void phaseChangeModel::correct
(
const scalar dt,
scalarField& availableMass,
volScalarField& dMass,
volScalarField& dEnergy
)
{
if (!active())
{
return;
}
correctModel
(
dt,
availableMass,
dMass,
dEnergy
);
latestMassPC_ = sum(dMass.primitiveField());
totalMassPC_ += latestMassPC_;
availableMass -= dMass;
dMass.correctBoundaryConditions();
if (writeTime())
{
scalar phaseChangeMass = getModelProperty<scalar>("phaseChangeMass");
phaseChangeMass += returnReduce(totalMassPC_, sumOp<scalar>());
setModelProperty<scalar>("phaseChangeMass", phaseChangeMass);
totalMassPC_ = 0.0;
}
}
void phaseChangeModel::correct
(
const scalar dt,
scalarField& availableMass,
volScalarField& dMass,
volScalarField& dEnergy
)
{
correctModel
(
dt,
availableMass,
dMass,
dEnergy
);
latestMassPC_ = sum(dMass.internalField());
totalMassPC_ += latestMassPC_;
availableMass -= dMass;
dMass.correctBoundaryConditions();
}
//**********************************************************************************************************************
int ChimeraPerseusCommand::driver(string chimeraFileName, vector<seqData>& sequences, string accnosFileName, int& numChimeras){
try {
vector<vector<double> > correctModel(4); //could be an option in the future to input own model matrix
for(int i=0;i<4;i++){ correctModel[i].resize(4); }
correctModel[0][0] = 0.000000; //AA
correctModel[1][0] = 11.619259; //CA
correctModel[2][0] = 11.694004; //TA
correctModel[3][0] = 7.748623; //GA
correctModel[1][1] = 0.000000; //CC
correctModel[2][1] = 7.619657; //TC
correctModel[3][1] = 12.852562; //GC
correctModel[2][2] = 0.000000; //TT
correctModel[3][2] = 10.964048; //TG
correctModel[3][3] = 0.000000; //GG
for(int i=0;i<4;i++){
for(int j=0;j<i;j++){
correctModel[j][i] = correctModel[i][j];
}
}
int numSeqs = sequences.size();
int alignLength = sequences[0].sequence.size();
ofstream chimeraFile;
ofstream accnosFile;
m->openOutputFile(chimeraFileName, chimeraFile);
m->openOutputFile(accnosFileName, accnosFile);
Perseus myPerseus;
vector<vector<double> > binMatrix = myPerseus.binomial(alignLength);
chimeraFile << "SequenceIndex\tName\tDiffsToBestMatch\tBestMatchIndex\tBestMatchName\tDiffstToChimera\tIndexofLeftParent\tIndexOfRightParent\tNameOfLeftParent\tNameOfRightParent\tDistanceToBestMatch\tcIndex\t(cIndex - singleDist)\tloonIndex\tMismatchesToChimera\tMismatchToTrimera\tChimeraBreakPoint\tLogisticProbability\tTypeOfSequence\n";
vector<bool> chimeras(numSeqs, 0);
for(int i=0;i<numSeqs;i++){
if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
vector<bool> restricted = chimeras;
vector<vector<int> > leftDiffs(numSeqs);
vector<vector<int> > leftMaps(numSeqs);
vector<vector<int> > rightDiffs(numSeqs);
vector<vector<int> > rightMaps(numSeqs);
vector<int> singleLeft, bestLeft;
vector<int> singleRight, bestRight;
int bestSingleIndex, bestSingleDiff;
vector<pwAlign> alignments(numSeqs);
int comparisons = myPerseus.getAlignments(i, sequences, alignments, leftDiffs, leftMaps, rightDiffs, rightMaps, bestSingleIndex, bestSingleDiff, restricted);
if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
int minMismatchToChimera, leftParentBi, rightParentBi, breakPointBi;
string dummyA, dummyB;
if(comparisons >= 2){
minMismatchToChimera = myPerseus.getChimera(sequences, leftDiffs, rightDiffs, leftParentBi, rightParentBi, breakPointBi, singleLeft, bestLeft, singleRight, bestRight, restricted);
if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
int minMismatchToTrimera = numeric_limits<int>::max();
int leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB;
if(minMismatchToChimera >= 3 && comparisons >= 3){
minMismatchToTrimera = myPerseus.getTrimera(sequences, leftDiffs, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, singleLeft, bestLeft, singleRight, bestRight, restricted);
if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
}
double singleDist = myPerseus.modeledPairwiseAlignSeqs(sequences[i].sequence, sequences[bestSingleIndex].sequence, dummyA, dummyB, correctModel);
if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
string type;
string chimeraRefSeq;
if(minMismatchToChimera - minMismatchToTrimera >= 3){
type = "trimera";
chimeraRefSeq = myPerseus.stitchTrimera(alignments, leftParentTri, middleParentTri, rightParentTri, breakPointTriA, breakPointTriB, leftMaps, rightMaps);
}
else{
type = "chimera";
chimeraRefSeq = myPerseus.stitchBimera(alignments, leftParentBi, rightParentBi, breakPointBi, leftMaps, rightMaps);
}
;
if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
double chimeraDist = myPerseus.modeledPairwiseAlignSeqs(sequences[i].sequence, chimeraRefSeq, dummyA, dummyB, correctModel);
if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
double cIndex = chimeraDist;//modeledPairwiseAlignSeqs(sequences[i].sequence, chimeraRefSeq);
double loonIndex = myPerseus.calcLoonIndex(sequences[i].sequence, sequences[leftParentBi].sequence, sequences[rightParentBi].sequence, breakPointBi, binMatrix);
if (m->control_pressed) { chimeraFile.close(); m->mothurRemove(chimeraFileName); accnosFile.close(); m->mothurRemove(accnosFileName); return 0; }
chimeraFile << i << '\t' << sequences[i].seqName << '\t' << bestSingleDiff << '\t' << bestSingleIndex << '\t' << sequences[bestSingleIndex].seqName << '\t';
chimeraFile << minMismatchToChimera << '\t' << leftParentBi << '\t' << rightParentBi << '\t' << sequences[leftParentBi].seqName << '\t' << sequences[rightParentBi].seqName << '\t';
chimeraFile << singleDist << '\t' << cIndex << '\t' << (cIndex - singleDist) << '\t' << loonIndex << '\t';
chimeraFile << minMismatchToChimera << '\t' << minMismatchToTrimera << '\t' << breakPointBi << '\t';
double probability = myPerseus.classifyChimera(singleDist, cIndex, loonIndex, alpha, beta);
chimeraFile << probability << '\t';
if(probability > cutoff){
chimeraFile << type << endl;
accnosFile << sequences[i].seqName << endl;
chimeras[i] = 1;
numChimeras++;
}
else{
chimeraFile << "good" << endl;
}
}
else{
chimeraFile << i << '\t' << sequences[i].seqName << "\t0\t0\tNull\t0\t0\t0\tNull\tNull\t0.0\t0.0\t0.0\t0\t0\t0\t0.0\t0.0\tgood" << endl;
}
//report progress
if((i+1) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(i+1) + "\n"); }
}
if((numSeqs) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(numSeqs) + "\n"); }
chimeraFile.close();
accnosFile.close();
return numSeqs;
}
catch(exception& e) {
m->errorOut(e, "ChimeraPerseusCommand", "driver");
exit(1);
}
}
