X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckrdp.h;h=cc23c2e9e8b0b794339a0dfa8fa91bae50f28c00;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=f436718ef8cc7ae5d63451edadd0eee960d3f9fc;hpb=c4fb347858dd8cfea4d2933f429fff4130dca65b;p=mothur.git

diff --git a/chimeracheckrdp.h b/chimeracheckrdp.h
index f436718..cc23c2e 100644
--- a/chimeracheckrdp.h
+++ b/chimeracheckrdp.h
@@ -14,7 +14,7 @@
 #include "chimera.h"
 #include "kmer.hpp"
 #include "kmerdb.hpp"
-#include "database.hpp"
+#include "alignmentdb.h"
 
 /***********************************************************/
 //This class was created using the algorythms described in 
@@ -25,45 +25,35 @@
 class ChimeraCheckRDP : public Chimera {
 	
 	public:
-		ChimeraCheckRDP(string, string);	
+		ChimeraCheckRDP(string, string, string, bool, int, int, string); //fasta, template, name, svg, increment, ksize, outputDir	
 		~ChimeraCheckRDP();
 		
-		void getChimeras();
-		void print(ostream&);
-		
-		void setCons(string){};
-		void setQuantiles(string q) {};
+		int getChimeras(Sequence*);
+		Sequence print(ostream&, ostream&);
 		
+		#ifdef USE_MPI
+		Sequence print(MPI_File&, MPI_File&);
+		#endif
 		
 	private:
 		
-		vector<linePair*> lines;
-		vector<Sequence*> querySeqs;
-		Database* templateDB;
+		Sequence* querySeq;
+		AlignmentDB* templateDB;
 		Kmer* kmer;
-		
-		vector< vector<sim> > IS;  //IS[0] is the vector of IS values for each window for querySeqs[0]
-		float chimeraCutoff;
-		
-		
-		//map<string, vector< map<int, int> > >:: iterator it;
-		//map<int, int>::iterator it2;
-		
-		vector<Sequence> closest;		//closest[0] is the closest overall seq to querySeqs[0].
-		
-		string fastafile, templateFile;
+		Sequence closest;		//closest is the closest overall seq to query
+
+		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);
+		vector<sim> findIS();
 		int calcKmers(map<int, int>, map<int, int>);
-		void getCutoff();
-		void makeSVGpic(vector<sim>, int);
+		void makeSVGpic(vector<sim>);
 		void readName(string);
-				
-		void createProcessesIS();
-		
 };
-
 /***********************************************************/
 
 #endif