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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/dbvar__feature__sorter_8cpp_source.html below:

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

65  if

(iter != sm_QuaGroupNameStrs.end()) {

74

vector<string> tokens;

76  size_t

num_tokens = tokens.size();

79  for

(

size_t i

= 0;

i

< num_tokens; ++

i

) {

104  const

objects::CSeq_feat::TData&

data

= feat.GetOriginalFeature().GetData();

105  if

(

data

.IsVariation()) {

130  static const string

kSorterName =

"variant_quality"

;

139  "Sort variants by variant quality"

);

166  if

(iter != sm_PilotGroupNameStrs.end()) {

175

vector<string> tokens;

177  size_t

num_tokens = tokens.size();

180  for

(

size_t i

= 0;

i

< num_tokens; ++

i

) {

220  const

objects::CSeq_feat::TData&

data

= feat.GetOriginalFeature().GetData();

221  if

(

data

.IsVariation()) {

222  string value

= feat.GetNamedQual(

"Pilot"

);

223  if

(

value

.empty()) {

261  static const string

kSorterName =

"pilot"

;

270  "Sort variants by pilot number"

);

297  if

(iter != sm_ClinGroupNameStrs.end()) {

306

vector<string> tokens;

308  size_t

num_tokens = tokens.size();

311  for

(

size_t i

= 0;

i

< num_tokens; ++

i

) {

351  const

objects::CSeq_feat::TData&

data

= feat.GetOriginalFeature().GetData();

352  if

(

data

.IsVariation()) {

354  const

objects::CVariation_ref& var = feat.GetData().GetVariation();

355  ITERATE

(objects::CVariation_ref::TPhenotype, pnt_iter, var.GetPhenotype()) {

356  if

((*pnt_iter)->CanGetClinical_significance()) {

357  switch

((*pnt_iter)->GetClinical_significance()) {

358  case

objects::CPhenotype::eClinical_significance_non_pathogenic:

361  case

objects::CPhenotype::eClinical_significance_pathogenic:

364  case

objects::CPhenotype::eClinical_significance_probable_pathogenic:

367  case

objects::CPhenotype::eClinical_significance_probable_non_pathogenic:

370  case

objects::CPhenotype::eClinical_significance_unknown:

373  case

objects::CPhenotype::eClinical_significance_untested:

376  case

objects::CPhenotype::eClinical_significance_other:

407  static const string

kSorterName =

"clinical_assertion"

;

416  "Sort variants by clinical assertion"

);

441  if

(iter != sm_SampleTypeNameStrs.end()) {

450

vector<string> tokens;

452  size_t

num_tokens = tokens.size();

455  for

(

size_t i

= 0;

i

< num_tokens; ++

i

) {

483  const

objects::CSeq_feat::TData&

data

= feat.GetOriginalFeature().GetData();

484  if

(

data

.IsVariation()) {

485  const string

& qual = feat.GetNamedQual(

"sampleset_type"

);

490

}

else if

(qual.empty()) {

518  static const string

kSorterName =

"sampleset_type"

;

527  "Sort variants by sampleset type"

);

555  if

(iter != sm_ValidationTypeNameStrs.end()) {

564

vector<string> tokens;

566  size_t

num_tokens = tokens.size();

569  for

(

int i

= 0;

i

< num_tokens; ++

i

) {

596  if

(feat.IsSetExts()) {

597  const

objects::CSeq_feat::TExts& exts = feat.GetExts();

598  ITERATE

(objects::CSeq_feat::TExts, iter, exts) {

599  if

( (*iter)->GetType().IsStr() &&

601

(*iter)->GetFieldRef(

"Status"

) &&

602

(*iter)->GetFieldRef(

"Status"

)->GetData().IsStr()) {

638  static const string

kSorterName =

"validation_status"

;

647  "Sort variants by validation status"

);

671  if

(iter != sm_ResolveStatusNameStrs.end()) {

680

vector<string> tokens;

682  size_t

num_tokens = tokens.size();

685  for

(

int i

= 0;

i

< num_tokens; ++

i

) {

711  const string

& status = feat.GetNamedQual(

"status"

);

729  static const string

kSorterName =

"grc_status"

;

738  "Sort GRC issues by resolution status"

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

virtual int GetGroupIdx(const objects::CMappedFeat &feat) const

Get the sorted group index for a given feature.

static const string & GetID()

virtual string GroupIdxToName(int idx) const

Convert group index into group name.

CDbvarClinicalAsstSorter(const string &sort_str)

virtual SSorterDescriptor GetThisDescr() const

Return a name for the sorter.

static SSorterDescriptor GetSorterDescr()

set< EGroup > m_SortGroups

Curently intended sorting groups.

@ eInvalid

maybe it is valid, but not considered

set< EGroup > m_SortGroups

Curently intended sorting groups.

static const string & GetID()

static SSorterDescriptor GetSorterDescr()

CDbvarPilotSorter(const string &sort_str)

virtual int GetGroupIdx(const objects::CMappedFeat &feat) const

Get the sorted group index for a given feature.

virtual SSorterDescriptor GetThisDescr() const

Return a name for the sorter.

@ eInvalid

maybe it is valid, but not considered

virtual string GroupIdxToName(int idx) const

Convert group index into group name.

static SSorterDescriptor GetSorterDescr()

static const string & GetID()

set< EGroup > m_SortGroups

Curently intended sorting groups.

virtual string GroupIdxToName(int idx) const

Convert group index into group name.

@ eInvalid

maybe it is valid, but not considered

CDbvarQualitySorter(const string &sort_str)

virtual int GetGroupIdx(const objects::CMappedFeat &feat) const

Get the sorted group index for a given feature.

virtual SSorterDescriptor GetThisDescr() const

Return a name for the sorter.

virtual string GroupIdxToName(int idx) const

Convert group index into group name.

set< EGroup > m_SortGroups

Curently intended sorting groups.

virtual SSorterDescriptor GetThisDescr() const

Return a name for the sorter.

CDbvarSamplesetTypeSorter(const string &sort_str)

@ eInvalid

maybe it is valid, but not considered

virtual int GetGroupIdx(const objects::CMappedFeat &feat) const

Get the sorted group index for a given feature.

static const string & GetID()

static SSorterDescriptor GetSorterDescr()

virtual string GroupIdxToName(int idx) const

Convert group index into group name.

static const string & GetID()

virtual int GetGroupIdx(const objects::CMappedFeat &feat) const

Get the sorted group index for a given feature.

CDbvarValidationSorter(const string &sort_str)

set< EGroup > m_SortGroups

Curently intended sorting groups.

virtual SSorterDescriptor GetThisDescr() const

Return a name for the sorter.

@ eDiffSample_DiffPlatform

@ eDiffSample_SamePlatform

@ eSameSample_DiffPlatform

@ eInvalid

maybe it is valid, but not considered

static SSorterDescriptor GetSorterDescr()

CGRCStatusSorter(const string &sort_str)

static const string & GetID()

virtual int GetGroupIdx(const objects::CMappedFeat &feat) const

Get the sorted group index for a given feature.

static SSorterDescriptor GetSorterDescr()

virtual string GroupIdxToName(int idx) const

Convert group index into group name.

virtual SSorterDescriptor GetThisDescr() const

Return a name for the sorter.

set< EGroup > m_SortGroups

Curently intended sorting groups.

class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...

TBase::const_iterator const_iterator

iterator_bool insert(const value_type &val)

static const TPilotGroupNameStr s_PilotGroupNameStrs[]

static const TResolveStatusNameStr s_ResolveStatusNameStrs[]

SStaticPair< CGRCStatusSorter::EGroup, const char * > TResolveStatusNameStr

CGRCStatusSorter implementation.

SStaticPair< CDbvarSamplesetTypeSorter::EGroup, const char * > TSampleTypeNameStr

CDbvarSamplesetTypeSorter implementation.

CStaticArrayMap< CDbvarSamplesetTypeSorter::EGroup, string > TSampleTypeNameMap

CStaticArrayMap< CDbvarQualitySorter::EGroup, string > TQuaGroupNameMap

static const TValidationTypeNameStr s_ValidationTypeNameStrs[]

static const TSampleTypeNameStr s_SampleTypeNameStrs[]

static const string & s_PilotGroupIdxToName(int idx)

static const string & s_ValidationTypeIdxToName(int idx)

static const string & s_QuaGroupIdxToName(int idx)

SStaticPair< CDbvarClinicalAsstSorter::EGroup, const char * > TClinGroupNameStr

CDbvarClinicalAsstSorter implementation.

CStaticArrayMap< CDbvarPilotSorter::EGroup, string > TPilotGroupNameMap

CStaticArrayMap< CDbvarClinicalAsstSorter::EGroup, string > TClinGroupNameMap

SStaticPair< CDbvarQualitySorter::EGroup, const char * > TQuaGroupNameStr

CDbvarQualitySorter implementation.

SStaticPair< CDbvarPilotSorter::EGroup, const char * > TPilotGroupNameStr

CDbvarPilotSorter implementation.

static const string & s_ResolveStatusIdxToName(int idx)

static const string & s_ClinGroupIdxToName(int idx)

SStaticPair< CDbvarValidationSorter::EGroup, const char * > TValidationTypeNameStr

CDbvarValidationSorter implementation.

DEFINE_STATIC_ARRAY_MAP(TQuaGroupNameMap, sm_QuaGroupNameStrs, s_QuaGroupNameStrs)

static const TClinGroupNameStr s_ClinGroupNameStrs[]

static const TQuaGroupNameStr s_QuaGroupNameStrs[]

CStaticArrayMap< CDbvarValidationSorter::EGroup, string > TValidationTypeNameMap

CStaticArrayMap< CGRCStatusSorter::EGroup, string > TResolveStatusNameMap

static const string & s_SampleTypeIdxToName(int idx)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

static void TokenizeWithEscape(const string &str, const string &delim, vector< string > &tokens, bool remove_escape=false)

Tokenize a string using the delim.

#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.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

const GenericPointer< typename T::ValueType > T2 value

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...


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