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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/pairwise__aln_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/alnmgr/pairwise_aln.cpp Source File

(

->IsDirect() ) {

(gap_second_from, it_second_from));

( !

->IsDirect() ) {

(gap_second_to, it_second_to));

(

->IsDirect() ) {

(it_second_to, gap_second_to));

( !

->IsDirect() ) {

(it_second_from, gap_second_from));

(left_shift != 0 || right_shift != 0) {

(

->IsReversed() ) {

(left_shift, right_shift);

new_row = new_dim - 1;

(

< new_row) {

(aln_rng_it->IsDirect()) {

bool IsSet(int flags) const

int GetPolicyFlags() const

const_iterator begin() const

pair< const_iterator, bool > find_2(position_type pos) const

returns an iterator pointing to a range containing "pos"; if such a range does not exists an iterator...

void push_back(const TAlignRange &r)

@ fMixedDir

contains at least one reversed range

const_iterator end() const

TPairwiseAlnVector m_PairwiseAlns

TDim GetDim(void) const

How many rows.

bool SplitStrands(void)

Split rows with mixed dir into separate rows returns true if the operation was performed.

A pairwise aln is a collection of ranges for a pair of rows.

const TAlnSeqIdIRef & GetFirstId(void) const

Get first sequence id.

const TAlnSeqIdIRef & GetSecondId(void) const

Get second sequence id.

CPairwiseAln iterator. Iterates over aligned ranges and gaps.

pair< TIterator, bool > TCheckedIterator

void x_Init(bool force_direct=false)

CPairwise_CI & operator++(void)

CConstRef< CPairwiseAln > m_Aln

static DLIST_TYPE *DLIST_NAME() last(DLIST_LIST_TYPE *list)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

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

TThisType & IntersectWith(const TThisType &r)

TThisType & SetToOpen(position_type toOpen)

position_type GetToOpen(void) const

static TThisType GetEmpty(void)

TThisType & SetOpen(position_type from, position_type toOpen)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

#define row(bind, expected)

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