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NCBI C++ ToolKit: src/gui/packages/pkg_sequence/table_data_vcf.cpp Source File

shared_ptr<INonAsnTrackData::TDataBlob>& vcf_blob);

shared_ptr<INonAsnTrackData::TDataBlob>& vcf_blob)

;

data_cols(all_col_names.begin(), all_col_names.end());

info_columns[info_column_name] = variant_CI.

(info_column_name);

(variant_CI.

(sample_column_name)) {

sample_columns[sample_column_name] = variant_CI.

(sample_column_name);

}

(std::exception& ex) {

m_DataLoadStatus(eNotReady)

<<

(job_id !=

)

;

= (col == 0 ?

:

);

= (col == 0 ?

:

);

= vcf_variant->GetID();

= vcf_variant->GetVariationTypeAsString();

= vcf_variant->GetAllAlleles_display();

(vcf_variant->GetInfoColumns().find(sColLabel) != vcf_variant->GetInfoColumns().end()) {

= vcf_variant->GetInfoColumns().at(sColLabel);

(

.empty()) {

(vcf_variant->GetSampleColumns().find(sColLabel) != vcf_variant->GetSampleColumns().end()) {

= vcf_variant->GetSampleColumns().at(sColLabel);

= vcf_variant->GetPos()+1;

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

IAppJobListener Interface for components that need to be notified about changes in Jobs.

CAppJobNotification Notification send by CAppJobEventTranslator.

CAppJobProgress Default implementation for IAppJobProgress - the class encapsulates a text message an...

Base class to build jobs with cancel functionality.

objects::CBioseq_Handle m_Handle

target sequence

virtual CConstIRef< IAppJobProgress > GetProgress()

return progress object, the function shall be synchronized internally.

int m_VcfLimit

-1: theoretically unlimited, practically there is one (kMaxObjNum) >0: any limit set from a user

shared_ptr< INonAsnTrackData::TDataBlob > m_VcfBlob

virtual CConstIRef< IAppJobError > GetError()

Returns IAppJobError object describing internal error that caused the Job to fail.

CRef< CObject > m_listVcfs

CTableDataVcfJob(CBioseq_Handle handle, const TSeqRange &range, int max_vcf, shared_ptr< INonAsnTrackData::TDataBlob > &vcf_blob)

virtual ~CTableDataVcfJob()

virtual CRef< CObject > GetResult()

Returns the Job Result.

virtual EJobState Run()

Function that does all the useful work, called by the Engine.

TSeqRange m_Range

target range

CRef< CAppJobError > m_Error

virtual string GetDescr() const

Returns a human readable description of the Job (optional)

virtual void GetStringValue(size_t row, size_t col, string &value) const

CRef< CObjectFor< TVcfDataList > > m_listVcfs

virtual double GetRealValue(size_t row, size_t col) const

TSeqRange m_Range

target range

vector< string > m_ColNames

virtual string GetColumnLabel(size_t col) const

virtual size_t GetColsCount() const

virtual size_t GetRowsCount() const

virtual string GetHtmlValue(size_t, size_t) const

EDataLoadStatus m_DataLoadStatus

CRef< objects::CScope > m_Scope

void OnJobNotification(CEvent *evt)

virtual SConstScopedObject GetRowObject(size_t row) const

virtual bool IsHtmlColumn(size_t col) const

CConstRef< objects::CVcfVariant > x_GetRowData(size_t row) const

objects::CBioseq_Handle m_Handle

target sequence

virtual ColumnType GetColumnType(size_t col) const

shared_ptr< INonAsnTrackData::TDataBlob > m_VcfBlob

static const int c_MaxRows

! until dynamic loading is implemented

virtual SConstScopedObject GetObjectValue(size_t row, size_t col) const

virtual long GetIntValue(size_t row, size_t col) const

string GetVariantID() const

string GetInfoField(const string &field_name) const

bool IsSetSample(const string &name) const

string GetSample(const string &name) const

bool IsSetInfoField(const string &field_name) const

unsigned GetPosition() const

const CVariantDescriptors & GetDescriptors() const

static const vector< string > & s_GetAllColNames()

contains sm_INFO, sm_SAMPLES

vector< string > GetInfoFieldNames() const

vector< string > GetSampleNames() const

API (CDeflineGenerator) for computing sequences' titles ("definitions").

#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)

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

static CAppJobDispatcher & GetInstance()

TColumns & SetInfoColumns()

virtual bool IsCanceled() const override

TColumns & SetSampleColumns()

bool DeleteJob(TJobID job_id)

when a Job is deleted the listener is not notified

EJobState

Job states (describe FSM)

TJobID StartJob(IAppJob &job, const string &engine_name, IEngineParams *params=NULL)

Starts a Job on the specified engine in "passive mode" - no notifications or progress reports will be...

#define ON_EVENT(type, id, handler)

#define END_EVENT_MAP()

Ends definition of Command Map.

#define BEGIN_EVENT_MAP(thisClass, baseClass)

Begins definition of Command Map for CEventHandler-derived class.

CRef< CObject > GetJobResult(TJobID job_id)

TJobState GetState() const

virtual bool Send(CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)

Sends an event synchronously.

void SetNormDone(float done)

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

T & GetData(void)

Get data as a reference.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

unsigned int

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

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

const GenericPointer< typename T::ValueType > T2 value

#define row(bind, expected)

vector< CRef< objects::CVcfVariant > > m_VcfVariants

vector< string > m_InfoFields

vector< string > m_SampleNames

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