Bad character rule:

   Upon mismatch ==>  skip alignments until

			(a) the mismatch becomes a match   or
			(b) pattern P moves past the mismatched char in text T

Example 1:

    T:   GCTTCTGCTACCTTTTGCGCGCGCGC
    P:   CCTTTTGC
             ^
	     | mismatch

    T:   GCTTCTGCTACCTTTTGCGCGCGCGC
    P:      CCTTTTGC
             ^
	     | mismatch becomes a match

Example 2:

    T:   GCTTCTGCTACCTTTTGCGCGCGCGC
    P:      CCTTTTGC
                  ^
		  | mismatch   (no A in P !)

    T:   GCTTCTGCTACCTTTTGCGCGCGCGC
    P:             CCTTTTGC
                   ^
		   | P moves past the mismatched char in text T


Bad suffix rule turns a mismatch into a match

========================================================================

Good suffix rule:

  Let t = substring matched by inned loop

  Upon mismatch ==>  skip alignments until:

			(a) there are no mismatches between P and t  or
			    (You can use a SUFFIX of t in this match !)
			(b) P moves past t

Example 1:

             t
            vvv
  T = CGTGCCTACTTACTTACTTACTTACGCGAA
  P = CTTACTTAC

  I.e.: shift P until you have another TAC

            vvv
  T = CGTGCCTACTTACTTACTTACTTACGCGAA
  P =     CTTACTTAC
            ^^^ P and t match

Example 2:

	       t
            vvvvvvv
  T = CGTGCCTACTTACTTACTTACTTACGCGAA
  P =     CTTACTTAC

            vvvvvvv
  T = CGTGCCTACTTACTTACTTACTTACGCGAA
  P =         CTTACTTAC
              ^^^^^ P and t (suffix of t) match

Good suffix rule tries to keep a match

=============================================================================

How to use these rules:

   When you have a mismatch:

	(1) bad character rule tells you to shift k1
	(2) good suffix rule tells you to shift k2

   Shift max(k1, k2)


Example 1:

  T = GTTATAGCTGATCGCGGCGTAGCGGCGAA
  P = GTAGCGGCG
              ^ mismatch

Bad char rule:

  T = GTTATAGCTGATCGCGGCGTAGCGGCGAA
  P =        GTAGCGGCG

Good suffix rule is void because t = EMPTY



Example 2:

		    t
                   vvv 
  T = GTTATAGCTGATCGCGGCGTAGCGGCGAA
  P =        GTAGCGGCG
                  ^
		  | mismatch

Bad char rule:

  T = GTTATAGCTGATCGCGGCGTAGCGGCGAA
  P =         GTAGCGGCG
                  ^
		  | match, shift 1

Good suffix rule:

                    t
                   vvv
  T = GTTATAGCTGATCGCGGCGTAGCGGCGAA
  P =           GTAGCGGCG
                   ^^^     shift 3

Result:

  T = GTTATAGCTGATCGCGGCGTAGCGGCGAA
  P =           GTAGCGGCG

We shift 3.




Example 3:

                   vvvvvv
  T = GTTATAGCTGATCGCGGCGTAGCGGCGAA
  P =           GTAGCGGCG
                  ^
		  | mismatch

Bad char rule:

  T = GTTATAGCTGATCGCGGCGTAGCGGCGAA
  P =              GTAGCGGCG
                  ^
		  | mismatch

Good suffix rule:

                   vvvvvv
  T = GTTATAGCTGATCGCGGCGTAGCGGCGAA
  P =                   GTAGCGGCG



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Bad Match Table (BMT)

      P = kuyulayu    ---> Unique:  k u y l a
          01234567    m = len(P) = 8
          ^^^^^^^^
	    idx  (use the LAST idx of a char)

BMT:
      Char     t (shift distance) = m - idx - 1
    ================================
     	k      8-0-1=7
	u      8-1-1=6, 8-3-1=4
	y      8-2-1=5, 8-6-1=1
	l      8-4-1=3
	a      8-5-1=2
	*      m = 8                * = wild card, not char in table

Last character shift distance:

     if (not exist before) t = m
     else (it exists)      use the last computed shift value

How to use the BMT:

    Bad Char Match shift distance d1:

         d1 = max{ 1, t(c) - k }   t(c) in table
                                   k = # macthed characters before mismatch

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