NCBI C++ ToolKit
Classes | Functions
loaderpatcher.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/plugin_manager_store.hpp>
#include <corelib/plugin_manager_impl.hpp>
#include <objtools/data_loaders/patcher/loaderpatcher.hpp>
#include <objmgr/data_loader_factory.hpp>
#include <objmgr/annot_name.hpp>
#include <objmgr/impl/data_source.hpp>
#include <objmgr/impl/tse_loadlock.hpp>
#include <objmgr/impl/tse_split_info.hpp>
#include <objmgr/impl/bioseq_info.hpp>
#include <objmgr/impl/bioseq_set_info.hpp>
#include <objmgr/impl/annot_finder.hpp>
#include <objmgr/impl/annot_object.hpp>
#include <objmgr/impl/seq_annot_info.hpp>
#include <objects/general/Int_fuzz.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/Annot_descr.hpp>
#include <objects/seq/Annotdesc.hpp>
#include <objects/seqedit/SeqEdit_Cmd.hpp>
#include <objects/seqedit/SeqEdit_Id.hpp>
#include <objects/seqedit/SeqEdit_Cmd_AddId.hpp>
#include <objects/seqedit/SeqEdit_Cmd_RemoveId.hpp>
#include <objects/seqedit/SeqEdit_Cmd_ResetIds.hpp>
#include <objects/seqedit/SeqEdit_Cmd_ChangeSeqAttr.hpp>
#include <objects/seqedit/SeqEdit_Cmd_ResetSetAttr.hpp>
#include <objects/seqedit/SeqEdit_Cmd_ChangeSetAttr.hpp>
#include <objects/seqedit/SeqEdit_Cmd_ResetSeqAttr.hpp>
#include <objects/seqedit/SeqEdit_Cmd_AddDescr.hpp>
#include <objects/seqedit/SeqEdit_Cmd_SetDescr.hpp>
#include <objects/seqedit/SeqEdit_Cmd_ResetDescr.hpp>
#include <objects/seqedit/SeqEdit_Cmd_AddDesc.hpp>
#include <objects/seqedit/SeqEdit_Cmd_RemoveDesc.hpp>
#include <objects/seqedit/SeqEdit_Cmd_AttachSeq.hpp>
#include <objects/seqedit/SeqEdit_Cmd_AttachSet.hpp>
#include <objects/seqedit/SeqEdit_Cmd_ResetSeqEntry.hpp>
#include <objects/seqedit/SeqEdit_Cmd_AttachSeqEntry.hpp>
#include <objects/seqedit/SeqEdit_Cmd_RemoveSeqEntry.hpp>
#include <objects/seqedit/SeqEdit_Cmd_AttachAnnot.hpp>
#include <objects/seqedit/SeqEdit_Cmd_RemoveAnnot.hpp>
#include <objects/seqedit/SeqEdit_Cmd_AddAnnot.hpp>
#include <objects/seqedit/SeqEdit_Cmd_ReplaceAnnot.hpp>
+ Include dependency graph for loaderpatcher.cpp:

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Classes

class  CDLPatcher_DataLoaderCF
 Data Loader Factory for BlastDbDataLoader. More...
 

Functions

void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_AddId &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_RemoveId &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_ResetIds &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_ChangeSeqAttr &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_ResetSeqAttr &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_ChangeSetAttr &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_ResetSetAttr &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_AddDescr &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_SetDescr &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_ResetDescr &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_AddDesc &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_RemoveDesc &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_AttachSeq &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_AttachSet &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_ResetSeqEntry &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_AttachSeqEntry &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_RemoveSeqEntry &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_AttachAnnot &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_RemoveAnnot &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_AddAnnot &cmd)
 
void x_ApplyCmd (CTSE_Info &tse, const CSeqEdit_Cmd_ReplaceAnnot &cmd)
 
static CBioObjectId s_Convert (const CSeqEdit_Id &id)
 
CBioseq_InfoGetBioseq (CTSE_Info &tse, const CBioObjectId &id)
 
CBioseq_set_InfoGetBioseq_set (CTSE_Info &tse, const CBioObjectId &id)
 
CBioseq_Base_InfoGetBase (CTSE_Info &tse, const CBioObjectId &id)
 
CSeq_entry_InfoGetSeq_entry (CTSE_Info &tse, const CBioObjectId &id)
 
template<typename T >
static void x_MakeRemove (CTSE_Info &tse, const CSeq_entry_Info &info, const CAnnotName &name, const T &old_value)
 
template<typename T >
static void x_MakeReplace (CTSE_Info &tse, const CSeq_entry_Info &info, const CAnnotName &name, const T &old_value, const T &new_value)
 
 USING_SCOPE (objects)
 
void DataLoaders_Register_Patcher (void)
 
const string kDataLoader_Patcher_DriverName ("dlpatcher")
 
void NCBI_EntryPoint_DataLoader_Patcher (CPluginManager< CDataLoader >::TDriverInfoList &info_list, CPluginManager< CDataLoader >::EEntryPointRequest method)
 
void NCBI_EntryPoint_xloader_Patcher (CPluginManager< objects::CDataLoader >::TDriverInfoList &info_list, CPluginManager< objects::CDataLoader >::EEntryPointRequest method)
 

Function Documentation

◆ DataLoaders_Register_Patcher()

void DataLoaders_Register_Patcher ( void  )

Definition at line 859 of file loaderpatcher.cpp.

References NCBI_EntryPoint_DataLoader_Patcher().

◆ GetBase()

CBioseq_Base_Info& GetBase ( CTSE_Info tse,
const CBioObjectId id 
)

◆ GetBioseq()

CBioseq_Info& GetBioseq ( CTSE_Info tse,
const CBioObjectId id 
)

◆ GetBioseq_set()

CBioseq_set_Info& GetBioseq_set ( CTSE_Info tse,
const CBioObjectId id 
)

Definition at line 413 of file loaderpatcher.cpp.

References NCBI_THROW, and CTSE_Info::x_FindBioObject().

Referenced by x_ApplyCmd().

◆ GetSeq_entry()

CSeq_entry_Info& GetSeq_entry ( CTSE_Info tse,
const CBioObjectId id 
)

◆ kDataLoader_Patcher_DriverName()

const string kDataLoader_Patcher_DriverName ( "dlpatcher"  )

◆ NCBI_EntryPoint_DataLoader_Patcher()

void NCBI_EntryPoint_DataLoader_Patcher ( CPluginManager< CDataLoader >::TDriverInfoList &  info_list,
CPluginManager< CDataLoader >::EEntryPointRequest  method 
)

◆ NCBI_EntryPoint_xloader_Patcher()

void NCBI_EntryPoint_xloader_Patcher ( CPluginManager< objects::CDataLoader >::TDriverInfoList &  info_list,
CPluginManager< objects::CDataLoader >::EEntryPointRequest  method 
)

Definition at line 973 of file loaderpatcher.cpp.

References NCBI_EntryPoint_DataLoader_Patcher().

◆ s_Convert()

static CBioObjectId s_Convert ( const CSeqEdit_Id id)
inlinestatic

◆ USING_SCOPE()

USING_SCOPE ( objects  )

◆ x_ApplyCmd() [1/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_AddAnnot cmd 
)

◆ x_ApplyCmd() [2/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_AddDesc cmd 
)

Definition at line 630 of file loaderpatcher.cpp.

References CBioseq_Base_Info::AddSeqdesc(), cmd, GetBase(), and s_Convert().

◆ x_ApplyCmd() [3/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_AddDescr cmd 
)

Definition at line 609 of file loaderpatcher.cpp.

References CBioseq_Base_Info::AddSeq_descr(), cmd, GetBase(), and s_Convert().

◆ x_ApplyCmd() [4/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_AddId cmd 
)

◆ x_ApplyCmd() [5/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_AttachAnnot cmd 
)

Definition at line 696 of file loaderpatcher.cpp.

References cmd, GetSeq_entry(), info, and s_Convert().

◆ x_ApplyCmd() [6/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_AttachSeq cmd 
)

Definition at line 652 of file loaderpatcher.cpp.

References cmd, GetSeq_entry(), info, and s_Convert().

◆ x_ApplyCmd() [7/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_AttachSeqEntry cmd 
)

Definition at line 673 of file loaderpatcher.cpp.

References cmd, GetBioseq_set(), info, CRef< C, Locker >::Reset(), and s_Convert().

◆ x_ApplyCmd() [8/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_AttachSet cmd 
)

Definition at line 660 of file loaderpatcher.cpp.

References cmd, GetSeq_entry(), info, and s_Convert().

◆ x_ApplyCmd() [9/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_ChangeSeqAttr cmd 
)

◆ x_ApplyCmd() [10/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_ChangeSetAttr cmd 
)

◆ x_ApplyCmd() [11/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_RemoveAnnot cmd 
)

◆ x_ApplyCmd() [12/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_RemoveDesc cmd 
)

◆ x_ApplyCmd() [13/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_RemoveId cmd 
)

◆ x_ApplyCmd() [14/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_RemoveSeqEntry cmd 
)

Definition at line 686 of file loaderpatcher.cpp.

References cmd, GetBioseq_set(), GetSeq_entry(), info, Ref(), and s_Convert().

◆ x_ApplyCmd() [15/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_ReplaceAnnot cmd 
)

◆ x_ApplyCmd() [16/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_ResetDescr cmd 
)

Definition at line 624 of file loaderpatcher.cpp.

References cmd, GetBase(), CBioseq_Base_Info::ResetDescr(), and s_Convert().

◆ x_ApplyCmd() [17/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_ResetIds cmd 
)

Definition at line 466 of file loaderpatcher.cpp.

References cmd, GetBioseq(), CBioseq_Info::ResetId(), and s_Convert().

◆ x_ApplyCmd() [18/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_ResetSeqAttr cmd 
)

◆ x_ApplyCmd() [19/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_ResetSeqEntry cmd 
)

Definition at line 667 of file loaderpatcher.cpp.

References cmd, GetSeq_entry(), info, and s_Convert().

◆ x_ApplyCmd() [20/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_ResetSetAttr cmd 
)

◆ x_ApplyCmd() [21/21]

void x_ApplyCmd ( CTSE_Info tse,
const CSeqEdit_Cmd_SetDescr cmd 
)

Definition at line 616 of file loaderpatcher.cpp.

References cmd, GetBase(), s_Convert(), and CBioseq_Base_Info::SetDescr().

◆ x_MakeRemove()

template<typename T >
static void x_MakeRemove ( CTSE_Info tse,
const CSeq_entry_Info info,
const CAnnotName name,
const T old_value 
)
inlinestatic

◆ x_MakeReplace()

template<typename T >
static void x_MakeReplace ( CTSE_Info tse,
const CSeq_entry_Info info,
const CAnnotName name,
const T old_value,
const T new_value 
)
inlinestatic
Modified on Mon Jul 15 05:36:04 2024 by modify_doxy.py rev. 669887