X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=3ddd02e5c24dc03cd8ff7549b6b03a32982562e9;hb=39ef0543b73cb12dfc64529522b66ad3df7527d0;hp=713ae9af7346dbcdffe38e3f38f9f93b1129984d;hpb=72a92a86c30876883e8af2af9803a3ecf38bdea7;p=mothur.git diff --git a/globaldata.cpp b/globaldata.cpp index 713ae9a..3ddd02e 100644 --- a/globaldata.cpp +++ b/globaldata.cpp @@ -1,20 +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 /*******************************************************/ @@ -27,52 +16,6 @@ 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){ @@ -80,9 +23,15 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ 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(); + labels.clear(); lines.clear(); groups.clear(); } //saves help request @@ -103,7 +52,8 @@ 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; } @@ -114,49 +64,32 @@ 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 == "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(); 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(); 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 @@ -168,7 +101,8 @@ 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; } @@ -179,83 +113,74 @@ 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 == "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(); line = value; + label = ""; splitAtDash(value, lines); allLines = 0; } if (key == "label") {//stores lines to be used in a vector labels.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); + } } //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"; } + 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"; } + 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"; } + 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"; } + 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 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"; @@ -265,7 +190,6 @@ 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); } - } /*******************************************************/ @@ -280,6 +204,7 @@ 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; } @@ -289,20 +214,23 @@ 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; } 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 = ""; @@ -311,7 +239,6 @@ GlobalData::GlobalData() { /*******************************************************/ /******************************************************/ - void GlobalData::clear() { //option definitions should go here... phylipfile = ""; @@ -324,27 +251,42 @@ void GlobalData::clear() { orderfile = ""; fastafile = ""; treefile = ""; + sharedfile = ""; cutoff = "10.00"; format = ""; precision = "100"; iters = "1000"; line = ""; label = ""; - jumble = "1"; + 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"; } -/*******************************************************/ + +//*******************************************************/ /******************************************************/ +void GlobalData::reset() { + cutoff = "10.00"; + precision = "100"; + iters = "1000"; + line = ""; + label = ""; + 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"; + calc = ""; + abund = "10"; +} +/*******************************************************/ +/******************************************************/ GlobalData::~GlobalData() { _uniqueInstance = 0; if(gListVector != NULL) { delete gListVector; } @@ -352,140 +294,3 @@ 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); - } - -} -/*******************************************************/ - -/******************************************************/