X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bootstrapsharedcommand.cpp;h=de9657420aabb0f8dd817a7bfe1fb4339bc3144e;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=56611a8f1e5af0eea6b64eef76e3ec1588b7298f;hpb=154e089bcd37c2c2f773e53ffb88a20170b27037;p=mothur.git diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp index 56611a8..de96574 100644 --- a/bootstrapsharedcommand.cpp +++ b/bootstrapsharedcommand.cpp @@ -17,207 +17,352 @@ #include "sharedthetayc.h" #include "sharedthetan.h" #include "sharedmorisitahorn.h" +#include "sharedbraycurtis.h" //********************************************************************************************************************** +vector 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(){ + vector 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(); - format = globaldata->getFormat(); - convert(globaldata->getIters(), iters); - validCalculator = new ValidCalculators(); - util = new SharedUtil(); + 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 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; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} + else { + vector myArray = setParameters(); + + OptionParser parser(option); + map parameters = parser.getParameters(); + map::iterator it; + + ValidParameters validParameter; - int i; - for (i=0; iEstimators.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] == "sorensonabund") { - 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()); + //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; } + } + + //initialize outputTypes + vector 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; } } } - } + + sharedfile = validParameter.validFile(parameters, "shared", true); + if (sharedfile == "not found") { + sharedfile = m->getSharedFile(); + if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); } + else { m->mothurOut("You have no current shared file and the shared parameter is required."); m->mothurOutEndLine(); abort = true; } + } + else if (sharedfile == "not open") { sharedfile = ""; abort = true; } + else { m->setSharedFile(sharedfile); } - ofstream* temp; - for (int i=0; i < treeCalculators.size(); i++) { - temp = new ofstream; - out.push_back(temp); + //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 + } + + //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") { m->splitAtDash(label, labels); allLines = 0; } + else { allLines = 1; } + } + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + m->splitAtDash(groups, Groups); + m->setGroups(Groups); + } + + calc = validParameter.validFile(parameters, "calc", false); + if (calc == "not found") { calc = "jclass-thetayc"; } + else { + if (calc == "default") { calc = "jclass-thetayc"; } + } + m->splitAtDash(calc, Estimators); + if (m->inUsersGroups("citation", Estimators)) { + ValidCalculators validCalc; validCalc.printCitations(Estimators); + //remove citation from list of calcs + for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } } + } + + string temp; + temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } + m->mothurConvert(temp, iters); + + 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; iisValidCalculator("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); + } + + //make a vector of tree* for each calculator + trees.resize(treeCalculators.size()); + } } - - //reset calc for next command - globaldata->setCalc(""); } 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); - } } //********************************************************************************************************************** - -BootSharedCommand::~BootSharedCommand(){ - delete input; - delete read; - delete util; -} - +BootSharedCommand::~BootSharedCommand(){} //********************************************************************************************************************** int BootSharedCommand::execute(){ try { - int count = 1; - EstOutput data; + if (abort == true) { if (calledHelp) { return 0; } return 2; } + + m->mothurOut("bootstrap.shared command is no longer available."); m->mothurOutEndLine(); + /* + //read first line + input = new InputData(sharedfile, "sharedfile"); + order = input->getSharedOrderVector(); + string lastLabel = order->getLabel(); + //if the users entered no valid calculators don't execute command if (treeCalculators.size() == 0) { return 0; } - if (format == "sharedfile") { - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); - - input = globaldata->ginput; - order = input->getSharedOrderVector(); - }else { - //you are using a list and a groupfile - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); - - input = globaldata->ginput; - SharedList = globaldata->gSharedList; - order = SharedList->getSharedOrderVector(); - } - + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set processedLabels; + set userLabels = labels; + //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){ - - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->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++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input;delete util; return 0; } + + if(allLines == 1 || labels.count(order->getLabel()) == 1){ - cout << order->getLabel() << '\t' << count << endl; + m->mothurOut(order->getLabel()); m->mothurOutEndLine(); + int error = process(order); + if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input;delete util; return 0; } - //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])); - } - - //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. + processedLabels.insert(order->getLabel()); + userLabels.erase(order->getLabel()); + } + + //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(); - //for each calculator - for(int i = 0 ; i < treeCalculators.size(); i++) { - - //initialize simMatrix - simMatrix.clear(); - simMatrix.resize(numGroups); - for (int m = 0; m < simMatrix.size(); m++) { - for (int j = 0; j < simMatrix.size(); j++) { - simMatrix[m].push_back(0.0); - } - } + 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++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input;delete util; return 0; } + + processedLabels.insert(order->getLabel()); + userLabels.erase(order->getLabel()); - //initialize index - index.clear(); - for (int g = 0; g < numGroups; g++) { index[g] = g; } - - for (int k = 0; k < lookup.size(); k++) { // pass cdd each set of groups to commpare - for (int l = k; l < lookup.size(); l++) { - if (k != l) { //we dont need to similiarity of a groups to itself - //get estimated similarity between 2 groups - data = treeCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs - //save values in similarity matrix - simMatrix[k][l] = data[0]; - simMatrix[l][k] = data[0]; - } - } - } - - //creates tree from similarity matrix and write out file - createTree(out[i]); - } - } - //close ostream for each calc - for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); } + //restore real lastlabel to save below + order->setLabel(saveLabel); } - + + + lastLabel = order->getLabel(); + //get next line to process - if (format == "sharedfile") { - order = input->getSharedOrderVector(); + delete order; + order = input->getSharedOrderVector(); + } + + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input; delete util; return 0; } + + //output error messages about any remaining user labels + set::iterator it; + bool needToRun = false; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + 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 { - //you are using a list and a groupfile - SharedList = input->getSharedListVector(); //get new list vector to process - if (SharedList != NULL) { - order = SharedList->getSharedOrderVector(); //gets new order vector with group info. - }else { - break; - } + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); } - count++; } + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input; delete util; return 0; } + + //run last line if you need to + if (needToRun == true) { + 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++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input; delete util; return 0; } + + delete order; + + } + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear();delete input; delete util; return 0; } + //reset groups parameter - globaldata->Groups.clear(); globaldata->setGroups(""); + 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 = 0.0; + + 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++) { @@ -229,7 +374,7 @@ void BootSharedCommand::createTree(ostream* out){ //set non-leaf node info and update leaves to know their parents //non-leaf t->tree[numGroups + i].setChildren(index[row], index[column]); - + //parents t->tree[index[row]].setParent(numGroups + i); t->tree[index[column]].setParent(numGroups + i); @@ -240,70 +385,176 @@ void BootSharedCommand::createTree(ostream* out){ //branchlengths t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves()); t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves()); - + //set your length to leaves to your childs length plus branchlength t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength()); - + //update index index[row] = numGroups+i; index[column] = numGroups+i; //zero out highest value that caused the merge. - simMatrix[row][column] = 0.0; - simMatrix[column][row] = 0.0; - + simMatrix[row][column] = -1000.0; + simMatrix[column][row] = -1000.0; + //merge values in simsMatrix for (int n = 0; n < simMatrix.size(); n++) { //row becomes merge of 2 groups simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2; simMatrix[n][row] = simMatrix[row][n]; //delete column - simMatrix[column][n] = 0.0; - simMatrix[n][column] = 0.0; + 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); + t->print(*out);*/ - //delete tree - delete t; + 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"; +} +/***********************************************************/ +int BootSharedCommand::process(SharedOrderVector* order) { + try{ + /* EstOutput data; + vector subset; + + //open an ostream for each calc to print to + for (int z = 0; z < treeCalculators.size(); z++) { + //create a new filename + 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++) { + + 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 o = 0; o < simMatrix.size(); o++) { + for (int j = 0; j < simMatrix.size(); j++) { + simMatrix[o].push_back(0.0); + } + } + + //initialize index + index.clear(); + for (int g = 0; g < numGroups; g++) { index[g] = g; } + + for (int k = 0; k < lookup.size(); k++) { // pass cdd each set of groups to commpare + for (int l = k; l < lookup.size(); l++) { + if (k != l) { //we dont need to similiarity of a groups to itself + subset.clear(); //clear out old pair of sharedrabunds + //add new pair of sharedrabunds + subset.push_back(lookup[k]); subset.push_back(lookup[l]); + + //get estimated similarity between 2 groups + data = treeCalculators[i]->getValues(subset); //saves the calculator outputs + //save values in similarity matrix + simMatrix[k][l] = data[0]; + simMatrix[l][k] = data[0]; + } + } + } + + tempTree = new Tree(); + + if (m->control_pressed) { delete tempTree; return 1; } + + //creates tree from similarity matrix and write out file + 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) { + m->errorOut(e, "BootSharedCommand", "process"); exit(1); - } + } } /***********************************************************/ +