X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=bootstrapsharedcommand.cpp;h=a94954ae6541e509723dd233ec235b7b384abb4e;hb=99bd02d78eaf21b01420c6f99e38efc7fa4e9e17;hp=6b1f338661820d5f205556f9e62b347664e5cb4d;hpb=ee27b6e01a979fdf832668eb87412b029f77e4d7;p=mothur.git diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp index 6b1f338..a94954a 100644 --- a/bootstrapsharedcommand.cpp +++ b/bootstrapsharedcommand.cpp @@ -22,50 +22,123 @@ //********************************************************************************************************************** -BootSharedCommand::BootSharedCommand(){ +BootSharedCommand::BootSharedCommand(string option){ try { globaldata = GlobalData::getInstance(); - format = globaldata->getFormat(); - convert(globaldata->getIters(), iters); - validCalculator = new ValidCalculators(); - util = new SharedUtil(); + abort = false; + allLines = 1; + lines.clear(); + labels.clear(); + Groups.clear(); + Estimators.clear(); + //allow user to run help + if(option == "help") { help(); abort = true; } - int i; - for (i=0; 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] == "sorabund") { - treeCalculators.push_back(new SorAbund()); - }else if (globaldata->Estimators[i] == "jclass") { - treeCalculators.push_back(new Jclass()); - }else if (globaldata->Estimators[i] == "sorclass") { - treeCalculators.push_back(new SorClass()); - }else if (globaldata->Estimators[i] == "jest") { - treeCalculators.push_back(new Jest()); - }else if (globaldata->Estimators[i] == "sorest") { - treeCalculators.push_back(new SorEst()); - }else if (globaldata->Estimators[i] == "thetayc") { - treeCalculators.push_back(new ThetaYC()); - }else if (globaldata->Estimators[i] == "thetan") { - treeCalculators.push_back(new ThetaN()); - }else if (globaldata->Estimators[i] == "morisitahorn") { - treeCalculators.push_back(new MorHorn()); - }else if (globaldata->Estimators[i] == "braycurtis") { - treeCalculators.push_back(new BrayCurtis()); + else { + //valid paramters for this command + string Array[] = {"line","label","calc","groups","iters"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser.getParameters(); + + ValidParameters validParameter; + + //check to make sure all parameters are valid for command + for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } + } + + //make sure the user has already run the read.otu command + if (globaldata->getSharedFile() == "") { + if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the bootstrap.shared command." << endl; abort = true; } + else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the bootstrap.shared command." << endl; abort = true; } + } + + //check for optional parameter and set defaults + // ...at some point should added some additional type checking... + line = validParameter.validFile(parameters, "line", false); + if (line == "not found") { line = ""; } + else { + if(line != "all") { splitAtDash(line, lines); allLines = 0; } + else { allLines = 1; } + } + + label = validParameter.validFile(parameters, "label", false); + if (label == "not found") { label = ""; } + else { + if(label != "all") { splitAtDash(label, labels); allLines = 0; } + else { allLines = 1; } + } + + //make sure user did not use both the line and label parameters + if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; } + //if the user has not specified any line or labels use the ones from read.otu + else if((line == "") && (label == "")) { + allLines = globaldata->allLines; + labels = globaldata->labels; + lines = globaldata->lines; + } + + groups = validParameter.validFile(parameters, "groups", false); + if (groups == "not found") { groups = ""; } + else { + splitAtDash(groups, Groups); + globaldata->Groups = Groups; + } + + calc = validParameter.validFile(parameters, "calc", false); + if (calc == "not found") { calc = "jclass-thetayc"; } + else { + if (calc == "default") { calc = "jclass-thetayc"; } + } + splitAtDash(calc, Estimators); + + string temp; + temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } + convert(temp, iters); + + if (abort == false) { + + validCalculator = new ValidCalculators(); + + 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); + } } } - - ofstream* temp; - for (int i=0; i < treeCalculators.size(); i++) { - temp = new ofstream; - out.push_back(temp); - } - - //reset calc for next command - globaldata->setCalc(""); } catch(exception& e) { @@ -77,30 +150,66 @@ BootSharedCommand::BootSharedCommand(){ exit(1); } } + +//********************************************************************************************************************** + +void BootSharedCommand::help(){ + try { + cout << "The bootstrap.shared command can only be executed after a successful read.otu command." << "\n"; + cout << "The bootstrap.shared command parameters are groups, calc, iters, line and label. You may not use line and label at the same time." << "\n"; + cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n"; + cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes." << "\n"; + cout << "The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, iters=yourIters)." << "\n"; + cout << "Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund, iters=100)." << "\n"; + cout << "The default value for groups is all the groups in your groupfile." << "\n"; + cout << "The default value for calc is jclass-thetayc. The default for iters is 1000." << "\n"; + } + catch(exception& e) { + cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } + catch(...) { + cout << "An unknown error has occurred in the BootSharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + exit(1); + } +} + //********************************************************************************************************************** BootSharedCommand::~BootSharedCommand(){ - delete input; - delete read; - delete util; + //made new in execute + if (abort == false) { + delete input; globaldata->ginput = NULL; + delete read; + delete util; + globaldata->gorder = NULL; + } } //********************************************************************************************************************** int BootSharedCommand::execute(){ try { - int count = 1; - EstOutput data; - vector subset; - //if the users entered no valid calculators don't execute command - if (treeCalculators.size() == 0) { return 0; } - + if (abort == true) { return 0; } + + int count = 1; + util = new SharedUtil(); + //read first line read = new ReadOTUFile(globaldata->inputFileName); read->read(&*globaldata); input = globaldata->ginput; order = input->getSharedOrderVector(); + SharedOrderVector* lastOrder = order; + + //if the users entered no valid calculators don't execute command + if (treeCalculators.size() == 0) { return 0; } + + //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label. + set processedLabels; + set userLabels = labels; + set userLines = lines; //set users groups util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup"); @@ -117,71 +226,59 @@ int BootSharedCommand::execute(){ tmap->makeSim(globaldata->gGroupmap); globaldata->gTreemap = tmap; - while(order != NULL){ + while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ + if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){ cout << order->getLabel() << '\t' << count << endl; + process(order); - //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. - - //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); - } - } - - //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]; - } - } - } - - //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(); } + 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); + + processedLabels.insert(lastOrder->getLabel()); + userLabels.erase(lastOrder->getLabel()); + } + + if (count != 1) { delete lastOrder; } + lastOrder = order; + //get next line to process order = input->getSharedOrderVector(); count++; } + //output error messages about any remaining user labels + set::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; + needToRun = true; + }else { + cout << ". Please refer to " << lastOrder->getLabel() << "." << endl; + } + } + + //run last line if you need to + if (needToRun == true) { + process(lastOrder); + cout << lastOrder->getLabel() << '\t' << count << endl; + } + + delete lastOrder; + //reset groups parameter - globaldata->Groups.clear(); globaldata->setGroups(""); + globaldata->Groups.clear(); return 0; } @@ -293,5 +390,73 @@ void BootSharedCommand::printSims() { } } /***********************************************************/ +void 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 = 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(Groups, lookup, order); //fills group vectors from order vector. + + //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); + } + } + + //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]; + } + } + } + + //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(); } + + } + 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"; + 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); + } +} +/***********************************************************/ +