X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=07999f6a1ff89499fd92b9429191704b51545f61;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=de30d3c5ac2e30ab6e44cb0f84cdb9e47c1eaf73;hpb=50ed3b6104d5821d6184f882e1e1423d47dcbf10;p=mothur.git diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp index de30d3c..07999f6 100644 --- a/treegroupscommand.cpp +++ b/treegroupscommand.cpp @@ -8,6 +8,10 @@ */ #include "treegroupscommand.h" +#include "sharedsobscollectsummary.h" +#include "sharedchao1.h" +#include "sharedace.h" +#include "sharednseqs.h" #include "sharedjabund.h" #include "sharedsorabund.h" #include "sharedjclass.h" @@ -16,191 +20,486 @@ #include "sharedsorest.h" #include "sharedthetayc.h" #include "sharedthetan.h" +#include "sharedkstest.h" +#include "whittaker.h" +#include "sharedochiai.h" +#include "sharedanderbergs.h" +#include "sharedkulczynski.h" +#include "sharedkulczynskicody.h" +#include "sharedlennon.h" #include "sharedmorisitahorn.h" #include "sharedbraycurtis.h" +#include "sharedjackknife.h" +#include "whittaker.h" +#include "odum.h" +#include "canberra.h" +#include "structeuclidean.h" +#include "structchord.h" +#include "hellinger.h" +#include "manhattan.h" +#include "structpearson.h" +#include "soergel.h" +#include "spearman.h" +#include "structkulczynski.h" +#include "structchi2.h" +#include "speciesprofile.h" +#include "hamming.h" +#include "gower.h" +#include "memchi2.h" +#include "memchord.h" +#include "memeuclidean.h" +#include "mempearson.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; calledHelp = 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(){ +TreeGroupCommand::TreeGroupCommand(string option) { try { globaldata = GlobalData::getInstance(); - format = globaldata->getFormat(); - validCalculator = new ValidCalculators(); - util = new SharedUtil(); - - int i; - for (i=0; iEstimators.size(); i++) { - if (validCalculator->isValidCalculator("treegroup", 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()); + abort = false; calledHelp = false; + allLines = 1; + labels.clear(); + Groups.clear(); + Estimators.clear(); + + //allow user to run help + if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; } + + else { + //valid paramters for this command + string Array[] = {"label","calc","groups", "phylip", "column", "name", "precision","cutoff","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + + OptionParser parser(option); + map parameters = parser. getParameters(); + + ValidParameters validParameter; + map::iterator it; + + //check to make sure all parameters are valid for command + 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("phylip"); + //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["phylip"] = inputDir + it->second; } } + + it = parameters.find("column"); + //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["column"] = inputDir + it->second; } + } + + it = parameters.find("name"); + //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["name"] = inputDir + it->second; } + } + } + + format = globaldata->getFormat(); + + //required parameters + phylipfile = validParameter.validFile(parameters, "phylip", true); + if (phylipfile == "not open") { abort = true; } + else if (phylipfile == "not found") { 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 { globaldata->newRead(); format = "column"; globaldata->setColumnFile(columnfile); } + + namefile = validParameter.validFile(parameters, "name", true); + if (namefile == "not open") { abort = true; } + else if (namefile == "not found") { namefile = ""; } + else { globaldata->setNameFile(namefile); } + + //error checking on files + if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { m->mothurOut("You must run the read.otu command or provide a distance file before running the tree.shared command."); m->mothurOutEndLine(); abort = true; } + else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; } + + if (columnfile != "") { + if (namefile == "") { m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); abort = true; } + } + + //check for optional parameter and set defaults + // ...at some point should added some additional type checking... + label = validParameter.validFile(parameters, "label", false); + if (label == "not found") { label = ""; } + else { + 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 { + m->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"; } + } + m->splitAtDash(calc, Estimators); + + string temp; + temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; } + convert(temp, precision); + + temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; } + convert(temp, cutoff); + cutoff += (5 / (precision * 10.0)); + + //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 += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it + } + + + if (abort == false) { + + validCalculator = new ValidCalculators(); + + if (format == "sharedfile") { + int i; + for (i=0; iisValidCalculator("treegroup", Estimators[i]) == true) { + if (Estimators[i] == "sharedsobs") { + treeCalculators.push_back(new SharedSobsCS()); + }else if (Estimators[i] == "sharedchao") { + treeCalculators.push_back(new SharedChao1()); + }else if (Estimators[i] == "sharedace") { + treeCalculators.push_back(new SharedAce()); + }else 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] == "kstest") { + treeCalculators.push_back(new KSTest()); + }else if (Estimators[i] == "sharednseqs") { + treeCalculators.push_back(new SharedNSeqs()); + }else if (Estimators[i] == "ochiai") { + treeCalculators.push_back(new Ochiai()); + }else if (Estimators[i] == "anderberg") { + treeCalculators.push_back(new Anderberg()); + }else if (Estimators[i] == "kulczynski") { + treeCalculators.push_back(new Kulczynski()); + }else if (Estimators[i] == "kulczynskicody") { + treeCalculators.push_back(new KulczynskiCody()); + }else if (Estimators[i] == "lennon") { + treeCalculators.push_back(new Lennon()); + }else if (Estimators[i] == "morisitahorn") { + treeCalculators.push_back(new MorHorn()); + }else if (Estimators[i] == "braycurtis") { + treeCalculators.push_back(new BrayCurtis()); + }else if (Estimators[i] == "whittaker") { + treeCalculators.push_back(new Whittaker()); + }else if (Estimators[i] == "odum") { + treeCalculators.push_back(new Odum()); + }else if (Estimators[i] == "canberra") { + treeCalculators.push_back(new Canberra()); + }else if (Estimators[i] == "structeuclidean") { + treeCalculators.push_back(new StructEuclidean()); + }else if (Estimators[i] == "structchord") { + treeCalculators.push_back(new StructChord()); + }else if (Estimators[i] == "hellinger") { + treeCalculators.push_back(new Hellinger()); + }else if (Estimators[i] == "manhattan") { + treeCalculators.push_back(new Manhattan()); + }else if (Estimators[i] == "structpearson") { + treeCalculators.push_back(new StructPearson()); + }else if (Estimators[i] == "soergel") { + treeCalculators.push_back(new Soergel()); + }else if (Estimators[i] == "spearman") { + treeCalculators.push_back(new Spearman()); + }else if (Estimators[i] == "structkulczynski") { + treeCalculators.push_back(new StructKulczynski()); + }else if (Estimators[i] == "speciesprofile") { + treeCalculators.push_back(new SpeciesProfile()); + }else if (Estimators[i] == "hamming") { + treeCalculators.push_back(new Hamming()); + }else if (Estimators[i] == "structchi2") { + treeCalculators.push_back(new StructChi2()); + }else if (Estimators[i] == "gower") { + treeCalculators.push_back(new Gower()); + }else if (Estimators[i] == "memchi2") { + treeCalculators.push_back(new MemChi2()); + }else if (Estimators[i] == "memchord") { + treeCalculators.push_back(new MemChord()); + }else if (Estimators[i] == "memeuclidean") { + treeCalculators.push_back(new MemEuclidean()); + }else if (Estimators[i] == "mempearson") { + treeCalculators.push_back(new MemPearson()); + } + } + } + } + } } - - //reset calc for next command - globaldata->setCalc(""); } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the TreeGroupCommand class function TreeGroupCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} + +//********************************************************************************************************************** + +void TreeGroupCommand::help(){ + try { + m->mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n"); + m->mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n"); + m->mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision 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 allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n"); + m->mothurOut("The phylip or column parameter are required if you do not run the read.otu command first, and only one may be used. If you use a column file the name filename is required. \n"); + m->mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n"); + m->mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n"); + m->mothurOut("Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\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.\n"); + m->mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n"); + validCalculator->printCalc("treegroup", cout); + m->mothurOut("Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n"); + m->mothurOut("Example tree.shared(phylip=abrecovery.dist).\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); + } + catch(exception& e) { + m->errorOut(e, "TreeGroupCommand", "help"); exit(1); - } + } } + + //********************************************************************************************************************** TreeGroupCommand::~TreeGroupCommand(){ - delete input; - delete read; - delete util; + globaldata->Groups.clear(); + if (abort == false) { + + if (format == "sharedfile") { delete read; delete input; globaldata->ginput = NULL; } + else { delete readMatrix; delete matrix; delete list; } + delete tmap; globaldata->gTreemap = NULL; + delete validCalculator; + } + } //********************************************************************************************************************** int TreeGroupCommand::execute(){ try { - int count = 1; - EstOutput data; - vector subset; + + if (abort == true) { if (calledHelp) { return 0; } return 2; } - //if the users entered no valid calculators don't execute command - if (treeCalculators.size() == 0) { return 0; } - if (format == "sharedfile") { - read = new ReadOTUFile(globaldata->inputFileName); - read->read(&*globaldata); + //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; } - input = globaldata->ginput; - order = input->getSharedOrderVector(); - }else { - //you are using a list and a groupfile + if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; globaldata->gGroupmap = NULL; } + //you have groups read = new ReadOTUFile(globaldata->inputFileName); read->read(&*globaldata); - + input = globaldata->ginput; - SharedList = globaldata->gSharedList; - order = SharedList->getSharedOrderVector(); - } + lookup = input->getSharedRAbundVectors(); + lastLabel = lookup[0]->getLabel(); + + if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); return 0; } + + //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; - //set users groups - util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup"); - numGroups = globaldata->Groups.size(); - groupNames = ""; - for (int i = 0; i < numGroups; i++) { groupNames += globaldata->Groups[i]; } + 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; - //clear globaldatas old tree names if any - globaldata->Treenames.clear(); + if (format == "column") { readMatrix = new ReadColumnMatrix(filename); } + else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); } + + readMatrix->setCutoff(cutoff); + + if(namefile != ""){ + nameMap = new NameAssignment(namefile); + nameMap->readMap(); + } + else{ + nameMap = NULL; + } + + readMatrix->read(nameMap); + list = readMatrix->getListVector(); + matrix = readMatrix->getMatrix(); + + //make treemap + tmap = new TreeMap(); + + if (m->control_pressed) { return 0; } + + tmap->makeSim(list); + globaldata->gTreemap = tmap; + + globaldata->Groups = tmap->namesOfGroups; - //fills globaldatas tree names - globaldata->Treenames = globaldata->Groups; + //clear globaldatas old tree names if any + globaldata->Treenames.clear(); - //create treemap class from groupmap for tree class to use - tmap = new TreeMap(); - tmap->makeSim(globaldata->gGroupmap); - globaldata->gTreemap = tmap; + //fills globaldatas tree names + globaldata->Treenames = globaldata->Groups; - while(order != NULL){ - - if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){ - - cout << order->getLabel() << '\t' << count << endl; - util->getSharedVectors(globaldata->Groups, lookup, order); //fills group vectors from order vector. + //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 + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "tre"; + outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); - //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); - } - } + createTree(); + + if (m->control_pressed) { return 0; } + + m->mothurOut("Tree complete. "); m->mothurOutEndLine(); + + } - //initialize index - index.clear(); - for (int g = 0; g < numGroups; g++) { index[g] = g; } - - //create a new filename - outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + order->getLabel() + ".tre"; - - for (int k = 0; k < lookup.size(); k++) { - for (int l = k; l < lookup.size(); l++) { - if (k != l) { //we dont need to similiarity of a groups to itself - //get estimated similarity between 2 groups - - subset.clear(); //clear out old pair of sharedrabunds - //add new pair of sharedrabunds - subset.push_back(lookup[k]); subset.push_back(lookup[l]); - - 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(); - } - } + //reset groups parameter + globaldata->Groups.clear(); - //get next line to process - if (format == "sharedfile") { - order = input->getSharedOrderVector(); - }else { - //you are using a list and a groupfile - SharedList = input->getSharedListVector(); //get new list vector to process - if (SharedList != NULL) { - order = SharedList->getSharedOrderVector(); //gets new order vector with group info. - }else { - break; - } - } - count++; + //set tree file as new current treefile + string current = ""; + itTypes = outputTypes.find("tree"); + if (itTypes != outputTypes.end()) { + if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); } } - //reset groups parameter - globaldata->Groups.clear(); globaldata->setGroups(""); + 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; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "TreeGroupCommand", "execute"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the TreeGroupCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } } //********************************************************************************************************************** -void TreeGroupCommand::createTree(){ +int TreeGroupCommand::createTree(){ try { //create tree t = new Tree(); @@ -208,8 +507,10 @@ void TreeGroupCommand::createTree(){ //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++) { + float largest = -1000.0; + + if (m->control_pressed) { delete t; return 1; } - float largest = 0.0; int row, column; //find largest value in sims matrix by searching lower triangle for (int j = 1; j < simMatrix.size(); j++) { @@ -241,9 +542,9 @@ void TreeGroupCommand::createTree(){ index[row] = numGroups+i; index[column] = numGroups+i; - //zero out highest value that caused the merge. - simMatrix[row][column] = 0.0; - simMatrix[column][row] = 0.0; + //remove highest value that caused the merge. + simMatrix[row][column] = -1000.0; + simMatrix[column][row] = -1000.0; //merge values in simsMatrix for (int n = 0; n < simMatrix.size(); n++) { @@ -251,51 +552,258 @@ void TreeGroupCommand::createTree(){ simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2; simMatrix[n][row] = simMatrix[row][n]; //delete column - simMatrix[column][n] = 0.0; - simMatrix[n][column] = 0.0; + simMatrix[column][n] = -1000.0; + simMatrix[n][column] = -1000.0; } } - + + //adjust tree to make sure root to tip length is .5 + int root = t->findRoot(); + t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves())); + //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) { - cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; - exit(1); - } - catch(...) { - cout << "An unknown error has occurred in the TreeGroupCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "TreeGroupCommand", "createTree"); exit(1); } } /***********************************************************/ -void TreeGroupCommand::printSims() { +void TreeGroupCommand::printSims(ostream& out) { try { - cout << "simsMatrix" << endl; + + //output column headers + //out << '\t'; + //for (int i = 0; i < lookup.size(); i++) { out << lookup[i]->getGroup() << '\t'; } + //out << endl; + + for (int m = 0; m < simMatrix.size(); m++) { + //out << lookup[m]->getGroup() << '\t'; for (int n = 0; n < simMatrix.size(); n++) { - cout << simMatrix[m][n] << '\t'; + out << simMatrix[m][n] << '\t'; } - cout << endl; + out << endl; } } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "TreeGroupCommand", "printSims"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the TreeGroupCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} +/***********************************************************/ +int TreeGroupCommand::makeSimsDist() { + try { + numGroups = list->size(); + + //initialize index + index.clear(); + for (int g = 0; g < numGroups; g++) { index[g] = g; } + + //initialize simMatrix + simMatrix.clear(); + simMatrix.resize(numGroups); + for (int k = 0; k < simMatrix.size(); k++) { + for (int j = 0; j < simMatrix.size(); j++) { + simMatrix[k].push_back(0.0); + } + } + + //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 1; } + + } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "TreeGroupCommand", "makeSimsDist"); exit(1); - } + } } + /***********************************************************/ +int TreeGroupCommand::makeSimsShared() { + try { + 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(); + process(lookup); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + } + + 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]; } + lookup = input->getSharedRAbundVectors(lastLabel); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + process(lookup); + + processedLabels.insert(lookup[0]->getLabel()); + userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); + } + + lastLabel = lookup[0]->getLabel(); + + //get next line to process + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + 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; + for (it = userLabels.begin(); it != userLabels.end(); it++) { + m->mothurOut("Your file does not include the label " + *it); + if (processedLabels.count(lastLabel) != 1) { + m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine(); + needToRun = true; + }else { + m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine(); + } + } + + //run last label if you need to + if (needToRun == true) { + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } + lookup = input->getSharedRAbundVectors(lastLabel); + + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); + process(lookup); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + } + + for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; } + + return 0; + } + catch(exception& e) { + m->errorOut(e, "TreeGroupCommand", "makeSimsShared"); + exit(1); + } +} + +/***********************************************************/ +int TreeGroupCommand::process(vector thisLookup) { + try{ + EstOutput data; + vector subset; + numGroups = thisLookup.size(); + + //for each calculator + for(int i = 0 ; i < treeCalculators.size(); i++) { + //initialize simMatrix + simMatrix.clear(); + simMatrix.resize(numGroups); + for (int k = 0; k < simMatrix.size(); k++) { + for (int j = 0; j < simMatrix.size(); j++) { + simMatrix[k].push_back(0.0); + } + } + + //initialize index + index.clear(); + for (int g = 0; g < numGroups; g++) { index[g] = g; } + + //create a new filename + 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++) { + if (k != l) { //we dont need to similiarity of a groups to itself + //get estimated similarity between 2 groups + + subset.clear(); //clear out old pair of sharedrabunds + //add new pair of sharedrabunds + subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); + + //if this calc needs all groups to calculate the pair load all groups + if (treeCalculators[i]->getNeedsAll()) { + //load subset with rest of lookup for those calcs that need everyone to calc for a pair + for (int w = 0; w < thisLookup.size(); w++) { + if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); } + } + } + + 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) { + m->errorOut(e, "TreeGroupCommand", "process"); + exit(1); + } +} +/***********************************************************/ + +