X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=da81879f48fff6fbe87ac67ba950afd84c03a69e;hb=f20505bcd9f07e0b5f967be0e8d414076d9a5678;hp=f09ea358b61c3e30b6880937a9f606969bfca63b;hpb=fd282e6b4be2560f5b1bd154a9e8d24b798eefaf;p=mothur.git diff --git a/globaldata.cpp b/globaldata.cpp index f09ea35..da81879 100644 --- a/globaldata.cpp +++ b/globaldata.cpp @@ -1,19 +1,9 @@ -#include -#include -#include -#include -#include -#include - -using namespace std; - #include "globaldata.hpp" #include "sparsematrix.hpp" +#include "tree.h" #include "rabundvector.hpp" #include "sabundvector.hpp" #include "listvector.hpp" -#include -#include /*******************************************************/ @@ -26,62 +16,22 @@ GlobalData* GlobalData::getInstance() { } /*******************************************************/ -/******************************************************/ - -ListVector* GlobalData::getListVector() { return gListVector; } -/*******************************************************/ - -/******************************************************/ -void GlobalData::setListVector(ListVector* lv){ - try { - if(gListVector != NULL){ delete gListVector; } - gListVector = new ListVector(*lv); - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the GlobalData class function setListVector. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} - -/*******************************************************/ - -/******************************************************/ - -SparseMatrix* GlobalData::getSparseMatrix() { return gSparseMatrix; } -/*******************************************************/ - -/******************************************************/ -void GlobalData::setSparseMatrix(SparseMatrix* sm){ - try{ - if(gSparseMatrix != NULL){ delete gSparseMatrix; } - gSparseMatrix = new SparseMatrix(*sm); - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the GlobalData class function setSparseMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - -} -/*******************************************************/ - /******************************************************/ //This function parses through the option string of the command to remove its parameters void GlobalData::parseGlobalData(string commandString, string optionText){ try { - allLines = 1; commandName = commandString; //save command name to be used by other classes + //set all non filename paramters to default + reset(); + //clears out data from previous read - if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.list")) { + if ((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) { clear(); + gGroupmap = NULL; + gTree.clear(); + labels.clear(); lines.clear(); groups.clear(); + allLines = 1; } //saves help request @@ -89,6 +39,11 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ helpRequest = optionText; } + if (commandName == "libshuff") { + iters = "10000"; + cutoff = "1.0"; + } + string key, value; //reads in parameters and values if((optionText != "") && (commandName != "help")){ @@ -96,15 +51,17 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ splitAtComma(value, optionText); splitAtEquals(key, value); - if (key == "phylipfile" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; } - if (key == "columnfile" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; } - if (key == "listfile" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; } - if (key == "rabundfile" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; } - if (key == "sabundfile" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; } - if (key == "fastafile" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; } - if (key == "namefile" ) { namefile = value; } - if (key == "orderfile" ) { orderfile = value; } - if (key == "groupfile" ) { groupfile = value; } + if (key == "phylip" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; } + if (key == "column" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; } + if (key == "list" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; } + if (key == "rabund" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; } + if (key == "sabund" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; } + if (key == "fasta" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; } + if (key == "tree" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; } + if (key == "shared" ) { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile"; } + if (key == "name" ) { namefile = value; } + if (key == "order" ) { orderfile = value; } + if (key == "group" ) { groupfile = value; } if (key == "cutoff" ) { cutoff = value; } if (key == "precision" ) { precision = value; } if (key == "iters" ) { iters = value; } @@ -112,63 +69,54 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ if (key == "freq" ) { freq = value; } if (key == "method" ) { method = value; } if (key == "fileroot" ) { fileroot = value; } + if (key == "abund" ) { abund = value; } + if (key == "random" ) { randomtree = value; } + if (key == "calc") { calc = value; } + if (key == "step") { step = value; } + if (key == "form") { form = value; } + if (key == "sorted") { sorted = value; } - if (key == "single") {//stores estimators in a vector - singleEstimators.clear(); //clears out old values - if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; } - splitAtDash(value, singleEstimators); - } - if (key == "rarefaction") {//stores estimators in a vector - rareEstimators.clear(); //clears out old values - if (value == "default") { value = "rarefraction"; } - splitAtDash(value, rareEstimators); - } - if (key == "shared") {//stores estimators in a vector - sharedEstimators.clear(); //clears out old values - if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; } - splitAtDash(value, sharedEstimators); - } - if (key == "summary") { //stores summaries to be used in a vector - summaryEstimators.clear(); - if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; } - splitAtDash(value, summaryEstimators); - } - if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector - sharedSummaryEstimators.clear(); - if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; } - splitAtDash(value, sharedSummaryEstimators); - } - if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector - sharedRareEstimators.clear(); - if (value == "default") { value = "sharedobserved"; } - splitAtDash(value, sharedRareEstimators); - } - if (key == "line") {//stores lines to be used in a vector + + + if (key == "line") {//stores lines to be used in a set lines.clear(); + labels.clear(); line = value; + label = ""; splitAtDash(value, lines); allLines = 0; } - if (key == "label") {//stores lines to be used in a vector + if (key == "label") {//stores labels to be used in a set labels.clear(); + lines.clear(); label = value; + line = ""; splitAtDash(value, labels); allLines = 0; } + + if (key == "groups") {//stores groups to be used in a vector + Groups.clear(); + groups = value; + splitAtDash(value, Groups); + } + } //saves the last parameter value = optionText; splitAtEquals(key, value); - if (key == "phylipfile" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; } - if (key == "columnfile" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; } - if (key == "listfile" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; } - if (key == "rabundfile" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; } - if (key == "sabundfile" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; } - if (key == "fastafile" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; } - if (key == "namefile" ) { namefile = value; } - if (key == "orderfile" ) { orderfile = value; } - if (key == "groupfile" ) { groupfile = value; } + if (key == "phylip" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; } + if (key == "column" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; } + if (key == "list" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; } + if (key == "rabund" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; } + if (key == "sabund" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; } + if (key == "fasta" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; } + if (key == "tree" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; } + if (key == "shared" ) { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile"; } + if (key == "name" ) { namefile = value; } + if (key == "order" ) { orderfile = value; } + if (key == "group" ) { groupfile = value; } if (key == "cutoff" ) { cutoff = value; } if (key == "precision" ) { precision = value; } if (key == "iters" ) { iters = value; } @@ -176,76 +124,87 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ if (key == "freq" ) { freq = value; } if (key == "method" ) { method = value; } if (key == "fileroot" ) { fileroot = value; } + if (key == "abund" ) { abund = value; } + if (key == "random" ) { randomtree = value; } + if (key == "calc") { calc = value; } + if (key == "step") { step = value; } + if (key == "form") { form = value; } + if (key == "sorted") { sorted = value; } - if (key == "single") {//stores estimators in a vector - singleEstimators.clear(); //clears out old values - if (value == "default") { value = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; } - splitAtDash(value, singleEstimators); - } - if (key == "rarefaction") {//stores estimators in a vector - rareEstimators.clear(); //clears out old values - if (value == "default") { value = "rarefraction"; } - splitAtDash(value, rareEstimators); - } - if (key == "shared") {//stores estimators in a vector - sharedEstimators.clear(); //clears out old values - if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; } - splitAtDash(value, sharedEstimators); - } - if (key == "summary") { //stores summaries to be used in a vector - summaryEstimators.clear(); - if (value == "default") { value = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; } - splitAtDash(value, summaryEstimators); - } - if (key == "sharedsummary") { //stores sharedSummaries to be used in a vector - sharedSummaryEstimators.clear(); - if (value == "default") { value = "sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; } - splitAtDash(value, sharedSummaryEstimators); - } - if (key == "sharedrarefaction") { //stores sharedrarefaction to be used in a vector - sharedRareEstimators.clear(); - if (value == "default") { value = "sharedobserved"; } - splitAtDash(value, sharedRareEstimators); - } - if (key == "line") {//stores lines to be used in a vector lines.clear(); + labels.clear(); line = value; - splitAtDash(value, lines); - allLines = 0; + label = ""; + if (line != "all") { splitAtDash(value, lines); allLines = 0; } + else { allLines = 1; } } if (key == "label") {//stores lines to be used in a vector labels.clear(); + lines.clear(); label = value; - splitAtDash(value, labels); - allLines = 0; + line = ""; + if (label != "all") { splitAtDash(value, labels); allLines = 0; } + else { allLines = 1; } + } + + if (key == "groups") {//stores groups to be used in a vector + Groups.clear(); + groups = value; + splitAtDash(value, Groups); } } //set format for shared if ((listfile != "") && (groupfile != "")) { format = "shared"; } + if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; } - //input defaults - if (commandString == "collect.single") { - if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); } + //input defaults for calculators + if (commandName == "collect.single") { + if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-qstat-logsd-bergerparker-bstick"; } + Estimators.clear(); + splitAtDash(calc, Estimators); } - if (commandString == "rarefaction.single") { - if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators); } + if (commandName == "rarefaction.single") { + if ((calc == "default") || (calc == "")) { calc = "sobs"; } + Estimators.clear(); + splitAtDash(calc, Estimators); } - if (commandString == "collect.shared") { - if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); } + if (commandName == "collect.shared") { + if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; } + Estimators.clear(); + splitAtDash(calc, Estimators); } - if (commandString == "summary.single") { - if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); } + if (commandName == "summary.single") { + if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-logsd-qstat-bergerparker-bstick"; } + Estimators.clear(); + splitAtDash(calc, Estimators); } - if (commandString == "summary.shared") { - if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); } + if (commandName == "summary.shared") { + if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; } + Estimators.clear(); + splitAtDash(calc, Estimators); } - if (commandString == "rarefaction.shared") { - if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); } + if (commandName == "rarefaction.shared") { + if ((calc == "default") || (calc == "")) { calc = "sharedobserved"; } + Estimators.clear(); + splitAtDash(calc, Estimators); + } + if (commandName == "venn") { + if ((calc == "default") || (calc == "")) { + if (format == "list") { calc = "sobs"; } + else { calc = "sharedsobs"; } + } + Estimators.clear(); + splitAtDash(calc, Estimators); } - + //if you have done a read.otu with a groupfile but don't want to use it anymore because you want to do single commands + if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) { + if (listfile != "") { format = "list"; } + else if (sabundfile != "") { format = "sabund"; } + else if (rabundfile != "") { format = "rabund"; } + } } catch(exception& e) { cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; @@ -255,7 +214,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; exit(1); } - } /*******************************************************/ @@ -269,6 +227,8 @@ string GlobalData::getSabundFile() { return sabundfile; } string GlobalData::getNameFile() { return namefile; } string GlobalData::getGroupFile() { return groupfile; } string GlobalData::getOrderFile() { return orderfile; } +string GlobalData::getTreeFile() { return treefile; } +string GlobalData::getSharedFile() { return sharedfile; } string GlobalData::getFastaFile() { return fastafile; } string GlobalData::getCutOff() { return cutoff; } string GlobalData::getFormat() { return format; } @@ -278,20 +238,26 @@ string GlobalData::getFileRoot() { return fileroot; } string GlobalData::getIters() { return iters; } string GlobalData::getJumble() { return jumble; } string GlobalData::getFreq() { return freq; } +string GlobalData::getAbund() { return abund; } +string GlobalData::getRandomTree() { return randomtree; } +string GlobalData::getGroups() { return groups; } +string GlobalData::getStep() { return step; } +string GlobalData::getForm() { return form; } +string GlobalData::getSorted() { return sorted; } void GlobalData::setListFile(string file) { listfile = file; inputFileName = file;} void GlobalData::setRabundFile(string file) { rabundfile = file; inputFileName = file;} void GlobalData::setSabundFile(string file) { sabundfile = file; inputFileName = file;} void GlobalData::setPhylipFile(string file) { phylipfile = file; inputFileName = file;} void GlobalData::setColumnFile(string file) { columnfile = file; inputFileName = file;} -//void GlobalData::setGroupFile(string file) { groupfile = file; } -void GlobalData::setNameFile(string file) { namefile = file; } -void GlobalData::setFormat(string Format) { format = Format; } - +void GlobalData::setNameFile(string file) { namefile = file; } +void GlobalData::setFormat(string Format) { format = Format; } +void GlobalData::setRandomTree(string Random) { randomtree = Random; } +void GlobalData::setGroups(string g) { groups = g; } +void GlobalData::setCalc(string Calc) { calc = Calc; } /*******************************************************/ /******************************************************/ - GlobalData::GlobalData() { //option definitions should go here... helpRequest = ""; @@ -300,7 +266,6 @@ GlobalData::GlobalData() { /*******************************************************/ /******************************************************/ - void GlobalData::clear() { //option definitions should go here... phylipfile = ""; @@ -312,27 +277,47 @@ void GlobalData::clear() { groupfile = ""; orderfile = ""; fastafile = ""; + treefile = ""; + sharedfile = ""; cutoff = "10.00"; format = ""; precision = "100"; iters = "1000"; line = ""; label = ""; - jumble = "0"; + groups = ""; + jumble = "1"; //0 means don't jumble, 1 means jumble. + randomtree = ""; //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile. freq = "100"; method = "furthest"; fileroot = ""; - single = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-rarefraction"; - rarefaction = "rarefaction"; - shared = "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; - sharedsummary = "sharedSobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN"; - summary = "summary-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; - sharedrarefaction = "sharedobserved"; + abund = "10"; + step = "0.01"; + form = "integral"; + sorted = "1"; //0 means don't sort, 1 means sort. } -/*******************************************************/ + +//*******************************************************/ /******************************************************/ +void GlobalData::reset() { + cutoff = "10.00"; + precision = "100"; + iters = "1000"; + groups = ""; + jumble = "1"; //0 means don't jumble, 1 means jumble. + sorted = "1"; //0 means don't sort, 1 means sort. + randomtree = ""; //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile. + freq = "100"; + method = "furthest"; + calc = ""; + abund = "10"; + step = "0.01"; + form = "integral"; +} +/*******************************************************/ +/******************************************************/ GlobalData::~GlobalData() { _uniqueInstance = 0; if(gListVector != NULL) { delete gListVector; } @@ -340,140 +325,3 @@ GlobalData::~GlobalData() { if(gorder != NULL) { delete gorder; } } /*******************************************************/ - -/******************************************************/ -//This function parses the estimator options and puts them in a vector -void GlobalData::splitAtDash(string& estim, vector& container) { - try { - string individual; - - while (estim.find_first_of('-') != -1) { - individual = estim.substr(0,estim.find_first_of('-')); - if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string - estim = estim.substr(estim.find_first_of('-')+1, estim.length()); - container.push_back(individual); - } - } - //get last one - container.push_back(estim); - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - -} -/*******************************************************/ - -/******************************************************/ -//This function parses the label options and puts them in a set -void GlobalData::splitAtDash(string& estim, set& container) { - try { - string individual; - - while (estim.find_first_of('-') != -1) { - individual = estim.substr(0,estim.find_first_of('-')); - if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string - estim = estim.substr(estim.find_first_of('-')+1, estim.length()); - container.insert(individual); - } - } - //get last one - container.insert(estim); - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - -} -/*******************************************************/ - -/******************************************************/ -//This function parses the line options and puts them in a set -void GlobalData::splitAtDash(string& estim, set& container) { - try { - string individual; - int lineNum; - - while (estim.find_first_of('-') != -1) { - individual = estim.substr(0,estim.find_first_of('-')); - if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string - estim = estim.substr(estim.find_first_of('-')+1, estim.length()); - convert(individual, lineNum); //convert the string to int - container.insert(lineNum); - } - } - //get last one - convert(estim, lineNum); //convert the string to int - container.insert(lineNum); - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the GlobalData class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - -} -/*******************************************************/ - -/******************************************************/ - -//This function splits up the various option parameters -void GlobalData::splitAtComma(string& prefix, string& suffix){ - try { - prefix = suffix.substr(0,suffix.find_first_of(',')); - if ((suffix.find_first_of(',')+2) <= suffix.length()) { //checks to make sure you don't have comma at end of string - suffix = suffix.substr(suffix.find_first_of(',')+2, suffix.length()); - } - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the GlobalData class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - -} -/*******************************************************/ - -/******************************************************/ -//This function separates the key value from the option value i.e. distfile = "96_..." -void GlobalData::splitAtEquals(string& key, string& value){ - try { - if(value.find_first_of('=') != -1){ - key = value.substr(0,value.find_first_of('=')); - if ((value.find_first_of('=')+1) <= value.length()) { - value = value.substr(value.find_first_of('=')+1, value.length()); - } - }else{ - key = value; - value = 1; - } - } - catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the GlobalData class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - -} -/*******************************************************/ - -/******************************************************/