ValidParameters::ValidParameters() {
try {
-
- parameters["phylip"] = "phylip";
- parameters["columnfile"] = "columnfile";
- parameters["listfile"] = "listfile";
- parameters["rabundfile"] = "rabundfile";
- parameters["sabundfile"] = "sabundfile";
- parameters["namefile"] = "namefile";
- parameters["groupfile"] = "groupfile";
- parameters["orderfile"] = "orderfile";
- parameters["fastafile"] = "fastafile";
- parameters["treefile"] = "treefile";
- parameters["fileroot"] = "fileroot";
- parameters["cutoff"] = "cutoff";
- parameters["method"] = "method";
- parameters["format"] = "format";
- parameters["precision"] = "precision";
- parameters["label"] = "label";
- parameters["line"] = "line";
- parameters["iters"] = "iters";
- parameters["jumble"] = "jumble";
- parameters["freq"] = "freq";
- parameters["single"] = "single";
- parameters["rarefaction"] = "rarefaction";
- parameters["sharedrarefaction"] = "sharedrarefaction";
- parameters["shared"] = "shared";
- parameters["summary"] = "summary";
- parameters["sharedsummary"] = "sharedsummary";
-
+ m = MothurOut::getInstance();
+ initParameterRanges();
+ commandName = "";
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ValidParameters", "ValidParameters");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ValidParameters class function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/***********************************************************************/
+
+ValidParameters::ValidParameters(string c) {
+ try {
+ m = MothurOut::getInstance();
+ initParameterRanges();
+ commandName = c;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ValidParameters", "ValidParameters");
exit(1);
- }
+ }
}
/***********************************************************************/
ValidParameters::~ValidParameters() {}
/***********************************************************************/
-bool ValidParameters::isValidParameter(string parameter) {
+bool ValidParameters::isValidParameter(string parameter, vector<string> cParams, string value) {
try {
-
- //is the parameter in the map
- if ((parameters.find(parameter)) != (parameters.end())) {
- return true;
- }else{
- cout << parameter << " is not a valid parameter in Mothur." << endl;
+ bool valid = false;
+ //vector<string> cParams = commandParameters[command];
+ int numParams = cParams.size();
+ for(int i = 0; i < numParams; i++) {
+ if(cParams.at(i).compare(parameter) == 0) {
+ valid = true;
+ i = numParams;
+ }
+ }
+ if(!valid) {
+ m->mothurOut(parameter + " is not a valid parameter."); m->mothurOutEndLine();
+ m->mothurOut("The valid parameters are: ");
+ for(int i = 0; i < numParams-1; i++)
+ m->mothurOut(cParams.at(i) + ", ");
+ m->mothurOut("and " + cParams.at(numParams-1) + ".\n");
return false;
}
+ if(parameterRanges.count(parameter) != 1)
+ return true;
+
+ int pVal;
+ double piSentinel = 3.14159;
+ vector<string> range = parameterRanges[parameter];
+
+ vector<string> values;
+ m->splitAtDash(value, values);
+
+ for(int i = 0; i < values.size(); i++) {
+ value = values.at(i);
+ valid = convertTest(value, pVal);
+
+ if(!valid)
+ return false;
+
+
+
+ /********************************************************************************************************
+ Special Cases
+ *********************************************************************************************************/
+
+ if(parameter.compare("precision") == 0) {
+ double logNum = log10((double)pVal);
+ double diff = (double)((int)logNum - logNum);
+ if(diff != 0) {
+ m->mothurOut("The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n");
+ return false;
+ }
+ }
+
+ /************************************************************************************************************/
+
+
+
+ double a,b,c,d,e;
+
+ if(range.at(1).compare("NA") == 0)
+ a = piSentinel;
+ else
+ a = atoi(range.at(1).c_str());
+
+ if(range.at(3).compare("NA") == 0)
+ b = piSentinel;
+ else
+ b = atoi(range.at(3).c_str());
+
+ if(range.at(4).compare("between") == 0)
+ c = 0;
+ else if(range.at(4).compare("only") == 0)
+ c = 1;
+ else {
+ m->mothurOut("The range can only be 'between' or 'only' the bounding numbers.\n");
+ return false;
+ }
+
+ if(range.at(0).compare(">") == 0)
+ d = 0;
+ else if(range.at(0).compare(">=") == 0 || range[3].compare("=>") == 0)
+ d = 1;
+ else {
+ m->mothurOut("The parameter value can only be '>', '>=', or '=>' the lower bounding number.\n");
+ return false;
+ }
+
+ if(range.at(2).compare("<") == 0)
+ e = 0;
+ else if(range.at(2).compare("<=") == 0 || range[4].compare("=<") == 0)
+ e = 1;
+ else {
+ m->mothurOut("The parameter value can only be '<', '<=', or '=<' the upper bounding number.\n");
+ return false;
+ }
+
+ bool a0 = pVal > a;
+ bool a1 = pVal >= a;
+ bool b0 = pVal < b;
+ bool b1 = pVal <= b;
+
+ if(c != 1) {
+ if(a != piSentinel && b == piSentinel) {
+ if(d == 0)
+ valid = a0;
+ else
+ valid = a1;
+ }
+ else if(a == piSentinel && b != piSentinel) {
+ if(e == 0)
+ valid = b0;
+ else
+ valid = b1;
+ }
+ else {
+ if(d == 0 && e == 0)
+ valid = (a0 && b0);
+ else if(d == 0 && e == 1)
+ valid = (a0 && b1);
+ else if(d == 1 && e == 0)
+ valid = (a1 && b0);
+ else
+ valid = (a1 && b1);
+ }
+ }
+ else {
+ if(a != piSentinel && b == piSentinel)
+ valid = (pVal == a);
+ else if(a == piSentinel && b != piSentinel)
+ valid = (pVal == b);
+ else
+ valid = (pVal == a || pVal == b);
+ }
+
+
+ if(!valid) {
+ m->mothurOut("The '" + parameter + "' parameter needs to be ");
+ if(c == 1)
+ m->mothurOut("either '" + toString(a) + "' or '" + toString(b) + "'.\n");
+ else {
+ if(a != piSentinel) {
+ m->mothurOut(">");
+ if(d != 0)
+ m->mothurOut("=");
+ m->mothurOut(" '" + toString(a) + "'");
+ }
+ if(b == piSentinel)
+ m->mothurOut( "'.\n");
+ else if(a != piSentinel)
+ m->mothurOut(" and ");
+ if(b != piSentinel) {
+ m->mothurOut("<");
+ if(e != 0)
+ m->mothurOut("=");
+ m->mothurOut(" '" + toString(b) + "'.\n");
+ }
+ }
+ return false;
+ }
+ }
+ return true;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ValidParameters", "isValidParameters");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/*******************************************************/
+
+/******************************************************/
+
+string ValidParameters::validFile(map<string, string>& container, string parameter, bool isFile) {
+ try {
+ int ableToOpen;
+
+ map<string, string>::iterator it;
+
+ it = container.find(parameter);
+ if(it != container.end()){ //no parameter given
+
+ if(isFile == true) {
+
+ 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"; }
+
+ return it->second;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ValidParameters", "validFile");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+/***********************************************************************/
+void ValidParameters::initParameterRanges() {
+ try {
+ int rangeSize = 5;
+
+ /**************************************************************************************************************
+ {">=" or "=>" or ">" if the value should be greater than or equal to or just greater than the lower bound,
+ A number representing the lower bound ("NA" if there is no lower bound),
+ "<=" or "=<" or "<" if the value shoud be less than or equal to or just less than the upper bound,
+ A number representing the upper bound ("NA" if there is no lower bound),
+ "between" if between lower and upper bounds or "only" if exactly one of the bounds};
+
+ # = parameter
+ # (>, >=) lower bound, # (<, <=) upperbound, # should be (between, only) lower and upper bounds.
+ ***********************************************************************************************************/
+
+ string precisionArray[] = {">=","10", "<","NA", "between"};
+ parameterRanges["precision"] = addParameters(precisionArray, rangeSize);
+
+ string itersArray[] = {">=","1", "<","NA", "between"};
+ parameterRanges["iters"] = addParameters(itersArray, rangeSize);
+
+ string abundArray[] = {">=","5", "<","NA", "between"};
+ parameterRanges["abund"] = addParameters(abundArray, rangeSize);
+
+ string softArray[] = {">=","0", "<=","100", "between"};
+ parameterRanges["soft"] = addParameters(softArray, rangeSize);
+
+ string sizeArray[] = {">=","1", "<","NA", "between"};
+ parameterRanges["size"] = addParameters(sizeArray, rangeSize);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ValidParameters", "initParameterRanges");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+
+/***********************************************************************/
+vector<string> ValidParameters::addParameters(string parameters[], int size) {
+ try {
+ vector<string> pVector (parameters, parameters+size);
+ return pVector;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ValidParameters", "addParameters");
exit(1);
}
}
-/***********************************************************************/
\ No newline at end of file
projects / mothur.git / blobdiff