double Perseus::basicPairwiseAlignSeqs(string query, string reference, string& qAlign, string& rAlign, pwModel model){
try {
double GAP = model.GAP_OPEN;
double MATCH = model.MATCH;
double MISMATCH = model.MISMATCH;
int queryLength = query.size();
int refLength = reference.size();
vector<vector<double> > alignMatrix(queryLength + 1);
vector<vector<char> > alignMoves(queryLength + 1);
for(int i=0;i<=queryLength;i++){
if (m->getControl_pressed()) { return 0; }
alignMatrix[i].resize(refLength + 1, 0);
alignMoves[i].resize(refLength + 1, 'x');
}
for(int i=0;i<=queryLength;i++){
if (m->getControl_pressed()) { return 0; }
alignMatrix[i][0] = GAP * i;
alignMoves[i][0] = 'u';
}
for(int i=0;i<=refLength;i++){
if (m->getControl_pressed()) { return 0; }
alignMatrix[0][i] = GAP * i;
alignMoves[0][i] = 'l';
}
for(int i=1;i<=queryLength;i++){
if (m->getControl_pressed()) { return 0; }
for(int j=1;j<=refLength;j++){
double nogapScore;
if(query[i-1] == reference[j-1]){ nogapScore = alignMatrix[i-1][j-1] + MATCH; }
else { nogapScore = alignMatrix[i-1][j-1] + MISMATCH; }
double leftScore;
if(i == queryLength) { leftScore = alignMatrix[i][j-1]; }
else { leftScore = alignMatrix[i][j-1] + GAP; }
double upScore;
if(j == refLength) { upScore = alignMatrix[i-1][j]; }
else { upScore = alignMatrix[i-1][j] + GAP; }
if(nogapScore > leftScore){
if(nogapScore > upScore){
alignMoves[i][j] = 'd';
alignMatrix[i][j] = nogapScore;
}
else{
alignMoves[i][j] = 'u';
alignMatrix[i][j] = upScore;
}
}
else{
if(leftScore > upScore){
alignMoves[i][j] = 'l';
alignMatrix[i][j] = leftScore;
}
else{
alignMoves[i][j] = 'u';
alignMatrix[i][j] = upScore;
}
}
}
}
int i = queryLength;
int j = refLength;
qAlign = "";
rAlign = "";
int diffs = 0;
int length = 0;
while(i > 0 && j > 0){
if (m->getControl_pressed()) { return 0; }
if(alignMoves[i][j] == 'd'){
qAlign = query[i-1] + qAlign;
rAlign = reference[j-1] + rAlign;
if(query[i-1] != reference[j-1]){ diffs++; }
length++;
i--;
j--;
}
else if(alignMoves[i][j] == 'u'){
qAlign = query[i-1] + qAlign;
if(j != refLength) { rAlign = '-' + rAlign; diffs++; length++; }
else { rAlign = '.' + rAlign; }
i--;
}
else if(alignMoves[i][j] == 'l'){
rAlign = reference[j-1] + rAlign;
if(i != queryLength){ qAlign = '-' + qAlign; diffs++; length++; }
else { qAlign = '.' + qAlign; }
j--;
}
}
while(i>0){
if (m->getControl_pressed()) { return 0; }
rAlign = '.' + rAlign;
qAlign = query[i-1] + qAlign;
i--;
}
while(j>0){
if (m->getControl_pressed()) { return 0; }
rAlign = reference[j-1] + rAlign;
qAlign = '.' + qAlign;
j--;
}
return double(diffs)/double(length);
}
catch(exception& e) {
m->errorOut(e, "Perseus", "basicPairwiseAlignSeqs");
exit(1);
}
}
int seqNoise::countDiffs(vector<int> query, vector<int> ref){
try {
//double MATCH = 5.0;
//double MISMATCH = -2.0;
//double GAP = -2.0;
vector<vector<double> > correctMatrix(4);
for(int i=0;i<4;i++){ correctMatrix[i].resize(4); }
correctMatrix[0][0] = 0.000000; //AA
correctMatrix[1][0] = 11.619259; //CA
correctMatrix[2][0] = 11.694004; //TA
correctMatrix[3][0] = 7.748623; //GA
correctMatrix[1][1] = 0.000000; //CC
correctMatrix[2][1] = 7.619657; //TC
correctMatrix[3][1] = 12.852562; //GC
correctMatrix[2][2] = 0.000000; //TT
correctMatrix[3][2] = 10.964048; //TG
correctMatrix[3][3] = 0.000000; //GG
for(int i=0;i<4;i++){
for(int j=0;j<i;j++){
correctMatrix[j][i] = correctMatrix[i][j];
}
}
int queryLength = query.size();
int refLength = ref.size();
vector<vector<double> > alignMatrix(queryLength + 1);
vector<vector<char> > alignMoves(queryLength + 1);
for(int i=0;i<=queryLength;i++){
if (m->control_pressed) { return 0; }
alignMatrix[i].resize(refLength + 1, 0);
alignMoves[i].resize(refLength + 1, 'x');
}
for(int i=0;i<=queryLength;i++){
if (m->control_pressed) { return 0; }
alignMatrix[i][0] = 15.0 * i;
alignMoves[i][0] = 'u';
}
for(int i=0;i<=refLength;i++){
if (m->control_pressed) { return 0; }
alignMatrix[0][i] = 15.0 * i;
alignMoves[0][i] = 'l';
}
for(int i=1;i<=queryLength;i++){
if (m->control_pressed) { return 0; }
for(int j=1;j<=refLength;j++){
double nogap;
nogap = alignMatrix[i-1][j-1] + correctMatrix[query[i-1]][ref[j-1]];
double gap;
double left;
if(i == queryLength){ //terminal gap
left = alignMatrix[i][j-1];
}
else{
if(ref[j-1] == getLastMatch('l', alignMoves, i, j, query, ref)){
gap = 4.0;
}
else{
gap = 15.0;
}
left = alignMatrix[i][j-1] + gap;
}
double up;
if(j == refLength){ //terminal gap
up = alignMatrix[i-1][j];
}
else{
if(query[i-1] == getLastMatch('u', alignMoves, i, j, query, ref)){
gap = 4.0;
}
else{
gap = 15.0;
}
up = alignMatrix[i-1][j] + gap;
}
if(nogap < left){
if(nogap < up){
alignMoves[i][j] = 'd';
alignMatrix[i][j] = nogap;
}
else{
alignMoves[i][j] = 'u';
alignMatrix[i][j] = up;
}
}
else{
if(left < up){
alignMoves[i][j] = 'l';
alignMatrix[i][j] = left;
}
else{
alignMoves[i][j] = 'u';
alignMatrix[i][j] = up;
}
}
}
}
int i = queryLength;
int j = refLength;
int diffs = 0;
// string alignA = "";
// string alignB = "";
// string bases = "ACTG";
while(i > 0 && j > 0){
if (m->control_pressed) { return 0; }
if(alignMoves[i][j] == 'd'){
// alignA = bases[query[i-1]] + alignA;
// alignB = bases[ref[j-1]] + alignB;
if(query[i-1] != ref[j-1]) { diffs++; }
i--;
j--;
}
else if(alignMoves[i][j] == 'u'){
if(j != refLength){
// alignA = bases[query[i-1]] + alignA;
// alignB = '-' + alignB;
diffs++;
}
i--;
}
else if(alignMoves[i][j] == 'l'){
if(i != queryLength){
// alignA = '-' + alignA;
// alignB = bases[ref[j-1]] + alignB;
diffs++;
}
j--;
}
}
// cout << diffs << endl;
// cout << alignA << endl;
// cout << alignB << endl;
// cout << endl;
return diffs;
}
catch(exception& e) {
m->errorOut(e, "seqNoise", "countDiffs");
exit(1);
}
}
double Perseus::modeledPairwiseAlignSeqs(string query, string reference, string& qAlign, string& rAlign, vector<vector<double> >& correctMatrix){
try {
int queryLength = query.size();
int refLength = reference.size();
vector<vector<double> > alignMatrix(queryLength + 1);
vector<vector<char> > alignMoves(queryLength + 1);
for(int i=0;i<=queryLength;i++){
if (m->getControl_pressed()) { return 0; }
alignMatrix[i].resize(refLength + 1, 0);
alignMoves[i].resize(refLength + 1, 'x');
}
for(int i=0;i<=queryLength;i++){
if (m->getControl_pressed()) { return 0; }
alignMatrix[i][0] = 15.0 * i;
alignMoves[i][0] = 'u';
}
for(int i=0;i<=refLength;i++){
if (m->getControl_pressed()) { return 0; }
alignMatrix[0][i] = 15.0 * i;
alignMoves[0][i] = 'l';
}
for(int i=1;i<=queryLength;i++){
if (m->getControl_pressed()) { return 0; }
for(int j=1;j<=refLength;j++){
double nogap;
nogap = alignMatrix[i-1][j-1] + correctMatrix[toInt(query[i-1])][toInt(reference[j-1])];
double gap;
double left;
if(i == queryLength){ //terminal gap
left = alignMatrix[i][j-1];
}
else{
if(reference[j-1] == getLastMatch('l', alignMoves, i, j, query, reference)){
gap = 4.0;
}
else{
gap = 15.0;
}
left = alignMatrix[i][j-1] + gap;
}
double up;
if(j == refLength){ //terminal gap
up = alignMatrix[i-1][j];
}
else{
if(query[i-1] == getLastMatch('u', alignMoves, i, j, query, reference)){
gap = 4.0;
}
else{
gap = 15.0;
}
up = alignMatrix[i-1][j] + gap;
}
if(nogap < left){
if(nogap < up){
alignMoves[i][j] = 'd';
alignMatrix[i][j] = nogap;
}
else{
alignMoves[i][j] = 'u';
alignMatrix[i][j] = up;
}
}
else{
if(left < up){
alignMoves[i][j] = 'l';
alignMatrix[i][j] = left;
}
else{
alignMoves[i][j] = 'u';
alignMatrix[i][j] = up;
}
}
}
}
int i = queryLength;
int j = refLength;
int alignLength = 0;
while(i > 0 && j > 0){
if (m->getControl_pressed()) { return 0; }
if(alignMoves[i][j] == 'd'){
qAlign = query[i-1] + qAlign;
rAlign = reference[j-1] + rAlign;
alignLength++;
i--;
j--;
}
else if(alignMoves[i][j] == 'u'){
if(j != refLength){
qAlign = query[i-1] + qAlign;
rAlign = '-' + rAlign;
alignLength++;
}
i--;
}
else if(alignMoves[i][j] == 'l'){
if(i != queryLength){
qAlign = '-' + qAlign;
rAlign = reference[j-1] + rAlign;
alignLength++;
}
j--;
}
}
return alignMatrix[queryLength][refLength] / (double)alignLength;
}
catch(exception& e) {
m->errorOut(e, "Perseus", "modeledPairwiseAlignSeqs");
exit(1);
}
}
double correctDist::getDist(vector<int>& seqA, vector<int>& seqB){
try {
int lengthA = seqA.size();
int lengthB = seqB.size();
vector<vector<double> > alignMatrix(lengthA+1);
vector<vector<char> > alignMoves(lengthA+1);
for(int i=0;i<=lengthA;i++){
alignMatrix[i].resize(lengthB+1, 0);
alignMoves[i].resize(lengthB+1, 'x');
}
for(int i=0;i<=lengthA;i++){
alignMatrix[i][0] = 15.0 * i;
alignMoves[i][0] = 'u';
}
for(int i=0;i<=lengthB;i++){
alignMatrix[0][i] = 15.0 * i;
alignMoves[0][i] = 'l';
}
for(int i=1;i<=lengthA;i++){
for(int j=1;j<=lengthB;j++){
if (m->control_pressed) { return 0; }
double nogap;
nogap = alignMatrix[i-1][j-1] + correctMatrix[seqA[i-1]][seqB[j-1]];
double gap;
double left;
if(i == lengthA){ //terminal gap
left = alignMatrix[i][j-1];
}
else{
if(seqB[j-1] == getLastMatch('l', alignMoves, i, j, seqA, seqB)){
gap = 4.0;
}
else{
gap = 15.0;
}
left = alignMatrix[i][j-1] + gap;
}
double up;
if(j == lengthB){ //terminal gap
up = alignMatrix[i-1][j];
}
else{
if(seqA[i-1] == getLastMatch('u', alignMoves, i, j, seqA, seqB)){
gap = 4.0;
}
else{
gap = 15.0;
}
up = alignMatrix[i-1][j] + gap;
}
if(nogap < left){
if(nogap < up){
alignMoves[i][j] = 'd';
alignMatrix[i][j] = nogap;
}
else{
alignMoves[i][j] = 'u';
alignMatrix[i][j] = up;
}
}
else{
if(left < up){
alignMoves[i][j] = 'l';
alignMatrix[i][j] = left;
}
else{
alignMoves[i][j] = 'u';
alignMatrix[i][j] = up;
}
}
}
}
int i = lengthA;
int j = lengthB;
int count = 0;
// string alignA = "";
// string alignB = "";
// string bases = "ACTG";
//
// for(int i=0;i<lengthA;i++){
// cout << bases[seqA[i]];
// }cout << endl;
//
// for(int i=0;i<lengthB;i++){
// cout << bases[seqB[i]];
// }cout << endl;
while(i > 0 && j > 0){
if (m->control_pressed) { return 0; }
if(alignMoves[i][j] == 'd'){
// alignA = bases[seqA[i-1]] + alignA;
// alignB = bases[seqB[j-1]] + alignB;
count++;
i--;
j--;
}
else if(alignMoves[i][j] == 'u'){
if(j != lengthB){
// alignA = bases[seqA[i-1]] + alignA;
// alignB = '-' + alignB;
count++;
}
i--;
}
else if(alignMoves[i][j] == 'l'){
if(i != lengthA){
// alignA = '-' + alignA;
// alignB = bases[seqB[j-1]] + alignB;
count++;
}
j--;
}
}
// cout << alignA << endl << alignB << endl;
return alignMatrix[lengthA][lengthB] / (double)count;
}
catch(exception& e) {
m->errorOut(e, "correctDist", "getDist");
exit(1);
}
}
