//**********************************************************************************************************************
NameAssignment::NameAssignment(string nameMapFile){
-
- openInputFile(nameMapFile, fileHandle);
+ m = MothurOut::getInstance();
+ m->openInputFile(nameMapFile, fileHandle);
}
-
+//**********************************************************************************************************************
+NameAssignment::NameAssignment(){ m = MothurOut::getInstance(); }
//**********************************************************************************************************************
void NameAssignment::readMap(){
try{
string firstCol, secondCol, skip;
// int index = 0;
-
-
-// map<string, string> data;
+
+
+ map<string, int>::iterator itData;
int rowIndex = 0;
-
+
while(fileHandle){
- fileHandle >> firstCol; //read from first column
+ fileHandle >> firstCol; m->gobble(fileHandle); //read from first column
fileHandle >> secondCol; //read from second column
+
+ itData = (*this).find(firstCol);
+ if (itData == (*this).end()) {
-// data[firstCol] = secondCol; //store data in map
-
- list.push_back(secondCol); //adds data's value to list
- (*this)[firstCol] = rowIndex++;
- gobble(fileHandle);
+ (*this)[firstCol] = rowIndex++;
+ list.push_back(secondCol); //adds data's value to list
+ reverse[rowIndex] = firstCol;
+
+ }else{ m->mothurOut(firstCol + " is already in namesfile. I will use first definition."); m->mothurOutEndLine(); }
+
+ m->gobble(fileHandle);
}
fileHandle.close();
-// map<string, string>::iterator it = data.begin();
-// for(it;it!=data.end();it++){
-// cout << it->first << endl;
-// (*this)[it->first] = rowIndex;
-// rowIndex++;
-// }
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the NameAssignment class Function readMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "NameAssignment", "readMap");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the NameAssignment class function readMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+void NameAssignment::push_back(string name) {
+ try{
+
+ int num = (*this).size();
+ (*this)[name] = num;
+ reverse[num] = name;
+
+ list.push_back(name);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NameAssignment", "push_back");
exit(1);
}
}
//**********************************************************************************************************************
-void NameAssignment::print(void){
+void NameAssignment::print(ostream& out){
try {
- map<string,int>::iterator it = (*this).begin();
- for(it;it!=(*this).end();it++){
- cout << it->first << '\t' << it->second << endl; //prints out keys and values of the map this.
+ map<string,int>::iterator it;
+//cout << (*this).size() << endl;
+ for(it = (*this).begin(); it!=(*this).end(); it++){
+ out << it->first << '\t' << it->second << endl; //prints out keys and values of the map this.
+ //out << it->first << '\t' << it->first << endl;
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the NameAssignment class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the NameAssignment class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "NameAssignment", "print");
exit(1);
}
}
//**********************************************************************************************************************
int NameAssignment::get(string key){
-
- return (*this)[key];
-
+ try {
+ map<string, int>::iterator itGet = (*this).find(key);
+
+ //if you can't find it
+ if (itGet == (*this).end()) { return -1; }
+
+ return (*this)[key];
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NameAssignment", "get");
+ exit(1);
+ }
}
+//**********************************************************************************************************************
+string NameAssignment::get(int key){
+ try {
+
+ map<int, string>::iterator itGet = reverse.find(key);
+
+ if (itGet == reverse.end()) { return "not found"; }
+
+ return reverse[key];
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NameAssignment", "get");
+ exit(1);
+ }
+}
//**********************************************************************************************************************