moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / maligner.h

diff --git a/maligner.h b/maligner.h
deleted file mode 100644 (file)
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
-