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NCBI C++ ToolKit: src/gui/widgets/loaders/columnar_vcf_iterator.cpp Source File

39

: m_Variants(&var_list)

57

: m_Variants(&var_list)

85  for

(

const auto

& it : cols_name) {

86  if

(!descr[it].

empty

()) {

87

unique_ptr<TSparseCI> new_iter = make_unique<TSparseCI>(&descr[it],

m_Start

);

92  auto

info_fields = descr.GetInfoFieldNames();

93  for

(

const auto

& it : info_fields) {

94  if

(!descr.GetInfoField(it).empty()) {

95

unique_ptr<TInfoCI> new_iter = make_unique<TInfoCI>(&descr.GetInfoField(it),

m_Start

);

100  auto

samples = descr.GetSampleNames();

104  for

(

const auto

& it : samples) {

105  if

(!descr.GetSample(it).empty()) {

106

unique_ptr<TInfoCI> new_iter = make_unique<TInfoCI>(&descr.GetSample(it),

m_Start

);

145  if

(++m_IndexIterator < m_IncludedItems->end()) {

161

it.second->advance();

164

it.second->advance();

167

it.second->advance();

226  if

(it->second->is_null())

229  return

it->second->value();

246  if

(it.second->is_null()) {

250

info_value += it.first;

251  string

key_val = it.second->value();

252  if

(!key_val.empty()) {

253

info_value +=

"="

+ key_val;

258  if

(info_value.back() ==

';'

)

259

info_value.pop_back();

267  return

(info_iter !=

m_InfoIterators

.end() && !info_iter->second->is_null());

278  if

(info_iter->second->is_null()) {

279

info_value =

"null"

;

281

info_value = info_iter->second->value();

302  if

(sample_it->is_null()) {

306

sample = sample_it->value();

318  if

(!sample_it.second->is_null()) {

319

sample += sample_it.second->value();

CVCFVariant_CI & operator++()

CVCFVariant_CI(const CVCFVariantsBase &var_list)

vector< pair< string, unique_ptr< TInfoCI > > > m_SampleIterators

vector< size_t >::const_iterator m_IndexIterator

string GetInfoField(const string &field_name) const

const vector< size_t > * m_IncludedItems

bool IsSetSample(const string &name) const

string GetSample(const string &name) const

bool IsSetInfoField(const string &field_name) const

unique_ptr< vector< size_t > > m_Elements

unordered_map< string, unique_ptr< TSparseCI > > m_Iterators

unordered_map< string, size_t > m_SampleIterMap

unordered_map< string, unique_ptr< TInfoCI > > m_InfoIterators

CConstRef< CVCFVariantsBase > m_Variants

string x_GetData(const string &col_name) const

unsigned GetPosition() const

bool x_IsSetData(const string &col_name) const

string GetSampleCols() const

bool operator!=(const CVCFVariant_CI &other) const

bool operator==(const CVCFVariant_CI &other) const

const CVariantDescriptors & GetDescriptors() const

TSeqPos GetLeftShiftedStartPos(const TSeqRange &range) const

static const vector< string > & s_GetColNames()

does not contain sm_INFO and sm_SAMPLES

static const string sm_INFO

const unsigned & GetMaxFeatLength() const

static const string sm_MissingValue

unique_ptr< vector< size_t > > Filter(const TSeqRange &range) const

const vector< size_t > * GetIncludedItems() const

size_t GetIndexForPosition(const unsigned &pos, CPosToIndex::EType type) const

unsigned GetPositionForIndex(const size_t &index) const

vector< string > GetInfoFieldNames() const

bvector_type::size_type size_type

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NCBI_THROW(exception_class, err_code, message)

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

bool NotEmpty(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

constexpr bool empty(list< Ts... >) noexcept

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