added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / suffixdb.hpp

diff --git a/suffixdb.hpp b/suffixdb.hpp
index 15114cf9a103707b67486864fd0d8b40f96e95c7..ca1ff42a11c6bcbd689e0e49e2cdfb36604e0807 100644 (file)
--- a/suffixdb.hpp
+++ b/suffixdb.hpp
@@ -20,17 +20,29 @@
 
 #include "mothur.h"
 #include "database.hpp"
-
-class SuffixTree;
+#include "suffixtree.hpp"
+//class SuffixTree;
 
 class SuffixDB : public Database {
        
 public:
-       SuffixDB(string);
-       Sequence* findClosestSequence(Sequence*);
+       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();
+       
+       void generateDB() {}; //adding sequences generates the db
+       void addSequence(Sequence);
+       vector<int> findClosestSequences(Sequence*, int);
 
 private:
        vector<SuffixTree> suffixForest;
+       int count;
 };
 
 #endif