Ejemplo n.º 1
0
void updateHomopolymers(int** aanHA, int** aanHB, int** aanMoves, int nI, int nJ, const char* acA, const char *acB)
{
  int nMove = aanMoves[nI][nJ];

  switch(nMove){
  case DIAG:
    if(acA[nI - 1] == acB[nJ - 1]){
      if(getLastMatch(aanMoves[nI - 1][nJ - 1], nI - 1, nJ - 1, acA, acB) == acA[nI - 1]){
	aanHA[nI][nJ] = aanHA[nI - 1][nJ - 1] + 1;
	aanHB[nI][nJ] = aanHB[nI - 1][nJ - 1] + 1;
      }
      else{
	aanHA[nI][nJ] = 1;
	aanHB[nI][nJ] = 1;
      }
    }
    else{
      aanHA[nI][nJ] = 0;
      aanHB[nI][nJ] = 0;
    }

    break;
  case LEFT:
    if(acB[nJ - 1] == getLastMatch(aanMoves[nI][nJ - 1], nI, nJ - 1, acA, acB)){
      aanHB[nI][nJ] = aanHB[nI][nJ - 1] + 1;
      aanHA[nI][nJ] = aanHA[nI][nJ - 1] + 1;
    }
    else{
      aanHA[nI][nJ] = 0;
      aanHB[nI][nJ] = 0;
    }
    break;

  case UP:
    /*GAP in B*/
    if(acA[nI - 1] == getLastMatch(aanMoves[nI - 1][nJ], nI - 1, nJ, acA, acB)){
      aanHA[nI][nJ] = aanHA[nI - 1][nJ] + 1;
      aanHB[nI][nJ] = aanHB[nI - 1][nJ] + 1;
    }
    else{
      aanHA[nI][nJ] = 0;
      aanHB[nI][nJ] = 0;
    }
    break;
  }
}
Ejemplo n.º 2
0
int returnHomopolymerA(int nMove, int** aanHA, int** aanMoves, int nI, int nJ, const char* acA, const char *acB)
{
  int retA = 0;

  switch(nMove){
  case DIAG:
    if(acA[nI - 1] == acB[nJ - 1]){
      if(getLastMatch(aanMoves[nI - 1][nJ - 1], nI - 1, nJ - 1, acA, acB) == acA[nI - 1]){
	retA = aanHA[nI - 1][nJ - 1] + 1;
      }
      else{
	retA = 1;
      }
    }
    else{
      retA = 0;
    }

    break;
  case LEFT:
    if(acB[nJ - 1] == getLastMatch(aanMoves[nI][nJ - 1], nI, nJ - 1, acA, acB)){
      retA = aanHA[nI][nJ - 1] + 1;
    }
    else{
      retA = 0;
    }
    break;

  case UP:
    /*GAP in B*/
    if(acA[nI - 1] == getLastMatch(aanMoves[nI - 1][nJ], nI - 1, nJ, acA, acB)){
      retA = aanHA[nI - 1][nJ] + 1;
    }
    else{
      retA = 0;
    }
    break;
  }
  
  return retA;
}
Ejemplo n.º 3
0
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);
	}
}
Ejemplo n.º 4
0
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);
	}
	
}
Ejemplo n.º 5
0
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);
	}	
}