#include "mothur.h"
#include "database.hpp"
-
-class SuffixTree;
+#include "suffixtree.hpp"
+//class SuffixTree;
class SuffixDB : public Database {
public:
- SuffixDB(string);
+ SuffixDB(int);
+ SuffixDB();
+ SuffixDB(const SuffixDB& sdb) : count(sdb.count), Database(sdb) {
+ for (int i = 0; i < sdb.suffixForest.size(); i++) {
+ SuffixTree temp(sdb.suffixForest[i]);
+ suffixForest.push_back(temp);
+ }
+ }
~SuffixDB();
- Sequence findClosestSequence(Sequence*);
+
+ void generateDB() {}; //adding sequences generates the db
+ void addSequence(Sequence);
+ vector<int> findClosestSequences(Sequence*, int);
private:
vector<SuffixTree> suffixForest;
+ int count;
};
#endif