#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 } |
Variables | |
| BEGIN_NCBI_NAMESPACE | |
| END_NCBI_NAMESPACE | |
Typedef Documentation
◆ INSDC_coord_len
| typedef uint32_t INSDC_coord_len |
Definition at line 57 of file wgsread.hpp.
◆ INSDC_coord_one
| typedef int32_t INSDC_coord_one |
Definition at line 56 of file wgsread.hpp.
◆ INSDC_coord_zero
| typedef int32_t INSDC_coord_zero |
Definition at line 55 of file wgsread.hpp.
◆ INSDC_quality_phred
| typedef uint8_t INSDC_quality_phred |
Definition at line 58 of file wgsread.hpp.
◆ NCBI_gb_state
| typedef uint32_t NCBI_gb_state |
Definition at line 53 of file wgsread.hpp.
◆ NCBI_WGS_component_props
| typedef int16_t NCBI_WGS_component_props |
Definition at line 60 of file wgsread.hpp.
◆ NCBI_WGS_feattype
| typedef uint8_t NCBI_WGS_feattype |
Definition at line 73 of file wgsread.hpp.
◆ NCBI_WGS_gap_linkage
| typedef int32_t NCBI_WGS_gap_linkage |
Definition at line 61 of file wgsread.hpp.
◆ NCBI_WGS_hash
| typedef int32_t NCBI_WGS_hash |
Definition at line 95 of file wgsread.hpp.
◆ NCBI_WGS_loc_strand
| typedef uint8_t NCBI_WGS_loc_strand |
Definition at line 75 of file wgsread.hpp.
◆ NCBI_WGS_seqtype
| typedef uint8_t 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 |
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.
