/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
 * 
 * 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/>.
 */
package jalview.analysis;

import java.awt.Color;
import java.util.*;

import jalview.datamodel.*;

/**
 * Calculates conservation values for a given set of sequences
 * 
 * @author $author$
 * @version $Revision$
 */
public class Conservation
{
  SequenceI[] sequences;

  int start;

  int end;

  Vector seqNums; // vector of int vectors where first is sequence checksum

  int maxLength = 0; // used by quality calcs

  boolean seqNumsChanged = false; // updated after any change via calcSeqNum;

  Hashtable[] total;

  boolean canonicaliseAa = true; // if true then conservation calculation will

  // map all symbols to canonical aa numbering
  // rather than consider conservation of that
  // symbol

  /** Stores calculated quality values */
  public Vector quality;

  /** Stores maximum and minimum values of quality values */
  public Double[] qualityRange = new Double[2];

  String consString = "";

  Sequence consSequence;

  Hashtable propHash;

  int threshold;

  String name = "";

  int[][] cons2;

  /**
   * Creates a new Conservation object.
   * 
   * @param name
   *          Name of conservation
   * @param propHash
   *          hash of properties for each symbol
   * @param threshold
   *          to count the residues in residueHash(). commonly used value is 3
   * @param sequences
   *          sequences to be used in calculation
   * @param start
   *          start residue position
   * @param end
   *          end residue position
   */
  public Conservation(String name, Hashtable propHash, int threshold,
          List<SequenceI> sequences, int start, int end)
  {
    this.name = name;
    this.propHash = propHash;
    this.threshold = threshold;
    this.start = start;
    this.end = end;

    maxLength = end - start + 1; // default width includes bounds of
    // calculation

    int s, sSize = sequences.size();
    SequenceI[] sarray = new SequenceI[sSize];
    this.sequences = sarray;
    try
    {
      for (s = 0; s < sSize; s++)
      {
        sarray[s] = (SequenceI) sequences.get(s);
        if (sarray[s].getLength() > maxLength)
        {
          maxLength = sarray[s].getLength();
        }
      }
    } catch (ArrayIndexOutOfBoundsException ex)
    {
      // bail - another thread has modified the sequence array, so the current
      // calculation is probably invalid.
      this.sequences = new SequenceI[0];
      maxLength = 0;
    }
  }

  /**
   * Translate sequence i into a numerical representation and store it in the
   * i'th position of the seqNums array.
   * 
   * @param i
   */
  private void calcSeqNum(int i)
  {
    String sq = null; // for dumb jbuilder not-inited exception warning
    int[] sqnum = null;

    int sSize = sequences.length;

    if ((i > -1) && (i < sSize))
    {
      sq = sequences[i].getSequenceAsString();

      if (seqNums.size() <= i)
      {
        seqNums.addElement(new int[sq.length() + 1]);
      }

      if (sq.hashCode() != ((int[]) seqNums.elementAt(i))[0])
      {
        int j;
        int len;
        seqNumsChanged = true;
        len = sq.length();

        if (maxLength < len)
        {
          maxLength = len;
        }

        sqnum = new int[len + 1]; // better to always make a new array -
        // sequence can change its length
        sqnum[0] = sq.hashCode();

        for (j = 1; j <= len; j++)
        {
          sqnum[j] = jalview.schemes.ResidueProperties.aaIndex[sq
                  .charAt(j - 1)];
        }

        seqNums.setElementAt(sqnum, i);
      }
      else
      {
        System.out.println("SEQUENCE HAS BEEN DELETED!!!");
      }
    }
    else
    {
      // JBPNote INFO level debug
      System.err
              .println("ERROR: calcSeqNum called with out of range sequence index for Alignment\n");
    }
  }

  /**
   * Calculates the conservation values for given set of sequences
   */
  public void calculate()
  {
    Hashtable resultHash, ht;
    int thresh, j, jSize = sequences.length;
    int[] values; // Replaces residueHash
    String type, res = null;
    char c;
    Enumeration enumeration2;

    total = new Hashtable[maxLength];

    for (int i = start; i <= end; i++)
    {
      values = new int[255];

      for (j = 0; j < jSize; j++)
      {
        if (sequences[j].getLength() > i)
        {
          c = sequences[j].getCharAt(i);

          if (canonicaliseAa)
          { // lookup the base aa code symbol
            c = (char) jalview.schemes.ResidueProperties.aaIndex[sequences[j]
                    .getCharAt(i)];
            if (c > 20)
            {
              c = '-';
            }
            else
            {
              // recover canonical aa symbol
              c = jalview.schemes.ResidueProperties.aa[c].charAt(0);
            }
          }
          else
          {
            // original behaviour - operate on ascii symbols directly
            // No need to check if its a '-'
            if (c == '.' || c == ' ')
            {
              c = '-';
            }

            if (!canonicaliseAa && 'a' <= c && c <= 'z')
            {
              c -= (32); // 32 = 'a' - 'A'
            }
          }
          values[c]++;
        }
        else
        {
          values['-']++;
        }
      }

      // What is the count threshold to count the residues in residueHash()
      thresh = (threshold * (jSize)) / 100;

      // loop over all the found residues
      resultHash = new Hashtable();
      for (char v = '-'; v < 'Z'; v++)
      {

        if (values[v] > thresh)
        {
          res = String.valueOf(v);

          // Now loop over the properties
          enumeration2 = propHash.keys();

          while (enumeration2.hasMoreElements())
          {
            type = (String) enumeration2.nextElement();
            ht = (Hashtable) propHash.get(type);

            // Have we ticked this before?
            if (!resultHash.containsKey(type))
            {
              if (ht.containsKey(res))
              {
                resultHash.put(type, ht.get(res));
              }
              else
              {
                resultHash.put(type, ht.get("-"));
              }
            }
            else if (((Integer) resultHash.get(type)).equals((Integer) ht
                    .get(res)) == false)
            {
              resultHash.put(type, new Integer(-1));
            }
          }
        }
      }

      if (total.length > 0)
      {
        total[i - start] = resultHash;
      }
    }
  }

  /*****************************************************************************
   * count conservation for the j'th column of the alignment
   * 
   * @return { gap count, conserved residue count}
   */
  public int[] countConsNGaps(int j)
  {
    int count = 0;
    int cons = 0;
    int nres = 0;
    int[] r = new int[2];
    char f = '$';
    int i, iSize = sequences.length;
    char c;

    for (i = 0; i < iSize; i++)
    {
      if (j >= sequences[i].getLength())
      {
        count++;
        continue;
      }

      c = sequences[i].getCharAt(j); // gaps do not have upper/lower case

      if (jalview.util.Comparison.isGap((c)))
      {
        count++;
      }
      else
      {
        nres++;

        if (nres == 1)
        {
          f = c;
          cons++;
        }
        else if (f == c)
        {
          cons++;
        }
      }
    }

    r[0] = (nres == cons) ? 1 : 0;
    r[1] = count;

    return r;
  }

  /**
   * Calculates the conservation sequence
   * 
   * @param consflag
   *          if true, poitiveve conservation; false calculates negative
   *          conservation
   * @param percentageGaps
   *          commonly used value is 25
   */
  public void verdict(boolean consflag, float percentageGaps)
  {
    StringBuffer consString = new StringBuffer();
    String type;
    Integer result;
    int[] gapcons;
    int totGaps, count;
    float pgaps;
    Hashtable resultHash;
    Enumeration enumeration;

    // NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
    // EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
    // DOES NOT EXIST IN JALVIEW 2.1.2
    for (int i = 0; i < start; i++)
    {
      consString.append('-');
    }

    for (int i = start; i <= end; i++)
    {
      gapcons = countConsNGaps(i);
      totGaps = gapcons[1];
      pgaps = ((float) totGaps * 100) / (float) sequences.length;

      if (percentageGaps > pgaps)
      {
        resultHash = total[i - start];

        // Now find the verdict
        count = 0;
        enumeration = resultHash.keys();

        while (enumeration.hasMoreElements())
        {
          type = (String) enumeration.nextElement();
          result = (Integer) resultHash.get(type);

          // Do we want to count +ve conservation or +ve and -ve cons.?
          if (consflag)
          {
            if (result.intValue() == 1)
            {
              count++;
            }
          }
          else
          {
            if (result.intValue() != -1)
            {
              count++;
            }
          }
        }

        if (count < 10)
        {
          consString.append(count); // Conserved props!=Identity
        }
        else
        {
          consString.append((gapcons[0] == 1) ? "*" : "+");
        }
      }
      else
      {
        consString.append('-');
      }
    }

    consSequence = new Sequence(name, consString.toString(), start, end);
  }

  /**
   * 
   * 
   * @return Conservation sequence
   */
  public Sequence getConsSequence()
  {
    return consSequence;
  }

  // From Alignment.java in jalview118
  public void findQuality()
  {
    findQuality(0, maxLength - 1);
  }

  /**
   * DOCUMENT ME!
   */
  private void percentIdentity2()
  {
    seqNums = new Vector();
    // calcSeqNum(s);
    int i = 0, iSize = sequences.length;
    // Do we need to calculate this again?
    for (i = 0; i < iSize; i++)
    {
      calcSeqNum(i);
    }

    if ((cons2 == null) || seqNumsChanged)
    {
      cons2 = new int[maxLength][24];

      // Initialize the array
      for (int j = 0; j < 24; j++)
      {
        for (i = 0; i < maxLength; i++)
        {
          cons2[i][j] = 0;
        }
      }

      int[] sqnum;
      int j = 0;

      while (j < sequences.length)
      {
        sqnum = (int[]) seqNums.elementAt(j);

        for (i = 1; i < sqnum.length; i++)
        {
          cons2[i - 1][sqnum[i]]++;
        }

        for (i = sqnum.length - 1; i < maxLength; i++)
        {
          cons2[i][23]++; // gap count
        }

        j++;
      }

      // unnecessary ?

      /*
       * for (int i=start; i <= end; i++) { int max = -1000; int maxi = -1; int
       * maxj = -1;
       * 
       * for (int j=0;j<24;j++) { if (cons2[i][j] > max) { max = cons2[i][j];
       * maxi = i; maxj = j; } } }
       */
    }
  }

  /**
   * Calculates the quality of the set of sequences
   * 
   * @param start
   *          Start residue
   * @param end
   *          End residue
   */
  public void findQuality(int start, int end)
  {
    quality = new Vector();

    double max = -10000;
    int[][] BLOSUM62 = jalview.schemes.ResidueProperties.getBLOSUM62();

    // Loop over columns // JBPNote Profiling info
    // long ts = System.currentTimeMillis();
    // long te = System.currentTimeMillis();
    percentIdentity2();

    int size = seqNums.size();
    int[] lengths = new int[size];
    double tot, bigtot, sr, tmp;
    double[] x, xx;
    int l, j, i, ii, i2, k, seqNum;

    for (l = 0; l < size; l++)
    {
      lengths[l] = ((int[]) seqNums.elementAt(l)).length - 1;
    }

    for (j = start; j <= end; j++)
    {
      bigtot = 0;

      // First Xr = depends on column only
      x = new double[24];

      for (ii = 0; ii < 24; ii++)
      {
        x[ii] = 0;

        for (i2 = 0; i2 < 24; i2++)
        {
          x[ii] += (((double) cons2[j][i2] * BLOSUM62[ii][i2]) + 4);
        }

        x[ii] /= size;
      }

      // Now calculate D for each position and sum
      for (k = 0; k < size; k++)
      {
        tot = 0;
        xx = new double[24];
        seqNum = (j < lengths[k]) ? ((int[]) seqNums.elementAt(k))[j + 1]
                : 23; // Sequence, or gap at the end

        // This is a loop over r
        for (i = 0; i < 23; i++)
        {
          sr = 0;

          sr = (double) BLOSUM62[i][seqNum] + 4;

          // Calculate X with another loop over residues
          // System.out.println("Xi " + i + " " + x[i] + " " + sr);
          xx[i] = x[i] - sr;

          tot += (xx[i] * xx[i]);
        }

        bigtot += Math.sqrt(tot);
      }

      // This is the quality for one column
      if (max < bigtot)
      {
        max = bigtot;
      }

      // bigtot = bigtot * (size-cons2[j][23])/size;
      quality.addElement(new Double(bigtot));

      // Need to normalize by gaps
    }

    double newmax = -10000;

    for (j = start; j <= end; j++)
    {
      tmp = ((Double) quality.elementAt(j)).doubleValue();
      tmp = ((max - tmp) * (size - cons2[j][23])) / size;

      // System.out.println(tmp+ " " + j);
      quality.setElementAt(new Double(tmp), j);

      if (tmp > newmax)
      {
        newmax = tmp;
      }
    }

    // System.out.println("Quality " + s);
    qualityRange[0] = new Double(0);
    qualityRange[1] = new Double(newmax);
  }

  /**
   * complete the given consensus and quuality annotation rows. Note: currently
   * this method will enlarge the given annotation row if it is too small,
   * otherwise will leave its length unchanged.
   * 
   * @param conservation
   *          conservation annotation row
   * @param quality2
   *          (optional - may be null)
   * @param istart
   *          first column for conservation
   * @param alWidth
   *          extent of conservation
   */
  public void completeAnnotations(AlignmentAnnotation conservation,
          AlignmentAnnotation quality2, int istart, int alWidth)
  {
    char[] sequence = getConsSequence().getSequence();
    float minR;
    float minG;
    float minB;
    float maxR;
    float maxG;
    float maxB;
    minR = 0.3f;
    minG = 0.0f;
    minB = 0f;
    maxR = 1.0f - minR;
    maxG = 0.9f - minG;
    maxB = 0f - minB; // scalable range for colouring both Conservation and
    // Quality

    float min = 0f;
    float max = 11f;
    float qmin = 0f;
    float qmax = 0f;

    char c;

    if (conservation.annotations != null
            && conservation.annotations.length < alWidth)
    {
      conservation.annotations = new Annotation[alWidth];
    }

    if (quality2 != null)
    {
      quality2.graphMax = qualityRange[1].floatValue();
      if (quality2.annotations != null
              && quality2.annotations.length < alWidth)
      {
        quality2.annotations = new Annotation[alWidth];
      }
      qmin = qualityRange[0].floatValue();
      qmax = qualityRange[1].floatValue();
    }

    for (int i = 0; i < alWidth; i++)
    {
      float value = 0;

      c = sequence[i];

      if (Character.isDigit(c))
      {
        value = (int) (c - '0');
      }
      else if (c == '*')
      {
        value = 11;
      }
      else if (c == '+')
      {
        value = 10;
      }

      float vprop = value - min;
      vprop /= max;
      conservation.annotations[i] = new Annotation(String.valueOf(c),
              String.valueOf(value), ' ', value, new Color(minR
                      + (maxR * vprop), minG + (maxG * vprop), minB
                      + (maxB * vprop)));

      // Quality calc
      if (quality2 != null)
      {
        value = ((Double) quality.elementAt(i)).floatValue();
        vprop = value - qmin;
        vprop /= qmax;
        quality2.annotations[i] = new Annotation(" ",
                String.valueOf(value), ' ', value, new Color(minR
                        + (maxR * vprop), minG + (maxG * vprop), minB
                        + (maxB * vprop)));
      }
    }
  }

  /**
   * construct and call the calculation methods on a new Conservation object
   * 
   * @param name
   *          - name of conservation
   * @param consHash
   *          - hash table of properties for each amino acid (normally
   *          ResidueProperties.propHash)
   * @param threshold
   *          - minimum number of conserved residues needed to indicate
   *          conservation (typically 3)
   * @param seqs
   * @param start
   *          first column in calculation window
   * @param end
   *          last column in calculation window
   * @param posOrNeg
   *          positive (true) or negative (false) conservation
   * @param consPercGaps
   *          percentage of gaps tolerated in column
   * @param calcQuality
   *          flag indicating if alignment quality should be calculated
   * @return Conservation object ready for use in visualization
   */
  public static Conservation calculateConservation(String name,
          Hashtable consHash, int threshold, List<SequenceI> seqs,
          int start, int end, boolean posOrNeg, int consPercGaps,
          boolean calcQuality)
  {
    Conservation cons = new Conservation(name, consHash, threshold, seqs,
            start, end);
    return calculateConservation(cons, posOrNeg, consPercGaps, calcQuality);
  }

  /**
   * @param b
   *          positive (true) or negative (false) conservation
   * @param consPercGaps
   *          percentage of gaps tolerated in column
   * @param calcQuality
   *          flag indicating if alignment quality should be calculated
   * @return Conservation object ready for use in visualization
   */
  public static Conservation calculateConservation(Conservation cons,
          boolean b, int consPercGaps, boolean calcQuality)
  {
    cons.calculate();
    cons.verdict(b, consPercGaps);

    if (calcQuality)
    {
      cons.findQuality();
    }

    return cons;
  }
}