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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/User__object_8hpp_source.html below:

NCBI C++ ToolKit: include/objects/general/User_object.hpp Source File

37 #ifndef OBJECTS_GENERAL_USER_OBJECT_HPP 38 #define OBJECTS_GENERAL_USER_OBJECT_HPP 67

EParseField parse = eParse_String);

69

EParseField parse = eParse_String);

93  const string

& delim =

"."

,

96  const string

& delim =

"."

,

104  const string

& delim =

"."

,

108  const string

& delim =

"."

,

113  bool

HasField(

const string

&

str

,

114  const string

& delim =

"."

,

135

eCategory_Unknown = -1,

141

eExperiment_Unknown = -1,

146 

ECategory GetCategory(

void

)

const

;

149 

EExperiment GetExperimentType(

void

)

const

;

162

eObjectType_Unknown = -1,

172

eObjectType_Unreviewed

175

EObjectType GetObjectType()

const

;

176  void

SetObjectType(EObjectType obj_type);

177  bool IsDBLink

()

const

{

return

GetObjectType() == eObjectType_DBLink; }

179  bool IsOriginalId

()

const

{

return

GetObjectType() == eObjectType_OriginalId; }

180  bool IsUnverified

()

const

{

return

GetObjectType() == eObjectType_Unverified; }

182  bool IsCleanup

()

const

{

return

GetObjectType() == eObjectType_Cleanup; }

184  bool IsFileTrack

()

const

{

return

GetObjectType() == eObjectType_FileTrack; }

186  bool IsUnreviewed

()

const

{

return

GetObjectType() == eObjectType_Unreviewed; }

190  void

AddUnverifiedOrganism();

191  void

RemoveUnverifiedOrganism();

193  void

AddUnverifiedFeature();

194  void

RemoveUnverifiedFeature();

196  void

AddUnverifiedMisassembled();

197  void

RemoveUnverifiedMisassembled();

199  void

AddUnverifiedContaminant();

200  void

RemoveUnverifiedContaminant();

203  bool

IsUnreviewedUnannotated()

const

;

204  void

AddUnreviewedUnannotated();

205  void

RemoveUnreviewedUnannotated();

207  void

UpdateNcbiCleanup(

int version

);

213  void

SetFileTrackURL(

const string

& url);

214  void

SetFileTrackUploadId(

const string

& upload_id);

220

eRefGeneTrackingStatus_Error = -1,

228

eRefGeneTrackingStatus_WGS

231

ERefGeneTrackingStatus GetRefGeneTrackingStatus()

const

;

232  void

ResetRefGeneTrackingStatus();

236  return

(

val

!= eRefGeneTrackingStatus_NotSet &&

val

!= eRefGeneTrackingStatus_Error);

239  void

SetRefGeneTrackingGenomicSource(

const string

& genomic_source);

240  const string

& GetRefGeneTrackingGenomicSource()

const

;

241  void

ResetRefGeneTrackingGenomicSource();

244  void

SetRefGeneTrackingGenerated(

bool val

=

true

);

245  bool

GetRefGeneTrackingGenerated()

const

;

246  void

ResetRefGeneTrackingGenerated();

249  void

SetRefGeneTrackingCollaborator(

const string

& collaborator);

250  const string

& GetRefGeneTrackingCollaborator()

const

;

251  void

ResetRefGeneTrackingCollaborator();

256  void

SetRefGeneTrackingCollaboratorURL(

const string

& collaborator_url);

257  const string

& GetRefGeneTrackingCollaboratorURL()

const

;

258  void

ResetRefGeneTrackingCollaboratorURL();

273  switch

(GetErrCode()) {

274  case

eUserFieldWithoutLabel:

return "User field without label"

;

275  case

eBadUserFieldData:

return "Unexpected data type"

;

292

m_Accession(accession),

305  const string

&

GetName

()

const

{

return

m_Name; }

314  bool IsEmpty

()

const

{

return

!(IsSetAccession() || IsSetComment() ||

315

IsSetName() || IsSetGI() ||

316

IsSetFrom() || IsSetTo()); }

339  void

ResetRefGeneTrackingIdenticalTo();

343  void

SetRefGeneTrackingAssembly(

const

TRefGeneTrackingAccessions& acc_list);

344

TRefGeneTrackingAccessions GetRefGeneTrackingAssembly()

const

;

345  void

ResetRefGeneTrackingAssembly();

353  bool

x_IsUnverifiedType(

const string

&

val

)

const

;

354  bool

x_IsUnverifiedType(

const string

&

val

,

const CUser_field

& field)

const

;

355  void

x_AddUnverifiedType(

const string

&

val

);

356  void

x_RemoveUnverifiedType(

const string

&

val

);

358  bool

x_IsUnreviewedType(

const string

&

val

)

const

;

359  bool

x_IsUnreviewedType(

const string

&

val

,

const CUser_field

& field)

const

;

360  void

x_AddUnreviewedType(

const string

&

val

);

361  void

x_RemoveUnreviewedType(

const string

&

val

);

364  void

x_SetRefGeneTrackingField(

const string

& field_name,

const string

&

value

);

365  const string

& x_GetRefGeneTrackingField(

const string

& field_name)

const

;

@ eBoth

Both preliminary and traceback stages.

CRefGeneTrackingAccession(const CRefGeneTrackingAccession &cpy)=delete

Prohibit copy constructor and assignment operator.

CRefGeneTrackingAccession & operator=(const CRefGeneTrackingAccession &value)=delete

bool IsSetComment() const

CRefGeneTrackingAccession(const string &accession, TGi gi=ZERO_GI, TSeqPos from=kInvalidSeqPos, TSeqPos to=kInvalidSeqPos, const string &comment=kEmptyStr, const string &acc_name=kEmptyStr)

const string & GetName() const

const string & GetComment() const

CRefGeneTrackingAccession()

~CRefGeneTrackingAccession()

const string & GetAccession() const

bool IsSetAccession() const

virtual const char * GetErrCodeString() const override

Get error code interpreted as text.

NCBI_EXCEPTION_DEFAULT(CRefGeneTrackingException, CException)

**** User-object ********************************************** * * a general object for a user defin...

@ eRefGeneTrackingStatus_INFERRED

@ eRefGeneTrackingStatus_VALIDATED

@ eRefGeneTrackingStatus_PREDICTED

@ eRefGeneTrackingStatus_NotSet

@ eRefGeneTrackingStatus_PROVISIONAL

@ eRefGeneTrackingStatus_PIPELINE

@ eRefGeneTrackingStatus_REVIEWED

bool IsRefGeneTracking() const

ECategory

enums for implicit typing of user objects

bool IsSetRefGeneTrackingIdenticalTo() const

bool IsSetRefGeneTrackingGenomicSource() const

@ eObjectType_RefGeneTracking

@ eObjectType_StructuredComment

@ eObjectType_AutodefOptions

@ eObjectType_ValidationSuppression

bool IsOriginalId() const

bool IsSetRefGeneTrackingCollaboratorURL() const

bool IsValidationSuppression() const

vector< CConstRef< CRefGeneTrackingAccession > > TRefGeneTrackingAccessions

bool IsAutodefOptions() const

bool IsSetRefGeneTrackingStatus() const

CUser_object_Base Tparent

CUser_object(const CUser_object &value)

Prohibit copy constructor and assignment operator.

ELabelContent

enum controlling what to return for a label this mirrors a request inside of feature::GetLabel()

EExperiment

sub-category experiment

bool IsUnverified() const

CUser_object(void)

constructor

bool IsSetRefGeneTrackingCollaborator() const

EParseField

how to interpret the value in the AddField() conversion functions below.

@ eParse_String

Add string even if all numbers.

bool IsUnreviewed() const

bool IsSetRefGeneTrackingAssembly() const

bool IsStructuredComment() const

CUser_object & operator=(const CUser_object &value)

static const char * str(char *buf, int n)

void SetField(objects::CUser_object &user, const string &field_name, const string &val)

unsigned int TSeqPos

Type for sequence locations and lengths.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

EErrCode

Error types that an application can generate.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

string GetLabel(const CSeq_id &id)

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.

ECase

Which type of string comparison.

@ eCase

Case sensitive compare.

#define NCBI_GENERAL_EXPORT

static const char label[]

const string version

version string

const GenericPointer< typename T::ValueType > T2 value

bool IsUnverifiedMisassembled(const CBioseq &seq)

bool IsUnverifiedOrganism(const CBioseq &seq)

bool IsUnverifiedContaminant(const CBioseq &seq)

bool IsUnverifiedFeature(const CBioseq &seq)

static void SetRefGeneTrackingStatus(CRef< CSeq_entry > entry, string status)

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