- if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
-
- //get next line to process
- lookup = input->getSharedRAbundVectors();
- }
-
- if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ //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 = labels;
+
+ //set norm to smallest group number
+ if (method == "totalgroup") {
+ if (norm == 0) {
+ norm = lookupFloat[0]->getNumSeqs();
+ for (int i = 1; i < lookupFloat.size(); i++) {
+ if (lookupFloat[i]->getNumSeqs() < norm) { norm = lookupFloat[i]->getNumSeqs(); }
+ }
+ }
+
+ m->mothurOut("Normalizing to " + toString(norm) + "."); m->mothurOutEndLine();
+ }
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } globaldata->Groups.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){
+
+ m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+ normalize(lookupFloat, out);
+
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+ }
+
+ if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookupFloat[0]->getLabel();
+
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
+ lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+ m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
+
+ normalize(lookupFloat, out);
+
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookupFloat[0]->setLabel(saveLabel);
+ }
+
+ lastLabel = lookupFloat[0]->getLabel();
+ //prevent memory leak
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; lookupFloat[i] = NULL; }
+
+ if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+
+ //get next line to process
+ lookupFloat = input->getSharedRAbundFloatVectors();