#include "pcacommand.h"
+//**********************************************************************************************************************
+vector<string> PCACommand::getValidParameters(){
+ try {
+ string Array[] = {"phylip", "outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PCACommand::PCACommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["pcoa"] = tempOutNames;
+ outputTypes["loadings"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "PCACommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PCACommand::getRequiredParameters(){
+ try {
+ string Array[] = {"phylip"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PCACommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PCACommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
PCACommand::PCACommand(string option) {
if (path == "") { parameters["phylip"] = inputDir + it->second; }
}
}
-
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["pcoa"] = tempOutNames;
+ outputTypes["loadings"] = tempOutNames;
+
//required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
}
}
- ofstream pcaData((fnameRoot+"pca").c_str(), ios::trunc);
+ ofstream pcaData((fnameRoot+"pcoa").c_str(), ios::trunc);
pcaData.setf(ios::fixed, ios::floatfield);
pcaData.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+"pca");
+ outputNames.push_back(fnameRoot+"pcoa");
+ outputTypes["pcoa"].push_back(fnameRoot+"pcoa");
- ofstream pcaLoadings((fnameRoot+"pca.loadings").c_str(), ios::trunc);
+ ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc);
pcaLoadings.setf(ios::fixed, ios::floatfield);
pcaLoadings.setf(ios::showpoint);
- outputNames.push_back(fnameRoot+"pca.loadings");
+ outputNames.push_back(fnameRoot+"pcoa.loadings");
+ outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings");
pcaLoadings << "axis\tloading\n";
for(int i=0;i<rank;i++){