X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=fb4887c73da88c0c631895e82f05090e97645761;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=2542431f111f85b5bc344d93388662364045a509;hpb=c24be04180aacf08ce518d02a5402d23e53d0b73;p=mothur.git diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp index 2542431..fb4887c 100644 --- a/treegroupscommand.cpp +++ b/treegroupscommand.cpp @@ -70,6 +70,26 @@ string TreeGroupCommand::getHelpString(){ } } //********************************************************************************************************************** +string TreeGroupCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "tree") { outputFileName = "tre"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "TreeGroupCommand", "getOutputFileNameTag"); + exit(1); + } +} +//********************************************************************************************************************** TreeGroupCommand::TreeGroupCommand(){ try { abort = true; calledHelp = true; @@ -266,8 +286,8 @@ TreeGroupCommand::TreeGroupCommand(string option) { TreeGroupCommand::~TreeGroupCommand(){ if (abort == false) { if (format == "sharedfile") { delete input; } - else { delete readMatrix; delete matrix; delete list; } - delete tmap; + else { delete list; } + delete ct; } } @@ -380,8 +400,16 @@ int TreeGroupCommand::execute(){ m->runParse = false; //create treemap class from groupmap for tree class to use - tmap = new TreeMap(); - tmap->makeSim(m->getAllGroups()); + ct = new CountTable(); + set nameMap; + map groupMap; + set gps; + for (int i = 0; i < m->getAllGroups().size(); i++) { + nameMap.insert(m->getAllGroups()[i]); + gps.insert(m->getAllGroups()[i]); + groupMap[m->getAllGroups()[i]] = m->getAllGroups()[i]; + } + ct->createTable(nameMap, groupMap, gps); //clear globaldatas old tree names if any m->Treenames.clear(); @@ -398,7 +426,8 @@ int TreeGroupCommand::execute(){ }else{ //read in dist file filename = inputfile; - + + ReadMatrix* readMatrix; if (format == "column") { readMatrix = new ReadColumnMatrix(filename); } else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); } @@ -408,22 +437,26 @@ int TreeGroupCommand::execute(){ nameMap = new NameAssignment(namefile); nameMap->readMap(); } - else{ - nameMap = NULL; - } + else{ nameMap = NULL; } readMatrix->read(nameMap); list = readMatrix->getListVector(); - matrix = readMatrix->getMatrix(); + SparseDistanceMatrix* dMatrix = readMatrix->getDMatrix(); //make treemap - tmap = new TreeMap(); - - if (m->control_pressed) { return 0; } - - tmap->makeSim(list); + ct = new CountTable(); + set nameMap; + map groupMap; + set gps; + for (int i = 0; i < list->getNumBins(); i++) { + string bin = list->get(i); + nameMap.insert(bin); + gps.insert(bin); + groupMap[bin] = bin; + } + ct->createTable(nameMap, groupMap, gps); - vector namesGroups = tmap->getNamesOfGroups(); + vector namesGroups = ct->getNamesOfGroups(); m->setGroups(namesGroups); //clear globaldatas old tree names if any @@ -437,12 +470,14 @@ int TreeGroupCommand::execute(){ if (m->control_pressed) { return 0; } - vector< vector > matrix = makeSimsDist(); + vector< vector > matrix = makeSimsDist(dMatrix); + delete readMatrix; + delete dMatrix; if (m->control_pressed) { return 0; } //create a new filename - string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "tre"; + string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("tree"); outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); Tree* newTree = createTree(matrix); @@ -482,13 +517,12 @@ int TreeGroupCommand::execute(){ Tree* TreeGroupCommand::createTree(vector< vector >& simMatrix){ try { //create tree - t = new Tree(tmap, simMatrix); + t = new Tree(ct, simMatrix); if (m->control_pressed) { delete t; t = NULL; return t; } //assemble tree - map empty; - t->assembleTree(empty); + t->assembleTree(); return t; } @@ -534,7 +568,7 @@ void TreeGroupCommand::printSims(ostream& out, vector< vector >& simMatr } } /***********************************************************/ -vector< vector > TreeGroupCommand::makeSimsDist() { +vector< vector > TreeGroupCommand::makeSimsDist(SparseDistanceMatrix* matrix) { try { numGroups = list->size(); @@ -549,13 +583,17 @@ vector< vector > TreeGroupCommand::makeSimsDist() { //go through sparse matrix and fill sims //go through each cell in the sparsematrix - 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); - - if (m->control_pressed) { return simMatrix; } + for (int i = 0; i < matrix->seqVec.size(); i++) { + for (int j = 0; j < matrix->seqVec[i].size(); j++) { + + //already checked everyone else in row + if (i < matrix->seqVec[i][j].index) { + simMatrix[i][matrix->seqVec[i][j].index] = -(matrix->seqVec[i][j].dist -1.0); + simMatrix[matrix->seqVec[i][j].index][i] = -(matrix->seqVec[i][j].dist -1.0); + if (m->control_pressed) { return simMatrix; } + } + } } return simMatrix; @@ -570,13 +608,6 @@ vector< vector > TreeGroupCommand::makeSimsDist() { int TreeGroupCommand::makeSimsShared() { try { - numGroups = lookup.size(); - lines.resize(processors); - for (int i = 0; i < processors; i++) { - lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups); - lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups); - } - if (subsample) { if (subsampleSize == -1) { //user has not set size, set size = smallest samples size subsampleSize = lookup[0]->getNumSeqs(); @@ -601,8 +632,17 @@ int TreeGroupCommand::makeSimsShared() { lookup = temp; m->setGroups(Groups); } + + if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; return 0; } } + numGroups = lookup.size(); + lines.resize(processors); + for (int i = 0; i < processors; i++) { + lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups); + lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups); + } + set processedLabels; set userLabels = labels; @@ -894,7 +934,7 @@ int TreeGroupCommand::process(vector thisLookup) { } //create a new filename - string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".ave.tre"; + string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".ave." + getOutputFileNameTag("tree"); outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); //creates tree from similarity matrix and write out file @@ -907,7 +947,7 @@ int TreeGroupCommand::process(vector thisLookup) { if (m->control_pressed) { break; } //create a new filename - string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".all.tre"; + string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".all." + getOutputFileNameTag("tree"); outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); ofstream outAll; @@ -948,7 +988,7 @@ int TreeGroupCommand::process(vector thisLookup) { Tree* conTree = consensus.getTree(trees); //create a new filename - string conFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".cons.tre"; + string conFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".cons." + getOutputFileNameTag("tree"); outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile); ofstream outTree; m->openOutputFile(conFile, outTree); @@ -976,7 +1016,7 @@ int TreeGroupCommand::process(vector thisLookup) { } //create a new filename - string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre"; + string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + getOutputFileNameTag("tree"); outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); //creates tree from similarity matrix and write out file