//**********************************************************************************************************************
-BootSharedCommand::BootSharedCommand(){
+BootSharedCommand::BootSharedCommand(string option){
try {
globaldata = GlobalData::getInstance();
- format = globaldata->getFormat();
- convert(globaldata->getIters(), iters);
- validCalculator = new ValidCalculators();
- util = new SharedUtil();
+ abort = false;
+ allLines = 1;
+ lines.clear();
+ labels.clear();
+ Groups.clear();
+ Estimators.clear();
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
- int i;
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("boot", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "jabund") {
- treeCalculators.push_back(new JAbund());
- }else if (globaldata->Estimators[i] == "sorabund") {
- treeCalculators.push_back(new SorAbund());
- }else if (globaldata->Estimators[i] == "jclass") {
- treeCalculators.push_back(new Jclass());
- }else if (globaldata->Estimators[i] == "sorclass") {
- treeCalculators.push_back(new SorClass());
- }else if (globaldata->Estimators[i] == "jest") {
- treeCalculators.push_back(new Jest());
- }else if (globaldata->Estimators[i] == "sorest") {
- treeCalculators.push_back(new SorEst());
- }else if (globaldata->Estimators[i] == "thetayc") {
- treeCalculators.push_back(new ThetaYC());
- }else if (globaldata->Estimators[i] == "thetan") {
- treeCalculators.push_back(new ThetaN());
- }else if (globaldata->Estimators[i] == "morisitahorn") {
- treeCalculators.push_back(new MorHorn());
- }else if (globaldata->Estimators[i] == "braycurtis") {
- treeCalculators.push_back(new BrayCurtis());
+ else {
+ //valid paramters for this command
+ string Array[] = {"line","label","calc","groups","iters"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ parser = new OptionParser();
+ parser->parse(option, parameters); delete parser;
+
+ ValidParameters* validParameter = new ValidParameters();
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter->isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //make sure the user has already run the read.otu command
+ if (globaldata->getSharedFile() == "") {
+ if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the bootstrap.shared command." << endl; abort = true; }
+ else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the bootstrap.shared command." << endl; abort = true; }
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ line = validParameter->validFile(parameters, "line", false);
+ if (line == "not found") { line = ""; }
+ else {
+ if(line != "all") { splitAtDash(line, lines); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ label = validParameter->validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //make sure user did not use both the line and label parameters
+ if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
+ //if the user has not specified any line or labels use the ones from read.otu
+ else if((line == "") && (label == "")) {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ lines = globaldata->lines;
+ }
+
+ groups = validParameter->validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ calc = validParameter->validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "jclass-thetayc"; }
+ else {
+ if (calc == "default") { calc = "jclass-thetayc"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ string temp;
+ temp = validParameter->validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ convert(temp, iters);
+
+ delete validParameter;
+
+ if (abort == false) {
+
+ validCalculator = new ValidCalculators();
+
+ int i;
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("boot", Estimators[i]) == true) {
+ if (Estimators[i] == "jabund") {
+ treeCalculators.push_back(new JAbund());
+ }else if (Estimators[i] == "sorabund") {
+ treeCalculators.push_back(new SorAbund());
+ }else if (Estimators[i] == "jclass") {
+ treeCalculators.push_back(new Jclass());
+ }else if (Estimators[i] == "sorclass") {
+ treeCalculators.push_back(new SorClass());
+ }else if (Estimators[i] == "jest") {
+ treeCalculators.push_back(new Jest());
+ }else if (Estimators[i] == "sorest") {
+ treeCalculators.push_back(new SorEst());
+ }else if (Estimators[i] == "thetayc") {
+ treeCalculators.push_back(new ThetaYC());
+ }else if (Estimators[i] == "thetan") {
+ treeCalculators.push_back(new ThetaN());
+ }else if (Estimators[i] == "morisitahorn") {
+ treeCalculators.push_back(new MorHorn());
+ }else if (Estimators[i] == "braycurtis") {
+ treeCalculators.push_back(new BrayCurtis());
+ }
+ }
}
+
+ delete validCalculator;
+
+ ofstream* tempo;
+ for (int i=0; i < treeCalculators.size(); i++) {
+ tempo = new ofstream;
+ out.push_back(tempo);
+ }
}
}
-
- ofstream* temp;
- for (int i=0; i < treeCalculators.size(); i++) {
- temp = new ofstream;
- out.push_back(temp);
- }
-
- //reset calc for next command
- globaldata->setCalc("");
}
catch(exception& e) {
exit(1);
}
}
+
+//**********************************************************************************************************************
+
+void BootSharedCommand::help(){
+ try {
+ cout << "The bootstrap.shared command can only be executed after a successful read.otu command." << "\n";
+ cout << "The bootstrap.shared command parameters are groups, calc, iters, line and label. You may not use line and label at the same time." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
+ cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes." << "\n";
+ cout << "The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, iters=yourIters)." << "\n";
+ cout << "Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund, iters=100)." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile." << "\n";
+ cout << "The default value for calc is jclass-thetayc. The default for iters is 1000." << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BootSharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
BootSharedCommand::~BootSharedCommand(){
- delete input;
- delete read;
- delete util;
+ //made new in execute
+ if (abort == false) {
+ delete input;
+ delete read;
+ delete util;
+ }
}
//**********************************************************************************************************************
int BootSharedCommand::execute(){
try {
- int count = 1;
- //if the users entered no valid calculators don't execute command
- if (treeCalculators.size() == 0) { return 0; }
-
+ if (abort == true) { return 0; }
+
+ int count = 1;
+ util = new SharedUtil();
+
//read first line
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
order = input->getSharedOrderVector();
SharedOrderVector* lastOrder = order;
+ //if the users entered no valid calculators don't execute command
+ if (treeCalculators.size() == 0) { return 0; }
+
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
- set<string> userLabels = globaldata->labels;
- set<int> userLines = globaldata->lines;
+ set<string> userLabels = labels;
+ set<int> userLines = lines;
//set users groups
util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
tmap->makeSim(globaldata->gGroupmap);
globaldata->gTreemap = tmap;
- while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
cout << order->getLabel() << '\t' << count << endl;
process(order);
delete lastOrder;
//reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+ globaldata->Groups.clear();
return 0;
}
//create a file for each calculator with the 1000 trees in it.
for (int p = 0; p < iters; p++) {
- util->getSharedVectorswithReplacement(globaldata->Groups, lookup, order); //fills group vectors from order vector.
+ util->getSharedVectorswithReplacement(Groups, lookup, order); //fills group vectors from order vector.
//for each calculator
for(int i = 0 ; i < treeCalculators.size(); i++) {
projects / mothur.git / blobdiff