/***********************************************************************/
-void Rarefact::getCurve(int increment = 1, int nIters = 1000){
+int Rarefact::getCurve(float percentFreq = 0.01, int nIters = 1000){
try {
RarefactionCurveData* rcd = new RarefactionCurveData();
for(int i=0;i<displays.size();i++){
rcd->registerDisplay(displays[i]);
}
-
+
+ //convert freq percentage to number
+ int increment = 1;
+ if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
+ else { increment = percentFreq; }
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ if(processors == 1){
+ driver(rcd, increment, nIters);
+ }else{
+ vector<int> procIters;
+
+ int numItersPerProcessor = nIters / processors;
+
+ //divide iters between processes
+ for (int i = 0; i < processors; i++) {
+ if(i == processors - 1){
+ numItersPerProcessor = nIters - i * numItersPerProcessor;
+ }
+ procIters.push_back(numItersPerProcessor);
+ }
+
+ createProcesses(procIters, rcd, increment);
+ }
+
+ #else
+ driver(rcd, increment, nIters);
+ #endif
+
+ for(int i=0;i<displays.size();i++){
+ displays[i]->close();
+ }
+
+ delete rcd;
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Rarefact", "getCurve");
+ exit(1);
+ }
+}
+/***********************************************************************/
+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++){
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);
lookup->set(binNumber, abundance);
rank->set(abundance, rank->get(abundance)+1);
- if((i == 0) || (i+1) % increment == 0){
+ if((i == 0) || ((i+1) % increment == 0) || (ends.count(i+1) != 0)){
rcd->updateRankData(rank);
}
}
- if(numSeqs % increment != 0){
+ 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;
}
- for(int i=0;i<displays.size();i++){
- displays[i]->close();
- }
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Rarefact class Function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Rarefact", "driver");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Rarefact class function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/**************************************************************************************************/
+
+int Rarefact::createProcesses(vector<int>& procIters, RarefactionCurveData* rcd, int increment) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ int process = 1;
+
+ vector<int> processIDS;
+
+ EstOutput results;
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ driver(rcd, increment, procIters[process]);
+
+ //pass numSeqs to parent
+ for(int i=0;i<displays.size();i++){
+ string tempFile = toString(getpid()) + toString(i) + ".rarefact.temp";
+ displays[i]->outputTempFiles(tempFile);
+ }
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ driver(rcd, increment, procIters[0]);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<(processors-1);i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //get data created by processes
+ for (int i=0;i<(processors-1);i++) {
+ for(int j=0;j<displays.size();j++){
+ string s = toString(processIDS[i]) + toString(j) + ".rarefact.temp";
+ displays[j]->inputTempFiles(s);
+ m->mothurRemove(s);
+ }
+ }
+
+ return 0;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Rarefact", "createProcesses");
exit(1);
}
}
-
/***********************************************************************/
-void Rarefact::getSharedCurve(int increment = 1, int nIters = 1000){
+int Rarefact::getSharedCurve(float percentFreq = 0.01, int nIters = 1000){
try {
- globaldata = GlobalData::getInstance();
SharedRarefactionCurveData* rcd = new SharedRarefactionCurveData();
+ label = lookup[0]->getLabel();
+
//register the displays
for(int i=0;i<displays.size();i++){
rcd->registerDisplay(displays[i]);
}
-
+
+ //if jumble is false all iters will be the same
+ if (m->jumble == false) { nIters = 1; }
+
+ //convert freq percentage to number
+ int increment = 1;
+ if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
+ else { increment = percentFreq; }
+
for(int iter=0;iter<nIters;iter++){
- //clear out old values for new iter
- lookup.clear();
-
- //create and initialize vector of sharedvectors, one for each group
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
- temp->setLabel(sharedorder->getLabel());
- temp->setGroup(globaldata->Groups[i]);
- lookup.push_back(temp);
- }
-
+
for(int i=0;i<displays.size();i++){
displays[i]->init(label);
}
-
- //sample all the members
- for(int i=0;i<numSeqs;i++){
- //get first sample
- individual chosen = sharedorder->get(i);
- int abundance;
-
- //set info for sharedvector in chosens group
- for (int j = 0; j < lookup.size(); j++) {
- if (chosen.group == lookup[j]->getGroup()) {
- abundance = lookup[j]->getAbundance(chosen.bin);
- lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
- break;
- }
- }
+
+ if (m->jumble == true) {
+ //randomize the groups
+ random_shuffle(lookup.begin(), lookup.end());
}
- //randomize the groups
- random_shuffle(lookup.begin(), lookup.end());
+ //make merge the size of lookup[0]
+ SharedRAbundVector* merge = new SharedRAbundVector(lookup[0]->size());
+
+ //make copy of lookup zero
+ for(int i = 0; i<lookup[0]->size(); i++) {
+ merge->set(i, lookup[0]->getAbundance(i), "merge");
+ }
vector<SharedRAbundVector*> subset;
//send each group one at a time
for (int k = 0; k < lookup.size(); k++) {
+ if (m->control_pressed) { delete merge; delete rcd; return 0; }
+
subset.clear(); //clears out old pair of sharedrabunds
//add in new pair of sharedrabunds
- subset.push_back(lookup[0]); subset.push_back(lookup[k]);
+ subset.push_back(merge); subset.push_back(lookup[k]);
rcd->updateSharedData(subset, k+1, numGroupComb);
- mergeVectors(lookup[0], lookup[k]);
+ mergeVectors(merge, lookup[k]);
}
//resets output files
for(int i=0;i<displays.size();i++){
displays[i]->reset();
}
+
+ delete merge;
}
for(int i=0;i<displays.size();i++){
displays[i]->close();
}
-
+
+ delete rcd;
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Rarefact class Function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Rarefact", "getSharedCurve");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Rarefact class function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
/**************************************************************************************/
try{
for (int k = 0; k < shared1->size(); k++) {
//merge new species into shared1
- if ((shared1->getAbundance(k) == 0) && (shared2->getAbundance(k) != 0)) {
- shared1->set(k, shared2->getAbundance(k), "combo"); //set to 'combo' since this vector now contains multiple groups
- }
+ shared1->set(k, (shared1->getAbundance(k) + shared2->getAbundance(k)), "combo"); //set to 'combo' since this vector now contains multiple groups
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the Rarefact class Function mergeVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "Rarefact", "mergeVectors");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the Rarefact class function mergeVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
projects / mothur.git / blobdiff