#include <ncbi_pch.hpp>
#include <gui/widgets/seq_graphic/dbvar_feature_sorter.hpp>
#include <gui/utils/track_info.hpp>
#include <objects/seqfeat/Variation_ref.hpp>
#include <objects/seqfeat/Phenotype.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/general/Object_id.hpp>
#include <objmgr/mapped_feat.hpp>
#include <util/static_map.hpp>

Include dependency graph for dbvar_feature_sorter.cpp:

Go to the SVN repository for this file.

Typedefs
typedef SStaticPair< CDbvarQualitySorter::EGroup, const char * >	TQuaGroupNameStr
	CDbvarQualitySorter implementation. More...

typedef CStaticArrayMap< CDbvarQualitySorter::EGroup, string >	TQuaGroupNameMap

typedef SStaticPair< CDbvarPilotSorter::EGroup, const char * >	TPilotGroupNameStr
	CDbvarPilotSorter implementation. More...

typedef CStaticArrayMap< CDbvarPilotSorter::EGroup, string >	TPilotGroupNameMap

typedef SStaticPair< CDbvarClinicalAsstSorter::EGroup, const char * >	TClinGroupNameStr
	CDbvarClinicalAsstSorter implementation. More...

typedef CStaticArrayMap< CDbvarClinicalAsstSorter::EGroup, string >	TClinGroupNameMap

typedef SStaticPair< CDbvarSamplesetTypeSorter::EGroup, const char * >	TSampleTypeNameStr
	CDbvarSamplesetTypeSorter implementation. More...

typedef CStaticArrayMap< CDbvarSamplesetTypeSorter::EGroup, string >	TSampleTypeNameMap

typedef SStaticPair< CDbvarValidationSorter::EGroup, const char * >	TValidationTypeNameStr
	CDbvarValidationSorter implementation. More...

typedef CStaticArrayMap< CDbvarValidationSorter::EGroup, string >	TValidationTypeNameMap

typedef SStaticPair< CGRCStatusSorter::EGroup, const char * >	TResolveStatusNameStr
	CGRCStatusSorter implementation. More...

typedef CStaticArrayMap< CGRCStatusSorter::EGroup, string >	TResolveStatusNameMap

Functions
	DEFINE_STATIC_ARRAY_MAP (TQuaGroupNameMap, sm_QuaGroupNameStrs, s_QuaGroupNameStrs)

static const string &	s_QuaGroupIdxToName (int idx)

	DEFINE_STATIC_ARRAY_MAP (TPilotGroupNameMap, sm_PilotGroupNameStrs, s_PilotGroupNameStrs)

static const string &	s_PilotGroupIdxToName (int idx)

	DEFINE_STATIC_ARRAY_MAP (TClinGroupNameMap, sm_ClinGroupNameStrs, s_ClinGroupNameStrs)

static const string &	s_ClinGroupIdxToName (int idx)

	DEFINE_STATIC_ARRAY_MAP (TSampleTypeNameMap, sm_SampleTypeNameStrs, s_SampleTypeNameStrs)

static const string &	s_SampleTypeIdxToName (int idx)

	DEFINE_STATIC_ARRAY_MAP (TValidationTypeNameMap, sm_ValidationTypeNameStrs, s_ValidationTypeNameStrs)

static const string &	s_ValidationTypeIdxToName (int idx)

	DEFINE_STATIC_ARRAY_MAP (TResolveStatusNameMap, sm_ResolveStatusNameStrs, s_ResolveStatusNameStrs)

static const string &	s_ResolveStatusIdxToName (int idx)

Typedef Documentation

◆ TClinGroupNameMap

typedef CStaticArrayMap<CDbvarClinicalAsstSorter::EGroup, string> TClinGroupNameMap

Definition at line 290 of file dbvar_feature_sorter.cpp.

◆ TClinGroupNameStr

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

CDbvarClinicalAsstSorter implementation.

sort group index to group name

Definition at line 278 of file dbvar_feature_sorter.cpp.

◆ TPilotGroupNameMap

typedef CStaticArrayMap<CDbvarPilotSorter::EGroup, string> TPilotGroupNameMap

Definition at line 159 of file dbvar_feature_sorter.cpp.

◆ TPilotGroupNameStr

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

CDbvarPilotSorter implementation.

sort group index to group name

Definition at line 147 of file dbvar_feature_sorter.cpp.

◆ TQuaGroupNameMap

typedef CStaticArrayMap<CDbvarQualitySorter::EGroup, string> TQuaGroupNameMap

Definition at line 58 of file dbvar_feature_sorter.cpp.

◆ TQuaGroupNameStr

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

CDbvarQualitySorter implementation.

sort group index to group name

Definition at line 51 of file dbvar_feature_sorter.cpp.

◆ TResolveStatusNameMap

typedef CStaticArrayMap<CGRCStatusSorter::EGroup, string> TResolveStatusNameMap

Definition at line 664 of file dbvar_feature_sorter.cpp.

◆ TResolveStatusNameStr

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

CGRCStatusSorter implementation.

sort group index to group name

Definition at line 657 of file dbvar_feature_sorter.cpp.

◆ TSampleTypeNameMap

typedef CStaticArrayMap<CDbvarSamplesetTypeSorter::EGroup, string> TSampleTypeNameMap

Definition at line 434 of file dbvar_feature_sorter.cpp.

◆ TSampleTypeNameStr

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

CDbvarSamplesetTypeSorter implementation.

sort group index to group name

Definition at line 425 of file dbvar_feature_sorter.cpp.

◆ TValidationTypeNameMap

typedef CStaticArrayMap<CDbvarValidationSorter::EGroup, string> TValidationTypeNameMap

Definition at line 548 of file dbvar_feature_sorter.cpp.

◆ TValidationTypeNameStr

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

CDbvarValidationSorter implementation.

sort group index to group name

Definition at line 536 of file dbvar_feature_sorter.cpp.

Function Documentation

◆ DEFINE_STATIC_ARRAY_MAP() [1/6]

DEFINE_STATIC_ARRAY_MAP	(	TClinGroupNameMap	,
		sm_ClinGroupNameStrs	,
		s_ClinGroupNameStrs
	)

◆ DEFINE_STATIC_ARRAY_MAP() [2/6]

DEFINE_STATIC_ARRAY_MAP	(	TPilotGroupNameMap	,
		sm_PilotGroupNameStrs	,
		s_PilotGroupNameStrs
	)

◆ DEFINE_STATIC_ARRAY_MAP() [3/6]

DEFINE_STATIC_ARRAY_MAP	(	TQuaGroupNameMap	,
		sm_QuaGroupNameStrs	,
		s_QuaGroupNameStrs
	)

◆ DEFINE_STATIC_ARRAY_MAP() [4/6]

DEFINE_STATIC_ARRAY_MAP	(	TResolveStatusNameMap	,
		sm_ResolveStatusNameStrs	,
		s_ResolveStatusNameStrs
	)

◆ DEFINE_STATIC_ARRAY_MAP() [5/6]

DEFINE_STATIC_ARRAY_MAP	(	TSampleTypeNameMap	,
		sm_SampleTypeNameStrs	,
		s_SampleTypeNameStrs
	)

◆ DEFINE_STATIC_ARRAY_MAP() [6/6]

DEFINE_STATIC_ARRAY_MAP	(	TValidationTypeNameMap	,
		sm_ValidationTypeNameStrs	,
		s_ValidationTypeNameStrs
	)

◆ s_ClinGroupIdxToName()

static const string& s_ClinGroupIdxToName ( int idx )

static

Definition at line 293 of file dbvar_feature_sorter.cpp.

References kEmptyStr.

Referenced by CDbvarClinicalAsstSorter::GroupIdxToName().

◆ s_PilotGroupIdxToName()

static const string& s_PilotGroupIdxToName ( int idx )

static

Definition at line 162 of file dbvar_feature_sorter.cpp.

References kEmptyStr.

Referenced by CDbvarPilotSorter::GroupIdxToName().

◆ s_QuaGroupIdxToName()

static const string& s_QuaGroupIdxToName ( int idx )

static

Definition at line 61 of file dbvar_feature_sorter.cpp.

References kEmptyStr.

Referenced by CDbvarQualitySorter::GroupIdxToName().

◆ s_ResolveStatusIdxToName()

static const string& s_ResolveStatusIdxToName ( int idx )

static

Definition at line 667 of file dbvar_feature_sorter.cpp.

References kEmptyStr.

Referenced by CGRCStatusSorter::GroupIdxToName().

◆ s_SampleTypeIdxToName()

static const string& s_SampleTypeIdxToName ( int idx )

static

Definition at line 437 of file dbvar_feature_sorter.cpp.

References kEmptyStr.

Referenced by CDbvarSamplesetTypeSorter::GroupIdxToName().

◆ s_ValidationTypeIdxToName()

static const string& s_ValidationTypeIdxToName ( int idx )

static

Definition at line 551 of file dbvar_feature_sorter.cpp.

References kEmptyStr.

Referenced by CDbvarValidationSorter::CDbvarValidationSorter(), CDbvarValidationSorter::GetGroupIdx(), and CDbvarValidationSorter::GroupIdxToName().

Variable Documentation

◆ s_ClinGroupNameStrs

const TClinGroupNameStr s_ClinGroupNameStrs[]

static

Initial value:

= {
    { CDbvarClinicalAsstSorter::eBenign, "Benign" },
    { CDbvarClinicalAsstSorter::ePathogenic, "Pathogenic" },
    { CDbvarClinicalAsstSorter::eLikelyPathogenic, "Likely Pathogenic" },
    { CDbvarClinicalAsstSorter::eLikelyBenign, "Likely Benign" },
    { CDbvarClinicalAsstSorter::eLikelyUnknown, "Likely Unknown" },
    { CDbvarClinicalAsstSorter::eNotTested, "Not Tested" },
    { CDbvarClinicalAsstSorter::eOther, "Other" },
}

Definition at line 279 of file dbvar_feature_sorter.cpp.

◆ s_PilotGroupNameStrs

const TPilotGroupNameStr s_PilotGroupNameStrs[]

static

Initial value:

= {
    { CDbvarPilotSorter::ePilot1, "Pilot1" },
    { CDbvarPilotSorter::ePilot2, "Pilot2" },
    { CDbvarPilotSorter::ePilot3, "Pilot3" },
    { CDbvarPilotSorter::ePilot4, "Pilot4" },
    { CDbvarPilotSorter::ePilot5, "Pilot5" },
    { CDbvarPilotSorter::eNotSet, "Pilot Not Set" },
    { CDbvarPilotSorter::eOther, "Others" },
}

Definition at line 148 of file dbvar_feature_sorter.cpp.

◆ s_QuaGroupNameStrs

const TQuaGroupNameStr s_QuaGroupNameStrs[]

static

Initial value:

= {
    { CDbvarQualitySorter::eHigh, "Variant Quality: High" },
    { CDbvarQualitySorter::eLow, "Variant Quality: Low" },
}

Definition at line 52 of file dbvar_feature_sorter.cpp.

◆ s_ResolveStatusNameStrs

const TResolveStatusNameStr s_ResolveStatusNameStrs[]

static

Initial value:

= {
    { CGRCStatusSorter::eResolved, "Resolved" },
    { CGRCStatusSorter::eOther, "Not resolved" },
}

Definition at line 658 of file dbvar_feature_sorter.cpp.

◆ s_SampleTypeNameStrs

const TSampleTypeNameStr s_SampleTypeNameStrs[]

static

Initial value:

= {
    { CDbvarSamplesetTypeSorter::eCase, "Sampleset: Case" },
    { CDbvarSamplesetTypeSorter::eControl, "Sampleset: Control" },
    { CDbvarSamplesetTypeSorter::eNotSet, "Sampleset: Not set" },
    { CDbvarSamplesetTypeSorter::eOther, "Sampleset: Other" },
}

Definition at line 426 of file dbvar_feature_sorter.cpp.

◆ s_ValidationTypeNameStrs

const TValidationTypeNameStr s_ValidationTypeNameStrs[]

static

Initial value:

= {
    { CDbvarValidationSorter::eSameSample_DiffPlatform, "validated in this sample using another platform" },
    { CDbvarValidationSorter::eDiffSample_DiffPlatform, "validated in a different sample using another platform" },
    { CDbvarValidationSorter::eDiffSample_SamePlatform, "seen in other samples from submitting lab using this platform" },
    { CDbvarValidationSorter::eSeenInPlubic, "seen in public data set" },
    { CDbvarValidationSorter::eNovel, "novel" },
    { CDbvarValidationSorter::eNotAssessed, "not assessed" },
    { CDbvarValidationSorter::eOther, "other" },
}

Definition at line 537 of file dbvar_feature_sorter.cpp.

Variables
static const TQuaGroupNameStr	s_QuaGroupNameStrs []

static const TPilotGroupNameStr	s_PilotGroupNameStrs []

static const TClinGroupNameStr	s_ClinGroupNameStrs []

static const TSampleTypeNameStr	s_SampleTypeNameStrs []

static const TValidationTypeNameStr	s_ValidationTypeNameStrs []

static const TResolveStatusNameStr	s_ResolveStatusNameStrs []

Typedefs

Functions

Variables

Typedef Documentation

◆ TClinGroupNameMap

◆ TClinGroupNameStr

◆ TPilotGroupNameMap

◆ TPilotGroupNameStr

◆ TQuaGroupNameMap

◆ TQuaGroupNameStr

◆ TResolveStatusNameMap

◆ TResolveStatusNameStr

◆ TSampleTypeNameMap

◆ TSampleTypeNameStr

◆ TValidationTypeNameMap

◆ TValidationTypeNameStr

Function Documentation

◆ DEFINE_STATIC_ARRAY_MAP() [1/6]

◆ DEFINE_STATIC_ARRAY_MAP() [2/6]

◆ DEFINE_STATIC_ARRAY_MAP() [3/6]

◆ DEFINE_STATIC_ARRAY_MAP() [4/6]

◆ DEFINE_STATIC_ARRAY_MAP() [5/6]

◆ DEFINE_STATIC_ARRAY_MAP() [6/6]

◆ s_ClinGroupIdxToName()

◆ s_PilotGroupIdxToName()

◆ s_QuaGroupIdxToName()

◆ s_ResolveStatusIdxToName()

◆ s_SampleTypeIdxToName()

◆ s_ValidationTypeIdxToName()

Variable Documentation

◆ s_ClinGroupNameStrs

◆ s_PilotGroupNameStrs

◆ s_QuaGroupNameStrs

◆ s_ResolveStatusNameStrs

◆ s_SampleTypeNameStrs

◆ s_ValidationTypeNameStrs