//**********************************************************************************************************************
-RareFactCommand::RareFactCommand(string option){
+RareFactCommand::RareFactCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
labels.clear();
Estimators.clear();
-
+
//allow user to run help
if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
}
//make sure the user has already run the read.otu command
- if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund, rabund or shared file before you can use the rarefact.single command."); mothurOutEndLine(); abort = true; }
+ if ((globaldata->getSharedFile() == "") && (globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { m->mothurOut("You must read a list, sabund, rabund or shared file before you can use the rarefact.single command."); m->mothurOutEndLine(); abort = true; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
}
catch(exception& e) {
- errorOut(e, "RareFactCommand", "RareFactCommand");
+ m->errorOut(e, "RareFactCommand", "RareFactCommand");
exit(1);
}
}
void RareFactCommand::help(){
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, 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");
+ m->mothurOut("The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
+ m->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");
+ m->mothurOut("The rarefaction.single command parameters are label, iters, freq, calc and abund. No parameters are required. \n");
+ m->mothurOut("The rarefaction.single command should be in the following format: \n");
+ m->mothurOut("rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
+ m->mothurOut("Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n");
+ m->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 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");
+ m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
}
catch(exception& e) {
- errorOut(e, "RareFactCommand", "help");
+ m->errorOut(e, "RareFactCommand", "help");
exit(1);
}
}
if (abort == true) { return 0; }
+ vector<string> outputNames;
+
if ((globaldata->getFormat() != "sharedfile")) { inputFileNames.push_back(globaldata->inputFileName); }
else { inputFileNames = parseSharedFile(globaldata->getSharedFile()); globaldata->setFormat("rabund"); }
globaldata->inputFileName = inputFileNames[p];
if (inputFileNames.size() > 1) {
- mothurOutEndLine(); mothurOut("Processing group " + groups[p]); mothurOutEndLine(); mothurOutEndLine();
+ m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
}
int i;
validCalculator = new ValidCalculators();
if (validCalculator->isValidCalculator("rarefaction", Estimators[i]) == true) {
if (Estimators[i] == "sobs") {
rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
+ outputNames.push_back(fileNameRoot+"rarefaction");
}else if (Estimators[i] == "chao") {
rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
+ outputNames.push_back(fileNameRoot+"r_chao");
}else if (Estimators[i] == "ace") {
if(abund < 5)
abund = 10;
rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
+ outputNames.push_back(fileNameRoot+"r_ace");
}else if (Estimators[i] == "jack") {
rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
+ outputNames.push_back(fileNameRoot+"r_jack");
}else if (Estimators[i] == "shannon") {
rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
+ outputNames.push_back(fileNameRoot+"r_shannon");
}else if (Estimators[i] == "npshannon") {
rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
+ outputNames.push_back(fileNameRoot+"r_npshannon");
}else if (Estimators[i] == "simpson") {
rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
+ outputNames.push_back(fileNameRoot+"r_simpson");
}else if (Estimators[i] == "bootstrap") {
rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
+ outputNames.push_back(fileNameRoot+"r_bootstrap");
}else if (Estimators[i] == "coverage") {
rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
+ outputNames.push_back(fileNameRoot+"r_coverage");
}else if (Estimators[i] == "nseqs") {
rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
+ outputNames.push_back(fileNameRoot+"r_nseqs");
}
}
}
rCurve->getCurve(freq, nIters);
delete rCurve;
- mothurOut(order->getLabel()); mothurOutEndLine();
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
}
rCurve->getCurve(freq, nIters);
delete rCurve;
- mothurOut(order->getLabel()); mothurOutEndLine();
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
rCurve->getCurve(freq, nIters);
delete rCurve;
- mothurOut(order->getLabel()); mothurOutEndLine();
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
delete order;
}
}
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "RareFactCommand", "execute");
+ m->errorOut(e, "RareFactCommand", "execute");
exit(1);
}
}
return filenames;
}
catch(exception& e) {
- errorOut(e, "RareFactCommand", "parseSharedFile");
+ m->errorOut(e, "RareFactCommand", "parseSharedFile");
exit(1);
}
}
projects / mothur.git / blobdiff