X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=626659501a531db80f5193bef33e88793414a874;hb=d04f948b1a2a1a2984fc4a45d04403b8c121c5bc;hp=6ce5ee9dfcb29dfd495bb7dc5f83aec8681eb3d6;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp index 6ce5ee9..6266595 100644 --- a/treegroupscommand.cpp +++ b/treegroupscommand.cpp @@ -19,7 +19,55 @@ #include "sharedmorisitahorn.h" #include "sharedbraycurtis.h" - +//********************************************************************************************************************** +vector TreeGroupCommand::getValidParameters(){ + try { + string Array[] = {"label","calc","groups", "phylip", "column", "name", "precision","cutoff","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "TreeGroupCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +TreeGroupCommand::TreeGroupCommand(){ + try { + abort = true; + globaldata = GlobalData::getInstance(); + //initialize outputTypes + vector tempOutNames; + outputTypes["tree"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector TreeGroupCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "TreeGroupCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector TreeGroupCommand::getRequiredFiles(){ + try { + string Array[] = {"phylip","column","shared","or"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "TreeGroupCommand", "getRequiredFiles"); + exit(1); + } +} //********************************************************************************************************************** TreeGroupCommand::TreeGroupCommand(string option) { @@ -50,6 +98,10 @@ TreeGroupCommand::TreeGroupCommand(string option) { 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 = ""; } @@ -58,7 +110,7 @@ TreeGroupCommand::TreeGroupCommand(string option) { it = parameters.find("phylip"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["phylip"] = inputDir + it->second; } } @@ -66,7 +118,7 @@ TreeGroupCommand::TreeGroupCommand(string option) { it = parameters.find("column"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["column"] = inputDir + it->second; } } @@ -74,7 +126,7 @@ TreeGroupCommand::TreeGroupCommand(string option) { it = parameters.find("name"); //user has given a template file if(it != parameters.end()){ - path = hasPath(it->second); + path = m->hasPath(it->second); //if the user has not given a path then, add inputdir. else leave path alone. if (path == "") { parameters["name"] = inputDir + it->second; } } @@ -86,12 +138,12 @@ TreeGroupCommand::TreeGroupCommand(string option) { phylipfile = validParameter.validFile(parameters, "phylip", true); if (phylipfile == "not open") { abort = true; } else if (phylipfile == "not found") { phylipfile = ""; } - else { format = "phylip"; globaldata->setPhylipFile(phylipfile); } + else { globaldata->newRead(); format = "phylip"; globaldata->setPhylipFile(phylipfile); } columnfile = validParameter.validFile(parameters, "column", true); if (columnfile == "not open") { abort = true; } else if (columnfile == "not found") { columnfile = ""; } - else { format = "column"; globaldata->setColumnFile(columnfile); } + else { globaldata->newRead(); format = "column"; globaldata->setColumnFile(columnfile); } namefile = validParameter.validFile(parameters, "name", true); if (namefile == "not open") { abort = true; } @@ -111,7 +163,7 @@ TreeGroupCommand::TreeGroupCommand(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; } } @@ -124,7 +176,7 @@ TreeGroupCommand::TreeGroupCommand(string option) { groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { - splitAtDash(groups, Groups); + m->splitAtDash(groups, Groups); globaldata->Groups = Groups; } @@ -133,7 +185,7 @@ TreeGroupCommand::TreeGroupCommand(string option) { else { if (calc == "default") { calc = "jclass-thetayc"; } } - splitAtDash(calc, Estimators); + m->splitAtDash(calc, Estimators); string temp; temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; } @@ -146,7 +198,7 @@ TreeGroupCommand::TreeGroupCommand(string option) { //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 + outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it } @@ -223,6 +275,7 @@ void TreeGroupCommand::help(){ //********************************************************************************************************************** TreeGroupCommand::~TreeGroupCommand(){ + globaldata->Groups.clear(); if (abort == false) { if (format == "sharedfile") { delete read; delete input; globaldata->ginput = NULL; } @@ -243,7 +296,8 @@ int TreeGroupCommand::execute(){ if (format == "sharedfile") { //if the users entered no valid calculators don't execute command if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; } - + + if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; globaldata->gGroupmap = NULL; } //you have groups read = new ReadOTUFile(globaldata->inputFileName); read->read(&*globaldata); @@ -257,8 +311,23 @@ int TreeGroupCommand::execute(){ //used in tree constructor globaldata->runParse = false; + //create treemap class from groupmap for tree class to use + tmap = new TreeMap(); + tmap->makeSim(globaldata->gGroupmap); + globaldata->gTreemap = tmap; + + //clear globaldatas old tree names if any + globaldata->Treenames.clear(); + + //fills globaldatas tree names + globaldata->Treenames = globaldata->Groups; + + if (m->control_pressed) { return 0; } + //create tree file makeSimsShared(); + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } }else{ //read in dist file filename = globaldata->inputFileName; @@ -282,6 +351,9 @@ int TreeGroupCommand::execute(){ //make treemap tmap = new TreeMap(); + + if (m->control_pressed) { return 0; } + tmap->makeSim(list); globaldata->gTreemap = tmap; @@ -296,14 +368,22 @@ int TreeGroupCommand::execute(){ //used in tree constructor globaldata->runParse = false; + if (m->control_pressed) { return 0; } + makeSimsDist(); + + if (m->control_pressed) { return 0; } //create a new filename - outputFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "tre"; - outputNames.push_back(outputFile); + outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "tre"; + outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); createTree(); + + if (m->control_pressed) { return 0; } + m->mothurOut("Tree complete. "); m->mothurOutEndLine(); + } //reset groups parameter @@ -323,7 +403,7 @@ int TreeGroupCommand::execute(){ } //********************************************************************************************************************** -void TreeGroupCommand::createTree(){ +int TreeGroupCommand::createTree(){ try { //create tree t = new Tree(); @@ -332,7 +412,9 @@ void TreeGroupCommand::createTree(){ //there are numGroups - 1 merges to do for (int i = 0; i < (numGroups - 1); i++) { float largest = -1000.0; - + + if (m->control_pressed) { delete t; return 1; } + int row, column; //find largest value in sims matrix by searching lower triangle for (int j = 1; j < simMatrix.size(); j++) { @@ -386,11 +468,17 @@ void TreeGroupCommand::createTree(){ //assemble tree t->assembleTree(); + if (m->control_pressed) { delete t; return 1; } + //print newick file t->createNewickFile(outputFile); //delete tree delete t; + + if (m->control_pressed) { remove(outputFile.c_str()); outputNames.pop_back(); return 1; } + + return 0; } catch(exception& e) { @@ -423,7 +511,7 @@ void TreeGroupCommand::printSims(ostream& out) { } } /***********************************************************/ -void TreeGroupCommand::makeSimsDist() { +int TreeGroupCommand::makeSimsDist() { try { numGroups = list->size(); @@ -434,9 +522,9 @@ void TreeGroupCommand::makeSimsDist() { //initialize simMatrix simMatrix.clear(); simMatrix.resize(numGroups); - for (int m = 0; m < simMatrix.size(); m++) { + for (int k = 0; k < simMatrix.size(); k++) { for (int j = 0; j < simMatrix.size(); j++) { - simMatrix[m].push_back(0.0); + simMatrix[k].push_back(0.0); } } @@ -445,10 +533,13 @@ void TreeGroupCommand::makeSimsDist() { for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){ //similairity = -(distance-1) simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0); - simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0); + simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0); + + if (m->control_pressed) { return 1; } + } - + return 0; } catch(exception& e) { m->errorOut(e, "TreeGroupCommand", "makeSimsDist"); @@ -457,25 +548,14 @@ void TreeGroupCommand::makeSimsDist() { } /***********************************************************/ -void TreeGroupCommand::makeSimsShared() { +int TreeGroupCommand::makeSimsShared() { try { - - //clear globaldatas old tree names if any - globaldata->Treenames.clear(); - - //fills globaldatas tree names - globaldata->Treenames = globaldata->Groups; - - //create treemap class from groupmap for tree class to use - tmap = new TreeMap(); - tmap->makeSim(globaldata->gGroupmap); - globaldata->gTreemap = tmap; - set processedLabels; set userLabels = labels; //as long as you are not at the end of the file or done wih the lines you want while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; } return 1; } if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); @@ -485,7 +565,7 @@ void TreeGroupCommand::makeSimsShared() { userLabels.erase(lookup[0]->getLabel()); } - if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = lookup[0]->getLabel(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } @@ -508,6 +588,8 @@ void TreeGroupCommand::makeSimsShared() { lookup = input->getSharedRAbundVectors(); } + if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; } return 1; } + //output error messages about any remaining user labels set::iterator it; bool needToRun = false; @@ -532,6 +614,8 @@ void TreeGroupCommand::makeSimsShared() { } for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; } + + return 0; } catch(exception& e) { m->errorOut(e, "TreeGroupCommand", "makeSimsShared"); @@ -540,7 +624,7 @@ void TreeGroupCommand::makeSimsShared() { } /***********************************************************/ -void TreeGroupCommand::process(vector thisLookup) { +int TreeGroupCommand::process(vector thisLookup) { try{ EstOutput data; vector subset; @@ -551,9 +635,9 @@ void TreeGroupCommand::process(vector thisLookup) { //initialize simMatrix simMatrix.clear(); simMatrix.resize(numGroups); - for (int m = 0; m < simMatrix.size(); m++) { + for (int k = 0; k < simMatrix.size(); k++) { for (int j = 0; j < simMatrix.size(); j++) { - simMatrix[m].push_back(0.0); + simMatrix[k].push_back(0.0); } } @@ -562,8 +646,8 @@ void TreeGroupCommand::process(vector thisLookup) { for (int g = 0; g < numGroups; g++) { index[g] = g; } //create a new filename - outputFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre"; - outputNames.push_back(outputFile); + outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre"; + outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); for (int k = 0; k < thisLookup.size(); k++) { for (int l = k; l < thisLookup.size(); l++) { @@ -575,16 +659,39 @@ void TreeGroupCommand::process(vector thisLookup) { subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); data = treeCalculators[i]->getValues(subset); //saves the calculator outputs + //cout << thisLookup[k]->getGroup() << '\t' << thisLookup[l]->getGroup() << '\t' << (1.0 - data[0]) << endl; + if (m->control_pressed) { return 1; } + //save values in similarity matrix simMatrix[k][l] = data[0]; simMatrix[l][k] = data[0]; } } } - + + //createdistance file from simMatrix + /*string o = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist"; + ofstream outDist; + m->openOutputFile(o, outDist); + outDist << simMatrix.size() << endl; + for (int k = 0; k < simMatrix.size(); k++) { + outDist << thisLookup[k]->getGroup() << '\t'; + for (int l = 0; l < k; l++) { + outDist << (1.0-simMatrix[k][l]) << '\t'; + } + outDist << endl; + } + outDist.close();*/ + + + if (m->control_pressed) { return 1; } //creates tree from similarity matrix and write out file createTree(); + + if (m->control_pressed) { return 1; } } + + return 0; } catch(exception& e) {