X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=suffixdb.hpp;h=3796801a73c852bd61b6785d453d1cce825a0e66;hp=3d0b01d187fe938451056e0ff10621c5a4c941b4;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=526a868606faa50caf86e7399f7554c0335b39e5

diff --git a/suffixdb.hpp b/suffixdb.hpp
index 3d0b01d..3796801 100644
--- 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