//**********************************************************************************************************************
RareFactCommand::RareFactCommand(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["rarefaction"] = tempOutNames;
outputTypes["r_chao"] = tempOutNames;
outputTypes["r_ace"] = tempOutNames;
outputTypes["r_jack"] = tempOutNames;
outputTypes["r_shannon"] = tempOutNames;
outputTypes["r_shannoneven"] = tempOutNames;
outputTypes["r_shannonrange"] = tempOutNames;
outputTypes["r_heip"] = tempOutNames;
outputTypes["r_smithwilson"] = tempOutNames;
outputTypes["r_npshannon"] = tempOutNames;
outputTypes["r_simpson"] = tempOutNames;
outputTypes["r_simpsoneven"] = tempOutNames;
outputTypes["r_invsimpson"] = tempOutNames;
outputTypes["r_bootstrap"] = tempOutNames;
outputTypes["r_coverage"] = tempOutNames;
outputTypes["r_nseqs"] = 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; }
}
it = parameters.find("rabund");
//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["rabund"] = inputDir + it->second; }
}
it = parameters.find("sabund");
//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["sabund"] = inputDir + it->second; }
}
it = parameters.find("list");
//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["list"] = inputDir + it->second; }
}
}
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
rabundfile = validParameter.validFile(parameters, "rabund", true);
if (rabundfile == "not open") { rabundfile = ""; abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
//is there are current file available for any of these?
//give priority to shared, then list, then rabund, then sabund
//if there is a current shared file, use it
sharedfile = m->getSharedFile();
if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
else {
listfile = m->getListFile();
if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
else {
rabundfile = m->getRabundFile();
if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
else {
sabundfile = m->getSabundFile();
if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine();
abort = true;
}
}
}
}
}
//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(inputfile); }
//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 = "sobs"; }
else {
if (calc == "default") { calc = "sobs"; }
}
m->splitAtDash(calc, Estimators);
if (m->inUsersGroups("citation", Estimators)) {
ValidCalculators validCalc; validCalc.printCitations(Estimators);
//remove citation from list of calcs
for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
}
string temp;
temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
m->mothurConvert(temp, freq);
temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
m->mothurConvert(temp, abund);
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
m->mothurConvert(temp, nIters);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "alpha", false); if (temp == "not found") { temp = "1"; }
m->mothurConvert(temp, alpha);
if ((alpha != 0) && (alpha != 1) && (alpha != 2)) { m->mothurOut("[ERROR]: Not a valid alpha value. Valid values are 0, 1 and 2."); m->mothurOutEndLine(); abort=true; }
temp = validParameter.validFile(parameters, "groupmode", false); if (temp == "not found") { temp = "T"; }
groupMode = m->isTrue(temp);
}
}
catch(exception& e) {
m->errorOut(e, "RareFactCommand", "RareFactCommand");
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);
}
}
SummaryCommand::SummaryCommand(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 (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {
abort = true;
}
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["summary"] = 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;
}
}
it = parameters.find("rabund");
//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["rabund"] = inputDir + it->second;
}
}
it = parameters.find("sabund");
//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["sabund"] = inputDir + it->second;
}
}
it = parameters.find("list");
//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["list"] = inputDir + it->second;
}
}
}
//check for required parameters
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") {
listfile = "";
abort = true;
}
else if (listfile == "not found") {
listfile = "";
}
else {
format = "list";
inputfile = listfile;
m->setListFile(listfile);
}
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") {
sabundfile = "";
abort = true;
}
else if (sabundfile == "not found") {
sabundfile = "";
}
else {
format = "sabund";
inputfile = sabundfile;
m->setSabundFile(sabundfile);
}
rabundfile = validParameter.validFile(parameters, "rabund", true);
if (rabundfile == "not open") {
rabundfile = "";
abort = true;
}
else if (rabundfile == "not found") {
rabundfile = "";
}
else {
format = "rabund";
inputfile = rabundfile;
m->setRabundFile(rabundfile);
}
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") {
sharedfile = "";
abort = true;
}
else if (sharedfile == "not found") {
sharedfile = "";
}
else {
format = "sharedfile";
inputfile = sharedfile;
m->setSharedFile(sharedfile);
}
if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
//is there are current file available for any of these?
//give priority to shared, then list, then rabund, then sabund
//if there is a current shared file, use it
sharedfile = m->getSharedFile();
if (sharedfile != "") {
inputfile = sharedfile;
format = "sharedfile";
m->mothurOut("Using " + sharedfile + " as input file for the shared parameter.");
m->mothurOutEndLine();
}
else {
listfile = m->getListFile();
if (listfile != "") {
inputfile = listfile;
format = "list";
m->mothurOut("Using " + listfile + " as input file for the list parameter.");
m->mothurOutEndLine();
}
else {
rabundfile = m->getRabundFile();
if (rabundfile != "") {
inputfile = rabundfile;
format = "rabund";
m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter.");
m->mothurOutEndLine();
}
else {
sabundfile = m->getSabundFile();
if (sabundfile != "") {
inputfile = sabundfile;
format = "sabund";
m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter.");
m->mothurOutEndLine();
}
else {
m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command.");
m->mothurOutEndLine();
abort = true;
}
}
}
}
}
//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(inputfile);
}
//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 = "sobs-chao-ace-jack-shannon-npshannon-simpson";
}
else {
if (calc == "default") {
calc = "sobs-chao-ace-jack-shannon-npshannon-simpson";
}
}
m->splitAtDash(calc, Estimators);
if (m->inUsersGroups("citation", Estimators)) {
ValidCalculators validCalc;
validCalc.printCitations(Estimators);
//remove citation from list of calcs
for (int i = 0; i < Estimators.size(); i++) {
if (Estimators[i] == "citation") {
Estimators.erase(Estimators.begin()+i);
break;
}
}
}
string temp;
temp = validParameter.validFile(parameters, "abund", false);
if (temp == "not found") {
temp = "10";
}
m->mothurConvert(temp, abund);
temp = validParameter.validFile(parameters, "size", false);
if (temp == "not found") {
temp = "0";
}
m->mothurConvert(temp, size);
temp = validParameter.validFile(parameters, "groupmode", false);
if (temp == "not found") {
temp = "T";
}
groupMode = m->isTrue(temp);
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; //we will set it to smallest group later
subsampleSize = -1;
}
else {
subsample = false;
subsampleSize = -1;
}
}
if (subsample == false) {
iters = 0;
}
else {
//if you did not set a samplesize and are not using a sharedfile
if ((subsampleSize == -1) && (format != "sharedfile")) {
m->mothurOut("[ERROR]: If you want to subsample with a list, rabund or sabund file, you must provide the sample size. You can do this by setting subsample=yourSampleSize.\n");
abort=true;
}
}
}
}
catch(exception& e) {
m->errorOut(e, "SummaryCommand", "SummaryCommand");
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);
}
}
TreeGroupCommand::TreeGroupCommand(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();
ValidParameters validParameter;
map<string, string>::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<string> 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; }
}
it = parameters.find("count");
//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["count"] = inputDir + it->second; }
}
}
//check for required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { phylipfile = ""; abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
else { inputfile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile); }
columnfile = validParameter.validFile(parameters, "column", true);
if (columnfile == "not open") { columnfile = ""; abort = true; }
else if (columnfile == "not found") { columnfile = ""; }
else { inputfile = columnfile; format = "column"; m->setColumnFile(columnfile); }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
else { inputfile = sharedfile; format = "sharedfile"; m->setSharedFile(sharedfile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { abort = true; countfile = ""; }
else if (countfile == "not found") { countfile = ""; }
else { m->setCountTableFile(countfile); }
if ((phylipfile == "") && (columnfile == "") && (sharedfile == "")) {
//is there are current file available for either of these?
//give priority to shared, then column, then phylip
sharedfile = m->getSharedFile();
if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
else {
columnfile = m->getColumnFile();
if (columnfile != "") { inputfile = columnfile; format = "column"; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
else {
phylipfile = m->getPhylipFile();
if (phylipfile != "") { inputfile = phylipfile; format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("No valid current files. You must provide a shared, phylip or column file."); 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 == "") && (countfile == "")){
namefile = m->getNameFile();
if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
else {
countfile = m->getCountTableFile();
if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("You need to provide a namefile or countfile 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; }
}
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
m->setGroups(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);
if (m->inUsersGroups("citation", Estimators)) {
ValidCalculators validCalc; validCalc.printCitations(Estimators);
//remove citation from list of calcs
for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
}
string temp;
temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
m->mothurConvert(temp, precision);
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; }
m->mothurConvert(temp, cutoff);
cutoff += (5 / (precision * 10.0));
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
m->mothurConvert(temp, processors);
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 = 1; }
if (subsample && (format != "sharedfile")) { m->mothurOut("[ERROR]: the subsample parameter can only be used with a shared file.\n"); abort=true; }
//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(inputfile); //if user entered a file with a path then preserve it
}
}
}
catch(exception& e) {
m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
exit(1);
}
}