X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=a0b80ecbbf77ef9e8b95b90b558656148651f9fc;hb=643cdf74ccd4fc2d565168716fb5645917dee834;hp=17b4908515179211b792a6d06801d2dc878a7bca;hpb=3659285c05daa94306a7b61dd97ec945b23d472b;p=mothur.git diff --git a/globaldata.cpp b/globaldata.cpp index 17b4908..a0b80ec 100644 --- a/globaldata.cpp +++ b/globaldata.cpp @@ -1,295 +1,173 @@ + +/* #include "globaldata.hpp" -#include "sparsematrix.hpp" -#include "tree.h" -#include "rabundvector.hpp" -#include "sabundvector.hpp" -#include "listvector.hpp" +#include "sharedlistvector.h" +#include "inputdata.h" +#include "fullmatrix.h" /*******************************************************/ -/******************************************************/ +/****************************************************** GlobalData* GlobalData::getInstance() { - if( _uniqueInstance == 0 ) { + if( _uniqueInstance == 0) { _uniqueInstance = new GlobalData(); } return _uniqueInstance; } /*******************************************************/ -/******************************************************/ -//This function parses through the option string of the command to remove its parameters -void GlobalData::parseGlobalData(string commandString, string optionText){ - try { - 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(); - allLines = 1; - } - - //saves help request - if (commandName =="help") { - helpRequest = optionText; - } - - string key, value; - //reads in parameters and values - if((optionText != "") && (commandName != "help")){ - while((optionText.find_first_of(',') != -1)) { //while there are parameters - splitAtComma(value, optionText); - splitAtEquals(key, 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; } - if (key == "jumble" ) { jumble = value; } - 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 == "line") {//stores lines to be used in a set - lines.clear(); - line = value; - label = ""; - splitAtDash(value, lines); - allLines = 0; - } - 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 - value = optionText; - splitAtEquals(key, 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; } - if (key == "jumble" ) { jumble = value; } - 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 == "line") {//stores lines to be used in a vector - lines.clear(); - line = value; - 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(); - label = value; - 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 for calculators - if (commandName == "collect.single") { - if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; } - Estimators.clear(); - splitAtDash(calc, Estimators); - } - if (commandName == "rarefaction.single") { - if ((calc == "default") || (calc == "")) { calc = "sobs"; } - Estimators.clear(); - splitAtDash(calc, Estimators); - } - if (commandName == "collect.shared") { - 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 ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; } - Estimators.clear(); - splitAtDash(calc, Estimators); - } - if (commandName == "summary.shared") { - 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 ((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"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } -} -/*******************************************************/ - -/******************************************************/ +/****************************************************** // These functions give you the option parameters of the commands -string GlobalData::getPhylipFile() { return phylipfile; } -string GlobalData::getColumnFile() { return columnfile; } -string GlobalData::getListFile() { return listfile; } -string GlobalData::getRabundFile() { return rabundfile; } -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; } -string GlobalData::getPrecision() { return precision; } -string GlobalData::getMethod() { return method; } -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;} +string GlobalData::getPhylipFile() { return phylipfile; } +string GlobalData::getColumnFile() { return columnfile; } +string GlobalData::getListFile() { return listfile; } +string GlobalData::getRabundFile() { return rabundfile; } +string GlobalData::getSabundFile() { return sabundfile; } +string GlobalData::getNameFile() { return namefile; } +string GlobalData::getGroupFile() { return groupfile; } +string GlobalData::getOrderFile() { return orderfile; } +string GlobalData::getOrderGroupFile() { return ordergroup; } +string GlobalData::getTreeFile() { return treefile; } +string GlobalData::getSharedFile() { return sharedfile; } +string GlobalData::getRelAbundFile() { return relAbundfile; } +string GlobalData::getFormat() { return format; } + +void GlobalData::setListFile(string file) { listfile = file; inputFileName = file; } +void GlobalData::setTreeFile(string file) { treefile = 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::setSharedFile(string file) { sharedfile = file; inputFileName = file; } +void GlobalData::setRelAbundFile(string file) { relAbundfile = file; inputFileName = file; } void GlobalData::setNameFile(string file) { namefile = file; } +void GlobalData::setOrderFile(string file) { orderfile = file; } +void GlobalData::setOrderGroupFile(string file) { ordergroup = 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() { + m = MothurOut::getInstance(); //option definitions should go here... - helpRequest = ""; clear(); + gListVector = NULL; + gSparseMatrix = NULL; + ginput = NULL; + gorder = NULL; + glist = NULL; + gSharedList = NULL; + sabund = NULL; + rabund = NULL; + gGroupmap = NULL; + gMatrix = NULL; + gTreemap = NULL; + gSequenceDB = NULL; + nameMap = NULL; + saveNextLabel = ""; } /*******************************************************/ -/******************************************************/ +/****************************************************** void GlobalData::clear() { //option definitions should go here... - phylipfile = ""; - columnfile = ""; + phylipfile = ""; //do we need this? + columnfile = ""; //do we need this? listfile = ""; rabundfile = ""; sabundfile = ""; - namefile = ""; - groupfile = ""; + namefile = ""; //do we need this? + groupfile = ""; //do we need this? orderfile = ""; - fastafile = ""; + ordergroup = ""; +// fastafile = ""; //do we need this? treefile = ""; sharedfile = ""; - cutoff = "10.00"; - format = ""; - 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"; - fileroot = ""; - abund = "10"; + relAbundfile = ""; + format = ""; + saveNextLabel = ""; } -//*******************************************************/ -/******************************************************/ -void GlobalData::reset() { - cutoff = "10.00"; - precision = "100"; - iters = "1000"; - 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"; -} /*******************************************************/ -/******************************************************/ +/****************************************************** +void GlobalData::newRead() { + try{ + //remove old file names + clear(); + + //free memory + if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; } + + if (gListVector != NULL) { delete gListVector; gListVector = NULL;} + + if (gSparseMatrix != NULL) { delete gSparseMatrix; gSparseMatrix = NULL; } + + if (ginput != NULL) { delete ginput; ginput = NULL;} + + if (gorder != NULL) { delete gorder; gorder = NULL; } + + if (glist != NULL) { delete glist; glist = NULL;} + + if (gSharedList != NULL) { delete gSharedList; gSharedList = NULL; } + + if (sabund != NULL) { delete sabund; sabund = NULL;} + + if (rabund != NULL) { delete rabund; rabund = NULL; } + + if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;} + + if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; } + + if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;} + + if (nameMap != NULL) { delete nameMap; nameMap = NULL; } + + + gTree.clear(); + Treenames.clear(); + labels.clear(); Groups.clear(); + allLines = 1; + runParse = true; + names.clear(); + } + catch(exception& e) { + m->errorOut(e, "GlobalData", "newRead"); + exit(1); + } +} + +//******************************************************/ + +/***************************************************** GlobalData::~GlobalData() { _uniqueInstance = 0; - if(gListVector != NULL) { delete gListVector; } - if(gSparseMatrix != NULL) { delete gSparseMatrix; } - if(gorder != NULL) { delete gorder; } + try { + if (gGroupmap != NULL) { delete gGroupmap; gGroupmap = NULL; } + if (gListVector != NULL) { delete gListVector; gListVector = NULL;} + if (gSparseMatrix != NULL) { delete gSparseMatrix; gSparseMatrix = NULL; } + if (ginput != NULL) { delete ginput; ginput = NULL;} + if (gorder != NULL) { delete gorder; gorder = NULL; } + if (glist != NULL) { delete glist; glist = NULL;} + if (gSharedList != NULL) { delete gSharedList; gSharedList = NULL; } + if (sabund != NULL) { delete sabund; sabund = NULL;} + if (rabund != NULL) { delete rabund; rabund = NULL; } + if (gMatrix != NULL) { delete gMatrix; gMatrix = NULL;} + if (gTreemap != NULL) { delete gTreemap; gTreemap = NULL; } + if (gSequenceDB != NULL) { delete gSequenceDB; gSequenceDB = NULL;} + if (nameMap != NULL) { delete nameMap; nameMap = NULL; } + } + catch(exception& e) { + m->errorOut(e, "GlobalData", "~GlobalData"); + exit(1); + } } /*******************************************************/ + +/*******************************************************/ + +