#include "getlistcountcommand.h"
+//**********************************************************************************************************************
+vector<string> GetListCountCommand::getValidParameters(){
+ try {
+ string Array[] = {"list","label","sort","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetListCountCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetListCountCommand::GetListCountCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["otu"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetListCountCommand", "GetListCountCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetListCountCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"list"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetListCountCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetListCountCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetListCountCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
GetListCountCommand::GetListCountCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["otu"] = tempOutNames;
+
string ranRead = globaldata->getListFile();
//if the user changes the input directory command factory will send this info to us in the output parameter
int GetListCountCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
globaldata->setFormat("list");
delete input;
delete list;
globaldata->gListVector = NULL;
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
return 0;
}
delete input;
delete list;
globaldata->gListVector = NULL;
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
return 0;
}
delete input;
delete list;
globaldata->gListVector = NULL;
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
return 0;
}
if (outputDir == "") { outputDir += m->hasPath(listfile); }
string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".otu";
m->openOutputFile(outputFileName, out);
- outputNames.push_back(outputFileName);
+ outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);
m->mothurOut(list->getLabel()); m->mothurOutEndLine();