#include "whittaker.h"
-
//**********************************************************************************************************************
-
+vector<string> CollectSharedCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"freq","label","calc","groups","all","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectSharedCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> CollectSharedCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectSharedCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> CollectSharedCommand::getRequiredFiles(){
+ try {
+ string AlignArray[] = {"shared"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectSharedCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CollectSharedCommand::CollectSharedCommand(){
+ try {
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sharedchao"] = tempOutNames;
+ outputTypes["sharedsobs"] = tempOutNames;
+ outputTypes["sharedace"] = tempOutNames;
+ outputTypes["jabund"] = tempOutNames;
+ outputTypes["sorabund"] = tempOutNames;
+ outputTypes["jclass"] = tempOutNames;
+ outputTypes["sorclass"] = tempOutNames;
+ outputTypes["jest"] = tempOutNames;
+ outputTypes["sorest"] = tempOutNames;
+ outputTypes["thetayc"] = tempOutNames;
+ outputTypes["thetan"] = tempOutNames;
+ outputTypes["kstest"] = tempOutNames;
+ outputTypes["whittaker"] = tempOutNames;
+ outputTypes["sharednseqs"] = tempOutNames;
+ outputTypes["ochiai"] = tempOutNames;
+ outputTypes["anderberg"] = tempOutNames;
+ outputTypes["skulczynski"] = tempOutNames;
+ outputTypes["kulczynskicody"] = tempOutNames;
+ outputTypes["lennon"] = tempOutNames;
+ outputTypes["morisitahorn"] = tempOutNames;
+ outputTypes["braycurtis"] = tempOutNames;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
CollectSharedCommand::CollectSharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sharedchao"] = tempOutNames;
+ outputTypes["sharedsobs"] = tempOutNames;
+ outputTypes["sharedace"] = tempOutNames;
+ outputTypes["jabund"] = tempOutNames;
+ outputTypes["sorabund"] = tempOutNames;
+ outputTypes["jclass"] = tempOutNames;
+ outputTypes["sorclass"] = tempOutNames;
+ outputTypes["jest"] = tempOutNames;
+ outputTypes["sorest"] = tempOutNames;
+ outputTypes["thetayc"] = tempOutNames;
+ outputTypes["thetan"] = tempOutNames;
+ outputTypes["kstest"] = tempOutNames;
+ outputTypes["whittaker"] = tempOutNames;
+ outputTypes["sharednseqs"] = tempOutNames;
+ outputTypes["ochiai"] = tempOutNames;
+ outputTypes["anderberg"] = tempOutNames;
+ outputTypes["skulczynski"] = tempOutNames;
+ outputTypes["kulczynskicody"] = tempOutNames;
+ outputTypes["lennon"] = tempOutNames;
+ outputTypes["morisitahorn"] = tempOutNames;
+ outputTypes["braycurtis"] = 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 = ""; }
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");
+ outputNames.push_back(fileNameRoot+"shared.chao"); outputTypes["sharedchao"].push_back(fileNameRoot+"shared.chao");
}else if (Estimators[i] == "sharedsobs") {
cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
- outputNames.push_back(fileNameRoot+"shared.sobs");
+ outputNames.push_back(fileNameRoot+"shared.sobs"); outputTypes["sharedsobs"].push_back(fileNameRoot+"shared.sobs");
}else if (Estimators[i] == "sharedace") {
cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
- outputNames.push_back(fileNameRoot+"shared.ace");
+ outputNames.push_back(fileNameRoot+"shared.ace"); outputTypes["sharedace"].push_back(fileNameRoot+"shared.ace");
}else if (Estimators[i] == "jabund") {
cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
- outputNames.push_back(fileNameRoot+"jabund");
+ outputNames.push_back(fileNameRoot+"jabund"); outputTypes["jabund"].push_back(fileNameRoot+"jabund");
}else if (Estimators[i] == "sorabund") {
cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
- outputNames.push_back(fileNameRoot+"sorabund");
+ outputNames.push_back(fileNameRoot+"sorabund"); outputTypes["sorabund"].push_back(fileNameRoot+"sorabund");
}else if (Estimators[i] == "jclass") {
cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
- outputNames.push_back(fileNameRoot+"jclass");
+ outputNames.push_back(fileNameRoot+"jclass"); outputTypes["jclass"].push_back(fileNameRoot+"jclass");
}else if (Estimators[i] == "sorclass") {
cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass")));
- outputNames.push_back(fileNameRoot+"sorclass");
+ outputNames.push_back(fileNameRoot+"sorclass"); outputTypes["sorclass"].push_back(fileNameRoot+"sorclass");
}else if (Estimators[i] == "jest") {
cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest")));
- outputNames.push_back(fileNameRoot+"jest");
+ outputNames.push_back(fileNameRoot+"jest"); outputTypes["jest"].push_back(fileNameRoot+"jest");
}else if (Estimators[i] == "sorest") {
cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest")));
- outputNames.push_back(fileNameRoot+"sorest");
+ outputNames.push_back(fileNameRoot+"sorest"); outputTypes["sorest"].push_back(fileNameRoot+"sorest");
}else if (Estimators[i] == "thetayc") {
cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc")));
- outputNames.push_back(fileNameRoot+"thetayc");
+ outputNames.push_back(fileNameRoot+"thetayc"); outputTypes["thetayc"].push_back(fileNameRoot+"thetayc");
}else if (Estimators[i] == "thetan") {
cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
- outputNames.push_back(fileNameRoot+"thetan");
+ outputNames.push_back(fileNameRoot+"thetan"); outputTypes["thetan"].push_back(fileNameRoot+"thetan");
}else if (Estimators[i] == "kstest") {
cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
- outputNames.push_back(fileNameRoot+"kstest");
+ outputNames.push_back(fileNameRoot+"kstest"); outputTypes["kstest"].push_back(fileNameRoot+"kstest");
}else if (Estimators[i] == "whittaker") {
cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
- outputNames.push_back(fileNameRoot+"whittaker");
+ outputNames.push_back(fileNameRoot+"whittaker"); outputTypes["whittaker"].push_back(fileNameRoot+"whittaker");
}else if (Estimators[i] == "sharednseqs") {
cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
- outputNames.push_back(fileNameRoot+"shared.nseqs");
+ outputNames.push_back(fileNameRoot+"shared.nseqs"); outputTypes["shared.nseqs"].push_back(fileNameRoot+"shared.nseqs");
}else if (Estimators[i] == "ochiai") {
cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
- outputNames.push_back(fileNameRoot+"ochiai");
+ outputNames.push_back(fileNameRoot+"ochiai"); outputTypes["ochiai"].push_back(fileNameRoot+"ochiai");
}else if (Estimators[i] == "anderberg") {
cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
- outputNames.push_back(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");
+ outputNames.push_back(fileNameRoot+"kulczynski"); outputTypes["kulczynski"].push_back(fileNameRoot+"kulczynski");
}else if (Estimators[i] == "kulczynskicody") {
cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody")));
- outputNames.push_back(fileNameRoot+"kulczynskicody");
+ outputNames.push_back(fileNameRoot+"kulczynskicody"); outputTypes["kulczynskicody"].push_back(fileNameRoot+"kulczynskicody");
}else if (Estimators[i] == "lennon") {
cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon")));
- outputNames.push_back(fileNameRoot+"lennon");
+ outputNames.push_back(fileNameRoot+"lennon"); outputTypes["lennon"].push_back(fileNameRoot+"lennon");
}else if (Estimators[i] == "morisitahorn") {
cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn")));
- outputNames.push_back(fileNameRoot+"morisitahorn");
+ outputNames.push_back(fileNameRoot+"morisitahorn"); outputTypes["morisitahorn"].push_back(fileNameRoot+"morisitahorn");
}else if (Estimators[i] == "braycurtis") {
cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
- outputNames.push_back(fileNameRoot+"braycurtis");
+ outputNames.push_back(fileNameRoot+"braycurtis"); outputTypes["braycurtis"].push_back(fileNameRoot+"braycurtis");
}
}
}
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()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
delete order;
globaldata->Groups.clear();
}
if (m->control_pressed) {
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
globaldata->Groups.clear();
return 0;
delete cCurve;
if (m->control_pressed) {
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
delete order;
globaldata->Groups.clear();
projects / mothur.git / blobdiff