//if the users entered no valid calculators don't execute command
if (treeCalculators.size() == 0) { return 0; }
- if (format == "sharedfile") {
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ //you have groups
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
- input = globaldata->ginput;
- order = input->getSharedOrderVector();
- }else {
- //you are using a list and a groupfile
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- SharedList = globaldata->gSharedList;
- order = SharedList->getSharedOrderVector();
- }
+ input = globaldata->ginput;
+ lookup = input->getSharedRAbundVectors();
+
+ if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; }
- //set users groups
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
numGroups = globaldata->Groups.size();
groupNames = "";
for (int i = 0; i < numGroups; i++) { groupNames += globaldata->Groups[i]; }
tmap->makeSim(globaldata->gGroupmap);
globaldata->gTreemap = tmap;
- 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;
- util->getSharedVectors(globaldata->Groups, lookup, order); //fills group vectors from order vector.
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
//for each calculator
for(int i = 0 ; i < treeCalculators.size(); i++) {
for (int g = 0; g < numGroups; g++) { index[g] = g; }
//create a new filename
- outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + order->getLabel() + ".tre";
+ outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".tre";
for (int k = 0; k < lookup.size(); k++) {
for (int l = k; l < lookup.size(); l++) {
}
//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;
- }
- }
+ lookup = input->getSharedRAbundVectors();
count++;
}