return (left->getGroup() < right->getGroup());
}
//**********************************************************************************************************************
+vector<string> SharedCommand::getValidParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+SharedCommand::SharedCommand(){
+ try {
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "SharedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SharedCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SharedCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SharedCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
SharedCommand::SharedCommand(string o) : outputDir(o) {
try {
globaldata = GlobalData::getInstance();
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+
//getting output filename
filename = globaldata->inputFileName;
if (outputDir == "") { outputDir += m->hasPath(filename); }
filename = outputDir + m->getRootName(m->getSimpleName(filename));
filename = filename + "shared";
+ outputTypes["shared"].push_back(filename);
m->openOutputFile(filename, out);
pickedGroups = false;
for (int i=0; i<groups.size(); i++) {
remove((fileroot + groups[i] + ".rabund").c_str());
outputNames.push_back((fileroot + groups[i] + ".rabund"));
+ outputTypes["rabund"].push_back((fileroot + groups[i] + ".rabund"));
}
}