#include "sensspeccommand.h"
+//**********************************************************************************************************************
+vector<string> SensSpecCommand::getValidParameters(){
+ try {
+ string Array[] = {"list", "phylip", "column", "name", "hard", "label", "cutoff", "precision", "outputdir", "inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SensSpecCommand::SensSpecCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sensspec"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "SensSpecCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SensSpecCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"list","phylip","column","or"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SensSpecCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SensSpecCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//***************************************************************************************************************
SensSpecCommand::SensSpecCommand(string option) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sensspec"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
if (abort == true) { return 0; }
setUpOutput();
+ outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);
if(format == "phylip") { processPhylip(); }
else if(format == "column") { processColumn(); }