41 #ifndef OBJECTS_INSDSEQ_INSDSEQ_BASE_HPP
42 #define OBJECTS_INSDSEQ_INSDSEQ_BASE_HPP
56 #ifndef BEGIN_objects_SCOPE
57 # define BEGIN_objects_SCOPE BEGIN_SCOPE(objects)
58 # define END_objects_SCOPE END_SCOPE(objects)
133 typedef list< CRef< CINSDXref > >
TXrefs;
153 e_secondary_accessions,
166 e_database_reference,
186 bool IsSetLocus(
void)
const;
193 bool CanGetLocus(
void)
const;
196 void ResetLocus(
void);
202 const TLocus& GetLocus(
void)
const;
224 bool IsSetLength(
void)
const;
231 bool CanGetLength(
void)
const;
234 void ResetLength(
void);
261 bool IsSetStrandedness(
void)
const;
268 bool CanGetStrandedness(
void)
const;
271 void ResetStrandedness(
void);
299 bool IsSetMoltype(
void)
const;
306 bool CanGetMoltype(
void)
const;
309 void ResetMoltype(
void);
315 const TMoltype& GetMoltype(
void)
const;
337 bool IsSetTopology(
void)
const;
344 bool CanGetTopology(
void)
const;
347 void ResetTopology(
void);
353 const TTopology& GetTopology(
void)
const;
375 bool IsSetDivision(
void)
const;
382 bool CanGetDivision(
void)
const;
385 void ResetDivision(
void);
391 const TDivision& GetDivision(
void)
const;
413 bool IsSetUpdate_date(
void)
const;
420 bool CanGetUpdate_date(
void)
const;
423 void ResetUpdate_date(
void);
451 bool IsSetCreate_date(
void)
const;
458 bool CanGetCreate_date(
void)
const;
461 void ResetCreate_date(
void);
489 bool IsSetUpdate_release(
void)
const;
496 bool CanGetUpdate_release(
void)
const;
499 void ResetUpdate_release(
void);
527 bool IsSetCreate_release(
void)
const;
534 bool CanGetCreate_release(
void)
const;
537 void ResetCreate_release(
void);
565 bool IsSetDefinition(
void)
const;
572 bool CanGetDefinition(
void)
const;
575 void ResetDefinition(
void);
603 bool IsSetPrimary_accession(
void)
const;
610 bool CanGetPrimary_accession(
void)
const;
613 void ResetPrimary_accession(
void);
641 bool IsSetEntry_version(
void)
const;
648 bool CanGetEntry_version(
void)
const;
651 void ResetEntry_version(
void);
679 bool IsSetAccession_version(
void)
const;
686 bool CanGetAccession_version(
void)
const;
689 void ResetAccession_version(
void);
717 bool IsSetOther_seqids(
void)
const;
724 bool CanGetOther_seqids(
void)
const;
727 void ResetOther_seqids(
void);
748 bool IsSetSecondary_accessions(
void)
const;
755 bool CanGetSecondary_accessions(
void)
const;
758 void ResetSecondary_accessions(
void);
781 bool IsSetProject(
void)
const;
788 bool CanGetProject(
void)
const;
791 void ResetProject(
void);
819 bool IsSetKeywords(
void)
const;
826 bool CanGetKeywords(
void)
const;
829 void ResetKeywords(
void);
835 const TKeywords& GetKeywords(
void)
const;
850 bool IsSetSegment(
void)
const;
857 bool CanGetSegment(
void)
const;
860 void ResetSegment(
void);
888 bool IsSetSource(
void)
const;
895 bool CanGetSource(
void)
const;
898 void ResetSource(
void);
904 const TSource& GetSource(
void)
const;
926 bool IsSetOrganism(
void)
const;
933 bool CanGetOrganism(
void)
const;
936 void ResetOrganism(
void);
942 const TOrganism& GetOrganism(
void)
const;
964 bool IsSetTaxonomy(
void)
const;
971 bool CanGetTaxonomy(
void)
const;
974 void ResetTaxonomy(
void);
980 const TTaxonomy& GetTaxonomy(
void)
const;
1002 bool IsSetReferences(
void)
const;
1009 bool CanGetReferences(
void)
const;
1012 void ResetReferences(
void);
1033 bool IsSetComment(
void)
const;
1040 bool CanGetComment(
void)
const;
1043 void ResetComment(
void);
1049 const TComment& GetComment(
void)
const;
1071 bool IsSetComment_set(
void)
const;
1078 bool CanGetComment_set(
void)
const;
1081 void ResetComment_set(
void);
1102 bool IsSetStruc_comments(
void)
const;
1109 bool CanGetStruc_comments(
void)
const;
1112 void ResetStruc_comments(
void);
1133 bool IsSetPrimary(
void)
const;
1140 bool CanGetPrimary(
void)
const;
1143 void ResetPrimary(
void);
1149 const TPrimary& GetPrimary(
void)
const;
1171 bool IsSetSource_db(
void)
const;
1178 bool CanGetSource_db(
void)
const;
1181 void ResetSource_db(
void);
1209 bool IsSetDatabase_reference(
void)
const;
1216 bool CanGetDatabase_reference(
void)
const;
1219 void ResetDatabase_reference(
void);
1247 bool IsSetFeature_table(
void)
const;
1254 bool CanGetFeature_table(
void)
const;
1257 void ResetFeature_table(
void);
1278 bool IsSetFeature_set(
void)
const;
1285 bool CanGetFeature_set(
void)
const;
1288 void ResetFeature_set(
void);
1310 bool IsSetSequence(
void)
const;
1317 bool CanGetSequence(
void)
const;
1320 void ResetSequence(
void);
1348 bool IsSetContig(
void)
const;
1355 bool CanGetContig(
void)
const;
1358 void ResetContig(
void);
1364 const TContig& GetContig(
void)
const;
1386 bool IsSetAlt_seq(
void)
const;
1393 bool CanGetAlt_seq(
void)
const;
1396 void ResetAlt_seq(
void);
1402 const TAlt_seq& GetAlt_seq(
void)
const;
1422 bool IsSetXrefs(
void)
const;
1429 bool CanGetXrefs(
void)
const;
1432 void ResetXrefs(
void);
1438 const TXrefs& GetXrefs(
void)
const;
1447 virtual void Reset(
void);
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
Base class for all serializable objects.
static void GetSegment(char *str, IndexblkPtr entry)
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.
unsigned int TSeqPos
Type for sequence locations and lengths.
static char UnassignedByte(void)
void ThrowUnassigned(TMemberIndex index) const
static string UnassignedString(void)
TSeqPos GetLength(const CSeq_id &id, CScope *scope)
Get sequence length if scope not null, else return max possible TSeqPos.
uint32_t Uint4
4-byte (32-bit) unsigned integer
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define NCBI_INSDSEQ_EXPORT
TSegment & SetSegment(void)
Assign a value to Segment data member.
bool IsSetEntry_version(void) const
Check if a value has been assigned to Entry_version data member.
TDivision & SetDivision(void)
Assign a value to Division data member.
bool CanGetSource_db(void) const
Check if it is safe to call GetSource_db method.
const TComment & GetComment(void) const
Get the Comment member data.
Tparent::CMemberIndex< E_memberIndex, 36 > TmemberIndex
TTaxonomy & SetTaxonomy(void)
Assign a value to Taxonomy data member.
bool IsSetDatabase_reference(void) const
Check if a value has been assigned to Database_reference data member.
TKeywords & SetKeywords(void)
Assign a value to Keywords data member.
TXrefs & SetXrefs(void)
Assign a value to Xrefs data member.
const TCreate_date & GetCreate_date(void) const
Get the Create_date member data.
TDatabase_reference & SetDatabase_reference(void)
Assign a value to Database_reference data member.
bool IsSetContig(void) const
Check if a value has been assigned to Contig data member.
bool CanGetAccession_version(void) const
Check if it is safe to call GetAccession_version method.
bool CanGetPrimary(void) const
Check if it is safe to call GetPrimary method.
bool CanGetComment(void) const
Check if it is safe to call GetComment method.
const TReferences & GetReferences(void) const
Get the References member data.
bool CanGetReferences(void) const
Check if it is safe to call GetReferences method.
const TSecondary_accessions & GetSecondary_accessions(void) const
Get the Secondary_accessions member data.
bool CanGetSegment(void) const
Check if it is safe to call GetSegment method.
bool IsSetAlt_seq(void) const
Check if a value has been assigned to Alt_seq data member.
bool IsSetPrimary_accession(void) const
Check if a value has been assigned to Primary_accession data member.
bool IsSetSource_db(void) const
Check if a value has been assigned to Source_db data member.
string TDatabase_reference
bool IsSetKeywords(void) const
Check if a value has been assigned to Keywords data member.
const TUpdate_date & GetUpdate_date(void) const
Get the Update_date member data.
list< CRef< CINSDComment > > TComment_set
list< CRef< CINSDComment > > m_Comment_set
bool IsSetComment_set(void) const
Check if a value has been assigned to Comment_set data member.
string m_Database_reference
bool IsSetLocus(void) const
Check if a value has been assigned to Locus data member.
const TUpdate_release & GetUpdate_release(void) const
Get the Update_release member data.
TCreate_release & SetCreate_release(void)
Assign a value to Create_release data member.
string m_Accession_version
list< CINSDSecondary_accn > TSecondary_accessions
bool IsSetMoltype(void) const
Check if a value has been assigned to Moltype data member.
const TFeature_table & GetFeature_table(void) const
Get the Feature_table member data.
list< CRef< CINSDFeature > > m_Feature_table
bool IsSetDivision(void) const
Check if a value has been assigned to Division data member.
const TEntry_version & GetEntry_version(void) const
Get the Entry_version member data.
list< CRef< CINSDXref > > TXrefs
bool CanGetPrimary_accession(void) const
Check if it is safe to call GetPrimary_accession method.
bool IsSetTaxonomy(void) const
Check if a value has been assigned to Taxonomy data member.
const TCreate_release & GetCreate_release(void) const
Get the Create_release member data.
bool CanGetDivision(void) const
Check if it is safe to call GetDivision method.
bool CanGetDefinition(void) const
Check if it is safe to call GetDefinition method.
bool CanGetEntry_version(void) const
Check if it is safe to call GetEntry_version method.
const TPrimary_accession & GetPrimary_accession(void) const
Get the Primary_accession member data.
bool IsSetSource(void) const
Check if a value has been assigned to Source data member.
const TOrganism & GetOrganism(void) const
Get the Organism member data.
bool IsSetReferences(void) const
Check if a value has been assigned to References data member.
const TSegment & GetSegment(void) const
Get the Segment member data.
bool CanGetSource(void) const
Check if it is safe to call GetSource method.
bool CanGetSequence(void) const
Check if it is safe to call GetSequence method.
const TTaxonomy & GetTaxonomy(void) const
Get the Taxonomy member data.
TOrganism & SetOrganism(void)
Assign a value to Organism data member.
list< CINSDSecondary_accn > m_Secondary_accessions
bool CanGetXrefs(void) const
Check if it is safe to call GetXrefs method.
TAlt_seq & SetAlt_seq(void)
Assign a value to Alt_seq data member.
bool IsSetStruc_comments(void) const
Check if a value has been assigned to Struc_comments data member.
const TComment_set & GetComment_set(void) const
Get the Comment_set member data.
TSecondary_accessions & SetSecondary_accessions(void)
Assign a value to Secondary_accessions data member.
TLength GetLength(void) const
Get the Length member data.
list< CINSDSeqid > m_Other_seqids
bool CanGetMoltype(void) const
Check if it is safe to call GetMoltype method.
const TMoltype & GetMoltype(void) const
Get the Moltype member data.
CINSDSeq_Base & operator=(const CINSDSeq_Base &)
bool IsSetProject(void) const
INSDSeq_project has been deprecated in favor of INSDSeq_xrefs .
const TDatabase_reference & GetDatabase_reference(void) const
Get the Database_reference member data.
bool IsSetCreate_date(void) const
Check if a value has been assigned to Create_date data member.
DECLARE_INTERNAL_TYPE_INFO()
bool CanGetStrandedness(void) const
Check if it is safe to call GetStrandedness method.
TPrimary & SetPrimary(void)
Assign a value to Primary data member.
bool CanGetContig(void) const
Check if it is safe to call GetContig method.
bool CanGetUpdate_date(void) const
Check if it is safe to call GetUpdate_date method.
const TContig & GetContig(void) const
Get the Contig member data.
TLength & SetLength(void)
Assign a value to Length data member.
list< CRef< CINSDXref > > m_Xrefs
TMoltype & SetMoltype(void)
Assign a value to Moltype data member.
bool CanGetLength(void) const
Check if it is safe to call GetLength method.
const TLocus & GetLocus(void) const
Get the Locus member data.
bool CanGetUpdate_release(void) const
Check if it is safe to call GetUpdate_release method.
const TPrimary & GetPrimary(void) const
Get the Primary member data.
bool IsSetFeature_set(void) const
Check if a value has been assigned to Feature_set data member.
const TXrefs & GetXrefs(void) const
Get the Xrefs member data.
bool IsSetComment(void) const
Check if a value has been assigned to Comment data member.
TFeature_table & SetFeature_table(void)
Assign a value to Feature_table data member.
TOther_seqids & SetOther_seqids(void)
Assign a value to Other_seqids data member.
list< CRef< CINSDReference > > m_References
TSource & SetSource(void)
Assign a value to Source data member.
bool CanGetProject(void) const
Check if it is safe to call GetProject method.
const TSource & GetSource(void) const
Get the Source member data.
const TSequence & GetSequence(void) const
Get the Sequence member data.
bool IsSetOrganism(void) const
Check if a value has been assigned to Organism data member.
bool IsSetFeature_table(void) const
Check if a value has been assigned to Feature_table data member.
TAccession_version & SetAccession_version(void)
Assign a value to Accession_version data member.
bool CanGetLocus(void) const
Check if it is safe to call GetLocus method.
list< CINSDKeyword > m_Keywords
const TStruc_comments & GetStruc_comments(void) const
Get the Struc_comments member data.
TCreate_date & SetCreate_date(void)
Assign a value to Create_date data member.
string m_Primary_accession
string TPrimary_accession
list< CRef< CINSDStrucComment > > TStruc_comments
TContig & SetContig(void)
Assign a value to Contig data member.
TPrimary_accession & SetPrimary_accession(void)
Assign a value to Primary_accession data member.
TLocus & SetLocus(void)
Assign a value to Locus data member.
bool IsSetSequence(void) const
Optional for contig, wgs, etc.
list< CRef< CINSDFeatureSet > > m_Feature_set
bool IsSetDefinition(void) const
Check if a value has been assigned to Definition data member.
TUpdate_date & SetUpdate_date(void)
Assign a value to Update_date data member.
bool IsSetXrefs(void) const
INSDSeq_xrefs provides cross-references from a sequence record to other database resources.
bool CanGetFeature_set(void) const
Check if it is safe to call GetFeature_set method.
bool IsSetLength(void) const
Check if a value has been assigned to Length data member.
bool CanGetOrganism(void) const
Check if it is safe to call GetOrganism method.
const TFeature_set & GetFeature_set(void) const
Get the Feature_set member data.
const TAccession_version & GetAccession_version(void) const
Get the Accession_version member data.
list< CRef< CINSDFeature > > TFeature_table
const TDivision & GetDivision(void) const
Get the Division member data.
bool CanGetFeature_table(void) const
Check if it is safe to call GetFeature_table method.
bool IsSetUpdate_release(void) const
Check if a value has been assigned to Update_release data member.
bool IsSetSecondary_accessions(void) const
Check if a value has been assigned to Secondary_accessions data member.
const TAlt_seq & GetAlt_seq(void) const
Get the Alt_seq member data.
TComment_set & SetComment_set(void)
Assign a value to Comment_set data member.
bool CanGetCreate_date(void) const
Check if it is safe to call GetCreate_date method.
const TStrandedness & GetStrandedness(void) const
Get the Strandedness member data.
list< CINSDKeyword > TKeywords
const TTopology & GetTopology(void) const
Get the Topology member data.
bool IsSetTopology(void) const
Check if a value has been assigned to Topology data member.
TUpdate_release & SetUpdate_release(void)
Assign a value to Update_release data member.
bool CanGetOther_seqids(void) const
Check if it is safe to call GetOther_seqids method.
string TAccession_version
bool CanGetAlt_seq(void) const
Check if it is safe to call GetAlt_seq method.
list< CRef< CINSDAltSeqData > > TAlt_seq
const TSource_db & GetSource_db(void) const
Get the Source_db member data.
TComment & SetComment(void)
Assign a value to Comment data member.
bool IsSetUpdate_date(void) const
Check if a value has been assigned to Update_date data member.
bool CanGetStruc_comments(void) const
Check if it is safe to call GetStruc_comments method.
TStrandedness & SetStrandedness(void)
Assign a value to Strandedness data member.
list< CINSDSeqid > TOther_seqids
TSource_db & SetSource_db(void)
Assign a value to Source_db data member.
bool IsSetStrandedness(void) const
Check if a value has been assigned to Strandedness data member.
void ResetLength(void)
Reset Length data member.
bool CanGetTopology(void) const
Check if it is safe to call GetTopology method.
bool CanGetKeywords(void) const
Check if it is safe to call GetKeywords method.
bool IsSetCreate_release(void) const
Check if a value has been assigned to Create_release data member.
bool CanGetSecondary_accessions(void) const
Check if it is safe to call GetSecondary_accessions method.
CINSDSeq_Base(const CINSDSeq_Base &)
list< CRef< CINSDAltSeqData > > m_Alt_seq
list< CRef< CINSDFeatureSet > > TFeature_set
bool CanGetDatabase_reference(void) const
Check if it is safe to call GetDatabase_reference method.
bool IsSetSegment(void) const
Check if a value has been assigned to Segment data member.
const TDefinition & GetDefinition(void) const
Get the Definition member data.
TTopology & SetTopology(void)
Assign a value to Topology data member.
list< CRef< CINSDReference > > TReferences
TDefinition & SetDefinition(void)
Assign a value to Definition data member.
TFeature_set & SetFeature_set(void)
Assign a value to Feature_set data member.
bool CanGetComment_set(void) const
Check if it is safe to call GetComment_set method.
const TKeywords & GetKeywords(void) const
Get the Keywords member data.
TStruc_comments & SetStruc_comments(void)
Assign a value to Struc_comments data member.
bool CanGetTaxonomy(void) const
Check if it is safe to call GetTaxonomy method.
bool CanGetCreate_release(void) const
Check if it is safe to call GetCreate_release method.
bool IsSetPrimary(void) const
Check if a value has been assigned to Primary data member.
TProject & SetProject(void)
Assign a value to Project data member.
TEntry_version & SetEntry_version(void)
Assign a value to Entry_version data member.
bool IsSetOther_seqids(void) const
Check if a value has been assigned to Other_seqids data member.
TSequence & SetSequence(void)
Assign a value to Sequence data member.
bool IsSetAccession_version(void) const
Check if a value has been assigned to Accession_version data member.
TReferences & SetReferences(void)
Assign a value to References data member.
const TOther_seqids & GetOther_seqids(void) const
Get the Other_seqids member data.
const TProject & GetProject(void) const
Get the Project member data.
list< CRef< CINSDStrucComment > > m_Struc_comments
CProject * GetProject(wxTreeCtrl &treeCtrl, const CItem &item)