int RareFactCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
map<string, set<int> > labelToEnds;
if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); }
else { inputFileNames = parseSharedFile(sharedfile, labelToEnds); format = "rabund"; }
if (m->control_pressed) { return 0; }
map<int, string> file2Group; //index in outputNames[i] -> group
for (int p = 0; p < inputFileNames.size(); p++) {
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
if (inputFileNames.size() > 1) {
m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
}
int i;
ValidCalculators validCalculator;
map<string, string> variables;
variables["[filename]"] = fileNameRoot;
for (i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("rarefaction", Estimators[i]) == true) {
if (Estimators[i] == "sobs") {
rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(getOutputFileName("rarefaction",variables))));
outputNames.push_back(getOutputFileName("rarefaction",variables)); outputTypes["rarefaction"].push_back(getOutputFileName("rarefaction",variables));
}else if (Estimators[i] == "chao") {
rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(getOutputFileName("r_chao",variables))));
outputNames.push_back(getOutputFileName("r_chao",variables)); outputTypes["r_chao"].push_back(getOutputFileName("r_chao",variables));
}else if (Estimators[i] == "ace") {
if(abund < 5)
abund = 10;
rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(getOutputFileName("r_ace",variables))));
outputNames.push_back(getOutputFileName("r_ace",variables)); outputTypes["r_ace"].push_back(getOutputFileName("r_ace",variables));
}else if (Estimators[i] == "jack") {
rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(getOutputFileName("r_jack",variables))));
outputNames.push_back(getOutputFileName("r_jack",variables)); outputTypes["r_jack"].push_back(getOutputFileName("r_jack",variables));
}else if (Estimators[i] == "shannon") {
rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(getOutputFileName("r_shannon",variables))));
outputNames.push_back(getOutputFileName("r_shannon",variables)); outputTypes["r_shannon"].push_back(getOutputFileName("r_shannon",variables));
}else if (Estimators[i] == "shannoneven") {
rDisplays.push_back(new RareDisplay(new ShannonEven(), new ThreeColumnFile(getOutputFileName("r_shannoneven",variables))));
outputNames.push_back(getOutputFileName("r_shannoneven",variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannoneven",variables));
}else if (Estimators[i] == "heip") {
rDisplays.push_back(new RareDisplay(new Heip(), new ThreeColumnFile(getOutputFileName("r_heip",variables))));
outputNames.push_back(getOutputFileName("r_heip",variables)); outputTypes["r_heip"].push_back(getOutputFileName("r_heip",variables));
}else if (Estimators[i] == "r_shannonrange") {
rDisplays.push_back(new RareDisplay(new RangeShannon(alpha), new ThreeColumnFile(getOutputFileName("r_shannonrange", variables))));
outputNames.push_back(getOutputFileName("r_shannonrange", variables)); outputTypes["r_shannoneven"].push_back(getOutputFileName("r_shannonrange", variables));
}else if (Estimators[i] == "smithwilson") {
rDisplays.push_back(new RareDisplay(new SmithWilson(), new ThreeColumnFile(getOutputFileName("r_smithwilson",variables))));
outputNames.push_back(getOutputFileName("r_smithwilson",variables)); outputTypes["r_smithwilson"].push_back(getOutputFileName("r_smithwilson",variables));
}else if (Estimators[i] == "npshannon") {
rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(getOutputFileName("r_npshannon",variables))));
outputNames.push_back(getOutputFileName("r_npshannon",variables)); outputTypes["r_npshannon"].push_back(getOutputFileName("r_npshannon",variables));
}else if (Estimators[i] == "simpson") {
rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(getOutputFileName("r_simpson",variables))));
outputNames.push_back(getOutputFileName("r_simpson",variables)); outputTypes["r_simpson"].push_back(getOutputFileName("r_simpson",variables));
}else if (Estimators[i] == "simpsoneven") {
rDisplays.push_back(new RareDisplay(new SimpsonEven(), new ThreeColumnFile(getOutputFileName("r_simpsoneven",variables))));
outputNames.push_back(getOutputFileName("r_simpsoneven",variables)); outputTypes["r_simpsoneven"].push_back(getOutputFileName("r_simpsoneven",variables));
}else if (Estimators[i] == "invsimpson") {
rDisplays.push_back(new RareDisplay(new InvSimpson(), new ThreeColumnFile(getOutputFileName("r_invsimpson",variables))));
outputNames.push_back(getOutputFileName("r_invsimpson",variables)); outputTypes["r_invsimpson"].push_back(getOutputFileName("r_invsimpson",variables));
}else if (Estimators[i] == "bootstrap") {
rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(getOutputFileName("r_bootstrap",variables))));
outputNames.push_back(getOutputFileName("r_bootstrap",variables)); outputTypes["r_bootstrap"].push_back(getOutputFileName("r_bootstrap",variables));
}else if (Estimators[i] == "coverage") {
rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(getOutputFileName("r_coverage",variables))));
outputNames.push_back(getOutputFileName("r_coverage",variables)); outputTypes["r_coverage"].push_back(getOutputFileName("r_coverage",variables));
}else if (Estimators[i] == "nseqs") {
rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(getOutputFileName("r_nseqs",variables))));
outputNames.push_back(getOutputFileName("r_nseqs",variables)); outputTypes["r_nseqs"].push_back(getOutputFileName("r_nseqs",variables));
}
if (inputFileNames.size() > 1) { file2Group[outputNames.size()-1] = groups[p]; }
}
}
//if the users entered no valid calculators don't execute command
if (rDisplays.size() == 0) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } return 0; }
input = new InputData(inputFileNames[p], format);
order = input->getOrderVector();
string lastLabel = order->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete input; delete order; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//as long as you are not at the end of the file or done wih the lines you want
while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete input; delete order; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if(allLines == 1 || labels.count(order->getLabel()) == 1){
m->mothurOut(order->getLabel()); m->mothurOutEndLine();
map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
set<int> ends;
if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
rCurve = new Rarefact(order, rDisplays, processors, ends);
rCurve->getCurve(freq, nIters);
delete rCurve;
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
}
if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = order->getLabel();
delete order;
order = (input->getOrderVector(lastLabel));
m->mothurOut(order->getLabel()); m->mothurOutEndLine();
map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
set<int> ends;
if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
rCurve = new Rarefact(order, rDisplays, processors, ends);
rCurve->getCurve(freq, nIters);
delete rCurve;
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
//restore real lastlabel to save below
order->setLabel(saveLabel);
}
lastLabel = order->getLabel();
delete order;
order = (input->getOrderVector());
}
if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//output error messages about any remaining user labels
set<string>::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();
}
}
if (m->control_pressed) { for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; } delete input; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//run last label if you need to
if (needToRun == true) {
if (order != NULL) { delete order; }
order = (input->getOrderVector(lastLabel));
m->mothurOut(order->getLabel()); m->mothurOutEndLine();
map<string, set<int> >::iterator itEndings = labelToEnds.find(order->getLabel());
set<int> ends;
if (itEndings != labelToEnds.end()) { ends = itEndings->second; }
rCurve = new Rarefact(order, rDisplays, processors, ends);
rCurve->getCurve(freq, nIters);
delete rCurve;
delete order;
}
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
rDisplays.clear();
delete input;
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
//create summary file containing all the groups data for each label - this function just combines the info from the files already created.
if ((sharedfile != "") && (groupMode)) { outputNames = createGroupFile(outputNames, file2Group); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
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) {
m->errorOut(e, "RareFactCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
CollectSharedCommand::CollectSharedCommand(string option) {
try {
abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters=parser.getParameters();
map<string,string>::iterator it;
ValidParameters validParameter;
//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<string> tempOutNames;
outputTypes["sharedchao"] = tempOutNames;
outputTypes["sharedsobs"] = tempOutNames;
outputTypes["sharedace"] = tempOutNames;
outputTypes["jabund"] = tempOutNames;
outputTypes["sorabund"] = tempOutNames;
outputTypes["jclass"] = tempOutNames;
outputTypes["sorclass"] = tempOutNames;
outputTypes["jest"] = tempOutNames;
outputTypes["sorest"] = tempOutNames;
outputTypes["thetayc"] = tempOutNames;
outputTypes["thetan"] = tempOutNames;
outputTypes["kstest"] = tempOutNames;
outputTypes["whittaker"] = tempOutNames;
outputTypes["sharednseqs"] = tempOutNames;
outputTypes["ochiai"] = tempOutNames;
outputTypes["anderberg"] = tempOutNames;
outputTypes["kulczynski"] = tempOutNames;
outputTypes["kulczynskicody"] = tempOutNames;
outputTypes["lennon"] = tempOutNames;
outputTypes["morisitahorn"] = tempOutNames;
outputTypes["braycurtis"] = tempOutNames;
outputTypes["odum"] = tempOutNames;
outputTypes["canberra"] = tempOutNames;
outputTypes["structeuclidean"] = tempOutNames;
outputTypes["structchord"] = tempOutNames;
outputTypes["hellinger"] = tempOutNames;
outputTypes["manhattan"] = tempOutNames;
outputTypes["structpearson"] = tempOutNames;
outputTypes["soergel"] = tempOutNames;
outputTypes["spearman"] = tempOutNames;
outputTypes["structkulczynski"] = tempOutNames;
outputTypes["speciesprofile"] = tempOutNames;
outputTypes["structchi2"] = tempOutNames;
outputTypes["hamming"] = tempOutNames;
outputTypes["gower"] = tempOutNames;
outputTypes["memchi2"] = tempOutNames;
outputTypes["memchord"] = tempOutNames;
outputTypes["memeuclidean"] = tempOutNames;
outputTypes["mempearson"] = 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; }
}
}
//get shared file
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") {
//if there is a current shared file, use it
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 sharedfile and the shared parameter is required."); m->mothurOutEndLine(); 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 = m->hasPath(sharedfile); }
//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; }
}
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
else {
if (calc == "default") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
}
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; } }
}
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
}
m->setGroups(Groups);
string temp;
temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
m->mothurConvert(temp, freq);
temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; }
all = m->isTrue(temp);
if (abort == false) {
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(sharedfile));
ValidCalculators validCalculator;
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("shared", Estimators[i]) == true) {
if (Estimators[i] == "sharedchao") {
cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
outputNames.push_back(fileNameRoot+"shared.chao"); outputTypes["sharedchao"].push_back(fileNameRoot+"shared.chao");
}else if (Estimators[i] == "sharedsobs") {
cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
outputNames.push_back(fileNameRoot+"shared.sobs"); outputTypes["sharedsobs"].push_back(fileNameRoot+"shared.sobs");
}else if (Estimators[i] == "sharedace") {
cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
outputNames.push_back(fileNameRoot+"shared.ace"); outputTypes["sharedace"].push_back(fileNameRoot+"shared.ace");
}else if (Estimators[i] == "jabund") {
cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
outputNames.push_back(fileNameRoot+"jabund"); outputTypes["jabund"].push_back(fileNameRoot+"jabund");
}else if (Estimators[i] == "sorabund") {
cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
outputNames.push_back(fileNameRoot+"sorabund"); outputTypes["sorabund"].push_back(fileNameRoot+"sorabund");
}else if (Estimators[i] == "jclass") {
cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
outputNames.push_back(fileNameRoot+"jclass"); outputTypes["jclass"].push_back(fileNameRoot+"jclass");
}else if (Estimators[i] == "sorclass") {
cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass")));
outputNames.push_back(fileNameRoot+"sorclass"); outputTypes["sorclass"].push_back(fileNameRoot+"sorclass");
}else if (Estimators[i] == "jest") {
cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest")));
outputNames.push_back(fileNameRoot+"jest"); outputTypes["jest"].push_back(fileNameRoot+"jest");
}else if (Estimators[i] == "sorest") {
cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest")));
outputNames.push_back(fileNameRoot+"sorest"); outputTypes["sorest"].push_back(fileNameRoot+"sorest");
}else if (Estimators[i] == "thetayc") {
cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc")));
outputNames.push_back(fileNameRoot+"thetayc"); outputTypes["thetayc"].push_back(fileNameRoot+"thetayc");
}else if (Estimators[i] == "thetan") {
cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
outputNames.push_back(fileNameRoot+"thetan"); outputTypes["thetan"].push_back(fileNameRoot+"thetan");
}else if (Estimators[i] == "kstest") {
cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
outputNames.push_back(fileNameRoot+"kstest"); outputTypes["kstest"].push_back(fileNameRoot+"kstest");
}else if (Estimators[i] == "whittaker") {
cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
outputNames.push_back(fileNameRoot+"whittaker"); outputTypes["whittaker"].push_back(fileNameRoot+"whittaker");
}else if (Estimators[i] == "sharednseqs") {
cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
outputNames.push_back(fileNameRoot+"shared.nseqs"); outputTypes["shared.nseqs"].push_back(fileNameRoot+"shared.nseqs");
}else if (Estimators[i] == "ochiai") {
cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
outputNames.push_back(fileNameRoot+"ochiai"); outputTypes["ochiai"].push_back(fileNameRoot+"ochiai");
}else if (Estimators[i] == "anderberg") {
cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
outputNames.push_back(fileNameRoot+"anderberg"); outputTypes["anderberg"].push_back(fileNameRoot+"anderberg");
}else if (Estimators[i] == "kulczynski") {
cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
outputNames.push_back(fileNameRoot+"kulczynski"); outputTypes["kulczynski"].push_back(fileNameRoot+"kulczynski");
}else if (Estimators[i] == "kulczynskicody") {
cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody")));
outputNames.push_back(fileNameRoot+"kulczynskicody"); outputTypes["kulczynskicody"].push_back(fileNameRoot+"kulczynskicody");
}else if (Estimators[i] == "lennon") {
cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon")));
outputNames.push_back(fileNameRoot+"lennon"); outputTypes["lennon"].push_back(fileNameRoot+"lennon");
}else if (Estimators[i] == "morisitahorn") {
cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn")));
outputNames.push_back(fileNameRoot+"morisitahorn"); outputTypes["morisitahorn"].push_back(fileNameRoot+"morisitahorn");
}else if (Estimators[i] == "braycurtis") {
cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
outputNames.push_back(fileNameRoot+"braycurtis"); outputTypes["braycurtis"].push_back(fileNameRoot+"braycurtis");
}else if (Estimators[i] == "odum") {
cDisplays.push_back(new CollectDisplay(new Odum(), new SharedOneColumnFile(fileNameRoot+"odum")));
outputNames.push_back(fileNameRoot+"odum"); outputTypes["odum"].push_back(fileNameRoot+"odum");
}else if (Estimators[i] == "canberra") {
cDisplays.push_back(new CollectDisplay(new Canberra(), new SharedOneColumnFile(fileNameRoot+"canberra")));
outputNames.push_back(fileNameRoot+"canberra"); outputTypes["canberra"].push_back(fileNameRoot+"canberra");
}else if (Estimators[i] == "structeuclidean") {
cDisplays.push_back(new CollectDisplay(new StructEuclidean(), new SharedOneColumnFile(fileNameRoot+"structeuclidean")));
outputNames.push_back(fileNameRoot+"structeuclidean"); outputTypes["structeuclidean"].push_back(fileNameRoot+"structeuclidean");
}else if (Estimators[i] == "structchord") {
cDisplays.push_back(new CollectDisplay(new StructChord(), new SharedOneColumnFile(fileNameRoot+"structchord")));
outputNames.push_back(fileNameRoot+"structchord"); outputTypes["structchord"].push_back(fileNameRoot+"structchord");
}else if (Estimators[i] == "hellinger") {
cDisplays.push_back(new CollectDisplay(new Hellinger(), new SharedOneColumnFile(fileNameRoot+"hellinger")));
outputNames.push_back(fileNameRoot+"hellinger"); outputTypes["hellinger"].push_back(fileNameRoot+"hellinger");
}else if (Estimators[i] == "manhattan") {
cDisplays.push_back(new CollectDisplay(new Manhattan(), new SharedOneColumnFile(fileNameRoot+"manhattan")));
outputNames.push_back(fileNameRoot+"manhattan"); outputTypes["manhattan"].push_back(fileNameRoot+"manhattan");
}else if (Estimators[i] == "structpearson") {
cDisplays.push_back(new CollectDisplay(new StructPearson(), new SharedOneColumnFile(fileNameRoot+"structpearson")));
outputNames.push_back(fileNameRoot+"structpearson"); outputTypes["structpearson"].push_back(fileNameRoot+"structpearson");
}else if (Estimators[i] == "soergel") {
cDisplays.push_back(new CollectDisplay(new Soergel(), new SharedOneColumnFile(fileNameRoot+"soergel")));
outputNames.push_back(fileNameRoot+"soergel"); outputTypes["soergel"].push_back(fileNameRoot+"soergel");
}else if (Estimators[i] == "spearman") {
cDisplays.push_back(new CollectDisplay(new Spearman(), new SharedOneColumnFile(fileNameRoot+"spearman")));
outputNames.push_back(fileNameRoot+"spearman"); outputTypes["spearman"].push_back(fileNameRoot+"spearman");
}else if (Estimators[i] == "structkulczynski") {
cDisplays.push_back(new CollectDisplay(new StructKulczynski(), new SharedOneColumnFile(fileNameRoot+"structkulczynski")));
outputNames.push_back(fileNameRoot+"structkulczynski"); outputTypes["structkulczynski"].push_back(fileNameRoot+"structkulczynski");
}else if (Estimators[i] == "speciesprofile") {
cDisplays.push_back(new CollectDisplay(new SpeciesProfile(), new SharedOneColumnFile(fileNameRoot+"speciesprofile")));
outputNames.push_back(fileNameRoot+"speciesprofile"); outputTypes["speciesprofile"].push_back(fileNameRoot+"speciesprofile");
}else if (Estimators[i] == "hamming") {
cDisplays.push_back(new CollectDisplay(new Hamming(), new SharedOneColumnFile(fileNameRoot+"hamming")));
outputNames.push_back(fileNameRoot+"hamming"); outputTypes["hamming"].push_back(fileNameRoot+"hamming");
}else if (Estimators[i] == "structchi2") {
cDisplays.push_back(new CollectDisplay(new StructChi2(), new SharedOneColumnFile(fileNameRoot+"structchi2")));
outputNames.push_back(fileNameRoot+"structchi2"); outputTypes["structchi2"].push_back(fileNameRoot+"structchi2");
}else if (Estimators[i] == "gower") {
cDisplays.push_back(new CollectDisplay(new Gower(), new SharedOneColumnFile(fileNameRoot+"gower")));
outputNames.push_back(fileNameRoot+"gower"); outputTypes["gower"].push_back(fileNameRoot+"gower");
}else if (Estimators[i] == "memchi2") {
cDisplays.push_back(new CollectDisplay(new MemChi2(), new SharedOneColumnFile(fileNameRoot+"memchi2")));
outputNames.push_back(fileNameRoot+"memchi2"); outputTypes["memchi2"].push_back(fileNameRoot+"memchi2");
}else if (Estimators[i] == "memchord") {
cDisplays.push_back(new CollectDisplay(new MemChord(), new SharedOneColumnFile(fileNameRoot+"memchord")));
outputNames.push_back(fileNameRoot+"memchord"); outputTypes["memchord"].push_back(fileNameRoot+"memchord");
}else if (Estimators[i] == "memeuclidean") {
cDisplays.push_back(new CollectDisplay(new MemEuclidean(), new SharedOneColumnFile(fileNameRoot+"memeuclidean")));
outputNames.push_back(fileNameRoot+"memeuclidean"); outputTypes["memeuclidean"].push_back(fileNameRoot+"memeuclidean");
}else if (Estimators[i] == "mempearson") {
cDisplays.push_back(new CollectDisplay(new MemPearson(), new SharedOneColumnFile(fileNameRoot+"mempearson")));
outputNames.push_back(fileNameRoot+"mempearson"); outputTypes["mempearson"].push_back(fileNameRoot+"mempearson");
}
}
}
}
}
}
catch(exception& e) {
m->errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
exit(1);
}
}
MatrixOutputCommand::MatrixOutputCommand(string option) {
try {
abort = false; calledHelp = false;
allLines = 1;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
map<string,string>::iterator it;
ValidParameters validParameter;
//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<string> tempOutNames;
outputTypes["phylip"] = 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") {
//if there is a current shared file, use it
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 sharedfile 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 += m->hasPath(sharedfile); //if user entered a file with a path then preserve it
}
//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; }
}
output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "lt"; }
if ((output != "lt") && (output != "square") && (output != "column")) { m->mothurOut(output + " is not a valid output form. Options are lt, column and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
mode = validParameter.validFile(parameters, "mode", false); if(mode == "not found"){ mode = "average"; }
if ((mode != "average") && (mode != "median")) { m->mothurOut(mode + " is not a valid mode. Options are average and medina. I will use average."); m->mothurOutEndLine(); output = "average"; }
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
m->setGroups(Groups);
}
string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "jclass-thetayc"; }
else {
if (calc == "default") { calc = "jclass-thetayc"; }
}
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; } }
}
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "subsample", false); if (temp == "not found") { temp = "F"; }
if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
else {
if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; } //we will set it to smallest group later
else { subsample = false; }
}
if (subsample == false) { iters = 0; }
if (abort == false) {
ValidCalculators validCalculator;
int i;
for (i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("matrix", Estimators[i]) == true) {
if (Estimators[i] == "sharedsobs") {
matrixCalculators.push_back(new SharedSobsCS());
}else if (Estimators[i] == "sharedchao") {
matrixCalculators.push_back(new SharedChao1());
}else if (Estimators[i] == "sharedace") {
matrixCalculators.push_back(new SharedAce());
}else if (Estimators[i] == "jabund") {
matrixCalculators.push_back(new JAbund());
}else if (Estimators[i] == "sorabund") {
matrixCalculators.push_back(new SorAbund());
}else if (Estimators[i] == "jclass") {
matrixCalculators.push_back(new Jclass());
}else if (Estimators[i] == "sorclass") {
matrixCalculators.push_back(new SorClass());
}else if (Estimators[i] == "jest") {
matrixCalculators.push_back(new Jest());
}else if (Estimators[i] == "sorest") {
matrixCalculators.push_back(new SorEst());
}else if (Estimators[i] == "thetayc") {
matrixCalculators.push_back(new ThetaYC());
}else if (Estimators[i] == "thetan") {
matrixCalculators.push_back(new ThetaN());
}else if (Estimators[i] == "kstest") {
matrixCalculators.push_back(new KSTest());
}else if (Estimators[i] == "sharednseqs") {
matrixCalculators.push_back(new SharedNSeqs());
}else if (Estimators[i] == "ochiai") {
matrixCalculators.push_back(new Ochiai());
}else if (Estimators[i] == "anderberg") {
matrixCalculators.push_back(new Anderberg());
}else if (Estimators[i] == "kulczynski") {
matrixCalculators.push_back(new Kulczynski());
}else if (Estimators[i] == "kulczynskicody") {
matrixCalculators.push_back(new KulczynskiCody());
}else if (Estimators[i] == "lennon") {
matrixCalculators.push_back(new Lennon());
}else if (Estimators[i] == "morisitahorn") {
matrixCalculators.push_back(new MorHorn());
}else if (Estimators[i] == "braycurtis") {
matrixCalculators.push_back(new BrayCurtis());
}else if (Estimators[i] == "whittaker") {
matrixCalculators.push_back(new Whittaker());
}else if (Estimators[i] == "odum") {
matrixCalculators.push_back(new Odum());
}else if (Estimators[i] == "canberra") {
matrixCalculators.push_back(new Canberra());
}else if (Estimators[i] == "structeuclidean") {
matrixCalculators.push_back(new StructEuclidean());
}else if (Estimators[i] == "structchord") {
matrixCalculators.push_back(new StructChord());
}else if (Estimators[i] == "hellinger") {
matrixCalculators.push_back(new Hellinger());
}else if (Estimators[i] == "manhattan") {
matrixCalculators.push_back(new Manhattan());
}else if (Estimators[i] == "structpearson") {
matrixCalculators.push_back(new StructPearson());
}else if (Estimators[i] == "soergel") {
matrixCalculators.push_back(new Soergel());
}else if (Estimators[i] == "spearman") {
matrixCalculators.push_back(new Spearman());
}else if (Estimators[i] == "structkulczynski") {
matrixCalculators.push_back(new StructKulczynski());
}else if (Estimators[i] == "speciesprofile") {
matrixCalculators.push_back(new SpeciesProfile());
}else if (Estimators[i] == "hamming") {
matrixCalculators.push_back(new Hamming());
}else if (Estimators[i] == "structchi2") {
matrixCalculators.push_back(new StructChi2());
}else if (Estimators[i] == "gower") {
matrixCalculators.push_back(new Gower());
}else if (Estimators[i] == "memchi2") {
matrixCalculators.push_back(new MemChi2());
}else if (Estimators[i] == "memchord") {
matrixCalculators.push_back(new MemChord());
}else if (Estimators[i] == "memeuclidean") {
matrixCalculators.push_back(new MemEuclidean());
}else if (Estimators[i] == "mempearson") {
matrixCalculators.push_back(new MemPearson());
}else if (Estimators[i] == "jsd") {
matrixCalculators.push_back(new JSD());
}else if (Estimators[i] == "rjsd") {
matrixCalculators.push_back(new RJSD());
}
}
}
}
}
}
catch(exception& e) {
m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
exit(1);
}
}
int TreeGroupCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
if (format == "sharedfile") {
ValidCalculators validCalculator;
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("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());
}else if (Estimators[i] == "jsd") {
treeCalculators.push_back(new JSD());
}else if (Estimators[i] == "rjsd") {
treeCalculators.push_back(new RJSD());
}
}
}
//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 = new InputData(sharedfile, "sharedfile");
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
m->runParse = false;
//create treemap class from groupmap for tree class to use
ct = new CountTable();
set<string> nameMap;
map<string, string> groupMap;
set<string> 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();
//fills globaldatas tree names
//m->Treenames = m->getGroups();
for (int k = 0; k < lookup.size(); k++) {
m->Treenames.push_back(lookup[k]->getGroup());
}
if (m->control_pressed) { return 0; }
//create tree file
makeSimsShared();
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}else{
//read in dist file
filename = inputfile;
ReadMatrix* readMatrix;
if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
readMatrix->setCutoff(cutoff);
ct = NULL;
nameMap = NULL;
if(namefile != ""){
nameMap = new NameAssignment(namefile);
nameMap->readMap();
readMatrix->read(nameMap);
}else if (countfile != "") {
ct = new CountTable();
ct->readTable(countfile, true, false);
readMatrix->read(ct);
}else {
readMatrix->read(nameMap);
}
list = readMatrix->getListVector();
SparseDistanceMatrix* dMatrix = readMatrix->getDMatrix();
//clear globaldatas old tree names if any
m->Treenames.clear();
//make treemap
if (ct != NULL) { delete ct; }
ct = new CountTable();
set<string> nameMap;
map<string, string> groupMap;
set<string> gps;
for (int i = 0; i < list->getNumBins(); i++) {
string bin = list->get(i);
nameMap.insert(bin);
gps.insert(bin);
groupMap[bin] = bin;
m->Treenames.push_back(bin);
}
ct->createTable(nameMap, groupMap, gps);
vector<string> namesGroups = ct->getNamesOfGroups();
m->setGroups(namesGroups);
//used in tree constructor
m->runParse = false;
if (m->control_pressed) { return 0; }
vector< vector<double> > matrix = makeSimsDist(dMatrix);
delete readMatrix;
delete dMatrix;
if (m->control_pressed) { return 0; }
//create a new filename
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
string outputFile = getOutputFileName("tree",variables);
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
Tree* newTree = createTree(matrix);
if (newTree != NULL) { writeTree(outputFile, newTree); delete newTree; }
if (m->control_pressed) { return 0; }
m->mothurOut("Tree complete. "); m->mothurOutEndLine();
}
//reset groups parameter
m->clearGroups();
//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); }
}
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) {
m->errorOut(e, "TreeGroupCommand", "execute");
exit(1);
}
}
int SummaryCommand::execute() {
try {
if (abort == true) {
if (calledHelp) {
return 0;
}
return 2;
}
if ((format != "sharedfile")) {
inputFileNames.push_back(inputfile);
}
else {
inputFileNames = parseSharedFile(sharedfile);
format = "rabund";
}
if (m->control_pressed) {
return 0;
}
int numLines = 0;
int numCols = 0;
map<string, string> groupIndex;
for (int p = 0; p < inputFileNames.size(); p++) {
numLines = 0;
numCols = 0;
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
string fileNameRoot = getOutputFileName("summary",variables);
variables["[tag]"] = "ave-std";
string fileNameAve = getOutputFileName("summary",variables);
outputNames.push_back(fileNameRoot);
outputTypes["summary"].push_back(fileNameRoot);
if (inputFileNames.size() > 1) {
m->mothurOutEndLine();
m->mothurOut("Processing group " + groups[p]);
m->mothurOutEndLine();
m->mothurOutEndLine();
groupIndex[fileNameRoot] = groups[p];
}
sumCalculators.clear();
ValidCalculators validCalculator;
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("summary", Estimators[i]) == true) {
if(Estimators[i] == "sobs") {
sumCalculators.push_back(new Sobs());
} else if(Estimators[i] == "chao") {
sumCalculators.push_back(new Chao1());
} else if(Estimators[i] == "coverage") {
sumCalculators.push_back(new Coverage());
} else if(Estimators[i] == "geometric") {
sumCalculators.push_back(new Geom());
} else if(Estimators[i] == "logseries") {
sumCalculators.push_back(new LogSD());
} else if(Estimators[i] == "qstat") {
sumCalculators.push_back(new QStat());
} else if(Estimators[i] == "bergerparker") {
sumCalculators.push_back(new BergerParker());
} else if(Estimators[i] == "bstick") {
sumCalculators.push_back(new BStick());
} else if(Estimators[i] == "ace") {
if(abund < 5)
abund = 10;
sumCalculators.push_back(new Ace(abund));
} else if(Estimators[i] == "jack") {
sumCalculators.push_back(new Jackknife());
} else if(Estimators[i] == "shannon") {
sumCalculators.push_back(new Shannon());
} else if(Estimators[i] == "shannoneven") {
sumCalculators.push_back(new ShannonEven());
} else if(Estimators[i] == "npshannon") {
sumCalculators.push_back(new NPShannon());
} else if(Estimators[i] == "heip") {
sumCalculators.push_back(new Heip());
} else if(Estimators[i] == "smithwilson") {
sumCalculators.push_back(new SmithWilson());
} else if(Estimators[i] == "simpson") {
sumCalculators.push_back(new Simpson());
} else if(Estimators[i] == "simpsoneven") {
sumCalculators.push_back(new SimpsonEven());
} else if(Estimators[i] == "invsimpson") {
sumCalculators.push_back(new InvSimpson());
} else if(Estimators[i] == "bootstrap") {
sumCalculators.push_back(new Bootstrap());
} else if (Estimators[i] == "nseqs") {
sumCalculators.push_back(new NSeqs());
} else if (Estimators[i] == "goodscoverage") {
sumCalculators.push_back(new GoodsCoverage());
} else if (Estimators[i] == "efron") {
sumCalculators.push_back(new Efron(size));
} else if (Estimators[i] == "boneh") {
sumCalculators.push_back(new Boneh(size));
} else if (Estimators[i] == "solow") {
sumCalculators.push_back(new Solow(size));
} else if (Estimators[i] == "shen") {
sumCalculators.push_back(new Shen(size, abund));
}
}
}
//if the users entered no valid calculators don't execute command
if (sumCalculators.size() == 0) {
for (int i = 0; i < outputNames.size(); i++) {
m->mothurRemove(outputNames[i]);
}
return 0;
}
ofstream outputFileHandle;
m->openOutputFile(fileNameRoot, outputFileHandle);
outputFileHandle << "label";
ofstream outAve;
if (subsample) {
m->openOutputFile(fileNameAve, outAve);
outputNames.push_back(fileNameAve);
outputTypes["summary"].push_back(fileNameAve);
outAve << "label\tmethod";
outAve.setf(ios::fixed, ios::floatfield);
outAve.setf(ios::showpoint);
if (inputFileNames.size() > 1) {
groupIndex[fileNameAve] = groups[p];
}
}
input = new InputData(inputFileNames[p], format);
sabund = input->getSAbundVector();
string lastLabel = sabund->getLabel();
for(int i=0; i<sumCalculators.size(); i++) {
if(sumCalculators[i]->getCols() == 1) {
outputFileHandle << '\t' << sumCalculators[i]->getName();
if (subsample) {
outAve << '\t' << sumCalculators[i]->getName();
}
numCols++;
}
else {
outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
if (subsample) {
outAve << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
}
numCols += 3;
}
}
outputFileHandle << endl;
if (subsample) {
outAve << endl;
}
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
if (m->control_pressed) {
outputFileHandle.close();
outAve.close();
for (int i = 0; i < outputNames.size(); i++) {
m->mothurRemove(outputNames[i]);
}
for(int i=0; i<sumCalculators.size(); i++) {
delete sumCalculators[i];
}
delete sabund;
delete input;
return 0;
}
while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) {
outputFileHandle.close();
outAve.close();
for (int i = 0; i < outputNames.size(); i++) {
m->mothurRemove(outputNames[i]);
}
for(int i=0; i<sumCalculators.size(); i++) {
delete sumCalculators[i];
}
delete sabund;
delete input;
return 0;
}
if(allLines == 1 || labels.count(sabund->getLabel()) == 1) {
m->mothurOut(sabund->getLabel());
m->mothurOutEndLine();
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
process(sabund, outputFileHandle, outAve);
if (m->control_pressed) {
outputFileHandle.close();
outAve.close();
for (int i = 0; i < outputNames.size(); i++) {
m->mothurRemove(outputNames[i]);
}
for(int i=0; i<sumCalculators.size(); i++) {
delete sumCalculators[i];
}
delete sabund;
delete input;
return 0;
}
numLines++;
}
if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = sabund->getLabel();
delete sabund;
sabund = input->getSAbundVector(lastLabel);
m->mothurOut(sabund->getLabel());
m->mothurOutEndLine();
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
process(sabund, outputFileHandle, outAve);
if (m->control_pressed) {
outputFileHandle.close();
outAve.close();
for (int i = 0; i < outputNames.size(); i++) {
m->mothurRemove(outputNames[i]);
}
for(int i=0; i<sumCalculators.size(); i++) {
delete sumCalculators[i];
}
delete sabund;
delete input;
return 0;
}
numLines++;
//restore real lastlabel to save below
sabund->setLabel(saveLabel);
}
lastLabel = sabund->getLabel();
delete sabund;
sabund = input->getSAbundVector();
}
if (m->control_pressed) {
outputFileHandle.close();
outAve.close();
for (int i = 0; i < outputNames.size(); i++) {
m->mothurRemove(outputNames[i]);
}
for(int i=0; i<sumCalculators.size(); i++) {
delete sumCalculators[i];
}
delete input;
return 0;
}
//output error messages about any remaining user labels
set<string>::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) {
if (sabund != NULL) {
delete sabund;
}
sabund = input->getSAbundVector(lastLabel);
m->mothurOut(sabund->getLabel());
m->mothurOutEndLine();
process(sabund, outputFileHandle, outAve);
if (m->control_pressed) {
outputFileHandle.close();
outAve.close();
for (int i = 0; i < outputNames.size(); i++) {
m->mothurRemove(outputNames[i]);
}
for(int i=0; i<sumCalculators.size(); i++) {
delete sumCalculators[i];
}
delete sabund;
delete input;
return 0;
}
numLines++;
delete sabund;
}
outputFileHandle.close();
if (subsample) {
outAve.close();
}
if (m->control_pressed) {
for (int i = 0; i < outputNames.size(); i++) {
m->mothurRemove(outputNames[i]);
}
for(int i=0; i<sumCalculators.size(); i++) {
delete sumCalculators[i];
}
delete input;
return 0;
}
delete input;
for(int i=0; i<sumCalculators.size(); i++) {
delete sumCalculators[i];
}
}
if (m->control_pressed) {
for (int i = 0; i < outputNames.size(); i++) {
m->mothurRemove(outputNames[i]);
}
return 0;
}
//create summary file containing all the groups data for each label - this function just combines the info from the files already created.
if ((sharedfile != "") && (groupMode)) {
vector<string> comboNames = createGroupSummaryFile(numLines, numCols, outputNames, groupIndex);
for (int i = 0; i < comboNames.size(); i++) {
outputNames.push_back(comboNames[i]);
}
}
if (m->control_pressed) {
for (int i = 0; i < outputNames.size(); i++) {
m->mothurRemove(outputNames[i]);
}
return 0;
}
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) {
m->errorOut(e, "SummaryCommand", "execute");
exit(1);
}
}
/////// need to fix to work with calcs and sequencedb
int DistanceCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
try {
ValidCalculators validCalculator;
Dist* distCalculator;
if (m->isTrue(countends) == true) {
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
}
}
}else {
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
}
}
}
MPI_Status status;
MPI_File outMPI;
int amode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
//char* filename = new char[file.length()];
//memcpy(filename, file.c_str(), file.length());
char filename[1024];
strcpy(filename, file.c_str());
MPI_File_open(MPI_COMM_SELF, filename, amode, MPI_INFO_NULL, &outMPI);
//delete filename;
int startTime = time(NULL);
string outputString = "";
size = 0;
if(startLine == 0){ outputString += toString(alignDB.getNumSeqs()) + "\n"; }
for(int i=startLine;i<endLine;i++){
string name = alignDB.get(i).getName();
if (name.length() < 10) { //pad with spaces to make compatible
while (name.length() < 10) { name += " "; }
}
outputString += name;
for(int j=0;j<alignDB.getNumSeqs();j++){
if (m->control_pressed) { delete distCalculator; return 0; }
distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
double dist = distCalculator->getDist();
outputString += "\t" + toString(dist);
}
outputString += "\n";
if(i % 100 == 0){
m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
}
//send results to parent
int length = outputString.length();
char* buf = new char[length];
memcpy(buf, outputString.c_str(), length);
MPI_File_write(outMPI, buf, length, MPI_CHAR, &status);
size += outputString.length();
outputString = "";
delete buf;
}
m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
MPI_File_close(&outMPI);
delete distCalculator;
return 1;
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "driverMPI");
exit(1);
}
}
/////// need to fix to work with calcs and sequencedb
int DistanceCommand::driverMPI(int startLine, int endLine, MPI_File& outMPI, float cutoff){
try {
ValidCalculators validCalculator;
Dist* distCalculator;
if (m->isTrue(countends) == true) {
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
}
}
}else {
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
}
}
}
MPI_Status status;
int startTime = time(NULL);
string outputString = "";
for(int i=startLine;i<endLine;i++){
for(int j=0;j<i;j++){
if (m->control_pressed) { delete distCalculator; return 0; }
//if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
//the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
double dist = distCalculator->getDist();
if(dist <= cutoff){
outputString += (alignDB.get(i).getName() + ' ' + alignDB.get(j).getName() + ' ' + toString(dist) + '\n');
}
}
if(i % 100 == 0){
m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
}
//send results to parent
int length = outputString.length();
char* buf = new char[length];
memcpy(buf, outputString.c_str(), length);
MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
outputString = "";
delete buf;
}
m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
delete distCalculator;
return 1;
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "driverMPI");
exit(1);
}
}
/////// need to fix to work with calcs and sequencedb
int DistanceCommand::driver(int startLine, int endLine, string dFileName, string square){
try {
ValidCalculators validCalculator;
Dist* distCalculator;
if (m->isTrue(countends) == true) {
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
}
}
}else {
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
}
}
}
int startTime = time(NULL);
//column file
ofstream outFile(dFileName.c_str(), ios::trunc);
outFile.setf(ios::fixed, ios::showpoint);
outFile << setprecision(4);
if(startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
for(int i=startLine;i<endLine;i++){
string name = alignDB.get(i).getName();
//pad with spaces to make compatible
if (name.length() < 10) { while (name.length() < 10) { name += " "; } }
outFile << name << '\t';
for(int j=0;j<alignDB.getNumSeqs();j++){
if (m->control_pressed) { delete distCalculator; outFile.close(); return 0; }
distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
double dist = distCalculator->getDist();
outFile << dist << '\t';
}
outFile << endl;
if(i % 100 == 0){
m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
}
}
m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
outFile.close();
delete distCalculator;
return 1;
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "driver");
exit(1);
}
}
/////// need to fix to work with calcs and sequencedb
int DistanceCommand::driver(int startLine, int endLine, string dFileName, float cutoff){
try {
ValidCalculators validCalculator;
Dist* distCalculator;
if (m->isTrue(countends) == true) {
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[i] == "eachgap") { distCalculator = new eachGapDist(); }
else if (Estimators[i] == "onegap") { distCalculator = new oneGapDist(); }
}
}
}else {
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
else if (Estimators[i] == "eachgap"){ distCalculator = new eachGapIgnoreTermGapDist(); }
else if (Estimators[i] == "onegap") { distCalculator = new oneGapIgnoreTermGapDist(); }
}
}
}
int startTime = time(NULL);
//column file
ofstream outFile(dFileName.c_str(), ios::trunc);
outFile.setf(ios::fixed, ios::showpoint);
outFile << setprecision(4);
if((output == "lt") && startLine == 0){ outFile << alignDB.getNumSeqs() << endl; }
for(int i=startLine;i<endLine;i++){
if(output == "lt") {
string name = alignDB.get(i).getName();
if (name.length() < 10) { //pad with spaces to make compatible
while (name.length() < 10) { name += " "; }
}
outFile << name;
}
for(int j=0;j<i;j++){
if (m->control_pressed) { delete distCalculator; outFile.close(); return 0; }
//if there was a column file given and we are appending, we don't want to calculate the distances that are already in the column file
//the alignDB contains the new sequences and then the old, so if i an oldsequence and j is an old sequence then break out of this loop
if ((i >= numNewFasta) && (j >= numNewFasta)) { break; }
distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
double dist = distCalculator->getDist();
if(dist <= cutoff){
if (output == "column") { outFile << alignDB.get(i).getName() << ' ' << alignDB.get(j).getName() << ' ' << dist << endl; }
}
if (output == "lt") { outFile << '\t' << dist; }
}
if (output == "lt") { outFile << endl; }
if(i % 100 == 0){
m->mothurOutJustToScreen(toString(i) + "\t" + toString(time(NULL) - startTime)+"\n");
}
}
m->mothurOutJustToScreen(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)+"\n");
outFile.close();
delete distCalculator;
return 1;
}
catch(exception& e) {
m->errorOut(e, "DistanceCommand", "driver");
exit(1);
}
}
int process(treeSharedData* params) {
try{
ValidCalculators validCalculator;
vector<Calculator*> treeCalculators;
for (int i=0; i<params->Estimators.size(); i++) {
if (validCalculator.isValidCalculator("treegroup", params->Estimators[i]) ) {
if (params->Estimators[i] == "sharedsobs") {
treeCalculators.push_back(new SharedSobsCS());
}else if (params->Estimators[i] == "sharedchao") {
treeCalculators.push_back(new SharedChao1());
}else if (params->Estimators[i] == "sharedace") {
treeCalculators.push_back(new SharedAce());
}else if (params->Estimators[i] == "jabund") {
treeCalculators.push_back(new JAbund());
}else if (params->Estimators[i] == "sorabund") {
treeCalculators.push_back(new SorAbund());
}else if (params->Estimators[i] == "jclass") {
treeCalculators.push_back(new Jclass());
}else if (params->Estimators[i] == "sorclass") {
treeCalculators.push_back(new SorClass());
}else if (params->Estimators[i] == "jest") {
treeCalculators.push_back(new Jest());
}else if (params->Estimators[i] == "sorest") {
treeCalculators.push_back(new SorEst());
}else if (params->Estimators[i] == "thetayc") {
treeCalculators.push_back(new ThetaYC());
}else if (params->Estimators[i] == "thetan") {
treeCalculators.push_back(new ThetaN());
}else if (params->Estimators[i] == "kstest") {
treeCalculators.push_back(new KSTest());
}else if (params->Estimators[i] == "sharednseqs") {
treeCalculators.push_back(new SharedNSeqs());
}else if (params->Estimators[i] == "ochiai") {
treeCalculators.push_back(new Ochiai());
}else if (params->Estimators[i] == "anderberg") {
treeCalculators.push_back(new Anderberg());
}else if (params->Estimators[i] == "kulczynski") {
treeCalculators.push_back(new Kulczynski());
}else if (params->Estimators[i] == "kulczynskicody") {
treeCalculators.push_back(new KulczynskiCody());
}else if (params->Estimators[i] == "lennon") {
treeCalculators.push_back(new Lennon());
}else if (params->Estimators[i] == "morisitahorn") {
treeCalculators.push_back(new MorHorn());
}else if (params->Estimators[i] == "braycurtis") {
treeCalculators.push_back(new BrayCurtis());
}else if (params->Estimators[i] == "whittaker") {
treeCalculators.push_back(new Whittaker());
}else if (params->Estimators[i] == "odum") {
treeCalculators.push_back(new Odum());
}else if (params->Estimators[i] == "canberra") {
treeCalculators.push_back(new Canberra());
}else if (params->Estimators[i] == "structeuclidean") {
treeCalculators.push_back(new StructEuclidean());
}else if (params->Estimators[i] == "structchord") {
treeCalculators.push_back(new StructChord());
}else if (params->Estimators[i] == "hellinger") {
treeCalculators.push_back(new Hellinger());
}else if (params->Estimators[i] == "manhattan") {
treeCalculators.push_back(new Manhattan());
}else if (params->Estimators[i] == "structpearson") {
treeCalculators.push_back(new StructPearson());
}else if (params->Estimators[i] == "soergel") {
treeCalculators.push_back(new Soergel());
}else if (params->Estimators[i] == "spearman") {
treeCalculators.push_back(new Spearman());
}else if (params->Estimators[i] == "structkulczynski") {
treeCalculators.push_back(new StructKulczynski());
}else if (params->Estimators[i] == "speciesprofile") {
treeCalculators.push_back(new SpeciesProfile());
}else if (params->Estimators[i] == "hamming") {
treeCalculators.push_back(new Hamming());
}else if (params->Estimators[i] == "structchi2") {
treeCalculators.push_back(new StructChi2());
}else if (params->Estimators[i] == "gower") {
treeCalculators.push_back(new Gower());
}else if (params->Estimators[i] == "memchi2") {
treeCalculators.push_back(new MemChi2());
}else if (params->Estimators[i] == "memchord") {
treeCalculators.push_back(new MemChord());
}else if (params->Estimators[i] == "memeuclidean") {
treeCalculators.push_back(new MemEuclidean());
}else if (params->Estimators[i] == "mempearson") {
treeCalculators.push_back(new MemPearson());
}else if (params->Estimators[i] == "jsd") {
treeCalculators.push_back(new JSD());
}else if (params->Estimators[i] == "rjsd") {
treeCalculators.push_back(new RJSD());
}
}
}
//if the users entered no valid calculators don't execute command
if (treeCalculators.size() == 0) { params->m->mothurOut("You have given no valid calculators.\n"); return 0; }
params->Estimators.clear();
for (int i=0; i<treeCalculators.size(); i++) { params->Estimators.push_back(treeCalculators[i]->getName()); }
vector< vector<seqDist> > calcDists; calcDists.resize(treeCalculators.size());
SubSample sample;
for (int thisIter = 0; thisIter < params->numIters; thisIter++) {
SharedRAbundVectors* thisItersLookup = new SharedRAbundVectors(*params->thisLookup);
vector<string> namesOfGroups = thisItersLookup->getNamesGroups();
if ((params->subsample && (!params->mainThread)) || (params->mainThread && (thisIter != 0) ) ) {
if (params->withReplacement) { sample.getSampleWithReplacement(thisItersLookup, params->subsampleSize); }
else { sample.getSample(thisItersLookup, params->subsampleSize); }
}
vector<SharedRAbundVector*> thisItersRabunds = thisItersLookup->getSharedRAbundVectors();
vector<string> thisItersGroupNames = params->thisLookup->getNamesGroups();
driverTreeShared(thisItersRabunds, calcDists, treeCalculators, params->m);
for (int i = 0; i < thisItersRabunds.size(); i++) { delete thisItersRabunds[i]; }
if ((params->subsample && (!params->mainThread)) || (params->mainThread && (thisIter != 0) ) ){
if((thisIter+1) % 100 == 0){ params->m->mothurOutJustToScreen(toString(thisIter+1)+"\n"); }
params->calcDistsTotals.push_back(calcDists);
for (int i = 0; i < calcDists.size(); i++) {
for (int j = 0; j < calcDists[i].size(); j++) {
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: Results: iter = " + toString(thisIter) + ", " + thisItersGroupNames[calcDists[i][j].seq1] + " - " + thisItersGroupNames[calcDists[i][j].seq2] + " distance = " + toString(calcDists[i][j].dist) + ".\n"); }
}
}
}else { //print results for whole dataset
for (int i = 0; i < calcDists.size(); i++) {
if (params->m->getControl_pressed()) { break; }
//initialize matrix
vector< vector<double> > matrix; //square matrix to represent the distance
matrix.resize(thisItersLookup->size());
for (int k = 0; k < thisItersLookup->size(); k++) { matrix[k].resize(thisItersLookup->size(), 0.0); }
for (int j = 0; j < calcDists[i].size(); j++) {
int row = calcDists[i][j].seq1;
int column = calcDists[i][j].seq2;
double dist = calcDists[i][j].dist;
matrix[row][column] = -(dist-1.0);
matrix[column][row] = -(dist-1.0);
}
params->matrices.push_back(matrix);
}
}
for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); }
delete thisItersLookup;
}
if((params->numIters) % 100 != 0){ params->m->mothurOutJustToScreen(toString(params->numIters)+"\n"); }
for (int i=0; i<treeCalculators.size(); i++) { delete treeCalculators[i]; }
return 0;
}
catch(exception& e) {
params->m->errorOut(e, "TreeGroupCommand", "process");
exit(1);
}
}