aligner.h

本程序是计算机视觉稠密匹配的程序

/*
 *
 *  All Contents Copyright 2000 by Jared Samet. All Rights Reserved.
 *
 */

#ifndef _ALIGNER_H
#define _ALIGNER_H

#ifdef _DEBUG
#define new DEBUG_NEW
#endif

typedef enum {C3D_WEST, C3D_NORTHWEST, C3D_NORTH, C3D_INVALID_DIR} C3D_DIRECTION;
typedef enum {C3D_A, C3D_B, C3D_C, C3D_INVALID_AR} C3D_ARRAY;

struct SArrayEntry
{
    int iScore;
    C3D_DIRECTION dirPrev;
    C3D_ARRAY arPrev;
};

struct SDPBox
{
    SArrayEntry A, B, C;
};

template<class T>
class CSteppedArray;

class CAligner
{
public:
	typedef int (*MATCH) (unsigned int left, unsigned int right);	// fn that returns the score if these two letters are matched
	CAligner(int iGapStart, int iGapContinue, MATCH Match, int iMinDisp, int iMaxDisp);
	virtual ~CAligner();						// bye-bye
	void Align(void);							// line 'em up! when it's done, check member fn's for results
	int AlignmentCount(void);		        	// how many alignments did it find?
	bool SetSequences(CSequence* pSeq1,			// change the sequences being aligned
					  CSequence* pSeq2);		
	bool isAligned(void);				        // have these been aligned yet?
	void DumpTable(void);
	void GetAlignment(int nAlignment,			// which one to get
					  CSequence** ppSeq1,		// (OUT) place to store * to the first sequence
					  CSequence** ppSeq2);		// (OUT) place to store * to the second seq

protected:			
    bool isValid(C3D_ARRAY arPrev, int iRow, int iCol);
    int m_iGapStart, m_iGapContinue, m_iMinDisp, m_iMaxDisp;
    int m_iLeftLen, m_iRightLen;
    MATCH m_Match;
    bool m_fAligned, m_fHaveSeqs;
    CSteppedArray<SDPBox> *m_pTable;
    CSequence *m_pSeqLeft, *m_pSeqRight;
};

#endif