#include "mothurout.h"
#include "tree.h"
+#include "counttable.h"
class TreeReader {
public:
- TreeReader(string tf);
- TreeReader(string tf, string gf);
+ TreeReader(string tf, string cf);
TreeReader(string tf, string gf, string nf);
~TreeReader() {}
vector<Tree*> getTrees() { return trees; }
- map<string, string> getNames() { return nameMap; } //dups -> unique
- map<string, string> getNameMap() { return names; } //unique -> dups list
-
private:
MothurOut* m;
vector<Tree*> trees;
- TreeMap* tmap;
- map<string, string> nameMap; //dupName -> uniqueName
- map<string, string> names;
+ CountTable* ct;
+ //map<string, string> nameMap; //dupName -> uniqueName
+ // map<string, string> names;
- string treefile, groupfile, namefile;
+ string treefile, groupfile, namefile, countfile;
bool readTrees();
int readNamesFile();