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

[mothur.git] / chimerarealigner.h

diff --git a/chimerarealigner.h b/chimerarealigner.h
deleted file mode 100644 (file)
index 5809f42..0000000
--- a/chimerarealigner.h
+++ /dev/null
@@ -1,59 +0,0 @@
-#ifndef CHIMERAREALIGNER_H
-#define CHIMERAREALIGNER_H
-
-/*
- *  chimerarealigner.h
- *  Mothur
- *
- *  Created by westcott on 2/12/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "chimera.h"
-#include "alignment.hpp"
-
-/***********************************************************/
-
-struct AlignCell {
-       int score;
-       char direction;
-       AlignCell() : score(0), direction('x') {};
-};
-
-/***********************************************************/
-
-struct  bases {
-       int A, T, G, C, Gap, Chars;
-       bases() : A(0), T(0), G(0), C(0), Gap(0), Chars(0){};
-};
-
-/***********************************************************/
-
-
-class ChimeraReAligner  {
-       
-public:
-       ChimeraReAligner();      
-       ~ChimeraReAligner();
-       
-       void reAlign(Sequence*, vector<string>);
-                               
-private:
-       void buildTemplateProfile(vector<string>);
-       void createAlignMatrix(int, int);
-       void fillAlignMatrix(string);
-       int calcMatchScore(bases, char);
-       string getNewAlignment(string);
-
-       int alignmentLength;
-       vector<bases> profile;
-       vector<vector<AlignCell> > alignMatrix;
-
-       MothurOut* m;
-};
-
-/***********************************************************/
-
-#endif
-