#include "whittaker.h"
#include "odum.h"
#include "canberra.h"
-#include "stricteuclidean.h"
-#include "strictchord.h"
+#include "structeuclidean.h"
+#include "structchord.h"
#include "hellinger.h"
#include "manhattan.h"
-#include "strictpearson.h"
+#include "structpearson.h"
#include "soergel.h"
#include "spearman.h"
-#include "strictkulczynski.h"
+#include "structkulczynski.h"
+#include "structchi2.h"
#include "speciesprofile.h"
#include "hamming.h"
+#include "gower.h"
+#include "memchi2.h"
+#include "memchord.h"
+#include "memeuclidean.h"
+#include "mempearson.h"
//**********************************************************************************************************************
vector<string> CollectSharedCommand::getValidParameters(){
outputTypes["braycurtis"] = tempOutNames;
outputTypes["odum"] = tempOutNames;
outputTypes["canberra"] = tempOutNames;
- outputTypes["stricteuclidean"] = tempOutNames;
- outputTypes["strictchord"] = tempOutNames;
+ outputTypes["structeuclidean"] = tempOutNames;
+ outputTypes["structchord"] = tempOutNames;
outputTypes["hellinger"] = tempOutNames;
outputTypes["manhattan"] = tempOutNames;
- outputTypes["strictpearson"] = tempOutNames;
+ outputTypes["structpearson"] = tempOutNames;
outputTypes["soergel"] = tempOutNames;
outputTypes["spearman"] = tempOutNames;
- outputTypes["strictkulczynski"] = tempOutNames;
+ outputTypes["structkulczynski"] = tempOutNames;
+ outputTypes["structchi2"] = tempOutNames;
outputTypes["speciesprofile"] = tempOutNames;
outputTypes["hamming"] = tempOutNames;
+ outputTypes["gower"] = tempOutNames;
+ outputTypes["memchi2"] = tempOutNames;
+ outputTypes["memchord"] = tempOutNames;
+ outputTypes["memeuclidean"] = tempOutNames;
+ outputTypes["mempearson"] = tempOutNames;
}
catch(exception& e) {
outputTypes["braycurtis"] = tempOutNames;
outputTypes["odum"] = tempOutNames;
outputTypes["canberra"] = tempOutNames;
- outputTypes["stricteuclidean"] = tempOutNames;
- outputTypes["strictchord"] = tempOutNames;
+ outputTypes["structeuclidean"] = tempOutNames;
+ outputTypes["structchord"] = tempOutNames;
outputTypes["hellinger"] = tempOutNames;
outputTypes["manhattan"] = tempOutNames;
- outputTypes["strictpearson"] = tempOutNames;
+ outputTypes["structpearson"] = tempOutNames;
outputTypes["soergel"] = tempOutNames;
outputTypes["spearman"] = tempOutNames;
- outputTypes["strictkulczynski"] = tempOutNames;
+ outputTypes["structkulczynski"] = tempOutNames;
outputTypes["speciesprofile"] = tempOutNames;
+ outputTypes["structchi2"] = tempOutNames;
outputTypes["hamming"] = tempOutNames;
-
+ outputTypes["gower"] = tempOutNames;
+ outputTypes["memchi2"] = tempOutNames;
+ outputTypes["memchord"] = tempOutNames;
+ outputTypes["memeuclidean"] = tempOutNames;
+ outputTypes["mempearson"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
}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");
- }else if (Estimators[i] == "stricteuclidean") {
- cDisplays.push_back(new CollectDisplay(new StrictEuclidean(), new SharedOneColumnFile(fileNameRoot+"stricteuclidean")));
- outputNames.push_back(fileNameRoot+"stricteuclidean"); outputTypes["stricteuclidean"].push_back(fileNameRoot+"stricteuclidean");
- }else if (Estimators[i] == "strictchord") {
- cDisplays.push_back(new CollectDisplay(new StrictChord(), new SharedOneColumnFile(fileNameRoot+"strictchord")));
- outputNames.push_back(fileNameRoot+"strictchord"); outputTypes["strictchord"].push_back(fileNameRoot+"strictchord");
+ }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");
+ }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");
}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");
}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");
- }else if (Estimators[i] == "strictpearson") {
- cDisplays.push_back(new CollectDisplay(new StrictPearson(), new SharedOneColumnFile(fileNameRoot+"strictpearson")));
- outputNames.push_back(fileNameRoot+"strictpearson"); outputTypes["strictpearson"].push_back(fileNameRoot+"strictpearson");
+ }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");
}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");
}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");
- }else if (Estimators[i] == "strictkulczynski") {
- cDisplays.push_back(new CollectDisplay(new StrictKulczynski(), new SharedOneColumnFile(fileNameRoot+"strictkulczynski")));
- outputNames.push_back(fileNameRoot+"strictkulczynski"); outputTypes["strictkulczynski"].push_back(fileNameRoot+"strictkulczynski");
+ }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");
}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");
}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");
+ }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");
+ }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");
+ }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");
+ }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");
+ }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");
+ }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");
}
}
projects / mothur.git / blobdiff