CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
- CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-np_shannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
}
}
//**********************************************************************************************************************
+string CollectCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "sobs") { outputFileName = "sobs"; }
+ else if (type == "chao") { outputFileName = "chao"; }
+ else if (type == "nseqs") { outputFileName = "nseqs"; }
+ else if (type == "coverage") { outputFileName = "coverage"; }
+ else if (type == "ace") { outputFileName = "ace"; }
+ else if (type == "jack") { outputFileName = "jack"; }
+ else if (type == "shannon") { outputFileName = "shannon"; }
+ else if (type == "shannoneven") { outputFileName = "shannoneven"; }
+ else if (type == "npshannon") { outputFileName = "npshannon"; }
+ else if (type == "heip") { outputFileName = "heip"; }
+ else if (type == "smithwilson") { outputFileName = "smithwilson"; }
+ else if (type == "simpson") { outputFileName = "simpson"; }
+ else if (type == "simpsoneven") { outputFileName = "simpsoneven"; }
+ else if (type == "invsimpson") { outputFileName = "invsimpson"; }
+ else if (type == "bootstrap") { outputFileName = "bootstrap"; }
+ else if (type == "geometric") { outputFileName = "geometric"; }
+ else if (type == "qstat") { outputFileName = "qstat"; }
+ else if (type == "logseries") { outputFileName = "logseries"; }
+ else if (type == "bergerparker") { outputFileName = "bergerparker"; }
+ else if (type == "bstick") { outputFileName = "bstick"; }
+ else if (type == "goodscoverage") { outputFileName = "goodscoverage"; }
+ else if (type == "efron") { outputFileName = "efron"; }
+ else if (type == "boneh") { outputFileName = "boneh"; }
+ else if (type == "solow") { outputFileName = "solow"; }
+ else if (type == "shen") { outputFileName = "shen"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
CollectCommand::CollectCommand(){
try {
abort = true; calledHelp = true;
outputTypes["jack"] = tempOutNames;
outputTypes["shannon"] = tempOutNames;
outputTypes["shannoneven"] = tempOutNames;
- outputTypes["np_shannon"] = tempOutNames;
+ outputTypes["npshannon"] = tempOutNames;
outputTypes["heip"] = tempOutNames;
outputTypes["smithwilson"] = tempOutNames;
outputTypes["simpson"] = tempOutNames;
outputTypes["jack"] = tempOutNames;
outputTypes["shannon"] = tempOutNames;
outputTypes["shannoneven"] = tempOutNames;
- outputTypes["np_shannon"] = tempOutNames;
+ outputTypes["npshannon"] = tempOutNames;
outputTypes["heip"] = tempOutNames;
outputTypes["smithwilson"] = tempOutNames;
outputTypes["simpson"] = tempOutNames;
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
- else { format = "list"; inputfile = listfile; }
+ else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
sabundfile = validParameter.validFile(parameters, "sabund", true);
if (sabundfile == "not open") { sabundfile = ""; abort = true; }
else if (sabundfile == "not found") { sabundfile = ""; }
- else { format = "sabund"; inputfile = sabundfile; }
+ else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
rabundfile = validParameter.validFile(parameters, "rabund", true);
if (rabundfile == "not open") { rabundfile = ""; abort = true; }
else if (rabundfile == "not found") { rabundfile = ""; }
- else { format = "rabund"; inputfile = rabundfile; }
+ else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
sharedfile = validParameter.validFile(parameters, "shared", true);
if (sharedfile == "not open") { sharedfile = ""; abort = true; }
else if (sharedfile == "not found") { sharedfile = ""; }
- else { format = "sharedfile"; inputfile = sharedfile; }
+ else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
}
m->splitAtDash(calc, Estimators);
+ if (m->inUsersGroups("citation", Estimators)) {
+ ValidCalculators validCalc; validCalc.printCitations(Estimators);
+ //remove citation from list of calcs
+ for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
+ }
string temp;
temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
- convert(temp, freq);
+ m->mothurConvert(temp, freq);
temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
- convert(temp, abund);
+ m->mothurConvert(temp, abund);
temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
- convert(temp, size);
+ m->mothurConvert(temp, size);
}
}
for (int p = 0; p < inputFileNames.size(); p++) {
- if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
for (int 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")));
- outputNames.push_back(fileNameRoot+"sobs"); outputTypes["sobs"].push_back(fileNameRoot+"sobs");
+ cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("sobs"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("sobs")); outputTypes["sobs"].push_back(fileNameRoot+getOutputFileNameTag("sobs"));
}else if (Estimators[i] == "chao") {
- cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
- outputNames.push_back(fileNameRoot+"chao"); outputTypes["chao"].push_back(fileNameRoot+"chao");
+ cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("chao"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("chao")); outputTypes["chao"].push_back(fileNameRoot+getOutputFileNameTag("chao"));
}else if (Estimators[i] == "nseqs") {
- cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
- outputNames.push_back(fileNameRoot+"nseqs"); outputTypes["nseqs"].push_back(fileNameRoot+"nseqs");
+ cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("nseqs"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("nseqs")); outputTypes["nseqs"].push_back(fileNameRoot+getOutputFileNameTag("nseqs"));
}else if (Estimators[i] == "coverage") {
- cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
- outputNames.push_back(fileNameRoot+"coverage"); outputTypes["coverage"].push_back(fileNameRoot+"coverage");
+ cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("coverage"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("coverage")); outputTypes["coverage"].push_back(fileNameRoot+getOutputFileNameTag("coverage"));
}else if (Estimators[i] == "ace") {
- cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
- outputNames.push_back(fileNameRoot+"ace"); outputTypes["ace"].push_back(fileNameRoot+"ace");
+ cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("ace"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("ace")); outputTypes["ace"].push_back(fileNameRoot+getOutputFileNameTag("ace"));
}else if (Estimators[i] == "jack") {
- cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
- outputNames.push_back(fileNameRoot+"jack"); outputTypes["jack"].push_back(fileNameRoot+"jack");
+ cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("jack"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("jack")); outputTypes["jack"].push_back(fileNameRoot+getOutputFileNameTag("jack"));
}else if (Estimators[i] == "shannon") {
- cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
- outputNames.push_back(fileNameRoot+"shannon"); outputTypes["shannon"].push_back(fileNameRoot+"shannon");
+ cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("shannon"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("shannon")); outputTypes["shannon"].push_back(fileNameRoot+getOutputFileNameTag("shannon"));
}else if (Estimators[i] == "shannoneven") {
- cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
- outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].push_back(fileNameRoot+"shannoneven");
+ cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("shannoneven"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("shannoneven")); outputTypes["shannoneven"].push_back(fileNameRoot+getOutputFileNameTag("shannoneven"));
}else if (Estimators[i] == "npshannon") {
- cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
- outputNames.push_back(fileNameRoot+"np_shannon"); outputTypes["np_shannon"].push_back(fileNameRoot+"np_shannon");
+ cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("npshannon"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("npshannon")); outputTypes["npshannon"].push_back(fileNameRoot+getOutputFileNameTag("npshannon"));
}else if (Estimators[i] == "heip") {
- cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
- outputNames.push_back(fileNameRoot+"heip"); outputTypes["heip"].push_back(fileNameRoot+"heip");
+ cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("heip"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("heip")); outputTypes["heip"].push_back(fileNameRoot+getOutputFileNameTag("heip"));
}else if (Estimators[i] == "smithwilson") {
- cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+"smithwilson")));
- outputNames.push_back(fileNameRoot+"smithwilson"); outputTypes["smithwilson"].push_back(fileNameRoot+"smithwilson");
+ cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("smithwilson"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("smithwilson")); outputTypes["smithwilson"].push_back(fileNameRoot+getOutputFileNameTag("smithwilson"));
}else if (Estimators[i] == "simpson") {
- cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
- outputNames.push_back(fileNameRoot+"simpson"); outputTypes["simpson"].push_back(fileNameRoot+"simpson");
+ cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("simpson"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("simpson")); outputTypes["simpson"].push_back(fileNameRoot+getOutputFileNameTag("simpson"));
}else if (Estimators[i] == "simpsoneven") {
- cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+"simpsoneven")));
- outputNames.push_back(fileNameRoot+"simpsoneven"); outputTypes["simpsoneven"].push_back(fileNameRoot+"simpsoneven");
+ cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("simpsoneven"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("simpsoneven")); outputTypes["simpsoneven"].push_back(fileNameRoot+getOutputFileNameTag("simpsoneven"));
}else if (Estimators[i] == "invsimpson") {
- cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"invsimpson")));
- outputNames.push_back(fileNameRoot+"invsimpson"); outputTypes["invsimpson"].push_back(fileNameRoot+"invsimpson");
+ cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("invsimpson"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("invsimpson")); outputTypes["invsimpson"].push_back(fileNameRoot+getOutputFileNameTag("invsimpson"));
}else if (Estimators[i] == "bootstrap") {
- cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
- outputNames.push_back(fileNameRoot+"bootstrap"); outputTypes["bootstrap"].push_back(fileNameRoot+"bootstrap");
+ cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("bootstrap"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("bootstrap")); outputTypes["bootstrap"].push_back(fileNameRoot+getOutputFileNameTag("bootstrap"));
}else if (Estimators[i] == "geometric") {
- cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
- outputNames.push_back(fileNameRoot+"geometric"); outputTypes["geometric"].push_back(fileNameRoot+"geometric");
+ cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("geometric"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("geometric")); outputTypes["geometric"].push_back(fileNameRoot+getOutputFileNameTag("geometric"));
}else if (Estimators[i] == "qstat") {
- cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
- outputNames.push_back(fileNameRoot+"qstat"); outputTypes["qstat"].push_back(fileNameRoot+"qstat");
+ cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("qstat"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("qstat")); outputTypes["qstat"].push_back(fileNameRoot+getOutputFileNameTag("qstat"));
}else if (Estimators[i] == "logseries") {
- cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
- outputNames.push_back(fileNameRoot+"logseries"); outputTypes["logseries"].push_back(fileNameRoot+"logseries");
+ cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("logseries"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("logseries")); outputTypes["logseries"].push_back(fileNameRoot+getOutputFileNameTag("logseries"));
}else if (Estimators[i] == "bergerparker") {
- cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
- outputNames.push_back(fileNameRoot+"bergerparker"); outputTypes["bergerparker"].push_back(fileNameRoot+"bergerparker");
+ cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("bergerparker"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("bergerparker")); outputTypes["bergerparker"].push_back(fileNameRoot+getOutputFileNameTag("bergerparker"));
}else if (Estimators[i] == "bstick") {
- cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
- outputNames.push_back(fileNameRoot+"bstick"); outputTypes["bstick"].push_back(fileNameRoot+"bstick");
+ cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+getOutputFileNameTag("bstick"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("bstick")); outputTypes["bstick"].push_back(fileNameRoot+getOutputFileNameTag("bstick"));
}else if (Estimators[i] == "goodscoverage") {
- cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
- outputNames.push_back(fileNameRoot+"goodscoverage"); outputTypes["goodscoverage"].push_back(fileNameRoot+"goodscoverage");
+ cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+getOutputFileNameTag("goodscoverage"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("goodscoverage")); outputTypes["goodscoverage"].push_back(fileNameRoot+getOutputFileNameTag("goodscoverage"));
}else if (Estimators[i] == "efron") {
- cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
- outputNames.push_back(fileNameRoot+"efron"); outputTypes["efron"].push_back(fileNameRoot+"efron");
+ cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+getOutputFileNameTag("efron"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("efron")); outputTypes["efron"].push_back(fileNameRoot+getOutputFileNameTag("efron"));
}else if (Estimators[i] == "boneh") {
- cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
- outputNames.push_back(fileNameRoot+"boneh"); outputTypes["boneh"].push_back(fileNameRoot+"boneh");
+ cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+getOutputFileNameTag("boneh"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("boneh")); outputTypes["boneh"].push_back(fileNameRoot+getOutputFileNameTag("boneh"));
}else if (Estimators[i] == "solow") {
- cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
- outputNames.push_back(fileNameRoot+"solow"); outputTypes["solow"].push_back(fileNameRoot+"solow");
+ cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+getOutputFileNameTag("solow"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("solow")); outputTypes["solow"].push_back(fileNameRoot+getOutputFileNameTag("solow"));
}else if (Estimators[i] == "shen") {
- cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
- outputNames.push_back(fileNameRoot+"shen"); outputTypes["shen"].push_back(fileNameRoot+"shen");
+ cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+getOutputFileNameTag("shen"))));
+ outputNames.push_back(fileNameRoot+getOutputFileNameTag("shen")); outputTypes["shen"].push_back(fileNameRoot+getOutputFileNameTag("shen"));
}
}
}
if (m->control_pressed) {
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
delete input;
delete order;
- m->Groups.clear();
+ m->clearGroups();
return 0;
}
if (m->control_pressed) {
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
delete input;
delete order;
- m->Groups.clear();
+ m->clearGroups();
return 0;
}
if (m->control_pressed) {
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
delete input;
- m->Groups.clear();
+ m->clearGroups();
return 0;
}
if (m->control_pressed) {
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
delete input;
delete order;
- m->Groups.clear();
+ m->clearGroups();
return 0;
}
delete order;
delete input;
}
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
//clears file before we start to write to it below
for (int i=0; i<lookup.size(); i++) {
- remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+ m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
}
projects / mothur.git / blobdiff