//**********************************************************************************************************************
vector<string> CollectSharedCommand::setParameters(){
try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); 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", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-skulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter pall("all", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pall);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","",false,true,true); 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", "sharedchao-sharedsobs-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-whittaker-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-structchi2-hamming-gower-memchi2-memchord-memeuclidean-mempearson", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan", "", "", "","",true,false,true); parameters.push_back(pcalc);
+ CommandParameter pall("all", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pall);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
exit(1);
}
}
+//**********************************************************************************************************************
+string CollectSharedCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "sharedchao") { pattern = "[filename],shared.chao"; }
+ else if (type == "sharedsobs") { pattern = "[filename],shared.sobs"; }
+ else if (type == "sharedace") { pattern = "[filename],shared.ace"; }
+ else if (type == "jabund") { pattern = "[filename],jabund"; }
+ else if (type == "sorabund") { pattern = "[filename],sorabund"; }
+ else if (type == "jclass") { pattern = "[filename],jclass"; }
+ else if (type == "sorclass") { pattern = "[filename],sorclass"; }
+ else if (type == "jest") { pattern = "[filename],jest"; }
+ else if (type == "sorest") { pattern = "[filename],sorest"; }
+ else if (type == "thetayc") { pattern = "[filename],thetayc"; }
+ else if (type == "thetan") { pattern = "[filename],thetan"; }
+ else if (type == "kstest") { pattern = "[filename],kstest"; }
+ else if (type == "whittaker") { pattern = "[filename],whittaker"; }
+ else if (type == "sharednseqs") { pattern = "[filename],shared.nseqs"; }
+ else if (type == "ochiai") { pattern = "[filename],ochiai"; }
+ else if (type == "anderberg") { pattern = "[filename],anderberg"; }
+ else if (type == "kulczynski") { pattern = "[filename],kulczynski"; }
+ else if (type == "kulczynskicody") { pattern = "[filename],kulczynskicody"; }
+ else if (type == "lennon") { pattern = "[filename],lennon"; }
+ else if (type == "morisitahorn") { pattern = "[filename],morisitahorn"; }
+ else if (type == "braycurtis") { pattern = "[filename],braycurtis"; }
+ else if (type == "odum") { pattern = "[filename],odum"; }
+ else if (type == "canberra") { pattern = "[filename],canberra"; }
+ else if (type == "structeuclidean") { pattern = "[filename],structeuclidean"; }
+ else if (type == "structchord") { pattern = "[filename],structchord"; }
+ else if (type == "hellinger") { pattern = "[filename],hellinger"; }
+ else if (type == "manhattan") { pattern = "[filename],manhattan"; }
+ else if (type == "structpearson") { pattern = "[filename],structpearson"; }
+ else if (type == "soergel") { pattern = "[filename],soergel"; }
+ else if (type == "spearman") { pattern = "[filename],spearman"; }
+ else if (type == "structkulczynski") { pattern = "[filename],structkulczynski";}
+ else if (type == "structchi2") { pattern = "[filename],structchi2"; }
+ else if (type == "speciesprofile") { pattern = "[filename],speciesprofile"; }
+ else if (type == "hamming") { pattern = "[filename],hamming"; }
+ else if (type == "gower") { pattern = "[filename],gower"; }
+ else if (type == "memchi2") { pattern = "[filename],memchi2"; }
+ else if (type == "memchord") { pattern = "[filename],memchord"; }
+ else if (type == "memeuclidean") { pattern = "[filename],memeuclidean"; }
+ else if (type == "mempearson") { pattern = "[filename],mempearson"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectSharedCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
CollectSharedCommand::CollectSharedCommand(){
try {
outputTypes["sharednseqs"] = tempOutNames;
outputTypes["ochiai"] = tempOutNames;
outputTypes["anderberg"] = tempOutNames;
- outputTypes["skulczynski"] = tempOutNames;
+ outputTypes["kulczynski"] = tempOutNames;
outputTypes["kulczynskicody"] = tempOutNames;
outputTypes["lennon"] = tempOutNames;
outputTypes["morisitahorn"] = tempOutNames;
outputTypes["sharednseqs"] = tempOutNames;
outputTypes["ochiai"] = tempOutNames;
outputTypes["anderberg"] = tempOutNames;
- outputTypes["skulczynski"] = tempOutNames;
+ outputTypes["kulczynski"] = tempOutNames;
outputTypes["kulczynskicody"] = tempOutNames;
outputTypes["lennon"] = tempOutNames;
outputTypes["morisitahorn"] = tempOutNames;
sharedfile = m->getSharedFile();
if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { 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 = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
}
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; } }
+ }
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
}
- m->Groups = Groups;
+ m->setGroups(Groups);
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, "all", false); if (temp == "not found") { temp = "false"; }
all = m->isTrue(temp);
if (abort == false) {
string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(sharedfile));
-
+ map<string, string> variables;
+ variables["[filename]"] = fileNameRoot;
+
ValidCalculators validCalculator;
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("shared", Estimators[i]) == true) {
if (Estimators[i] == "sharedchao") {
- cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
- outputNames.push_back(fileNameRoot+"shared.chao"); outputTypes["sharedchao"].push_back(fileNameRoot+"shared.chao");
+ cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(getOutputFileName("sharedchao", variables))));
+ outputNames.push_back(getOutputFileName("sharedchao", variables)); outputTypes["sharedchao"].push_back(getOutputFileName("sharedchao", variables));
}else if (Estimators[i] == "sharedsobs") {
- cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
- outputNames.push_back(fileNameRoot+"shared.sobs"); outputTypes["sharedsobs"].push_back(fileNameRoot+"shared.sobs");
+ cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(getOutputFileName("sharedsobs", variables))));
+ outputNames.push_back(getOutputFileName("sharedsobs", variables)); outputTypes["sharedsobs"].push_back(getOutputFileName("sharedsobs", variables));
}else if (Estimators[i] == "sharedace") {
- cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
- outputNames.push_back(fileNameRoot+"shared.ace"); outputTypes["sharedace"].push_back(fileNameRoot+"shared.ace");
+ cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(getOutputFileName("sharedace", variables))));
+ outputNames.push_back(getOutputFileName("sharedace", variables)); outputTypes["sharedace"].push_back(getOutputFileName("sharedace", variables));
}else if (Estimators[i] == "jabund") {
- cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
- outputNames.push_back(fileNameRoot+"jabund"); outputTypes["jabund"].push_back(fileNameRoot+"jabund");
+ cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(getOutputFileName("jabund", variables))));
+ outputNames.push_back(getOutputFileName("jabund", variables)); outputTypes["jabund"].push_back(getOutputFileName("jabund", variables));
}else if (Estimators[i] == "sorabund") {
- cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
- outputNames.push_back(fileNameRoot+"sorabund"); outputTypes["sorabund"].push_back(fileNameRoot+"sorabund");
+ cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(getOutputFileName("sorabund", variables))));
+ outputNames.push_back(getOutputFileName("sorabund", variables)); outputTypes["sorabund"].push_back(getOutputFileName("sorabund", variables));
}else if (Estimators[i] == "jclass") {
- cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
- outputNames.push_back(fileNameRoot+"jclass"); outputTypes["jclass"].push_back(fileNameRoot+"jclass");
+ cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(getOutputFileName("jclass", variables))));
+ outputNames.push_back(getOutputFileName("jclass", variables)); outputTypes["jclass"].push_back(getOutputFileName("jclass", variables));
}else if (Estimators[i] == "sorclass") {
- cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass")));
- outputNames.push_back(fileNameRoot+"sorclass"); outputTypes["sorclass"].push_back(fileNameRoot+"sorclass");
+ cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(getOutputFileName("sorclass", variables))));
+ outputNames.push_back(getOutputFileName("sorclass", variables)); outputTypes["sorclass"].push_back(getOutputFileName("sorclass", variables));
}else if (Estimators[i] == "jest") {
- cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest")));
- outputNames.push_back(fileNameRoot+"jest"); outputTypes["jest"].push_back(fileNameRoot+"jest");
+ cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(getOutputFileName("jest", variables))));
+ outputNames.push_back(getOutputFileName("jest", variables)); outputTypes["jest"].push_back(getOutputFileName("jest", variables));
}else if (Estimators[i] == "sorest") {
- cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest")));
- outputNames.push_back(fileNameRoot+"sorest"); outputTypes["sorest"].push_back(fileNameRoot+"sorest");
+ cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(getOutputFileName("sorest", variables))));
+ outputNames.push_back(getOutputFileName("sorest", variables)); outputTypes["sorest"].push_back(getOutputFileName("sorest", variables));
}else if (Estimators[i] == "thetayc") {
- cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc")));
- outputNames.push_back(fileNameRoot+"thetayc"); outputTypes["thetayc"].push_back(fileNameRoot+"thetayc");
+ cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(getOutputFileName("thetayc", variables))));
+ outputNames.push_back(getOutputFileName("thetayc", variables)); outputTypes["thetayc"].push_back(getOutputFileName("thetayc", variables));
}else if (Estimators[i] == "thetan") {
- cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
- outputNames.push_back(fileNameRoot+"thetan"); outputTypes["thetan"].push_back(fileNameRoot+"thetan");
+ cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(getOutputFileName("thetan", variables))));
+ outputNames.push_back(getOutputFileName("thetan", variables)); outputTypes["thetan"].push_back(getOutputFileName("thetan", variables));
}else if (Estimators[i] == "kstest") {
- cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
- outputNames.push_back(fileNameRoot+"kstest"); outputTypes["kstest"].push_back(fileNameRoot+"kstest");
+ cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(getOutputFileName("kstest", variables))));
+ outputNames.push_back(getOutputFileName("kstest", variables)); outputTypes["kstest"].push_back(getOutputFileName("kstest", variables));
}else if (Estimators[i] == "whittaker") {
- cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
- outputNames.push_back(fileNameRoot+"whittaker"); outputTypes["whittaker"].push_back(fileNameRoot+"whittaker");
+ cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(getOutputFileName("whittaker", variables))));
+ outputNames.push_back(getOutputFileName("whittaker", variables)); outputTypes["whittaker"].push_back(getOutputFileName("whittaker", variables));
}else if (Estimators[i] == "sharednseqs") {
- cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
- outputNames.push_back(fileNameRoot+"shared.nseqs"); outputTypes["shared.nseqs"].push_back(fileNameRoot+"shared.nseqs");
+ cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(getOutputFileName("sharednseqs", variables))));
+ outputNames.push_back(getOutputFileName("sharednseqs", variables)); outputTypes["shared.nseqs"].push_back(getOutputFileName("sharednseqs", variables));
}else if (Estimators[i] == "ochiai") {
- cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
- outputNames.push_back(fileNameRoot+"ochiai"); outputTypes["ochiai"].push_back(fileNameRoot+"ochiai");
+ cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(getOutputFileName("ochiai", variables))));
+ outputNames.push_back(getOutputFileName("ochiai", variables)); outputTypes["ochiai"].push_back(getOutputFileName("ochiai", variables));
}else if (Estimators[i] == "anderberg") {
- cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
- outputNames.push_back(fileNameRoot+"anderberg"); outputTypes["anderberg"].push_back(fileNameRoot+"anderberg");
- }else if (Estimators[i] == "skulczynski") {
- cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
- outputNames.push_back(fileNameRoot+"kulczynski"); outputTypes["kulczynski"].push_back(fileNameRoot+"kulczynski");
+ cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(getOutputFileName("anderberg", variables))));
+ outputNames.push_back(getOutputFileName("anderberg", variables)); outputTypes["anderberg"].push_back(getOutputFileName("anderberg", variables));
+ }else if (Estimators[i] == "kulczynski") {
+ cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(getOutputFileName("kulczynski", variables))));
+ outputNames.push_back(getOutputFileName("kulczynski", variables)); outputTypes["kulczynski"].push_back(getOutputFileName("kulczynski", variables));
}else if (Estimators[i] == "kulczynskicody") {
- cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody")));
- outputNames.push_back(fileNameRoot+"kulczynskicody"); outputTypes["kulczynskicody"].push_back(fileNameRoot+"kulczynskicody");
+ cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(getOutputFileName("kulczynskicody", variables))));
+ outputNames.push_back(getOutputFileName("kulczynskicody", variables)); outputTypes["kulczynskicody"].push_back(getOutputFileName("kulczynskicody", variables));
}else if (Estimators[i] == "lennon") {
- cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon")));
- outputNames.push_back(fileNameRoot+"lennon"); outputTypes["lennon"].push_back(fileNameRoot+"lennon");
+ cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(getOutputFileName("lennon", variables))));
+ outputNames.push_back(getOutputFileName("lennon", variables)); outputTypes["lennon"].push_back(getOutputFileName("lennon", variables));
}else if (Estimators[i] == "morisitahorn") {
- cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn")));
- outputNames.push_back(fileNameRoot+"morisitahorn"); outputTypes["morisitahorn"].push_back(fileNameRoot+"morisitahorn");
+ cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(getOutputFileName("morisitahorn", variables))));
+ outputNames.push_back(getOutputFileName("morisitahorn", variables)); outputTypes["morisitahorn"].push_back(getOutputFileName("morisitahorn", variables));
}else if (Estimators[i] == "braycurtis") {
- cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
- outputNames.push_back(fileNameRoot+"braycurtis"); outputTypes["braycurtis"].push_back(fileNameRoot+"braycurtis");
+ cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(getOutputFileName("braycurtis", variables))));
+ outputNames.push_back(getOutputFileName("braycurtis", variables)); outputTypes["braycurtis"].push_back(getOutputFileName("braycurtis", variables));
}else if (Estimators[i] == "odum") {
- cDisplays.push_back(new CollectDisplay(new Odum(), new SharedOneColumnFile(fileNameRoot+"odum")));
- outputNames.push_back(fileNameRoot+"odum"); outputTypes["odum"].push_back(fileNameRoot+"odum");
+ cDisplays.push_back(new CollectDisplay(new Odum(), new SharedOneColumnFile(getOutputFileName("odum", variables))));
+ outputNames.push_back(getOutputFileName("odum", variables)); outputTypes["odum"].push_back(getOutputFileName("odum", variables));
}else if (Estimators[i] == "canberra") {
- cDisplays.push_back(new CollectDisplay(new Canberra(), new SharedOneColumnFile(fileNameRoot+"canberra")));
- outputNames.push_back(fileNameRoot+"canberra"); outputTypes["canberra"].push_back(fileNameRoot+"canberra");
+ cDisplays.push_back(new CollectDisplay(new Canberra(), new SharedOneColumnFile(getOutputFileName("canberra", variables))));
+ outputNames.push_back(getOutputFileName("canberra", variables)); outputTypes["canberra"].push_back(getOutputFileName("canberra", variables));
}else if (Estimators[i] == "structeuclidean") {
- cDisplays.push_back(new CollectDisplay(new StructEuclidean(), new SharedOneColumnFile(fileNameRoot+"structeuclidean")));
- outputNames.push_back(fileNameRoot+"structeuclidean"); outputTypes["structeuclidean"].push_back(fileNameRoot+"structeuclidean");
+ cDisplays.push_back(new CollectDisplay(new StructEuclidean(), new SharedOneColumnFile(getOutputFileName("structeuclidean", variables))));
+ outputNames.push_back(getOutputFileName("structeuclidean", variables)); outputTypes["structeuclidean"].push_back(getOutputFileName("structeuclidean", variables));
}else if (Estimators[i] == "structchord") {
- cDisplays.push_back(new CollectDisplay(new StructChord(), new SharedOneColumnFile(fileNameRoot+"structchord")));
- outputNames.push_back(fileNameRoot+"structchord"); outputTypes["structchord"].push_back(fileNameRoot+"structchord");
+ cDisplays.push_back(new CollectDisplay(new StructChord(), new SharedOneColumnFile(getOutputFileName("structchord", variables))));
+ outputNames.push_back(getOutputFileName("structchord", variables)); outputTypes["structchord"].push_back(getOutputFileName("structchord", variables));
}else if (Estimators[i] == "hellinger") {
- cDisplays.push_back(new CollectDisplay(new Hellinger(), new SharedOneColumnFile(fileNameRoot+"hellinger")));
- outputNames.push_back(fileNameRoot+"hellinger"); outputTypes["hellinger"].push_back(fileNameRoot+"hellinger");
+ cDisplays.push_back(new CollectDisplay(new Hellinger(), new SharedOneColumnFile(getOutputFileName("hellinger", variables))));
+ outputNames.push_back(getOutputFileName("hellinger", variables)); outputTypes["hellinger"].push_back(getOutputFileName("hellinger", variables));
}else if (Estimators[i] == "manhattan") {
- cDisplays.push_back(new CollectDisplay(new Manhattan(), new SharedOneColumnFile(fileNameRoot+"manhattan")));
- outputNames.push_back(fileNameRoot+"manhattan"); outputTypes["manhattan"].push_back(fileNameRoot+"manhattan");
+ cDisplays.push_back(new CollectDisplay(new Manhattan(), new SharedOneColumnFile(getOutputFileName("manhattan", variables))));
+ outputNames.push_back(getOutputFileName("manhattan", variables)); outputTypes["manhattan"].push_back(getOutputFileName("manhattan", variables));
}else if (Estimators[i] == "structpearson") {
- cDisplays.push_back(new CollectDisplay(new StructPearson(), new SharedOneColumnFile(fileNameRoot+"structpearson")));
- outputNames.push_back(fileNameRoot+"structpearson"); outputTypes["structpearson"].push_back(fileNameRoot+"structpearson");
+ cDisplays.push_back(new CollectDisplay(new StructPearson(), new SharedOneColumnFile(getOutputFileName("structpearson", variables))));
+ outputNames.push_back(getOutputFileName("structpearson", variables)); outputTypes["structpearson"].push_back(getOutputFileName("structpearson", variables));
}else if (Estimators[i] == "soergel") {
- cDisplays.push_back(new CollectDisplay(new Soergel(), new SharedOneColumnFile(fileNameRoot+"soergel")));
- outputNames.push_back(fileNameRoot+"soergel"); outputTypes["soergel"].push_back(fileNameRoot+"soergel");
+ cDisplays.push_back(new CollectDisplay(new Soergel(), new SharedOneColumnFile(getOutputFileName("soergel", variables))));
+ outputNames.push_back(getOutputFileName("soergel", variables)); outputTypes["soergel"].push_back(getOutputFileName("soergel", variables));
}else if (Estimators[i] == "spearman") {
- cDisplays.push_back(new CollectDisplay(new Spearman(), new SharedOneColumnFile(fileNameRoot+"spearman")));
- outputNames.push_back(fileNameRoot+"spearman"); outputTypes["spearman"].push_back(fileNameRoot+"spearman");
+ cDisplays.push_back(new CollectDisplay(new Spearman(), new SharedOneColumnFile(getOutputFileName("spearman", variables))));
+ outputNames.push_back(getOutputFileName("spearman", variables)); outputTypes["spearman"].push_back(getOutputFileName("spearman", variables));
}else if (Estimators[i] == "structkulczynski") {
- cDisplays.push_back(new CollectDisplay(new StructKulczynski(), new SharedOneColumnFile(fileNameRoot+"structkulczynski")));
- outputNames.push_back(fileNameRoot+"structkulczynski"); outputTypes["structkulczynski"].push_back(fileNameRoot+"structkulczynski");
+ cDisplays.push_back(new CollectDisplay(new StructKulczynski(), new SharedOneColumnFile(getOutputFileName("structkulczynski", variables))));
+ outputNames.push_back(getOutputFileName("structkulczynski", variables)); outputTypes["structkulczynski"].push_back(getOutputFileName("structkulczynski", variables));
}else if (Estimators[i] == "speciesprofile") {
- cDisplays.push_back(new CollectDisplay(new SpeciesProfile(), new SharedOneColumnFile(fileNameRoot+"speciesprofile")));
- outputNames.push_back(fileNameRoot+"speciesprofile"); outputTypes["speciesprofile"].push_back(fileNameRoot+"speciesprofile");
+ cDisplays.push_back(new CollectDisplay(new SpeciesProfile(), new SharedOneColumnFile(getOutputFileName("speciesprofile", variables))));
+ outputNames.push_back(getOutputFileName("speciesprofile", variables)); outputTypes["speciesprofile"].push_back(getOutputFileName("speciesprofile", variables));
}else if (Estimators[i] == "hamming") {
- cDisplays.push_back(new CollectDisplay(new Hamming(), new SharedOneColumnFile(fileNameRoot+"hamming")));
- outputNames.push_back(fileNameRoot+"hamming"); outputTypes["hamming"].push_back(fileNameRoot+"hamming");
+ cDisplays.push_back(new CollectDisplay(new Hamming(), new SharedOneColumnFile(getOutputFileName("hamming", variables))));
+ outputNames.push_back(getOutputFileName("hamming", variables)); outputTypes["hamming"].push_back(getOutputFileName("hamming", variables));
}else if (Estimators[i] == "structchi2") {
- cDisplays.push_back(new CollectDisplay(new StructChi2(), new SharedOneColumnFile(fileNameRoot+"structchi2")));
- outputNames.push_back(fileNameRoot+"structchi2"); outputTypes["structchi2"].push_back(fileNameRoot+"structchi2");
+ cDisplays.push_back(new CollectDisplay(new StructChi2(), new SharedOneColumnFile(getOutputFileName("structchi2", variables))));
+ outputNames.push_back(getOutputFileName("structchi2", variables)); outputTypes["structchi2"].push_back(getOutputFileName("structchi2", variables));
}else if (Estimators[i] == "gower") {
- cDisplays.push_back(new CollectDisplay(new Gower(), new SharedOneColumnFile(fileNameRoot+"gower")));
- outputNames.push_back(fileNameRoot+"gower"); outputTypes["gower"].push_back(fileNameRoot+"gower");
+ cDisplays.push_back(new CollectDisplay(new Gower(), new SharedOneColumnFile(getOutputFileName("gower", variables))));
+ outputNames.push_back(getOutputFileName("gower", variables)); outputTypes["gower"].push_back(getOutputFileName("gower", variables));
}else if (Estimators[i] == "memchi2") {
- cDisplays.push_back(new CollectDisplay(new MemChi2(), new SharedOneColumnFile(fileNameRoot+"memchi2")));
- outputNames.push_back(fileNameRoot+"memchi2"); outputTypes["memchi2"].push_back(fileNameRoot+"memchi2");
+ cDisplays.push_back(new CollectDisplay(new MemChi2(), new SharedOneColumnFile(getOutputFileName("memchi2", variables))));
+ outputNames.push_back(getOutputFileName("memchi2", variables)); outputTypes["memchi2"].push_back(getOutputFileName("memchi2", variables));
}else if (Estimators[i] == "memchord") {
- cDisplays.push_back(new CollectDisplay(new MemChord(), new SharedOneColumnFile(fileNameRoot+"memchord")));
- outputNames.push_back(fileNameRoot+"memchord"); outputTypes["memchord"].push_back(fileNameRoot+"memchord");
+ cDisplays.push_back(new CollectDisplay(new MemChord(), new SharedOneColumnFile(getOutputFileName("memchord", variables))));
+ outputNames.push_back(getOutputFileName("memchord", variables)); outputTypes["memchord"].push_back(getOutputFileName("memchord", variables));
}else if (Estimators[i] == "memeuclidean") {
- cDisplays.push_back(new CollectDisplay(new MemEuclidean(), new SharedOneColumnFile(fileNameRoot+"memeuclidean")));
- outputNames.push_back(fileNameRoot+"memeuclidean"); outputTypes["memeuclidean"].push_back(fileNameRoot+"memeuclidean");
+ cDisplays.push_back(new CollectDisplay(new MemEuclidean(), new SharedOneColumnFile(getOutputFileName("memeuclidean", variables))));
+ outputNames.push_back(getOutputFileName("memeuclidean", variables)); outputTypes["memeuclidean"].push_back(getOutputFileName("memeuclidean", variables));
}else if (Estimators[i] == "mempearson") {
- cDisplays.push_back(new CollectDisplay(new MemPearson(), new SharedOneColumnFile(fileNameRoot+"mempearson")));
- outputNames.push_back(fileNameRoot+"mempearson"); outputTypes["mempearson"].push_back(fileNameRoot+"mempearson");
+ cDisplays.push_back(new CollectDisplay(new MemPearson(), new SharedOneColumnFile(getOutputFileName("mempearson", variables))));
+ outputNames.push_back(getOutputFileName("mempearson", variables)); outputTypes["mempearson"].push_back(getOutputFileName("mempearson", variables));
}
}
//set users groups
SharedUtil* util = new SharedUtil();
- util->setGroups(m->Groups, m->namesOfGroups, "collect");
+ Groups = m->getGroups();
+ vector<string> allGroups = m->getAllGroups();
+ util->setGroups(Groups, allGroups, "collect");
+ m->setGroups(Groups);
+ m->setAllGroups(allGroups);
delete util;
while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) {
- 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();
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
delete order; delete input;
- m->Groups.clear();
+ m->clearGroups();
return 0;
}
}
if (m->control_pressed) {
- 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();
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
- m->Groups.clear();
+ m->clearGroups();
delete input;
return 0;
}
delete cCurve;
if (m->control_pressed) {
- 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();
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
delete order;
delete input;
- m->Groups.clear();
+ m->clearGroups();
return 0;
}
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
//reset groups parameter
- m->Groups.clear();
+ m->clearGroups();
delete input;
m->mothurOutEndLine();
projects / mothur.git / blobdiff