NCBI C++ ToolKit
Classes | Typedefs | Functions | Variables
sub_cache_create.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/ncbiargs.hpp>
#include <corelib/request_ctx.hpp>
#include <corelib/ncbifile.hpp>
#include <corelib/ncbistr.hpp>
#include <corelib/ncbitime.hpp>
#include <corelib/ncbi_signal.hpp>
#include <corelib/ncbi_process.hpp>
#include <objtools/data_loaders/asn_cache/asn_cache.hpp>
#include <objtools/data_loaders/asn_cache/file_names.hpp>
#include <objtools/data_loaders/asn_cache/chunk_file.hpp>
#include <objtools/data_loaders/asn_cache/seq_id_chunk_file.hpp>
#include <objtools/data_loaders/asn_cache/asn_cache_util.hpp>
#include <serial/iterator.hpp>
#include <connect/ncbi_pipe.hpp>
#include <dbapi/simple/sdbapi.hpp>
#include <util/file_manifest.hpp>
#include <util/compress/zlib.hpp>
#include <util/compress/stream.hpp>
#include <objects/seqset/Bioseq_set.hpp>
#include <objects/seq/Seq_inst.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/bioseq_handle.hpp>
#include <objmgr/seq_entry_handle.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <misc/data_loaders_util/data_loaders_util.hpp>
#include <db/bdb/bdb_cursor.hpp>
#include <string>
#include <vector>
#include <cstdlib>
#include <algorithm>
#include <functional>
+ Include dependency graph for sub_cache_create.cpp:

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Classes

struct  SSeqIdIndex
 Indexing primitives. More...
 
struct  SBlobLocator
 
struct  SSubcacheIndexData
 
struct  SBlobCopier
 
struct  SBlobInserter
 
class  CAsnSubCacheCreateApplication
 
struct  CAsnSubCacheCreateApplication::SBlobVersion
 

Typedefs

typedef deque< SSubcacheIndexDataTBlobLocationList
 
typedef SSubcacheIndexDataTBlobLocationEntry
 
typedef map< SSeqIdIndex, TBlobLocationEntryTIndexMapById
 
typedef TIndexMapById::iterator TIndexRef
 
typedef list< TIndexRefTIndexRefList
 
typedef vector< pair< SBlobLocator, TBlobLocationEntry > > TIndexMapByBlob
 
typedef set< CSeq_id_Handle, CSeq_id_Handle::PLessOrderedTCachedSeqIds
 

Functions

 USING_SCOPE (objects)
 
void ExtractExtraIds (CBioseq_Handle bsh, vector< CSeq_id_Handle > &extra_ids, bool extract_delta, bool extract_products)
 
bool s_RemoveAnnotsFromEntry (CSeq_entry &entry)
 
bool TrimEntry (CConstRef< CSeq_entry > &entry, CBioseq_Handle bsh)
 If entry is a large nucprot set, Optionally create a new trimmed Seq-entry containing only the needed Bioseq. More...
 
void VerifyMolType (CBioseq_Handle bsh)
 
bool HasNameAndAccession (const CSeq_id_Handle &idh)
 
CSeq_id_Handle StrippedAccVer (const CSeq_id_Handle &idh)
 
static void s_ReadIdsFromFile (CNcbiIstream &istr, TIndexMapById &index_map, TBlobLocationList &blob_locations, TCachedSeqIds &cached_seq_ids)
 
static bool s_ShouldFetchOneByOne (TIndexMapById &ids)
 
int main (int argc, const char *argv[])
 

Variables

 USING_NCBI_SCOPE
 
static bool s_TrimLargeNucprots = false
 
static bool s_RemoveAnnot = false
 
static CSeq_inst::EMol s_MolType = CSeq_inst::eMol_not_set
 

Typedef Documentation

◆ TBlobLocationEntry

Definition at line 210 of file sub_cache_create.cpp.

◆ TBlobLocationList

Definition at line 209 of file sub_cache_create.cpp.

◆ TCachedSeqIds

Definition at line 215 of file sub_cache_create.cpp.

◆ TIndexMapByBlob

Definition at line 214 of file sub_cache_create.cpp.

◆ TIndexMapById

Definition at line 211 of file sub_cache_create.cpp.

◆ TIndexRef

Definition at line 212 of file sub_cache_create.cpp.

◆ TIndexRefList

typedef list<TIndexRef> TIndexRefList

Definition at line 213 of file sub_cache_create.cpp.

Function Documentation

◆ ExtractExtraIds()

void ExtractExtraIds ( CBioseq_Handle  bsh,
vector< CSeq_id_Handle > &  extra_ids,
bool  extract_delta,
bool  extract_products 
)

◆ HasNameAndAccession()

bool HasNameAndAccession ( const CSeq_id_Handle idh)

◆ main()

int main ( int  argc,
const char *  argv[] 
)

◆ s_ReadIdsFromFile()

static void s_ReadIdsFromFile ( CNcbiIstream istr,
TIndexMapById index_map,
TBlobLocationList blob_locations,
TCachedSeqIds cached_seq_ids 
)
static

◆ s_RemoveAnnotsFromEntry()

bool s_RemoveAnnotsFromEntry ( CSeq_entry entry)

◆ s_ShouldFetchOneByOne()

static bool s_ShouldFetchOneByOne ( TIndexMapById ids)
static

◆ StrippedAccVer()

CSeq_id_Handle StrippedAccVer ( const CSeq_id_Handle idh)

◆ TrimEntry()

bool TrimEntry ( CConstRef< CSeq_entry > &  entry,
CBioseq_Handle  bsh 
)

◆ USING_SCOPE()

USING_SCOPE ( objects  )

◆ VerifyMolType()

void VerifyMolType ( CBioseq_Handle  bsh)

Variable Documentation

◆ s_MolType

Definition at line 267 of file sub_cache_create.cpp.

Referenced by VerifyMolType().

◆ s_RemoveAnnot

bool s_RemoveAnnot = false
static

Definition at line 266 of file sub_cache_create.cpp.

Referenced by CAsnSubCacheCreateApplication::Run(), and TrimEntry().

◆ s_TrimLargeNucprots

bool s_TrimLargeNucprots = false
static

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 95 of file sub_cache_create.cpp.

Modified on Sun Feb 25 03:09:06 2024 by modify_doxy.py rev. 669887