41 #ifndef OBJECTS_DOCSUM_SS_BASE_HPP
42 #define OBJECTS_DOCSUM_SS_BASE_HPP
52 #ifndef BEGIN_objects_SCOPE
53 # define BEGIN_objects_SCOPE BEGIN_SCOPE(objects)
54 # define END_objects_SCOPE END_SCOPE(objects)
105 eAttlist_subSnpClass_snp = 1,
106 eAttlist_subSnpClass_in_del = 2,
107 eAttlist_subSnpClass_heterozygous = 3,
108 eAttlist_subSnpClass_microsatellite = 4,
109 eAttlist_subSnpClass_named_locus = 5,
110 eAttlist_subSnpClass_no_variation = 6,
111 eAttlist_subSnpClass_mixed = 7,
112 eAttlist_subSnpClass_multinucleotide_polymorphism = 8
121 eAttlist_orient_forward = 1,
122 eAttlist_orient_reverse = 2
131 eAttlist_strand_top = 1,
132 eAttlist_strand_bottom = 2
139 eAttlist_molType_genomic = 1,
140 eAttlist_molType_cDNA = 2,
141 eAttlist_molType_mito = 3,
142 eAttlist_molType_chloro = 4,
143 eAttlist_molType_unknown = 5
152 eAttlist_methodClass_dHPLC = 1,
153 eAttlist_methodClass_hybridize = 2,
154 eAttlist_methodClass_computed = 3,
155 eAttlist_methodClass_sSCP = 4,
156 eAttlist_methodClass_other = 5,
157 eAttlist_methodClass_unknown = 6,
158 eAttlist_methodClass_rFLP = 7,
159 eAttlist_methodClass_sequence = 8
168 eAttlist_validated_by_submitter = 1,
169 eAttlist_validated_by_frequency = 2,
170 eAttlist_validated_by_cluster = 3
210 e_clinicalSignificance
225 bool IsSetSsId(
void)
const;
232 bool CanGetSsId(
void)
const;
235 void ResetSsId(
void);
241 TSsId GetSsId(
void)
const;
253 TSsId& SetSsId(
void);
263 bool IsSetHandle(
void)
const;
270 bool CanGetHandle(
void)
const;
273 void ResetHandle(
void);
279 const THandle& GetHandle(
void)
const;
302 bool IsSetBatchId(
void)
const;
309 bool CanGetBatchId(
void)
const;
312 void ResetBatchId(
void);
340 bool IsSetLocSnpId(
void)
const;
347 bool CanGetLocSnpId(
void)
const;
350 void ResetLocSnpId(
void);
356 const TLocSnpId& GetLocSnpId(
void)
const;
378 bool IsSetSubSnpClass(
void)
const;
385 bool CanGetSubSnpClass(
void)
const;
388 void ResetSubSnpClass(
void);
415 bool IsSetOrient(
void)
const;
422 bool CanGetOrient(
void)
const;
425 void ResetOrient(
void);
452 bool IsSetStrand(
void)
const;
459 bool CanGetStrand(
void)
const;
462 void ResetStrand(
void);
490 bool IsSetMolType(
void)
const;
497 bool CanGetMolType(
void)
const;
500 void ResetMolType(
void);
529 bool IsSetBuildId(
void)
const;
536 bool CanGetBuildId(
void)
const;
539 void ResetBuildId(
void);
566 bool IsSetMethodClass(
void)
const;
573 bool CanGetMethodClass(
void)
const;
576 void ResetMethodClass(
void);
603 bool IsSetValidated(
void)
const;
610 bool CanGetValidated(
void)
const;
613 void ResetValidated(
void);
642 bool IsSetLinkoutUrl(
void)
const;
649 bool CanGetLinkoutUrl(
void)
const;
652 void ResetLinkoutUrl(
void);
680 bool IsSetSsAlias(
void)
const;
687 bool CanGetSsAlias(
void)
const;
690 void ResetSsAlias(
void);
696 const TSsAlias& GetSsAlias(
void)
const;
730 bool IsSetAlleleOrigin(
void)
const;
737 bool CanGetAlleleOrigin(
void)
const;
740 void ResetAlleleOrigin(
void);
778 bool IsSetClinicalSignificance(
void)
const;
785 bool CanGetClinicalSignificance(
void)
const;
788 void ResetClinicalSignificance(
void);
879 bool IsSetSeq5(
void)
const;
886 bool CanGetSeq5(
void)
const;
889 void ResetSeq5(
void);
895 const TSeq5& GetSeq5(
void)
const;
908 TSeq5& SetSeq5(
void);
920 bool IsSetObserved(
void)
const;
927 bool CanGetObserved(
void)
const;
930 void ResetObserved(
void);
936 const TObserved& GetObserved(
void)
const;
960 bool IsSetSeq3(
void)
const;
967 bool CanGetSeq3(
void)
const;
970 void ResetSeq3(
void);
976 const TSeq3& GetSeq3(
void)
const;
989 TSeq3& SetSeq3(
void);
1012 e__allMandatory = 0,
1028 bool IsSetAttlist(
void)
const;
1035 bool CanGetAttlist(
void)
const;
1038 void ResetAttlist(
void);
1044 const TAttlist& GetAttlist(
void)
const;
1065 bool IsSetSequence(
void)
const;
1072 bool CanGetSequence(
void)
const;
1075 void ResetSequence(
void);
1096 virtual void Reset(
void);
1141 if (!CanGetSsId()) {
1175 return IsSetHandle();
1181 if (!CanGetHandle()) {
1197 m_Handle = std::forward<CSs_Base::C_Attlist::THandle>(
value);
1205 if (!IsSetHandle()) {
1222 return IsSetBatchId();
1235 if (!CanGetBatchId()) {
1252 if (!IsSetBatchId()) {
1269 return IsSetLocSnpId();
1275 if (!CanGetLocSnpId()) {
1291 m_LocSnpId = std::forward<CSs_Base::C_Attlist::TLocSnpId>(
value);
1299 if (!IsSetLocSnpId()) {
1316 return IsSetSubSnpClass();
1329 if (!CanGetSubSnpClass()) {
1332 return m_SubSnpClass;
1338 m_SubSnpClass =
value;
1346 if (!IsSetSubSnpClass()) {
1351 return m_SubSnpClass;
1363 return IsSetOrient();
1376 if (!CanGetOrient()) {
1393 if (!IsSetOrient()) {
1410 return IsSetStrand();
1423 if (!CanGetStrand()) {
1440 if (!IsSetStrand()) {
1457 return IsSetMolType();
1470 if (!CanGetMolType()) {
1487 if (!IsSetMolType()) {
1504 return IsSetBuildId();
1517 if (!CanGetBuildId()) {
1534 if (!IsSetBuildId()) {
1551 return IsSetMethodClass();
1564 if (!CanGetMethodClass()) {
1567 return m_MethodClass;
1573 m_MethodClass =
value;
1581 if (!IsSetMethodClass()) {
1586 return m_MethodClass;
1598 return IsSetValidated();
1611 if (!CanGetValidated()) {
1620 m_Validated =
value;
1628 if (!IsSetValidated()) {
1645 return IsSetLinkoutUrl();
1651 if (!CanGetLinkoutUrl()) {
1654 return m_LinkoutUrl;
1660 m_LinkoutUrl =
value;
1667 m_LinkoutUrl = std::forward<CSs_Base::C_Attlist::TLinkoutUrl>(
value);
1675 if (!IsSetLinkoutUrl()) {
1680 return m_LinkoutUrl;
1692 return IsSetSsAlias();
1698 if (!CanGetSsAlias()) {
1714 m_SsAlias = std::forward<CSs_Base::C_Attlist::TSsAlias>(
value);
1722 if (!IsSetSsAlias()) {
1739 return IsSetAlleleOrigin();
1752 if (!CanGetAlleleOrigin()) {
1755 return m_AlleleOrigin;
1761 m_AlleleOrigin =
value;
1769 if (!IsSetAlleleOrigin()) {
1774 return m_AlleleOrigin;
1786 return IsSetClinicalSignificance();
1792 if (!CanGetClinicalSignificance()) {
1795 return m_ClinicalSignificance;
1801 m_ClinicalSignificance =
value;
1808 m_ClinicalSignificance = std::forward<CSs_Base::C_Attlist::TClinicalSignificance>(
value);
1816 if (!IsSetClinicalSignificance()) {
1821 return m_ClinicalSignificance;
1839 if (!CanGetSeq5()) {
1855 m_Seq5 = std::forward<CSs_Base::C_Sequence::TSeq5>(
value);
1880 return IsSetObserved();
1886 if (!CanGetObserved()) {
1902 m_Observed = std::forward<CSs_Base::C_Sequence::TObserved>(
value);
1910 if (!IsSetObserved()) {
1933 if (!CanGetSeq3()) {
1949 m_Seq3 = std::forward<CSs_Base::C_Sequence::TSeq3>(
value);
Base class for all serializable objects.
data for an individual submission to dbSNP
SBlastSequence GetSequence(const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)
Retrieves a sequence using the object manager.
static char UnassignedByte(void)
void ThrowUnassigned(TMemberIndex index) const
#define ENUM_METHOD_NAME(EnumName)
static string UnassignedString(void)
ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)
Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...
uint32_t Uint4
4-byte (32-bit) unsigned integer
int64_t Int8
8-byte (64-bit) signed integer
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define NCBI_DOCSUM_EXPORT
TBatchId GetBatchId(void) const
Get the BatchId member data.
TClinicalSignificance & SetClinicalSignificance(void)
Assign a value to ClinicalSignificance data member.
EAttlist_subSnpClass m_SubSnpClass
bool CanGetAttlist(void) const
Check if it is safe to call GetAttlist method.
C_Attlist(const C_Attlist &)
TObserved & SetObserved(void)
Assign a value to Observed data member.
TSequence & SetSequence(void)
Assign a value to Sequence data member.
void SetHandle(THandle &&value)
TAlleleOrigin & SetAlleleOrigin(void)
Assign a value to AlleleOrigin data member.
void ResetBatchId(void)
Reset BatchId data member.
bool IsSetLinkoutUrl(void) const
append loc-snp-id to this base URL to construct a pointer to submitter data.
const TLinkoutUrl & GetLinkoutUrl(void) const
Get the LinkoutUrl member data.
EAttlist_subSnpClass
SubSNP classification by type of variation.
TStrand & SetStrand(void)
Assign a value to Strand data member.
TMethodClass & SetMethodClass(void)
Assign a value to MethodClass data member.
EAttlist_strand
strand is defined as TOP/BOTTOM by nature of flanking nucleotide sequence
bool CanGetClinicalSignificance(void) const
Check if it is safe to call GetClinicalSignificance method.
bool IsSetClinicalSignificance(void) const
<xsd:simpleType> <xsd:restriction base="xsd:string"> <xsd:enumeration value="unknown"/> <xsd:enumerat...
TBuildId GetBuildId(void) const
Get the BuildId member data.
void ResetSequence(void)
Reset Sequence data member.
C_Sequence(const C_Sequence &)
const TSeq3 & GetSeq3(void) const
Get the Seq3 member data.
DECLARE_INTERNAL_TYPE_INFO()
bool IsSetAttlist(void) const
Check if a value has been assigned to Attlist data member.
bool IsSetBatchId(void) const
dbSNP number for batch submission Check if a value has been assigned to BatchId data member.
TAlleleOrigin GetAlleleOrigin(void) const
Get the AlleleOrigin member data.
const TLocSnpId & GetLocSnpId(void) const
Get the LocSnpId member data.
bool CanGetOrient(void) const
Check if it is safe to call GetOrient method.
TOrient & SetOrient(void)
Assign a value to Orient data member.
TBuildId & SetBuildId(void)
Assign a value to BuildId data member.
CRef< TSequence > m_Sequence
const TSeq5 & GetSeq5(void) const
Get the Seq5 member data.
void SetHandle(const THandle &value)
Assign a value to Handle data member.
bool CanGetBuildId(void) const
Check if it is safe to call GetBuildId method.
EAttlist_orient
orientation of refsnp cluster members to refsnp cluster sequence
EAttlist_validated
subsnp has been experimentally validated by submitter
bool CanGetSequence(void) const
Check if it is safe to call GetSequence method.
bool CanGetValidated(void) const
Check if it is safe to call GetValidated method.
void ResetAlleleOrigin(void)
Reset AlleleOrigin data member.
bool IsSetHandle(void) const
Tag for the submitting laboratory Check if a value has been assigned to Handle data member.
TMolType & SetMolType(void)
Assign a value to MolType data member.
const TObserved & GetObserved(void) const
Get the Observed member data.
TValidated & SetValidated(void)
Assign a value to Validated data member.
C_Sequence & operator=(const C_Sequence &)
TLocSnpId & SetLocSnpId(void)
Assign a value to LocSnpId data member.
const TClinicalSignificance & GetClinicalSignificance(void) const
Get the ClinicalSignificance member data.
void ResetAttlist(void)
Reset Attlist data member.
TStrand GetStrand(void) const
Get the Strand member data.
bool CanGetBatchId(void) const
Check if it is safe to call GetBatchId method.
DECLARE_INTERNAL_TYPE_INFO()
Tparent::CMemberIndex< E_memberIndex, 3 > TmemberIndex
bool CanGetHandle(void) const
Check if it is safe to call GetHandle method.
Tparent::CMemberIndex< E_memberIndex, 16 > TmemberIndex
const THandle & GetHandle(void) const
Get the Handle member data.
void ResetOrient(void)
Reset Orient data member.
const TSsAlias & GetSsAlias(void) const
Get the SsAlias member data.
void ResetMolType(void)
Reset MolType data member.
CSs_Base & operator=(const CSs_Base &)
C_Attlist & operator=(const C_Attlist &)
void ResetSsId(void)
Reset SsId data member.
TBatchId & SetBatchId(void)
Assign a value to BatchId data member.
CRef< TAttlist > m_Attlist
bool CanGetAlleleOrigin(void) const
Check if it is safe to call GetAlleleOrigin method.
TAttlist & SetAttlist(void)
Assign a value to Attlist data member.
void ResetStrand(void)
Reset Strand data member.
bool IsSetSeq5(void) const
5' sequence that flanks the variation Check if a value has been assigned to Seq5 data member.
void ResetMethodClass(void)
Reset MethodClass data member.
bool IsSetSeq3(void) const
3' sequence that flanks the variation Check if a value has been assigned to Seq3 data member.
TSsId GetSsId(void) const
Get the SsId member data.
TSsId & SetSsId(void)
Assign a value to SsId data member.
bool IsSetAlleleOrigin(void) const
<xsd:simpleType> <xsd:restriction base="xsd:string"> <xsd:enumeration value="unknown"/> <xsd:enumerat...
bool CanGetSsId(void) const
Check if it is safe to call GetSsId method.
bool IsSetObserved(void) const
list of all nucleotide alleles observed in ss-list members, correcting for reverse complementation of...
bool CanGetLocSnpId(void) const
Check if it is safe to call GetLocSnpId method.
EAttlist_molType TMolType
TSubSnpClass & SetSubSnpClass(void)
Assign a value to SubSnpClass data member.
bool IsSetOrient(void) const
Check if a value has been assigned to Orient data member.
bool IsSetSsId(void) const
dbSNP accession number for submission Check if a value has been assigned to SsId data member.
EAttlist_molType m_MolType
EAttlist_validated m_Validated
EAttlist_methodClass
class of method used to assay for the variation
bool CanGetLinkoutUrl(void) const
Check if it is safe to call GetLinkoutUrl method.
EAttlist_subSnpClass TSubSnpClass
bool CanGetSeq5(void) const
Check if it is safe to call GetSeq5 method.
bool CanGetObserved(void) const
Check if it is safe to call GetObserved method.
TSsAlias & SetSsAlias(void)
Assign a value to SsAlias data member.
bool CanGetSsAlias(void) const
Check if it is safe to call GetSsAlias method.
TSubSnpClass GetSubSnpClass(void) const
Get the SubSnpClass member data.
bool IsSetSsAlias(void) const
Check if a value has been assigned to SsAlias data member.
bool CanGetSeq3(void) const
Check if it is safe to call GetSeq3 method.
void ResetValidated(void)
Reset Validated data member.
THandle & SetHandle(void)
Assign a value to Handle data member.
bool CanGetStrand(void) const
Check if it is safe to call GetStrand method.
EAttlist_methodClass TMethodClass
TMethodClass GetMethodClass(void) const
Get the MethodClass member data.
bool IsSetLocSnpId(void) const
submission (ss#) submitter ID Check if a value has been assigned to LocSnpId data member.
void ResetBuildId(void)
Reset BuildId data member.
bool IsSetMolType(void) const
moltype from Batch table Check if a value has been assigned to MolType data member.
TMolType GetMolType(void) const
Get the MolType member data.
bool IsSetSubSnpClass(void) const
Check if a value has been assigned to SubSnpClass data member.
bool IsSetStrand(void) const
Check if a value has been assigned to Strand data member.
string TClinicalSignificance
bool CanGetSubSnpClass(void) const
Check if it is safe to call GetSubSnpClass method.
bool IsSetBuildId(void) const
dbSNP build number when ss# was added to a refSNP (rs#) cluster Check if a value has been assigned to...
TValidated GetValidated(void) const
Get the Validated member data.
TLinkoutUrl & SetLinkoutUrl(void)
Assign a value to LinkoutUrl data member.
TSeq3 & SetSeq3(void)
Assign a value to Seq3 data member.
string m_ClinicalSignificance
bool IsSetValidated(void) const
Check if a value has been assigned to Validated data member.
CSs_Base(const CSs_Base &)
const TSequence & GetSequence(void) const
Get the Sequence member data.
EAttlist_validated TValidated
bool CanGetMethodClass(void) const
Check if it is safe to call GetMethodClass method.
const TAttlist & GetAttlist(void) const
Get the Attlist member data.
bool CanGetMolType(void) const
Check if it is safe to call GetMolType method.
TSeq5 & SetSeq5(void)
Assign a value to Seq5 data member.
void ResetSubSnpClass(void)
Reset SubSnpClass data member.
bool IsSetSequence(void) const
Check if a value has been assigned to Sequence data member.
EAttlist_methodClass m_MethodClass
bool IsSetMethodClass(void) const
Check if a value has been assigned to MethodClass data member.
Tparent::CMemberIndex< E_memberIndex, 4 > TmemberIndex
DECLARE_INTERNAL_TYPE_INFO()
TOrient GetOrient(void) const
Get the Orient member data.
const GenericPointer< typename T::ValueType > T2 value