41 #ifndef OBJECTS_GENOMECOLL_GC_ASSEMBLYDESC_BASE_HPP
42 #define OBJECTS_GENOMECOLL_GC_ASSEMBLYDESC_BASE_HPP
53 #ifndef BEGIN_objects_SCOPE
54 # define BEGIN_objects_SCOPE BEGIN_SCOPE(objects)
55 # define END_objects_SCOPE END_SCOPE(objects)
95 eRelease_type_genbank = 1,
96 eRelease_type_refseq = 2
104 eRelease_status_new = 0,
105 eRelease_status_gpipe = 5,
106 eRelease_status_public = 10,
107 eRelease_status_suppressed = 15,
108 eRelease_status_hup = 100,
109 eRelease_status_withdrawn = 105
117 eRelease_level_major = 0,
118 eRelease_level_patch = 1,
119 eRelease_level_minor = 2,
120 eRelease_level_other = 255
137 typedef list< CRef< CSeq_annot > >
TAnnot;
166 e_submitter_organization
182 bool IsSetProjects(
void)
const;
189 bool CanGetProjects(
void)
const;
192 void ResetProjects(
void);
198 const TProjects& GetProjects(
void)
const;
214 bool IsSetName(
void)
const;
221 bool CanGetName(
void)
const;
224 void ResetName(
void);
230 const TName& GetName(
void)
const;
243 TName& SetName(
void);
252 bool IsSetSubmitter_name(
void)
const;
259 bool CanGetSubmitter_name(
void)
const;
262 void ResetSubmitter_name(
void);
290 bool IsSetDisplay_name(
void)
const;
297 bool CanGetDisplay_name(
void)
const;
300 void ResetDisplay_name(
void);
328 bool IsSetLong_name(
void)
const;
335 bool CanGetLong_name(
void)
const;
338 void ResetLong_name(
void);
366 bool IsSetFilesafe_name(
void)
const;
373 bool CanGetFilesafe_name(
void)
const;
376 void ResetFilesafe_name(
void);
404 bool IsSetWgs_acc_prefix(
void)
const;
411 bool CanGetWgs_acc_prefix(
void)
const;
414 void ResetWgs_acc_prefix(
void);
442 bool IsSetWgs_acc_number(
void)
const;
449 bool CanGetWgs_acc_number(
void)
const;
452 void ResetWgs_acc_number(
void);
479 bool IsSetRelease_type(
void)
const;
486 bool CanGetRelease_type(
void)
const;
489 void ResetRelease_type(
void);
516 bool IsSetRelease_status(
void)
const;
523 bool CanGetRelease_status(
void)
const;
526 void ResetRelease_status(
void);
555 bool IsSetAnnot(
void)
const;
562 bool CanGetAnnot(
void)
const;
565 void ResetAnnot(
void);
571 const TAnnot& GetAnnot(
void)
const;
587 bool IsSetSynonyms(
void)
const;
594 bool CanGetSynonyms(
void)
const;
597 void ResetSynonyms(
void);
603 const TSynonyms& GetSynonyms(
void)
const;
619 bool IsSetSubmitter_date(
void)
const;
626 bool CanGetSubmitter_date(
void)
const;
629 void ResetSubmitter_date(
void);
669 bool IsSetDescr(
void)
const;
676 bool CanGetDescr(
void)
const;
679 void ResetDescr(
void);
685 const TDescr& GetDescr(
void)
const;
708 bool IsSetPartial(
void)
const;
715 bool CanGetPartial(
void)
const;
718 void ResetPartial(
void);
747 bool IsSetCoverage(
void)
const;
754 bool CanGetCoverage(
void)
const;
757 void ResetCoverage(
void);
784 bool IsSetRelease_level(
void)
const;
791 bool CanGetRelease_level(
void)
const;
794 void ResetRelease_level(
void);
797 void SetDefaultRelease_level(
void);
826 bool IsSetSubmitter_organization(
void)
const;
833 bool CanGetSubmitter_organization(
void)
const;
836 void ResetSubmitter_organization(
void);
858 virtual void Reset(
void);
953 m_Name = std::forward<CGC_AssemblyDesc_Base::TName>(
value);
CGC_AssemblyDesc_Base –.
@Seq_descr.hpp User-defined methods of the data storage class.
Base class for all serializable objects.
static CStringUTF8 UnassignedStringUTF8(void)
static char UnassignedByte(void)
void ThrowUnassigned(TMemberIndex index) const
#define ENUM_METHOD_NAME(EnumName)
static string UnassignedString(void)
TSeqPos GetCoverage(const CSeq_loc &loc, CScope *scope)
Get number of unique bases in the location.
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_GENOME_COLLECTION_EXPORT
list< CRef< CSeq_annot > > TAnnot
bool CanGetSubmitter_date(void) const
Check if it is safe to call GetSubmitter_date method.
CStringUTF8 TSubmitter_organization
ERelease_level
release level: Most of releases are major
TPartial & SetPartial(void)
Assign a value to Partial data member.
const TName & GetName(void) const
Get the Name member data.
TCoverage & SetCoverage(void)
Assign a value to Coverage data member.
bool IsSetRelease_status(void) const
Check if a value has been assigned to Release_status data member.
const TSubmitter_name & GetSubmitter_name(void) const
Get the Submitter_name member data.
bool CanGetPartial(void) const
Check if it is safe to call GetPartial method.
void ResetPartial(void)
Reset Partial data member.
bool IsSetPartial(void) const
flag: is this assembly partial? **NOTE: not set = not known!! Check if a value has been assigned to P...
CGC_AssemblyDesc_Base(const CGC_AssemblyDesc_Base &)
TDisplay_name & SetDisplay_name(void)
Assign a value to Display_name data member.
bool CanGetName(void) const
Check if it is safe to call GetName method.
TCoverage GetCoverage(void) const
Get the Coverage member data.
bool CanGetRelease_type(void) const
Check if it is safe to call GetRelease_type method.
ERelease_type
release type: RefSeq / GenBank.
bool CanGetSubmitter_organization(void) const
Check if it is safe to call GetSubmitter_organization method.
TRelease_type GetRelease_type(void) const
Get the Release_type member data.
DECLARE_INTERNAL_TYPE_INFO()
TFilesafe_name & SetFilesafe_name(void)
Assign a value to Filesafe_name data member.
bool IsSetAnnot(void) const
in alt-loci units - contain alignment of this sequence to the primary unit Check if a value has been ...
TRelease_level GetRelease_level(void) const
Get the Release_level member data.
TName & SetName(void)
Assign a value to Name data member.
list< CRef< CGC_DbTagAlias > > m_Synonyms
bool IsSetProjects(void) const
project ID for this genome this is the ID for this asssembly and may reflect the submitter/source Che...
TPartial GetPartial(void) const
Get the Partial member data.
list< CRef< CGC_DbTagAlias > > TSynonyms
void ResetRelease_type(void)
Reset Release_type data member.
list< CRef< CSeq_annot > > m_Annot
const TSynonyms & GetSynonyms(void) const
Get the Synonyms member data.
void ResetWgs_acc_number(void)
Reset Wgs_acc_number data member.
bool CanGetDescr(void) const
Check if it is safe to call GetDescr method.
CGC_AssemblyDesc_Base & operator=(const CGC_AssemblyDesc_Base &)
const TDisplay_name & GetDisplay_name(void) const
Get the Display_name member data.
bool CanGetAnnot(void) const
Check if it is safe to call GetAnnot method.
const TFilesafe_name & GetFilesafe_name(void) const
Get the Filesafe_name member data.
const TLong_name & GetLong_name(void) const
Get the Long_name member data.
TRelease_status & SetRelease_status(void)
Assign a value to Release_status data member.
TAnnot & SetAnnot(void)
Assign a value to Annot data member.
bool IsSetFilesafe_name(void) const
Check if a value has been assigned to Filesafe_name data member.
bool CanGetDisplay_name(void) const
Check if it is safe to call GetDisplay_name method.
bool IsSetWgs_acc_number(void) const
Check if a value has been assigned to Wgs_acc_number data member.
CStringUTF8 m_Submitter_organization
bool CanGetRelease_status(void) const
Check if it is safe to call GetRelease_status method.
ERelease_status
release status (numeric values have gaps for possible additional states
TProjects & SetProjects(void)
Assign a value to Projects data member.
const TSubmitter_date & GetSubmitter_date(void) const
Get the Submitter_date member data.
TWgs_acc_number GetWgs_acc_number(void) const
Get the Wgs_acc_number member data.
bool CanGetRelease_level(void) const
Check if it is safe to call GetRelease_level method.
bool IsSetSubmitter_organization(void) const
organization which submitted this assembly.
TSubmitter_organization & SetSubmitter_organization(void)
Assign a value to Submitter_organization data member.
bool IsSetDescr(void) const
Various attributes assigned at this level: biosrc, comments, publications...
bool IsSetRelease_type(void) const
Check if a value has been assigned to Release_type data member.
bool CanGetFilesafe_name(void) const
Check if it is safe to call GetFilesafe_name method.
const TDescr & GetDescr(void) const
Get the Descr member data.
Tparent::CMemberIndex< E_memberIndex, 19 > TmemberIndex
void ResetRelease_status(void)
Reset Release_status data member.
bool CanGetWgs_acc_prefix(void) const
Check if it is safe to call GetWgs_acc_prefix method.
void ResetRelease_level(void)
Reset Release_level data member.
TLong_name & SetLong_name(void)
Assign a value to Long_name data member.
bool CanGetCoverage(void) const
Check if it is safe to call GetCoverage method.
bool IsSetSynonyms(void) const
Synonyms: Other releases of same assembly Check if a value has been assigned to Synonyms data member.
TRelease_type & SetRelease_type(void)
Assign a value to Release_type data member.
bool IsSetRelease_level(void) const
Check if a value has been assigned to Release_level data member.
TRelease_status GetRelease_status(void) const
Get the Release_status member data.
bool IsSetLong_name(void) const
Check if a value has been assigned to Long_name data member.
bool IsSetName(void) const
Names of the assembly Check if a value has been assigned to Name data member.
void SetDefaultRelease_level(void)
Assign default value to Release_level data member.
CRef< TSubmitter_date > m_Submitter_date
const TProjects & GetProjects(void) const
Get the Projects member data.
const TSubmitter_organization & GetSubmitter_organization(void) const
Get the Submitter_organization member data.
bool IsSetWgs_acc_prefix(void) const
Check if a value has been assigned to Wgs_acc_prefix data member.
bool IsSetSubmitter_name(void) const
Check if a value has been assigned to Submitter_name data member.
bool CanGetLong_name(void) const
Check if it is safe to call GetLong_name method.
void ResetCoverage(void)
Reset Coverage data member.
TWgs_acc_number & SetWgs_acc_number(void)
Assign a value to Wgs_acc_number data member.
const TWgs_acc_prefix & GetWgs_acc_prefix(void) const
Get the Wgs_acc_prefix member data.
TSynonyms & SetSynonyms(void)
Assign a value to Synonyms data member.
bool CanGetSynonyms(void) const
Check if it is safe to call GetSynonyms method.
const TAnnot & GetAnnot(void) const
Get the Annot member data.
TRelease_level & SetRelease_level(void)
Assign a value to Release_level data member.
bool CanGetProjects(void) const
Check if it is safe to call GetProjects method.
bool CanGetWgs_acc_number(void) const
Check if it is safe to call GetWgs_acc_number method.
list< CRef< CGC_Project > > TProjects
TWgs_acc_prefix & SetWgs_acc_prefix(void)
Assign a value to Wgs_acc_prefix data member.
TSubmitter_name & SetSubmitter_name(void)
Assign a value to Submitter_name data member.
list< CRef< CGC_Project > > m_Projects
bool IsSetDisplay_name(void) const
Check if a value has been assigned to Display_name data member.
bool IsSetSubmitter_date(void) const
Submitter release date Check if a value has been assigned to Submitter_date data member.
bool IsSetCoverage(void) const
level of coverage for this assembly **NOTE: not set = not known!! Check if a value has been assigned ...
bool CanGetSubmitter_name(void) const
Check if it is safe to call GetSubmitter_name method.
void SetPartial(CSeq_loc &loc, CRef< CSeq_feat > feat, CSeq_loc::TStrand strand, bool partial_start, bool partial_stop)