map<string,int>::iterator itA = nameMap->find(firstName);
map<string,int>::iterator itB = nameMap->find(secondName);
- if(itA == nameMap->end()){
- cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);
- }
- if(itB == nameMap->end()){
- cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);
- }
-//if (((itA->second == 8) && (itB->second == 1588)) || ((itA->second == 1588) && (itB->second == 8))) { cout << "found it" << endl; }
+ if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1); }
+ if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1); }
if (distance == -1) { distance = 1000000; }
else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
map<string,int>::iterator itA = nameMap->find(firstName);
map<string,int>::iterator itB = nameMap->find(secondName);
- if(itA == nameMap->end()){
- cerr << "BError: Sequence '" << firstName << "' was not found in the names file, please correct\n";
- }
- if(itB == nameMap->end()){
- cerr << "BError: Sequence '" << secondName << "' was not found in the names file, please correct\n";
- }
+ if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1); }
+ if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1); }
if (distance == -1) { distance = 1000000; }
else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.