globaldata = GlobalData::getInstance();
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
- util = new SharedUtil();
int i;
delete input;
delete read;
delete venn;
- delete util;
+ for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
}
//**********************************************************************************************************************
if (format == "sharedfile") {
//you have groups
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
input = globaldata->ginput;
- order = input->getSharedOrderVector();
- }else if (format == "shared") {
- //you are using a list and a groupfile
- read = new ReadPhilFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
+ lookup = input->getSharedRAbundVectors();
}else if (format == "list") {
//you are using just a list file and have only one group
- read = new ReadPhilFile(globaldata->inputFileName);
+ read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
- ordersingle = globaldata->gorder;
+ sabund = globaldata->sabund;
input = globaldata->ginput;
}
if (format != "list") {
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "venn");
- globaldata->setGroups("");
-
- while(order != NULL){
+ while(lookup[0] != NULL){
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
- cout << order->getLabel() << '\t' << count << endl;
- venn->getPic(order, vennCalculators);
-
- }
-
- //get next line to process
- if (format == "sharedfile") {
- order = input->getSharedOrderVector();
- }else {
- //you are using a list and a groupfile
- SharedList = input->getSharedListVector(); //get new list vector to process
- if (SharedList != NULL) {
- order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
- }else {
- break;
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+
+ 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 > 3; i--) { delete lookup[i]; lookup.pop_back(); }
}
+
+ //util->getSharedVectors(globaldata->Groups, lookup, order); //fills group vectors from order vector.
+ venn->getPic(lookup, vennCalculators);
}
+
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
+ //get next line to process
+ lookup = input->getSharedRAbundVectors();
count++;
}
globaldata->Groups.clear();
}else{
- while(ordersingle != NULL){
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){
+ while(sabund != NULL){
+
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
- cout << ordersingle->getLabel() << '\t' << count << endl;
- venn->getPic(ordersingle, vennCalculators);
-
+ cout << sabund->getLabel() << '\t' << count << endl;
+ venn->getPic(sabund, vennCalculators);
}
- ordersingle = (input->getOrderVector());
+ delete sabund;
+ sabund = input->getSAbundVector();
count++;
}
}
+ globaldata->setGroups("");
return 0;
}
catch(exception& e) {
}
}
-//**********************************************************************************************************************
-
+//**********************************************************************************************************************
\ No newline at end of file