}
}
+//**********************************************************************************************************************
+string PCOACommand::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 == "pcoa") { outputFileName = "pcoa.axes"; }
+ else if (type == "loadings") { outputFileName = "pcoa.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, "PCOACommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
PCOACommand::PCOACommand(){
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
phylipfile = m->getPhylipFile();
if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setPhylipFile(phylipfile); }
filename = phylipfile;
output(fbase, names, G, d);
- 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; }
if (metric) {
vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa 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(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
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; }
}
}
}
}
- ofstream pcaData((fnameRoot+"pcoa.axes").c_str(), ios::trunc);
+ ofstream pcaData;
+ string pcoaDataFile = fnameRoot+getOutputFileNameTag("pcoa");
+ m->openOutputFile(pcoaDataFile, pcaData);
pcaData.setf(ios::fixed, ios::floatfield);
pcaData.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+"pcoa.axes");
- outputTypes["pcoa"].push_back(fnameRoot+"pcoa.axes");
+ outputNames.push_back(pcoaDataFile);
+ outputTypes["pcoa"].push_back(pcoaDataFile);
- ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc);
+ ofstream pcaLoadings;
+ string loadingsFile = fnameRoot+getOutputFileNameTag("loadings");
+ m->openOutputFile(loadingsFile, pcaLoadings);
pcaLoadings.setf(ios::fixed, ios::floatfield);
pcaLoadings.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+"pcoa.loadings");
- outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings");
+ outputNames.push_back(loadingsFile);
+ outputTypes["loadings"].push_back(loadingsFile);
pcaLoadings << "axis\tloading\n";
for(int i=0;i<rank;i++){