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NCBI C++ ToolKit: src/gui/widgets/seq_graphic/denseg_graphic_ds.cpp Source File

=

;

objects::CSeq_align& align, objects::CScope& scope,

anchor)

(align.GetSegs().IsDenseg());

(align.CheckNumRows() == 2);

(align.GetSegs().GetDenseg().CheckNumSegs() > 0);

(!align.GetSegs().GetDenseg().IsSetWidths());

(bsh.IsProtein()) {

(iter->first) {

objects::CBioseq_Handle&

try_reverse_dir)

pre_iter = curr_iter;

(try_reverse_dir ||

(try_reverse_dir ||

try_reverse_dir)

(curr_iter && ((reversed && aln_pos < curr_iter->GetRange().GetFrom()) ||

(!reversed && aln_pos > curr_iter->

().

()))) {

pre_iter = curr_iter;

((reversed && aln_pos > curr_iter->

().

()) ||

(!reversed && aln_pos < curr_iter->GetRange().GetFrom())) {

(try_reverse_dir ||

(try_reverse_dir ||

mis_str_idx = 0;

curr_seq_idx = 0;

TCigar::const_iterator c_iter = cigars.begin();

(

<

&& c_iter != cigars.end()) {

span = c_iter->second;

(c_iter->first) {

(curr_p + span >

) {

left_over = span -

;

.replace(curr_seq_idx, left_over, mismatch_str, mis_str_idx, left_over);

mis_str_idx += left_over;

curr_seq_idx += left_over;

(curr_p + span >

) {

left_over = curr_p -

;

curr_seq_idx += left_over;

(curr_p + span >

&& curr_seq_idx > 0) {

.replace(curr_seq_idx, span, span,

);

curr_seq_idx += span;

}

(exception& e) {

curr_seq_idx = 0;

(curr_iter &&

<

) {

off = curr_f -

;

(curr_seq_idx <

.length())

.replace(curr_seq_idx, off, off,

);

(

< curr_f + span) {

(curr_seq_idx <

.length())

.replace(curr_seq_idx, left_over, left_over,

);

row_f = row_t - left_over + 1;

row_t = row_f + left_over - 1;

seq_vec.

(row_f, row_t + 1, tmp_str);

0,

(tmp_str.length()), tmp_seq);

(tmp_str, tmp_seq);

(curr_seq_idx <

.length())

.replace(curr_seq_idx, left_over, tmp_str, 0, left_over);

curr_seq_idx += left_over;

anchor_direct)

= (size_t)seq_rng.

();

= (size_t)seq_rng.

();

mis_str_idx = 0;

curr_seq_idx = 0;

TCigar::const_iterator c_iter = cigars.begin();

(

<

&& c_iter != cigars.end()) {

span = c_iter->second;

(c_iter->first) {

(curr_p + span >

) {

left_over = span -

;

+= mismatch_str.substr(mis_str_idx, left_over);

mis_str_idx += left_over;

curr_seq_idx += left_over;

(curr_p + span >

) {

left_over = curr_p -

;

+= anchor_seq.substr(curr_seq_idx, left_over);

curr_seq_idx += left_over;

(curr_p + span >

&& curr_seq_idx > 0) {

curr_seq_idx += span;

(curr_p + span >

) {

left_over = span -

;

+= mismatch_str.substr(mis_str_idx, left_over);

mis_str_idx += left_over;

(!anchor_direct && reversed) {

( !cigar_str.empty() ) {

is_bam = !

(cigar_str[0]);

c_len = cigar_str.length();

len_start = is_bam ?

+ 1 :

;

len_end = len_start;

type_index =

;

(len_end < c_len && cigar_str[len_end] <

) {

type_index = len_end;

cigar.emplace_back(c_op,

);

(!cigar.empty()) {

((*iter)->GetType().IsStr() &&

(cigar_field && cigar_field->

().

()) {

((*iter)->GetType().IsStr() &&

(mismatch_field && mismatch_field->

().

()) {

virtual TNumrow GetNumRows(void) const

number of rows in alignment

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

bool m_IsCigarUnambiguous

string x_GetMismatchStr() const

virtual const TCigar * GetCigar() const

Get CIGAR vector.

virtual bool IsCigarUnambiguous() const

Check if cigar doesn't have ambiguous M's.

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

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

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

virtual TSignedSeqPos GetSeqPosFromSeqPos(TNumrow for_row, TNumrow row, TSeqPos seq_pos) const

virtual TNumrow GetAnchor(void) const

virtual TSeqPos GetAlnStart(void) const

CRef< objects::CScope > m_Scope

string x_GetCigarStr() const

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

map< TNumrow, objects::CBioseq_Handle > m_BioseqHandles

IAlnExplorer::TNumrow TNumrow

virtual TSignedRange GetAlnRange(void) const

virtual TSeqPos GetAlnStop(void) const

virtual TSeqPos GetSeqLength(TNumrow row) const

CConstRef< objects::CSeq_align > m_Alignment

virtual string & GetAlnSeqString(TNumrow row, string &buffer, const TSignedRange &aln_rng) const

virtual bool IsPositiveStrand(TNumrow row) const

virtual bool IsNegativeStrand(TNumrow row) const

virtual TSignedRange GetSeqAlnRange(TNumrow row) const

virtual TSeqPos GetSeqStop(TNumrow row) const

CDensegGraphicDataSource(const objects::CSeq_align &align, objects::CScope &scope, TNumrow anchor)

CDensegGraphicDataSource.

virtual TSeqPos GetBaseWidth(TNumrow row) const

virtual string & GetSeqString(string &buffer, TNumrow row, const TSignedRange &seq_rng, const TSignedRange &aln_rng, bool anchor_direct) const

Get sequence string for a given row in sequence range.

string & x_GetAlnStringFromCigar(TNumrow row, string &buffer, const TSignedRange &aln_range) const

virtual ~CDensegGraphicDataSource()

virtual EPolyATail HasPolyATail() const

Check if there is any unaligned polyA tail.

virtual TSeqPos GetSeqStart(TNumrow row) const

virtual IAlnExplorer::EAlignType GetAlignType() const

Implementation of IAlnSegmentIterator for CDense_seg.

static SIZE_TYPE ReverseComplement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Return a field reference representing the tokenized key, or a NULL reference if the key doesn't exist...

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)

vector< TCigarPair > TCigar

IAlnExplorer::TSignedRange TSignedRange

IAlnExplorer::TNumrow TNumrow

EPolyATail

Cetantiy of having unaligned polyA tail.

virtual string & GetSeqString(string &buffer, TNumrow row, const TSignedRange &seq_rng, const TSignedRange &aln_rng, bool anchor_direct) const

Get sequence string for a given row in sequence range.

Alignment segment iterator interface.

@ eAllSegments

Iterate all segments.

@ eSkipGaps

Skip gap segments (show only aligned ranges)

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

@ fReversed

The selected row is reversed (relative to the anchor).

virtual TSegTypeFlags GetType(void) const =0

Get current segment type.

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

static const string kMismatch

USING_SCOPE(ncbi::objects)

static const string kCigar

static const string kTracebacks

unsigned int TSeqPos

Type for sequence locations and lengths.

#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)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Error(CExceptionArgs_Base &args)

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ 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).

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

position_type GetLength(void) const

bool NotEmpty(void) const

position_type GetToOpen(void) const

static TThisType GetWhole(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static size_t StringToSizet(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to size_t.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool IsStr(void) const

Check if variant Str is selected.

list< CRef< CUser_object > > TExt

#define row(bind, expected)

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