//**********************************************************************************************************************
-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;
+ 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[] = {"label","calc","groups"};
+ 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->getSharedFile() == "") {
+ mothurOut("You must read a list and a group, or a shared before you can use the summary.shared command."); mothurOutEndLine(); abort = true;
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ }
+
+ //if the user has not specified any labels use the ones from read.otu
+ if(label == "") {
+ allLines = globaldata->allLines;
+ labels = globaldata->labels;
+ }
+
+ 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;
+ }
+
+ 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);
+ mult = false;
}
}
- //reset calc for next command
- globaldata->setCalc("");
-
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SummarySharedCommand", "SummarySharedCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SummarySharedCommand class function SummarySharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+//**********************************************************************************************************************
+
+void SummarySharedCommand::help(){
+ try {
+ mothurOut("The summary.shared command can only be executed after a successful read.otu command.\n");
+ mothurOut("The summary.shared command parameters are label and calc. No parameters are required.\n");
+ mothurOut("The summary.shared command should be in the following format: \n");
+ mothurOut("summary.shared(label=yourLabel, calc=yourEstimators, groups=yourGroups).\n");
+ mothurOut("Example summary.shared(label=unique-.01-.03, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
+ validCalculator->printCalc("sharedsummary", cout);
+ mothurOut("The default value for calc is sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan\n");
+ mothurOut("The default value for groups is all the groups in your groupfile.\n");
+ mothurOut("The label parameter is used to analyze specific labels in your input.\n");
+ mothurOut("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");
+ mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
+ }
+ catch(exception& e) {
+ errorOut(e, "SummarySharedCommand", "help");
exit(1);
- }
+ }
}
+
//**********************************************************************************************************************
SummarySharedCommand::~SummarySharedCommand(){
- delete input;
- delete read;
+ if (abort == false) {
+ delete read;
+ delete validCalculator;
+ }
}
//**********************************************************************************************************************
int SummarySharedCommand::execute(){
try {
- int count = 1;
+
+ if (abort == true) { return 0; }
//if the users entered no valid calculators don't execute command
if (sumCalculators.size() == 0) { return 0; }
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- vector<SharedRAbundVector*> lastLookup = lookup;
+ string lastLabel = lookup[0]->getLabel();
//output estimator names as column headers
outputFileHandle << "label" <<'\t' << "comparison" << '\t';
}
if (lookup.size() < 2) {
- cout << "I cannot run the command without at least 2 valid groups.";
+ mothurOut("I cannot run the command without at least 2 valid groups.");
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
//close files and clean up
outputFileHandle.close(); remove(outputFileName.c_str());
if (mult == true) { outAll.close(); remove(outAllFileName.c_str()); }
return 0;
+ //if you only have 2 groups you don't need a .sharedmultiple file
+ }else if ((lookup.size() == 2) && (mult == true)) {
+ mult = false;
+ outAll.close();
+ remove(outAllFileName.c_str());
}
//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<string> userLabels = labels;
+
//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))) {
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
- cout << lookup[0]->getLabel() << '\t' << count << endl;
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
process(lookup);
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- process(lastLookup);
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ process(lookup);
- processedLabels.insert(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
}
- //prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
+
+ lastLabel = lookup[0]->getLabel();
//get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
- count++;
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- process(lastLookup);
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ process(lookup);
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
- 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();
if (mult == true) { outAll.close(); }
+
+ for(int i=0;i<sumCalculators.size();i++){ delete sumCalculators[i]; }
+
+ delete input; globaldata->ginput = NULL;
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SummarySharedCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SummarySharedCommand", "process");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SummarySharedCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
-/***********************************************************/
\ No newline at end of file
+/***********************************************************/
projects / mothur.git / blobdiff