NCBI C++ ToolKit
Classes | Typedefs | Enumerations | Functions | Variables
wgsread.hpp File Reference
#include <corelib/ncbistd.hpp>
#include <corelib/ncbimtx.hpp>
#include <util/range.hpp>
#include <util/rangemap.hpp>
#include <util/simple_buffer.hpp>
#include <serial/serialbase.hpp>
#include <sra/readers/sra/vdbread.hpp>
#include <objects/seq/seq_id_handle.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Seq_data.hpp>
#include <sra/readers/sra/snpread.hpp>
#include <sra/readers/sra/limited_resource_map.hpp>
#include <map>
#include <list>
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Classes

class  CAsnBinData
 
struct  SWGSDb_Defs
 
class  CWGSDb_Impl
 
struct  CWGSDb_Impl::SProtAccInfo
 
class  CWGSDb
 
class  CWGSSeqIterator
 
struct  CWGSSeqIterator::SVersionSelector
 
struct  CWGSSeqIterator::SWGSContigGapInfo
 
struct  CWGSSeqIterator::SSegment
 
class  CWGSScaffoldIterator
 
class  CWGSGiIterator
 
class  CWGSProteinIterator
 
class  CWGSFeatureIterator
 

Typedefs

typedef uint32_t NCBI_gb_state
 
typedef int32_t INSDC_coord_zero
 
typedef int32_t INSDC_coord_one
 
typedef uint32_t INSDC_coord_len
 
typedef uint8_t INSDC_quality_phred
 
typedef int16_t NCBI_WGS_component_props
 
typedef int32_t NCBI_WGS_gap_linkage
 
typedef uint8_t NCBI_WGS_seqtype
 
typedef uint8_t NCBI_WGS_feattype
 
typedef uint8_t NCBI_WGS_loc_strand
 
typedef int32_t NCBI_WGS_hash
 

Enumerations

enum  { NCBI_WGS_seqtype_contig = 0 , NCBI_WGS_seqtype_scaffold = 1 , NCBI_WGS_seqtype_protein = 2 , NCBI_WGS_seqtype_mrna = 3 }
 
enum  { NCBI_WGS_loc_strand_unknown = 0 , NCBI_WGS_loc_strand_plus = 1 , NCBI_WGS_loc_strand_minus = 2 , NCBI_WGS_loc_strand_both = 3 }
 
enum  {
  NCBI_gb_state_eWGSGenBankLive = 0 , NCBI_gb_state_eWGSGenBankSuppressed = 1 , NCBI_gb_state_eWGSGenBankReplaced = 2 , NCBI_gb_state_eWGSGenBankWithdrawn = 3 ,
  NCBI_gb_state_eWGSGenBankUnverified = 4 , NCBI_gb_state_eWGSGenBankMissing = 5 , NCBI_gb_state_eWGSGenBankMigrated = 6
}
 

Functions

 BEGIN_NAMESPACE (objects)
 
 DECLARE_SAFE_FLAGS (SWGSDb_Defs::EFlags)
 
 DECLARE_SAFE_FLAGS (CWGSDb_Impl::EGnlIdFlags)
 
 DECLARE_SAFE_FLAGS (CWGSDb_Impl::EAllowRowType)
 
 DECLARE_SAFE_FLAGS (CWGSSeqIterator::EInstSegmentFlags)
 
 DECLARE_SAFE_FLAGS (CWGSSeqIterator::EIncludeFlags)
 
 END_NAMESPACE (objects)
 

Variables

 BEGIN_NCBI_NAMESPACE
 
 END_NCBI_NAMESPACE
 

Typedef Documentation

◆ INSDC_coord_len

Definition at line 57 of file wgsread.hpp.

◆ INSDC_coord_one

Definition at line 56 of file wgsread.hpp.

◆ INSDC_coord_zero

Definition at line 55 of file wgsread.hpp.

◆ INSDC_quality_phred

Definition at line 58 of file wgsread.hpp.

◆ NCBI_gb_state

Definition at line 53 of file wgsread.hpp.

◆ NCBI_WGS_component_props

Definition at line 60 of file wgsread.hpp.

◆ NCBI_WGS_feattype

Definition at line 73 of file wgsread.hpp.

◆ NCBI_WGS_gap_linkage

Definition at line 61 of file wgsread.hpp.

◆ NCBI_WGS_hash

Definition at line 95 of file wgsread.hpp.

◆ NCBI_WGS_loc_strand

Definition at line 75 of file wgsread.hpp.

◆ NCBI_WGS_seqtype

Definition at line 64 of file wgsread.hpp.

Enumeration Type Documentation

◆ anonymous enum

anonymous enum
Enumerator
NCBI_WGS_seqtype_contig 
NCBI_WGS_seqtype_scaffold 
NCBI_WGS_seqtype_protein 
NCBI_WGS_seqtype_mrna 

Definition at line 65 of file wgsread.hpp.

◆ anonymous enum

anonymous enum
Enumerator
NCBI_WGS_loc_strand_unknown 
NCBI_WGS_loc_strand_plus 
NCBI_WGS_loc_strand_minus 
NCBI_WGS_loc_strand_both 

Definition at line 76 of file wgsread.hpp.

◆ anonymous enum

anonymous enum
Enumerator
NCBI_gb_state_eWGSGenBankLive 
NCBI_gb_state_eWGSGenBankSuppressed 
NCBI_gb_state_eWGSGenBankReplaced 
NCBI_gb_state_eWGSGenBankWithdrawn 
NCBI_gb_state_eWGSGenBankUnverified 
NCBI_gb_state_eWGSGenBankMissing 
NCBI_gb_state_eWGSGenBankMigrated 

Definition at line 85 of file wgsread.hpp.

Function Documentation

◆ BEGIN_NAMESPACE()

BEGIN_NAMESPACE ( objects  )

◆ DECLARE_SAFE_FLAGS() [1/5]

DECLARE_SAFE_FLAGS ( CWGSDb_Impl::EAllowRowType  )

◆ DECLARE_SAFE_FLAGS() [2/5]

DECLARE_SAFE_FLAGS ( CWGSDb_Impl::EGnlIdFlags  )

◆ DECLARE_SAFE_FLAGS() [3/5]

DECLARE_SAFE_FLAGS ( CWGSSeqIterator::EIncludeFlags  )

◆ DECLARE_SAFE_FLAGS() [4/5]

DECLARE_SAFE_FLAGS ( CWGSSeqIterator::EInstSegmentFlags  )

◆ DECLARE_SAFE_FLAGS() [5/5]

DECLARE_SAFE_FLAGS ( SWGSDb_Defs::EFlags  )

◆ END_NAMESPACE()

END_NAMESPACE ( objects  )

Variable Documentation

◆ BEGIN_NCBI_NAMESPACE

BEGIN_NCBI_NAMESPACE

Definition at line 97 of file wgsread.hpp.

◆ END_NCBI_NAMESPACE

END_NCBI_NAMESPACE

Definition at line 1603 of file wgsread.hpp.

Modified on Fri May 24 14:53:44 2024 by modify_doxy.py rev. 669887