#include "mempearson.h"
//**********************************************************************************************************************
-vector<string> TreeGroupCommand::getValidParameters(){
+vector<string> TreeGroupCommand::setParameters(){
try {
- string Array[] = {"label","calc","groups", "phylip", "column", "name", "precision","cutoff","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);
+ CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "getValidParameters");
+ m->errorOut(e, "TreeGroupCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-TreeGroupCommand::TreeGroupCommand(){
+string TreeGroupCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- globaldata = GlobalData::getInstance();
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["tree"] = tempOutNames;
+ string helpString = "";
+ ValidCalculators validCalculator;
+ helpString += "The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n";
+ helpString += "The tree.shared command parameters are shared, groups, calc, phylip, column, name, cutoff, precision and label.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
+ helpString += "The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n";
+ helpString += "The phylip or column parameter are required if you do not provide a sharedfile, and only one may be used. If you use a column file the name filename is required. \n";
+ helpString += "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n";
+ helpString += "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
+ helpString += "Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n";
+ helpString += "The default value for groups is all the groups in your groupfile.\n";
+ helpString += "The default value for calc is jclass-thetayc.\n";
+ helpString += "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n";
+ helpString += validCalculator.printCalc("treegroup");
+ helpString += "Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n";
+ helpString += "Example tree.shared(phylip=abrecovery.dist).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
+ m->errorOut(e, "TreeGroupCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> TreeGroupCommand::getRequiredParameters(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "getRequiredParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-vector<string> TreeGroupCommand::getRequiredFiles(){
+TreeGroupCommand::TreeGroupCommand(){
try {
- string Array[] = {"phylip","column","shared","or"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "getRequiredFiles");
+ m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
exit(1);
}
}
TreeGroupCommand::TreeGroupCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
abort = false; calledHelp = false;
allLines = 1;
- labels.clear();
- Groups.clear();
- Estimators.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"label","calc","groups", "phylip", "column", "name", "precision","cutoff","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser. getParameters();
}
}
- format = globaldata->getFormat();
-
- //required parameters
+ //check for required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
- if (phylipfile == "not open") { abort = true; }
+ if (phylipfile == "not open") { phylipfile = ""; abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
- else { globaldata->newRead(); format = "phylip"; globaldata->setPhylipFile(phylipfile); }
+ else { inputfile = phylipfile; format = "phylip"; }
columnfile = validParameter.validFile(parameters, "column", true);
- if (columnfile == "not open") { abort = true; }
+ if (columnfile == "not open") { columnfile = ""; abort = true; }
else if (columnfile == "not found") { columnfile = ""; }
- else { globaldata->newRead(); format = "column"; globaldata->setColumnFile(columnfile); }
+ else { inputfile = columnfile; format = "column"; }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { inputfile = sharedfile; format = "sharedfile"; }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
- else { globaldata->setNameFile(namefile); }
- //error checking on files
- if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { m->mothurOut("You must run the read.otu command or provide a distance file before running the tree.shared command."); m->mothurOutEndLine(); abort = true; }
+ 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 == "") { m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); abort = true; }
+ if (namefile == "") {
+ namefile = m->getNameFile();
+ if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
}
-
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
else { allLines = 1; }
}
- //if the user has not specified any labels use the ones from read.otu
- if(label == "") {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- }
-
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->Groups = Groups;
}
calc = validParameter.validFile(parameters, "calc", false);
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
- outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(inputfile); //if user entered a file with a path then preserve it
}
-
-
- if (abort == false) {
-
- validCalculator = new ValidCalculators();
-
- if (format == "sharedfile") {
- int i;
- for (i=0; 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());
- }
- }
- }
- }
- }
}
}
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void TreeGroupCommand::help(){
- try {
- m->mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n");
- m->mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n");
- m->mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision and label.\n");
- m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
- m->mothurOut("The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n");
- m->mothurOut("The phylip or column parameter are required if you do not run the read.otu command first, and only one may be used. If you use a column file the name filename is required. \n");
- m->mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
- m->mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
- m->mothurOut("Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n");
- m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
- m->mothurOut("The default value for calc is jclass-thetayc.\n");
- m->mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n");
- validCalculator->printCalc("treegroup", cout);
- m->mothurOut("Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n");
- m->mothurOut("Example tree.shared(phylip=abrecovery.dist).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "TreeGroupCommand", "help");
- exit(1);
- }
-}
-
-
//**********************************************************************************************************************
TreeGroupCommand::~TreeGroupCommand(){
- globaldata->Groups.clear();
if (abort == false) {
-
- if (format == "sharedfile") { delete read; delete input; globaldata->ginput = NULL; }
+ if (format == "sharedfile") { delete input; }
else { delete readMatrix; delete matrix; delete list; }
- delete tmap; globaldata->gTreemap = NULL;
- delete validCalculator;
+ delete tmap;
}
}
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());
+ }
+ }
+ }
+
//if the users entered no valid calculators don't execute command
if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
- if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; globaldata->gGroupmap = NULL; }
- //you have groups
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
+ 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
- globaldata->runParse = false;
+ m->runParse = false;
//create treemap class from groupmap for tree class to use
tmap = new TreeMap();
- tmap->makeSim(globaldata->gGroupmap);
- globaldata->gTreemap = tmap;
+ tmap->makeSim(m->namesOfGroups);
//clear globaldatas old tree names if any
- globaldata->Treenames.clear();
+ m->Treenames.clear();
//fills globaldatas tree names
- globaldata->Treenames = globaldata->Groups;
+ m->Treenames = m->Groups;
if (m->control_pressed) { return 0; }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
}else{
//read in dist file
- filename = globaldata->inputFileName;
+ filename = inputfile;
if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
if (m->control_pressed) { return 0; }
tmap->makeSim(list);
- globaldata->gTreemap = tmap;
- globaldata->Groups = tmap->namesOfGroups;
+ m->Groups = tmap->namesOfGroups;
//clear globaldatas old tree names if any
- globaldata->Treenames.clear();
+ m->Treenames.clear();
//fills globaldatas tree names
- globaldata->Treenames = globaldata->Groups;
+ m->Treenames = m->Groups;
//used in tree constructor
- globaldata->runParse = false;
+ m->runParse = false;
if (m->control_pressed) { return 0; }
if (m->control_pressed) { return 0; }
//create a new filename
- outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "tre";
+ outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "tre";
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
createTree();
}
//reset groups parameter
- globaldata->Groups.clear();
+ m->Groups.clear();
//set tree file as new current treefile
string current = "";
int TreeGroupCommand::createTree(){
try {
//create tree
- t = new Tree();
+ t = new Tree(tmap);
//do merges and create tree structure by setting parents and children
//there are numGroups - 1 merges to do
for (int g = 0; g < numGroups; g++) { index[g] = g; }
//create a new filename
- outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
+ outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
for (int k = 0; k < thisLookup.size(); k++) {
projects / mothur.git / blobdiff