Collaboration diagram for SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >:

[legend]

Classes
struct	weight

Public Member Functions
void	clearAlignment ()
void	clear ()
	SmithWaterman (Atype A, QualityType qualities, Btype *B, int m, int n, int allowedInsertDelete=INT_MAX, int direction=1, readIndexType MOffset=0, referenceIndexType NOffset=0)
void	setRead (Atype *A)
void	setReadQuality (QualityType *qualities)
void	setReference (Btype *B)
void	setReadLength (int m)
void	setReadOffset (readIndexType MOffset)
void	setReferenceLength (int n)
void	setReferenceOffset (referenceIndexType NOffset)
void	setAllowedInsertDelete (int allowedInsertDelete=INT_MAX)
void	setDirection (int direction)
void	clearH ()
void	populateH ()
void	printH (bool prettyPrint=true)
void	debugPrint (bool doPrintH=true)
void	populateAlignment ()
int	getSumQ ()
int	getSumQForward ()
int	getSumQBackward ()
void	rollCigarForward (CigarRoller &cigar)
void	rollCigarBackward (CigarRoller &cigar)
int	getSoftClipCount ()
void	rollCigar (CigarRoller &cigar)
bool	localAlignment (uint32_t bandSize, Atype &read, readIndexType readLength, QualityType &quality, Btype &reference, referenceIndexType referenceLength, referenceIndexType referenceOffset, CigarRoller &cigarRoller, uint32_t &softClipCount, referenceIndexType &cigarStartingPoint, int &sumQ)

Public Attributes
HCellType	H [maxReadLengthH][maxReferenceLengthH]
Atype *	A
Btype *	B
QualityType *	qualities
int	m
int	n
readIndexType	MOffset
referenceIndexType	NOffset
weight	w
int	allowedInsertDelete
int	direction
int	gapOpenCount
int	gapCloseCount
int	gapExtendCount
vector< pair< int, int > >	alignment
HCellType	maxCostValue
pair< int, int >	maxCostPosition

Detailed Description

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>
class SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >

Definition at line 127 of file SmithWaterman.h.

Constructor & Destructor Documentation

◆ SmithWaterman() [1/2]

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::SmithWaterman ( )

inline

Definition at line 204 of file SmithWaterman.h.

    {
        clear();
        clearH();
    }

◆ SmithWaterman() [2/2]

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::SmithWaterman	(	Atype *	A,
		QualityType *	qualities,
		Btype *	B,
		int	m,
		int	n,
		int	allowedInsertDelete = INT_MAX,
		int	direction = 1,
		readIndexType	MOffset = 0,
		referenceIndexType	NOffset = 0 )

inline

Definition at line 211 of file SmithWaterman.h.

                                       :
            A(A),
            qualities(qualities),
            B(B),
            m(m),
            n(n),
            allowedInsertDelete(allowedInsertDelete),
            direction(direction),
            MOffset(MOffset),
            NOffset(NOffset),
            maxCostValue((HCellType) 0)
    {
    }

Member Function Documentation

◆ clear()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::clear ( )

inline

Definition at line 185 of file SmithWaterman.h.

    {
        maxCostPosition.first = 0;
        maxCostPosition.second = 0;
        A = NULL;
        B = NULL;
        qualities = NULL;
        m = 0;
        n = 0;
        MOffset = 0;
        NOffset = 0;
        allowedInsertDelete = 0;
        direction = 0;
        gapOpenCount = 0;
        gapCloseCount = 0;
        gapExtendCount = 0;
    }

◆ clearAlignment()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::clearAlignment ( )

inline

Definition at line 170 of file SmithWaterman.h.

    {
        alignment.clear();
    }

◆ clearH()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::clearH ( )

inline

Definition at line 295 of file SmithWaterman.h.

    {
        memset(H, 0, sizeof(H));
    }

◆ debugPrint()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::debugPrint ( bool doPrintH = true )

inline

Definition at line 369 of file SmithWaterman.h.

    {
        if (doPrintH) printH();
        cout << "maxCostPosition = " << maxCostPosition << std::endl;
        if (alignment.empty()) cout << "alignment vector is empty.\n";
        else
        {
            cout << "alignment vector:\n";
            for (vector<pair<int,int> >::iterator i=alignment.begin(); i < alignment.end(); i++)
            {
                cout << (i - alignment.begin()) << ": " << *i << "\n";
            }
        }
        cout << std::endl;
    }

◆ getSoftClipCount()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::getSoftClipCount ( )

inline

Definition at line 680 of file SmithWaterman.h.

    {
        if (direction>0)
        {
            // invariant: assert(maxCostPosition == alignment.front());
            return m - maxCostPosition.first;
        }
        else
        {
//          return alignment.back().first;  // nope, this always returns 0
            // XXX BE CAREFUL... not sure this is right, either.
//          return n - maxCostPosition.second;
            return m - maxCostPosition.first;
        }
    }

◆ getSumQ()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::getSumQ ( )

inline

Definition at line 448 of file SmithWaterman.h.

    {
        if (direction>0) return getSumQForward();
        else return getSumQBackward();
    }

◆ getSumQBackward()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::getSumQBackward ( )

inline

Definition at line 497 of file SmithWaterman.h.

    {
        int sumQ = 0;
        vector<pair<int,int> >::iterator i;
 
        for (i=alignment.begin(); i < alignment.end() - 1; i++)
        {
#if defined(DEBUG_GETSUMQ)
            cout << *i << ": ";
#endif
            if ((*(i+1)).first == ((*i).first-1) && (*(i+1)).second == ((*i).second - 1))
            {
                // match/mismatch
#if defined(DEBUG_GETSUMQ)
                cout << "Match/Mismatch";
#endif
                if ((*A)[MOffset + m - (*i).first] != (*B)[NOffset + n - (*i).second])
                    sumQ += (*qualities)[MOffset + m - (*i).first] - '!';
            }
            else if ((*(i+1)).first == ((*i).first-1) && (*(i+1)).second == ((*i).second))
            {
                // insert?
#if defined(DEBUG_GETSUMQ)
                cout << "Insert?";
#endif
                sumQ += 50;
            }
            else if ((*(i+1)).first == ((*i).first) && (*(i+1)).second == ((*i).second - 1))
            {
                // delete?
#if defined(DEBUG_GETSUMQ)
                cout << "Delete?";
#endif
                sumQ += 50;
            }
        }
#if defined(DEBUG_GETSUMQ)
        cout << endl;
#endif
        return sumQ;
    }

◆ getSumQForward()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::getSumQForward ( )

inline

Definition at line 454 of file SmithWaterman.h.

    {
        int sumQ = 0;
        vector<pair<int,int> >::reverse_iterator i;
 
        for (i=alignment.rbegin(); i < alignment.rend() - 1; i++)
        {
// #define DEBUG_GETSUMQ
#if defined(DEBUG_GETSUMQ)
            cout << *i << ": ";
#endif
            if ((*(i+1)).first == ((*i).first+1) && (*(i+1)).second == ((*i).second + 1))
            {
                // match/mismatch
#if defined(DEBUG_GETSUMQ)
                cout << "Match/Mismatch";
#endif
                if ((*A)[MOffset + (*i).first] != (*B)[NOffset + (*i).second])
                    sumQ += (*qualities)[MOffset + (*i).first] - '!';
            }
            else if ((*(i+1)).first == ((*i).first+1) && (*(i+1)).second == ((*i).second))
            {
                // insert?
#if defined(DEBUG_GETSUMQ)
                cout << "Insert";
#endif
                sumQ += 50;
            }
            else if ((*(i+1)).first == ((*i).first) && (*(i+1)).second == ((*i).second + 1))
            {
                // delete?
#if defined(DEBUG_GETSUMQ)
                cout << "Delete";
#endif
                sumQ += 50;
            }
        }
#if defined(DEBUG_GETSUMQ)
        cout << endl;
#endif
        return sumQ;
    }

◆ localAlignment()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

bool SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::localAlignment	(	uint32_t	bandSize,
		Atype &	read,
		readIndexType	readLength,
		QualityType &	quality,
		Btype &	reference,
		referenceIndexType	referenceLength,
		referenceIndexType	referenceOffset,
		CigarRoller &	cigarRoller,
		uint32_t &	softClipCount,
		referenceIndexType &	cigarStartingPoint,
		int &	sumQ )

inline

Definition at line 713 of file SmithWaterman.h.

    {
 
        clear();
 
        cigarRoller.clear();
 
        setDirection(+1);
        setAllowedInsertDelete(bandSize);
 
        setRead(&read);
        setReadOffset(0);
        setReadLength(readLength);
 
        setReadQuality(&quality);
 
        setReference(&reference);
        setReferenceOffset(referenceOffset);
        setReferenceLength(referenceLength);
 
        populateH();
 
        softClipCount = getSoftClipCount();
 
        populateAlignment();
 
        rollCigar(cigarRoller);
 
        sumQ = getSumQ();
 
        return false;
 
    };

◆ populateAlignment()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::populateAlignment ( )

inline

Definition at line 389 of file SmithWaterman.h.

    {
        alignment.clear();
        int i = m, j = n;
 
        i = maxCostPosition.first;
        j = maxCostPosition.second;
 
        //
        // Stop when we either reach zero cost cell or
        // when we reach the upper left corner of H.
        // A zero cost cell to the lower right means we
        // are soft clipping that end.
        //
        while (H[i][j] > 0 || (i>0 && j>0))
        {
// #define DEBUG_ALIGNMENT_VECTOR
#if defined(DEBUG_ALIGNMENT_VECTOR)
            cout << "alignment.push_back(" << i << ", " << j << ")" << endl;
#endif
            alignment.push_back(pair<int,int>(i,j));
            if (H[i-1][j-1]>=H[i-1][j] && H[i-1][j-1]>=H[i][j-1])
            {
                // diagonal upper left cell is biggest
                i--;
                j--;
            }
            else if (H[i-1][j] < H[i][j-1])
            {
                // upper cell is biggest
                j--;
            }
            else
            {
                // left cell is biggest
                i--;
            }
        }
        alignment.push_back(pair<int,int>(i,j));
#if defined(DEBUG_ALIGNMENT_VECTOR)
        cout << "alignment.push_back(" << i << ", " << j << ")" << endl;
        cout << "alignment.size(): " << alignment.size() << endl;
#endif
    }

◆ populateH()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::populateH ( )

inline

Definition at line 300 of file SmithWaterman.h.

    {
 
        maxCostValue = 0;
 
        for (int i=1; i<=m ; i++)
        {
 
            // implement a banded Smith-Waterman approach:
            int low = MAX(1, i - allowedInsertDelete);
            int high = MIN(n, i + allowedInsertDelete);
 
            for (int j=low; j<=high ; j++)
            {
                HCellType c;
                c = 0;
                if (direction>0) c = MAX(c, H[i-1][j-1] + (((*A)[MOffset + i-1]==(*B)[NOffset + j-1]) ? w.match : w.misMatch));
                else c = MAX(c, H[i-1][j-1] + (((*A)[MOffset + m-i+0]==(*B)[NOffset + n-j+0]) ? w.match : w.misMatch));
                c = MAX(c, H[i-1][j] + w.del);
                c = MAX(c, H[i][j-1] + w.insert);
                H[i][j] = c;
                if (c>maxCostValue)
                {
                    maxCostValue = c;
                    maxCostPosition.first = i;
                    maxCostPosition.second = j;
                }
            }
        }
    }

◆ printH()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::printH ( bool prettyPrint = true )

inline

Definition at line 334 of file SmithWaterman.h.

    {
        // print the scoring matrix:
        for (int i=-1; i<=m ; i++)
        {
            for (int j=-1; j<=n ; j++)
            {
                if (prettyPrint) cout << setw(3);
                if (i==-1 && j==-1)
                {
                    if (prettyPrint) cout << " ";
                    else cout << "\t";
                }
                else if (j==-1)
                {
                    if (!prettyPrint) cout << "\t";
                    if (i==0) cout << "-";
                    else cout << (*A)[MOffset + direction>0 ? i-1 : m - i];
                }
                else if (i==-1)
                {
                    if (!prettyPrint) cout << "\t";
                    if (j==0) cout << "-";
                    else cout << (*B)[NOffset + direction>0 ? j-1 : n - j];
                }
                else
                {
                    if (!prettyPrint) cout << "\t";
                    cout << H[i][j];
                }
            }
            cout << endl;
        }
    }

◆ rollCigar()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::rollCigar ( CigarRoller & cigar )

inline

Definition at line 696 of file SmithWaterman.h.

    {
        if (direction>0) rollCigarForward(cigar);
        else rollCigarBackward(cigar);
    }

◆ rollCigarBackward()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::rollCigarBackward ( CigarRoller & cigar )

inline

Definition at line 625 of file SmithWaterman.h.

    {
        vector<pair<int,int> >::iterator i;
 
        // if there is soft clipping, allow for it (::Add will
        // ignore if the count is 0):
        cigar.Add(CigarRoller::softClip, getSoftClipCount());
 
        i = alignment.begin();
 
        for (i=alignment.begin();
                i < alignment.end() - 1;
                i++)
        {
#if defined(DEBUG_CIGAR)
            cout << *i << ": ";
#endif
            if ((*(i+1)).first == ((*i).first-1) && (*(i+1)).second == ((*i).second - 1))
            {
                // match/mismatch
#if defined(DEBUG_CIGAR)
                cout << "Match/Mismatch";
#endif
                cigar.Add(CigarRoller::match, 1);
            }
            else if ((*(i+1)).first == ((*i).first-1) && (*(i+1)).second == ((*i).second))
            {
                // insert?
#if defined(DEBUG_CIGAR)
                cout << "Insert?";
#endif
                cigar.Add(CigarRoller::insert, 1);
            }
            else if ((*(i+1)).first == ((*i).first) && (*(i+1)).second == ((*i).second - 1))
            {
                // delete?
#if defined(DEBUG_CIGAR)
                cout << "Delete?";
#endif
                cigar.Add(CigarRoller::del, 1);
            }
        }
#if defined(DEBUG_CIGAR)
        cout << endl;
#endif
    }

◆ rollCigarForward()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::rollCigarForward ( CigarRoller & cigar )

inline

Definition at line 574 of file SmithWaterman.h.

    {
        vector<pair<int,int> >::reverse_iterator i;
 
        for (i=alignment.rbegin(); i < alignment.rend() - 1; i++)
        {
// #define DEBUG_CIGAR
#if defined(DEBUG_CIGAR)
            cout << *i << ": ";
#endif
            if ((*(i+1)).first == ((*i).first+1) && (*(i+1)).second == ((*i).second + 1))
            {
                // match/mismatch
#if defined(DEBUG_CIGAR)
                cout << "Match/Mismatch";
#endif
                cigar.Add(CigarRoller::match, 1);
            }
            else if ((*(i+1)).first == ((*i).first+1) && (*(i+1)).second == ((*i).second))
            {
                // insert?
#if defined(DEBUG_CIGAR)
                cout << "Insert";
#endif
                cigar.Add(CigarRoller::insert, 1);
            }
            else if ((*(i+1)).first == ((*i).first) && (*(i+1)).second == ((*i).second + 1))
            {
                // delete?
#if defined(DEBUG_CIGAR)
                cout << "Delete";
#endif
                cigar.Add(CigarRoller::del, 1);
            }
        }
        // if there is soft clipping, allow for it (::Add will
        // ignore if the count is 0):
        cigar.Add(CigarRoller::softClip, getSoftClipCount());
#if defined(DEBUG_CIGAR)
        cout << endl;
#endif
    }

◆ setAllowedInsertDelete()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setAllowedInsertDelete ( int allowedInsertDelete = INT_MAX )

inline

Definition at line 281 of file SmithWaterman.h.

    {
        this->allowedInsertDelete = allowedInsertDelete;
    }

◆ setDirection()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setDirection ( int direction )

inline

Definition at line 290 of file SmithWaterman.h.

    {
        this->direction = direction;
    }

◆ setRead()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setRead ( Atype * A )

inline

Definition at line 234 of file SmithWaterman.h.

    {
        this->A = A;
    }

◆ setReadLength()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setReadLength ( int m )

inline

Definition at line 250 of file SmithWaterman.h.

    {
        this->m = m;
    }

◆ setReadOffset()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setReadOffset ( readIndexType MOffset )

inline

Definition at line 254 of file SmithWaterman.h.

    {
        this->MOffset = MOffset;
    }

◆ setReadQuality()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setReadQuality ( QualityType * qualities )

inline

Definition at line 238 of file SmithWaterman.h.

    {
        this->qualities = qualities;
    }

◆ setReference()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setReference ( Btype * B )

inline

Definition at line 242 of file SmithWaterman.h.

    {
        this->B = B;
    }

◆ setReferenceLength()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setReferenceLength ( int n )

inline

Definition at line 263 of file SmithWaterman.h.

    {
        this->n = n;
    }

◆ setReferenceOffset()

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

void SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::setReferenceOffset ( referenceIndexType NOffset )

inline

Definition at line 267 of file SmithWaterman.h.

    {
        this->NOffset = NOffset;
    }

Member Data Documentation

◆ A

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

Atype* SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::A

Definition at line 156 of file SmithWaterman.h.

◆ alignment

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

vector<pair<int,int> > SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::alignment

Definition at line 169 of file SmithWaterman.h.

◆ allowedInsertDelete

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::allowedInsertDelete

Definition at line 164 of file SmithWaterman.h.

◆ B

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

Btype* SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::B

Definition at line 157 of file SmithWaterman.h.

◆ direction

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::direction

Definition at line 165 of file SmithWaterman.h.

◆ gapCloseCount

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::gapCloseCount

Definition at line 167 of file SmithWaterman.h.

◆ gapExtendCount

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::gapExtendCount

Definition at line 168 of file SmithWaterman.h.

◆ gapOpenCount

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::gapOpenCount

Definition at line 166 of file SmithWaterman.h.

◆ H

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

HCellType SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::H[maxReadLengthH][maxReferenceLengthH]

Definition at line 155 of file SmithWaterman.h.

◆ m

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::m

Definition at line 160 of file SmithWaterman.h.

◆ maxCostPosition

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

pair<int,int> SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::maxCostPosition

Definition at line 176 of file SmithWaterman.h.

◆ maxCostValue

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

HCellType SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::maxCostValue

Definition at line 175 of file SmithWaterman.h.

◆ MOffset

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

readIndexType SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::MOffset

Definition at line 161 of file SmithWaterman.h.

◆ n

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

int SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::n

Definition at line 160 of file SmithWaterman.h.

◆ NOffset

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

referenceIndexType SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::NOffset

Definition at line 162 of file SmithWaterman.h.

◆ qualities

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

QualityType* SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::qualities

Definition at line 158 of file SmithWaterman.h.

◆ w

template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>

weight SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >::w

Definition at line 163 of file SmithWaterman.h.

The documentation for this class was generated from the following file:

general/SmithWaterman.h

Classes

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SmithWaterman() [1/2]

◆ SmithWaterman() [2/2]

Member Function Documentation

◆ clear()

◆ clearAlignment()

◆ clearH()

◆ debugPrint()

◆ getSoftClipCount()

◆ getSumQ()

◆ getSumQBackward()

◆ getSumQForward()

◆ localAlignment()

◆ populateAlignment()

◆ populateH()

◆ printH()

◆ rollCigar()

◆ rollCigarBackward()

◆ rollCigarForward()

◆ setAllowedInsertDelete()

◆ setDirection()

◆ setRead()

◆ setReadLength()

◆ setReadOffset()

◆ setReadQuality()

◆ setReference()

◆ setReferenceLength()

◆ setReferenceOffset()

Member Data Documentation

◆ A

◆ alignment

◆ allowedInsertDelete

◆ B

◆ direction

◆ gapCloseCount

◆ gapExtendCount

◆ gapOpenCount

◆ H

◆ m

◆ maxCostPosition

◆ maxCostValue

◆ MOffset

◆ n

◆ NOffset

◆ qualities

◆ w