X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=2c02ca9ad560f73ecea8277420fb569b04844d82;hb=c5c7502f435e1413c19e373dab1dfebcaa67588d;hp=bc836e854cb3c4f1b7cc184789b0d49d6e8e3f45;hpb=d037597badc8d18e235c59f0c1114180edb7f98f;p=mothur.git diff --git a/globaldata.cpp b/globaldata.cpp index bc836e8..2c02ca9 100644 --- a/globaldata.cpp +++ b/globaldata.cpp @@ -1,20 +1,6 @@ -#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 +#include "sparsematrix.hpp" /*******************************************************/ @@ -27,62 +13,23 @@ 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.tree")) { clear(); + gGroupmap = NULL; + gTree.clear(); + Treenames.clear(); + labels.clear(); lines.clear(); groups.clear(); + allLines = 1; } //saves help request @@ -90,6 +37,11 @@ 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")){ @@ -103,7 +55,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ 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 == "treefile" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; } + 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; } @@ -114,54 +67,34 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ if (key == "freq" ) { freq = value; } if (key == "method" ) { method = value; } if (key == "fileroot" ) { fileroot = value; } - if (key == "randomtree" ) { randomtree = value; } - if (key == "groups" ) { groups = 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 == "scaler") { scaler = 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 set lines.clear(); + labels.clear(); line = value; label = ""; splitAtDash(value, lines); allLines = 0; } - if (key == "label") {//stores lines to be used in a set + 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 lines to be used in a vector + + if (key == "groups") {//stores groups to be used in a vector Groups.clear(); groups = value; splitAtDash(value, Groups); @@ -178,7 +111,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ 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 == "treefile" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; } + 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; } @@ -189,76 +123,88 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ if (key == "freq" ) { freq = value; } if (key == "method" ) { method = value; } if (key == "fileroot" ) { fileroot = value; } - if (key == "randomtree" ) { randomtree = 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 == "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 == "scaler") { scaler = value; } + if (key == "line") {//stores lines to be used in a vector lines.clear(); + labels.clear(); line = value; label = ""; - splitAtDash(value, lines); - allLines = 0; + 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; line = ""; - splitAtDash(value, labels); - allLines = 0; + 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 + //input defaults for calculators if (commandName == "collect.single") { - if (singleEstimators.size() == 0) { splitAtDash(single, singleEstimators); } + if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-qstat-logsd-bergerparker-bstick"; } + Estimators.clear(); + splitAtDash(calc, Estimators); } if (commandName == "rarefaction.single") { - if (rareEstimators.size() == 0) { splitAtDash(rarefaction, rareEstimators); } + if ((calc == "default") || (calc == "")) { calc = "sobs"; } + Estimators.clear(); + splitAtDash(calc, Estimators); } if (commandName == "collect.shared") { - if (sharedEstimators.size() == 0) { splitAtDash(shared, sharedEstimators); } + if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; } + Estimators.clear(); + splitAtDash(calc, Estimators); } if (commandName == "summary.single") { - if (summaryEstimators.size() == 0) { splitAtDash(summary, summaryEstimators); } + if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-logsd-qstat-bergerparker-bstick"; } + Estimators.clear(); + splitAtDash(calc, Estimators); } if (commandName == "summary.shared") { - if (sharedSummaryEstimators.size() == 0) { splitAtDash(sharedsummary, sharedSummaryEstimators); } + if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; } + Estimators.clear(); + splitAtDash(calc, Estimators); } if (commandName == "rarefaction.shared") { - if (sharedRareEstimators.size() == 0) { splitAtDash(sharedrarefaction, sharedRareEstimators); } + 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 (commandName == "tree.groups") { + if (calc != "") { + Estimators.clear(); + splitAtDash(calc, Estimators); + }else { cout << "You have not specified any calculators." << endl; } } @@ -268,7 +214,6 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ 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"; @@ -278,7 +223,6 @@ 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); } - } /*******************************************************/ @@ -293,6 +237,7 @@ 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; } @@ -302,22 +247,27 @@ 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; } +string GlobalData::getScaler() { return scaler; } 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::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 = ""; @@ -326,7 +276,6 @@ GlobalData::GlobalData() { /*******************************************************/ /******************************************************/ - void GlobalData::clear() { //option definitions should go here... phylipfile = ""; @@ -339,28 +288,47 @@ void GlobalData::clear() { orderfile = ""; fastafile = ""; treefile = ""; + sharedfile = ""; cutoff = "10.00"; format = ""; precision = "100"; iters = "1000"; line = ""; label = ""; + groups = ""; jumble = "1"; //0 means don't jumble, 1 means jumble. - randomtree = "0"; //0 means user will enter some user trees, 1 means they just want the random tree distribution. + 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 = "sobs"; - 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. + scaler = "log2"; } -/*******************************************************/ + +//*******************************************************/ /******************************************************/ +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; } @@ -369,139 +337,143 @@ GlobalData::~GlobalData() { } /*******************************************************/ -/******************************************************/ -//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) { +void GlobalData::parseTreeFile() { + //only takes names from the first tree and assumes that all trees use the same names. try { - string individual; + string filename = treefile; + ifstream filehandle; + openInputFile(filename, filehandle); + int c, comment; + comment = 0; - 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); + //if you are not a nexus file + if ((c = filehandle.peek()) != '#') { + while((c = filehandle.peek()) != ';') { + while ((c = filehandle.peek()) != ';') { + // get past comments + if(c == '[') { + comment = 1; + } + if(c == ']'){ + comment = 0; + } + if((c == '(') && (comment != 1)){ break; } + filehandle.get(); + } + + readTreeString(filehandle); + } + //if you are a nexus file + }else if ((c = filehandle.peek()) == '#') { + string holder = ""; + + // get past comments + while(holder != "translate" && holder != "Translate"){ + if(holder == "[" || holder == "[!"){ + comment = 1; + } + if(holder == "]"){ + comment = 0; + } + filehandle >> holder; + + //if there is no translate then you must read tree string otherwise use translate to get names + if(holder == "tree" && comment != 1){ + //pass over the "tree rep.6878900 = " + while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF) ) {;} + + if (c == EOF ) { break; } + filehandle.putback(c); //put back first ( of tree. + readTreeString(filehandle); + break; + } + } + + //use nexus translation rather than parsing tree to save time + if ((holder == "translate") || (holder == "Translate")) { +cout << "there is a translate " << endl; + string number, name, h; + h = ""; // so it enters the loop the first time + while((h != ";") && (number != ";")) { + filehandle >> number; + filehandle >> name; + + //c = , until done with translation then c = ; + h = name.substr(name.length()-1, name.length()); + name.erase(name.end()-1); //erase the comma + Treenames.push_back(number); + } + if (number == ";") { Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name } } - //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"; + cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. 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"; + cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. 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) { +/*******************************************************/ +void GlobalData::readTreeString(ifstream& filehandle) { try { - string individual; - int lineNum; + int c; + string name; //k - 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); + while((c = filehandle.peek()) != ';') { + //if you are a name + if ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space + name = ""; + c = filehandle.get(); + // k = c; +//cout << k << endl; + while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) { + name += c; + c = filehandle.get(); + // k = c; +//cout << " in name while " << k << endl; + } + +//cout << "name = " << name << endl; + Treenames.push_back(name); + filehandle.putback(c); +//k = c; +//cout << " after putback" << k << endl; + } + + if (c == ':') { //read until you reach the end of the branch length + while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) { + c = filehandle.get(); + // k = c; + //cout << " in branch while " << k << endl; + } + filehandle.putback(c); } - } - //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); - } - -} -/*******************************************************/ - -/******************************************************/ + c = filehandle.get(); + if (c == ';') { break; } + // k = c; +//cout << k << endl; -//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"; + cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. 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"; + cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. 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); - } - -} /*******************************************************/ -/******************************************************/ +