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NCBI C++ ToolKit: src/gui/widgets/aln_table/alnspan_vertmodel.cpp Source File

( sparce_aln, threshold );

( spliced_seg, scope, threshold );

( input_aligns.size() == 1 && input_aligns[0]->GetSegs().IsSpliced() ){

*

( &input_aligns[0]->GetSegs().GetSpliced() )

( input_aligns.size() > 0 ){

container.

( **ait );

(

<<

<< e.what() );

(

<<

);

,

( *sparse_aln, threshold );

*handle -> GetBioseqHandle().

(),

vector< IAlnSegmentIterator* > iters;

vector<bool> seq_touched(

,

);

(a_range.

() < (

)pos && ++it) {

(!seq_touched[

])

seq_touched[

] =

;

}

(too < next_pos) {

vector<string> seq_spans;

seg_has_gap =

;

seg_has_unaln =

;

seg_is_translated =

;

seg_has_unaln = seq_touched[

];

[0]->GetAlnSeqString(

, seq_span, seq_range, seg_is_translated);

(seg_is_translated) {

seq_span.swap(new_seq);

(!seq_span.empty()) {

seq_spans.push_back(seq_span);

(seq_spans.size() <= 1) {

(seq_spans.empty()) {

(

<<

<< pos <<

<< (next_pos - 1) <<

);

(newRow.

== 0) {

aln_spans.push_back(newRow);

length = next_pos - pos;

= (

)seq_spans.size();

f_mismatch =

;

(

j = 1; j <

; j++) {

(

< (

)seq_spans[j].length());

(seq_spans[j][

] != seq_spans[0][

]) {

(new_span_type != f_span_type) {

(span_start >

- 1)

(

<<

<< pos <<

<< span_start <<

<<

);

newRow.

= f_span_type;

aln_spans.push_back(newRow);

f_span_type = new_span_type;

}

(

< length);

(

row_to_delete = 0; row_to_delete <

; row_to_delete++) {

iters[row_to_delete];

TAlnSpans::iterator iter = aln_spans.begin();

(; iter != aln_spans.end();) {

(from == -1 || to == -1) {

}

(iter->type &

) {

vector<bool> seq_strand(

,

);

(

seq_ix = 0; seq_ix <

; seq_ix++) {

seq_strand[seq_ix] =

[0]->IsPositiveStrand(seq_ix);

(

seq_ix = 0; seq_ix <

; seq_ix++) {

vector<TSignedSeqPos> seq_pos(

, -1);

(

seq_ix = 0; seq_ix <

; seq_ix++) {

(!span_row.

[seq_ix].Empty()) {

splice3, splice5;

(seq_strand[seq_ix]) {

(cur_seq_pos > 0 && cur_span_from > cur_seq_pos) {

gap_row.

[seq_ix] =

seq_ix, intron, seq_pos[seq_ix], cur_span_from - 1

(intron.length() > 1) {

splice5 = intron.substr(0, 2);

splice3 = intron.substr(intron.length() - 2);

iter = rows.insert(iter, gap_row);

seq_pos[seq_ix] = cur_span_to + 1;

(cur_seq_pos > 0 && cur_span_to < cur_seq_pos) {

gap_row.

[seq_ix] =

seq_ix, intron, cur_span_to + 1, seq_pos[seq_ix]

(intron.length() > 1) {

splice5 = intron.substr(0, 2);

splice3 = intron.substr(intron.length() - 2);

iter = rows.insert(iter, gap_row);

seq_pos[seq_ix] = cur_span_from - 1;

TAlnSpans::iterator iter = rows.begin();

TAlnSpans::iterator

= rows.end();

(; iter != rows.end();

= iter, ++iter) {

|| iter->type ==

merge_prev =

;

merge_next =

;

TAlnSpans::iterator

= iter + 1;

(

>= (

)merged_row.

.size()) {

}

(

>= (

)

->ranges.size()) {

(

>= (

)merged_row.

.size()) {

}

(

>= (

)

->ranges.size()) {

TAlnSpans::iterator from = merge_prev ? iter :

;

TAlnSpans::iterator to = merge_next ? (

+ 1) :

;

rows.erase(from, to);

TAlnSpans::iterator iter = rows.begin();

(; iter != rows.end();) {

(pos < (

)iter->aln_range.GetFrom()) {

pos = iter->aln_range.GetTo() + 1;

warning_cnt = 0;

TAlnSpans::iterator iter =

.begin();

(iter->length == 0) {

iter->length = iter->aln_range.GetLength() /

;

(iter->length == 0) {

(warning_cnt < 10) {

(warning_cnt == 10) {

(

<<

);

((double)(iter->length - iter->mismatch)) / iter->length

iter->identity = floor(identity * 10000 + 0.5) / 100.0;

iter->identity = 0.0;

(from == -1 || to == -1) {

}

(iter->type &

) {

span_row.

.push_back(loc);

loc->

().SetStrand(

loc->

().SetStrand(

span_row.

.push_back(loc);

product_length = 0;

( poly_a < start ){

span_rows.push_back( newRow );

( poly_a < start -1 ){

newRow.

= start - 1 - poly_a;

span_rows.push_back( newRow );

newRow.

= start - 1;

span_rows.push_back( newRow );

(chunk.

()) {

span_rows.push_back(newRow);

prod_pos += prod_len;

span_rows.push_back(newRow);

prod_pos += prod_len;

(aln_to < aln_from)

(aln_to, aln_from);

from += 3 - from % 3;

}

(off == 2) {

[0]->GetAlnSeqString(1, p_str, seq_range,

);

(g_str.size() == p_str.size());

(

= 0;

< g_str.size(); ++

) {

(

< p_str.size()) {

(g_str[

] != p_str[

])

newRow.

+= (g_str.size() - p_str.size());

span_rows.push_back(newRow);

prod_pos += prod_len;

newRow.

= prod_len;

span_rows.push_back( newRow );

prod_pos += prod_len;

span_rows.push_back( newRow );

( poly_a >= product_length ){

( stop < poly_a ){

( stop+1 < poly_a ){

newRow.

= (poly_a - stop) + 1;

span_rows.push_back( newRow );

newRow.

= (product_length - poly_a);

span_rows.push_back( newRow );

( stop < product_length - 1){

newRow.

= product_length - stop;

span_rows.push_back( newRow );

(

&& aln_row : span_rows) {

(!aln_row.ranges.empty() && aln_row.ranges[0].NotEmpty()) {

aln_from =

[0]->GetAlnPosFromSeqPos((

)0, aln_row.ranges[0].GetFrom());

aln_to =

[0]->GetAlnPosFromSeqPos((

)0, aln_row.ranges[0].GetTo());

(aln_to < aln_from)

(aln_to, aln_from);

aln_row.aln_range.Set(aln_from, aln_to + 1);

(

.size());

(

.size());

(

);

(

);

(

);

(

);

(

);

(

& dst,

& src)

( !dst.empty() ) {

,

( extra_col ){

wxVariant( spanRow.

);

wxVariant( spanRow.

);

wxVariant( spanRow.

);

wxVariant( spanRow.

);

|| col >= (

)spanRow.

.size()

|| spanRow.

[col].Empty()

,

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void BuildAln(TAnchoredAlnVec &in_alns, CAnchoredAln &out_aln, const CAlnUserOptions &options, TAlnSeqIdIRef pseudo_seqid=TAlnSeqIdIRef())

Build anchored alignment from a set of alignmnets.

void CreateAnchoredAlnVec(_TAlnStats &aln_stats, TAnchoredAlnVec &out_vec, const CAlnUserOptions &options)

Create anchored alignment from each seq-align in the stats.

static void s_Append(string &dst, const string &src)

const_iterator insert(const CSeq_align &seq_align)

Insert new CSeq_align into the list.

size_type size(void) const

Container mapping seq-aligns to vectors of participating seq-ids.

void push_back(const CSeq_align &aln)

Adding an alignment.

void x_ConvertRowsToSpans(TAlnSpans &rows)

finally, convert our spans into rows for display

void x_MergeRows(TAlnSpans &rows)

CRange< TSignedSeqPos > m_AlnRange

void SetThreshold(int th)

virtual int GetNumColumns() const

Returns the number of columns in the model.

TAlnSpans m_AlnSpans

the alignments we represent

void SetShowIndels(bool indel)

virtual wxVariant GetValueAt(int i, int j) const

vector< string > m_ColNames

const SSpanRow & GetData(size_t row) const

access a given row's data

void x_PopulateRows(TAlnSpans &rows)

virtual int GetNumRows() const

Returns the number of rows in the model.

virtual wxString GetColumnName(int aColIx) const

Returns a default name for the column using spreadsheet conventions: A, B, C, ...

CRef< CSpliced_seg > m_SplicedSeg

vector< CRef< CSparseAln > > m_SparseAlns

virtual wxString GetColumnType(int aColIx) const

Tries to extract actual type from row 0 value if it exists.

vector< SSpanRow > TAlnSpans

void x_InsertIntrons(TAlnSpans &rows)

CAnchoredAln m_AnchoredAln

CRef< IAlnMultiDataSource > m_AlnSrc

void x_PopulateRowsSpliced(TAlnSpans &rows)

Helper class which collects seq-align statistics: seq-ids participating in alignments and rows,...

bool CanBeAnchored(void) const

Check if there are any ids which can be used as anchors for the whole set of alignments.

Options for different alignment manager operations.

@ ePreserveRows

Preserve all rows as they were in the input (e.g.

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

TDim GetDim(void) const

How many rows.

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

TSeqPos GetSeqStop(TDim row) const

TDim CheckNumRows(void) const

TSeqPos GetSeqStart(TDim row) const

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

virtual void x_FireDataChanged()

IAlignRowHandle provides an abstract way to access alignment row data.

virtual bool UsesAATranslation() const =0

virtual const objects::CBioseq_Handle & GetBioseqHandle() const =0

virtual bool CanGetSeqString() const =0

virtual string & GetAlnSeqString(string &buffer, const IAlnExplorer::TSignedRange &aln_rng) const =0

IAlnMultiDataSource - interface to a data source representing an abstract multiple alignment.

virtual IAlnExplorer::EAlignType GetAlignType() const =0

virtual TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

virtual const IAlignRowHandle * GetRowHandle(TNumrow row) const =0

virtual bool IsPositiveStrand(TNumrow row) const =0

virtual TSeqPos GetAlnStart(void) const =0

virtual bool CanGetId(TNumrow row) const =0

virtual IAlnSegmentIterator * CreateSegmentIterator(TNumrow row, const IAlnExplorer::TSignedRange &range, IAlnSegmentIterator::EFlags flags) const =0

virtual TNumrow GetNumRows(void) const =0

number of rows in alignment

virtual TSeqPos GetAlnStop(void) const =0

virtual const objects::CSeq_id & GetSeqId(TNumrow row) const =0

Alignment segment iterator interface.

@ eAllSegments

Iterate all segments.

@ fIndel

Either anchor or the selected row is not present in the segment.

@ fGap

Both anchor row and the selected row are not included in the segment (some other row is present and t...

virtual TSegTypeFlags GetType(void) const =0

Get current segment type.

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

virtual int GetGenCode(IAlnExplorer::TNumrow row) const =0

bool IsConsensusSplice(const string &splice5, const string &splice3)

Consensus splice is GY..AG or AT..AC.

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

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

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

position_type GetLength(void) const

position_type GetToOpen(void) const

static position_type GetPositionMax(void)

static TThisType GetEmpty(void)

TThisType & Set(position_type from, position_type to)

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

CRange< TSignedSeqPos > TSignedSeqRange

#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.

@ fWithCommas

Use commas as thousands separator.

static const char label[]

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.

void SetTo(TTo value)

Assign a value to To data member.

const TProtpos & GetProtpos(void) const

Get the variant data.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

bool IsSetParts(void) const

basic seqments always are in biologic order Check if a value has been assigned to Parts data member.

TMatch GetMatch(void) const

Get the variant data.

const TProduct_id & GetProduct_id(void) const

Get the Product_id member data.

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

TProduct_length GetProduct_length(void) const

Get the Product_length member data.

bool IsSetPoly_a(void) const

start of poly(A) tail on the transcript For sense transcripts: aligned product positions < poly-a <= ...

TDiag GetDiag(void) const

Get the variant data.

TProduct_type GetProduct_type(void) const

Get the Product_type member data.

TMismatch GetMismatch(void) const

Get the variant data.

TAmin GetAmin(void) const

Get the Amin member data.

const TParts & GetParts(void) const

Get the Parts member data.

const TProduct_start & GetProduct_start(void) const

Get the Product_start member data.

TGenomic_ins GetGenomic_ins(void) const

Get the variant data.

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

list< CRef< CSpliced_exon_chunk > > TParts

bool IsSetProduct_length(void) const

length of the product, in bases/residues from this (or from poly-a if present), a 3' unaligned length...

TPoly_a GetPoly_a(void) const

Get the Poly_a member data.

TProduct_ins GetProduct_ins(void) const

Get the variant data.

TNucpos GetNucpos(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

@ e_Product_ins

insertion in product sequence (i.e. gap in the genomic sequence)

@ e_Diag

both sequences are represented, there is sufficient similarity between product and genomic sequences....

@ e_Genomic_ins

insertion in genomic sequence (i.e. gap in the product sequence)

@ e_Match

both sequences represented, product and genomic sequences match

@ e_Mismatch

both sequences represented, product and genomic sequences do not match

unsigned int

A callback function used to compare two keys in a database.

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n th

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

const CharType(& source)[N]

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

vector< CRef< CAnchoredAln > > TAnchoredAlnVec

Collection of anchored alignments.

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

#define row(bind, expected)

the alignment we store with its parsed data

vector< CConstRef< objects::CSeq_loc > > locs

vector< string > str_ranges

visible values

vector< TSignedSeqRange > ranges

wxString ToWxString(const string &s)

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