globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
Estimators.clear();
else {
//valid paramters for this command
- string Array[] = {"freq","line","label","calc","abund","size"};
+ string Array[] = {"freq","label","calc","abund","size"};
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 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 collect.single command parameters are label, freq, calc and abund. No parameters are required. \n");
+ mothurOut("The collect.single command should be in the following format: \n");
+ mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
+ mothurOut("Example collect(label=unique-.01-.03, 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);
- 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) {
try {
if (abort == true) { return 0; }
-
- int count = 1;
//if the users entered no valid calculators don't execute command
if (cDisplays.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;
- 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){
cCurve = new Collect(order, cDisplays);
cCurve->getCurve(freq);
mothurOut(order->getLabel()); 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
- }
+ }
+ //you have a label the user want that is smaller than this label and the last label has not already been processed
if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
delete order;
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));