+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = globaldata->labels;
+
+ while((SharedList != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+ if (m->control_pressed) {
+ delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
+ out.close(); remove(filename.c_str());
+ for (int i=0; i<groups.size(); i++) { remove((fileroot + groups[i] + ".rabund").c_str()); }
+ return 1;
+ }
+
+ if(globaldata->allLines == 1 || globaldata->labels.count(SharedList->getLabel()) == 1){
+
+ lookup = SharedList->getSharedRAbundVector();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (pickedGroups) { //check for otus with no seqs in them
+ eliminateZeroOTUS(lookup);
+ }
+
+ if (m->control_pressed) {
+ delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
+ out.close(); remove(filename.c_str());
+ for (int i=0; i<groups.size(); i++) { remove((fileroot + groups[i] + ".rabund").c_str()); }
+ return 1;
+ }
+
+ printSharedData(lookup); //prints info to the .shared file
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
+ processedLabels.insert(SharedList->getLabel());
+ userLabels.erase(SharedList->getLabel());
+ }
+
+ if ((anyLabelsToProcess(SharedList->getLabel(), userLabels, errorOff) == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = SharedList->getLabel();
+
+ delete SharedList;
+ SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
+
+ lookup = SharedList->getSharedRAbundVector();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (pickedGroups) { //check for otus with no seqs in them
+ eliminateZeroOTUS(lookup);
+ }
+
+
+ if (m->control_pressed) {
+ delete input; delete SharedList; globaldata->ginput = NULL; globaldata->gSharedList = NULL;
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
+ out.close(); remove(filename.c_str());
+ for (int i=0; i<groups.size(); i++) { remove((fileroot + groups[i] + ".rabund").c_str()); }
+ return 1;
+ }
+
+ printSharedData(lookup); //prints info to the .shared file
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
+ processedLabels.insert(SharedList->getLabel());
+ userLabels.erase(SharedList->getLabel());
+
+ //restore real lastlabel to save below
+ SharedList->setLabel(saveLabel);
+ }
+
+
+ lastLabel = SharedList->getLabel();
+
+ delete SharedList;
+ SharedList = input->getSharedListVector(); //get new list vector to process
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ if (processedLabels.count(lastLabel) != 1) {
+ needToRun = true;
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (SharedList != NULL) { delete SharedList; }
+ SharedList = input->getSharedListVector(lastLabel); //get new list vector to process
+
+ lookup = SharedList->getSharedRAbundVector();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (pickedGroups) { //check for otus with no seqs in them
+ eliminateZeroOTUS(lookup);
+ }
+
+ if (m->control_pressed) {
+ delete input; globaldata->ginput = NULL;
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { delete it3->second; }
+ out.close(); remove(filename.c_str());
+ for (int i=0; i<groups.size(); i++) { remove((fileroot + groups[i] + ".rabund").c_str()); }
+ return 1;
+ }
+
+ printSharedData(lookup); //prints info to the .shared file
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ delete SharedList;
+ }
+
+ globaldata->gSharedList = NULL;
+
+ out.close();
+
+ for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
+ delete it3->second;
+ }
+
+
+ //change format to shared to speed up commands
+ globaldata->setFormat("sharedfile");
+ globaldata->setListFile("");
+ globaldata->setGroupFile("");
+ globaldata->setSharedFile(filename);
+
+ if (m->control_pressed) {
+ delete input; globaldata->ginput = NULL;
+ remove(filename.c_str());
+ for (int i=0; i<groups.size(); i++) { remove((fileroot + groups[i] + ".rabund").c_str()); }
+ return 1;
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOut(filename); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+