X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.h;fp=maligner.h;h=6277e7300a02fbe815468e223298f5f969813a51;hb=05a0195e07c42c996592ee1c8abb63adedb7f493;hp=0000000000000000000000000000000000000000;hpb=d2fc851cdaf57874b3ac8261b220fad35750daad;p=mothur.git

diff --git a/maligner.h b/maligner.h
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+++ b/maligner.h
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+#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"
+
+/***********************************************************************/
+//This class was modeled after the chimeraMaligner written by the Broad Institute
+/***********************************************************************/
+struct score_struct {
+	int prev;
+	int score;
+	int row;
+	int col;
+};
+/***********************************************************************/
+struct trace_struct {
+	int col;
+	int oldCol;
+	int row;
+};
+/***********************************************************************/
+struct results {
+	int regionStart;
+	int regionEnd;
+	string parent;
+	float queryToParent;
+	float queryToParentLocal;
+	float divR;
+};
+
+/**********************************************************************/
+class Maligner {
+
+	public:
+		
+		Maligner(vector<Sequence*>, int, int, int, float, int);
+		~Maligner() {};
+		
+		string getResults(Sequence*);
+		float getPercentID() {	return percentIdenticalQueryChimera;	}
+		vector<results> getOutput()  {	return outputResults;			}
+		
+				
+	private:
+		DeCalculator* decalc;
+		Sequence* query;
+		vector<Sequence*> refSeqs;
+		vector<Sequence*> db;
+		int numWanted, matchScore, misMatchPenalty, minCoverage;
+		float minDivR, percentIdenticalQueryChimera;
+		vector<results> outputResults;
+		
+		vector<Sequence*> minCoverageFilter(vector<Sequence*>);  //removes top matches that do not have minimum coverage with query.
+		int computeChimeraPenalty();
+		void 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>, vector<Sequence*>);
+		string constructChimericSeq(vector<trace_struct>, vector<Sequence*>);
+		float computePercentID(string, string);
+		
+};
+
+/***********************************************************************/
+
+#endif
+