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[mothur.git] / 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"
+#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
+