#include "sharedbraycurtis.h"
#include "sharedjackknife.h"
#include "whittaker.h"
-
+#include "odum.h"
+#include "canberra.h"
+#include "structeuclidean.h"
+#include "structchord.h"
+#include "hellinger.h"
+#include "manhattan.h"
+#include "structpearson.h"
+#include "soergel.h"
+#include "spearman.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(){
//**********************************************************************************************************************
CollectSharedCommand::CollectSharedCommand(){
try {
- abort = true;
- //initialize outputTypes
+ abort = true; calledHelp = true;
vector<string> tempOutNames;
outputTypes["sharedchao"] = tempOutNames;
outputTypes["sharedsobs"] = tempOutNames;
outputTypes["lennon"] = tempOutNames;
outputTypes["morisitahorn"] = tempOutNames;
outputTypes["braycurtis"] = tempOutNames;
+ outputTypes["odum"] = tempOutNames;
+ outputTypes["canberra"] = tempOutNames;
+ outputTypes["structeuclidean"] = tempOutNames;
+ outputTypes["structchord"] = tempOutNames;
+ outputTypes["hellinger"] = tempOutNames;
+ outputTypes["manhattan"] = tempOutNames;
+ outputTypes["structpearson"] = tempOutNames;
+ outputTypes["soergel"] = tempOutNames;
+ outputTypes["spearman"] = 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) {
CollectSharedCommand::CollectSharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
Estimators.clear();
Groups.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
outputTypes["lennon"] = tempOutNames;
outputTypes["morisitahorn"] = tempOutNames;
outputTypes["braycurtis"] = tempOutNames;
-
+ outputTypes["odum"] = tempOutNames;
+ outputTypes["canberra"] = tempOutNames;
+ outputTypes["structeuclidean"] = tempOutNames;
+ outputTypes["structchord"] = tempOutNames;
+ outputTypes["hellinger"] = tempOutNames;
+ outputTypes["manhattan"] = tempOutNames;
+ outputTypes["structpearson"] = tempOutNames;
+ outputTypes["soergel"] = tempOutNames;
+ outputTypes["spearman"] = 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] == "braycurtis") {
cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
outputNames.push_back(fileNameRoot+"braycurtis"); outputTypes["braycurtis"].push_back(fileNameRoot+"braycurtis");
+ }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");
+ }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] == "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] == "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] == "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");
}
+
}
}
}
int CollectSharedCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//if the users entered no valid calculators don't execute command
if (cDisplays.size() == 0) { return 0; }
projects / mothur.git / blobdiff