X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.cpp;h=b76542aec7907c0cc3ef80b896c5308985c1c73d;hb=8f92612d5a69f5245e63a20657e7d93519c0769e;hp=1d60a4a35a8e7252e8f318a4997f91abdf102a51;hpb=16bea3130e36addc54e2116dfbcd02d706ebee45;p=mothur.git diff --git a/errorchecking.cpp b/errorchecking.cpp index 1d60a4a..b76542a 100644 --- a/errorchecking.cpp +++ b/errorchecking.cpp @@ -38,6 +38,128 @@ void ErrorCheck::refresh() { 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; */ + } /*******************************************************/ @@ -73,6 +195,7 @@ 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 @@ -81,7 +204,48 @@ bool ErrorCheck::checkInput(string input) { //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; } @@ -102,8 +266,8 @@ bool ErrorCheck::checkInput(string input) { if (parameter == "fileroot" ) { fileroot = value; } if (parameter == "line" ) { line = value; } if (parameter == "label" ) { label = value; } + if (parameter == "abund" ) { abund = value; } if (parameter == "random" ) { randomtree = value; } - } //gets the last parameter and value @@ -112,7 +276,47 @@ bool ErrorCheck::checkInput(string input) { 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; } @@ -134,7 +338,7 @@ bool ErrorCheck::checkInput(string input) { if (parameter == "line" ) { line = value; } if (parameter == "label" ) { label = value; } if (parameter == "random" ) { randomtree = value; } - + if (parameter == "abund" ) { abund = value; } } } @@ -163,8 +367,8 @@ 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; } @@ -183,6 +387,12 @@ bool ErrorCheck::checkInput(string input) { } //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; } @@ -198,7 +408,7 @@ bool ErrorCheck::checkInput(string input) { 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; } @@ -276,6 +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