X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayer.h;h=58e1656e6b995ae97d879863c0f2becc092ef9d1;hb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;hp=4095b86a4b0855e31b05bbfd775504801cc4ed1f;hpb=5a1e62397b91f57d0d3aff635891df04b8999a88;p=mothur.git

diff --git a/chimeraslayer.h b/chimeraslayer.h
index 4095b86..58e1656 100644
--- a/chimeraslayer.h
+++ b/chimeraslayer.h
@@ -23,12 +23,13 @@
 class ChimeraSlayer : public Chimera {
 	
 	public:
-		ChimeraSlayer(string);	
+		ChimeraSlayer(string, bool, string);	
 		~ChimeraSlayer();
 		
 		int getChimeras(Sequence*);
-		void print(ostream&);
+		int print(ostream&, ostream&);
 		void printHeader(ostream&);
+		int doPrep();
 		
 	private:
 		Sequence* querySeq;
@@ -36,12 +37,15 @@ class ChimeraSlayer : public Chimera {
 		Maligner* maligner;
 		Slayer* slayer;
 		map<int, int>  spotMap;
+		Database* databaseRight;
+		Database* databaseLeft;
 		
 		vector<data_struct>  chimeraResults;
-		string chimeraFlags, searchMethod;
-		string fastafile;
+		string chimeraFlags, searchMethod, fastafile;
+		bool realign;
 	
 		void printBlock(data_struct, ostream&);
+		
 };
 
 /************************************************************************/