X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bootstrapsharedcommand.cpp;h=de9657420aabb0f8dd817a7bfe1fb4339bc3144e;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=b44ce4b15d8f4121db33d12285616da1c8fde8f7;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp index b44ce4b..de96574 100644 --- a/bootstrapsharedcommand.cpp +++ b/bootstrapsharedcommand.cpp @@ -21,45 +21,110 @@ //********************************************************************************************************************** +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); + 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 { + 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 { - 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 myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); + map::iterator it; ValidParameters validParameter; //check to make sure all parameters are valid for command - for (map::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 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 @@ -67,21 +132,15 @@ BootSharedCommand::BootSharedCommand(string option) { 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); @@ -89,19 +148,27 @@ BootSharedCommand::BootSharedCommand(string option) { 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; iisValidCalculator("boot", Estimators[i]) == true) { @@ -148,51 +215,19 @@ BootSharedCommand::BootSharedCommand(string option) { 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(); @@ -204,14 +239,16 @@ int BootSharedCommand::execute(){ 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(); @@ -219,24 +256,27 @@ int BootSharedCommand::execute(){ globaldata->gTreemap = tmap; 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){ m->mothurOut(order->getLabel()); m->mothurOutEndLine(); - process(order); + 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()); } //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(); - process(order); + 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()); @@ -253,6 +293,9 @@ int BootSharedCommand::execute(){ 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; @@ -266,24 +309,40 @@ int BootSharedCommand::execute(){ } } + 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(); - process(order); + 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(); + //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; } @@ -294,13 +353,15 @@ int BootSharedCommand::execute(){ } //********************************************************************************************************************** -void BootSharedCommand::createTree(ostream* out, Tree* t){ +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; } + float largest = -1000.0; int row, column; //find largest value in sims matrix by searching lower triangle @@ -354,9 +415,13 @@ void BootSharedCommand::createTree(ostream* out, Tree* t){ //assemble tree t->assembleTree(); + + if (m->control_pressed) { return 1; } //print newick file - t->print(*out); + t->print(*out);*/ + + return 0; } catch(exception& e) { @@ -382,17 +447,17 @@ void BootSharedCommand::printSims() { } } /***********************************************************/ -void BootSharedCommand::process(SharedOrderVector* order) { +int BootSharedCommand::process(SharedOrderVector* order) { try{ - EstOutput data; + /* 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 + 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(); @@ -400,18 +465,22 @@ void BootSharedCommand::process(SharedOrderVector* order) { //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. + 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); } } @@ -437,29 +506,32 @@ void BootSharedCommand::process(SharedOrderVector* order) { 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(); - //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++) { 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 + 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; @@ -467,16 +539,14 @@ void BootSharedCommand::process(SharedOrderVector* order) { 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; } catch(exception& e) {