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

idx = (

)(score / 5);

kScoreName =

;

<

ValType>

vector<ValType>& vec)

(vec.empty())

;

= (float)(gr.

() ? gr.

() : 1.0);

= (float)(gr.

() ? gr.

() : 0.0);

ranges += iter.GetRange();

vector<ValType>::const_iterator iter_gr = vec.

();

unsigned_char =

;

(

(ValType) == 1) unsigned_char =

;

(iter_gr != vec.end() && pos <

.GetToOpen()) {

= (

char)((*iter_gr) *

+

);

val_i = (

)((*iter_gr) *

+

);

(val_i > 255)

= 255;

= (

char)val_i;

(graph_iter && graph_iter.

() == 1) {

reverse =

;

seq_graph = mapper.

(*seq_graph);

(graph.

())

std::reverse(values.begin(), values.end());

std::reverse(values.begin(), values.end());

std::reverse(values.begin(), values.end());

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 s_AddGraphToMap(CSGAlnQualityScore::TScoreColl &score, const TSeqRange &range, const CSeq_graph &gr, const vector< ValType > &vec)

Seq-loc and seq-align mapper exceptions.

size_t GetSize(void) const

const_iterator begin() const

position_type GetFrom() const

class CRgbaColor provides a simple abstraction for managing colors.

virtual const string & GetScoringMethod() const

virtual IAlnScoreIterator * GetScoreIterator(int row) const

void x_RetrieveQualityMap(IAlnExplorer::TNumrow row, bool remap)

CRef< CAlnInfo > m_AlnInfo

virtual int GetSupportedColorTypes() const

virtual bool IsCacheable() const

static const string & GetScoreName()

virtual bool IsAverageable() const

virtual bool HasScores() const

virtual CRgbaColor GetColorForScore(float score, IScoringMethod::EColorType type) const

virtual void CalculateScores()

CAlignOhterScore.

CRange< TSeqPos > GetSeqRange(TDim row) const

GetSeqRange NB: On a Spliced-seg, in case the product-type is protein, these only return the amin par...

TSeqPos GetSeqStop(TDim row) const

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

TSeqPos GetSeqStart(TDim row) const

ENa_strand GetSeqStrand(TDim row) const

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

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

static objects::SAnnotSelector GetAnnotSelector(TAnnotFlags flags=0)

request an annotation selector for a given type

void SetFrom(TSeqPos start)

void push_back(const attr_type &attr)

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

const CSeq_graph & GetMappedGraph(void) const

Graph mapped to the master sequence.

SAnnotSelector & AddUnnamedAnnots(void)

Add unnamed annots to set of annots names to look for.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

bool IsSetComp(void) const

compression (residues/value) Check if a value has been assigned to Comp data member.

bool IsSetB(void) const

display = (a x value) + b Check if a value has been assigned to B data member.

const TInt & GetInt(void) const

Get the variant data.

bool IsSetA(void) const

for scaling values Check if a value has been assigned to A data member.

const TGraph & GetGraph(void) const

Get the Graph member data.

const TValues & GetValues(void) const

Get the Values member data.

TB GetB(void) const

Get the B member data.

const TByte & GetByte(void) const

Get the variant data.

const TReal & GetReal(void) const

Get the variant data.

const TValues & GetValues(void) const

Get the Values member data.

E_Choice Which(void) const

Which variant is currently selected.

const TValues & GetValues(void) const

Get the Values member data.

const TLoc & GetLoc(void) const

Get the Loc member data.

TA GetA(void) const

Get the A member data.

TComp GetComp(void) const

Get the Comp member data.

unsigned int

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

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

#define row(bind, expected)

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