ValidParameters::ValidParameters() {
try {
- initCommandParameters();
+ m = MothurOut::getInstance();
initParameterRanges();
-
}
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";
- exit(1);
- }
}
/***********************************************************************/
ValidParameters::~ValidParameters() {}
-
/***********************************************************************/
-bool ValidParameters::isValidParameter(string parameter, string command, string value) {
+bool ValidParameters::isValidParameter(string parameter, vector<string> cParams, string value) {
try {
bool valid = false;
- vector<string> cParams = commandParameters[command];
+ //vector<string> cParams = commandParameters[command];
int numParams = cParams.size();
- for(int i = 0; i < numParams; i++)
- {
- if(cParams.at(i).compare(parameter) == 0)
- {
+ for(int i = 0; i < numParams; i++) {
+ if(cParams.at(i).compare(parameter) == 0) {
valid = true;
i = numParams;
}
}
- if(!valid)
- {
- cout << "'" << parameter << "' is not a valid parameter for the " << command << " command.\n";
+ 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;
}
int pVal;
double piSentinel = 3.14159;
vector<string> range = parameterRanges[parameter];
-
- valid = convertTest(value, pVal);
-
- if(!valid)
- return false;
+ vector<string> values;
+ splitAtDash(value, values);
+ for(int i = 0; i < values.size(); i++) {
+ value = values.at(i);
+ valid = convertTest(value, pVal);
- /********************************************************************************************************
- Special Cases
- *********************************************************************************************************/
-
- if(parameter.compare("precision") == 0)
- {
- double logNum = log10((double)pVal);
- double diff = (double)((int)logNum - logNum);
- if(diff != 0)
- {
- cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
+ 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
- {
- cout << "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
- {
- cout << "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
- {
- cout << "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)
- return true;
- if(a != piSentinel && b == piSentinel)
- {
- if(d == 0)
- valid = a0;
- else
- valid = a1;
+ /************************************************************************************************************/
+
+
+
+ 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;
}
- else if(a == piSentinel && b != piSentinel)
- {
- if(e == 0)
- valid = b0;
- else
- valid = b1;
+
+ 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;
}
- 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);
+
+ 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;
}
- }
- else
- {
- if(a == piSentinel && b == piSentinel)
- return true;
- 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)
- return true;
-
- else
- {
- cout << "The '" << parameter << "' parameter needs to be ";
- if(c == 1)
- cout << "either '" << a << "' or '" << b << "'.\n";
- else
- {
- if(a != piSentinel)
- {
- cout << ">";
- if(d != 0)
- cout << "=";
- cout << " '" << a << "'";
+
+ 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;
}
- if(b == piSentinel)
- cout << ".\n";
- else if(a != piSentinel)
- cout << " and ";
- if(b != piSentinel)
- {
- cout << "<";
- if(e != 0)
- cout << "=";
- cout << " '" << b << ".\n";
+ 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);
}
}
- return false;
+ 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";
- 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";
+ m->errorOut(e, "ValidParameters", "isValidParameters");
exit(1);
}
}
+/*******************************************************/
-/***********************************************************************/
-
-/***********************************************************************/
-void ValidParameters::initCommandParameters() {
- try {
- //{"parameter1","parameter2",...,"last parameter"};
-
- string readdistArray[] = {"phylip","name","cutoff","precision"};
- commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
-
- string readotuArray[] = {"list","order","group","shared", "sabund"};
- commandParameters["read.otu"] = addParameters(readotuArray, sizeof(readotuArray)/sizeof(string));
-
- string clusterArray[] = {"cutoff","precision","method"};
- commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string));
-
- string deconvoluteArray[] = {"fasta"};
- commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
-
- string collectsingleArray[] = {"freq","line","label","single","precision","abund"};
- commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
-
- string collectsharedArray[] = {"jumble","freq","line","label","shared","groups"};
- commandParameters["collect.shared"] = addParameters(collectsharedArray, sizeof(collectsharedArray)/sizeof(string));
+/******************************************************/
- string getgroupArray[] = {};
- commandParameters["get.group"] = addParameters(getgroupArray, sizeof(getgroupArray)/sizeof(string));
+string ValidParameters::validFile(map<string, string> container, string parameter, bool isFile) {
+ try {
+ int ableToOpen;
+ ifstream in;
+ map<string, string>::iterator it;
- string getlabelArray[] = {};
- commandParameters["get.label"] = addParameters(getlabelArray, sizeof(getlabelArray)/sizeof(string));
+ it = container.find(parameter);
+ if(it != container.end()){ //no parameter given
- string getlineArray[] = {};
- commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string));
+ if(isFile == true) {
+
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
+
+ if (pid == 0) {
+ #endif
- string rarefactionsingleArray[] = {"iters","freq","line","label","rarefaction","abund"};
- commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
+ ableToOpen = openInputFile(it->second, in);
+ in.close();
- string rarefactionsharedArray[] = {"iters","jumble","line","label","sharedrarefaction"};
- commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
-
- string libshuffArray[] = {"iters","groups","step","form","cutoff"};
- commandParameters["libshuff"] = addParameters(libshuffArray, sizeof(libshuffArray)/sizeof(string));
+ #ifdef USE_MPI
+ MPI_Bcast(&ableToOpen, 1, MPI_INT, 0, MPI_COMM_WORLD); //send ableToOPen
+ }else {
+ MPI_Bcast(&ableToOpen, 1, MPI_INT, 0, MPI_COMM_WORLD); //get ableToOPen
+ }
+ #endif
+
+ if (ableToOpen == 1) { return "not open"; }
+ }
+ }else { return "not found"; }
- string summarysingleArray[] = {"line","label","summary","abund"};
- commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
-
- string summarysharedArray[] = {"jumble","line","label","sharedsummary"};
- commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
-
- string quitArray[] = {};
- commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
-
+ return it->second;
+
}
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";
- 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";
+ m->errorOut(e, "ValidParameters", "validFile");
exit(1);
}
}
string itersArray[] = {">=","10", "<","NA", "between"};
parameterRanges["iters"] = addParameters(itersArray, rangeSize);
- string jumbleArray[] = {">","0", "<","1", "only"};
- parameterRanges["jumble"] = addParameters(jumbleArray, rangeSize);
-
- string freqArray[] = {">","1", "<","NA", "between"};
+ string freqArray[] = {">=","1", "<","NA", "between"};
parameterRanges["freq"] = addParameters(freqArray, rangeSize);
- string lineArray[] = {">=","1", "<","NA", "between"};
- parameterRanges["line"] = addParameters(lineArray, rangeSize);
+ //string lineArray[] = {">=","1", "<","NA", "between"};
+ //parameterRanges["line"] = addParameters(lineArray, 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- 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";
+ m->errorOut(e, "ValidParameters", "initParameterRanges");
exit(1);
}
}
return pVector;
}
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";
- 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";
+ m->errorOut(e, "ValidParameters", "addParameters");
exit(1);
}
}
-
projects / mothur.git / blobdiff