41 #ifndef OBJECTS_GBSEQ_GBSEQ_BASE_HPP
42 #define OBJECTS_GBSEQ_GBSEQ_BASE_HPP
56 #ifndef BEGIN_objects_SCOPE
57 # define BEGIN_objects_SCOPE BEGIN_SCOPE(objects)
58 # define END_objects_SCOPE END_SCOPE(objects)
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);
779 bool IsSetProject(
void)
const;
786 bool CanGetProject(
void)
const;
789 void ResetProject(
void);
817 bool IsSetKeywords(
void)
const;
824 bool CanGetKeywords(
void)
const;
827 void ResetKeywords(
void);
833 const TKeywords& GetKeywords(
void)
const;
848 bool IsSetSegment(
void)
const;
855 bool CanGetSegment(
void)
const;
858 void ResetSegment(
void);
886 bool IsSetSource(
void)
const;
893 bool CanGetSource(
void)
const;
896 void ResetSource(
void);
902 const TSource& GetSource(
void)
const;
924 bool IsSetOrganism(
void)
const;
931 bool CanGetOrganism(
void)
const;
934 void ResetOrganism(
void);
940 const TOrganism& GetOrganism(
void)
const;
962 bool IsSetTaxonomy(
void)
const;
969 bool CanGetTaxonomy(
void)
const;
972 void ResetTaxonomy(
void);
978 const TTaxonomy& GetTaxonomy(
void)
const;
1000 bool IsSetReferences(
void)
const;
1007 bool CanGetReferences(
void)
const;
1010 void ResetReferences(
void);
1031 bool IsSetComment(
void)
const;
1038 bool CanGetComment(
void)
const;
1041 void ResetComment(
void);
1047 const TComment& GetComment(
void)
const;
1069 bool IsSetComment_set(
void)
const;
1076 bool CanGetComment_set(
void)
const;
1079 void ResetComment_set(
void);
1100 bool IsSetStruc_comments(
void)
const;
1107 bool CanGetStruc_comments(
void)
const;
1110 void ResetStruc_comments(
void);
1131 bool IsSetPrimary(
void)
const;
1138 bool CanGetPrimary(
void)
const;
1141 void ResetPrimary(
void);
1147 const TPrimary& GetPrimary(
void)
const;
1169 bool IsSetSource_db(
void)
const;
1176 bool CanGetSource_db(
void)
const;
1179 void ResetSource_db(
void);
1207 bool IsSetDatabase_reference(
void)
const;
1214 bool CanGetDatabase_reference(
void)
const;
1217 void ResetDatabase_reference(
void);
1245 bool IsSetFeature_table(
void)
const;
1252 bool CanGetFeature_table(
void)
const;
1255 void ResetFeature_table(
void);
1276 bool IsSetFeature_set(
void)
const;
1283 bool CanGetFeature_set(
void)
const;
1286 void ResetFeature_set(
void);
1308 bool IsSetSequence(
void)
const;
1315 bool CanGetSequence(
void)
const;
1318 void ResetSequence(
void);
1346 bool IsSetContig(
void)
const;
1353 bool CanGetContig(
void)
const;
1356 void ResetContig(
void);
1362 const TContig& GetContig(
void)
const;
1384 bool IsSetAlt_seq(
void)
const;
1391 bool CanGetAlt_seq(
void)
const;
1394 void ResetAlt_seq(
void);
1400 const TAlt_seq& GetAlt_seq(
void)
const;
1415 bool IsSetXrefs(
void)
const;
1422 bool CanGetXrefs(
void)
const;
1425 void ResetXrefs(
void);
1431 const TXrefs& GetXrefs(
void)
const;
1440 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_GBSEQ_EXPORT
bool IsSetStruc_comments(void) const
Check if a value has been assigned to Struc_comments data member.
const TAccession_version & GetAccession_version(void) const
Get the Accession_version member data.
bool IsSetTaxonomy(void) const
Check if a value has been assigned to Taxonomy data member.
TAlt_seq & SetAlt_seq(void)
Assign a value to Alt_seq data member.
list< CRef< CGBFeatureSet > > m_Feature_set
TOrganism & SetOrganism(void)
Assign a value to Organism data member.
TSource_db & SetSource_db(void)
Assign a value to Source_db data member.
TSequence & SetSequence(void)
Assign a value to Sequence data member.
bool CanGetDatabase_reference(void) const
Check if it is safe to call GetDatabase_reference method.
bool IsSetEntry_version(void) const
Check if a value has been assigned to Entry_version data member.
bool CanGetUpdate_release(void) const
Check if it is safe to call GetUpdate_release method.
string TAccession_version
bool CanGetMoltype(void) const
Check if it is safe to call GetMoltype method.
bool CanGetSecondary_accessions(void) const
Check if it is safe to call GetSecondary_accessions method.
string m_Database_reference
const TUpdate_release & GetUpdate_release(void) const
Get the Update_release member data.
string m_Primary_accession
Tparent::CMemberIndex< E_memberIndex, 36 > TmemberIndex
bool CanGetSource_db(void) const
Check if it is safe to call GetSource_db method.
bool CanGetPrimary_accession(void) const
Check if it is safe to call GetPrimary_accession method.
TComment & SetComment(void)
Assign a value to Comment data member.
TTopology & SetTopology(void)
Assign a value to Topology data member.
bool IsSetPrimary(void) const
Check if a value has been assigned to Primary data member.
TComment_set & SetComment_set(void)
Assign a value to Comment_set data member.
const TOther_seqids & GetOther_seqids(void) const
Get the Other_seqids member data.
list< CRef< CGBAltSeqData > > TAlt_seq
const TCreate_date & GetCreate_date(void) const
Get the Create_date member data.
bool CanGetTopology(void) const
Check if it is safe to call GetTopology method.
TEntry_version & SetEntry_version(void)
Assign a value to Entry_version data member.
bool IsSetCreate_release(void) const
Check if a value has been assigned to Create_release data member.
CGBSeq_Base & operator=(const CGBSeq_Base &)
bool CanGetCreate_date(void) const
Check if it is safe to call GetCreate_date method.
list< CRef< CGBFeature > > m_Feature_table
TUpdate_release & SetUpdate_release(void)
Assign a value to Update_release data member.
TFeature_set & SetFeature_set(void)
Assign a value to Feature_set data member.
const TDatabase_reference & GetDatabase_reference(void) const
Get the Database_reference member data.
const TProject & GetProject(void) const
Get the Project member data.
bool IsSetSecondary_accessions(void) const
Check if a value has been assigned to Secondary_accessions data member.
const TComment_set & GetComment_set(void) const
Get the Comment_set member data.
const TEntry_version & GetEntry_version(void) const
Get the Entry_version member data.
bool CanGetOther_seqids(void) const
Check if it is safe to call GetOther_seqids method.
bool CanGetStrandedness(void) const
Check if it is safe to call GetStrandedness method.
const TPrimary & GetPrimary(void) const
Get the Primary member data.
TReferences & SetReferences(void)
Assign a value to References data member.
bool IsSetSource(void) const
Check if a value has been assigned to Source data member.
TUpdate_date & SetUpdate_date(void)
Assign a value to Update_date data member.
TMoltype & SetMoltype(void)
Assign a value to Moltype data member.
TKeywords & SetKeywords(void)
Assign a value to Keywords data member.
bool IsSetKeywords(void) const
Check if a value has been assigned to Keywords data member.
list< CRef< CGBComment > > m_Comment_set
list< CRef< CGBAltSeqData > > m_Alt_seq
TLength GetLength(void) const
Get the Length member data.
TCreate_date & SetCreate_date(void)
Assign a value to Create_date data member.
bool IsSetUpdate_date(void) const
Check if a value has been assigned to Update_date data member.
bool IsSetTopology(void) const
Check if a value has been assigned to Topology data member.
list< CRef< CGBStrucComment > > TStruc_comments
list< CGBSecondary_accn > TSecondary_accessions
bool CanGetReferences(void) const
Check if it is safe to call GetReferences method.
bool IsSetAccession_version(void) const
Check if a value has been assigned to Accession_version data member.
const TSecondary_accessions & GetSecondary_accessions(void) const
Get the Secondary_accessions member data.
bool IsSetDefinition(void) const
Check if a value has been assigned to Definition data member.
TDatabase_reference & SetDatabase_reference(void)
Assign a value to Database_reference data member.
TLength & SetLength(void)
Assign a value to Length data member.
void ResetLength(void)
Reset Length data member.
bool IsSetFeature_table(void) const
Check if a value has been assigned to Feature_table data member.
list< CRef< CGBReference > > m_References
list< CRef< CGBComment > > TComment_set
bool CanGetOrganism(void) const
Check if it is safe to call GetOrganism method.
bool IsSetAlt_seq(void) const
Check if a value has been assigned to Alt_seq data member.
list< CGBKeyword > TKeywords
list< CRef< CGBStrucComment > > m_Struc_comments
list< CRef< CGBFeatureSet > > TFeature_set
TLocus & SetLocus(void)
Assign a value to Locus data member.
bool CanGetKeywords(void) const
Check if it is safe to call GetKeywords method.
bool CanGetLocus(void) const
Check if it is safe to call GetLocus method.
const TSegment & GetSegment(void) const
Get the Segment member data.
const TFeature_table & GetFeature_table(void) const
Get the Feature_table member data.
TContig & SetContig(void)
Assign a value to Contig data member.
TFeature_table & SetFeature_table(void)
Assign a value to Feature_table data member.
const TXrefs & GetXrefs(void) const
Get the Xrefs member data.
bool CanGetSegment(void) const
Check if it is safe to call GetSegment method.
bool CanGetTaxonomy(void) const
Check if it is safe to call GetTaxonomy method.
TSegment & SetSegment(void)
Assign a value to Segment data member.
const TFeature_set & GetFeature_set(void) const
Get the Feature_set member data.
list< CRef< CGBXref > > TXrefs
list< CGBKeyword > m_Keywords
TProject & SetProject(void)
Assign a value to Project data member.
const TAlt_seq & GetAlt_seq(void) const
Get the Alt_seq member data.
list< CGBSeqid > TOther_seqids
bool CanGetSequence(void) const
Check if it is safe to call GetSequence method.
bool IsSetOther_seqids(void) const
Check if a value has been assigned to Other_seqids data member.
bool IsSetSource_db(void) const
Check if a value has been assigned to Source_db data member.
bool IsSetSegment(void) const
Check if a value has been assigned to Segment data member.
const TSource_db & GetSource_db(void) const
Get the Source_db member data.
bool IsSetPrimary_accession(void) const
Check if a value has been assigned to Primary_accession data member.
bool IsSetSequence(void) const
Optional for contig, wgs, etc.
bool CanGetComment(void) const
Check if it is safe to call GetComment method.
list< CRef< CGBXref > > m_Xrefs
const TSource & GetSource(void) const
Get the Source member data.
bool IsSetFeature_set(void) const
Check if a value has been assigned to Feature_set data member.
TAccession_version & SetAccession_version(void)
Assign a value to Accession_version data member.
const TOrganism & GetOrganism(void) const
Get the Organism member data.
TSecondary_accessions & SetSecondary_accessions(void)
Assign a value to Secondary_accessions data member.
const TMoltype & GetMoltype(void) const
Get the Moltype member data.
const TStruc_comments & GetStruc_comments(void) const
Get the Struc_comments member data.
DECLARE_INTERNAL_TYPE_INFO()
const TLocus & GetLocus(void) const
Get the Locus member data.
CGBSeq_Base(const CGBSeq_Base &)
bool CanGetProject(void) const
Check if it is safe to call GetProject method.
TOther_seqids & SetOther_seqids(void)
Assign a value to Other_seqids data member.
bool CanGetPrimary(void) const
Check if it is safe to call GetPrimary method.
TPrimary_accession & SetPrimary_accession(void)
Assign a value to Primary_accession data member.
const TCreate_release & GetCreate_release(void) const
Get the Create_release member data.
TSource & SetSource(void)
Assign a value to Source data member.
string TDatabase_reference
TStruc_comments & SetStruc_comments(void)
Assign a value to Struc_comments data member.
TCreate_release & SetCreate_release(void)
Assign a value to Create_release data member.
bool CanGetDivision(void) const
Check if it is safe to call GetDivision method.
bool CanGetComment_set(void) const
Check if it is safe to call GetComment_set method.
const TReferences & GetReferences(void) const
Get the References member data.
TStrandedness & SetStrandedness(void)
Assign a value to Strandedness data member.
string m_Accession_version
string TPrimary_accession
bool IsSetReferences(void) const
Check if a value has been assigned to References data member.
bool IsSetDatabase_reference(void) const
Check if a value has been assigned to Database_reference data member.
list< CGBSeqid > m_Other_seqids
bool IsSetProject(void) const
Check if a value has been assigned to Project data member.
bool CanGetContig(void) const
Check if it is safe to call GetContig method.
bool CanGetEntry_version(void) const
Check if it is safe to call GetEntry_version method.
bool CanGetXrefs(void) const
Check if it is safe to call GetXrefs method.
bool IsSetCreate_date(void) const
Check if a value has been assigned to Create_date data member.
bool CanGetUpdate_date(void) const
Check if it is safe to call GetUpdate_date method.
TXrefs & SetXrefs(void)
Assign a value to Xrefs data member.
const TKeywords & GetKeywords(void) const
Get the Keywords member data.
const TTopology & GetTopology(void) const
Get the Topology member data.
TTaxonomy & SetTaxonomy(void)
Assign a value to Taxonomy data member.
bool IsSetLocus(void) const
Check if a value has been assigned to Locus data member.
bool CanGetFeature_table(void) const
Check if it is safe to call GetFeature_table method.
bool IsSetOrganism(void) const
Check if a value has been assigned to Organism data member.
list< CGBSecondary_accn > m_Secondary_accessions
TDivision & SetDivision(void)
Assign a value to Division data member.
list< CRef< CGBFeature > > TFeature_table
bool IsSetMoltype(void) const
Check if a value has been assigned to Moltype data member.
bool IsSetXrefs(void) const
Check if a value has been assigned to Xrefs data member.
const TTaxonomy & GetTaxonomy(void) const
Get the Taxonomy member data.
bool CanGetLength(void) const
Check if it is safe to call GetLength method.
TDefinition & SetDefinition(void)
Assign a value to Definition data member.
const TPrimary_accession & GetPrimary_accession(void) const
Get the Primary_accession member data.
const TComment & GetComment(void) const
Get the Comment member data.
bool IsSetLength(void) const
Check if a value has been assigned to Length data member.
const TSequence & GetSequence(void) const
Get the Sequence member data.
const TDefinition & GetDefinition(void) const
Get the Definition member data.
bool IsSetUpdate_release(void) const
Check if a value has been assigned to Update_release data member.
bool CanGetCreate_release(void) const
Check if it is safe to call GetCreate_release method.
list< CRef< CGBReference > > TReferences
const TDivision & GetDivision(void) const
Get the Division member data.
bool IsSetContig(void) const
Check if a value has been assigned to Contig data member.
const TUpdate_date & GetUpdate_date(void) const
Get the Update_date member data.
bool IsSetComment(void) const
Check if a value has been assigned to Comment data member.
bool CanGetSource(void) const
Check if it is safe to call GetSource method.
bool IsSetComment_set(void) const
Check if a value has been assigned to Comment_set data member.
bool IsSetDivision(void) const
Check if a value has been assigned to Division data member.
bool IsSetStrandedness(void) const
Check if a value has been assigned to Strandedness data member.
bool CanGetFeature_set(void) const
Check if it is safe to call GetFeature_set method.
bool CanGetAlt_seq(void) const
Check if it is safe to call GetAlt_seq method.
bool CanGetAccession_version(void) const
Check if it is safe to call GetAccession_version method.
bool CanGetStruc_comments(void) const
Check if it is safe to call GetStruc_comments method.
TPrimary & SetPrimary(void)
Assign a value to Primary data member.
const TContig & GetContig(void) const
Get the Contig member data.
const TStrandedness & GetStrandedness(void) const
Get the Strandedness member data.
bool CanGetDefinition(void) const
Check if it is safe to call GetDefinition method.
CProject * GetProject(wxTreeCtrl &treeCtrl, const CItem &item)