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NCBI C++ ToolKit: include/objects/genomecoll/GC_AssemblyDesc_.hpp Source File

eRelease_type_genbank = 1,

eRelease_type_refseq = 2

eRelease_status_new = 0,

eRelease_status_gpipe = 5,

eRelease_status_public = 10,

eRelease_status_suppressed = 15,

eRelease_status_hup = 100,

eRelease_status_withdrawn = 105

eRelease_level_major = 0,

eRelease_level_patch = 1,

eRelease_level_minor = 2,

eRelease_level_other = 255

list< CRef< CSeq_annot > >

;

e_submitter_organization

IsSetProjects(

)

;

CanGetProjects(

)

;

ResetProjects(

);

& GetProjects(

)

;

IsSetName(

)

;

CanGetName(

)

;

ResetName(

);

& GetName(

)

;

& SetName(

);

IsSetSubmitter_name(

)

;

CanGetSubmitter_name(

)

;

ResetSubmitter_name(

);

IsSetDisplay_name(

)

;

CanGetDisplay_name(

)

;

ResetDisplay_name(

);

IsSetLong_name(

)

;

CanGetLong_name(

)

;

ResetLong_name(

);

& GetLong_name(

)

;

IsSetFilesafe_name(

)

;

CanGetFilesafe_name(

)

;

ResetFilesafe_name(

);

IsSetWgs_acc_prefix(

)

;

CanGetWgs_acc_prefix(

)

;

ResetWgs_acc_prefix(

);

IsSetWgs_acc_number(

)

;

CanGetWgs_acc_number(

)

;

ResetWgs_acc_number(

);

IsSetRelease_type(

)

;

CanGetRelease_type(

)

;

ResetRelease_type(

);

IsSetRelease_status(

)

;

CanGetRelease_status(

)

;

ResetRelease_status(

);

IsSetAnnot(

)

;

CanGetAnnot(

)

;

ResetAnnot(

);

& GetAnnot(

)

;

& SetAnnot(

);

IsSetSynonyms(

)

;

CanGetSynonyms(

)

;

ResetSynonyms(

);

& GetSynonyms(

)

;

IsSetSubmitter_date(

)

;

CanGetSubmitter_date(

)

;

ResetSubmitter_date(

);

IsSetDescr(

)

;

CanGetDescr(

)

;

ResetDescr(

);

& GetDescr(

)

;

& SetDescr(

);

IsSetPartial(

)

;

CanGetPartial(

)

;

ResetPartial(

);

IsSetCoverage(

)

;

CanGetCoverage(

)

;

ResetCoverage(

);

IsSetRelease_level(

)

;

CanGetRelease_level(

)

;

ResetRelease_level(

);

SetDefaultRelease_level(

);

IsSetSubmitter_organization(

)

;

CanGetSubmitter_organization(

)

;

ResetSubmitter_organization(

);

Reset(

);

= std::forward<CGC_AssemblyDesc_Base::TName>(

);

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.

const GenericPointer< typename T::ValueType > T2 value

void SetPartial(CSeq_loc &loc, CRef< CSeq_feat > feat, CSeq_loc::TStrand strand, bool partial_start, bool partial_stop)

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