+ m->errorOut(e, "SensSpecCommand", "process");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int SensSpecCommand::process(set<string>& seqPairSet, string label, bool& getCutoff, string& origCutoff, int numSeqs){
+ try {
+ int numDists = (numSeqs * (numSeqs-1) / 2);
+
+ ifstream columnFile;
+ m->openInputFile(distFile, columnFile);
+ string seqNameA, seqNameB, seqPairString;
+ double distance;
+
+ truePositives = 0;
+ falsePositives = 0;
+ trueNegatives = numDists;
+ falseNegatives = 0;
+
+ if(getCutoff == 1){
+ if(label != "unique"){
+ origCutoff = label;
+ convert(label, cutoff);
+ if(hard == 0){ cutoff += (0.49 / double(precision)); }
+ }
+ else{
+ origCutoff = "unique";
+ cutoff = 0.0000;
+ }
+ }
+
+ m->mothurOut(label); m->mothurOutEndLine();
+
+ while(columnFile){
+ columnFile >> seqNameA >> seqNameB >> distance;
+ if(seqNameA < seqNameB) { seqPairString = seqNameA + '\t' + seqNameB; }
+ else { seqPairString = seqNameB + '\t' + seqNameA; }
+
+ set<string>::iterator it = seqPairSet.find(seqPairString);
+
+ if(distance <= cutoff){
+ if(it != seqPairSet.end()){
+ truePositives++;
+ seqPairSet.erase(it);
+ }
+ else{
+ falseNegatives++;
+ }
+ trueNegatives--;
+ }
+ else if(it != seqPairSet.end()){
+ falsePositives++;
+ trueNegatives--;
+ seqPairSet.erase(it);
+ }
+
+ m->gobble(columnFile);
+ }
+ falsePositives += seqPairSet.size();
+
+ outputStatistics(label, origCutoff);
+
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "process");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+int SensSpecCommand::processColumn(){
+ try{
+ string origCutoff = "";
+ bool getCutoff = 0;
+ if(cutoff == -1.00) { getCutoff = 1; }
+ else { origCutoff = toString(cutoff); cutoff += (0.49 / double(precision)); }
+
+ set<string> seqPairSet;
+ int numSeqs = 0;
+
+ InputData input(listFile, "list");
+ ListVector* list = input.getListVector();
+ 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;
+ set<string> userLabels = labels;
+
+
+ while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete list; return 0; }
+
+ if(allLines == 1 || labels.count(list->getLabel()) == 1){
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //process
+ numSeqs = fillSeqPairSet(seqPairSet, list);
+ process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
+ }
+
+ if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = list->getLabel();
+
+ delete list;
+ list = input.getListVector(lastLabel);
+
+ processedLabels.insert(list->getLabel());
+ userLabels.erase(list->getLabel());
+
+ //process
+ numSeqs = fillSeqPairSet(seqPairSet, list);
+ process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
+
+ //restore real lastlabel to save below
+ list->setLabel(saveLabel);
+ }
+
+ lastLabel = list->getLabel();
+
+ delete list;
+ list = input.getListVector();
+ }
+
+
+ //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();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ if (list != NULL) { delete list; }
+ list = input.getListVector(lastLabel);
+
+ //process
+ numSeqs = fillSeqPairSet(seqPairSet, list);
+ delete list;
+ process(seqPairSet, list->getLabel(), getCutoff, origCutoff, numSeqs);
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "processColumn");