ValidParameters::ValidParameters() {
try {
+ m = MothurOut::getInstance();
initParameterRanges();
+ commandName = "";
}
catch(exception& e) {
- errorOut(e, "ValidParameters", "ValidParameters");
+ 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");
exit(1);
}
}
}
}
if(!valid) {
- mothurOut(parameter + " is not a valid parameter."); mothurOutEndLine();
- mothurOut("The valid parameters are: ");
+ m->mothurOut(parameter + " is not a valid parameter."); m->mothurOutEndLine();
+ m->mothurOut("The valid parameters are: ");
for(int i = 0; i < numParams-1; i++)
- mothurOut(cParams.at(i) + ", ");
- mothurOut("and " + cParams.at(numParams-1) + ".\n");
+ m->mothurOut(cParams.at(i) + ", ");
+ m->mothurOut("and " + cParams.at(numParams-1) + ".\n");
return false;
}
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);
double logNum = log10((double)pVal);
double diff = (double)((int)logNum - logNum);
if(diff != 0) {
- mothurOut("The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n");
+ m->mothurOut("The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n");
return false;
}
}
else if(range.at(4).compare("only") == 0)
c = 1;
else {
- mothurOut("The range can only be 'between' or 'only' the bounding numbers.\n");
+ m->mothurOut("The range can only be 'between' or 'only' the bounding numbers.\n");
return false;
}
else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0)
d = 1;
else {
- mothurOut("The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n");
+ m->mothurOut("The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n");
return false;
}
else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0)
e = 1;
else {
- mothurOut("The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n");
+ m->mothurOut("The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n");
return false;
}
if(!valid) {
- mothurOut("The '" + parameter + "' parameter needs to be ");
+ m->mothurOut("The '" + parameter + "' parameter needs to be ");
if(c == 1)
- mothurOut("either '" + toString(a) + "' or '" + toString(b) + "'.\n");
+ m->mothurOut("either '" + toString(a) + "' or '" + toString(b) + "'.\n");
else {
if(a != piSentinel) {
- mothurOut(">");
+ m->mothurOut(">");
if(d != 0)
- mothurOut("=");
- mothurOut(" '" + toString(a) + "'");
+ m->mothurOut("=");
+ m->mothurOut(" '" + toString(a) + "'");
}
if(b == piSentinel)
- mothurOut( "'.\n");
+ m->mothurOut( "'.\n");
else if(a != piSentinel)
- mothurOut(" and ");
+ m->mothurOut(" and ");
if(b != piSentinel) {
- mothurOut("<");
+ m->mothurOut("<");
if(e != 0)
- mothurOut("=");
- mothurOut(" '" + toString(b) + "'.\n");
+ m->mothurOut("=");
+ m->mothurOut(" '" + toString(b) + "'.\n");
}
}
return false;
return true;
}
catch(exception& e) {
- errorOut(e, "ValidParameters", "isValidParameters");
+ m->errorOut(e, "ValidParameters", "isValidParameters");
exit(1);
}
}
/******************************************************/
-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(it != container.end()){ //no parameter given
+
if(isFile == true) {
- ableToOpen = openInputFile(it->second, in);
- if (ableToOpen == 1) { return "not open"; }
+
+ int pos = (it->second).find(".tx.");
+ if (pos != string::npos) { m->sharedHeaderMode = "tax"; }
+ else { m->sharedHeaderMode = "otu"; }
+
+ #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 (commandName == "") { processors = 1; }
+
+ if (pid == 0) {
+ #endif
+ 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";
+ }
+
+ //check phylip file to make sure its really phylip and not column
+ if ((it->first == "phylip") && (ableToOpen != 1)) {
+ ifstream inPhylip;
+ m->openInputFile(it->second, inPhylip);
+
+ string numTest, name;
+ inPhylip >> numTest >> name;
+ inPhylip.close();
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ". I suspect you entered a column formatted file as a phylip file, aborting."); m->mothurOutEndLine(); return "not found"; }
+ }
+
+ //check for blank file
+ if (ableToOpen != 1) {
+ if (m->isBlank(container[parameter])) {
+ m->mothurOut("[ERROR]: " + container[parameter] + " is blank, aborting."); m->mothurOutEndLine(); return "not found";
+ }
+ }
+
}
}else { return "not found"; }
}
catch(exception& e) {
- errorOut(e, "ValidParameters", "validFile");
+ m->errorOut(e, "ValidParameters", "validFile");
exit(1);
}
}
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);
parameterRanges["size"] = addParameters(sizeArray, rangeSize);
}
catch(exception& e) {
- errorOut(e, "ValidParameters", "initParameterRanges");
+ m->errorOut(e, "ValidParameters", "initParameterRanges");
exit(1);
}
}
return pVector;
}
catch(exception& e) {
- errorOut(e, "ValidParameters", "addParameters");
+ m->errorOut(e, "ValidParameters", "addParameters");
exit(1);
}
}
projects / mothur.git / blobdiff