#include <ncbi_pch.hpp>#include <gui/objutils/na_utils.hpp>#include <gui/objutils/utils.hpp>#include <objmgr/scope.hpp>#include <objmgr/object_manager.hpp>#include <objmgr/align_ci.hpp>#include <objmgr/annot_ci.hpp>#include <objmgr/util/sequence.hpp>#include <objects/seqtable/Seq_table.hpp>#include <objects/seqtable/SeqTable_column.hpp>#include <objects/seqtable/SeqTable_column_info.hpp>#include <objects/seq/Annot_descr.hpp>#include <objects/seq/Annotdesc.hpp>#include <gui/objutils/gui_eutils_client.hpp>#include <misc/xmlwrapp/xmlwrapp.hpp>
Include dependency graph for na_utils.cpp:
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Classes | |
| class | CNADocSumIterator |
| help class for iterating through the NA DocSum one by one. More... | |
Macros | |
| #define | USE_GI_CACHING |
Enumerations | |
| enum | EAlignType { fAlign_DNA = 0x01 , fAlign_Protein = 0x02 , fAlign_Mixed = 0x04 , fAlign_Invalid = 0x80000000 } |
Functions | |
| USING_SCOPE (objects) | |
| DEFINE_CLASS_STATIC_FAST_MUTEX (CNAUtils::sm_NAAtoUidCacheMutex) | |
| DEFINE_CLASS_STATIC_FAST_MUTEX (CNAUtils::sm_UidtoMetaDataCacheMutex) | |
| DEFINE_CLASS_STATIC_FAST_MUTEX (CNAUtils::sm_UidtoGiCacheMutex) | |
| static string | s_GetFeatSubtypeStr (int subtype) |
| static bool | s_MatchHeaders (const char **header_names, const set< string > &headers) |
| static string | s_EEDBToString (CNAUtils::EEntrezDB eedb) |
| static string | s_MakeUidtoGiCacheKey (TEntrezId uid, CNAUtils::EEntrezDB eedb) |
Variables | |
| static const int | kRetMax = 5000 |
| static const char * | kSnpSubtypeStr = "variation_snp" |
| const size_t | kChunkSize = 256 |
Macro Definition Documentation
◆ USE_GI_CACHING
| #define USE_GI_CACHING |
Definition at line 1011 of file na_utils.cpp.
Enumeration Type Documentation
◆ EAlignType
| enum EAlignType |
| Enumerator | |
|---|---|
| fAlign_DNA | |
| fAlign_Protein | |
| fAlign_Mixed | |
| fAlign_Invalid | |
Definition at line 68 of file na_utils.cpp.
Function Documentation
◆ DEFINE_CLASS_STATIC_FAST_MUTEX() [1/3]
| DEFINE_CLASS_STATIC_FAST_MUTEX | ( | CNAUtils::sm_NAAtoUidCacheMutex | ) |
◆ DEFINE_CLASS_STATIC_FAST_MUTEX() [2/3]
| DEFINE_CLASS_STATIC_FAST_MUTEX | ( | CNAUtils::sm_UidtoGiCacheMutex | ) |
◆ DEFINE_CLASS_STATIC_FAST_MUTEX() [3/3]
| DEFINE_CLASS_STATIC_FAST_MUTEX | ( | CNAUtils::sm_UidtoMetaDataCacheMutex | ) |
◆ s_EEDBToString()
|
static |
Definition at line 756 of file na_utils.cpp.
References CNAUtils::EEDB_Nucleotide, and CNAUtils::EEDB_Protein.
Referenced by s_MakeUidtoGiCacheKey(), CNAUtils::x_GetAllGIs(), CNAUtils::x_GetAllNAIds(), and CNAUtils::x_GetAllNAIdsWithContext().
◆ s_GetFeatSubtypeStr()
Definition at line 142 of file na_utils.cpp.
References CSeqFeatData::eSubtype_variation, CSeqFeatData::GetFeatList(), CFeatList::GetStoragekey(), and kSnpSubtypeStr.
Referenced by CDataTrackUtils::GetFeatSubtypes(), and CNAUtils::GetNATrackInfo().
◆ s_MakeUidtoGiCacheKey()
|
static |
Definition at line 1091 of file na_utils.cpp.
References NStr::NumericToString(), and s_EEDBToString().
Referenced by CNAUtils::x_GetAllGIs().
◆ s_MatchHeaders()
Definition at line 241 of file na_utils.cpp.
Referenced by CDataTrackUtils::GetSeqTableSubtype().
◆ USING_SCOPE()
| USING_SCOPE | ( | objects | ) |
Variable Documentation
◆ kChunkSize
| const size_t kChunkSize = 256 |
Definition at line 587 of file na_utils.cpp.
Referenced by BOOST_AUTO_TEST_CASE(), CNAUtils::GetAllNAMetaData(), CPileUpGraph::GetNumberOfReads(), CTestProtProd_EntrezNeighbors::RunTest(), sx_AddBits(), CFlatGatherer::x_GatherSequence(), and CSplitQueryTestFixture::x_ValidateChunkBounds().
◆ kRetMax
Definition at line 55 of file na_utils.cpp.
Referenced by CNAUtils::x_GetNAId(), and CNAUtils::x_Init().
◆ kSnpSubtypeStr
|
static |
Definition at line 56 of file na_utils.cpp.
Referenced by CDataTrackUtils::FeatSubtypes2TrackSubtypes(), and s_GetFeatSubtypeStr().
