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);
  }
  public static float compare(SequenceI ii, SequenceI jj, int start, int end) {

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

     int ilen = end-start+1;
     int jlen = end-start+1;

     if ( si.substring(start + ilen).equals("-") ||
          si.substring(start + ilen).equals(".") ||
          si.substring(start + ilen).equals(" ")) {

       ilen--;

       while (si.substring(start + ilen,start + ilen+1).equals("-")  ||
              si.substring(start + ilen,start + ilen+1).equals(".")  ||
              si.substring(start + ilen,start + ilen+1).equals(" ")) {
         ilen--;
       }
     }

     if ( sj.substring(start + jlen).equals("-")  ||
          sj.substring(start + jlen).equals(".")  ||
          sj.substring(start + jlen).equals(" ")) {
       jlen--;

       while (sj.substring(start + jlen,start + jlen+1).equals("-")  ||
              sj.substring(start + jlen,start + jlen+1).equals(".")  ||
              sj.substring(start + jlen,start + jlen+1).equals(" ")) {
         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;
  }

  /**    */
  public static float PID(Sequence s1 , Sequence s2) {
    int res = 0;
    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++) {
      String str1 = "";
      String str2 = "";

      if (i < s1.getSequence().length()) {
        str1 = s1.getSequence().substring(i,i+1);
      } else {
        str1 = ".";
      }

      if (i < s2.getSequence().length()) {
        str2 = s2.getSequence().substring(i,i+1);
      } else {
        str2 = ".";
      }

      if (!(str1.equals(".") ||
            str1.equals("-") ||
            str1.equals(" "))   &&
          !(str2.equals(".") ||
            str2.equals("-") ||
            str2.equals(" "))) {

        if (!str1.equals(str2)) {
          bad++;
        }
      }
    }

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