//**********************************************************************************************************************
+vector<string> BootSharedCommand::setParameters(){
+ try {
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
+ CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-BootSharedCommand::BootSharedCommand(string option){
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BootSharedCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string BootSharedCommand::getHelpString(){
try {
- globaldata = GlobalData::getInstance();
- abort = false;
- allLines = 1;
- lines.clear();
- labels.clear();
- Groups.clear();
- Estimators.clear();
+ string helpString = "";
+ helpString += "The bootstrap.shared command parameters are shared, groups, calc, iters and label. shared is required.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
+ helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like trees created for, and is also separated by dashes.\n";
+ helpString += "The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels, iters=yourIters).\n";
+ helpString += "Example bootstrap.shared(groups=A-B-C, calc=jabund-sorabund, iters=100).\n";
+ helpString += "The default value for groups is all the groups in your groupfile.\n";
+ helpString += "The default value for calc is jclass-thetayc. The default for iters is 1000.\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BootSharedCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+BootSharedCommand::BootSharedCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "BootSharedCommand", "BootSharedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+BootSharedCommand::BootSharedCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"line","label","calc","groups","iters"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
- parser = new OptionParser();
- parser->parse(option, parameters); delete parser;
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
- ValidParameters* validParameter = new ValidParameters();
+ ValidParameters validParameter;
//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; }
+ 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; }
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("shared");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["shared"] = inputDir + it->second; }
+ }
}
- //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; }
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not found") { m->mothurOut("shared is a required parameter."); m->mothurOutEndLine(); sharedfile = ""; abort = true; }
+ else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += m->hasPath(sharedfile); //if user entered a file with a path then preserve it
}
- label = validParameter->validFile(parameters, "label", false);
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->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);
+
+ groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->splitAtDash(groups, Groups);
+ m->Groups = Groups;
}
- calc = validParameter->validFile(parameters, "calc", false);
+ calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "jclass-thetayc"; }
else {
if (calc == "default") { calc = "jclass-thetayc"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
string temp;
- temp = validParameter->validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
convert(temp, iters);
-
- delete validParameter;
-
+
if (abort == false) {
+ //used in tree constructor
+ m->runParse = false;
+
validCalculator = new ValidCalculators();
+
+ //NOTE: if you add a calc to this if statement you must add it to the setParameters function
+ //or it will not be visible in the gui
int i;
for (i=0; i<Estimators.size(); i++) {
if (validCalculator->isValidCalculator("boot", Estimators[i]) == true) {
for (int i=0; i < treeCalculators.size(); i++) {
tempo = new ofstream;
out.push_back(tempo);
- }
+ }
+
+ //make a vector of tree* for each calculator
+ trees.resize(treeCalculators.size());
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function BootSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BootSharedCommand", "BootSharedCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function BootSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- 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(){
- //made new in execute
- if (abort == false) {
- delete input;
- delete read;
- delete util;
- }
-}
-
+BootSharedCommand::~BootSharedCommand(){}
//**********************************************************************************************************************
int BootSharedCommand::execute(){
try {
- if (abort == true) { return 0; }
-
- int count = 1;
- util = new SharedUtil();
-
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ m->mothurOut("bootstrap.shared command is no longer available."); m->mothurOutEndLine();
+ /*
//read first line
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
- input = globaldata->ginput;
+ input = new InputData(sharedfile, "sharedfile");
order = input->getSharedOrderVector();
- SharedOrderVector* lastOrder = order;
+ string lastLabel = order->getLabel();
//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 = labels;
- set<int> userLines = lines;
//set users groups
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
- numGroups = globaldata->Groups.size();
+ util = new SharedUtil();
+ util->setGroups(m->Groups, m->namesOfGroups, "treegroup");
+
+ numGroups = m->Groups.size();
//clear globaldatas old tree names if any
globaldata->Treenames.clear();
//fills globaldatas tree names
- globaldata->Treenames = globaldata->Groups;
+ globaldata->Treenames = m->Groups;
//create treemap class from groupmap for tree class to use
tmap = new TreeMap();
tmap->makeSim(globaldata->gGroupmap);
globaldata->gTreemap = tmap;
- while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
-
- if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
+ while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input;delete util; return 0; }
+
+ if(allLines == 1 || labels.count(order->getLabel()) == 1){
- cout << order->getLabel() << '\t' << count << endl;
- process(order);
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ int error = process(order);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input;delete util; return 0; }
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
- userLines.erase(count);
}
- //you have a label the user want that is smaller than this line and the last line has not already been processed
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
-
- cout << lastOrder->getLabel() << '\t' << count << endl;
- process(lastOrder);
+ //you have a label the user want that is smaller than this label and the last label has not already been processed
+ if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = order->getLabel();
+
+ delete order;
+ order = input->getSharedOrderVector(lastLabel);
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ int error = process(order);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input;delete util; return 0; }
- processedLabels.insert(lastOrder->getLabel());
- userLabels.erase(lastOrder->getLabel());
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
+
+ //restore real lastlabel to save below
+ order->setLabel(saveLabel);
}
- if (count != 1) { delete lastOrder; }
- lastOrder = order;
+
+ lastLabel = order->getLabel();
//get next line to process
+ delete order;
order = input->getSharedOrderVector();
- count++;
}
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input; delete util; return 0; }
+
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastOrder->getLabel()) != 1) {
- cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input; delete util; return 0; }
+
//run last line if you need to
if (needToRun == true) {
- process(lastOrder);
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ if (order != NULL) { delete order; }
+ order = input->getSharedOrderVector(lastLabel);
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ int error = process(order);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); delete input; delete util; return 0; }
+
+ delete order;
+
}
- delete lastOrder;
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear();delete input; delete util; return 0; }
//reset groups parameter
globaldata->Groups.clear();
+
+ //set first tree file as new current treefile
+ string currentTree = "";
+ itTypes = outputTypes.find("tree");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); }
+ }
+
+ delete input;
+ delete util;
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+*/
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BootSharedCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
-void BootSharedCommand::createTree(ostream* out){
+int BootSharedCommand::createTree(ostream* out, Tree* t){
try {
- //create tree
- t = new Tree();
-
+ /*
//do merges and create tree structure by setting parents and children
//there are numGroups - 1 merges to do
for (int i = 0; i < (numGroups - 1); i++) {
- float largest = -1.0;
+ if (m->control_pressed) { return 1; }
+
+ float largest = -1000.0;
int row, column;
//find largest value in sims matrix by searching lower triangle
for (int j = 1; j < simMatrix.size(); j++) {
index[column] = numGroups+i;
//zero out highest value that caused the merge.
- simMatrix[row][column] = -1.0;
- simMatrix[column][row] = -1.0;
+ simMatrix[row][column] = -1000.0;
+ simMatrix[column][row] = -1000.0;
//merge values in simsMatrix
for (int n = 0; n < simMatrix.size(); n++) {
simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
simMatrix[n][row] = simMatrix[row][n];
//delete column
- simMatrix[column][n] = -1.0;
- simMatrix[n][column] = -1.0;
+ simMatrix[column][n] = -1000.0;
+ simMatrix[n][column] = -1000.0;
}
}
+
+ //adjust tree to make sure root to tip length is .5
+ int root = t->findRoot();
+ t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
//assemble tree
t->assembleTree();
+
+ if (m->control_pressed) { return 1; }
//print newick file
- t->print(*out);
-
- //delete tree
- delete t;
+ t->print(*out);*/
+
+ return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BootSharedCommand", "createTree");
exit(1);
}
}
/***********************************************************/
void BootSharedCommand::printSims() {
try {
- cout << "simsMatrix" << endl;
- for (int m = 0; m < simMatrix.size(); m++) {
+ m->mothurOut("simsMatrix"); m->mothurOutEndLine();
+ for (int k = 0; k < simMatrix.size(); k++) {
for (int n = 0; n < simMatrix.size(); n++) {
- cout << simMatrix[m][n] << '\t';
+ m->mothurOut(toString(simMatrix[k][n])); m->mothurOut("\t");
}
- cout << endl;
+ m->mothurOutEndLine();
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BootSharedCommand", "printSims");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
-void BootSharedCommand::process(SharedOrderVector* order) {
+int BootSharedCommand::process(SharedOrderVector* order) {
try{
- EstOutput data;
+ /* EstOutput data;
vector<SharedRAbundVector*> subset;
-
+
//open an ostream for each calc to print to
for (int z = 0; z < treeCalculators.size(); z++) {
//create a new filename
- outputFile = getRootName(globaldata->inputFileName) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
- openOutputFile(outputFile, *(out[z]));
+ outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
+ m->openOutputFile(outputFile, *(out[z]));
+ outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
}
+ m->mothurOut("Generating bootstrap trees..."); cout.flush();
+
//create a file for each calculator with the 1000 trees in it.
for (int p = 0; p < iters; p++) {
- util->getSharedVectorswithReplacement(Groups, lookup, order); //fills group vectors from order vector.
+ if (m->control_pressed) { return 1; }
+
+ util->getSharedVectorswithReplacement(m->Groups, lookup, order); //fills group vectors from order vector.
+
//for each calculator
for(int i = 0 ; i < treeCalculators.size(); i++) {
-
+
+ if (m->control_pressed) { return 1; }
+
//initialize simMatrix
simMatrix.clear();
simMatrix.resize(numGroups);
- for (int m = 0; m < simMatrix.size(); m++) {
+ for (int o = 0; o < simMatrix.size(); o++) {
for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[m].push_back(0.0);
+ simMatrix[o].push_back(0.0);
}
}
}
}
}
-
+
+ tempTree = new Tree();
+
+ if (m->control_pressed) { delete tempTree; return 1; }
+
//creates tree from similarity matrix and write out file
- createTree(out[i]);
+ createTree(out[i], tempTree);
+
+ if (m->control_pressed) { delete tempTree; return 1; }
+
+ //save trees for consensus command.
+ trees[i].push_back(tempTree);
}
}
+
+ m->mothurOut("\tDone."); m->mothurOutEndLine();
+
+
+ //create consensus trees for each bootstrapped tree set
+ for (int k = 0; k < trees.size(); k++) {
+
+ m->mothurOut("Generating consensus tree for " + treeCalculators[k]->getName()); m->mothurOutEndLine();
+
+ if (m->control_pressed) { return 1; }
+
+ //set global data to calc trees
+ globaldata->gTree = trees[k];
+
+ string filename = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
+ consensus = new ConcensusCommand(filename);
+ consensus->execute();
+ delete consensus;
+
+ outputNames.push_back(filename + ".cons.pairs");
+ outputNames.push_back(filename + ".cons.tre");
+
+ }
+
+
+
//close ostream for each calc
for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); }
-
+ */
+ return 0;
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "BootSharedCommand", "process");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
projects / mothur.git / blobdiff