int ConsensusSeqsCommand::readNames(){
try{
-
- ifstream in;
- m->openInputFile(namefile, in);
-
- string thisname, repnames;
- map<string, string>::iterator it;
-
- bool error = false;
-
- while(!in.eof()){
-
- if (m->control_pressed) { break; }
-
- in >> thisname; m->gobble(in); //read from first column
- in >> repnames; //read from second column
-
- it = nameMap.find(thisname);
+ map<string, string> temp;
+ map<string, string>::iterator it;
+ bool error = false;
+
+ m->readNames(namefile, temp); //use central buffered read
+
+ for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end(); itTemp++) {
+ string thisname, repnames;
+ thisname = itTemp->first;
+ repnames = itTemp->second;
+
+ it = nameMap.find(thisname);
if (it != nameMap.end()) { //then this sequence was in the fastafile
-
+ nameFileMap[thisname] = repnames; //for later when outputting the new namesFile if the list file is unique
+
vector<string> splitRepNames;
m->splitAtComma(repnames, splitRepNames);
- nameFileMap[thisname] = repnames; //for later when outputting the new namesFile if the list file is unique
for (int i = 0; i < splitRepNames.size(); i++) { nameMap[splitRepNames[i]] = thisname; }
}else{ m->mothurOut("[ERROR]: " + thisname + " is not in the fasta file, please correct."); m->mothurOutEndLine(); error = true; }
-
- m->gobble(in);
- }
-
- in.close();
-
+ }
+
if (error) { m->control_pressed = true; }
return 0;