TreeMap* gTreemap;
SequenceDB* gSequenceDB;
string inputFileName, argv;
- bool allLines, runParse;
+ bool allLines, runParse, jumble;
vector<string> Estimators, Groups; //holds estimators to be used
set<int> lines; //hold lines to be used
set<string> labels; //holds labels to be used
string getNameFile(); //do we need this?
string getGroupFile(); //do we need this?
string getOrderFile();
-// string getFastaFile();
string getTreeFile();
string getSharedFile();
string getFormat(); //do we need this?
-// string getCandidateFile();
-// string getTemplateFile();
+
void setListFile(string);
-// void setFastaFile(string);
void setTreeFile(string);
-// void setCandidateFile(string);
-// void setTemplateFile(string);
void setGroupFile(string); //do we need this?
void setPhylipFile(string);
void setColumnFile(string);