NCBI C++ ToolKit
Classes | Macros | Enumerations | Functions | Variables
wgsmaster.cpp File Reference
#include <ncbi_pch.hpp>
#include <objtools/data_loaders/genbank/impl/wgsmaster.hpp>
#include <objtools/data_loaders/genbank/blob_id.hpp>
#include <objtools/error_codes.hpp>
#include <objmgr/data_loader.hpp>
#include <objmgr/impl/tse_split_info.hpp>
#include <objmgr/impl/tse_chunk_info.hpp>
#include <objmgr/impl/tse_loadlock.hpp>
#include <objmgr/impl/bioseq_set_info.hpp>
#include <objmgr/impl/tse_assigner.hpp>
#include <objmgr/objmgr_exception.hpp>
#include <objects/general/general__.hpp>
+ Include dependency graph for wgsmaster.cpp:

Go to the source code of this file.

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Classes

class  CWGSBioseqUpdater_Base
 
class  CWGSBioseqUpdaterChunk
 
class  CWGSBioseqUpdaterDescr
 
class  CWGSMasterInfo
 
class  CWGSMasterChunkInfo
 
class  CWGSMasterDescrSetter
 

Macros

#define NCBI_USE_ERRCODE_X   Objtools_Rd_Process
 

Enumerations

enum  EDescrType { eDescrTypeDefault , eDescrTypeRefSeq }
 

Functions

static bool s_GoodLetters (CTempString s)
 
static bool s_GoodDigits (CTempString s)
 
static bool s_IsGoodDescr (const CSeqdesc &desc, int mask, const TUserObjectTypesSet &uo_types)
 
bool HasWGSMasterMark (const CTSE_Info &info)
 
CSeq_id_Handle GetWGSMasterSeq_id (const CSeq_id_Handle &idh)
 
EDescrType GetDescrType (const CSeq_id_Handle &master_seq_idh)
 
int GetForceDescrMask (EDescrType type)
 
int GetOptionalDescrMask (EDescrType type)
 
void AddMasterDescr (CBioseq_Info &seq, const CSeq_descr &src, EDescrType type)
 
bool s_HasMasterId (const CBioseq_Info &seq, const CSeq_id_Handle &master_idh)
 
CConstRef< CSeq_descrGetWGSMasterDescr (CDataLoader *loader, const CSeq_id_Handle &master_idh)
 

Variables

static const bool kAddMasterDescrToTSE = true
 
static const char kMasterDescrMark [] = "WithMasterDescr"
 
 BEGIN_LOCAL_NAMESPACE
 
static const int kForceDescrMask = ((1<<CSeqdesc::e_User))
 
static const int kRefSeqOptionalDescrMask
 
static const int kOptionalDescrMask
 
static const int kGoodDescrMask = kForceDescrMask | kRefSeqOptionalDescrMask | kOptionalDescrMask
 
 END_LOCAL_NAMESPACE
 

Macro Definition Documentation

◆ NCBI_USE_ERRCODE_X

#define NCBI_USE_ERRCODE_X   Objtools_Rd_Process

Definition at line 45 of file wgsmaster.cpp.

Enumeration Type Documentation

◆ EDescrType

enum EDescrType
Enumerator
eDescrTypeDefault 
eDescrTypeRefSeq 

Definition at line 266 of file wgsmaster.cpp.

Function Documentation

◆ AddMasterDescr()

void AddMasterDescr ( CBioseq_Info seq,
const CSeq_descr src,
EDescrType  type 
)

◆ GetDescrType()

EDescrType GetDescrType ( const CSeq_id_Handle master_seq_idh)
inline

◆ GetForceDescrMask()

int GetForceDescrMask ( EDescrType  type)

◆ GetOptionalDescrMask()

int GetOptionalDescrMask ( EDescrType  type)

Definition at line 287 of file wgsmaster.cpp.

References eDescrTypeRefSeq, kOptionalDescrMask, and kRefSeqOptionalDescrMask.

Referenced by AddMasterDescr().

◆ GetWGSMasterDescr()

CConstRef<CSeq_descr> GetWGSMasterDescr ( CDataLoader loader,
const CSeq_id_Handle master_idh 
)

◆ GetWGSMasterSeq_id()

CSeq_id_Handle GetWGSMasterSeq_id ( const CSeq_id_Handle idh)

◆ HasWGSMasterMark()

bool HasWGSMasterMark ( const CTSE_Info info)

◆ s_GoodDigits()

static bool s_GoodDigits ( CTempString  s)
static

Definition at line 78 of file wgsmaster.cpp.

References isdigit(), and ITERATE.

Referenced by GetWGSMasterSeq_id().

◆ s_GoodLetters()

static bool s_GoodLetters ( CTempString  s)
static

Definition at line 67 of file wgsmaster.cpp.

References isalpha(), and ITERATE.

Referenced by GetWGSMasterSeq_id().

◆ s_HasMasterId()

bool s_HasMasterId ( const CBioseq_Info seq,
const CSeq_id_Handle master_idh 
)

Definition at line 324 of file wgsmaster.cpp.

References CBioseq_Info::GetId(), GetWGSMasterSeq_id(), and ITERATE.

Referenced by CWGSBioseqUpdater_Base::HasMasterId().

◆ s_IsGoodDescr()

static bool s_IsGoodDescr ( const CSeqdesc desc,
int  mask,
const TUserObjectTypesSet uo_types 
)
static

Variable Documentation

◆ BEGIN_LOCAL_NAMESPACE

BEGIN_LOCAL_NAMESPACE

Definition at line 63 of file wgsmaster.cpp.

◆ END_LOCAL_NAMESPACE

END_LOCAL_NAMESPACE

Definition at line 550 of file wgsmaster.cpp.

◆ kAddMasterDescrToTSE

const bool kAddMasterDescrToTSE = true
static

Definition at line 51 of file wgsmaster.cpp.

Referenced by CWGSMasterSupport::AddWGSMaster().

◆ kForceDescrMask

const int kForceDescrMask = ((1<<CSeqdesc::e_User))
static

Definition at line 94 of file wgsmaster.cpp.

Referenced by GetForceDescrMask().

◆ kGoodDescrMask

◆ kMasterDescrMark

const char kMasterDescrMark[] = "WithMasterDescr"
static

◆ kOptionalDescrMask

const int kOptionalDescrMask
static
Initial value:
@ e_Embl
EMBL specific information.
Definition: Seqdesc_.hpp:127
@ e_Update_date
date of last update
Definition: Seqdesc_.hpp:129
@ e_Genbank
GenBank specific info.
Definition: Seqdesc_.hpp:121
@ e_Molinfo
info on the molecule and techniques
Definition: Seqdesc_.hpp:134
@ e_Create_date
date entry first created/released
Definition: Seqdesc_.hpp:128
@ e_Source
source of materials, includes Org-ref
Definition: Seqdesc_.hpp:133

Definition at line 99 of file wgsmaster.cpp.

Referenced by GetOptionalDescrMask().

◆ kRefSeqOptionalDescrMask

const int kRefSeqOptionalDescrMask
static
Initial value:
= ((1<<CSeqdesc::e_Pub) |
@ e_Pub
a reference to the publication
Definition: Seqdesc_.hpp:122
@ e_Comment
a more extensive comment
Definition: Seqdesc_.hpp:117

Definition at line 96 of file wgsmaster.cpp.

Referenced by GetForceDescrMask(), and GetOptionalDescrMask().

Modified on Sat Mar 02 10:55:18 2024 by modify_doxy.py rev. 669887