//**********************************************************************************************************************
-RareFactCommand::RareFactCommand(){
+RareFactCommand::RareFactCommand(string option){
try {
globaldata = GlobalData::getInstance();
- string fileNameRoot;
- fileNameRoot = getRootName(globaldata->inputFileName);
- validCalculator = new ValidCalculators();
+ abort = false;
+ allLines = 1;
+ lines.clear();
+ labels.clear();
+ Estimators.clear();
- int i;
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("rarefaction", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "sobs") {
- rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
- }else if (globaldata->Estimators[i] == "chao") {
- rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"r_chao")));
- }else if (globaldata->Estimators[i] == "ace") {
- convert(globaldata->getAbund(), abund);
- if(abund < 5)
- abund = 10;
- rDisplays.push_back(new RareDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"r_ace")));
- }else if (globaldata->Estimators[i] == "jack") {
- rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
- }else if (globaldata->Estimators[i] == "shannon") {
- rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
- }else if (globaldata->Estimators[i] == "npshannon") {
- rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
- }else if (globaldata->Estimators[i] == "simpson") {
- rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
- }else if (globaldata->Estimators[i] == "bootstrap") {
- rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
- }else if (globaldata->Estimators[i] == "coverage") {
- rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
- }else if (globaldata->Estimators[i] == "nseqs") {
- rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
+ //allow user to run help
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"iters","freq","line","label","calc","abund"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ 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() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the rarefaction.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);
+ 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 {
+ if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ 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 == "")) {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ lines = globaldata->lines;
+ }
+
+ calc = validParameter.validFile(parameters, "calc", false);
+ if (calc == "not found") { calc = "sobs"; }
+ else {
+ if (calc == "default") { calc = "sobs"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ string temp;
+ 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"; }
+ convert(temp, abund);
+
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ convert(temp, nIters);
+
+ if (abort == false) {
+
+ string fileNameRoot = getRootName(globaldata->inputFileName);
+ int i;
+ validCalculator = new ValidCalculators();
+
+
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("rarefaction", Estimators[i]) == true) {
+ if (Estimators[i] == "sobs") {
+ rDisplays.push_back(new RareDisplay(new Sobs(), new ThreeColumnFile(fileNameRoot+"rarefaction")));
+ }else if (Estimators[i] == "chao") {
+ rDisplays.push_back(new RareDisplay(new Chao1(), new ThreeColumnFile(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")));
+ }else if (Estimators[i] == "jack") {
+ rDisplays.push_back(new RareDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"r_jack")));
+ }else if (Estimators[i] == "shannon") {
+ rDisplays.push_back(new RareDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"r_shannon")));
+ }else if (Estimators[i] == "npshannon") {
+ rDisplays.push_back(new RareDisplay(new NPShannon(), new ThreeColumnFile(fileNameRoot+"r_npshannon")));
+ }else if (Estimators[i] == "simpson") {
+ rDisplays.push_back(new RareDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"r_simpson")));
+ }else if (Estimators[i] == "bootstrap") {
+ rDisplays.push_back(new RareDisplay(new Bootstrap(), new ThreeColumnFile(fileNameRoot+"r_bootstrap")));
+ }else if (Estimators[i] == "coverage") {
+ rDisplays.push_back(new RareDisplay(new Coverage(), new ThreeColumnFile(fileNameRoot+"r_coverage")));
+ }else if (Estimators[i] == "nseqs") {
+ rDisplays.push_back(new RareDisplay(new NSeqs(), new ThreeColumnFile(fileNameRoot+"r_nseqs")));
+ }
+ }
}
}
+
}
- //reset calc for next command
- globaldata->setCalc("");
-
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "RareFactCommand", "RareFactCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the RareFactCommand class function RareFactCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+//**********************************************************************************************************************
+
+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, 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 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("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
+ }
+ catch(exception& e) {
+ errorOut(e, "RareFactCommand", "help");
exit(1);
- }
-
+ }
}
//**********************************************************************************************************************
RareFactCommand::~RareFactCommand(){
- delete order;
- delete input;
- delete rCurve;
- delete read;
+ if (abort == false) {
+ globaldata->gorder = NULL;
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ }
}
//**********************************************************************************************************************
int RareFactCommand::execute(){
try {
+
+ if (abort == true) { return 0; }
+
int count = 1;
//if the users entered no valid calculators don't execute command
read->read(&*globaldata);
order = globaldata->gorder;
+ string lastLabel = order->getLabel();
input = globaldata->ginput;
-
- while(order != NULL){
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+ //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))) {
+
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
rCurve = new Rarefact(order, rDisplays);
- convert(globaldata->getFreq(), freq);
- convert(globaldata->getIters(), nIters);
rCurve->getCurve(freq, nIters);
+ delete rCurve;
+ 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(lastLabel));
+
+ rCurve = new Rarefact(order, rDisplays);
+ rCurve->getCurve(freq, nIters);
delete rCurve;
- cout << order->getLabel() << '\t' << count << endl;
+ mothurOut(order->getLabel()); mothurOutEndLine();
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
}
+ lastLabel = order->getLabel();
+
delete order;
order = (input->getOrderVector());
count++;
+ }
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ needToRun = true;
+ }else {
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ }
}
-
+
+ //run last line if you need to
+ if (needToRun == true) {
+ if (order != NULL) { delete order; }
+ order = (input->getOrderVector(lastLabel));
+
+ rCurve = new Rarefact(order, rDisplays);
+ rCurve->getCurve(freq, nIters);
+ delete rCurve;
+
+ mothurOut(order->getLabel()); mothurOutEndLine();
+ delete order;
+ }
+
+
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the RareFactCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "RareFactCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the RareFactCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff