package jalview.ws.datamodel.alphafold;

import java.awt.Color;
import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;

import org.json.simple.JSONObject;

import jalview.analysis.AverageDistanceEngine;
import jalview.bin.Console;
import jalview.datamodel.Annotation;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactListImpl;
import jalview.datamodel.ContactListProviderI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileFormatException;
import jalview.io.FileParse;
import jalview.util.MapList;
import jalview.util.MapUtils;
import jalview.ws.dbsources.EBIAlfaFold;

public class PAEContactMatrix extends MappableContactMatrix<PAEContactMatrix> implements ContactMatrixI
{
  int maxrow = 0, maxcol = 0;

  float[][] elements;

  float maxscore;


  @SuppressWarnings("unchecked")
  public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj) throws FileFormatException
  {
    setRefSeq(_refSeq);
    // convert the lists to primitive arrays and store

    if (!MapUtils.containsAKey(pae_obj, "predicted_aligned_error", "pae"))
    {
      parse_version_1_pAE(pae_obj);
      return;
    }
    else
    {
      parse_version_2_pAE(pae_obj);
    }
  }

  /**
   * construct a sequence associated PAE matrix directly from a float array
   * 
   * @param _refSeq
   * @param matrix
   */
  public PAEContactMatrix(SequenceI _refSeq, float[][] matrix)
  {
    setRefSeq(_refSeq);
    maxcol = 0;
    for (float[] row : matrix)
    {
      if (row.length > maxcol)
      {
        maxcol = row.length;
      }
      maxscore = row[0];
      for (float f : row)
      {
        if (maxscore < f)
        {
          maxscore = f;
        }
      }
    }
    maxrow = matrix.length;
    elements = matrix;

  }

  /**
   * new matrix with specific mapping to a reference sequence
   * @param newRefSeq
   * @param newFromMapList
   * @param elements2
   */
  public PAEContactMatrix(SequenceI newRefSeq,
          MapList newFromMapList, float[][] elements2)
  {
    this(newRefSeq,elements2);
    toSeq = newFromMapList;
  }

  /**
   * parse a sane JSON representation of the pAE
   * 
   * @param pae_obj
   */
  @SuppressWarnings("unchecked")
  private void parse_version_2_pAE(Map<String, Object> pae_obj)
  {
    maxscore = -1;
    // look for a maxscore element - if there is one...
    try
    {
      // this is never going to be reached by the integer rounding.. or is it ?
      maxscore = ((Double) MapUtils.getFirst(pae_obj,
              "max_predicted_aligned_error", "max_pae")).floatValue();
    } catch (Throwable t)
    {
      // ignore if a key is not found.
    }
    List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
            .getFirst(pae_obj, "predicted_aligned_error", "pae"));
    elements = new float[scoreRows.size()][scoreRows.size()];
    int row = 0, col = 0;
    for (List<Long> scoreRow : scoreRows)
    {
      Iterator<Long> scores = scoreRow.iterator();
      while (scores.hasNext())
      {
        Object d = scores.next();

        if (d instanceof Double)
        {
          elements[row][col++] = ((Double) d).longValue();
        }
        else
        {
          elements[row][col++] = (float) ((Long) d).longValue();
        }
        
        if (maxscore < elements[row][col - 1])
        {
          maxscore = elements[row][col - 1];
        }
      }
      row++;
      col = 0;
    }
    maxcol = length;
    maxrow = length;
  }

  /**
   * v1 format got ditched 28th July 2022 see
   * https://alphafold.ebi.ac.uk/faq#:~:text=We%20updated%20the%20PAE%20JSON%20file%20format%20on%2028th%20July%202022
   * 
   * @param pae_obj
   */
  @SuppressWarnings("unchecked")
  private void parse_version_1_pAE(Map<String, Object> pae_obj)
  {
    // assume indices are with respect to range defined by _refSeq on the
    // dataset refSeq
    Iterator<Long> rows = ((List<Long>) pae_obj.get("residue1")).iterator();
    Iterator<Long> cols = ((List<Long>) pae_obj.get("residue2")).iterator();
    // two pass - to allocate the elements array
    while (rows.hasNext())
    {
      int row = rows.next().intValue();
      int col = cols.next().intValue();
      if (maxrow < row)
      {
        maxrow = row;
      }
      if (maxcol < col)
      {
        maxcol = col;
      }

    }
    rows = ((List<Long>) pae_obj.get("residue1")).iterator();
    cols = ((List<Long>) pae_obj.get("residue2")).iterator();
    Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
            .iterator();
    elements = new float[maxrow][maxcol];
    while (scores.hasNext())
    {
      float escore = scores.next().floatValue();
      int row = rows.next().intValue();
      int col = cols.next().intValue();
      if (maxrow < row)
      {
        maxrow = row;
      }
      if (maxcol < col)
      {
        maxcol = col;
      }
      elements[row - 1][col - 1] = escore;
    }

    maxscore = ((Double) MapUtils.getFirst(pae_obj,
            "max_predicted_aligned_error", "max_pae")).floatValue();
  }

  @Override
  public ContactListI getContactList(final int column)
  {
//    final int _column;
//    if (toSeq != null)
//    {
//      int[] word = toSeq.locateInTo(column, column);
//      if (word == null)
//      {
//        return null;
//      }
//      _column = word[0];
//    }
//    else
//    {
//      _column = column;
//    }
    if (column < 0 || column >= elements.length)
    {
      return null;
    }

    return new ContactListImpl(new ContactListProviderI()
    {
      @Override
      public int getPosition()
      {
        return column;
      }

      @Override
      public int getContactHeight()
      {
        return maxcol - 1;
      }

      @Override
      public double getContactAt(int mcolumn)
      {
        if (mcolumn < 0 || mcolumn >= elements[column].length)
        {
          return -1;
        }
        return elements[column][mcolumn];
      }
    });
  }

  @Override
  protected double getElementAt(int _column, int i)
  {
    return elements[_column][i];
  }
  @Override
  public float getMin()
  {
    return 0;
  }

  @Override
  public float getMax()
  {
    return maxscore;
  }

  @Override
  public String getAnnotDescr()
  {
    return "Predicted Alignment Error"+((refSeq==null) ? "" : (" for " + refSeq.getName()));
  }

  @Override
  public String getAnnotLabel()
  {
    StringBuilder label = new StringBuilder("PAE Matrix");
    //if (this.getReferenceSeq() != null)
    //{
    //  label.append(":").append(this.getReferenceSeq().getDisplayId(false));
    //}
    return label.toString();
  }

  public static final String PAEMATRIX = "PAE_MATRIX";

  @Override
  public String getType()
  {
    return PAEMATRIX;
  }

  @Override
  public int getWidth()
  {
    return length;
  }

  @Override
  public int getHeight()
  {
    return length;
  }
  List<BitSet> groups=null;
  @Override
  public boolean hasGroups()
  {
    return groups!=null;
  }
  String newick=null;
  @Override
  public String getNewick()
  {
    return newick;
  }
  @Override
  public boolean hasTree()
  {
    return newick!=null && newick.length()>0;
  }
  boolean abs;
  double thresh;
  String treeType=null;
  public void makeGroups(float thresh,boolean abs)
  {
    AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null, this);
    double height = clusterer.findHeight(clusterer.getTopNode());
    newick = new jalview.io.NewickFile(clusterer.getTopNode(),false,true).print();
    treeType = "UPGMA";
    Console.trace("Newick string\n"+newick);

    List<BinaryNode> nodegroups;
    if (abs ? height > thresh : 0 < thresh && thresh < 1)
    {
      float cut = abs ? (float) (thresh / height) : thresh;
      Console.debug("Threshold "+cut+" for height="+height);

      nodegroups = clusterer.groupNodes(cut);
    }
    else
    {
      nodegroups = new ArrayList<BinaryNode>();
      nodegroups.add(clusterer.getTopNode());
    }
    this.abs=abs;
    this.thresh=thresh;
    groups = new ArrayList<>();
    for (BinaryNode root:nodegroups)
    {
      BitSet gpset=new BitSet();
      for (BinaryNode leaf:clusterer.findLeaves(root))
      {
        gpset.set((Integer)leaf.element());
      }
      groups.add(gpset);
    }
  }
  @Override
  public void updateGroups(List<BitSet> colGroups)
  {
    if (colGroups!=null)
    {
      groups=colGroups;
    }    
  }
  @Override
  public BitSet getGroupsFor(int column)
  {
    if (groups != null)
    {
      for (BitSet gp : groups)
      {
        if (gp.get(column))
        {
          return gp;
        }
      }
    }
    return ContactMatrixI.super.getGroupsFor(column);
  }

  HashMap<BitSet,Color> colorMap = new HashMap<>();
  @Override 
  public Color getColourForGroup(BitSet bs)
  {
    if (bs==null) {
      return Color.white;
    }
    Color groupCol=colorMap.get(bs);
    if (groupCol==null)
    {
      return Color.white;
    }
    return groupCol;
  }
  @Override 
  public void setColorForGroup(BitSet bs,Color color)
  {
    colorMap.put(bs,color);
  }
  public void restoreGroups(List<BitSet> newgroups, String treeMethod,
          String tree, double thresh2)
  {
    treeType=treeMethod;
    groups = newgroups;
    thresh=thresh2;
    newick =tree;
    
  }
  @Override
  public boolean hasCutHeight() {
    return groups!=null && thresh!=0;
  }
  @Override
  public double getCutHeight()
  {
    return thresh;
  }
  @Override
  public String getTreeMethod()
  {
    return treeType;
  }

  public static void validateContactMatrixFile(String fileName) throws FileFormatException,IOException
  {
    FileInputStream infile=null;
    try {
      infile = new FileInputStream(new File(fileName));
    } catch (Throwable t)
    {
      new IOException("Couldn't open "+fileName,t);      
    }
    
    
    JSONObject paeDict=null;
    try {
      paeDict = EBIAlfaFold.parseJSONtoPAEContactMatrix(infile);
    } catch (Throwable t)
    {
      new FileFormatException("Couldn't parse "+fileName+" as a JSON dict or array containing a dict");
    }
    
    PAEContactMatrix matrix = new PAEContactMatrix(new SequenceDummy("Predicted"), (Map<String,Object>)paeDict);
    if (matrix.getWidth()<=0)
    {
      throw new FileFormatException("No data in PAE matrix read from '"+fileName+"'");
    }
  }

  @Override
  protected PAEContactMatrix newMappableContactMatrix(
          SequenceI newRefSeq, MapList newFromMapList)
  {
      return new PAEContactMatrix(newRefSeq, newFromMapList,
              elements);
  } 
}