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

objects::SAnnotSelector& sel,

sel,

.GetVisSeqRange(),

.GetScale(), fixed_scale, y_limits,

&

=

&

(

.object.GetObject());

(

.scope.GetObject(),

);

sid(

);

slabel(

);

objects::SAnnotSelector& sel,

sel.SetCollectNames();

(iter->IsNamed()) {

(iter->GetName().find(

) == string::npos) {

graph_iter(handle, range, sel);

(iter->IsNamed()) {

(iter->GetName().find(

) == string::npos &&

iter->GetName().find(

) == string::npos) {

objects::SAnnotSelector& sel,

handle.GetRangeSeq_loc(range.

(), range.

());

it(handle.GetScope(), *loc, sel);

valid_graph =

;

CSeq_annot::TDesc::Tdata::const_iterator d_iter = descs.begin();

(; d_iter != descs.end(); ++d_iter) {

((*d_iter)->IsUser()) {

valid_graph = col_span.

(annot, 0)

&& col_pos.

(annot, 0)

&& col_val.

(annot, 0);

}

(

exception&) {

(it->

().find(

) == string::npos) {

->GetData(the_map);

->m_ObjectList.emplace_back(hist.GetPointer());

(

& from,

& to)

valid_graph =

;

CSeq_annot::TDesc::Tdata::const_iterator d_iter = descs.begin();

(; d_iter != descs.end(); ++d_iter) {

(!(*d_iter)->IsUser())

runtime_error(

);

= (double)val_i;

to = from + span - 1;

range.

(from, to);

(!table_reader.

())

TDMaps::iterator iter = d_maps.find(g_title);

(iter == d_maps.end()) {

iter = d_maps.insert(

g_desc, g_name))).first;

(!table_reader.

(0, curr_range))

(curr_range.

() > to)

(!table_reader.

(

(rows - 1), curr_range))

(curr_range.

() < from)

r_end =

(rows - 1);

= (r_start + r_end) / 2;

}

((

)pos != from && r_start < r_end - 1);

= (r_start + r_end) / 2 ;

first_row =

;

(; (size_t)

< rows; ++

) {

last_row =

(

, (

)rows - 1);

(table_reader.

(first_row,

)) {

.Init(

.GetTo(), table_reader.

(first_row));

(table_reader.

(last_row,

)) {

}

(exception& e) {

.push_back(fref);

->m_ObjectList.swap(glyphs);

->m_ObjectList.swap(glyphs);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const TAnnotNames & GetAnnotNames(void) const

CSeq_annot_Handle GetAnnot(void) const

CAppJobError Default implementation for IAppJobError - encapsulates a text error message.

CRef< TData > GetData(const string &data_key)

Retrieves TData from in-memory cache or if not found calls TData::Init to initialize new TData instan...

static CGraphCache & GetInstance()

static int GetNearestLevel(const set< int > &levels, double zoom)

static void CalcGraphLevels(const string &annotName, objects::CScope &scope, const objects::CSeq_loc &loc, set< int > &levels)

static EType TypeStrToValue(const string &type)

void SetInterpolationMethod(EInterpolationMethod interpolation_method)

void InitDataPoints(const TModelPoint &first_point, const TModelPoint &last_point)

@ eInterpolation_Piecewise

void SetAnnotName(const string &name)

void SetAxisMaxFixed(TDataType max)

void SetFixedScale(bool value)

void SetDesc(const string &desc)

CRef< CHistParams > GetHistParams() const

void SetConfig(const CSeqGraphicConfig &config)

void SetAxisMinFixed(TDataType min)

void Map(int &from, int &to)

CPosMapper(TSeqPos src_f, TSeqPos src_t, TSeqPos target_f, bool reversed)

CRenderingContext offers the basic context and utility methods for rendering layout objects in featur...

objects::SAnnotSelector m_Sel

our annotation selector

objects::CScope & GetScope(void) const

CSGAnnotJob inline methods.

int m_GraphLevel

coverate graph level

int GetGraphLevel() const

TSeqRange m_Range

target range

IAppJob::EJobState x_CreateHistFromGraph(CSeqGlyph::TObjects &glyphs, const objects::SAnnotSelector &sel, TModelUnit window, bool fixed_scale, const TAxisLimits &y_limits)

objects::CBioseq_Handle m_Handle

target sequence

IAppJob::EJobState x_LoadCoverageGraph(CSeqGlyph::TObjects &glyphs, int level, TModelUnit window, const string &title, bool fixed_scale, const TAxisLimits &y_limits)

TJobID x_LaunchJob(IAppJob &job, int report_period=1, const string &pool="ObjManagerEngine")

Launch either a background or foreground job.

bool m_Adaptive

adaptive/exact annot selector

int m_Depth

annotation resolving depth

objects::CBioseq_Handle m_Handle

virtual string GetExtensionLabel() const

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

virtual ISGDataSource * CreateDS(SConstScopedObject &object) const

create an instance of the layout track type using default settings.

virtual string GetExtensionIdentifier() const

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

virtual bool IsSharable() const

check if the data source can be shared.

void LoadSeqGraphs(const string &annotName, objects::SAnnotSelector &sel, CRenderingContext &ctx, bool fixed_scale, const TAxisLimits &y_limits, CConstRef< CSeqGraphicConfig > config)

void GetSeqtableAnnots(objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names) const

CSGGraphDS(objects::CScope &scope, const objects::CSeq_id &id)

CSGGraphDS.

bool m_SeqTable

create graph from seq-table

void GetAnnotNames(objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names, bool seq_table=false) const

CSGJobResult – the data structure holding the seqgraphic job results.

CConstRef< CSeqGraphicConfig > m_Config

bool m_FixedScale

use global scale or dynamic scale

IAppJob::EJobState x_LoadGraph()

bool m_SeqTable

create graph from seq-table

IAppJob::EJobState x_LoadSeqTable()

TModelUnit m_Window

current window for smear bars

static void GetAnnotNames(const objects::CBioseq_Handle &handle, const TSeqRange &range, objects::SAnnotSelector &sel, TAnnotNameTitleMap &names, bool seq_table=false)

CSGSeqGraphJob.

IAppJob::EJobState x_LoadGraphFromCoverageGraph()

virtual EJobState x_Execute()

method truly doing the job.

static void GetSeqtableAnnots(const objects::CBioseq_Handle &handle, const TSeqRange &range, objects::SAnnotSelector &sel, TAnnotNameTitleMap &names)

list< CRef< CSeqGlyph > > TObjects

virtual void SetTaskName(const string &name)

virtual void SetTaskCompleted(int completed)

set total finished task number.

TJobToken m_Token

Job token recognizable by job listener.

CRef< CAppJobError > m_Error

CTableFieldHandle< double > m_col_val_real

CRef< CPosMapper > m_mapper

void SetMapper(CPosMapper *mapper)

CHistogramData::EInterpolationMethod m_InterpolationMethod

const string & GetGraphStyle() const

CSeqTableReader(CSeq_annot_Handle &annot)

CTableFieldHandle< int > m_col_val_int

bool GetRange(int row, TSeqRange &range)

CSeq_annot_Handle m_annot

vector< char > m_byte_vals

const CHistogramData::EInterpolationMethod GetInterpolationMethod() const

CTableFieldHandle< int > m_col_span

CTableFieldHandle< int > m_col_pos

bool IsSet(const CFeat_CI &feat_ci) const

bool TryGet(const CFeat_CI &feat_ci, Value &v) const

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...

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

container_type::value_type value_type

static const struct name_t names[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#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 ERR_POST(message)

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

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

static string GetAnnotName(const objects::CSeq_annot_Handle &annot_handle)

static const string & GetUnnamedAnnot()

Get the commonly used symbol representing a unnnamed annotation.

static string GetAnnotComment(const objects::CSeq_annot_Handle &annot_handle)

static void SetResolveDepth(objects::SAnnotSelector &sel, bool adaptive, int depth=-1)

help function for setting selector resolve depth.

virtual void AddRange(TSeqRange range, CntType score=1, bool expand=false)

EJobState

Job states (describe FSM)

ENa_strand GetStrand(void) const

Get the location's strand.

TRange GetTotalRange(void) const

bool IsSeq_table(void) const

size_t GetSeq_tableNumRows(void) const

const CSeq_annot::TDesc & Seq_annot_GetDesc(void) const

bool Seq_annot_CanGetDesc(void) const

const string & GetName(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

const CSeq_loc & GetOriginalLocation(void) const

const CSeq_loc & GetMappedLocation(void) const

bool IsMapped(void) const

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

TObjectType * Release(void)

Release a reference to the object and return a pointer to the object.

TThisType & Set(position_type from, position_type to)

static TThisType GetWhole(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

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.

@ eField_id_location_from

interval from

const Tdata & Get(void) const

Get the member data.

list< CRef< CAnnotdesc > > Tdata

double value_type

The numeric datatype used by the parser.

const GenericPointer< typename T::ValueType > T2 value

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

static SLJIT_INLINE sljit_ins lb(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

CHistogramGlyph::TMap m_Map

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