(iter != sm_QuaGroupNameStrs.end()) {
74vector<string> tokens;
76 size_tnum_tokens = tokens.size();
79 for(
size_t i= 0;
i< num_tokens; ++
i) {
104 constobjects::CSeq_feat::TData&
data= feat.GetOriginalFeature().GetData();
105 if(
data.IsVariation()) {
130 static const stringkSorterName =
"variant_quality";
139 "Sort variants by variant quality");
166 if(iter != sm_PilotGroupNameStrs.end()) {
175vector<string> tokens;
177 size_tnum_tokens = tokens.size();
180 for(
size_t i= 0;
i< num_tokens; ++
i) {
220 constobjects::CSeq_feat::TData&
data= feat.GetOriginalFeature().GetData();
221 if(
data.IsVariation()) {
222 string value= feat.GetNamedQual(
"Pilot");
223 if(
value.empty()) {
261 static const stringkSorterName =
"pilot";
270 "Sort variants by pilot number");
297 if(iter != sm_ClinGroupNameStrs.end()) {
306vector<string> tokens;
308 size_tnum_tokens = tokens.size();
311 for(
size_t i= 0;
i< num_tokens; ++
i) {
351 constobjects::CSeq_feat::TData&
data= feat.GetOriginalFeature().GetData();
352 if(
data.IsVariation()) {
354 constobjects::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 caseobjects::CPhenotype::eClinical_significance_non_pathogenic:
361 caseobjects::CPhenotype::eClinical_significance_pathogenic:
364 caseobjects::CPhenotype::eClinical_significance_probable_pathogenic:
367 caseobjects::CPhenotype::eClinical_significance_probable_non_pathogenic:
370 caseobjects::CPhenotype::eClinical_significance_unknown:
373 caseobjects::CPhenotype::eClinical_significance_untested:
376 caseobjects::CPhenotype::eClinical_significance_other:
407 static const stringkSorterName =
"clinical_assertion";
416 "Sort variants by clinical assertion");
441 if(iter != sm_SampleTypeNameStrs.end()) {
450vector<string> tokens;
452 size_tnum_tokens = tokens.size();
455 for(
size_t i= 0;
i< num_tokens; ++
i) {
483 constobjects::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 stringkSorterName =
"sampleset_type";
527 "Sort variants by sampleset type");
555 if(iter != sm_ValidationTypeNameStrs.end()) {
564vector<string> tokens;
566 size_tnum_tokens = tokens.size();
569 for(
int i= 0;
i< num_tokens; ++
i) {
596 if(feat.IsSetExts()) {
597 constobjects::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 stringkSorterName =
"validation_status";
647 "Sort variants by validation status");
671 if(iter != sm_ResolveStatusNameStrs.end()) {
680vector<string> tokens;
682 size_tnum_tokens = tokens.size();
685 for(
int i= 0;
i< num_tokens; ++
i) {
711 const string& status = feat.GetNamedQual(
"status");
729 static const stringkSorterName =
"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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