X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.h;fp=maligner.h;h=fc00e99faf3ad3931f76606c34ffb65b69eb4de7;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/maligner.h b/maligner.h
new file mode 100644
index 0000000..fc00e99
--- /dev/null
+++ b/maligner.h
@@ -0,0 +1,59 @@
+#ifndef MALIGNER_H
+#define MALIGNER_H
+/*
+ *  maligner.h
+ *  Mothur
+ *
+ *  Created by westcott on 9/23/09.
+ *  Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+ 
+#include "decalc.h"
+#include "chimera.h"
+#include "database.hpp"
+
+/***********************************************************************/
+//This class was modeled after the chimeraMaligner written by the Broad Institute
+/**********************************************************************/
+class Maligner {
+
+	public:
+		
+		Maligner(vector<Sequence>, int, int, float, int, int); //int, int, int, , string, Database*, Database*
+		~Maligner() {};
+		
+		string getResults(Sequence, DeCalculator);
+		float getPercentID() {	return percentIdenticalQueryChimera;	}
+		vector<results> getOutput()  {	return outputResults;			}
+		
+				
+	private:
+		Sequence query;
+		vector<Sequence> refSeqs;
+		vector<Sequence> db;
+		int minCoverage, minSimilarity, matchScore, misMatchPenalty;
+		float minDivR, percentIdenticalQueryChimera;
+		vector<results> outputResults;
+		map<int, int> spotMap;
+		vector<int> unalignedMap;
+		vector<Sequence> minCoverageFilter(vector<Sequence>);  //removes top matches that do not have minimum coverage with query.
+		int computeChimeraPenalty();
+		vector<Sequence> verticalFilter(vector<Sequence>);
+		
+		vector< vector<score_struct> > buildScoreMatrix(int, 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>);
+		string constructChimericSeq(vector<trace_struct>, vector<Sequence>);
+		string constructAntiChimericSeq(vector<trace_struct>, vector<Sequence>);
+		float computePercentID(string, string);
+		string chimeraMaligner(int, DeCalculator);
+		MothurOut* m;
+		
+};
+
+/***********************************************************************/
+
+#endif
+