+//***************************************************************************************************************
+
+string SensSpecCommand::preProcessList(){
+ try {
+ set<string> uniqueNames;
+ //get unique names from distance file
+ if (format == "phylip") {
+
+ ifstream phylipFile;
+ m->openInputFile(distFile, phylipFile);
+ string numTest;
+ int pNumSeqs;
+ phylipFile >> numTest;
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+ else {
+ m->mothurConvert(numTest, pNumSeqs);
+ }
+ phylipFile >> pNumSeqs; m->gobble(phylipFile);
+
+ string seqName;
+ double distance;
+
+ for(int i=0;i<pNumSeqs;i++){
+
+ if (m->control_pressed) { return ""; }
+
+ phylipFile >> seqName;
+ uniqueNames.insert(seqName);
+
+ for(int j=0;j<i;j++){
+ phylipFile >> distance;
+ }
+ m->gobble(phylipFile);
+ }
+ phylipFile.close();
+ }else {
+ ifstream columnFile;
+ m->openInputFile(distFile, columnFile);
+ string seqNameA, seqNameB;
+ double distance;
+
+ while(columnFile){
+ if (m->control_pressed) { return ""; }
+ columnFile >> seqNameA >> seqNameB >> distance;
+ uniqueNames.insert(seqNameA); uniqueNames.insert(seqNameB);
+ m->gobble(columnFile);
+ }
+ columnFile.close();
+ }
+
+ //read list file, if numSeqs > unique names then remove redundant names
+ string newListFile = listFile + ".temp";
+ ofstream out;
+ m->openOutputFile(newListFile, out);
+ ifstream in;
+ m->openInputFile(listFile, in);
+
+ bool wroteSomething = false;
+
+ while(!in.eof()){
+
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(newListFile); return ""; }
+
+ //read in list vector
+ ListVector list(in);
+
+ //listfile is already unique
+ if (list.getNumSeqs() == uniqueNames.size()) { in.close(); out.close(); m->mothurRemove(newListFile); return ""; }
+
+ //make a new list vector
+ ListVector newList;
+ newList.setLabel(list.getLabel());
+
+ //for each bin
+ for (int i = 0; i < list.getNumBins(); i++) {
+
+ //parse out names that are in accnos file
+ string binnames = list.get(i);
+ vector<string> bnames;
+ m->splitAtComma(binnames, bnames);
+
+ string newNames = "";
+ for (int i = 0; i < bnames.size(); i++) {
+ string name = bnames[i];
+ //if that name is in the .accnos file, add it
+ if (uniqueNames.count(name) != 0) { newNames += name + ","; }
+ }
+
+ //if there are names in this bin add to new list
+ if (newNames != "") {
+ newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
+ newList.push_back(newNames);
+ }
+ }
+
+ //print new listvector
+ if (newList.getNumBins() != 0) {
+ wroteSomething = true;
+ newList.print(out);
+ }
+
+ m->gobble(in);
+ }
+ in.close();
+ out.close();
+
+ if (wroteSomething) { return newListFile; }
+ return "";
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "preProcessList");
+ exit(1);
+ }
+}
+