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NCBI C++ ToolKit: include/util/align_range.hpp Source File

first_direct =

)

!(*

==

);

(new_to < new_from) {

new_to = new_from - 1;

(new_to < new_from) {

new_to = new_from - 1;

CAlignRange Represents an element of pairwise alignment of two sequences.

Include a standard set of the NCBI C++ Toolkit most basic headers.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

bool IsAbutting(const TThisType &r) const

void SetReversed(bool reversed=true)

position_type GetFirstPosBySecondPos(position_type pos) const

bool FirstContains(position_type pos) const

bool IntersectingWith(const CRange< position_type > &r) const

static TThisType GetEmpty(void)

position_type m_FirstFrom

position_type m_Length

start on the aligned sequence

CRange< Position > TRange

position_type m_SecondFrom

start

TThisType & IntersectWith(const CRange< position_type > &r)

TRange GetFirstRange() const

int m_Flags

length of the segment

TThisType IntersectionWith(const CRange< position_type > &r) const

Intersection.

CAlignRange(position_type first_from, position_type second_from, position_type len, bool direct=true, bool first_direct=true)

TRange GetSecondRange() const

static position_type GetPositionMin(void)

position_type GetFirstToOpen(void) const

TThisType & IntersectSecondWith(const CRange< position_type > &r)

TThisType & SetLength(position_type len)

bool IsFirstDirect() const

position_type GetFirstTo(void) const

TThisType & Set(position_type first_from, position_type second_from, position_type len)

static position_type GetEmptyTo(void)

TThisType CombinationWithAbutting(const TThisType &r) const

TThisType & SetSecondFrom(position_type second_from)

bool SecondContains(position_type pos) const

static position_type GetEmptyLength(void)

static position_type GetEmptyToOpen(void)

bool operator==(const TThisType &r) const

static position_type GetEmptyFrom(void)

bool NotEmpty(void) const

position_type GetSecondFrom(void) const

TThisType & CombineWithAbutting(const TThisType &r)

CAlignRange< Position > TThisType

bool operator!=(const TThisType &r) const

void SetFirstReversed(bool reversed=true)

void SetDirect(bool direct=true)

TThisType & SetFirstFrom(position_type from)

static position_type GetPositionMax(void)

void SetFirstDirect(bool direct=true)

bool IsFirstReversed() const

position_type GetSecondTo(void) const

position_type GetFirstFrom(void) const

position_type GetSecondToOpen(void) const

position_type GetLength(void) const

position_type GetSecondPosByFirstPos(position_type pos) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TTo GetTo(void) const

Get the To member data.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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