}
}
//**********************************************************************************************************************
+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;
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+"npshannon")));
- outputNames.push_back(fileNameRoot+"npshannon"); outputTypes["npshannon"].push_back(fileNameRoot+"npshannon");
+ 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"));
}
}
}
projects / mothur.git / blobdiff