);
    seqs[4].addSequenceFeature(seqFeature4);

    for (Sequence seq : seqs)
    {
      seq.setDatasetSequence(seq);
      expectedSeqs.put(seq.getName(), seq);
    }

    // create and add sequence groups
    ArrayList<SequenceI> grpSeqs = new ArrayList<SequenceI>();
    grpSeqs.add(seqs[1]);
    grpSeqs.add(seqs[2]);
    grpSeqs.add(seqs[3]);
    grpSeqs.add(seqs[4]);
    SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1883305585",
            null, true, true, false, 21, 29);
    ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
            "zappo", seqGrp);
    seqGrp.cs = scheme;
    seqGrp.setShowNonconserved(false);
    seqGrp.setDescription(null);

    expectedGrps.put(seqGrp.getName(), 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("", "", '\u0000', 0);
    annot[6] = new Annotation("", "", '\u0000', 0);
    annot[7] = new Annotation("", "", '\u0000', 0);
    annot[8] = new Annotation("β", "", 'E', 0);
    annot[9] = new Annotation("β", "", 'E', 0);
    annot[10] = new Annotation("β", "", 'E', 0);
    annot[11] = new Annotation("β", "", 'E', 0);
    annot[12] = new Annotation("β", "", 'E', 0);
    annot[13] = new Annotation("β", "", 'E', 0);
    annot[14] = new Annotation("β", "", 'E', 0);
    annot[15] = new Annotation("β", "", 'E', 0);
    annot[16] = new Annotation("", "", '\u0000', 0);
    annot[17] = new Annotation("", "", '\u0000', 0);
    annot[18] = new Annotation("", "", '\u0000', 0);
    annot[19] = new Annotation("", "", '\u0000', 0);
    annot[20] = new Annotation("", "", '\u0000', 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("α", "", 'H', 0);
    annot[27] = new Annotation("α", "", 'H', 0);
    annot[28] = new Annotation("α", "", 'H', 0);
    annot[29] = new Annotation("α", "", 'H', 0);
    annot[30] = new Annotation("α", "", 'H', 0);
    annot[31] = new Annotation("", "", '\u0000', 0);
    annot[32] = new Annotation("", "", '\u0000', 0);
    annot[33] = new Annotation("", "", '\u0000', 0);
    annot[34] = new Annotation("", "", '\u0000', 0);

    AlignmentAnnotation alignAnnot = new AlignmentAnnotation(
            "Secondary Structure", "New description", annot);
    expectedAnnots.put(alignAnnot.label, alignAnnot);

    expectedColSel.hideColumns(32, 33);
    expectedColSel.hideColumns(34, 34);

    TEST_SEQ_HEIGHT = expectedSeqs.size();
    TEST_GRP_HEIGHT = expectedGrps.size();
    TEST_ANOT_HEIGHT = expectedAnnots.size();
    TEST_CS_HEIGHT = expectedColSel.getHiddenColumns().size();

    AlignExportSettingI exportSettings = new AlignExportSettingI()
    {
      @Override
      public boolean isExportHiddenSequences()
      {
        return true;
      }

      @Override
      public boolean isExportHiddenColumns()
      {
        return true;
      }

      @Override
      public boolean isExportGroups()
      {
        return true;
      }

      @Override
      public boolean isExportFeatures()
      {
        return true;
      }

      @Override
      public boolean isExportAnnotations()
      {
        return true;
      }

      @Override
      public boolean isCancelled()
      {
        return false;
      }
    };

    AppletFormatAdapter formatAdapter = new AppletFormatAdapter();
    try
    {
      alignment = (Alignment) formatAdapter.readFile(TEST_JSON_FILE,
              AppletFormatAdapter.FILE, JSONFile.FILE_DESC);
      jf = (JSONFile) formatAdapter.getAlignFile();

      AlignFrame af = new AlignFrame(alignment, jf.getHiddenSequences(),
              jf.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
              AlignFrame.DEFAULT_HEIGHT);
      af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
      String colourSchemeName = jf.getGlobalColourScheme();
      ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
              colourSchemeName, alignment);
      af.changeColour(cs);
      af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());

      formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
      String jsonOutput = formatAdapter.formatSequences(JSONFile.FILE_DESC,
              af.alignPanel.getAlignment(), false);

      formatAdapter = new AppletFormatAdapter();
      testAlignment = formatAdapter.readFile(jsonOutput,
              AppletFormatAdapter.PASTE, JSONFile.FILE_DESC);
      testJsonFile = (JSONFile) formatAdapter.getAlignFile();
      // System.out.println(jsonOutput);
    } catch (IOException e)
    {
      e.printStackTrace();
    }

  }

  @BeforeMethod(alwaysRun = true)
  public void methodSetup()
  {
    passedCount = 0;
  }

  @AfterTest
  public void tearDown() throws Exception
  {
    testJsonFile = null;
    alignment = null;
    expectedSeqs = null;
    expectedAnnots = null;
    expectedGrps = null;
    testAlignment = null;
    jf = null;
  }

  @Test(groups = { "Functional" })
  public void roundTripTest()
  {
    assertNotNull("JSON roundtrip test failed!", testJsonFile);
  }

  @Test(groups = { "Functional" })
  public void testSeqParsed()
  {
    assertNotNull("Couldn't read supplied alignment data.", testAlignment);
    Assert.assertNotNull(testAlignment.getSequences());
    for (SequenceI seq : testAlignment.getSequences())
    {
      SequenceI expectedSeq = expectedSeqs.get(seq.getName());
      AssertJUnit.assertTrue(
              "Failed Sequence Test  for >>> " + seq.getName(),
              isSeqMatched(expectedSeq, seq));
      passedCount++;
    }
    AssertJUnit.assertEquals("Some Sequences did not pass the test",
            TEST_SEQ_HEIGHT, passedCount);
  }

  @Test(groups = { "Functional" })
  public void hiddenColsTest()
  {
    ColumnSelection cs = testJsonFile.getColumnSelection();
    Assert.assertNotNull(cs);
    Assert.assertNotNull(cs.getHiddenColumns());
    List<int[]> hiddenCols = cs.getHiddenColumns();
    Assert.assertEquals(hiddenCols.size(), TEST_CS_HEIGHT);
    Assert.assertEquals(hiddenCols, expectedColSel.getHiddenColumns(),
            "Mismatched hidden columns!");
  }

  @Test(groups = { "Functional" })
  public void hiddenSeqsTest()
  {
    Assert.assertNotNull(testJsonFile.getHiddenSequences(),
            "Hidden sequence Expected but found Null");
    Assert.assertEquals(jf.getHiddenSequences().length, 1, "Hidden sequece");
  }

  @Test(groups = { "Functional" })
  public void colorSchemeTest()
  {
    Assert.assertNotNull(testJsonFile.getGlobalColourScheme(),
            "Colourscheme is null, parsing failed!");
    Assert.assertEquals(testJsonFile.getGlobalColourScheme(), "Zappo",
            "Zappo colour scheme expected!");
  }

  @Test(groups = { "Functional" })
  public void isShowSeqFeaturesSet()
  {
    Assert.assertTrue(testJsonFile.isShowSeqFeatures(),
            "Sequence feature isDisplayed setting expected to be true");
  }

  @Test(groups = { "Functional" })
  public void testGrpParsed()
  {
    Assert.assertNotNull(testAlignment.getGroups());
    for (SequenceGroup seqGrp : testAlignment.getGroups())
    {
      SequenceGroup expectedGrp = expectedGrps.get(seqGrp.getName());
      AssertJUnit.assertTrue(
              "Failed SequenceGroup Test for >>> " + seqGrp.getName(),
              isGroupMatched(expectedGrp, seqGrp));
      passedCount++;
    }
    AssertJUnit.assertEquals("Some SequenceGroups did not pass the test",
            TEST_GRP_HEIGHT, passedCount);
  }

  @Test(groups = { "Functional" })
  public void testAnnotationParsed()
  {
    Assert.assertNotNull(testAlignment.getAlignmentAnnotation());
    for (AlignmentAnnotation annot : testAlignment.getAlignmentAnnotation())
    {
      AlignmentAnnotation expectedAnnot = expectedAnnots.get(annot.label);
      AssertJUnit.assertTrue("Failed AlignmentAnnotation Test for >>> "
              + annot.label, isAnnotationMatched(expectedAnnot, annot));
      passedCount++;
    }
    AssertJUnit.assertEquals("Some Sequences did not pass the test",
            TEST_ANOT_HEIGHT, passedCount);
  }

  public boolean isAnnotationMatched(AlignmentAnnotation eAnnot,
          AlignmentAnnotation annot)
  {
    if (!eAnnot.label.equals(annot.label)
            || !eAnnot.description.equals(annot.description)
            || eAnnot.annotations.length != annot.annotations.length)
    {
      return false;
    }

    for (int x = 0; x < annot.annotations.length; x++)
    {
      Annotation y = annot.annotations[x];
      Annotation z = annot.annotations[x];

      if (!y.displayCharacter.equals(z.displayCharacter)
              || y.value != z.value
              || y.secondaryStructure != z.secondaryStructure)
      {
        return false;
      }
    }
    return true;
  }

  public boolean isSeqMatched(SequenceI expectedSeq, SequenceI actualSeq)
  {
    System.out.println("Testing >>> " + actualSeq.getName());

    if (expectedSeq.getName().equals(actualSeq.getName())
            && expectedSeq.getSequenceAsString().equals(
                    actualSeq.getSequenceAsString())
            && expectedSeq.getStart() == actualSeq.getStart()
            && expectedSeq.getEnd() == actualSeq.getEnd()
            && featuresMatched(expectedSeq, actualSeq))
    {
      return true;
    }
    return false;
  }

  public boolean isGroupMatched(SequenceGroup expectedGrp,
          SequenceGroup actualGrp)
  {

    System.out.println("Testing >>> " + actualGrp.getName());
    System.out.println(expectedGrp.getName() + " | " + actualGrp.getName());
    System.out.println(expectedGrp.getColourText() + " | "
            + actualGrp.getColourText());
    System.out.println(expectedGrp.getDisplayBoxes() + " | "
            + actualGrp.getDisplayBoxes());
    System.out.println(expectedGrp.getIgnoreGapsConsensus() + " | "
            + actualGrp.getIgnoreGapsConsensus());
    System.out.println(expectedGrp.getSequences().size() + " | "
            + actualGrp.getSequences().size());
    System.out.println(expectedGrp.getStartRes() + " | "
            + actualGrp.getStartRes());
    System.out.println(expectedGrp.getEndRes() + " | "
            + actualGrp.getEndRes());
    System.out.println(expectedGrp.cs + " | " + actualGrp.cs);

    if (expectedGrp.getName().equals(actualGrp.getName())
            && expectedGrp.getColourText() == actualGrp.getColourText()
            && expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
            && expectedGrp.getIgnoreGapsConsensus() == actualGrp
                    .getIgnoreGapsConsensus()
            && (expectedGrp.cs.getClass().equals(actualGrp.cs.getClass()))
            && expectedGrp.getSequences().size() == actualGrp
                    .getSequences().size()
            && expectedGrp.getStartRes() == actualGrp.getStartRes()
            && expectedGrp.getEndRes() == actualGrp.getEndRes())
    {
      return true;
    }
    return false;
  }

  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;
      for (SequenceFeature in : inFeature)
      {
        for (SequenceFeature out : outFeature)
        {
          System.out.println(out.getType() + " | " + in.getType());
          System.out.println(out.getBegin() + " | " + in.getBegin());
          System.out.println(out.getEnd() + " | " + in.getEnd());

          if (inFeature.length == outFeature.length
                  && in.getBegin() == out.getBegin()
                  && in.getEnd() == out.getEnd()
                  && in.getScore() == out.getScore()
                  && in.getFeatureGroup().equals(out.getFeatureGroup())
                  && in.getType().equals(out.getType()))
          {

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