try {
m = MothurOut::getInstance();
initParameterRanges();
+ commandName = "";
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ValidParameters", "ValidParameters");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+ValidParameters::ValidParameters(string c) {
+ try {
+ m = MothurOut::getInstance();
+ initParameterRanges();
+ commandName = c;
}
catch(exception& e) {
m->errorOut(e, "ValidParameters", "ValidParameters");
vector<string> range = parameterRanges[parameter];
vector<string> values;
- splitAtDash(value, values);
+ m->splitAtDash(value, values);
for(int i = 0; i < values.size(); i++) {
value = values.at(i);
/******************************************************/
-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;
+
map<string, string>::iterator it;
it = container.find(parameter);
if(isFile == true) {
#ifdef USE_MPI
- int pid;
+ 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 (commandName == "") { processors = 1; }
if (pid == 0) {
#endif
-
- ableToOpen = openInputFile(it->second, in);
-
- if (ableToOpen == 1) { return "not open"; }
+ ifstream in;
+ ableToOpen = m->openInputFile(it->second, in, "noerror");
in.close();
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(it->second);
+ m->mothurOut("Unable to open " + it->second + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ container[parameter] = tryPath;
+ }
+ }
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(it->second);
+ m->mothurOut("Unable to open " + it->second + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ container[parameter] = tryPath;
+ in2.close();
+ }
+ }
+
+
+
#ifdef USE_MPI
+ for(int i = 1; i < processors; i++) {
+ MPI_Send(&ableToOpen, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+
+ int length = container[parameter].length();
+ MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+ MPI_Send(&(container[parameter][0]), length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+
+ }
+ }else {
+ MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+
+ int length;
+ MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ //recieve container
+ char* tempBuf = new char[length];
+ MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+
+ container[parameter] = tempBuf;
+ if (container[parameter].length() > length) { container[parameter] = container[parameter].substr(0, length); }
+ delete tempBuf;
}
+
#endif
-
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + container[parameter]); m->mothurOutEndLine();
+ return "not open";
+ }
}
}else { return "not found"; }
string precisionArray[] = {">=","10", "<","NA", "between"};
parameterRanges["precision"] = addParameters(precisionArray, rangeSize);
- string itersArray[] = {">=","10", "<","NA", "between"};
+ string itersArray[] = {">=","1", "<","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);