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
- if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the collect.single command." << endl; abort = true; }
+ if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the collect.single command."); mothurOutEndLine(); abort = true; }
//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; }
}
//make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
+ if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
//if the user has not specified any line or labels use the ones from read.otu
else if((line == "") && (label == "")) {
allLines = globaldata->allLines;
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;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the CollectCommand class function CollectCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "CollectCommand", "CollectCommand");
exit(1);
- }
-
+ }
}
//**********************************************************************************************************************
void CollectCommand::help(){
try {
- cout << "The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. " << "\n";
- cout << "The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n";
- cout << "The collect.single command parameters are label, line, freq, calc and abund. No parameters are required, but you may not use " << "\n";
- cout << "both the line and label parameters at the same time. The collect.single command should be in the following format: " << "\n";
- cout << "collect.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators)." << "\n";
- cout << "Example collect(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-chao-ace-jack)." << "\n";
- cout << "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson." << "\n";
+ mothurOut("The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. \n");
+ mothurOut("The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
+ mothurOut("The collect.single command parameters are label, line, freq, calc and abund. No parameters are required, but you may not use \n");
+ mothurOut("both the line and label parameters at the same time. The collect.single command should be in the following format: \n");
+ mothurOut("collect.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
+ mothurOut("Example collect(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n");
+ mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n");
validCalculator->printCalc("single", cout);
- cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
+ mothurOut("The label and line parameters are used to analyze specific lines in your input.\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "CollectCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the CollectCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
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;
+ }
}
//**********************************************************************************************************************
read->read(&*globaldata);
order = globaldata->gorder;
- lastOrder = order;
+ string lastLabel = order->getLabel();
input = globaldata->ginput;
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
cCurve->getCurve(freq);
delete cCurve;
- cout << order->getLabel() << '\t' << count << endl;
+ mothurOut(order->getLabel() + "\t" + toString(count)); mothurOutEndLine();
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
userLines.erase(count);
//you have a label the user want that is smaller than this line and the last line has not already been processed
}
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
- cCurve = new Collect(lastOrder, cDisplays);
+ if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+
+ delete order;
+ order = (input->getOrderVector(lastLabel));
+
+ cCurve = new Collect(order, cDisplays);
cCurve->getCurve(freq);
delete cCurve;
- cout << lastOrder->getLabel() << '\t' << count << endl;
- processedLabels.insert(lastOrder->getLabel());
- userLabels.erase(lastOrder->getLabel());
+ mothurOut(order->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
}
- if (count != 1) { delete lastOrder; }
- lastOrder = order;
+ lastLabel = order->getLabel();
+
+ delete order;
order = (input->getOrderVector());
count++;
}
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastOrder->getLabel()) != 1) {
- cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
}
//run last line if you need to
if (needToRun == true) {
- cCurve = new Collect(lastOrder, cDisplays);
+ delete order;
+ order = (input->getOrderVector(lastLabel));
+
+ mothurOut(order->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+
+ cCurve = new Collect(order, cDisplays);
cCurve->getCurve(freq);
delete cCurve;
-
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ delete order;
}
- delete lastOrder;
+
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CollectCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "CollectCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the CollectCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************