NCBI C++ ToolKit
Typedefs | Enumerations | Functions | Variables
osg_resolve_base.cpp File Reference
#include <ncbi_pch.hpp>
#include "osg_resolve.hpp"
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/Textseq_id.hpp>
#include <objects/id2/id2__.hpp>
#include <objtools/pubseq_gateway/impl/cassandra/bioseq_info/record.hpp>
#include "pubseq_gateway_convert_utils.hpp"
#include "osg_connection.hpp"
#include "osg_getblob_base.hpp"
#include "insdc_utils.hpp"
#include "pubseq_gateway_logging.hpp"
+ Include dependency graph for osg_resolve_base.cpp:

Go to the source code of this file.

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Typedefs

typedef int TAllowSeqType
 

Enumerations

enum  EAlligSeqType { fAllow_contig = 1 , fAllow_scaffold = 2 , fAllow_protein = 4 }
 

Functions

 BEGIN_NAMESPACE (psg)
 
 BEGIN_NAMESPACE (osg)
 
static bool IsWGSGeneral (const CDbtag &dbtag)
 
static bool IsWGSAccession (const string &acc, const CTextseq_id &id, TAllowSeqType allow_seq_type)
 
static bool IsWGSProtAccession (const CTextseq_id &id)
 
static bool IsWGSAccession (const CTextseq_id &id)
 
 END_NAMESPACE (osg)
 
 END_NAMESPACE (psg)
 

Variables

 BEGIN_NCBI_NAMESPACE
 
static const char kSpecialId_label [] = "LABEL"
 
static const char kSpecialId_taxid [] = "TAXID"
 
static const char kSpecialId_hash [] = "HASH"
 
static const char kSpecialId_length [] = "Seq-inst.length"
 
static const char kSpecialId_type [] = "Seq-inst.mol"
 
static const size_t kTypePrefixLen = 4
 
static const size_t kNumLettersV1 = 4
 
static const size_t kNumLettersV2 = 6
 
static const size_t kVersionDigits = 2
 
static const size_t kPrefixLenV1 = kNumLettersV1 + kVersionDigits
 
static const size_t kPrefixLenV2 = kNumLettersV2 + kVersionDigits
 
static const size_t kMinRowDigitsV1 = 6
 
static const size_t kMaxRowDigitsV1 = 8
 
static const size_t kMinRowDigitsV2 = 7
 
static const size_t kMaxRowDigitsV2 = 9
 
static const size_t kMinProtAccLen = 8
 
static const size_t kMaxProtAccLen = 10
 
 END_NCBI_NAMESPACE
 

Typedef Documentation

◆ TAllowSeqType

typedef int TAllowSeqType

Definition at line 317 of file osg_resolve_base.cpp.

Enumeration Type Documentation

◆ EAlligSeqType

Enumerator
fAllow_contig 
fAllow_scaffold 
fAllow_protein 

Definition at line 312 of file osg_resolve_base.cpp.

Function Documentation

◆ BEGIN_NAMESPACE() [1/2]

BEGIN_NAMESPACE ( osg  )

◆ BEGIN_NAMESPACE() [2/2]

BEGIN_NAMESPACE ( psg  )

◆ END_NAMESPACE() [1/2]

END_NAMESPACE ( osg  )

◆ END_NAMESPACE() [2/2]

END_NAMESPACE ( psg  )

◆ IsWGSAccession() [1/2]

static bool IsWGSAccession ( const CTextseq_id id)
static

◆ IsWGSAccession() [2/2]

static bool IsWGSAccession ( const string acc,
const CTextseq_id id,
TAllowSeqType  allow_seq_type 
)
static

◆ IsWGSGeneral()

static bool IsWGSGeneral ( const CDbtag dbtag)
static

◆ IsWGSProtAccession()

static bool IsWGSProtAccession ( const CTextseq_id id)
static

Definition at line 393 of file osg_resolve_base.cpp.

References kMaxProtAccLen, and kMinProtAccLen.

Referenced by IsWGSAccession().

Variable Documentation

◆ BEGIN_NCBI_NAMESPACE

BEGIN_NCBI_NAMESPACE

Definition at line 48 of file osg_resolve_base.cpp.

◆ END_NCBI_NAMESPACE

END_NCBI_NAMESPACE

Definition at line 465 of file osg_resolve_base.cpp.

◆ kMaxProtAccLen

const size_t kMaxProtAccLen = 10
static

Definition at line 292 of file osg_resolve_base.cpp.

Referenced by IsWGSProtAccession().

◆ kMaxRowDigitsV1

const size_t kMaxRowDigitsV1 = 8
static

Definition at line 287 of file osg_resolve_base.cpp.

Referenced by IsWGSAccession().

◆ kMaxRowDigitsV2

const size_t kMaxRowDigitsV2 = 9
static

Definition at line 289 of file osg_resolve_base.cpp.

Referenced by IsWGSAccession().

◆ kMinProtAccLen

const size_t kMinProtAccLen = 8
static

Definition at line 291 of file osg_resolve_base.cpp.

Referenced by IsWGSProtAccession().

◆ kMinRowDigitsV1

const size_t kMinRowDigitsV1 = 6
static

Definition at line 286 of file osg_resolve_base.cpp.

Referenced by IsWGSAccession().

◆ kMinRowDigitsV2

const size_t kMinRowDigitsV2 = 7
static

Definition at line 288 of file osg_resolve_base.cpp.

◆ kNumLettersV1

const size_t kNumLettersV1 = 4
static

Definition at line 281 of file osg_resolve_base.cpp.

Referenced by IsWGSAccession(), and IsWGSGeneral().

◆ kNumLettersV2

const size_t kNumLettersV2 = 6
static

Definition at line 282 of file osg_resolve_base.cpp.

Referenced by IsWGSAccession(), and IsWGSGeneral().

◆ kPrefixLenV1

const size_t kPrefixLenV1 = kNumLettersV1 + kVersionDigits
static

Definition at line 284 of file osg_resolve_base.cpp.

Referenced by IsWGSAccession(), and IsWGSGeneral().

◆ kPrefixLenV2

const size_t kPrefixLenV2 = kNumLettersV2 + kVersionDigits
static

Definition at line 285 of file osg_resolve_base.cpp.

Referenced by IsWGSAccession(), and IsWGSGeneral().

◆ kSpecialId_hash

const char kSpecialId_hash[] = "HASH"
static

Definition at line 80 of file osg_resolve_base.cpp.

Referenced by CPSGS_OSGResolveBase::ProcessResolveReply().

◆ kSpecialId_label

const char kSpecialId_label[] = "LABEL"
static

Definition at line 78 of file osg_resolve_base.cpp.

Referenced by CPSGS_OSGResolveBase::ProcessResolveReply().

◆ kSpecialId_length

const char kSpecialId_length[] = "Seq-inst.length"
static

Definition at line 81 of file osg_resolve_base.cpp.

Referenced by CPSGS_OSGResolveBase::ProcessResolveReply().

◆ kSpecialId_taxid

const char kSpecialId_taxid[] = "TAXID"
static

Definition at line 79 of file osg_resolve_base.cpp.

Referenced by CPSGS_OSGResolveBase::ProcessResolveReply().

◆ kSpecialId_type

const char kSpecialId_type[] = "Seq-inst.mol"
static

Definition at line 82 of file osg_resolve_base.cpp.

Referenced by CPSGS_OSGResolveBase::ProcessResolveReply().

◆ kTypePrefixLen

const size_t kTypePrefixLen = 4
static

Definition at line 280 of file osg_resolve_base.cpp.

Referenced by IsWGSGeneral().

◆ kVersionDigits

const size_t kVersionDigits = 2
static

Definition at line 283 of file osg_resolve_base.cpp.

Referenced by IsWGSAccession().

Modified on Wed Feb 21 09:57:11 2024 by modify_doxy.py rev. 669887