X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeracheckrdp.h;h=cc23c2e9e8b0b794339a0dfa8fa91bae50f28c00;hp=0ba851a9d6906b48a44b66d311882e0a88c8c400;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=9c23307c583d4e8595f75278c13e708788f2f058

diff --git a/chimeracheckrdp.h b/chimeracheckrdp.h
index 0ba851a..cc23c2e 100644
--- a/chimeracheckrdp.h
+++ b/chimeracheckrdp.h
@@ -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&, 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>);