#include "getsabundcommand.h"
//**********************************************************************************************************************
-
+vector<string> GetSAbundCommand::getValidParameters(){
+ try {
+ string Array[] = {"label","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetSAbundCommand::GetSAbundCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetSAbundCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetSAbundCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"list","rabund"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
GetSAbundCommand::GetSAbundCommand(string option) {
try {
globaldata = GlobalData::getInstance();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+
//if the user changes the output directory command factory will send this info to us in the output parameter
string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
set<string> processedLabels;
set<string> userLabels = labels;
- if (m->control_pressed) { out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
sabund->print(out);
delete sabund;
- if (m->control_pressed) { out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
sabund->print(out);
delete sabund;
- if (m->control_pressed) { out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
sabund->print(out);
delete sabund;
- if (m->control_pressed) { out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
delete order;
}
m->mothurOutEndLine();
m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(filename); m->mothurOutEndLine();
+ m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["sabund"].push_back(filename);
m->mothurOutEndLine();
return 0;