ValidCalculators* validCalculator = new ValidCalculators();
- if (sharedfile != "") {
-
- for (int i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("treegroup", Estimators[i]) == true) {
- if (Estimators[i] == "sharedsobs") {
- calculators.push_back(new SharedSobsCS());
- }else if (Estimators[i] == "sharedchao") {
- calculators.push_back(new SharedChao1());
- }else if (Estimators[i] == "sharedace") {
- calculators.push_back(new SharedAce());
- }else if (Estimators[i] == "jabund") {
- calculators.push_back(new JAbund());
- }else if (Estimators[i] == "sorabund") {
- calculators.push_back(new SorAbund());
- }else if (Estimators[i] == "jclass") {
- calculators.push_back(new Jclass());
- }else if (Estimators[i] == "sorclass") {
- calculators.push_back(new SorClass());
- }else if (Estimators[i] == "jest") {
- calculators.push_back(new Jest());
- }else if (Estimators[i] == "sorest") {
- calculators.push_back(new SorEst());
- }else if (Estimators[i] == "thetayc") {
- calculators.push_back(new ThetaYC());
- }else if (Estimators[i] == "thetan") {
- calculators.push_back(new ThetaN());
- }else if (Estimators[i] == "kstest") {
- calculators.push_back(new KSTest());
- }else if (Estimators[i] == "sharednseqs") {
- calculators.push_back(new SharedNSeqs());
- }else if (Estimators[i] == "ochiai") {
- calculators.push_back(new Ochiai());
- }else if (Estimators[i] == "anderberg") {
- calculators.push_back(new Anderberg());
- }else if (Estimators[i] == "kulczynski") {
- calculators.push_back(new Kulczynski());
- }else if (Estimators[i] == "kulczynskicody") {
- calculators.push_back(new KulczynskiCody());
- }else if (Estimators[i] == "lennon") {
- calculators.push_back(new Lennon());
- }else if (Estimators[i] == "morisitahorn") {
- calculators.push_back(new MorHorn());
- }else if (Estimators[i] == "braycurtis") {
- calculators.push_back(new BrayCurtis());
- }else if (Estimators[i] == "whittaker") {
- calculators.push_back(new Whittaker());
- }else if (Estimators[i] == "odum") {
- calculators.push_back(new Odum());
- }else if (Estimators[i] == "canberra") {
- calculators.push_back(new Canberra());
- }else if (Estimators[i] == "structeuclidean") {
- calculators.push_back(new StructEuclidean());
- }else if (Estimators[i] == "structchord") {
- calculators.push_back(new StructChord());
- }else if (Estimators[i] == "hellinger") {
- calculators.push_back(new Hellinger());
- }else if (Estimators[i] == "manhattan") {
- calculators.push_back(new Manhattan());
- }else if (Estimators[i] == "structpearson") {
- calculators.push_back(new StructPearson());
- }else if (Estimators[i] == "soergel") {
- calculators.push_back(new Soergel());
- }else if (Estimators[i] == "spearman") {
- calculators.push_back(new Spearman());
- }else if (Estimators[i] == "structkulczynski") {
- calculators.push_back(new StructKulczynski());
- }else if (Estimators[i] == "speciesprofile") {
- calculators.push_back(new SpeciesProfile());
- }else if (Estimators[i] == "hamming") {
- calculators.push_back(new Hamming());
- }else if (Estimators[i] == "structchi2") {
- calculators.push_back(new StructChi2());
- }else if (Estimators[i] == "gower") {
- calculators.push_back(new Gower());
- }else if (Estimators[i] == "memchi2") {
- calculators.push_back(new MemChi2());
- }else if (Estimators[i] == "memchord") {
- calculators.push_back(new MemChord());
- }else if (Estimators[i] == "memeuclidean") {
- calculators.push_back(new MemEuclidean());
- }else if (Estimators[i] == "mempearson") {
- calculators.push_back(new MemPearson());
- }
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("treegroup", Estimators[i]) == true) {
+ if (Estimators[i] == "sharedsobs") {
+ calculators.push_back(new SharedSobsCS());
+ }else if (Estimators[i] == "sharedchao") {
+ calculators.push_back(new SharedChao1());
+ }else if (Estimators[i] == "sharedace") {
+ calculators.push_back(new SharedAce());
+ }else if (Estimators[i] == "jabund") {
+ calculators.push_back(new JAbund());
+ }else if (Estimators[i] == "sorabund") {
+ calculators.push_back(new SorAbund());
+ }else if (Estimators[i] == "jclass") {
+ calculators.push_back(new Jclass());
+ }else if (Estimators[i] == "sorclass") {
+ calculators.push_back(new SorClass());
+ }else if (Estimators[i] == "jest") {
+ calculators.push_back(new Jest());
+ }else if (Estimators[i] == "sorest") {
+ calculators.push_back(new SorEst());
+ }else if (Estimators[i] == "thetayc") {
+ calculators.push_back(new ThetaYC());
+ }else if (Estimators[i] == "thetan") {
+ calculators.push_back(new ThetaN());
+ }else if (Estimators[i] == "kstest") {
+ calculators.push_back(new KSTest());
+ }else if (Estimators[i] == "sharednseqs") {
+ calculators.push_back(new SharedNSeqs());
+ }else if (Estimators[i] == "ochiai") {
+ calculators.push_back(new Ochiai());
+ }else if (Estimators[i] == "anderberg") {
+ calculators.push_back(new Anderberg());
+ }else if (Estimators[i] == "kulczynski") {
+ calculators.push_back(new Kulczynski());
+ }else if (Estimators[i] == "kulczynskicody") {
+ calculators.push_back(new KulczynskiCody());
+ }else if (Estimators[i] == "lennon") {
+ calculators.push_back(new Lennon());
+ }else if (Estimators[i] == "morisitahorn") {
+ calculators.push_back(new MorHorn());
+ }else if (Estimators[i] == "braycurtis") {
+ calculators.push_back(new BrayCurtis());
+ }else if (Estimators[i] == "whittaker") {
+ calculators.push_back(new Whittaker());
+ }else if (Estimators[i] == "odum") {
+ calculators.push_back(new Odum());
+ }else if (Estimators[i] == "canberra") {
+ calculators.push_back(new Canberra());
+ }else if (Estimators[i] == "structeuclidean") {
+ calculators.push_back(new StructEuclidean());
+ }else if (Estimators[i] == "structchord") {
+ calculators.push_back(new StructChord());
+ }else if (Estimators[i] == "hellinger") {
+ calculators.push_back(new Hellinger());
+ }else if (Estimators[i] == "manhattan") {
+ calculators.push_back(new Manhattan());
+ }else if (Estimators[i] == "structpearson") {
+ calculators.push_back(new StructPearson());
+ }else if (Estimators[i] == "soergel") {
+ calculators.push_back(new Soergel());
+ }else if (Estimators[i] == "spearman") {
+ calculators.push_back(new Spearman());
+ }else if (Estimators[i] == "structkulczynski") {
+ calculators.push_back(new StructKulczynski());
+ }else if (Estimators[i] == "speciesprofile") {
+ calculators.push_back(new SpeciesProfile());
+ }else if (Estimators[i] == "hamming") {
+ calculators.push_back(new Hamming());
+ }else if (Estimators[i] == "structchi2") {
+ calculators.push_back(new StructChi2());
+ }else if (Estimators[i] == "gower") {
+ calculators.push_back(new Gower());
+ }else if (Estimators[i] == "memchi2") {
+ calculators.push_back(new MemChi2());
+ }else if (Estimators[i] == "memchord") {
+ calculators.push_back(new MemChord());
+ }else if (Estimators[i] == "memeuclidean") {
+ calculators.push_back(new MemEuclidean());
+ }else if (Estimators[i] == "mempearson") {
+ calculators.push_back(new MemPearson());
}
}
}
}else { //user provided distance matrix
-
- //for each calculator
- for(int i = 0 ; i < calculators.size(); i++) {
- //create a new filename
- ofstream out;
- string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + calculators[i]->getName() + ".amova";
- m->openOutputFile(outputFile, out);
- outputNames.push_back(outputFile); outputTypes["amova"].push_back(outputFile);
-
- //print headers
- out << "groupsCompared\tMeanSquaredWithin\tMeanSquaredAmong\tFstatistic\tpValue" << endl;
- out.close();
- }
+
+ if (outputDir == "") { outputDir = m->hasPath(phylipfile); }
+
+ //create a new filename
+ ofstream out;
+ string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "amova";
+ m->openOutputFile(outputFile, out);
+ outputNames.push_back(outputFile); outputTypes["amova"].push_back(outputFile);
+
+ //print headers
+ out << "groupsCompared\tMeanSquaredWithin\tMeanSquaredAmong\tFstatistic\tpValue" << endl;
+ out.close();
ReadPhylipVector readMatrix(phylipfile);
vector< vector<double> > completeMatrix;
}
//append files
- for(int i = 0 ; i < calculators.size(); i++) {
- string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + calculators[i]->getName() + ".amova";
-
- for (int j = 0; j < processIDS.size(); j++) {
- m->appendFiles((outputFile + toString(processIDS[j])), outputFile);
- remove((outputFile + toString(processIDS[j])).c_str());
- }
+ string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "amova";
+ for (int j = 0; j < processIDS.size(); j++) {
+ m->appendFiles((outputFile + toString(processIDS[j])), outputFile);
+ remove((outputFile + toString(processIDS[j])).c_str());
}
+
}
#else
driver(0, namesOfGroupCombos.size(), names, "", completeMatrix);
matrix.resize(numGroups);
for (int k = 0; k < matrix.size(); k++) { for (int j = 0; j < matrix.size(); j++) { matrix[k].push_back(1.0); } }
- if (thisCombosLookup.size() != 0) {
+ if (thisCombosLookup.size() == 0) {
m->mothurOut("[ERROR]: Missing shared info for sets. Skipping comparison."); m->mothurOutEndLine();
}else{
int AmovaCommand::driver(int start, int num, vector<string> names, string pidValue, vector< vector<double> >& completeMatrix) {
try {
- //for each calculator
- for(int i = 0 ; i < calculators.size(); i++) {
+ //create a new filename
+ ofstream out;
+ string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "amova" + pidValue;
+ m->openOutputFileAppend(outputFile, out);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ //for each combo
+ for (int c = start; c < (start+num); c++) {
- //create a new filename
- ofstream out;
- string outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + calculators[i]->getName() + ".amova" + pidValue;
- m->openOutputFileAppend(outputFile, out);
- out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ if (m->control_pressed) { out.close(); return 0; }
- //for each combo
- for (int c = start; c < (start+num); c++) {
-
- if (m->control_pressed) { out.close(); return 0; }
-
- //get set names
- vector<string> setNames;
- for (int j = 0; j < namesOfGroupCombos[c].size(); j++) { setNames.push_back(namesOfGroupCombos[c][j]); }
-
- vector<string> thisCombosSets; //what set each line in the distance matrix is from to be used when calculating SSWithin
- set<int> indexes;
- for (int k = 0; k < names.size(); k++) {
- //is this group for a set we want to compare??
- if (m->inUsersGroups(designMap->getGroup(names[k]), setNames)) {
- thisCombosSets.push_back(designMap->getGroup(names[k]));
- indexes.insert(k); //save indexes of valid rows in matrix for submatrix
- }
+ //get set names
+ vector<string> setNames;
+ for (int j = 0; j < namesOfGroupCombos[c].size(); j++) { setNames.push_back(namesOfGroupCombos[c][j]); }
+
+ vector<string> thisCombosSets; //what set each line in the distance matrix is from to be used when calculating SSWithin
+ set<int> indexes;
+ for (int k = 0; k < names.size(); k++) {
+ //is this group for a set we want to compare??
+ if (m->inUsersGroups(designMap->getGroup(names[k]), setNames)) {
+ thisCombosSets.push_back(designMap->getGroup(names[k]));
+ indexes.insert(k); //save indexes of valid rows in matrix for submatrix
}
+ }
+
+ int numGroups = thisCombosSets.size();
+
+ //calc the distance matrix
+ matrix.clear();
+ matrix.resize(numGroups);
+
+ for (int k = 0; k < matrix.size(); k++) { for (int j = 0; j < matrix.size(); j++) { matrix[k].push_back(1.0); } }
+
+ if (thisCombosSets.size() == 0) {
+ m->mothurOut("[ERROR]: Missing distance info for sets. Skipping comparison."); m->mothurOutEndLine();
+ }else{
- int numGroups = thisCombosSets.size();
-
- //calc the distance matrix
- matrix.clear();
- matrix.resize(numGroups);
- for (int k = 0; k < matrix.size(); k++) { for (int j = 0; j < matrix.size(); j++) { matrix[k].push_back(1.0); } }
+ if (setNames.size() == 2) { out << setNames[0] << "-" << setNames[1] << '\t'; }
+ else { out << "all" << '\t'; }
- if (thisCombosSets.size() != 0) {
- m->mothurOut("[ERROR]: Missing distance info for sets. Skipping comparison."); m->mothurOutEndLine();
- }else{
+ //fill submatrix
+ int rowCount = 0;
+ for (int j = 0; j < completeMatrix.size(); j++) {
- if (setNames.size() == 2) { out << setNames[0] << "-" << setNames[1] << '\t'; }
- else { out << "all" << '\t'; }
-
- //fill submatrix
- int rowCount = 0;
- int columnCount = 0;
- for (int j = 0; j < completeMatrix.size(); j++) {
-
- if (indexes.count(j) != 0) { //we want at least part of this row
- for (int k = 0; k < completeMatrix[j].size(); k++) {
-
- if (indexes.count(k) != 0) { //we want this distance
- matrix[rowCount][columnCount] = completeMatrix[j][k];
- matrix[columnCount][rowCount] = completeMatrix[j][k];
- columnCount++;
- }
+ if (indexes.count(j) != 0) { //we want at least part of this row
+ int columnCount = 0;
+ for (int k = 0; k < completeMatrix[j].size(); k++) {
+
+ if (indexes.count(k) != 0) { //we want this distance
+ matrix[rowCount][columnCount] = completeMatrix[j][k];
+ matrix[columnCount][rowCount] = completeMatrix[j][k];
+ columnCount++;
}
- rowCount++;
}
+ rowCount++;
}
-
- //calc amova
- calcAmova(out, setNames.size(), thisCombosSets);
}
+
+ //calc amova
+ calcAmova(out, setNames.size(), thisCombosSets);
}
-
- out.close();
- }
+ }
+ out.close();
+
+
return 0;
}
pValue = count / (float) iters;
out << MSWithin << '\t' << MSAmoung << '\t' << FStatistic << '\t' << pValue << endl;
-
+ //cout << "ssAmong = " << SSAmoung << '\t' << "sswithin = " << SSWithin << '\t' << "ssTotal = " << SSTotal << '\t' << "pvalue = " << pValue << endl;
return 0;
}
catch(exception& e) {
projects / mothur.git / commitdiff