X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.h;fp=maligner.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=fc00e99faf3ad3931f76606c34ffb65b69eb4de7;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/maligner.h b/maligner.h
deleted file mode 100644
index fc00e99..0000000
--- a/maligner.h
+++ /dev/null
@@ -1,59 +0,0 @@
-#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
-