X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeracheckrdp.h;h=25db15b6738f4909a3a02e939d9a114b9d63fa29;hp=7563c023d0b774917b25bbec62390b43d180922d;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=e729387d0813f82e9cd907dfeeef1afab399ba84

diff --git a/chimeracheckrdp.h b/chimeracheckrdp.h
index 7563c02..25db15b 100644
--- a/chimeracheckrdp.h
+++ b/chimeracheckrdp.h
@@ -14,9 +14,10 @@
 #include "chimera.h"
 #include "kmer.hpp"
 #include "kmerdb.hpp"
-#include "database.hpp"
+#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. 
 
 /***********************************************************/
@@ -24,45 +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