/******************************************************/
-string ValidParameters::validFile(map<string, string> container, string parameter, bool isFile) {
+string ValidParameters::validFile(map<string, string>& container, string parameter, bool isFile) {
try {
int ableToOpen;
ifstream in;
if(it != container.end()){ //no parameter given
if(isFile == true) {
+
+ #ifdef USE_MPI
+ int pid, processors;
+ MPI_Status status;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+ MPI_Comm_size(MPI_COMM_WORLD, &processors);
+
+ if (pid == 0) {
+ #endif
- ableToOpen = openInputFile(it->second, in);
-
- if (ableToOpen == 1) { return "not open"; }
+ ableToOpen = openInputFile(it->second, in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + getSimpleName(it->second);
+ m->mothurOut("Unable to open " + it->second + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ableToOpen = openInputFile(tryPath, in, "noerror");
+ container[parameter] = tryPath;
+ }
+ }
+
in.close();
+
+ #ifdef USE_MPI
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&ableToOpen, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ }
+ }else {
+ MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ }
+
+ MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
+ #endif
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + container[parameter]); m->mothurOutEndLine();
+ return "not open";
+ }
}
}else { return "not found"; }
string itersArray[] = {">=","10", "<","NA", "between"};
parameterRanges["iters"] = addParameters(itersArray, rangeSize);
- string freqArray[] = {">=","1", "<","NA", "between"};
- parameterRanges["freq"] = addParameters(freqArray, rangeSize);
-
- //string lineArray[] = {">=","1", "<","NA", "between"};
- //parameterRanges["line"] = addParameters(lineArray, rangeSize);
-
string abundArray[] = {">=","5", "<","NA", "between"};
parameterRanges["abund"] = addParameters(abundArray, rangeSize);