X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.cpp;h=b76542aec7907c0cc3ef80b896c5308985c1c73d;hb=8f92612d5a69f5245e63a20657e7d93519c0769e;hp=7d63e9b5a53b77afcb277963f31418ac8bdfccd9;hpb=a043f0e4bff221df24e9e95bc09f59d87de5b7b8;p=mothur.git diff --git a/errorchecking.cpp b/errorchecking.cpp index 7d63e9b..b76542a 100644 --- a/errorchecking.cpp +++ b/errorchecking.cpp @@ -17,7 +17,12 @@ ErrorCheck::ErrorCheck() { globaldata = GlobalData::getInstance(); validCommand = new ValidCommands(); validParameter = new ValidParameters(); - validCalculator = new ValidCalculators(); +} +/*******************************************************/ + +/******************************************************/ + +void ErrorCheck::refresh() { columnfile = globaldata->getColumnFile(); phylipfile = globaldata->getPhylipFile(); listfile = globaldata->getListFile(); @@ -31,8 +36,132 @@ ErrorCheck::ErrorCheck() { cutoff = globaldata->getCutOff(); format = globaldata->getFormat(); method = globaldata->getMethod(); + randomtree = globaldata->getRandomTree(); + sharedfile = globaldata->getSharedFile(); + + + +/* string p[] = { + "phylip", //0 + "column", //1 + "list", //2 + "rabund", //3 + "sabund", //4 + "name", //5 + "order", //6 + "group", //7 + "fasta", //8 + "treefile", //9 + "cutoff", //10 + "precision", //11 + "iters", //12 + "jumble", //13 + "freq", //14 + "method", //15 + "fileroot", //16 + "line", //17 + "label", //18 + "single", //19 + "rarefaction", //20 + "shared", //21 + "summary", //22 + "sharedrarefaction", //23 + "sharedsummary", //24 + "groups", //25 + "abund", //26 + }; + + string c0[] = {p[0],p[5],p[10],p[11]}; + string c1[] = {p[2],p[6],p[7]}; + string c2[] = {p[10],p[11],p[15]}; + string c3[] = {p[8]}; + string c4[] = {p[14],p[17],p[18],p[19],p[26]}; + string c5[] = {p[13],p[14],p[17],p[18],p[21],p[25]}; + string c6[] = {""}; + string c7[] = {""}; + string c8[] = {""}; + string c9[] = {p[12],p[14],p[17],p[18],p[20],p[26]}; + string c10[] = {p[12],p[13],p[17],p[18],p[23]}; + string c11[] = {p[17],p[18],p[22],p[26]}; + string c12[] = {p[13],p[17],p[18],p[24]}; + string c13[] = {""}; + + vector v0 (c0, c0+sizeof(c0)/sizeof(string)); + vector v1 (c1, c1+sizeof(c1)/sizeof(string)); + vector v2 (c2, c2+sizeof(c2)/sizeof(string)); + vector v3 (c3, c3+sizeof(c3)/sizeof(string)); + vector v4 (c4, c4+sizeof(c4)/sizeof(string)); + vector v5 (c5, c5+sizeof(c5)/sizeof(string)); + vector v6 (c6, c6+sizeof(c6)/sizeof(string)); + vector v7 (c7, c7+sizeof(c7)/sizeof(string)); + vector v8 (c8, c8+sizeof(c8)/sizeof(string)); + vector v9 (c9, c9+sizeof(c9)/sizeof(string)); + vector v10 (c10, c10+sizeof(c10)/sizeof(string)); + vector v11 (c11, c11+sizeof(c11)/sizeof(string)); + vector v12 (c12, c12+sizeof(c12)/sizeof(string)); + vector v13 (c13, c13+sizeof(c13)/sizeof(string)); + + vector > allCommands; + allCommands.push_back(v0); + allCommands.push_back(v1); + allCommands.push_back(v2); + allCommands.push_back(v3); + allCommands.push_back(v4); + allCommands.push_back(v5); + allCommands.push_back(v6); + allCommands.push_back(v7); + allCommands.push_back(v8); + allCommands.push_back(v9); + allCommands.push_back(v10); + allCommands.push_back(v11); + allCommands.push_back(v12); + allCommands.push_back(v13); + + string commands[] = { + "read.dist", //0 + "read.otu", //1 + "cluster", //2 + "deconvolute", //3 + "collect.single", //4 + "collect.shared", //5 + "get.group", //6 + "get.label", //7 + "get.line", //8 + "rarefaction.single", //9 + "rarefaction.shared", //10 + "summary.single", //11 + "summary.shared", //12 + "quit" //13 + }; + + for(int i = 0; i < allCommands.size(); i++) + commandParameters[commands[i]] = allCommands.at(i); + + //{Lowerbound(piSent if no lowerbound), Upperbound(piSent if no upperbound), 1 if only the first 2 values, 0 if greater than, 0 if less than}; + piSent = 3.14159; + double ip0[] = {10, piSent, 0, 1, 0}; + double ip1[] = {10, piSent, 0, 1, 0}; + double ip2[] = {0, 1, 1, 0, 0}; + double ip3[] = {1, piSent, 0, 0, 0}; + double ip4[] = {1, piSent, 0, 1, 0}; + double ip5[] = {5, piSent, 0, 1, 0}; + + vector ipv0 (ip0, ip0+sizeof(ip0)/sizeof(double)); + vector ipv1 (ip1, ip1+sizeof(ip1)/sizeof(double)); + vector ipv2 (ip2, ip2+sizeof(ip2)/sizeof(double)); + vector ipv3 (ip3, ip3+sizeof(ip3)/sizeof(double)); + vector ipv4 (ip4, ip4+sizeof(ip4)/sizeof(double)); + vector ipv5 (ip5, ip5+sizeof(ip5)/sizeof(double)); + intParams[p[11]] = ipv0; + intParams[p[12]] = ipv1; + intParams[p[13]] = ipv2; + intParams[p[14]] = ipv3; + intParams[p[17]] = ipv4; + intParams[p[26]] = ipv5; */ + } + /*******************************************************/ /******************************************************/ @@ -46,7 +175,10 @@ ErrorCheck::~ErrorCheck() {} bool ErrorCheck::checkInput(string input) { errorFree = true; clear(); - + + //refresh variable + refresh(); + //get command name and parameters int openParen = input.find_first_of('('); int closeParen = input.find_last_of(')'); @@ -63,15 +195,57 @@ bool ErrorCheck::checkInput(string input) { if (validCommand->isValidCommand(commandName) != true) { return false; } string parameter, value; + //reads in parameters and values if((optionText != "") && (commandName != "help")){ while((optionText.find_first_of(',') != -1) && (errorFree)) { //while there are parameters - globaldata->splitAtComma(value, optionText); - globaldata->splitAtEquals(parameter, value); + splitAtComma(value, optionText); + splitAtEquals(parameter, value); //is it a valid parameter if (validParameter->isValidParameter(parameter) != true) { return false; } - + //if(!validCommandParameter(parameter,commandName)) { + // cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n"; + // return false; + //} + //if(!validParameterValue(value, parameter)) { + // if(parameter.compare("precision") == 0) + // cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n"; + // else { + /* vector bounds = intParams[parameter]; + double a = bounds.at(0); + double b = bounds.at(1); + double c = bounds.at(2); + double d = bounds.at(3); + double e = bounds.at(4); + cout << "The '" << parameter << "' parameter needs to be "; + if(c == 1) + cout << "either '" << a << "' or '" << b << "'.\n"; + else + { + if(a != piSent) + { + cout << ">"; + if(d != 0) + cout << "="; + cout << " '" << a << "'"; + } + if(b == piSent) + cout << ".\n"; + else if(a != piSent) + cout << " and "; + if(b != piSent) + { + cout << "<"; + if(e != 0) + cout << "="; + cout << " '" << b << ".\n"; + } + } + } + return false; + } */ + if (parameter == "phylip" ) { phylipfile = value; } if (parameter == "column" ) { columnfile = value; } if (parameter == "list" ) { listfile = value; } @@ -80,8 +254,9 @@ bool ErrorCheck::checkInput(string input) { if (parameter == "name" ) { namefile = value; } if (parameter == "order" ) { orderfile = value; } if (parameter == "fasta" ) { fastafile = value; } - if (parameter == "treefile" ) { treefile = value; } + if (parameter == "tree" ) { treefile = value; } if (parameter == "group" ) { groupfile = value; } + if (parameter == "shared" ) { sharedfile = value; } if (parameter == "cutoff" ) { cutoff = value; } if (parameter == "precision" ) { precision = value; } if (parameter == "iters" ) { iters = value; } @@ -91,56 +266,57 @@ bool ErrorCheck::checkInput(string input) { if (parameter == "fileroot" ) { fileroot = value; } if (parameter == "line" ) { line = value; } if (parameter == "label" ) { label = value; } - - if (parameter == "single") {//stores estimators in a vector - singleEsimators.clear(); //clears out old values - globaldata->splitAtDash(value, singleEsimators); - for (int i = 0; i < singleEsimators.size(); i++) { //loop through estimators - //is it a valid calculator - if (validCalculator->isValidCalculator(parameter, singleEsimators[i]) != true) { return false; } - } - } - if (parameter == "rarefaction") {//stores estimators in a vector - rareEstimators.clear(); //clears out old values - globaldata->splitAtDash(value, rareEstimators); - for (int i = 0; i < rareEstimators.size(); i++) { //loop through estimators - //is it a valid calculator - if (validCalculator->isValidCalculator(parameter, rareEstimators[i]) != true) { return false; } - } - } - if (parameter == "shared") {//stores estimators in a vector - sharedEstimators.clear(); //clears out old values - globaldata->splitAtDash(value, sharedEstimators); - for (int i = 0; i < sharedEstimators.size(); i++) { //loop through estimators - //is it a valid calculator - if (validCalculator->isValidCalculator(parameter, sharedEstimators[i]) != true) { return false; } - } - } - if (parameter == "summary") { //stores summaries to be used in a vector - summaryEstimators.clear(); //clears out old values - globaldata->splitAtDash(value, summaryEstimators); - for (int i = 0; i < summaryEstimators.size(); i++) { //loop through estimators - //is it a valid calculator - if (validCalculator->isValidCalculator(parameter, summaryEstimators[i]) != true) { return false; } - } - } - if (parameter == "sharedrarefaction") { //stores summaries to be used in a vector - sharedRareEstimators.clear(); //clears out old values - globaldata->splitAtDash(value, sharedRareEstimators); - for (int i = 0; i < sharedRareEstimators.size(); i++) { //loop through estimators - //is it a valid calculator - if (validCalculator->isValidCalculator(parameter, sharedRareEstimators[i]) != true) { return false; } - } - } + if (parameter == "abund" ) { abund = value; } + if (parameter == "random" ) { randomtree = value; } } //gets the last parameter and value if (errorFree) { //gets the last parameter and value value = optionText; - globaldata->splitAtEquals(parameter, value); + splitAtEquals(parameter, value); //is it a valid parameter if (validParameter->isValidParameter(parameter) != true) { return false; } - + // if(!validCommandParameter(parameter,commandName)) { + // cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n"; + // return false; + // } + /* if(!validParameterValue(value, parameter)) { + if(parameter.compare("precision") == 0) + cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n"; + else { + vector bounds = intParams[parameter]; + double a = bounds.at(0); + double b = bounds.at(1); + double c = bounds.at(2); + double d = bounds.at(3); + double e = bounds.at(4); + cout << "The '" << parameter << "' parameter needs to be "; + if(c == 1) + cout << "either '" << a << "' or '" << b << "'.\n"; + else + { + if(a != piSent) + { + cout << ">"; + if(d != 0) + cout << "="; + cout << " '" << a << "'"; + } + if(b == piSent) + cout << ".\n"; + else if(a != piSent) + cout << " and "; + if(b != piSent) + { + cout << "<"; + if(e != 0) + cout << "="; + cout << " '" << b << ".\n"; + } + } + } + return false; + }*/ if (parameter == "phylip" ) { phylipfile = value; } if (parameter == "column" ) { columnfile = value; } if (parameter == "list" ) { listfile = value; } @@ -149,8 +325,9 @@ bool ErrorCheck::checkInput(string input) { if (parameter == "name" ) { namefile = value; } if (parameter == "order" ) { orderfile = value; } if (parameter == "group" ) { groupfile = value; } + if (parameter == "shared" ) { sharedfile = value; } if (parameter == "fasta" ) { fastafile = value; } - if (parameter == "treefile" ) { treefile = value; } + if (parameter == "tree" ) { treefile = value; } if (parameter == "cutoff" ) { cutoff = value; } if (parameter == "precision" ) { precision = value; } if (parameter == "iters" ) { iters = value; } @@ -160,54 +337,13 @@ bool ErrorCheck::checkInput(string input) { if (parameter == "fileroot" ) { fileroot = value; } if (parameter == "line" ) { line = value; } if (parameter == "label" ) { label = value; } - - if (parameter == "single") {//stores estimators in a vector - singleEsimators.clear(); //clears out old values - globaldata->splitAtDash(value, singleEsimators); - for (int i = 0; i < singleEsimators.size(); i++) { //loop through estimators - //is it a valid calculator - if (validCalculator->isValidCalculator(parameter, singleEsimators[i]) != true) { return false; } - } - } - if (parameter == "rarefaction") {//stores estimators in a vector - rareEstimators.clear(); //clears out old values - globaldata->splitAtDash(value, rareEstimators); - for (int i = 0; i < rareEstimators.size(); i++) { //loop through estimators - //is it a valid calculator - if (validCalculator->isValidCalculator(parameter, rareEstimators[i]) != true) { return false; } - } - } - if (parameter == "shared") {//stores estimators in a vector - sharedEstimators.clear(); //clears out old values - globaldata->splitAtDash(value, sharedEstimators); - for (int i = 0; i < sharedEstimators.size(); i++) { //loop through estimators - //is it a valid calculator - if (validCalculator->isValidCalculator(parameter, sharedEstimators[i]) != true) { return false; } - } - } - if (parameter == "summary") { //stores summaries to be used in a vector - summaryEstimators.clear(); //clears out old values - globaldata->splitAtDash(value, summaryEstimators); - for (int i = 0; i < summaryEstimators.size(); i++) { //loop through estimators - //is it a valid calculator - if (validCalculator->isValidCalculator(parameter, summaryEstimators[i]) != true) { return false; } - } - } - if (parameter == "sharedrarefaction") { //stores summaries to be used in a vector - sharedRareEstimators.clear(); //clears out old values - globaldata->splitAtDash(value, sharedRareEstimators); - for (int i = 0; i < sharedRareEstimators.size(); i++) { //loop through estimators - //is it a valid calculator - if (validCalculator->isValidCalculator(parameter, sharedRareEstimators[i]) != true) { return false; } - } - } - + if (parameter == "random" ) { randomtree = value; } + if (parameter == "abund" ) { abund = value; } } } //make sure the user does not use both the line and label parameters if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; } - if (commandName == "read.dist") { validateReadFiles(); @@ -220,6 +356,9 @@ bool ErrorCheck::checkInput(string input) { validateReadFiles(); validateReadPhil(); } + }else if (commandName == "read.shared") { + //you want to do shared commands with just the shared file + validateReadFiles(); }else if (commandName == "read.tree") { validateTreeFiles(); //checks the treefile and groupfile parameters }else if (commandName == "deconvolute") { @@ -228,13 +367,32 @@ bool ErrorCheck::checkInput(string input) { } //are you trying to cluster before you have read something - if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) || - (commandName == "cluster") && (globaldata->getListVector() == NULL)) { + if (((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL)) || + ((commandName == "cluster") && (globaldata->getListVector() == NULL))) { cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl; errorFree = false; } + if (commandName == "parsimony") { + //are you trying to use parsimony without reading a tree or saying you want random distribution + if (randomtree == "") { + if (globaldata->gTree.size() == 0) { + cout << "You must read a treefile and a groupfile or set the randomtree parameter to the output filename you wish, before you may execute the parsimony command." << endl; return false; } + } + } + + if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) { + if (globaldata->gTree.size() == 0) {//no trees were read + cout << "You must execute the read.tree command, before you may execute the unifrac.weighted or unifrac.unweighted command." << endl; return false; } + } + //check for valid method + if(commandName == "get.group") { + if ((globaldata->getGroupFile() == "")) { cout << "You must read a group before you can use the get.group command." << endl; return false; } + } + if (commandName == "get.label" || commandName == "get.line") { + if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the get.label or get.line command." << endl; return false; } + } if (commandName == "cluster") { if ((method == "furthest") || (method == "nearest") || (method == "average")) { } else {cout << "Not a valid clustering method. Valid clustering algorithms are furthest, nearest or average." << endl; return false; } @@ -245,11 +403,12 @@ bool ErrorCheck::checkInput(string input) { } if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){ - if (globaldata->getListFile() == "") { cout << "You must read a list and a group before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; } - else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; } + if (globaldata->getSharedFile() == "") { + if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; } + else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; } + } } - - + return errorFree; } @@ -305,6 +464,12 @@ void ErrorCheck::validateReadFiles() { //unable to open if (ableToOpen == 1) { errorFree = false; } else { globaldata->inputFileName = fastafile; } + }else if (sharedfile != "") { + ableToOpen = openInputFile(sharedfile, filehandle); + filehandle.close(); + //unable to open + if (ableToOpen == 1) { errorFree = false; } + else { globaldata->inputFileName = sharedfile; } }else{ //no file given errorFree = false; } @@ -321,6 +486,113 @@ void ErrorCheck::validateReadFiles() { } /*******************************************************/ +/****************************************************** +//This function checks to see if the given paramter +//is a valid paramter for the given command. +bool ErrorCheck::validCommandParameter(string parameter, string commandName) { + try { + for(int i = 0; i < commandParameters[commandName].size(); i++) + if(parameter.compare(commandParameters[commandName][i]) == 0) + return true; + return false; + } + + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} +/*******************************************************/ + +/****************************************************** +//This function checks to see if the given paramter value +//is convertable into an int if that parameter requires it. +bool ErrorCheck::validParameterValue(string value, string parameter) { + try { + int pVal; + if(intParams.count(parameter) == 1) + { + vector bounds = intParams[parameter]; + bool valid = convertTest(value, pVal); + if(!valid) + return false; + if(parameter.compare("precision") == 0) + { + double logNum = log10((double)pVal); + double diff = (double)((int)logNum - logNum); + if(diff != 0) + return false; + } + double a = bounds.at(0); + double b = bounds.at(1); + double c = bounds.at(2); + double d = bounds.at(3); + double e = bounds.at(4); + bool a0 = pVal > a; + bool a1 = pVal >= a; + bool b0 = pVal < b; + bool b1 = pVal <= b; + + if(c != 1) + { + if(a == piSent && b == piSent) + return true; + if(a != piSent && b == piSent) + { + if(d == 0) + return a0; + else + return a1; + } + else if(a == piSent && b != piSent) + { + if(e == 0) + return b0; + else + return b1; + } + else + { + if(d == 0 && e == 0) + return (a0 && b0); + else if(d == 0 && e == 1) + return (a0 && b1); + else if(d == 1 && e == 0) + return (a1 && b0); + else + return (a1 && b1); + } + } + else + { + if(a == piSent && b == piSent) + return true; + if(a != piSent && b == piSent) + return (pVal == a); + else if(a == piSent && b != piSent) + return (pVal == b); + else + return (pVal == a || pVal == b); + } + } + return true; + } + + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the ErrorCheck class function validateReadFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} +/*******************************************************/ + /******************************************************/ //This function checks to make sure the user entered appropriate // format parameters on a distfile read @@ -490,6 +762,7 @@ void ErrorCheck::clear() { namefile = ""; groupfile = ""; orderfile = ""; + sharedfile = ""; line = ""; label = ""; method = "furthest";