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

objects::CScope& scope)

m_AnchorDirect(

)

gaps.reserve(gaps.size() + ins_vec.size());

(

= ins_vec.begin();

!= ins_vec.end(); ++

) {

gap.

=

->GetFirstFrom();

gap.

=

->GetLength();

stable_sort(gaps.begin(), gaps.end());

gap_it->shift = shift;

shift += gap_it->len;

CPairwiseAln::const_iterator seg_it = pw.

();

TGapRanges::const_iterator gap = gaps.begin();

first_direct =

;

second_direct =

;

(seg_it != pw.

()) {

(gap != gaps.end() &&

(gap->row ==

) {

gap->second_from, gap->len, gap->direct);

shift = gap->shift + gap->len;

(gap != gaps.end()) {

(gap->row ==

) {

last_to, gap->len, gap->direct);

shift = gap->shift + gap->len;

k_unasigned_base_width = 0;

base_width = k_unasigned_base_width;

(base_width == k_unasigned_base_width) {

(base_width != 1) {

T::eBackwards;

try_reverse_dir)

try_reverse_dir)

errstr =

+

(

).AsFastaString() +

;

( ref )

ref->GetGcode();

na_remainder = na.size() % 3;

na_size = na.size() - na_remainder;

aa.resize(na_size / 3 + (na_remainder ? 1 : 0));

( na.empty() )

;

(

na_i = 0; na_i < na_size; ) {

(

= 0;

< 3; ++

, ++na_i) {

force_translation)

&rq_seq_range,

force_translation)

seq_range = rq_seq_range;

(seq_range.

() % 3 > 0) {

force_translation =

;

(tr_to > tr_from) {

( force_translation ) {

force_translation)

(pairwise_aln.

()) {

translate = force_translation || pairwise_aln.

()->IsProtein();

buf_size = aln_range.

();

is_first_seg =

;

trim_from = 0;

( row_r.

() ) {

is_first_seg =

;

(base_width == 1) {

vec_size - row_r.

(), s);

(tr_from % 3 > 0) {

(tr_from == split_codon_pos) {

( is_first_seg ) trim_from = tr_from % 3;

tr_from -= tr_from % 3;

off += 3 - (tr_from % 3);

tr_from += 3 - (tr_from % 3);

split_codon_pos = tr_to;

(tr_to == split_codon_pos) {

( is_first_seg ) trim_from = 3 - (tr_to % 3);

off -= 3 - (tr_to % 3);

tr_to += 3 - (tr_to % 3);

(tr_from % 3 > 0) {

split_codon_pos = tr_from;

trim_to = 3 - (tr_from % 3);

tr_from += 3 - (tr_from % 3);

prot_r.

(tr_from / 3, tr_to / 3);

vec_size - prot_r.

(), s);

=

(buf_size - off, s.size());

is_first_seg =

;

(translate && (

)aln_range.

() >= trim_from + trim_to) {

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

CRange< position_type > GetSecondRange() const

class CAlignRangeCollectionList<TAlignRange> represent a sorted collection of TAlignRange.

const_iterator begin() const

ESearchDirection

adding empty ranges is considered valid, they are simply ignored

@ fMixedDir

contains at least one reversed range

@ fInvalid

collection was modified and not validated

@ fReversed

contains at least one direct range

@ fUnsorted

one or more policies violated

const TInsertions & GetInsertions() const

Each insertion shows where the 'first' sequence has a gap while the 'second' sequence has the inserti...

vector< TAlignRange > TInsertions

const_iterator end() const

CAlignRange Represents an element of pairwise alignment of two sequences.

Query-anchored alignment can be 2 or multi-dimentional.

const TPairwiseAlnVector & GetPairwiseAlns(void) const

The vector of pairwise alns.

TDim GetDim(void) const

How many rows.

void SetAnchorRow(TDim anchor_row)

Modify anchor row (never do this unless you are creating a new alignment and know what you're doing).

TPairwiseAlnVector & SetPairwiseAlns(void)

Modify pairwise alns.

void SetScore(int score)

Set the total score.

TDim GetAnchorRow(void) const

Which is the anchor row?

int GetScore(void) const

What is the total score?

void SetDim(TDim dim)

Modify the number of rows.

int GetGenCode(int def=1) const

static const CTrans_table & GetTransTable(int id)

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

int GetSecondBaseWidth(void) const

Base width of the second row.

const TAlnSeqIdIRef & GetFirstId(void) const

Get first sequence id.

const TAlnSeqIdIRef & GetSecondId(void) const

Get second sequence id.

TSignedSeqPos GetSeqAlnStart(TNumrow row) const

TRng GetAlnRange(void) const

Get whole alignment range.

const TAlnRngColl & GetAlignCollection(TNumrow row)

Get pairwise alignment for the row.

TSignedSeqPos GetSeqAlnStop(TNumrow row) const

void x_Build(const CAnchoredAln &src_align)

void SetGapChar(TResidue gap_char)

Gap character modifier.

static void TranslateNAToAA(const string &na, string &aa, int gen_code=kDefaultGenCode)

TRange GetSeqRange(TNumrow row) const

Get sequence range in sequence coords.

CAnchoredAln::TDim TDim

Synonym of TNumrow.

CSparseAln(const CAnchoredAln &anchored_aln, objects::CScope &scope)

Constructor.

CRef< CAnchoredAln > m_Aln

TSeqPos GetSeqStop(TNumrow row) const

virtual IAlnSegmentIterator * CreateSegmentIterator(TNumrow row, const TSignedRange &range, IAlnSegmentIterator::EFlags flags) const

Create segment iterator.

string & GetAlnSeqString(TNumrow row, string &buffer, const TSignedRange &rq_aln_rng, bool force_translation=false) const

Fetch alignment sequence data.

TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

Map sequence position to alignment coordinates.

int x_GetGenCode(TNumrow row) const

TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

vector< objects::CBioseq_Handle > m_BioseqHandles

bool IsTranslated(void) const

Wheather the alignment is translated (heterogenous), e.g. nuc-prot.

vector< TRng > m_SecondRanges

bool IsPositiveStrand(TNumrow row) const

Check direction of the row.

TDim GetDim(void) const

Alignment dimension (number of sequence rows in the alignment)

const objects::CBioseq_Handle & GetBioseqHandle(TNumrow row) const

Get bioseq handle for the row.

virtual ~CSparseAln(void)

Destructor.

CRef< objects::CScope > m_Scope

TSeqPos GetSeqStart(TNumrow row) const

TSignedRange GetSeqAlnRange(TNumrow row) const

Get sequence range in alignment coords (strand ignored).

CRef< objects::CScope > GetScope(void) const

Scope accessor.

vector< CRef< CSeqVector > > m_SeqVectors

CSeqVector & x_GetSeqVector(TNumrow row) const

string & GetSeqString(TNumrow row, string &buffer, TSeqPos seq_from, TSeqPos seq_to, bool force_translation=false) const

Fetch sequence data for the given row and range.

bool IsNegativeStrand(TNumrow row) const

const objects::CSeq_id & GetSeqId(TNumrow row) const

Get seq-id for the row.

Implementation of IAlnSegmentIterator for CSparseAln.

char GetCodonResidue(int state) const

static int NextCodonState(int state, unsigned char ch)

CRange< TSignedSeqPos > TSignedRange

objects::CSeqVector::TResidue TResidue

ESearchDirection

Position search options.

@ eRight

Towards higher aln coord (always to the right)

@ eLeft

Towards lower aln coord (always to the left)

@ eBackwards

Towards lower seq coord (to the left if plus strand, right if minus)

@ eForward

Towards higher seq coord (to the right if plus strand, left if minus)

Alignment segment iterator interface.

@ eSkipInserts

Iterate segments where at least some rows are aligned (including gap segments)

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const CBioSource * GetBioSource(const CBioseq &bioseq)

Retrieve the BioSource object for a given bioseq handle.

const COrg_ref * GetOrg_refOrNull(const CBioseq_Handle &handle)

Return the pointer to org-ref associated with a given sequence or null if there is no org-ref associa...

@ eStrand_Plus

Plus strand.

@ eStrand_Minus

Minus strand.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

bool IsProtein(void) const

void SetCoding(TCoding coding)

void SetIupacCoding(void)

Set coding to either Iupacaa or Iupacna depending on molecule type.

bool IsNucleotide(void) const

void Reset(void)

Reset reference object.

position_type GetLength(void) const

TThisType & CombineWith(const TThisType &r)

position_type GetToOpen(void) const

position_type GetFirstToOpen(void) const

TThisType & SetLength(position_type len)

bool IsFirstDirect() const

TThisType & SetSecondFrom(position_type second_from)

position_type GetSecondFrom(void) const

TThisType & SetOpen(position_type from, position_type toOpen)

void SetDirect(bool direct=true)

TThisType & SetFirstFrom(position_type from)

void SetFirstDirect(bool direct=true)

position_type GetFirstFrom(void) const

position_type GetSecondToOpen(void) const

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

TFrom GetFrom(void) const

Get the From member data.

@ e_not_set

No variant selected.

const struct ncbi::grid::netcache::search::fields::SIZE size

vector< SGapRange > TGapRanges

USING_SCOPE(ncbi::objects)

CSparseAln::TAlnRngColl::ESearchDirection GetCollectionSearchDirection(CSparseAln::ESearchDirection dir)

#define row(bind, expected)

TSignedSeqPos second_from

bool operator<(const SGapRange &rg) const

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