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/** Global sequence alignment with an affine gap penalty using the
* Needleman-Wunsch algorithm and the improvement by Gotoh.
* @author Shaun Jackman <sjackman@bcgsc.ca>
*/
#include "alignGlobal.h"
#include "Sequence.h"
#include <algorithm>
#include <cassert>
#include <cctype>
#include <climits>
#include <cstdlib> // for abort
using namespace std;
/** A character representing a gap. */
static const char GAP = '*';
/** The score of a match. */
static const int MATCH = 5;
/** The penalty of a mismatch. */
static const int MISMATCH = -4;
/** The penalty of opening a gap. */
static const int GAP_OPEN = -12;
/** The penalty of extending a gap. */
static const int GAP_EXTEND = -4;
/** Return the score of the alignment of a and b.
* @param [out] consensus the consensus of a and b
* @return the score
*/
static int score(char a, char b, char& c)
{
if (a == b) {
c = a;
return MATCH;
} else {
c = ambiguityOr(a, b);
return c == a || c == b ? MATCH : MISMATCH;
}
}
/** Return the score of the alignment of a and b. */
static int score(char a, char b)
{
char c;
return score(a, b, c);
}
/** Find the optimal alignment from the score matrices.
* @param[out] align the alignment
* @return the number of matches
*/
static unsigned backtrack(int** f, int** g, int** h,
const string& seqA, const string& seqB, NWAlignment& align)
{
string alignmentA, alignmentB, consensus;
unsigned matches = 0;
unsigned i = seqA.size(), j = seqB.size();
while (i > 0 && j > 0) {
int fij = f[i][j];
char a = seqA[i-1], b = seqB[j-1], c;
int s = score(a, b, c);
if (fij == f[i-1][j-1] + s) {
alignmentA += a;
alignmentB += b;
consensus += c;
if (s == MATCH)
matches++;
i--;
j--;
} else if (fij == f[i-1][j] + GAP_OPEN
|| fij == g[i-1][j] + GAP_EXTEND) {
while (g[i][j] == g[i-1][j] + GAP_EXTEND) {
char a = seqA[i-1];
alignmentA += a;
alignmentB += GAP;
consensus += tolower(a);
i--;
assert(i > 0);
}
assert(g[i][j] == f[i-1][j] + GAP_OPEN);
char a = seqA[i-1];
alignmentA += a;
alignmentB += GAP;
consensus += tolower(a);
i--;
} else if (fij == f[i][j-1] + GAP_OPEN
|| fij == h[i][j-1] + GAP_EXTEND) {
while (h[i][j] == h[i][j-1] + GAP_EXTEND) {
char b = seqB[j-1];
alignmentA += GAP;
alignmentB += b;
consensus += tolower(b);
j--;
assert(j > 0);
}
assert(h[i][j] == f[i][j-1] + GAP_OPEN);
char b = seqB[j-1];
alignmentA += GAP;
alignmentB += b;
consensus += tolower(b);
j--;
} else {
assert(false);
abort();
}
}
while (i > 0) {
char a = seqA[i-1];
alignmentA += a;
alignmentB += GAP;
consensus += tolower(a);
i--;
}
while (j > 0) {
char b = seqB[j-1];
alignmentA += GAP;
alignmentB += b;
consensus += tolower(b);
j--;
}
reverse(alignmentA.begin(), alignmentA.end());
reverse(alignmentB.begin(), alignmentB.end());
reverse(consensus.begin(), consensus.end());
align.query_align = alignmentA;
align.target_align = alignmentB;
align.match_align = consensus;
return matches;
}
/** Find the optimal global alignment of the two sequences using the
* Needleman-Wunsch algorithm and the improvement by Gotoh to use an
* affine gap penalty rather than a linear gap penalty.
* @param[out] align the alignment
* @return the number of matches
*/
unsigned alignGlobal(const string& seqA, const string& seqB,
NWAlignment& align)
{
unsigned lenA = seqA.size();
unsigned lenB = seqB.size();
int** f = new int*[lenA + 1];
int** g = new int*[lenA + 1];
int** h = new int*[lenA + 1];
for (unsigned i = 0; i <= lenA; i++) {
f[i] = new int[lenB + 1];
g[i] = new int[lenB + 1];
h[i] = new int[lenB + 1];
}
// Initialize the score matrix.
for (unsigned i = 0; i <= lenA; i++) {
f[i][0] = g[i][0] = i == 0 ? 0
: GAP_OPEN + GAP_EXTEND * ((int)i - 1);
h[i][0] = INT_MIN/2;
}
for (unsigned j = 0; j <= lenB; j++) {
f[0][j] = h[0][j] = j == 0 ? 0
: GAP_OPEN + GAP_EXTEND * ((int)j - 1);
g[0][j] = INT_MIN/2;
}
// Calculate the score matrix.
for (unsigned i = 1; i <= lenA; i++) {
for (unsigned j = 1; j <= lenB; j++) {
g[i][j] = max(
f[i-1][j] + GAP_OPEN,
g[i-1][j] + GAP_EXTEND);
h[i][j] = max(
f[i][j-1] + GAP_OPEN,
h[i][j-1] + GAP_EXTEND);
f[i][j] = max(
f[i-1][j-1] + score(seqA[i-1], seqB[j-1]),
max(g[i][j], h[i][j]));
}
}
// Find the best alignment.
unsigned matches = backtrack(f, g, h, seqA, seqB, align);
for (unsigned i = 0; i <= lenA; i++) {
delete[] f[i];
delete[] g[i];
delete[] h[i];
}
delete[] f;
delete[] g;
delete[] h;
return matches;
}
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