globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
Estimators.clear();
else {
//valid paramters for this command
- string Array[] = {"iters","freq","line","label","calc","abund"};
+ string Array[] = {"iters","freq","label","calc","abund"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
- 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);
if (label == "not found") { label = ""; }
else {
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- 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 == "")) {
+ //if the user has not specified any labels use the ones from read.otu
+ if(label == "") {
allLines = globaldata->allLines;
labels = globaldata->labels;
- lines = globaldata->lines;
}
calc = validParameter.validFile(parameters, "calc", false);
try {
mothurOut("The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
mothurOut("The rarefaction.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 rarefaction.single command parameters are label, line, iters, 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 rarefaction.single command should be in the following format: \n");
- mothurOut("rarefaction.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
- mothurOut("Example rarefaction.single(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n");
+ mothurOut("The rarefaction.single command parameters are label, iters, freq, calc and abund. No parameters are required. \n");
+ mothurOut("The rarefaction.single command should be in the following format: \n");
+ mothurOut("rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
+ mothurOut("Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n");
mothurOut("The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness.\n");
validCalculator->printCalc("rarefaction", cout);
- mothurOut("The label and line parameters are used to analyze specific lines in your input.\n");
+ mothurOut("The label parameter is used to analyze specific labels in your input.\n");
mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
}
catch(exception& e) {
if (abort == true) { return 0; }
- int count = 1;
-
//if the users entered no valid calculators don't execute command
if (rDisplays.size() == 0) { return 0; }
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
- set<int> userLines = lines;
//as long as you are not at the end of the file or done wih the lines you want
- while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
+ if(allLines == 1 || labels.count(order->getLabel()) == 1){
rCurve = new Rarefact(order, rDisplays);
rCurve->getCurve(freq, nIters);
mothurOut(order->getLabel()); mothurOutEndLine();
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
- userLines.erase(count);
}
if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
delete order;
order = (input->getOrderVector());
- count++;
}
//output error messages about any remaining user labels
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
if (order != NULL) { delete order; }
order = (input->getOrderVector(lastLabel));