/**
 ** Copyright (c) 2007-2010 Illumina, Inc.
 **
 ** This software is covered by the "Illumina Genome Analyzer Software
 ** License Agreement" and the "Illumina Source Code License Agreement",
 ** and certain third party copyright/licenses, and any user of this
 ** source file is bound by the terms therein (see accompanying files
 ** Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
 ** Illumina_Source_Code_License_Agreement.pdf and third party
 ** copyright/license notices).
 **
 ** This file is part of the Consensus Assessment of Sequence And VAriation
 ** (CASAVA) software package.
 **
 **/

#ifndef TRIMMER_H
#define TRIMMER_H

#include "TrimmerErrors.h"

class CTrimmer
{
public:
    /****************************************************************************
    Function:    Default Constructor
    Arguments:   None
    Globals:     None
    ****************************************************************************/
    CTrimmer()
        : m_Adaptor(0)
        , m_AdaptorLength(0)
        , m_Read(0)
        , m_ReadLength(0)
        , m_ScoreMatrix(0)
        , m_PathMatrix(0)
        , m_Reverser(0)
    {};

    /****************************************************************************
    Function:    Destructor
    Description: Deallocates and resets all member variables.
    ****************************************************************************/
    virtual ~CTrimmer();

    /****************************************************************************
    Function:    Setup
    Description:
    Arguments:
        Input:
       Output:
    Globals:     None
    ****************************************************************************/
    int Setup(const char adaptorString[],  // Null terminated string
              const int  similarityMatrix[NSYMBOLS][NSYMBOLS]);

    /****************************************************************************
    Function:    Run
    Description:
    Arguments:
        Input:
       Output:
    Globals:     None
    ****************************************************************************/
    int Run(const char readString[], // Null terminated string
            int &      suffixPosition,
            int &      maxScore);

    /****************************************************************************
    Function:    GetMatch
    Description: Accessor
    Arguments:
        Input:
       Output:
    Globals:     None
    ****************************************************************************/
    const char * GetMatch() const; // Null terminated string

private:
    int m_SimilarityMatrix[NSYMBOLS][NSYMBOLS];
    // Wikipedia contributors, "Similarity matrix," Wikipedia, The Free Encyclopedia,
    // http://en.wikipedia.org/w/index.php?title=Similarity_matrix&oldid=160829209
    /*************************************************************************
    * Enumeration of symbols: L, A, C, G, T, N
    * 0 = L (L is for lambda, the null character)
    * 1 = A
    * 2 = C
    * 3 = G
    * 4 = T
    * 5 = N
    *************************************************************************/
    int *            m_Adaptor;
    int              m_AdaptorLength;
    int *            m_Read;
    int              m_ReadLength;
    int **           m_ScoreMatrix;
    unsigned char ** m_PathMatrix;
    char *           m_Reverser;

    void getCode(const char anyString[],
                 int *      anyCode) const;

    int initAdaptor(const char adaptorString[]); // Null terminated string
    void initSimilarityMatrix(const int similarityMatrix[NSYMBOLS][NSYMBOLS]);

    int initScoreMatrix();
    void makeScoreMatrix();
    int getMaxScoreAndLocation(int & iMax,        // m_ScoreMatrix[iMax, jMax] is a max element
                               int & jMax) const; // along its outer boundary
    int getSuffixPosition(int i,                  // m_ScoreMatrix[i, j] is a max element
                          int j);                 // along its outer boundary
    void deallocRun();
};

/* ******* */
/* Inlines */
/* ******* */
inline const char * CTrimmer::GetMatch() const {return m_Reverser;}

#endif // TRIMMER_H