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);
}
}
//**********************************************************************************************************************
int RemoveRareCommand::processSabund(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "pick" + m->getExtension(sabundfile);
outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
InputData input(sabundfile, "sabund");
SAbundVector* sabund = input.getSAbundVector();
string lastLabel = sabund->getLabel();
set<string> processedLabels;
set<string> userLabels = labels;
while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) { delete sabund; out.close(); return 0; }
if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
if (sabund->getMaxRank() > nseqs) {
for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }
}else { sabund->clear(); }
if (sabund->getNumBins() > 0) { sabund->print(out); }
}
if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = sabund->getLabel();
delete sabund;
sabund = input.getSAbundVector(lastLabel);
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
if (sabund->getMaxRank() > nseqs) {
for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }
}else { sabund->clear(); }
if (sabund->getNumBins() > 0) { sabund->print(out); }
//restore real lastlabel to save below
sabund->setLabel(saveLabel);
}
lastLabel = sabund->getLabel();
delete sabund;
sabund = input.getSAbundVector();
}
if (m->control_pressed) { out.close(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
//run last label if you need to
if (needToRun == true) {
if (sabund != NULL) { delete sabund; }
sabund = input.getSAbundVector(lastLabel);
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
if (sabund->getMaxRank() > nseqs) {
for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }
}else { sabund->clear(); }
if (sabund->getNumBins() > 0) { sabund->print(out); }
delete sabund;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveRareCommand", "processSabund");
exit(1);
}
}