//**********************************************************************************************************************
-SummarySharedCommand::SummarySharedCommand(){
+SummarySharedCommand::SummarySharedCommand(string option){
try {
globaldata = GlobalData::getInstance();
- outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
- openOutputFile(outputFileName, outputFileHandle);
- format = globaldata->getFormat();
- validCalculator = new ValidCalculators();
- mult = false;
+ abort = false;
+ allLines = 1;
+ lines.clear();
+ labels.clear();
+ Estimators.clear();
- int i;
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("sharedsummary", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "sharedsobs") {
- sumCalculators.push_back(new SharedSobsCS());
- }else if (globaldata->Estimators[i] == "sharedchao") {
- sumCalculators.push_back(new SharedChao1());
- }else if (globaldata->Estimators[i] == "sharedace") {
- sumCalculators.push_back(new SharedAce());
- }else if (globaldata->Estimators[i] == "jabund") {
- sumCalculators.push_back(new JAbund());
- }else if (globaldata->Estimators[i] == "sorabund") {
- sumCalculators.push_back(new SorAbund());
- }else if (globaldata->Estimators[i] == "jclass") {
- sumCalculators.push_back(new Jclass());
- }else if (globaldata->Estimators[i] == "sorclass") {
- sumCalculators.push_back(new SorClass());
- }else if (globaldata->Estimators[i] == "jest") {
- sumCalculators.push_back(new Jest());
- }else if (globaldata->Estimators[i] == "sorest") {
- sumCalculators.push_back(new SorEst());
- }else if (globaldata->Estimators[i] == "thetayc") {
- sumCalculators.push_back(new ThetaYC());
- }else if (globaldata->Estimators[i] == "thetan") {
- sumCalculators.push_back(new ThetaN());
- }else if (globaldata->Estimators[i] == "kstest") {
- sumCalculators.push_back(new KSTest());
- }else if (globaldata->Estimators[i] == "sharednseqs") {
- sumCalculators.push_back(new SharedNSeqs());
- }else if (globaldata->Estimators[i] == "ochiai") {
- sumCalculators.push_back(new Ochiai());
- }else if (globaldata->Estimators[i] == "anderberg") {
- sumCalculators.push_back(new Anderberg());
- }else if (globaldata->Estimators[i] == "kulczynski") {
- sumCalculators.push_back(new Kulczynski());
- }else if (globaldata->Estimators[i] == "kulczynskicody") {
- sumCalculators.push_back(new KulczynskiCody());
- }else if (globaldata->Estimators[i] == "lennon") {
- sumCalculators.push_back(new Lennon());
- }else if (globaldata->Estimators[i] == "morisitahorn") {
- sumCalculators.push_back(new MorHorn());
- }else if (globaldata->Estimators[i] == "braycurtis") {
- sumCalculators.push_back(new BrayCurtis());
- }else if (globaldata->Estimators[i] == "whittaker") {
- sumCalculators.push_back(new Whittaker());
+ //allow user to run help
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"line","label","calc","groups"};
+ 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->getSharedFile() == "") {
+ if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the summary.shared command." << endl; abort = true; }
+ else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the summary.shared 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 = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
+ else {
+ if (calc == "default") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
+ }
+ splitAtDash(calc, Estimators);
+
+ groups = validParameter->validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ delete validParameter;
+
+ if (abort == false) {
+
+ validCalculator = new ValidCalculators();
+ int i;
+
+ for (i=0; i<Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("sharedsummary", Estimators[i]) == true) {
+ if (Estimators[i] == "sharedsobs") {
+ sumCalculators.push_back(new SharedSobsCS());
+ }else if (Estimators[i] == "sharedchao") {
+ sumCalculators.push_back(new SharedChao1());
+ }else if (Estimators[i] == "sharedace") {
+ sumCalculators.push_back(new SharedAce());
+ }else if (Estimators[i] == "jabund") {
+ sumCalculators.push_back(new JAbund());
+ }else if (Estimators[i] == "sorabund") {
+ sumCalculators.push_back(new SorAbund());
+ }else if (Estimators[i] == "jclass") {
+ sumCalculators.push_back(new Jclass());
+ }else if (Estimators[i] == "sorclass") {
+ sumCalculators.push_back(new SorClass());
+ }else if (Estimators[i] == "jest") {
+ sumCalculators.push_back(new Jest());
+ }else if (Estimators[i] == "sorest") {
+ sumCalculators.push_back(new SorEst());
+ }else if (Estimators[i] == "thetayc") {
+ sumCalculators.push_back(new ThetaYC());
+ }else if (Estimators[i] == "thetan") {
+ sumCalculators.push_back(new ThetaN());
+ }else if (Estimators[i] == "kstest") {
+ sumCalculators.push_back(new KSTest());
+ }else if (Estimators[i] == "sharednseqs") {
+ sumCalculators.push_back(new SharedNSeqs());
+ }else if (Estimators[i] == "ochiai") {
+ sumCalculators.push_back(new Ochiai());
+ }else if (Estimators[i] == "anderberg") {
+ sumCalculators.push_back(new Anderberg());
+ }else if (Estimators[i] == "kulczynski") {
+ sumCalculators.push_back(new Kulczynski());
+ }else if (Estimators[i] == "kulczynskicody") {
+ sumCalculators.push_back(new KulczynskiCody());
+ }else if (Estimators[i] == "lennon") {
+ sumCalculators.push_back(new Lennon());
+ }else if (Estimators[i] == "morisitahorn") {
+ sumCalculators.push_back(new MorHorn());
+ }else if (Estimators[i] == "braycurtis") {
+ sumCalculators.push_back(new BrayCurtis());
+ }else if (Estimators[i] == "whittaker") {
+ sumCalculators.push_back(new Whittaker());
+ }
+ }
}
+
+ outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
+ openOutputFile(outputFileName, outputFileHandle);
+ format = globaldata->getFormat();
+ mult = false;
}
}
- //reset calc for next command
- globaldata->setCalc("");
}
catch(exception& e) {
exit(1);
}
}
+
+//**********************************************************************************************************************
+
+void SummarySharedCommand::help(){
+ try {
+ cout << "The summary.shared command can only be executed after a successful read.otu command." << "\n";
+ cout << "The summary.shared command parameters are label, line and calc. No parameters are required, but you may not use " << "\n";
+ cout << "both the line and label parameters at the same time. The summary.shared command should be in the following format: " << "\n";
+ cout << "summary.shared(label=yourLabel, line=yourLines, calc=yourEstimators, groups=yourGroups)." << "\n";
+ cout << "Example summary.shared(label=unique-.01-.03, line=0,5,10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan)." << "\n";
+ validCalculator->printCalc("sharedsummary", cout);
+ cout << "The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan" << "\n";
+ cout << "The default value for groups is all the groups in your groupfile." << "\n";
+ cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
+ cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SummarySharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
SummarySharedCommand::~SummarySharedCommand(){
delete input;
delete read;
+ delete validCalculator;
}
//**********************************************************************************************************************
int SummarySharedCommand::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;
//as long as you are not at the end of the file or done wih the lines you want
- while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
+ if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
cout << lookup[0]->getLabel() << '\t' << count << endl;
process(lookup);
for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
//reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+ globaldata->Groups.clear();
//close files
outputFileHandle.close();
projects / mothur.git / blobdiff