string Array[] = {"freq","line","label","calc","abund","size"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- parser = new OptionParser();
- parser->parse(option, parameters); delete parser;
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
- ValidParameters* validParameter = new ValidParameters();
+ ValidParameters validParameter;
//check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter->isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//make sure the user has already run the read.otu command
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
- line = validParameter->validFile(parameters, "line", false);
+ line = validParameter.validFile(parameters, "line", false);
if (line == "not found") { line = ""; }
else {
if(line != "all") { splitAtDash(line, lines); allLines = 0; }
else { allLines = 1; }
}
- label = validParameter->validFile(parameters, "label", false);
+ label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
if(label != "all") { splitAtDash(label, labels); allLines = 0; }
lines = globaldata->lines;
}
- calc = validParameter->validFile(parameters, "calc", false);
+ calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
else {
if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
splitAtDash(calc, Estimators);
string temp;
- temp = validParameter->validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
+ temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
convert(temp, freq);
- temp = validParameter->validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
+ temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
convert(temp, abund);
- temp = validParameter->validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
+ temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
convert(temp, size);
-
- delete validParameter;
-
-
+
if (abort == false) {
string fileNameRoot = getRootName(globaldata->inputFileName);
int i;
//**********************************************************************************************************************
CollectCommand::~CollectCommand(){
- delete order;
- delete input;
- delete cCurve;
- delete read;
- delete validCalculator;
+ if (abort == false) {
+ //delete order;
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ globaldata->gorder = NULL;
+ }
}
//**********************************************************************************************************************
userLabels.erase(lastOrder->getLabel());
}
- if (count != 1) { delete lastOrder; }
+ if (count != 1) { delete lastOrder; }
lastOrder = order;
order = (input->getOrderVector());
count++;