X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=validparameter.cpp;h=7d1af2551c7a6717c1d3ea807af0e56de0fc218e;hp=61fd0445e81f9ae277f3c54f9c69ce313646e66d;hb=615301e57c25e241356a9c2380648d117709458d;hpb=81ff02ef4064fe4dec986ea3110c1cb8e1285fe6 diff --git a/validparameter.cpp b/validparameter.cpp index 61fd044..7d1af25 100644 --- a/validparameter.cpp +++ b/validparameter.cpp @@ -13,30 +13,27 @@ 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); - } + } } /***********************************************************************/ @@ -44,298 +41,342 @@ ValidParameters::ValidParameters() { ValidParameters::~ValidParameters() {} /***********************************************************************/ -bool ValidParameters::isValidParameter(string parameter, string command) { +bool ValidParameters::isValidParameter(string parameter, vector cParams, string value) { try { + bool valid = false; + //vector 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 << ", "; + int pVal; + double piSentinel = 3.14159; + vector range = parameterRanges[parameter]; + + vector 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.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 << ", "; + } + + /************************************************************************************************************/ + + + + 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 == "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 << ", "; + else if(a == piSentinel && b != piSentinel) { + if(e == 0) + valid = b0; + else + valid = b1; } - 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(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 == "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(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.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 << ", "; + return false; + } + } + return true; + } + catch(exception& e) { + m->errorOut(e, "ValidParameters", "isValidParameters"); + exit(1); + } +} +/*******************************************************/ + +/******************************************************/ + +string ValidParameters::validFile(map& container, string parameter, bool isFile) { + try { + int ableToOpen; + + map::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 == "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 << ", "; + + //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.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 << ", "; + + + + #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 == "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 << ", "; + + #endif + + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + container[parameter]); m->mothurOutEndLine(); + return "not open"; } - 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 << ", "; + + //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::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::initialUnifracunweighted() { - unifracunweighted["iters"] = "iters"; - unifracunweighted["groups"] = "groups"; -} + /***********************************************************************/ -void ValidParameters::initialLibshuff() { - libshuff["cutoff"] = "cutoff"; - libshuff["iters"] = "iters"; - libshuff["groups"] = "groups"; - libshuff["step"] = "step"; - libshuff["form"] = "form"; +vector ValidParameters::addParameters(string parameters[], int size) { + try { + vector pVector (parameters, parameters+size); + return pVector; + } + catch(exception& e) { + m->errorOut(e, "ValidParameters", "addParameters"); + exit(1); + } } -/***********************************************************************/ +