--- /dev/null
+#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
+