X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=bellerophon.h;h=36555bf0d406addb3cc7685ee55fdac341dffe68;hp=b79089c97c87e13e8f93288707ef9b374595d34a;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=8c3489da5da7fb7274f34bfa091c54aa496e75bd

diff --git a/bellerophon.h b/bellerophon.h
index b79089c..36555bf 100644
--- a/bellerophon.h
+++ b/bellerophon.h
@@ -12,47 +12,53 @@
 
 
 #include "chimera.h"
-#include "filterseqscommand.h"
+#include "sparsematrix.hpp"
 #include "sequence.hpp"
 #include "dist.h"
 
-struct Preference {
-		string name;
-		vector<string> leftParent; //keep the name of closest left associated with the two scores
-		vector<string> rightParent; //keep the name of closest right associated with the two scores
-		vector<float> score;  //so you can keep last score and calc this score and keep whichever is bigger.
-		vector<float> closestLeft;  //keep the closest left associated with the two scores
-		vector<float> closestRight; //keep the closest right associated with the two scores
-		int midpoint;
-
-};
-
+typedef list<PCell>::iterator MatData;
+typedef map<int, float> SeqMap;  //maps sequence to all distance for that seqeunce
 
 /***********************************************************/
 
 class Bellerophon : public Chimera {
 	
 	public:
-		Bellerophon(string);	
-		~Bellerophon() {};
+		Bellerophon(string, bool, bool, int, int, int, string);	//fastafile, filter, correction, window, increment, processors, outputDir);	
+		~Bellerophon() { delete distCalculator; for (int i = 0; i < seqs.size(); i++) { delete seqs[i];  }  seqs.clear(); }
 		
-		void getChimeras();
-		void print(ostream&);
-		
-		void setCons(string){};
-		void setQuantiles(string) {};
+		int getChimeras();
+		int print(ostream&, ostream&, string);
 		
+		#ifdef USE_MPI
+		int print(MPI_File&, MPI_File&, string);
+		#endif
 		
 	private:
+		struct linePair {
+			unsigned long long start;
+			int num;
+			linePair(unsigned long long i, int j) : start(i), num(j) {}
+		};
+		
+		vector<linePair> lines;
+	
 		Dist* distCalculator;
-		FilterSeqsCommand* filterSeqs;
-		vector<Sequence> seqs;
-		vector<Preference> pref;
+		vector<Sequence*> seqs;
+		vector< vector<Preference> > pref; //pref[0] = preference scores for all seqs in window 0.
 		string fastafile;
-		int iters;
+		int iters, count, window, increment, numSeqs, processors; //iters = number of windows
+		bool correction;
 		
-		void generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
+		int generatePreferences(vector<SeqMap>, vector<SeqMap>, int);
 		int createSparseMatrix(int, int, SparseMatrix*, vector<Sequence>);
+		vector<Preference> getBestPref();
+		int driverChimeras(vector<int>, linePair);
+		int createProcesses(vector<int>);
+		int writePrefs(string, linePair);
+		int readPrefs(string);
+		vector<string> getBestWindow(linePair line);
+		int fillPref(int, vector<string>&);
 };
 
 /***********************************************************/