ValidParameters::ValidParameters() {
try {
- initialReaddist();
- initialReadotu();
- initialReadtree();
- initialCluster();
- initialDeconvolute();
- initialParsimony();
- initialCollectsingle();
- initialCollectshared();
- initialRarefactsingle();
- initialRarefactshared();
- initialSummarysingle();
- initialSummaryshared();
- initialUnifracweighted();
- initialUnifracunweighted();
- initialLibshuff();
+ 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, string command) {
+bool ValidParameters::isValidParameter(string parameter, vector<string> cParams, string value) {
try {
+ 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;
- if (command == "read.dist") {
- //is it valid
- if ((readdist.find(parameter)) != (readdist.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = readdist.begin(); it != readdist.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "read.otu") {
- //is it valid
- if ((readotu.find(parameter)) != (readotu.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = readotu.begin(); it != readotu.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- //are you looking for a calculator for a rarefaction parameter
- }else if (command == "read.tree") {
- //is it valid
- if ((readtree.find(parameter)) != (readtree.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = readtree.begin(); it != readtree.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- //are you looking for a calculator for a summary parameter
- }else if (command == "cluster") {
- //is it valid
- if ((cluster.find(parameter)) != (cluster.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = cluster.begin(); it != cluster.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; } //are you looking for a calculator for a sharedsummary parameter
- }else if (command == "deconvolute") {
- //is it valid
- if ((deconvolute.find(parameter)) != (deconvolute.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = deconvolute.begin(); it != deconvolute.end(); it++) {
- cout << it->first;
- }
- cout << endl;
- return false; }
- }else if (command == "parsimony") {
- //is it valid
- if ((parsimony.find(parameter)) != (parsimony.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = parsimony.begin(); it != parsimony.end(); it++) {
- cout << it->first << ", ";
- }
- cout << endl;
- return false; }
- }else if (command == "collect.single") {
- //is it valid
- if ((collectsingle.find(parameter)) != (collectsingle.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = collectsingle.begin(); it != collectsingle.end(); it++) {
- cout << it->first << ", ";
+ 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;
}
- cout << endl;
- return false; }
- }else if (command == "collect.shared") {
- //is it valid
- if ((collectshared.find(parameter)) != (collectshared.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = collectshared.begin(); it != collectshared.end(); it++) {
- cout << it->first << ", ";
+ }
+
+ /************************************************************************************************************/
+
+
+
+ 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;
}
- cout << endl;
- return false; }
- }else if (command == "rarefaction.single") {
- //is it valid
- if ((rarefactsingle.find(parameter)) != (rarefactsingle.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = rarefactsingle.begin(); it != rarefactsingle.end(); it++) {
- cout << it->first << ", ";
+ else if(a == piSentinel && b != piSentinel) {
+ if(e == 0)
+ valid = b0;
+ else
+ valid = b1;
}
- cout << endl;
- return false; }
- }else if (command == "rarefaction.shared") {
- //is it valid
- if ((rarefactshared.find(parameter)) != (rarefactshared.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = rarefactshared.begin(); it != rarefactshared.end(); it++) {
- cout << it->first << ", ";
+ 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);
}
- cout << endl;
- return false; }
- }else if (command == "summary.single") {
- //is it valid
- if ((summarysingle.find(parameter)) != (summarysingle.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = summarysingle.begin(); it != summarysingle.end(); it++) {
- cout << it->first << ", ";
+ }
+ 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");
+ }
}
- cout << endl;
- return false; }
- }else if (command == "summary.shared") {
- //is it valid
- if ((summaryshared.find(parameter)) != (summaryshared.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = summaryshared.begin(); it != summaryshared.end(); it++) {
- cout << it->first << ", ";
+ return false;
+ }
+ }
+ return true;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ValidParameters", "isValidParameters");
+ exit(1);
+ }
+}
+/*******************************************************/
+
+/******************************************************/
+
+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;
+ }
}
- cout << endl;
- return false; }
- }else if (command == "unifrac.weighted") {
- //is it valid
- if ((unifracweighted.find(parameter)) != (unifracweighted.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = unifracweighted.begin(); it != unifracweighted.end(); it++) {
- cout << it->first << ", ";
+
+ //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();
+ }
}
- cout << endl;
- return false; }
- }else if (command == "unifrac.unweighted") {
- //is it valid
- if ((unifracunweighted.find(parameter)) != (unifracunweighted.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = unifracunweighted.begin(); it != unifracunweighted.end(); it++) {
- cout << it->first << ", ";
+
+
+
+ #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;
}
- cout << endl;
- return false; }
- }else if (command == "libshuff") {
- //is it valid
- if ((libshuff.find(parameter)) != (libshuff.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = libshuff.begin(); it != libshuff.end(); it++) {
- cout << it->first << ", ";
+
+ #endif
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + container[parameter]); m->mothurOutEndLine();
+ return "not open";
}
- cout << endl;
- return false; }
- }else if (command == "heatmap") {
- //is it valid
- if ((heatmap.find(parameter)) != (heatmap.end())) {
- return true;
- }else {
- cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
- for (it = heatmap.begin(); it != heatmap.end(); it++) {
- cout << it->first << ", ";
+
+ //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"; }
}
- cout << endl;
- return false; }
-
- //not a valid paramter
- }else if (command == "help") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
- }else if (command == "quit") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
- }else if (command == "get.group") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
- }else if (command == "get.label") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
- }else if (command == "get.line") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl; }
-
- return false;
+
+ //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) {
- 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);
}
}
/***********************************************************************/
-void ValidParameters::initialReaddist() {
- readdist["phylip"] = "phylip";
- readdist["column"] = "column";
- readdist["name"] = "name";
- readdist["group"] = "group";
- readdist["cutoff"] = "cutoff";
- readdist["precision"] = "precision";
-}
-/***********************************************************************/
-void ValidParameters::initialReadotu() {
- readotu["list"] = "list";
- readotu["rabund"] = "rabund";
- readotu["sabund"] = "sabund";
- readotu["shared"] = "shared";
- readotu["group"] = "group";
- readotu["order"] = "order";
- readotu["label"] = "label";
- readotu["line"] = "line";
-}
-/***********************************************************************/
-void ValidParameters::initialReadtree() {
- readtree["group"] = "group";
- readtree["tree"] = "tree";
-}
-/***********************************************************************/
-void ValidParameters::initialCluster() {
- cluster["cutoff"] = "cutoff";
- cluster["method"] = "method";
- cluster["precision"] = "precision";
-}
-/***********************************************************************/
-void ValidParameters::initialDeconvolute() {
- deconvolute["fasta"] = "fasta";
-}
-/***********************************************************************/
-void ValidParameters::initialParsimony() {
- parsimony["iters"] = "iters";
- parsimony["random"] = "random";
- parsimony["groups"] = "groups";
-}
-/***********************************************************************/
-void ValidParameters::initialCollectsingle() {
- collectsingle["label"] = "label";
- collectsingle["line"] = "line";
- collectsingle["freq"] = "freq";
- collectsingle["calc"] = "calc";
-}
-/***********************************************************************/
-void ValidParameters::initialCollectshared() {
- collectshared["label"] = "label";
- collectshared["line"] = "line";
- collectshared["freq"] = "freq";
- collectshared["calc"] = "calc";
- collectshared["jumble"] = "jumble";
-}
-/***********************************************************************/
-void ValidParameters::initialRarefactsingle() {
- rarefactsingle["label"] = "label";
- rarefactsingle["line"] = "line";
- rarefactsingle["freq"] = "freq";
- rarefactsingle["calc"] = "calc";
- rarefactsingle["iters"] = "iters";
-}
-/***********************************************************************/
-void ValidParameters::initialRarefactshared() {
- rarefactshared["label"] = "label";
- rarefactshared["line"] = "line";
- rarefactshared["jumble"] = "jumble";
- rarefactshared["calc"] = "calc";
- rarefactshared["iters"] = "iters";
-}
-/***********************************************************************/
-void ValidParameters::initialSummarysingle() {
- summarysingle["label"] = "label";
- summarysingle["line"] = "line";
- summarysingle["calc"] = "calc";
-}
-/***********************************************************************/
-void ValidParameters::initialSummaryshared() {
- summaryshared["label"] = "label";
- summaryshared["line"] = "line";
- summaryshared["calc"] = "calc";
- summaryshared["jumble"] = "jumble";
-}
-/***********************************************************************/
-void ValidParameters::initialUnifracweighted() {
- unifracweighted["iters"] = "iters";
- unifracweighted["groups"] = "groups";
-}
/***********************************************************************/
-void ValidParameters::initialUnifracunweighted() {
- unifracunweighted["iters"] = "iters";
- unifracunweighted["groups"] = "groups";
+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);
+ }
}
+
/***********************************************************************/
-void ValidParameters::initialLibshuff() {
- libshuff["cutoff"] = "cutoff";
- libshuff["iters"] = "iters";
- libshuff["groups"] = "groups";
- libshuff["step"] = "step";
- libshuff["form"] = "form";
-}
+
/***********************************************************************/
-void ValidParameters::initialHeatmap() {
- heatmap["label"] = "label";
- heatmap["line"] = "line";
+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);
+ }
}
-/***********************************************************************/
projects / mothur.git / blobdiff