void Match::Getchar(char revChar)
{
if(!Matched)
{
char curMachingChar = Key.charAt(curIndex);
curIndex = charMatch(revChar, curMachingChar, _IgnoreCase)? curIndex+1 : 0;
Matched = (curIndex >= keyLength)? true : false;
}
}
bool bandedGlobalAlign(const int & k, const string & U, const string & V,
vector<int> & L, vector<int> & R,
vector<vector<int> > & s, vector<vector<char> > & l,
int & NumOfError) {
int n = U.size();
int m = V.size();
int d = m >= n ? m - n : n - m;
setLR(k, m, n, L, R);
for (int i = 0; i <= n; i++) {
for (int j = 0; j < R[i] - L[i] + 1; j++) {
s[i][j] = 0;
l[i][j] = DIAG;
}
}
s[0][0] = 0;
for (int j = L[0]; j <= R[0]; j++) {
s[0][slCOL(0, j)] = j * w[INDEL];
l[0][slCOL(0, j)] = LEFT;
}
char maxl;
int s1, s2, s3, s1Col, s2Col, s3Col, maxs;
for (int i = 1; i <= n; i++) {
s[i][0] = i * w[INDEL];
l[i][0] = UP;
for (int j = L[i]; j <= R[i]; j++) {
s1 = -inf;
s2 = -inf;
s3 = -inf;
s1Col = slCOL(i - 1, j) - 1;
s2Col = slCOL(i - 1, j);
s3Col = slCOL(i, j) - 1;
if (j - 1 >= L[i - 1] && j - 1 <= R[i - 1]) {
s1 = s[i - 1][s1Col] + w[charMatch(U[I], V[J])];
}
if (j >= L[i - 1] && j <= R[i - 1]) {
s2 = s[i - 1][s2Col] + w[INDEL];
}
if (j - 1 >= L[i] && j - 1 <= R[i]) {
s3 = s[i][s3Col] + w[INDEL];
}
max(s1, s2, s3, maxs, maxl);
s[i][slCOL(i, j)] = maxs;
l[i][slCOL(i, j)] = maxl;
}
}
int nDiff = 0;
int p = n, q = m;
//rU.clear();
//rV.clear();
while (p >= 0 && q >= 0 && (p + q != 0)) { // trace back from s[n][m] to s[0][0]
if (l[p][slCOL(p, q)] == DIAG) {
//rU.push_back(U[P]);
//rV.push_back(V[Q]);
if (U[P] != V[Q])
nDiff++;
p = p - 1;
q = q - 1;
} else if (l[p][slCOL(p, q)] == UP) {
//rU.push_back(U[P]);
//rV.push_back('-');
p = p - 1;
nDiff++;
} else if (l[p][slCOL(p, q)] == LEFT) {
//rU.push_back('-');
//rV.push_back(V[Q]);
q = q - 1;
nDiff++;
}
if (nDiff > d + k) {
return false;
}
}
NumOfError = nDiff;
return true;
}