+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 {
+ 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;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+CollectSharedCommand::CollectSharedCommand(string option) {