working on pam

[mothur.git] / suffixdb.hpp

diff --git a/suffixdb.hpp b/suffixdb.hpp
index 3d0b01d187fe938451056e0ff10621c5a4c941b4..3796801a73c852bd61b6785d453d1cce825a0e66 100644 (file)
--- a/suffixdb.hpp
+++ b/suffixdb.hpp
@@ -9,7 +9,7 @@
  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
  *
  *     This is a child class of the Database abstract datatype.  The class is basically a database of suffix trees and an
- *     encapsulation of the method for finding the most similar tree to an inputted sequence.  the suffixForest objecct
+ *     encapsulation of the method for finding the most similar tree to an inputted sequence.  the suffixForest object
  *     is a vector of SuffixTrees, with each template sequence being represented by a different SuffixTree.  The class also
  *     provides a method to take an unaligned sequence and find the closest sequence in the suffixForest.  The search
  *     method is inspired by the article and Perl source code provided at http://www.ddj.com/web-development/184416093.  I 
@@ -20,17 +20,22 @@
 
 #include "mothur.h"
 #include "database.hpp"
-
-class SuffixTree;
+#include "suffixtree.hpp"
 
 class SuffixDB : public Database {
        
 public:
-       SuffixDB(string);
-       Sequence* findClosestSequence(Sequence*);
+       SuffixDB(int);
+       SuffixDB();
+       ~SuffixDB();
+       
+       void generateDB() {}; //adding sequences generates the db
+       void addSequence(Sequence);
+       vector<int> findClosestSequences(Sequence*, int);
 
 private:
        vector<SuffixTree> suffixForest;
+       int count;
 };
 
 #endif