/***********************************************************************/
Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i, int snp) :
- windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){}
+ windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){ m = MothurOut::getInstance(); }
/***********************************************************************/
string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
try {
for (int i = 0; i < refSeqs.size(); i++) {
for (int j = i+1; j < refSeqs.size(); j++) {
+
+ if (m->control_pressed) { return "no"; }
//make copies of query and each parent because runBellerophon removes gaps and messes them up
Sequence* q = new Sequence(query->getName(), query->getAligned());
map<int, int> spots; //map from spot in original sequence to spot in filtered sequence for query and both parents
vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
+ if (m->control_pressed) {
+ delete q;
+ delete leftParent;
+ delete rightParent;
+ return "no";
+ }
+
vector<data_struct> selectedDivs;
for (int k = 0; k < divs.size(); k++) {
vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
vector<snps> snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd);
+ if (m->control_pressed) {
+ delete q;
+ delete leftParent;
+ delete rightParent;
+ return "no";
+ }
+
int numSNPSLeft = snpsLeft.size();
int numSNPSRight = snpsRight.size();
float BS_A, BS_B;
bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B);
+
+ if (m->control_pressed) {
+ delete q;
+ delete leftParent;
+ delete rightParent;
+ return "no";
+ }
divs[k].bsa = BS_A;
divs[k].bsb = BS_B;
}
}
catch(exception& e) {
- errorOut(e, "Slayer", "getResults");
+ m->errorOut(e, "Slayer", "getResults");
exit(1);
}
}
//check window size
if (length < (2*windowSize+windowStep)) {
- mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); mothurOutEndLine();
+ m->mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); m->mothurOutEndLine();
windowSize = length / 4;
}
for (int i = windowSize-1; i <= (length - windowSize); i += windowStep) {
+ if (m->control_pressed) { return data; }
+
int breakpoint = i;
int leftLength = breakpoint + 1;
int rightLength = length - leftLength;
}
catch(exception& e) {
- errorOut(e, "Slayer", "runBellerophon");
+ m->errorOut(e, "Slayer", "runBellerophon");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "Slayer", "getSNPS");
+ m->errorOut(e, "Slayer", "getSNPS");
exit(1);
}
}
/***********************************************************************/
-void Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB) {
+int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB) {
try {
srand((unsigned)time( NULL ));
for (int i = 0; i < iters; i++) {
//random sampling with replacement.
+ if (m->control_pressed) { return 0; }
+
vector<snps> selectedLeft;
for (int j = 0; j < numLeft; j++) {
BSA = ((float) count_A / (float) iters) * 100;
BSB = ((float) count_B / (float) iters) * 100;
//cout << "bsa = " << BSA << " bsb = " << BSB << endl;
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "Slayer", "bootstrapSNPS");
+ m->errorOut(e, "Slayer", "bootstrapSNPS");
exit(1);
}
}
return percentID;
}
catch(exception& e) {
- errorOut(e, "Slayer", "snpQA");
+ m->errorOut(e, "Slayer", "snpQA");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "Slayer", "snpQB");
+ m->errorOut(e, "Slayer", "snpQB");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "Slayer", "snpAB");
+ m->errorOut(e, "Slayer", "snpAB");
exit(1);
}
}
return percentID;
}
catch(exception& e) {
- errorOut(e, "Slayer", "computePercentID");
+ m->errorOut(e, "Slayer", "computePercentID");
exit(1);
}
}
return maskMap;
}
catch(exception& e) {
- errorOut(e, "Slayer", "verticalFilter");
+ m->errorOut(e, "Slayer", "verticalFilter");
exit(1);
}
}