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

[mothur.git] / alignment.hpp

diff --git a/alignment.hpp b/alignment.hpp
deleted file mode 100644 (file)
index 7a943fd..0000000
--- a/alignment.hpp
+++ /dev/null
@@ -1,57 +0,0 @@
-#ifndef DPALIGNMENT_H
-#define DPALIGNMENT_H
-
-/*
- *  dpalignment.h
- *  
- *
- *  Created by Pat Schloss on 12/15/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- *  This is a class for an abstract datatype for classes that implement various types of alignment     algorithms.
- *     As of 12/18/08 these included alignments based on blastn, needleman-wunsch, and the     Gotoh algorithms
- * 
- */
-
-#include "mothur.h"
-#include "alignmentcell.hpp"
-
-/**************************************************************************************************/
-
-class Alignment {
-       
-public:
-       Alignment(int);
-       Alignment();
-       virtual ~Alignment();
-       virtual void align(string, string) = 0;
-       
-       
-//     float getAlignmentScore();
-       string getSeqAAln();
-       string getSeqBAln();
-       int getCandidateStartPos();
-       int getCandidateEndPos();
-       int getTemplateStartPos();
-       int getTemplateEndPos();
-       
-       int getPairwiseLength();
-       void resize(int);
-       int getnRows() { return nRows; }
-//     int getLongestTemplateGap();
-
-protected:
-       void traceBack();
-       string seqA, seqAaln;
-       string seqB, seqBaln;
-       int seqAstart, seqAend;
-       int seqBstart, seqBend;
-       int pairwiseLength;
-       int nRows, nCols, lA, lB;
-       vector<vector<AlignmentCell> > alignment;
-       MothurOut* m;
-};
-
-/**************************************************************************************************/
-
-#endif