#include "sharedthetayc.h"
#include "sharedthetan.h"
#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
//**********************************************************************************************************************
+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(){
+ 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();
- 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<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; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
+
+ ValidParameters validParameter;
- 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] == "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<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; }
}
}
- }
+
+ 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; 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);
+ }
+
+ //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<string> processedLabels;
+ set<string> 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<string>::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++) {
//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);
//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<SharedRAbundVector*> 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);
- }
+ }
}
/***********************************************************/
+
projects / mothur.git / blobdiff