//**********************************************************************************************************************
-CollectCommand::CollectCommand(){
+CollectCommand::CollectCommand(string option){
try {
globaldata = GlobalData::getInstance();
- string fileNameRoot;
- fileNameRoot = getRootName(globaldata->inputFileName);
- convert(globaldata->getFreq(), freq);
- int i;
- validCalculator = new ValidCalculators();
+ abort = false;
+ allLines = 1;
+ lines.clear();
+ labels.clear();
+ Estimators.clear();
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("single", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "sobs") {
- cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
- }else if (globaldata->Estimators[i] == "chao") {
- cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
- }else if (globaldata->Estimators[i] == "nseqs") {
- cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
- }else if (globaldata->Estimators[i] == "coverage") {
- cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
- }else if (globaldata->Estimators[i] == "ace") {
- convert(globaldata->getAbund(), abund);
- cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
- }else if (globaldata->Estimators[i] == "jack") {
- cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
- }else if (globaldata->Estimators[i] == "shannon") {
- cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
- }else if (globaldata->Estimators[i] == "npshannon") {
- cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
- }else if (globaldata->Estimators[i] == "simpson") {
- cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
- }else if (globaldata->Estimators[i] == "bootstrap") {
- cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
- }else if (globaldata->Estimators[i] == "geometric") {
- cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
- }else if (globaldata->Estimators[i] == "qstat") {
- cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
- }else if (globaldata->Estimators[i] == "logseries") {
- cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
- }else if (globaldata->Estimators[i] == "bergerparker") {
- cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
- }else if (globaldata->Estimators[i] == "bstick") {
- cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
- }else if (globaldata->Estimators[i] == "goodscoverage") {
- cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
- }else if (globaldata->Estimators[i] == "efron") {
- convert(globaldata->getSize(), size);
- cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
- }else if (globaldata->Estimators[i] == "boneh") {
- convert(globaldata->getSize(), size);
- cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
- }else if (globaldata->Estimators[i] == "solow") {
- convert(globaldata->getSize(), size);
- cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
- }else if (globaldata->Estimators[i] == "shen") {
- convert(globaldata->getSize(), size);
- cDisplays.push_back(new CollectDisplay(new Shen(size), new OneColumnFile(fileNameRoot+"shen")));
+ //allow user to run help
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ 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;
+
+ ValidParameters* validParameter = new ValidParameters();
+
+ //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; }
+ }
+
+ //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; }
+
+ //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 != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; 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-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"; }
+ convert(temp, freq);
+
+ 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"; }
+ convert(temp, size);
+
+ delete validParameter;
+
+
+ if (abort == false) {
+ string fileNameRoot = getRootName(globaldata->inputFileName);
+ int i;
+ validCalculator = new ValidCalculators();
+
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("single", Estimators[i]) == true) {
+ if (Estimators[i] == "sobs") {
+ cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
+ }else if (Estimators[i] == "chao") {
+ cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
+ }else if (Estimators[i] == "nseqs") {
+ cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
+ }else if (Estimators[i] == "coverage") {
+ cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
+ }else if (Estimators[i] == "ace") {
+ cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
+ }else if (Estimators[i] == "jack") {
+ cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
+ }else if (Estimators[i] == "shannon") {
+ cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
+ }else if (Estimators[i] == "npshannon") {
+ cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
+ }else if (Estimators[i] == "simpson") {
+ cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
+ }else if (Estimators[i] == "bootstrap") {
+ cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
+ }else if (Estimators[i] == "geometric") {
+ cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
+ }else if (Estimators[i] == "qstat") {
+ cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
+ }else if (Estimators[i] == "logseries") {
+ cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
+ }else if (Estimators[i] == "bergerparker") {
+ cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
+ }else if (Estimators[i] == "bstick") {
+ cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
+ }else if (Estimators[i] == "goodscoverage") {
+ cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
+ }else if (Estimators[i] == "efron") {
+ cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
+ }else if (Estimators[i] == "boneh") {
+ cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
+ }else if (Estimators[i] == "solow") {
+ cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
+ }else if (Estimators[i] == "shen") {
+ cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
+ }
+ }
}
}
}
- //reset calc for next command
- globaldata->setCalc("");
}
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";
}
}
+//**********************************************************************************************************************
+
+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";
+ 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";
+ }
+ 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";
+ 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);
+ }
+}
//**********************************************************************************************************************
delete input;
delete cCurve;
delete read;
+ delete validCalculator;
}
//**********************************************************************************************************************
int CollectCommand::execute(){
try {
+
+ if (abort == true) { return 0; }
+
int count = 1;
//if the users entered no valid calculators don't execute command
//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 = globaldata->labels;
- set<int> userLines = globaldata->lines;
+ set<string> userLabels = labels;
+ set<int> userLines = lines;
- while((order != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
cCurve = new Collect(order, cDisplays);
cCurve->getCurve(freq);
projects / mothur.git / blobdiff