X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeracheckrdp.h;h=25db15b6738f4909a3a02e939d9a114b9d63fa29;hp=e31cae7672ef016839e7eb736a5ac0bd1cde65a8;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=1244c4907c07baea86b0f0676d098a29d2e95a39

diff --git a/chimeracheckrdp.h b/chimeracheckrdp.h
index e31cae7..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. 
 
 /***********************************************************/
@@ -24,48 +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]
-		
-		//map of vector of maps- I know its a little convaluted but I am trying to save time 
-		//I think that since the window is only sliding 10 bases there is a good probability that the closest seq to each fragment
-		//will be the same for several windows so I want to save the vector of maps containing its kmer info rather than regenerating it.
-		//So...
-		map<string, vector< map<int, int> > > seqKmerInfo;  // outer map - sequence name -> kmer info 
-															// kmer info: inner vector of maps - each entry in the vector is a map of the kmers up to that spot in the unaligned seq
-															//example:  seqKmerInfo["ecoli"][50] = map containing the kmers found in the first 50 + kmersize characters of ecoli.
-															//i chose to store the kmers numbers in a map so you wouldn't have to check for dupilcate entries and could easily find the 
-															//kmers 2 seqs had in common.  There may be a better way to do this thats why I am leaving so many comments...
-		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;
-		
-		
-		vector<sim> findIS(int);
-		int calcKmers(map<int, int>, map<int, int>);		
-		vector< vector<sim> > createProcessesIS(vector<Sequence*>, vector<linePair*>);
-		
+		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 calcKmers(map<int, int>, map<int, int>);
+		void makeSVGpic(vector<sim>);
+		void readName(string);
 };
-
 /***********************************************************/
 
 #endif