X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=globaldata.cpp;h=ae1b0e2ebbb463fefc32a2f8ad3fd1816b01109d;hb=3117b1c3109121dff476997d3c5db5b47a77729b;hp=3ddd02e5c24dc03cd8ff7549b6b03a32982562e9;hpb=39ef0543b73cb12dfc64529522b66ad3df7527d0;p=mothur.git diff --git a/globaldata.cpp b/globaldata.cpp index 3ddd02e..ae1b0e2 100644 --- a/globaldata.cpp +++ b/globaldata.cpp @@ -1,9 +1,6 @@ #include "globaldata.hpp" -#include "sparsematrix.hpp" #include "tree.h" -#include "rabundvector.hpp" -#include "sabundvector.hpp" -#include "listvector.hpp" +#include "sparsematrix.hpp" /*******************************************************/ @@ -20,7 +17,6 @@ GlobalData* GlobalData::getInstance() { //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 @@ -31,7 +27,9 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ clear(); gGroupmap = NULL; gTree.clear(); + Treenames.clear(); labels.clear(); lines.clear(); groups.clear(); + allLines = 1; } //saves help request @@ -39,6 +37,14 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ helpRequest = optionText; } + if (commandName == "libshuff") { + iters = "10000"; + cutoff = "1.0"; + } + + //set default value for cutoff + if (commandName == "distance") { cutoff = "1.0"; } + string key, value; //reads in parameters and values if((optionText != "") && (commandName != "help")){ @@ -51,7 +57,9 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ 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 == "fasta" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; } + if (key == "nexus" ) { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus"; } + if (key == "clustal" ) { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; } 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; } @@ -66,11 +74,25 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ if (key == "fileroot" ) { fileroot = value; } if (key == "abund" ) { abund = value; } if (key == "random" ) { randomtree = value; } - if (key == "calc") { calc = value; } + if (key == "calc") { calc = value; } + if (key == "step") { step = value; } + if (key == "form") { form = value; } + if (key == "sorted") { sorted = value; } + if (key == "vertical") { vertical = value; } + if (key == "trump") { trump = value; } + if (key == "filter") { filter = value; } + if (key == "soft") { soft = value; } + if (key == "scale") { scale = value; } + if (key == "ends" ) { ends = value; } + if (key == "processors" ) { processors = value; } + + + if (key == "line") {//stores lines to be used in a set lines.clear(); + labels.clear(); line = value; label = ""; splitAtDash(value, lines); @@ -78,6 +100,7 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ } if (key == "label") {//stores labels to be used in a set labels.clear(); + lines.clear(); label = value; line = ""; splitAtDash(value, labels); @@ -101,6 +124,8 @@ 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 == "nexus" ) { nexusfile = value; inputFileName = value; fileroot = value; format = "nexus"; } + if (key == "clustal" ) { clustalfile = value; inputFileName = value; fileroot = value; format = "clustal"; } 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; } @@ -115,23 +140,37 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ if (key == "fileroot" ) { fileroot = value; } if (key == "abund" ) { abund = value; } if (key == "random" ) { randomtree = value; } - if (key == "calc") { calc = value; } + if (key == "calc") { calc = value; } + if (key == "step") { step = value; } + if (key == "form") { form = value; } + if (key == "sorted") { sorted = value; } + if (key == "vertical") { vertical = value; } + if (key == "trump") { trump = value; } + if (key == "filter") { filter = value; } + if (key == "soft") { soft = value; } + if (key == "scale") { scale = value; } + if (key == "ends" ) { ends = value; } + if (key == "processors" ) { processors = 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; @@ -145,7 +184,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ //input defaults for calculators if (commandName == "collect.single") { - if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; } + + if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; } Estimators.clear(); splitAtDash(calc, Estimators); } @@ -155,17 +195,18 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ splitAtDash(calc, Estimators); } if (commandName == "collect.shared") { - if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan"; } + + if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; } Estimators.clear(); splitAtDash(calc, Estimators); } if (commandName == "summary.single") { - if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson"; } + if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-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"; } + if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; } Estimators.clear(); splitAtDash(calc, Estimators); } @@ -174,6 +215,26 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ Estimators.clear(); splitAtDash(calc, Estimators); } + if (commandName == "distance") { + if ((calc == "default") || (calc == "")) { calc = "onegap"; } + 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.shared") || (commandName == "bootstrap.shared")) { + if (calc != "") { + Estimators.clear(); + splitAtDash(calc, Estimators); + }else { cout << "You have not specified any calculators." << endl; } + } + //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")) { @@ -206,6 +267,8 @@ string GlobalData::getOrderFile() { return orderfile; } string GlobalData::getTreeFile() { return treefile; } string GlobalData::getSharedFile() { return sharedfile; } string GlobalData::getFastaFile() { return fastafile; } +string GlobalData::getNexusFile() { return nexusfile; } +string GlobalData::getClustalFile() { return clustalfile; } string GlobalData::getCutOff() { return cutoff; } string GlobalData::getFormat() { return format; } string GlobalData::getPrecision() { return precision; } @@ -217,6 +280,16 @@ 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::getTrump() { return trump; } +string GlobalData::getSoft() { return soft; } +string GlobalData::getFilter() { return filter; } +string GlobalData::getScale() { return scale; } +string GlobalData::getEnds() { return ends; } +string GlobalData::getProcessors() { return processors; } + 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;} @@ -227,6 +300,9 @@ 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; } +void GlobalData::setEnds(string e) { ends = e; } +void GlobalData::setProcessors(string p) { processors = p; } + /*******************************************************/ @@ -235,6 +311,8 @@ GlobalData::GlobalData() { //option definitions should go here... helpRequest = ""; clear(); + gListVector == NULL; + gSparseMatrix == NULL; } /*******************************************************/ @@ -250,6 +328,8 @@ void GlobalData::clear() { groupfile = ""; orderfile = ""; fastafile = ""; + nexusfile = ""; + clustalfile = ""; treefile = ""; sharedfile = ""; cutoff = "10.00"; @@ -265,6 +345,17 @@ void GlobalData::clear() { method = "furthest"; fileroot = ""; abund = "10"; + step = "0.01"; + form = "integral"; + sorted = "T"; //F means don't sort, T means sort. + vertical = ""; + trump = ""; + filter = ""; + soft = ""; + scale = "log10"; + ends = "T"; //yes + processors = "1"; + } //*******************************************************/ @@ -274,15 +365,18 @@ void GlobalData::reset() { cutoff = "10.00"; precision = "100"; iters = "1000"; - line = ""; - label = ""; groups = ""; jumble = "1"; //0 means don't jumble, 1 means jumble. + sorted = "T"; //F means don't sort, T 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"; + abund = "10"; + step = "0.01"; + form = "integral"; + ends = "T"; + processors = "1"; } /*******************************************************/ @@ -294,3 +388,144 @@ GlobalData::~GlobalData() { if(gorder != NULL) { delete gorder; } } /*******************************************************/ + +/*******************************************************/ +void GlobalData::parseTreeFile() { + //only takes names from the first tree and assumes that all trees use the same names. + try { + string filename = treefile; + ifstream filehandle; + openInputFile(filename, filehandle); + int c, comment; + comment = 0; + + //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")) { + + 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 + } + } + + } + catch(exception& e) { + 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 parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} +/*******************************************************/ + +/*******************************************************/ +void GlobalData::readTreeString(ifstream& filehandle) { + try { + int c; + string name; //k + + 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); + } + c = filehandle.get(); + if (c == ';') { break; } + // k = c; +//cout << k << endl; + + } + } + catch(exception& e) { + 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 parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} + +/*******************************************************/ + +/*******************************************************/ + +