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);
}
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) {
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++){