X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeracheckrdp.h;h=25db15b6738f4909a3a02e939d9a114b9d63fa29;hp=e12e7d3d9d6cf3a08e44d453e7ea5afd2a34f06b;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=5a1e62397b91f57d0d3aff635891df04b8999a88

diff --git a/chimeracheckrdp.h b/chimeracheckrdp.h
index e12e7d3..25db15b 100644
--- a/chimeracheckrdp.h
+++ b/chimeracheckrdp.h
@@ -17,7 +17,7 @@
 #include "alignmentdb.h"
 
 /***********************************************************/
-//This class was created using the algorythms described in 
+//This class was created using the algorithms described in 
 //CHIMERA_CHECK version 2.7 written by Niels Larsen. 
 
 /***********************************************************/
@@ -25,15 +25,17 @@
 class ChimeraCheckRDP : public Chimera {
 	
 	public:
-		ChimeraCheckRDP(string, string);	
+		ChimeraCheckRDP(string, string, string, bool, int, int, string); //fasta, template, name, svg, increment, ksize, outputDir	
 		~ChimeraCheckRDP();
 		
 		int getChimeras(Sequence*);
-		void print(ostream&);
-		void doPrep();
+		Sequence print(ostream&, ostream&);
 		
-	private:
+		#ifdef USE_MPI
+		Sequence print(MPI_File&, MPI_File&);
+		#endif
 		
+	private:
 		
 		Sequence* querySeq;
 		AlignmentDB* templateDB;
@@ -43,6 +45,9 @@ class ChimeraCheckRDP : public Chimera {
 		vector<sim>  IS;  //IS is the vector of IS values for each window for query
 		string fastafile;
 		map<string, string> names;
+		string name;
+		bool svg;
+		int kmerSize, increment;
 		
 		vector<sim> findIS();
 		int calcKmers(map<int, int>, map<int, int>);