package jalview.util;

import jalview.datamodel.*;

public class Comparison {

  public static float compare(SequenceI ii, SequenceI jj)
  {
    return Comparison.compare(ii,jj,0,ii.getLength()-1);
  }
  /**
   * this was supposed to be an ungapped pid calculation
   * @param ii SequenceI
   * @param jj SequenceI
   * @param start int
   * @param end int
   * @return float
   */
  public static float compare(SequenceI ii, SequenceI jj, int start, int end) {

     String si   = ii.getSequence();
     String sj   = jj.getSequence();

     int ilen = si.length()-1;
     int jlen = sj.length()-1;

     while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
     {
       ilen--;
     }

     while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
     {
       jlen--;
     }

     int   count = 0;
     int   match = 0;
     float pid   = -1;

     if (ilen > jlen) {

       for (int j = 0; j < jlen; j++) {
         if (si.substring(start + j,start + j+1).equals(sj.substring(start + j,start + j+1))) {
           match++;
         }
         count++;
       }
       pid = (float)match/(float)ilen * 100;
     } else {
       for (int j = 0; j < jlen; j++) {
         if (si.substring(start + j,start + j+1).equals(sj.substring(start + j,start + j+1))) {
           match++;
         }
         count++;
       }
       pid = (float)match/(float)jlen * 100;
     }

    return pid;
  }

  /**
   * this is a gapped PID calculation
   *
   * @param s1 SequenceI
   * @param s2 SequenceI
   * @return float
   */
  public static float PID(SequenceI s1 , SequenceI s2)
  {
    int len;

    if (s1.getSequence().length() > s2.getSequence().length())
      len = s1.getSequence().length();
    else
      len = s2.getSequence().length();


    int bad = 0;

    for (int i = 0; i < len; i++)
    {
      char chr1;
      char chr2;

      if (i < s1.getSequence().length())
        chr1 = s1.getSequence().charAt(i);
      else
        chr1 = '.';


      if (i < s2.getSequence().length())
        chr2 = s2.getSequence().charAt(i);
      else
        chr2 = '.';


      if (!(jalview.util.Comparison.isGap( chr1 ))  &&  !(jalview.util.Comparison.isGap( chr2 )))
      {
        if (chr1!=chr2)
          bad++;
      }
    }

    return (float)100*(len-bad)/len;
  }

  // Another pid with region specification

  public static float PID(SequenceI s1 , SequenceI s2, int start, int end)
  {
    int len;

    if (s1.getSequence().length() > s2.getSequence().length())
      len = s1.getSequence().length();
    else
      len = s2.getSequence().length();

    if (end<len)
      len=end;

    if (len<start) {
      start = len - 1; // we just use a single residue for the difference
    }

    int bad = 0;

    for (int i = start; i < len; i++)
    {
      char chr1;
      char chr2;

      if (i < s1.getSequence().length())
        chr1 = s1.getSequence().charAt(i);
      else
        chr1 = '.';


      if (i < s2.getSequence().length())
        chr2 = s2.getSequence().charAt(i);
      else
        chr2 = '.';


      if (!(jalview.util.Comparison.isGap( chr1 ))  &&  !(jalview.util.Comparison.isGap( chr2 )))
      {
        if (chr1!=chr2)
          bad++;
      }
    }

    return (float)100*(len-bad)/len;
  }


  public static String GapChars = " .-";
  public static boolean isGap(char c)
  {
    return  (c != '.' && c != '-' && c != ' ') ? false : true;
  }
}