ValidParameters::ValidParameters() {
try {
- initCommandParameters();
+ 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, 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) {
}
}
if(!valid) {
- cout << "'" << parameter << "' is not a valid parameter for the " << command << " command.\n";
- cout << "The valid paramters for the " << command << " command 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++)
- cout << cParams.at(i) << ", ";
- cout << "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) {
- cout << "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 {
- cout << "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 {
- cout << "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 {
- cout << "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) {
- cout << "The '" << parameter << "' parameter needs to be ";
+ m->mothurOut("The '" + parameter + "' parameter needs to be ");
if(c == 1)
- cout << "either '" << a << "' or '" << b << "'.\n";
+ m->mothurOut("either '" + toString(a) + "' or '" + toString(b) + "'.\n");
else {
if(a != piSentinel) {
- cout << ">";
+ m->mothurOut(">");
if(d != 0)
- cout << "=";
- cout << " '" << a << "'";
+ m->mothurOut("=");
+ m->mothurOut(" '" + toString(a) + "'");
}
if(b == piSentinel)
- cout << "'.\n";
+ m->mothurOut( "'.\n");
else if(a != piSentinel)
- cout << " and ";
+ m->mothurOut(" and ");
if(b != piSentinel) {
- cout << "<";
+ m->mothurOut("<");
if(e != 0)
- cout << "=";
- cout << " '" << b << "'.\n";
+ 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","column", "name","cutoff","precision", "group"};
- commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
-
- string readotuArray[] = {"list","order","shared", "line", "label","group","sabund", "rabund"};
- commandParameters["read.otu"] = addParameters(readotuArray, sizeof(readotuArray)/sizeof(string));
-
- string readtreeArray[] = {"tree","group"};
- commandParameters["read.tree"] = addParameters(readtreeArray, sizeof(readtreeArray)/sizeof(string));
-
- string clusterArray[] = {"cutoff","precision","method"};
- commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string));
-
- string deconvoluteArray[] = {"fasta"};
- commandParameters["unique.seqs"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
-
- string collectsingleArray[] = {"freq","line","label","calc","abund","size"};
- commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
-
- string collectsharedArray[] = {"freq","line","label","calc","groups"};
- commandParameters["collect.shared"] = addParameters(collectsharedArray, sizeof(collectsharedArray)/sizeof(string));
-
- string getgroupArray[] = {};
- commandParameters["get.group"] = addParameters(getgroupArray, sizeof(getgroupArray)/sizeof(string));
-
- string getlabelArray[] = {};
- commandParameters["get.label"] = addParameters(getlabelArray, sizeof(getlabelArray)/sizeof(string));
-
- string getlineArray[] = {};
- commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string));
-
- string getsabundArray[] = {"line", "label"};
- commandParameters["get.sabund"] = addParameters(getsabundArray, sizeof(getsabundArray)/sizeof(string));
-
- string getrabundArray[] = {"line", "label"};
- commandParameters["get.rabund"] = addParameters(getrabundArray, sizeof(getrabundArray)/sizeof(string));
-
- string rarefactionsingleArray[] = {"iters","freq","line","label","calc","abund"};
- commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
+/******************************************************/
- string rarefactionsharedArray[] = {"iters","jumble","line","label","calc","groups"};
- commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
-
- string libshuffArray[] = {"iters","groups","step","form","cutoff"};
- commandParameters["libshuff"] = addParameters(libshuffArray, sizeof(libshuffArray)/sizeof(string));
+string ValidParameters::validFile(map<string, string>& container, string parameter, bool isFile) {
+ try {
+ int ableToOpen;
- string summarysingleArray[] = {"line","label","calc","abund","size"};
- commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
-
- string summarysharedArray[] = {"line","label","calc","groups"};
- commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
-
- string parsimonyArray[] = {"random","groups","iters"};
- commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string));
-
- string unifracWeightedArray[] = {"groups","iters"};
- commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string));
-
- string unifracUnweightedArray[] = {"groups","iters"};
- commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
-
- string heatmapArray[] = {"groups","line","label","sorted","scale"};
- commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
+ map<string, string>::iterator it;
- string filterseqsArray[] = {"fasta", "trump", "soft", "hard", "vertical"};
- commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
+ it = container.find(parameter);
+ if(it != container.end()){ //no parameter given
- string summaryseqsArray[] = {"fasta"};
- commandParameters["summary.seqs"] = addParameters(summaryseqsArray, sizeof(summaryseqsArray)/sizeof(string));
-
- string screenseqsArray[] = {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength", "name", "group"};
- commandParameters["screen.seqs"] = addParameters(screenseqsArray, sizeof(screenseqsArray)/sizeof(string));
-
- string reverseseqsArray[] = {"fasta"};
- commandParameters["reverse.seqs"] = addParameters(reverseseqsArray, sizeof(reverseseqsArray)/sizeof(string));
-
- string trimseqsArray[] = {"fasta", "flip", "oligos", "forward", "reverse", "barcode"};
- commandParameters["trim.seqs"] = addParameters(trimseqsArray, sizeof(trimseqsArray)/sizeof(string));
+ 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();
+ }
+ }
+
+
- string vennArray[] = {"groups","line","label","calc"};
- commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string));
-
- string binseqsArray[] = {"fasta","line","label","name", "group"};
- commandParameters["bin.seqs"] = addParameters(binseqsArray, sizeof(binseqsArray)/sizeof(string));
-
- string distsharedArray[] = {"line","label","calc","groups"};
- commandParameters["dist.shared"] = addParameters(distsharedArray, sizeof(distsharedArray)/sizeof(string));
-
- string getOTURepArray[] = {"fasta","list","line","label","name", "group"};
- commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
-
- string treeGroupsArray[] = {"line","label","calc","groups", "phylip", "column", "name"};
- commandParameters["tree.shared"] = addParameters(treeGroupsArray, sizeof(treeGroupsArray)/sizeof(string));
-
- string bootstrapArray[] = {"line","label","calc","groups","iters"};
- commandParameters["bootstrap.shared"] = addParameters(bootstrapArray, sizeof(bootstrapArray)/sizeof(string));
-
- string concensusArray[] = {};
- commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
-
- string distanceArray[] = {"fasta", "calc", "countends", "cutoff", "processors"};
- commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
-
- string AlignArray[] = {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
- commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
+ #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"; }
- 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 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 jumbleArray[] = {">","0", "<","1", "only"};
- parameterRanges["jumble"] = addParameters(jumbleArray, 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) {
- 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