int Rarefact::driver(RarefactionCurveData* rcd, int increment, int nIters = 1000){
try {
for(int iter=0;iter<nIters;iter++){
for(int i=0;i<displays.size();i++){
displays[i]->init(label);
}
RAbundVector* lookup = new RAbundVector(order->getNumBins());
SAbundVector* rank = new SAbundVector(order->getMaxRank()+1);
random_shuffle(order->begin(), order->end());
for(int i=0;i<numSeqs;i++){
if (m->control_pressed) { delete lookup; delete rank; delete rcd; return 0; }
int binNumber = order->get(i);
int abundance = lookup->get(binNumber);
rank->set(abundance, rank->get(abundance)-1);
abundance++;
lookup->set(binNumber, abundance);
rank->set(abundance, rank->get(abundance)+1);
if((i == 0) || ((i+1) % increment == 0) || (ends.count(i+1) != 0)){
rcd->updateRankData(rank);
}
}
if((numSeqs % increment != 0) || (ends.count(numSeqs) != 0)){
rcd->updateRankData(rank);
}
for(int i=0;i<displays.size();i++){
displays[i]->reset();
}
delete lookup;
delete rank;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "Rarefact", "driver");
exit(1);
}
}
int Collect::getCurve(float percentFreq = 0.01){
try {
RAbundVector* lookup = new RAbundVector(order->getNumBins());
SAbundVector* rank = new SAbundVector(order->getMaxRank()+1);
CollectorsCurveData* ccd = new CollectorsCurveData();
//sets displays label
for(int i=0;i<displays.size();i++){ displays[i]->init(label); }
ccd->registerDisplays(displays);
//convert freq percentage to number
int increment = 1;
if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
else { increment = percentFreq; }
for(int i=0;i<numSeqs;i++){
if (m->getControl_pressed()) { delete lookup; delete rank; delete ccd; return 1; }
int binNumber = order->get(i);
int abundance = lookup->get(binNumber);
rank->set(abundance, rank->get(abundance)-1);
abundance++;
lookup->set(binNumber, abundance);
rank->set(abundance, rank->get(abundance)+1); //increment rank(abundance)
if((i == 0) || (i+1) % increment == 0){ ccd->updateRankData(rank); }
}
if(numSeqs % increment != 0){ ccd->updateRankData(rank); }
for(int i=0;i<displays.size();i++){ displays[i]->reset(); }
delete lookup; delete rank; delete ccd;
return 0;
}
catch(exception& e) {
m->errorOut(e, "Collect", "getCurve");
exit(1);
}
}
TEST(Test_Container_SharedRabundVector, GetSabundVector) {
vector<int> abunds(10, 5);
SharedRAbundVector temp(abunds);
EXPECT_EQ(temp.getNumBins(), 10);
EXPECT_EQ(temp.getNumSeqs(), 50);
EXPECT_EQ(temp.getMaxRank(), 5);
SAbundVector sabund = temp.getSAbundVector();
EXPECT_EQ(sabund.getNumBins(), 10);
EXPECT_EQ(sabund.getNumSeqs(), 50);
EXPECT_EQ(sabund.getMaxRank(), 5);
EXPECT_EQ(sabund.get(5), 10);
}