exit(1);
}
}
+//**********************************************************************************************************************
+string PCACommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "pca") { outputFileName = "pca.axes"; }
+ else if (type == "loadings") { outputFileName = "pca.loadings"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
PCACommand::PCACommand(){
try {
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else { m->splitAtDash(groups, Groups); }
- m->Groups = Groups;
+ m->setGroups(Groups);
}
//as long as you are not at the end of the file or done wih the lines you want
while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } lookupFloat.clear(); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } lookupFloat.clear(); return 0; }
if(labels.count(lookupFloat[0]->getLabel()) == 1){
processedLabels.insert(lookupFloat[0]->getLabel());
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete input; for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } lookupFloat.clear(); return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete input; for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } lookupFloat.clear(); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } } lookupFloat.clear();
delete input;
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ 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();
vector< vector<double> > matrix(numSamples);
vector<double> colMeans(numOTUs);
-
//fill matrix with shared relative abundances, re-center
for (int i = 0; i < lookupFloat.size(); i++) {
matrix[i].resize(numOTUs, 0);
string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile));
string outputFileName = fbase + lookupFloat[0]->getLabel();
- output(outputFileName, m->Groups, X, d);
+ output(outputFileName, m->getGroups(), X, d);
if (metric) {
vector< vector<double> > PCAEuclidDists = linearCalc.calculateEuclidianDistance(X, i); //G is the pca file
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
double corr = linearCalc.calcPearson(PCAEuclidDists, observedEuclideanDistance);
m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine();
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
}
}
dsum += d[i];
}
- ofstream pcaData((fnameRoot+".pca.axes").c_str(), ios::trunc);
+ ofstream pcaData;
+ m->openOutputFile((fnameRoot+"."+getOutputFileNameTag("pca")), pcaData);
pcaData.setf(ios::fixed, ios::floatfield);
pcaData.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+".pca.axes");
- outputTypes["pca"].push_back(fnameRoot+".pca.axes");
+ outputNames.push_back(fnameRoot+"."+getOutputFileNameTag("pca"));
+ outputTypes["pca"].push_back(fnameRoot+"."+getOutputFileNameTag("pca"));
- ofstream pcaLoadings((fnameRoot+".pca.loadings").c_str(), ios::trunc);
+ ofstream pcaLoadings;
+ m->openOutputFile((fnameRoot+"."+getOutputFileNameTag("loadings")), pcaLoadings);
pcaLoadings.setf(ios::fixed, ios::floatfield);
pcaLoadings.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+".pca.loadings");
- outputTypes["loadings"].push_back(fnameRoot+".pca.loadings");
+ outputNames.push_back(fnameRoot+"."+getOutputFileNameTag("loadings"));
+ outputTypes["loadings"].push_back(fnameRoot+"."+getOutputFileNameTag("loadings"));
pcaLoadings << "axis\tloading\n";
for(int i=0;i<numEigenValues;i++){
}
pcaData << endl;
- for(int i=0;i<numEigenValues;i++){
+ for(int i=0;i<name_list.size();i++){
pcaData << name_list[i] << '\t';
for(int j=0;j<numEigenValues;j++){
pcaData << G[i][j] << '\t';