//**********************************************************************************************************************
vector<string> PCACommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
- CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","pca-loadings",false,false,true); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","pca-loadings",false,false,true); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmetric);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ 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); }
exit(1);
}
}
+//**********************************************************************************************************************
+string PCACommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "pca") { pattern = "[filename],[distance],pca.axes"; }
+ else if (type == "loadings") { pattern = "[filename],[distance],pca.loadings"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getOutputPattern");
+ 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);
}
if (m->control_pressed) { return 0; }
string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile));
- string outputFileName = fbase + lookupFloat[0]->getLabel();
- output(outputFileName, m->Groups, X, d);
+ //string outputFileName = fbase + lookupFloat[0]->getLabel();
+ output(fbase, lookupFloat[0]->getLabel(), m->getGroups(), X, d);
if (metric) {
}
/*********************************************************************************************************************************/
-void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
+void PCACommand::output(string fbase, string label, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
try {
int numEigenValues = d.size();
dsum += d[i];
}
- ofstream pcaData((fnameRoot+".pca.axes").c_str(), ios::trunc);
+ ofstream pcaData;
+ map<string, string> variables;
+ variables["[filename]"] = fbase;
+ variables["[distance]"] = label;
+ string pcaFileName = getOutputFileName("pca",variables);
+ m->openOutputFile(pcaFileName, 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(pcaFileName);
+ outputTypes["pca"].push_back(pcaFileName);
- ofstream pcaLoadings((fnameRoot+".pca.loadings").c_str(), ios::trunc);
+ ofstream pcaLoadings;
+ string loadingsFilename = getOutputFileName("loadings",variables);
+ m->openOutputFile(loadingsFilename, 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(loadingsFilename);
+ outputTypes["loadings"].push_back(loadingsFilename);
pcaLoadings << "axis\tloading\n";
for(int i=0;i<numEigenValues;i++){