//**********************************************************************************************************************
+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);
+ 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 {
+ 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 {
- globaldata = GlobalData::getInstance();
- abort = false;
- allLines = 1;
- labels.clear();
- Groups.clear();
- Estimators.clear();
+ 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[] = {"label","calc","groups","iters","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
ValidParameters validParameter;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ 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); }
+
//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 += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
- }
-
-
- //make sure the user has already run the read.otu command
- if (globaldata->getSharedFile() == "") {
- if (globaldata->getListFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the bootstrap.shared command."); m->mothurOutEndLine(); abort = true; }
- else if (globaldata->getGroupFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the bootstrap.shared command."); m->mothurOutEndLine(); abort = true; }
+ outputDir += m->hasPath(sharedfile); //if user entered a file with a path then preserve it
}
//check for optional parameter and set defaults
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; }
}
-
- //if the user has not specified any labels use the ones from read.otu
- if(label == "") {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- }
-
+
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->splitAtDash(groups, Groups);
+ m->setGroups(Groups);
}
calc = validParameter.validFile(parameters, "calc", false);
else {
if (calc == "default") { calc = "jclass-thetayc"; }
}
- splitAtDash(calc, Estimators);
+ 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"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
if (abort == false) {
//used in tree constructor
- globaldata->runParse = false;
+ 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) {
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void BootSharedCommand::help(){
- try {
- m->mothurOut("The bootstrap.shared command can only be executed after a successful read.otu command.\n");
- m->mothurOut("The bootstrap.shared command parameters are groups, calc, iters and label.\n");
- m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
- m->mothurOut("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");
- m->mothurOut("The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels, iters=yourIters).\n");
- m->mothurOut("Example bootstrap.shared(groups=A-B-C, calc=jabund-sorabund, iters=100).\n");
- m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
- m->mothurOut("The default value for calc is jclass-thetayc. The default for iters is 1000.\n");
- }
- catch(exception& e) {
- m->errorOut(e, "BootSharedCommand", "help");
- exit(1);
- }
-}
-
//**********************************************************************************************************************
-
-BootSharedCommand::~BootSharedCommand(){
- //made new in execute
- if (abort == false) {
- delete input; globaldata->ginput = NULL;
- delete read;
- delete util;
- globaldata->gorder = NULL;
- }
-}
-
+BootSharedCommand::~BootSharedCommand(){}
//**********************************************************************************************************************
int BootSharedCommand::execute(){
try {
- if (abort == true) { return 0; }
-
- 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();
string lastLabel = order->getLabel();
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();
globaldata->gTreemap = tmap;
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(); return 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){
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(); return 0; }
+ 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());
}
//you have a label the user want that is smaller than this label and the last label has not already been processed
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ 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(); return 0; }
+ 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());
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 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; }
//output error messages about any remaining user labels
set<string>::iterator it;
}
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 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; }
//run last line if you need to
if (needToRun == true) {
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(); return 0; }
+ 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++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 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; }
//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;
}
int BootSharedCommand::createTree(ostream* out, Tree* t){
try {
-
+ /*
//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++) {
if (m->control_pressed) { return 1; }
//print newick file
- t->print(*out);
+ t->print(*out);*/
return 0;
/***********************************************************/
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 = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
- openOutputFile(outputFile, *(out[z]));
- outputNames.push_back(outputFile);
+ 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();
if (m->control_pressed) { return 1; }
- util->getSharedVectorswithReplacement(globaldata->Groups, lookup, order); //fills group vectors from order vector.
+ util->getSharedVectorswithReplacement(m->Groups, lookup, order); //fills group vectors from order vector.
//for each calculator
}
m->mothurOut("\tDone."); m->mothurOutEndLine();
- //delete globaldata's tree
- //for (int m = 0; m < globaldata->gTree.size(); m++) { delete globaldata->gTree[m]; }
- //globaldata->gTree.clear();
-
+
//create consensus trees for each bootstrapped tree set
for (int k = 0; k < trees.size(); k++) {
//set global data to calc trees
globaldata->gTree = trees[k];
- string filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
+ 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");
- //delete globaldata's tree
- //for (int m = 0; m < globaldata->gTree.size(); m++) { delete globaldata->gTree[m]; }
- //globaldata->gTree.clear();
-
}
//close ostream for each calc
for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); }
-
+ */
return 0;
}
projects / mothur.git / blobdiff