/*
 * Jalview - A Sequence Alignment Editor and Viewer (2.11.5.0)
 * Copyright (C) 2025 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.structures.models;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertFalse;
import static org.testng.Assert.assertNotNull;
import static org.testng.Assert.assertTrue;

import java.awt.Color;
import java.io.IOException;
import java.util.Arrays;
import java.util.BitSet;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;

import jalview.api.AlignmentViewPanel;
import jalview.api.SequenceRenderer;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.ChimeraCommands;
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.schemes.JalviewColourScheme;
import jalview.structure.AtomSpec;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI.AtomSpecType;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import junit.extensions.PA;

/**
 * Unit tests for non-abstract methods of abstract base class
 * 
 * @author gmcarstairs
 *
 */
public class AAStructureBindingModelTest
{

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

  /*
   * Scenario: Jalview has 4 sequences, corresponding to 1YCS (chains A and B), 3A6S|B, 1OOT|A
   */
  private static final String PDB_1 = "HEADER    COMPLEX (ANTI-ONCOGENE/ANKYRIN REPEATS) 30-SEP-96   1YCS              \n"
          + "ATOM      2  CA  VAL A  97      24.134   4.926  45.821  1.00 47.43           C  \n"
          + "ATOM      9  CA  PRO A  98      25.135   8.584  46.217  1.00 41.60           C  \n"
          + "ATOM     16  CA  SER A  99      28.243   9.596  44.271  1.00 39.63           C  \n"
          + "ATOM     22  CA  GLN A 100      31.488  10.133  46.156  1.00 35.60           C  \n"
          // artificial jump in residue numbering to prove it is correctly
          // mapped:
          + "ATOM     31  CA  LYS A 102      33.323  11.587  43.115  1.00 41.69           C  \n"
          + "ATOM   1857  CA  GLU B 374       9.193 -16.005  95.870  1.00 54.22           C  \n"
          + "ATOM   1866  CA  ILE B 375       7.101 -14.921  92.847  1.00 46.82           C  \n"
          + "ATOM   1874  CA  VAL B 376      10.251 -13.625  91.155  1.00 47.80           C  \n"
          + "ATOM   1881  CA  LYS B 377      11.767 -17.068  91.763  1.00 50.21           C  \n"
          + "ATOM   1890  CA  PHE B 378       8.665 -18.948  90.632  1.00 44.85           C  \n";

  private static final String PDB_2 = "HEADER    HYDROLASE                               09-SEP-09   3A6S              \n"
          + "ATOM      2  CA  MET B   1      15.366 -11.648  24.854  1.00 32.05           C  \n"
          + "ATOM     10  CA  LYS B   2      16.846  -9.215  22.340  1.00 25.68           C  \n"
          + "ATOM     19  CA  LYS B   3      15.412  -6.335  20.343  1.00 19.42           C  \n"
          + "ATOM     28  CA  LEU B   4      15.629  -5.719  16.616  1.00 15.49           C  \n"
          + "ATOM     36  CA  GLN B   5      14.412  -2.295  15.567  1.00 12.19           C  \n";

  private static final String PDB_3 = "HEADER    STRUCTURAL GENOMICS                     04-MAR-03   1OOT              \n"
          + "ATOM      2  CA  SER A   7      29.427   3.330  -6.578  1.00 32.50           C  \n"
          + "ATOM      8  CA  PRO A   8      29.975   3.340  -2.797  1.00 17.62           C  \n"
          + "ATOM     16  CA ALYS A   9      26.958   3.024  -0.410  0.50  8.78           C  \n"
          + "ATOM     33  CA  ALA A  10      26.790   4.320   3.172  1.00 11.98           C  \n"
          + "ATOM     39  CA AVAL A  12      24.424   3.853   6.106  0.50 13.83           C  \n";

  /**
   * Multichain PDB with identical sequences imported - Binding should correctly
   * recover chain mappings for each derived sequence
   */
  private static final String PDB_4_MC = "HEADER    HYDROLASE                               09-SEP-09   3A6S              \n"
          + "ATOM      2  CA  MET A   1      15.366 -11.648  24.854  1.00 32.05           C  \n"
          + "ATOM     10  CA  LYS A   2      16.846  -9.215  22.340  1.00 25.68           C  \n"
          + "ATOM     19  CA  LYS A   3      15.412  -6.335  20.343  1.00 19.42           C  \n"
          + "ATOM     28  CA  LEU A   4      15.629  -5.719  16.616  1.00 15.49           C  \n"
          + "ATOM     36  CA  GLN A   5      14.412  -2.295  15.567  1.00 12.19           C  \n"
          + "ATOM   1030  CA  MET B   1      18.869  -7.572   3.432  1.00 31.52           C  \n"
          + "ATOM   1038  CA  LYS B   2      19.182 -10.025   6.313  1.00 26.41           C  \n"
          + "ATOM   1047  CA  LYS B   3      17.107 -12.963   7.534  1.00 19.71           C  \n"
          + "ATOM   1056  CA  LEU B   4      16.142 -13.579  11.164  1.00 14.81           C  \n"
          + "ATOM   1064  CA  GLN B   5      14.648 -17.005  11.785  1.00 13.38           C  \n";

  // TODO: JAL-2227 - import mmCIF PISA assembly & identify master/copy chains

  @Test(groups = { "Functional" })
  public void testImportPDBPreservesChainMappings() throws IOException
  {
    AlignmentI importedAl = new jalview.io.FormatAdapter().readFile(
            PDB_4_MC, DataSourceType.PASTE, FileFormats.getInstance()
                    .forName(jalview.io.FileFormat.PDB.toString()));
    // ideally, we would match on the actual data for the 'File' handle for
    // pasted files,
    // see JAL-623 - pasting is still not correctly handled...
    PDBEntry importedPDB = new PDBEntry("3A6S", "", Type.PDB, "Paste");
    AAStructureBindingModel binder = new AAStructureBindingModel(
            new StructureSelectionManager(), new PDBEntry[]
            { importedPDB },
            new SequenceI[][]
            { importedAl.getSequencesArray() }, null)
    {

      @Override
      public void updateColours(Object source)
      {
      }

      @Override
      public void releaseReferences(Object svl)
      {
      }

      @Override
      public String[] getStructureFiles()
      {
        return null;
      }

      @Override
      public void highlightAtoms(List<AtomSpec> atoms)
      {
      }

      @Override
      public SequenceRenderer getSequenceRenderer(
              AlignmentViewPanel alignment)
      {
        return null;
      }

      @Override
      protected List<String> executeCommand(StructureCommandI command,
              boolean getReply)
      {
        return null;
      }

      @Override
      protected String getModelIdForFile(String chainId)
      {
        return "";
      }

      @Override
      protected ViewerType getViewerType()
      {
        return null;
      }
    };
    String[][] chains = binder.getChains();
    assertFalse(chains == null || chains[0] == null,
            "No chains discovered by binding");
    assertEquals(chains[0].length, 2);
    assertEquals(chains[0][0], "A");
    assertEquals(chains[0][1], "B");
  }

  AAStructureBindingModel testee;

  AlignmentI al = null;

  /**
   * Set up test conditions with three aligned sequences,
   */
  @BeforeMethod(alwaysRun = true)
  public void setUp()
  {
    SequenceI seq1a = new Sequence("1YCS|A", "-VPSQK");
    SequenceI seq1b = new Sequence("1YCS|B", "EIVKF-");
    SequenceI seq2 = new Sequence("3A6S", "MK-KLQ");
    SequenceI seq3 = new Sequence("1OOT", "SPK-AV");
    al = new Alignment(new SequenceI[] { seq1a, seq1b, seq2, seq3 });
    al.setDataset(null);

    /*
     * give pdb files the name generated by Jalview for PASTE source
     */
    PDBEntry[] pdbFiles = new PDBEntry[3];
    pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
    pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
    pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
    SequenceI[][] seqs = new SequenceI[3][];
    seqs[0] = new SequenceI[] { seq1a, seq1b };
    seqs[1] = new SequenceI[] { seq2 };
    seqs[2] = new SequenceI[] { seq3 };
    StructureSelectionManager ssm = new StructureSelectionManager();

    ssm.setMapping(new SequenceI[] { seq1a, seq1b }, null, PDB_1,
            DataSourceType.PASTE, null);
    ssm.setMapping(new SequenceI[] { seq2 }, null, PDB_2,
            DataSourceType.PASTE, null);
    ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
            DataSourceType.PASTE, null);

    testee = newBindingModel(pdbFiles, seqs, ssm, null);
  }

  /**
   * A helper method to construct the test target object
   * 
   * @param pdbFiles
   * @param seqs
   * @param ssm
   * @param alignPanel
   */
  protected AAStructureBindingModel newBindingModel(PDBEntry[] pdbFiles,
          SequenceI[][] seqs, StructureSelectionManager ssm,
          AlignmentViewPanel avp)
  {
    AAStructureBindingModel model = new AAStructureBindingModel(ssm,
            pdbFiles, seqs, null)
    {
      @Override
      public String[] getStructureFiles()
      {
        String[] files = new String[getPdbCount()];
        for (int i = 0; i < this.getPdbCount(); i++)
        {
          files[i] = getPdbEntry(i).getFile();
        }
        return files;
      }

      @Override
      public void updateColours(Object source)
      {
      }

      @Override
      public void releaseReferences(Object svl)
      {
      }

      @Override
      public void highlightAtoms(List<AtomSpec> atoms)
      {
      }

      @Override
      public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
      {
        return avp == null ? null
                : new jalview.gui.SequenceRenderer(avp.getAlignViewport());
      }

      @Override
      protected List<String> executeCommand(StructureCommandI command,
              boolean getReply)
      {
        return null;
      }

      /*
       * for this test, let structure model ids be 0, 1, ...
       * corresponding to first, second etc pdbfile
       */
      @Override
      protected String getModelIdForFile(String pdbfile)
      {
        for (int i = 0; i < this.getPdbCount(); i++)
        {
          if (pdbfile.equals(this.getPdbEntry(i).getFile()))
          {
            return String.valueOf(i);
          }
        }
        return "";
      }

      @Override
      protected ViewerType getViewerType()
      {
        return null;
      }
    };
    PA.setValue(model, "commandGenerator", new ChimeraCommands());
    return model;
  }

  /**
   * Verify that the method determines that columns 2, 5 and 6 of the alignment
   * are alignable in structure
   */
  @Test(groups = { "Functional" })
  public void testFindSuperposableResidues()
  {
    /*
     * create a data bean to hold data per structure file
     */
    AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[testee
            .getStructureFiles().length];
    for (int i = 0; i < structs.length; i++)
    {
      structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
              "0");
    }
    /*
     * initialise BitSet of 'superposable columns' to true (would be false for
     * hidden columns)
     */
    BitSet matched = new BitSet();
    for (int i = 0; i < al.getWidth(); i++)
    {
      matched.set(i);
    }

    int refStructure = testee.findSuperposableResidues(al, matched,
            structs);

    assertEquals(refStructure, 0);

    /*
     * only ungapped, structure-mapped columns are superposable
     */
    assertFalse(matched.get(0)); // gap in first sequence
    assertTrue(matched.get(1));
    assertFalse(matched.get(2)); // gap in third sequence
    assertFalse(matched.get(3)); // gap in fourth sequence
    assertTrue(matched.get(4));
    assertTrue(matched.get(5)); // gap in second sequence

    assertEquals(structs[0].pdbId, "1YCS");
    assertEquals(structs[1].pdbId, "3A6S");
    assertEquals(structs[2].pdbId, "1OOT");
    assertEquals(structs[0].chain, "A"); // ? struct has chains A _and_ B
    assertEquals(structs[1].chain, "B");
    assertEquals(structs[2].chain, "A");
    // the 0's for unsuperposable positions propagate down the columns:
    assertEquals(Arrays.toString(structs[0].pdbResNo),
            "[0, 97, 98, 99, 100, 102]");
    assertEquals(Arrays.toString(structs[1].pdbResNo),
            "[0, 2, 0, 3, 4, 5]");
    assertEquals(Arrays.toString(structs[2].pdbResNo),
            "[0, 8, 0, 0, 10, 12]");
  }

  @Test(groups = { "Functional" })
  public void testFindSuperposableResidues_hiddenColumn()
  {
    AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[al
            .getHeight()];
    for (int i = 0; i < structs.length; i++)
    {
      structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
              "0");
    }
    /*
     * initialise BitSet of 'superposable columns' to true (would be false for
     * hidden columns)
     */
    BitSet matched = new BitSet();
    for (int i = 0; i < al.getWidth(); i++)
    {
      matched.set(i);
    }

    // treat column 5 of the alignment as hidden
    matched.clear(4);

    int refStructure = testee.findSuperposableResidues(al, matched,
            structs);

    assertEquals(refStructure, 0);

    // only ungapped, structure-mapped columns are not superposable
    assertFalse(matched.get(0));
    assertTrue(matched.get(1));
    assertFalse(matched.get(2));
    assertFalse(matched.get(3));
    assertFalse(matched.get(4)); // superposable, but hidden, column
    assertTrue(matched.get(5));
  }

  @Test(groups = { "Functional" })
  public void testBuildColoursMap()
  {
    /*
     * load these sequences, coloured by Strand propensity,
     * with columns 2-4 hidden
     */
    String fasta = ">seq1\nMHRSQSSSGG\n>seq2\nMVRSNGGSSS";
    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
            DataSourceType.PASTE);
    AlignmentI al = af.getViewport().getAlignment();
    af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
    ColumnSelection cs = new ColumnSelection();
    cs.addElement(2);
    cs.addElement(3);
    cs.addElement(4);
    af.getViewport().setColumnSelection(cs);
    af.hideSelColumns_actionPerformed(null);
    SequenceI seq1 = al.getSequenceAt(0);
    SequenceI seq2 = al.getSequenceAt(1);
    SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
    PDBEntry[] pdbFiles = new PDBEntry[2];
    pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "seq1.pdb");
    pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "seq2.pdb");
    StructureSelectionManager ssm = new StructureSelectionManager();

    /*
     * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
     */
    HashMap<Integer, int[]> map = new HashMap<>();
    for (int pos = 1; pos <= seq1.getLength(); pos++)
    {
      map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
    }
    StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
            "A", map, null);
    ssm.addStructureMapping(sm1);
    StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
            "B", map, null);
    ssm.addStructureMapping(sm2);

    AAStructureBindingModel binding = newBindingModel(pdbFiles, seqs, ssm,
            af.alignPanel);

    /*
     * method under test builds a map of structures residues by colour
     * verify the map holds what it should
     */
    Map<Object, AtomSpecModel> colours = binding.buildColoursMap(ssm, seqs,
            af.alignPanel);
    ChimeraCommands helper = new ChimeraCommands();

    /*
     * M colour is #82827d (see strand.html help page)
     * sequence residue 1 mapped to structure residue 21
     */
    Color mColor = new Color(0x82827d);
    AtomSpecModel atomSpec = colours.get(mColor);
    assertNotNull(atomSpec);
    assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
            "#0:21.A|#1:21.B");

    /*
     * H colour is #60609f, seq1.2 mapped to structure 0 residue 22
     */
    Color hColor = new Color(0x60609f);
    atomSpec = colours.get(hColor);
    assertNotNull(atomSpec);
    assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
            "#0:22.A");

    /*
     * V colour is #ffff00, seq2.2 mapped to structure 1 residue 22
     */
    Color vColor = new Color(0xffff00);
    atomSpec = colours.get(vColor);
    assertNotNull(atomSpec);
    assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
            "#1:22.B");

    /*
     * hidden columns are Gray (128, 128, 128)
     * sequence positions 3-5 mapped to structure residues 23-25
     */
    Color gray = new Color(128, 128, 128);
    atomSpec = colours.get(gray);
    assertNotNull(atomSpec);
    assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
            "#0:23-25.A|#1:23-25.B");

    /*
     * S and G are both coloured #4949b6, structure residues 26-30
     */
    Color sgColour = new Color(0x4949b6);
    atomSpec = colours.get(sgColour);
    assertNotNull(atomSpec);
    assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
            "#0:26-30.A|#1:26-30.B");
  }
}