X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=maligner.h;h=fc00e99faf3ad3931f76606c34ffb65b69eb4de7;hp=abe18a3cb1ad6c6b65d41077b8dd1fb56d802f96;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=5a1e62397b91f57d0d3aff635891df04b8999a88

diff --git a/maligner.h b/maligner.h
index abe18a3..fc00e99 100644
--- a/maligner.h
+++ b/maligner.h
@@ -11,6 +11,7 @@
  
 #include "decalc.h"
 #include "chimera.h"
+#include "database.hpp"
 
 /***********************************************************************/
 //This class was modeled after the chimeraMaligner written by the Broad Institute
@@ -19,36 +20,36 @@ class Maligner {
 
 	public:
 		
-		Maligner(vector<Sequence*>, int, int, int, float, int, int, string);
+		Maligner(vector<Sequence>, int, int, float, int, int); //int, int, int, , string, Database*, Database*
 		~Maligner() {};
 		
-		string getResults(Sequence*, DeCalculator*);
+		string getResults(Sequence, DeCalculator);
 		float getPercentID() {	return percentIdenticalQueryChimera;	}
 		vector<results> getOutput()  {	return outputResults;			}
 		
 				
 	private:
-		Sequence* query;
-		vector<Sequence*> refSeqs;
-		vector<Sequence*> db;
-		int numWanted, matchScore, misMatchPenalty, minCoverage, minSimilarity;
-		string searchMethod;
+		Sequence query;
+		vector<Sequence> refSeqs;
+		vector<Sequence> db;
+		int minCoverage, minSimilarity, matchScore, misMatchPenalty;
 		float minDivR, percentIdenticalQueryChimera;
 		vector<results> outputResults;
 		map<int, int> spotMap;
-		
-		vector<Sequence*> minCoverageFilter(vector<Sequence*>);  //removes top matches that do not have minimum coverage with query.
+		vector<int> unalignedMap;
+		vector<Sequence> minCoverageFilter(vector<Sequence>);  //removes top matches that do not have minimum coverage with query.
 		int computeChimeraPenalty();
-		void verticalFilter(vector<Sequence*>);
+		vector<Sequence> verticalFilter(vector<Sequence>);
 		
 		vector< vector<score_struct> > buildScoreMatrix(int, int);
-		void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence*>, int);
+		void fillScoreMatrix(vector<vector<score_struct> >&, vector<Sequence>, int);
 		vector<score_struct> extractHighestPath(vector<vector<score_struct> >);
-		vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>, vector<Sequence*>);
-		string constructChimericSeq(vector<trace_struct>, vector<Sequence*>);
+		vector<trace_struct> mapTraceRegionsToAlignment(vector<score_struct>);
+		string constructChimericSeq(vector<trace_struct>, vector<Sequence>);
+		string constructAntiChimericSeq(vector<trace_struct>, vector<Sequence>);
 		float computePercentID(string, string);
-		string chimeraMaligner(int, DeCalculator*);
-		vector<Sequence*> getBlastSeqs(Sequence*, int);
+		string chimeraMaligner(int, DeCalculator);
+		MothurOut* m;
 		
 };