input = globaldata->ginput;
list = globaldata->gListVector;
- ListVector* lastList = list;
+ string lastLabel = list->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
userLines.erase(count);
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
+ if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete list;
+ list = input->getListVector(lastLabel);
- error = process(lastList, count);
+ error = process(list, count);
if (error == 1) { return 0; }
- processedLabels.insert(lastList->getLabel());
- userLabels.erase(lastList->getLabel());
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
}
- if (count != 1) { delete lastList; }
- lastList = list;
-
+ lastLabel = list->getLabel();
+
+ delete list;
list = input->getListVector();
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastList->getLabel()) != 1) {
- cout << ". I will use " << lastList->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- error = process(lastList, count);
- if (error == 1) { return 0; }
+ delete list;
+ list = input->getListVector(lastLabel);
+
+ error = process(list, count);
+ if (error == 1) { return 0; }
+
+ delete list;
}
- delete lastList;
return 0;
}
catch(exception& e) {
read->read(&*globaldata);
input = globaldata->ginput;
order = input->getSharedOrderVector();
- SharedOrderVector* lastOrder = order;
+ string lastLabel = order->getLabel();
//if the users entered no valid calculators don't execute command
if (treeCalculators.size() == 0) { return 0; }
}
//you have a label the user want that is smaller than this line and the last line has not already been processed
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
-
- cout << lastOrder->getLabel() << '\t' << count << endl;
- process(lastOrder);
+ if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+
+ delete order;
+ order = input->getSharedOrderVector(lastLabel);
+ cout << order->getLabel() << '\t' << count << endl;
+ process(order);
- processedLabels.insert(lastOrder->getLabel());
- userLabels.erase(lastOrder->getLabel());
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
}
- if (count != 1) { delete lastOrder; }
- lastOrder = order;
+
+ lastLabel = order->getLabel();
//get next line to process
+ delete order;
order = input->getSharedOrderVector();
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastOrder->getLabel()) != 1) {
- cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- process(lastOrder);
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ delete order;
+ order = input->getSharedOrderVector(lastLabel);
+ cout << order->getLabel() << '\t' << count << endl;
+ process(order);
+ delete order;
+
}
-
- delete lastOrder;
//reset groups parameter
globaldata->Groups.clear();
read->read(&*globaldata);
order = globaldata->gorder;
- lastOrder = order;
+ string lastLabel = order->getLabel();
input = globaldata->ginput;
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
//you have a label the user want that is smaller than this line and the last line has not already been processed
}
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
- cCurve = new Collect(lastOrder, cDisplays);
+ if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+
+ delete order;
+ order = (input->getOrderVector(lastLabel));
+
+ cCurve = new Collect(order, cDisplays);
cCurve->getCurve(freq);
delete cCurve;
- cout << lastOrder->getLabel() << '\t' << count << endl;
- processedLabels.insert(lastOrder->getLabel());
- userLabels.erase(lastOrder->getLabel());
+ cout << order->getLabel() << '\t' << count << endl;
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
}
- if (count != 1) { delete lastOrder; }
- lastOrder = order;
+ lastLabel = order->getLabel();
+
+ delete order;
order = (input->getOrderVector());
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastOrder->getLabel()) != 1) {
- cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cCurve = new Collect(lastOrder, cDisplays);
+ delete order;
+ order = (input->getOrderVector(lastLabel));
+
+ cout << order->getLabel() << '\t' << count << endl;
+
+ cCurve = new Collect(order, cDisplays);
cCurve->getCurve(freq);
delete cCurve;
-
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ delete order;
}
- delete lastOrder;
+
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
return 0;
}
GlobalData* globaldata;
ReadOTUFile* read;
OrderVector* order;
- OrderVector* lastOrder;
InputData* input;
Collect* cCurve;
ValidCalculators* validCalculator;
input = globaldata->ginput;
order = input->getSharedOrderVector();
- SharedOrderVector* lastOrder = order;
+ string lastLabel = order->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
//you have a label the user want that is smaller than this line and the last line has not already been processed
}
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
+ if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete order;
+ order = input->getSharedOrderVector(lastLabel);
+
//create collectors curve
- cCurve = new Collect(lastOrder, cDisplays);
+ cCurve = new Collect(order, cDisplays);
cCurve->getSharedCurve(freq);
delete cCurve;
- cout << lastOrder->getLabel() << '\t' << count << endl;
- processedLabels.insert(lastOrder->getLabel());
- userLabels.erase(lastOrder->getLabel());
+ cout << order->getLabel() << '\t' << count << endl;
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
}
- if (count != 1) { delete lastOrder; }
- lastOrder = order;
+
+ lastLabel = order->getLabel();
//get next line to process
+ delete order;
order = input->getSharedOrderVector();
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastOrder->getLabel()) != 1) {
- cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cCurve = new Collect(lastOrder, cDisplays);
+ delete order;
+ order = input->getSharedOrderVector(lastLabel);
+
+ cCurve = new Collect(order, cDisplays);
cCurve->getCurve(freq);
delete cCurve;
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ cout << order->getLabel() << '\t' << count << endl;
+ delete order;
}
- delete lastOrder;
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
//reset groups parameter
input = globaldata->ginput;
list = globaldata->gListVector;
- ListVector* lastList = list;
+ string lastLabel = list->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
userLines.erase(count);
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
- cout << lastList->getLabel() << '\t' << count << endl;
- error = process(lastList);
+ if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete list;
+ list = input->getListVector(lastLabel);
+
+ cout << list->getLabel() << '\t' << count << endl;
+ error = process(list);
if (error == 1) { return 0; } //there is an error in hte input files, abort command
- processedLabels.insert(lastList->getLabel());
- userLabels.erase(lastList->getLabel());
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
}
- if (count != 1) { delete lastList; }
- lastList = list;
+ lastLabel = list->getLabel();
+
+ delete list;
list = input->getListVector();
count++;
}
bool needToRun = false;
for (set<string>::iterator it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastList->getLabel()) != 1) {
- cout << ". I will use " << lastList->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastList->getLabel() << '\t' << count << endl;
- error = process(lastList);
+ delete list;
+ list = input->getListVector(lastLabel);
+
+ cout << list->getLabel() << '\t' << count << endl;
+ error = process(list);
if (error == 1) { return 0; } //there is an error in hte input files, abort command
+ delete list;
}
- delete lastList;
delete matrix;
globaldata->gSparseMatrix = NULL;
- delete list;
globaldata->gListVector = NULL;
return 0;
input = globaldata->ginput;
list = globaldata->gListVector;
- ListVector* lastList = list;
+ string lastLabel = list->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
userLines.erase(count);
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
- cout << lastList->getLabel() << '\t' << count << endl;
+ if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete list;
+ list = input->getListVector(lastLabel);
+
+ cout << list->getLabel() << '\t' << count << endl;
rabund = new RAbundVector();
- *rabund = (lastList->getRAbundVector());
+ *rabund = (list->getRAbundVector());
rabund->print(out);
delete rabund;
- processedLabels.insert(lastList->getLabel());
- userLabels.erase(lastList->getLabel());
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
}
- if (count != 1) { delete lastList; }
- lastList = list;
+ lastLabel = list->getLabel();
+ delete list;
list = input->getListVector();
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastList->getLabel()) != 1) {
- cout << ". I will use " << lastList->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastList->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastList->getLabel() << '\t' << count << endl;
+ delete list;
+ list = input->getListVector(lastLabel);
+
+ cout << list->getLabel() << '\t' << count << endl;
rabund = new RAbundVector();
- *rabund = (lastList->getRAbundVector());
+ *rabund = (list->getRAbundVector());
rabund->print(out);
delete rabund;
+ delete list;
}
- delete lastList;
out.close();
return 0;
read->read(&*globaldata);
order = globaldata->gorder;
- lastOrder = order;
+ string lastLabel = order->getLabel();
input = globaldata->ginput;
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
userLines.erase(count);
}
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete order;
+ order = (input->getOrderVector(lastLabel));
+
+ cout << order->getLabel() << '\t' << count << endl;
sabund = new SAbundVector();
- *sabund = (lastOrder->getSAbundVector());
+ *sabund = (order->getSAbundVector());
sabund->print(out);
delete sabund;
- processedLabels.insert(lastOrder->getLabel());
- userLabels.erase(lastOrder->getLabel());
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
}
- if (count != 1) { delete lastOrder; }
- lastOrder = order;
-
+
+ lastLabel = order->getLabel();
+
+ delete order;
order = (input->getOrderVector());
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastOrder->getLabel()) != 1) {
- cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ delete order;
+ order = (input->getOrderVector(lastLabel));
+
+ cout << order->getLabel() << '\t' << count << endl;
sabund = new SAbundVector();
- *sabund = (lastOrder->getSAbundVector());
+ *sabund = (order->getSAbundVector());
sabund->print(out);
delete sabund;
+ delete order;
}
- delete lastOrder; globaldata->gorder = NULL;
+ globaldata->gorder = NULL;
out.close();
return 0;
ofstream out;
ReadOTUFile* read;
OrderVector* order;
- OrderVector* lastOrder;
InputData* input;
SAbundVector* sabund;
if (abort == true) { return 0; }
int count = 1;
- RAbundVector* lastRAbund;
- vector<SharedRAbundVector*> lastLookup;
+ string lastLabel;
if (format == "sharedfile") {
//you have groups
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- lastLookup = lookup;
+ lastLabel = lookup[0]->getLabel();
}else if (format == "list") {
//you are using just a list file and have only one group
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
rabund = globaldata->rabund;
- lastRAbund = globaldata->rabund;
+ lastLabel = rabund->getLabel();
input = globaldata->ginput;
}
userLines.erase(count);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastLookup);
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ cout << lastLabel << '\t' << count << endl;
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ heatmap->getPic(lookup);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
}
+ lastLabel = lookup[0]->getLabel();
//prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
-
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
//get next line to process
lookup = input->getSharedRAbundVectors();
count++;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastLookup);
+ cout << lastLabel << '\t' << count << endl;
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ heatmap->getPic(lookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
+
//reset groups parameter
globaldata->Groups.clear();
userLines.erase(count);
}
- if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastRAbund->getLabel()) != 1)) {
+ if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- cout << lastRAbund->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastRAbund);
+ cout << lastLabel << '\t' << count << endl;
+ delete rabund;
+ rabund = input->getRAbundVector(lastLabel);
- processedLabels.insert(lastRAbund->getLabel());
- userLabels.erase(lastRAbund->getLabel());
+ heatmap->getPic(rabund);
+
+ processedLabels.insert(rabund->getLabel());
+ userLabels.erase(rabund->getLabel());
}
- if (count != 1) { delete lastRAbund; }
- lastRAbund = rabund;
-
+
+
+ lastLabel = rabund->getLabel();
+ delete rabund;
rabund = input->getRAbundVector();
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastRAbund->getLabel()) != 1) {
- cout << ". I will use " << lastRAbund->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastRAbund->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastRAbund->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastRAbund);
+ cout << lastLabel << '\t' << count << endl;
+ delete rabund;
+ rabund = input->getRAbundVector(lastLabel);
+
+ heatmap->getPic(rabund);
+ delete rabund; globaldata->rabund = NULL;
}
- delete lastRAbund; globaldata->rabund = NULL;
-
}
delete input; globaldata->ginput = NULL;
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- vector<SharedRAbundVector*> lastLookup = lookup;
+ string lastLabel = lookup[0]->getLabel();
if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0;}
userLines.erase(count);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastLookup, heatCalculators);
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lookup, heatCalculators);
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
}
//prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
+
+ lastLabel = lookup[0]->getLabel();
//get next line to process
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel<< "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- heatmap->getPic(lastLookup, heatCalculators);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ heatmap->getPic(lookup, heatCalculators);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
//reset groups parameter
globaldata->Groups.clear();
InputData::InputData(string fName, string f) : format(f){
openInputFile(fName, fileHandle);
+ filename = fName;
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the InputData class function getListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+ListVector* InputData::getListVector(string label){
+ try {
+ ifstream in;
+ string thisLabel;
+ openInputFile(filename, in);
+
+ if(in){
+
+ if (format == "list") {
+
+ while (in.eof() != true) {
+
+ list = new ListVector(in);
+ thisLabel = list->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete list; }
+ gobble(in);
+ }
+ }
+
+ in.close();
+ return list;
+ }
+ else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the InputData class function getListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
+
/***********************************************************************/
SharedListVector* InputData::getSharedListVector(){
exit(1);
}
}
+/***********************************************************************/
+
+SharedListVector* InputData::getSharedListVector(string label){
+ try {
+ ifstream in;
+ string thisLabel;
+ openInputFile(filename, in);
+
+ if(in){
+
+ if (format == "shared") {
+
+ while (in.eof() != true) {
+
+ SharedList = new SharedListVector(in);
+ thisLabel = SharedList->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete SharedList; }
+ gobble(in);
+ }
+
+ }
+
+ in.close();
+ return SharedList;
+
+ }else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the InputData class function getSharedListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+
/***********************************************************************/
}
}
+/***********************************************************************/
+
+SharedOrderVector* InputData::getSharedOrderVector(string label){
+ try {
+ ifstream in;
+ string thisLabel;
+ openInputFile(filename, in);
+
+ if(in){
+
+ if (format == "sharedfile") {
+
+ while (in.eof() != true) {
+
+ SharedOrder = new SharedOrderVector(in);
+ thisLabel = SharedOrder->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete SharedOrder; }
+ gobble(in);
+ }
+
+ }
+
+ in.close();
+ return SharedOrder;
+
+ }else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the InputData class function getSharedOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
/***********************************************************************/
OrderVector* InputData::getOrderVector(){
try {
if(fileHandle){
- if(format == "list") {
+ if((format == "list") || (format == "listorder")) {
input = new ListVector(fileHandle);
}
else if (format == "shared") {
else if(format == "sabund"){
input = new SAbundVector(fileHandle);
}
- else if(format == "listorder"){
- input = new ListVector(fileHandle);
- }
-
+
gobble(fileHandle);
output = new OrderVector();
*output = (input->getOrderVector());
exit(1);
}
}
+
+/***********************************************************************/
+OrderVector* InputData::getOrderVector(string label){
+ try {
+
+ ifstream in;
+ string thisLabel;
+ openInputFile(filename, in);
+
+ if(in){
+ if((format == "list") || (format == "listorder")) {
+
+ while (in.eof() != true) {
+
+ input = new ListVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+ }
+ }
+ else if (format == "shared") {
+
+ while (in.eof() != true) {
+
+ input = new SharedListVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+ }
+
+ }
+ else if(format == "rabund"){
+
+ while (in.eof() != true) {
+
+ input = new RAbundVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+ }
+
+ }
+ else if(format == "order"){
+
+ while (in.eof() != true) {
+
+ input = new OrderVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+ }
+
+ }
+ else if(format == "sabund"){
+
+ while (in.eof() != true) {
+
+ input = new SAbundVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+
+ }
+
+ }
+
+ in.close();
+
+ output = new OrderVector();
+ *output = (input->getOrderVector());
+
+ return output;
+
+ }
+ else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the InputData class function getOrderVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
/***********************************************************************/
//this is used when you don't need the order vector
vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(){
exit(1);
}
}
+/***********************************************************************/
+vector<SharedRAbundVector*> InputData::getSharedRAbundVectors(string label){
+ try {
+ ifstream in;
+ string thisLabel;
+
+ openInputFile(filename, in);
+
+ if(in){
+ if (format == "sharedfile") {
+ while (in.eof() != true) {
+
+ SharedRAbundVector* SharedRAbund = new SharedRAbundVector(in);
+ if (SharedRAbund != NULL) {
+ thisLabel = SharedRAbund->getLabel();
+ //if you are at the last label
+ if (thisLabel == label) { in.close(); return SharedRAbund->getSharedRAbundVectors(); }
+ else {
+ //so you don't loose this memory
+ vector<SharedRAbundVector*> lookup = SharedRAbund->getSharedRAbundVectors();
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ delete SharedRAbund;
+ }
+ }else{ break; }
+ gobble(in);
+
+ }
+ }else if (format == "shared") {
+ while (in.eof() != true) {
+
+ SharedList = new SharedListVector(in);
+ if (SharedList != NULL) {
+ thisLabel = SharedList->getLabel();
+ //if you are at the last label
+ if (thisLabel == label) { in.close(); return SharedList->getSharedRAbundVector(); }
+ else {
+ //so you don't loose this memory
+ delete SharedList;
+ }
+ }else{ break; }
+ gobble(in);
+
+ }
+
+ }
+ }
+
+ //this is created to signal to calling function that the input file is at eof
+ vector<SharedRAbundVector*> null; null.push_back(NULL);
+ in.close();
+ return null;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the InputData class function getSharedRAbundVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
/***********************************************************************/
exit(1);
}
}
+/***********************************************************************/
+SAbundVector* InputData::getSAbundVector(string label){
+ try {
+
+ ifstream in;
+ string thisLabel;
+ openInputFile(filename, in);
+
+ if(in){
+ if (format == "list") {
+
+ while (in.eof() != true) {
+
+ input = new ListVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+ }
+ }
+ else if (format == "shared") {
+
+ while (in.eof() != true) {
+
+ input = new SharedListVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+ }
+
+ }
+ else if(format == "rabund"){
+
+ while (in.eof() != true) {
+
+ input = new RAbundVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+ }
+
+ }
+ else if(format == "order"){
+
+ while (in.eof() != true) {
+
+ input = new OrderVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+ }
+
+ }
+ else if(format == "sabund"){
+
+ while (in.eof() != true) {
+
+ input = new SAbundVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+
+ }
+
+ }
+
+ in.close();
+
+ sabund = new SAbundVector();
+ *sabund = (input->getSAbundVector());
+
+ return sabund;
+
+ }
+ else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the InputData class function getSAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
/***********************************************************************/
RAbundVector* InputData::getRAbundVector(){
}
}
/***********************************************************************/
+RAbundVector* InputData::getRAbundVector(string label){
+ try {
+
+ ifstream in;
+ string thisLabel;
+ openInputFile(filename, in);
+
+ if(in){
+ if (format == "list") {
+
+ while (in.eof() != true) {
+
+ input = new ListVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+ }
+ }
+ else if (format == "shared") {
+
+ while (in.eof() != true) {
+
+ input = new SharedListVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+ }
+
+ }
+ else if(format == "rabund"){
+
+ while (in.eof() != true) {
+
+ input = new RAbundVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+ }
+
+ }
+ else if(format == "order"){
+
+ while (in.eof() != true) {
+
+ input = new OrderVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+ }
+
+ }
+ else if(format == "sabund"){
+
+ while (in.eof() != true) {
+
+ input = new SAbundVector(in);
+ thisLabel = input->getLabel();
+
+ //if you are at the last label
+ if (thisLabel == label) { break; }
+ //so you don't loose this memory
+ else { delete input; }
+ gobble(in);
+
+ }
+
+ }
+
+ in.close();
+
+ rabund = new RAbundVector();
+ *rabund = (input->getRAbundVector());
+
+ return rabund;
+ }
+ else{
+ return NULL;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the InputData class Function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the InputData class function getRAbundVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************************/
InputData(string, string, string);
~InputData();
ListVector* getListVector();
+ ListVector* getListVector(string); //pass the label you want
SharedListVector* getSharedListVector();
- OrderVector* getOrderVector();
+ SharedListVector* getSharedListVector(string); //pass the label you want
+ OrderVector* getOrderVector();
+ OrderVector* getOrderVector(string); //pass the label you want
SharedOrderVector* getSharedOrderVector();
+ SharedOrderVector* getSharedOrderVector(string); //pass the label you want
SAbundVector* getSAbundVector();
+ SAbundVector* getSAbundVector(string); //pass the label you want
RAbundVector* getRAbundVector();
+ RAbundVector* getRAbundVector(string); //pass the label you want
vector<SharedRAbundVector*> getSharedRAbundVectors();
+ vector<SharedRAbundVector*> getSharedRAbundVectors(string); //pass the label you want
private:
string format;
SAbundVector* sabund;
RAbundVector* rabund;
map<string,int> orderMap;
+ string filename;
};
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- vector<SharedRAbundVector*> lastLookup = lookup;
+ string lastLabel = lookup[0]->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
userLines.erase(count);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- process(lastLookup);
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ process(lookup);
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
}
- //prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
+
+ lastLabel = lookup[0]->getLabel();
//get next line to process
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- process(lastLookup);
- }
-
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ process(lookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
//reset groups parameter
globaldata->Groups.clear();
read->read(&*globaldata);
order = globaldata->gorder;
- OrderVector* lastOrder = order;
+ string lastLabel = order->getLabel();
input = globaldata->ginput;
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
userLines.erase(count);
}
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
- rCurve = new Rarefact(lastOrder, rDisplays);
+ if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete order;
+ order = (input->getOrderVector(lastLabel));
+
+ rCurve = new Rarefact(order, rDisplays);
rCurve->getCurve(freq, nIters);
delete rCurve;
- cout << lastOrder->getLabel() << '\t' << count << endl;
- processedLabels.insert(lastOrder->getLabel());
- userLabels.erase(lastOrder->getLabel());
+ cout << order->getLabel() << '\t' << count << endl;
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
}
- if (count != 1) { delete lastOrder; }
- lastOrder = order;
-
+ lastLabel = order->getLabel();
+
+ delete order;
order = (input->getOrderVector());
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastOrder->getLabel()) != 1) {
- cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- rCurve = new Rarefact(lastOrder, rDisplays);
+ delete order;
+ order = (input->getOrderVector(lastLabel));
+
+ rCurve = new Rarefact(order, rDisplays);
rCurve->getCurve(freq, nIters);
delete rCurve;
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ cout << order->getLabel() << '\t' << count << endl;
+ delete order;
}
- delete lastOrder;
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
return 0;
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- vector<SharedRAbundVector*> lastLookup = lookup;
+ string lastLabel = lookup[0]->getLabel();
if (lookup.size() < 2) {
cout << "I cannot run the command without at least 2 valid groups.";
userLines.erase(count);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- rCurve = new Rarefact(lastLookup, rDisplays);
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ rCurve = new Rarefact(lookup, rDisplays);
rCurve->getSharedCurve(freq, nIters);
delete rCurve;
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
}
- //prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
+
+ lastLabel = lookup[0]->getLabel();
//get next line to process
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- rCurve = new Rarefact(lastLookup, rDisplays);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ rCurve = new Rarefact(lookup, rDisplays);
rCurve->getSharedCurve(freq, nIters);
delete rCurve;
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
-
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
//reset groups parameter
input = globaldata->ginput;
SharedList = globaldata->gSharedList;
- SharedListVector* lastList = SharedList;
+ string lastLabel = SharedList->getLabel();
vector<SharedRAbundVector*> lookup;
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
userLines.erase(count);
}
- if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastList->getLabel()) != 1)) {
- lookup = lastList->getSharedRAbundVector();
+ if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete SharedList;
+ SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
+
+ lookup = SharedList->getSharedRAbundVector();
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- processedLabels.insert(lastList->getLabel());
- userLabels.erase(lastList->getLabel());
+ processedLabels.insert(SharedList->getLabel());
+ userLabels.erase(SharedList->getLabel());
}
- if (count != 1) { delete lastList; }
- lastList = SharedList;
-
+
+ lastLabel = SharedList->getLabel();
+
+ delete SharedList;
SharedList = input->getSharedListVector(); //get new list vector to process
count++;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
//cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastList->getLabel()) != 1) {
+ if (processedLabels.count(lastLabel) != 1) {
//cout << ". I will use " << lastList->getLabel() << "." << endl;
needToRun = true;
}else {
//run last line if you need to
if (needToRun == true) {
- lookup = lastList->getSharedRAbundVector();
+ delete SharedList;
+ SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
+
+ lookup = SharedList->getSharedRAbundVector();
printSharedData(lookup); //prints info to the .shared file
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
-
+ delete SharedList;
}
- delete lastList; globaldata->gSharedList = NULL;
+ globaldata->gSharedList = NULL;
delete read;
out.close();
/***********************************************************************/
SharedRAbundVector::SharedRAbundVector() : DataVector(), maxRank(0), numBins(0), numSeqs(0) {globaldata = GlobalData::getInstance();}
+/***********************************************************************/
+
+SharedRAbundVector::~SharedRAbundVector() {
+ //for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
+}
/***********************************************************************/
//SharedRAbundVector(string, vector<int>);
SharedRAbundVector(const SharedRAbundVector& bv) : DataVector(bv), data(bv.data), maxRank(bv.maxRank), numBins(bv.numBins), numSeqs(bv.numSeqs){};
SharedRAbundVector(ifstream&);
- ~SharedRAbundVector(){};
+ ~SharedRAbundVector();
int getNumBins();
int getNumSeqs();
read->read(&*globaldata);
sabund = globaldata->sabund;
- SAbundVector* lastSAbund = sabund;
+ string lastLabel = sabund->getLabel();
input = globaldata->ginput;
for(int i=0;i<sumCalculators.size();i++){
outputFileHandle << endl;
}
- if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) {
-
- cout << lastSAbund->getLabel() << '\t' << count << endl;
- processedLabels.insert(lastSAbund->getLabel());
- userLabels.erase(lastSAbund->getLabel());
+ if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete sabund;
+ sabund = input->getSAbundVector(lastLabel);
+
+ cout << sabund->getLabel() << '\t' << count << endl;
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
- outputFileHandle << lastSAbund->getLabel();
+ outputFileHandle << sabund->getLabel();
for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(lastSAbund);
+ vector<double> data = sumCalculators[i]->getValues(sabund);
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
}
outputFileHandle << endl;
}
- if (count != 1) { delete lastSAbund; }
- lastSAbund = sabund;
-
+ lastLabel = sabund->getLabel();
+
+ delete sabund;
sabund = input->getSAbundVector();
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastSAbund->getLabel()) != 1) {
- cout << ". I will use " << lastSAbund->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastSAbund->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastSAbund->getLabel() << '\t' << count << endl;
- outputFileHandle << lastSAbund->getLabel();
+ delete sabund;
+ sabund = input->getSAbundVector(lastLabel);
+
+ cout << sabund->getLabel() << '\t' << count << endl;
+ outputFileHandle << sabund->getLabel();
for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(lastSAbund);
+ vector<double> data = sumCalculators[i]->getValues(sabund);
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
}
outputFileHandle << endl;
+ delete sabund;
}
outputFileHandle.close();
- delete lastSAbund;
return 0;
}
catch(exception& e) {
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- vector<SharedRAbundVector*> lastLookup = lookup;
+ string lastLabel = lookup[0]->getLabel();
//output estimator names as column headers
outputFileHandle << "label" <<'\t' << "comparison" << '\t';
userLines.erase(count);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- process(lastLookup);
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ process(lookup);
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
}
- //prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
+
+ lastLabel = lookup[0]->getLabel();
//get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- process(lastLookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ process(lookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
//reset groups parameter
globaldata->Groups.clear();
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- lastLookup = lookup;
+ lastLabel = lookup[0]->getLabel();
if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0; }
userLines.erase(count);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- process(lastLookup);
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ process(lookup);
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
}
- //prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
+ lastLabel = lookup[0]->getLabel();
//get next line to process
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- process(lastLookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ process(lookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; }
}
catch(exception& e) {
InputData* input;
ValidCalculators* validCalculator;
vector<SharedRAbundVector*> lookup;
- vector<SharedRAbundVector*> lastLookup;
+ string lastLabel;
string format, outputFile, groupNames, filename;
int numGroups;
ofstream out;
if (abort == true) { return 0; }
int count = 1;
- SAbundVector* lastSAbund;
- vector<SharedRAbundVector*> lastLookup;
-
+ string lastLabel;
+
//if the users entered no valid calculators don't execute command
if (vennCalculators.size() == 0) { return 0; }
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- lastLookup = lookup;
+ lastLabel = lookup[0]->getLabel();
}else if (format == "list") {
//you are using just a list file and have only one group
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
sabund = globaldata->sabund;
- lastSAbund = globaldata->sabund;
+ lastLabel = sabund->getLabel();
input = globaldata->ginput;
}
venn->getPic(lookup, vennCalculators);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
- if (lastLookup.size() > 4) {
+ if (lookup.size() > 4) {
cout << "Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile." << endl;
- for (int i = lastLookup.size(); i > 4; i--) { lastLookup.pop_back(); } //no memmory leak because pop_back calls destructor
+ for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
}
- venn->getPic(lastLookup, vennCalculators);
+ venn->getPic(lookup, vennCalculators);
}
- //prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
+
+ lastLabel = lookup[0]->getLabel();
//get next line to process
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- if (lastLookup.size() > 4) {
- cout << "Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile." << endl;
- for (int i = lastLookup.size(); i > 3; i--) { delete lastLookup[i]; lastLookup.pop_back(); }
- }
- venn->getPic(lastLookup, vennCalculators);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ if (lookup.size() > 4) {
+ cout << "Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile." << endl;
+ for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
+ }
+ venn->getPic(lookup, vennCalculators);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
//reset groups parameter
globaldata->Groups.clear();
userLines.erase(count);
}
- if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) {
-
- cout << lastSAbund->getLabel() << '\t' << count << endl;
- venn->getPic(lastSAbund, vennCalculators);
+ if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete sabund;
+ sabund = input->getSAbundVector(lastLabel);
+
+ cout << sabund->getLabel() << '\t' << count << endl;
+ venn->getPic(sabund, vennCalculators);
- processedLabels.insert(lastSAbund->getLabel());
- userLabels.erase(lastSAbund->getLabel());
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
}
- if (count != 1) { delete lastSAbund; }
- lastSAbund = sabund;
-
+ lastLabel = sabund->getLabel();
+
+ delete sabund;
sabund = input->getSAbundVector();
count++;
}
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastSAbund->getLabel()) != 1) {
- cout << ". I will use " << lastSAbund->getLabel() << "." << endl;
+ if (processedLabels.count(lastLabel) != 1) {
+ cout << ". I will use " << lastLabel << "." << endl;
needToRun = true;
}else {
- cout << ". Please refer to " << lastSAbund->getLabel() << "." << endl;
+ cout << ". Please refer to " << lastLabel << "." << endl;
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastSAbund->getLabel() << '\t' << count << endl;
- venn->getPic(lastSAbund, vennCalculators);
+ delete sabund;
+ sabund = input->getSAbundVector(lastLabel);
+
+ cout << sabund->getLabel() << '\t' << count << endl;
+ venn->getPic(sabund, vennCalculators);
+ delete sabund;
+
}
- delete lastSAbund;
+
}
for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
projects / mothur.git / commitdiff