vector<uNumber> Aligner::alignReadGreedy(const string& read, bool& overlapFound, uint errors, bool r){
vector<pair<kmer,uint>> listOverlap(getNOverlap(read,tryNumber));
if(listOverlap.empty()){++noOverlapRead;++readNumber;return {};}
overlapFound=true;
vector<uNumber> pathBegin,pathEnd;
for(uint start(0); start<(uint)listOverlap.size(); ++start){
pathBegin={};
uint errorBegin(checkBeginGreedy(read,listOverlap[start],pathBegin,errors));
if(errorBegin<=errors){
pathEnd={};
uint errorsEnd(checkEndGreedy(read,listOverlap[start],pathEnd,errors-errorBegin));
if(errorsEnd+errorBegin<=errors){
alignedRead++;
readNumber++;
pathBegin.insert(pathBegin.end(), pathEnd.begin(),pathEnd.end());
return pathBegin;
}
}
}
//TODO TEST this
//if(!rc){return alignReadGreedy(reverseComplements(read), overlapFound,errors, true);}
notAligned++;
readNumber++;
return {};
}
int DynamicObject::checkForCollision(StaticObject** objects, int numObjects,double* xShift, double* yShift, int* objCollidedWith, int* numCollided){
if(objects == NULL || numObjects == 0) return 0;
int i;
int retVal = 0;
int hitNE = -1;
int hitSE = -1;
int hitNW = -1;
int hitSW = -1;
//loop through the blocks and find any blocks that intercept a corner of the ball
//it can be assumed that a particular corner will not intersect more than 1 block
for(i = 0; i < numObjects; i++){
if(objects[i] == this) continue;
if(nwOverlap(objects[i])) hitNW = i;
if(swOverlap(objects[i])) hitSW = i;
if(neOverlap(objects[i])) hitNE = i;
if(seOverlap(objects[i])) hitSE = i;
}
if(hitNE != -1 && hitSW != -1){ //if hit directly at intersection of 2 blocks
if(movingSE()){
if(xShift != NULL) *xShift = getEOverlap(objects[hitNE]);
if(yShift != NULL) *yShift = getSOverlap(objects[hitSW]);
}
else if(movingNW()){
if(xShift != NULL) *xShift = getWOverlap(objects[hitSW]);
if(yShift != NULL) *yShift = getNOverlap(objects[hitNE]);
}
else{ //hope for the best
if(xShift != NULL) *xShift = 0;
if(yShift != NULL) *yShift = 0;
}
retVal = (X_AXIS | Y_AXIS);
}
else if(hitNW != -1 && hitSE != -1){
if(movingSW()){
if(xShift != NULL) *xShift = getWOverlap(objects[hitNW]);
if(yShift != NULL) *yShift = getSOverlap(objects[hitSE]);
}
else if(movingNE()){
if(xShift != NULL) *xShift = getEOverlap(objects[hitSE]);
if(yShift != NULL) *yShift = getNOverlap(objects[hitNW]);
}
else{ //hope for the best
if(xShift != NULL) *xShift = 0;
if(yShift != NULL) *yShift = 0;
}
retVal = (X_AXIS | Y_AXIS);
}
else if(hitNW != -1 && hitSW != -1){
if(xShift != NULL) *xShift = getWOverlap(objects[hitNW]);
retVal = X_AXIS;
}
else if(hitNW != -1 && hitNE != -1){
if(yShift != NULL) *yShift = getNOverlap(objects[hitNW]);
retVal = Y_AXIS;
}
else if(hitSE != -1 && hitNE != -1){
if(xShift != NULL) *xShift = getEOverlap(objects[hitNE]);
retVal = X_AXIS;
}
else if(hitSE != -1 && hitSW != -1){
if(yShift != NULL) *yShift = getSOverlap(objects[hitSE]);
retVal = Y_AXIS;
}
else if(hitSE != -1){
double x = getEOverlap(objects[hitSE]);
double y = getSOverlap(objects[hitSE]);
if(movingSE()){
if(-1*x > -1*y){ //impact on south side of ball
retVal = Y_AXIS;
if(yShift != NULL) *yShift = y;
}
else if(-1*x < -1*y){ //impact on East side of ball
retVal = X_AXIS;
if(xShift != NULL) *xShift = x;
}
else{
retVal = X_AXIS | Y_AXIS;
if(xShift != NULL) *xShift = x;
if(yShift != NULL) *yShift = y;
}
}
else if(movingSW()){
retVal = Y_AXIS;
if(yShift != NULL) *yShift = y;
}
else if(movingNE()){
retVal = X_AXIS;
if(xShift != NULL) *xShift = x;
}
else{
// printf("Level: Something wrong in SE\n");
}
}
else if(hitSW != -1){
double x = getWOverlap(objects[hitSW]);
double y = getSOverlap(objects[hitSW]);
if(movingSW()){
if(x > -1*y){ //impact on south side of ball
retVal = Y_AXIS;
if(yShift != NULL) *yShift = y;
}
else if(x < -1*y){ //impact on west side of ball
retVal = X_AXIS;
if(xShift != NULL) *xShift = x;
}
else{
retVal = X_AXIS | Y_AXIS;
if(xShift != NULL) *xShift = x;
if(yShift != NULL) *yShift = y;
}
}
else if(movingSE()){
retVal = Y_AXIS;
if(yShift != NULL) *yShift = y;
}
else if(movingNW()){
retVal = X_AXIS;
if(xShift != NULL) *xShift = x;
}
else{
// printf("Level: Something wrong in SW\n");
}
}
else if(hitNE != -1){
double x = getEOverlap(objects[hitNE]);
double y = getNOverlap(objects[hitNE]);
if(movingNE()){
if(-1*x > y){ //impact on North side of ball
retVal = Y_AXIS;
if(yShift != NULL) *yShift = y;
}
else if(-1*x < y){ //impact on East side of ball
retVal = X_AXIS;
if(xShift != NULL) *xShift = x;
}
else{
retVal = X_AXIS | Y_AXIS;
if(xShift != NULL) *xShift = x;
if(yShift != NULL) *yShift = y;
}
}
else if(movingNW()){
retVal = Y_AXIS;
if(yShift != NULL) *yShift = y;
}
else if(movingSE()){
retVal = X_AXIS;
if(xShift != NULL) *xShift = x;
}
else{
// printf("Level: Something wrong in SE\n");
}
}
else if(hitNW != -1){
double x = getWOverlap(objects[hitNW]);
double y = getNOverlap(objects[hitNW]);
if(movingNW()){
if(x > y){ //impact on North side of ball
retVal = Y_AXIS;
if(yShift != NULL) *yShift = y;
}
else if(x < y){ //impact on West side of ball
retVal = X_AXIS;
if(xShift != NULL) *xShift = x;
}
else{
retVal = X_AXIS | Y_AXIS;
if(xShift != NULL) *xShift = x;
if(yShift != NULL) *yShift = y;
}
}
else if(movingNE()){
retVal = Y_AXIS;
if(yShift != NULL) *yShift = y;
}
else if(movingSW()){
retVal = X_AXIS;
if(xShift != NULL) *xShift = x;
}
else{
// printf("Level: Something wrong in SE\n");
}
}
else retVal = 0;
if(objCollidedWith != NULL){
i = 0;
if(hitNE != -1){
objCollidedWith[i] = hitNE;
i++;
}
if(hitSE != -1){
objCollidedWith[i] = hitSE;
i++;
}
if(hitNW != -1){
objCollidedWith[i] = hitNW;
i++;
}
if(hitSW != -1){
objCollidedWith[i] = hitSW;
i++;
}
if(numCollided != NULL) *numCollided = i;
}
return retVal;
}