while(fileHandle && lt == 1){ //let's assume it's a triangular matrix...
- if (m->control_pressed) { out.close(); remove(tempOutFile.c_str()); fileHandle.close(); delete reading; return 0; }
+ if (m->control_pressed) { out.close(); m->mothurRemove(tempOutFile); fileHandle.close(); delete reading; return 0; }
fileHandle >> firstName >> secondName >> distance; // get the row and column names and distance
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 == 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; }
string outfile = m->getRootName(squareFile) + "sorted.dist.temp";
//use the unix sort
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
string command = "sort -n " + squareFile + " -o " + outfile;
system(command.c_str());
#else //sort using windows sort
system(command.c_str());
#endif
- if (m->control_pressed) { remove(tempOutFile.c_str()); remove(outfile.c_str()); delete reading; return 0; }
+ if (m->control_pressed) { m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
//output to new file distance for each row and save positions in file where new row begins
ifstream in;
while(!in.eof()) {
- if (m->control_pressed) { in.close(); out.close(); remove(distFile.c_str()); remove(tempOutFile.c_str()); remove(outfile.c_str()); delete reading; return 0; }
+ if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
in >> first >> second >> dist; m->gobble(in);
in.close();
out.close();
- if (m->control_pressed) { remove(distFile.c_str()); remove(tempOutFile.c_str()); remove(outfile.c_str()); delete reading; return 0; }
+ if (m->control_pressed) { m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
- remove(tempOutFile.c_str());
- remove(outfile.c_str());
+ m->mothurRemove(tempOutFile);
+ m->mothurRemove(outfile);
reading->finish();
delete reading;
list->setLabel("0");
- if (m->control_pressed) { remove(distFile.c_str()); return 0; }
+ if (m->control_pressed) { m->mothurRemove(distFile); return 0; }
return 1;