void antisandbox::startDetect(){
printf("========= Checks for AntiSandbox =======\n");
isCWSandbox();
isAnubis();
checkProcess();
checkFile();
checkRegistry();
findWindows();
}
//***************************************************************************************************************
//seqs have already been masked
vector< vector<float> > DeCalculator::getQuantiles(vector<Sequence*> seqs, vector<int> windowSizesTemplate, int window, vector<float> probProfile, int increment, int start, int end) {
try {
vector< vector<float> > quan;
//percentage of mismatched pairs 1 to 100
quan.resize(100);
//for each sequence
for(int i = start; i < end; i++){
m->mothurOut("Processing sequence " + toString(i)); m->mothurOutEndLine();
Sequence* query = new Sequence(seqs[i]->getName(), seqs[i]->getAligned());
//compare to every other sequence in template
for(int j = 0; j < i; j++){
Sequence* subject = new Sequence(seqs[j]->getName(), seqs[j]->getAligned());
if (m->control_pressed) { delete query; delete subject; return quan; }
map<int, int> trim;
map<int, int>::iterator it;
trimSeqs(query, subject, trim);
it = trim.begin();
int front = it->first; int back = it->second;
//reset window for each new comparison
windowSizesTemplate[i] = window;
vector<int> win = findWindows(query, front, back, windowSizesTemplate[i], increment);
vector<float> obsi = calcObserved(query, subject, win, windowSizesTemplate[i]);
vector<float> q = findQav(win, windowSizesTemplate[i], probProfile);
float alpha = getCoef(obsi, q);
vector<float> exp = calcExpected(q, alpha);
float de = calcDE(obsi, exp);
float dist = calcDist(query, subject, front, back);
//cout << i << '\t' << j << '\t' << dist << '\t' << de << endl;
dist = ceil(dist);
//quanMember newScore(de, i, j);
quan[dist].push_back(de);
delete subject;
}
delete query;
}
return quan;
}
catch(exception& e) {
m->errorOut(e, "DeCalculator", "getQuantiles");
exit(1);
}
}
//***************************************************************************************************************
int Ccode::getChimeras(Sequence* query) {
try {
closest.clear();
refCombo = 0;
sumRef.clear();
varRef.clear();
varQuery.clear();
sdRef.clear();
sdQuery.clear();
sumQuery.clear();
sumSquaredRef.clear();
sumSquaredQuery.clear();
averageRef.clear();
averageQuery.clear();
anova.clear();
isChimericConfidence.clear();
isChimericTStudent.clear();
isChimericANOVA.clear();
trim.clear();
spotMap.clear();
windowSizes = window;
windows.clear();
querySeq = query;
//find closest matches to query
closest = findClosest(query, numWanted);
if (m->control_pressed) { return 0; }
//initialize spotMap
for (int i = 0; i < query->getAligned().length(); i++) { spotMap[i] = i; }
//mask sequences if the user wants to
if (seqMask != "") {
decalc->setMask(seqMask);
decalc->runMask(query);
//mask closest
for (int i = 0; i < closest.size(); i++) { decalc->runMask(closest[i].seq); }
spotMap = decalc->getMaskMap();
}
if (filter) {
vector<Sequence*> temp;
for (int i = 0; i < closest.size(); i++) { temp.push_back(closest[i].seq); }
temp.push_back(query);
createFilter(temp, 0.5);
for (int i = 0; i < temp.size(); i++) {
if (m->control_pressed) { return 0; }
runFilter(temp[i]);
}
//update spotMap
map<int, int> newMap;
int spot = 0;
for (int i = 0; i < filterString.length(); i++) {
if (filterString[i] == '1') {
//add to newMap
newMap[spot] = spotMap[i];
spot++;
}
}
spotMap = newMap;
}
//trim sequences - this follows ccodes remove_extra_gaps
trimSequences(query);
if (m->control_pressed) { return 0; }
//windows are equivalent to words - ccode paper recommends windows are between 5% and 20% on alignment length().
//Our default will be 10% and we will warn if user tries to use a window above or below these recommendations
windows = findWindows();
if (m->control_pressed) { return 0; }
//remove sequences that are more than 20% different and less than 0.5% different - may want to allow user to specify this later
removeBadReferenceSeqs(closest);
if (m->control_pressed) { return 0; }
//find the averages for each querys references
getAverageRef(closest); //fills sumRef, averageRef, sumSquaredRef and refCombo.
getAverageQuery(closest, query); //fills sumQuery, averageQuery, sumSquaredQuery.
if (m->control_pressed) { return 0; }
//find the averages for each querys references
findVarianceRef(); //fills varRef and sdRef also sets minimum error rate to 0.001 to avoid divide by 0.
if (m->control_pressed) { return 0; }
//find the averages for the query
findVarianceQuery(); //fills varQuery and sdQuery also sets minimum error rate to 0.001 to avoid divide by 0.
if (m->control_pressed) { return 0; }
determineChimeras(); //fills anova, isChimericConfidence, isChimericTStudent and isChimericANOVA.
if (m->control_pressed) { return 0; }
return 0;
}
catch(exception& e) {
m->errorOut(e, "Ccode", "getChimeras");
exit(1);
}
}