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NCBI C++ ToolKit: src/objtools/data_loaders/patcher/loaderpatcher.cpp Source File

param(data_loader, db_engine, saver);

m_DataLoader(param.m_DataLoader),

m_DBEngine (param.m_DBEngine),

m_EditSaver (param.m_EditSaver)

(!sblobid.empty()) {

(!sblobid.empty()) {

(!sblobid.empty()) {

& blob_id = (*lock).GetBlobId();

entry->

(*orig_entry);

nlock->

(lock, entry);

(

.Which()) {

);

(

.Which()) {

);

);

);

);

);

(

.GetData().Which()) {

.SetInst_Length(

.GetData().GetLength());

.SetInst_Ext(

&

(

.GetData().GetExt()));

.SetInst_Seq_data(

&

(

.GetData().GetSeq_data()));

(

.GetWhat()) {

.ResetInst_Repr();

.ResetInst_Mol();

.ResetInst_Length();

.ResetInst_Fuzz();

.ResetInst_Topology();

.ResetInst_Strand();

.ResetInst_Ext();

.ResetInst_Hist();

.ResetInst_Seq_data();

(

.GetData().Which()) {

.SetColl(

&

(

.GetData().GetColl()));

.SetLevel(

.GetData().GetLevel());

.SetRelease(

&

(

.GetData().GetRelease()));

.SetDate(

&

(

.GetData().GetDate()));

(

.GetWhat()) {

.ResetRelease();

.SelectSeq(seq);

(

.IsSetSeq_entry())

index =

.GetIndex();

.AddEntry(*entry, index,

);

.RemoveEntry(

(&entry_info));

.AddAnnot(annot);

<

T>

);

(

.GetNamed()) {

(

.GetData().Which()) {

);

(

.GetNamed()) {

(

.IsSetSearch_param() &&

(

.GetData().Which()) {

annot_obj = finder.

(

, annot_name,

.GetSearch_param().GetObj().GetFeat());

annot_obj = finder.

(

, annot_name,

.GetSearch_param().GetObj().GetAlign());

annot_obj = finder.

(

, annot_name,

.GetSearch_param().GetObj().GetGraph());

);

);

}

(

.IsSetSearch_param() &&

.GetSearch_param().Which()

.GetSearch_param().GetDescr()));

);

(

.GetData().Which()) {

annot->

(

.GetData().GetFeat());

annot->

(

.GetData().GetAlign());

annot->

(

.GetData().GetGraph());

);

<

T>

& old_value,

& new_value)

);

(

.GetNamed()) {

(

.GetData().Which()) {

.GetData().GetFeat().GetOvalue(),

.GetData().GetFeat().GetNvalue());

.GetData().GetAlign().GetOvalue(),

.GetData().GetAlign().GetNvalue());

.GetData().GetGraph().GetOvalue(),

.GetData().GetGraph().GetNvalue());

);

void(*TArgFuncType)(list<CPluginManager<CDataLoader>

::EEntryPointRequest);

RegisterEntryPoint<CDataLoader>((TArgFuncType)

& data_loader =

& db_engine =

( !data_loader.empty() && !db_engine.empty() ) {

TDLManager dl_manager;

TDLManager::GetDefaultDrvVers(),

TDBManager db_manager;

TDBManager::GetDefaultDrvVers(),

& edit_saver =

( !edit_saver.empty() ) {

TESManager es_manager;

es = es_manager.CreateInstance(edit_saver,

TESManager::GetDefaultDrvVers(),

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void SetNamed(const string &name)

const CSeq_annot_Info & GetSeq_annot_Info(void) const

TIndex GetAnnotIndex(void) const

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &d)

const TDescr & GetDescr(void) const

void AddSeq_descr(const TDescr &v)

bool AddSeqdesc(CSeqdesc &d)

const CSeq_entry_Info & GetParentSeq_entry_Info(void) const

bool RemoveId(const CSeq_id_Handle &id)

bool AddId(const CSeq_id_Handle &id)

Data Loader Factory for BlastDbDataLoader.

virtual ~CDLPatcher_DataLoaderCF(void)

Destructor.

CDLPatcher_DataLoaderCF(void)

Constructor.

virtual CDataLoader * CreateAndRegister(CObjectManager &om, const TPluginManagerParamTree *params) const

Create and register a data loader.

CObjectManager::TPriority GetPriority(const TPluginManagerParamTree *params) const

const string & GetDriverName(void) const

CObjectManager::EIsDefault GetIsDefault(const TPluginManagerParamTree *params) const

bool ValidParams(const TPluginManagerParamTree *params) const

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CRef< CDataLoader >, CRef< IEditsDBEngine >, CRef< IEditSaver > saver=CRef< IEditSaver >(), CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

void x_PatchLockSet(const TTSE_LockSet &orig_locks, TTSE_LockSet &new_locks)

virtual TEditSaver GetEditSaver() const

virtual ~CDataLoaderPatcher()

virtual void GetChunks(const TChunkSet &chunks)

CDataLoaderPatcher(const string &loader_name, const SParam &param)

CRef< IEditsDBEngine > m_DBEngine

CRef< CDataLoader > m_DataLoader

CRef< IEditSaver > m_EditSaver

bool x_IsPatchNeeded(const CTSE_Info &tse)

TTSE_Lock x_PatchLock(const TTSE_Lock &lock)

virtual TTSE_Lock GetBlobById(const TBlobId &blob_id)

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

virtual TTSE_LockSet GetExternalRecords(const CBioseq_Info &bioseq)

Request from a datasource set of blobs with external annotations.

virtual bool CanGetBlobById(void) const

virtual TTSE_LockSet GetRecords(const CSeq_id_Handle &idh, EChoice choice)

Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call wi...

virtual TTSE_LockSet GetDetailedRecords(const CSeq_id_Handle &idh, const SRequestDetails &details)

Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call wi...

void x_ApplyPatches(CTSE_Info &tse)

virtual TBlobId GetBlobIdFromString(const string &str) const

virtual TBlobVersion GetBlobVersion(const TBlobId &id)

static string GetLoaderNameFromArgs(const SParam &param)

virtual void GetChunk(TChunk chunk_info)

CTSE_LoadLock GetTSE_LoadLock(const TBlobId &blob_id)

Data loader exceptions, used by GenBank loader.

CSeqEdit_Cmd_AddAnnot –.

CSeqEdit_Cmd_AddDesc –.

CSeqEdit_Cmd_AddDescr –.

CSeqEdit_Cmd_AttachAnnot –.

CSeqEdit_Cmd_AttachSeqEntry –.

CSeqEdit_Cmd_AttachSeq –.

CSeqEdit_Cmd_AttachSet –.

CSeqEdit_Cmd_ChangeSeqAttr –.

CSeqEdit_Cmd_ChangeSetAttr –.

CSeqEdit_Cmd_RemoveAnnot –.

CSeqEdit_Cmd_RemoveDesc –.

CSeqEdit_Cmd_RemoveId –.

CSeqEdit_Cmd_RemoveSeqEntry –.

CSeqEdit_Cmd_ReplaceAnnot –.

CSeqEdit_Cmd_ResetDescr –.

CSeqEdit_Cmd_ResetIds –.

CSeqEdit_Cmd_ResetSeqAttr –.

CSeqEdit_Cmd_ResetSeqEntry –.

CSeqEdit_Cmd_ResetSetAttr –.

CSeqEdit_Cmd_SetDescr –.

const CAnnotObject_Info * Find(const CSeq_entry_Info &entry, const CAnnotName &name, const CSeq_feat &feat)

void Remove(TAnnotIndex index)

pair< TAnnotIndex, bool > Add(const CSeq_feat &new_obj)

bool Replace(TAnnotIndex index, const CSeq_feat &new_obj)

@Seq_descr.hpp User-defined methods of the data storage class.

CConstRef< TObject > GetSeq_entrySkeleton(void) const

const TBlobId & GetBlobId(void) const

CTSE_Info & Assign(const CTSE_Lock &tse)

CTSE_Info_Object * x_FindBioObject(const CBioObjectId &uniq_id) const

bool IsLoaded(void) const

definition of a Culling tree

virtual bool HasBlob(const string &blobid) const =0

list< CRef< CSeqEdit_Cmd > > TCommands

virtual void GetCommands(const string &blobid, TCommands &cmds) const =0

virtual bool FindSeqId(const CSeq_id_Handle &id, string &blobid) const =0

iterator_bool insert(const value_type &val)

static const char * str(char *buf, int n)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

string ToString(void) const

TLoader * GetLoader(void) const

Get pointer to the loader.

virtual TBlobId GetBlobIdFromString(const string &str) const

string GetName(void) const

CDataSource * GetDataSource(void) const

virtual bool CanGetBlobById(void) const

virtual TTSE_Lock GetBlobById(const TBlobId &blob_id)

EChoice

main blob is blob with sequence all other blobs are external and contain external annotations

virtual TTSE_LockSet GetRecords(const CSeq_id_Handle &idh, EChoice choice)

Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call wi...

virtual TTSE_LockSet GetDetailedRecords(const CSeq_id_Handle &idh, const SRequestDetails &details)

Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call wi...

EIsDefault

Flag defining if the data loader is included in the "default" group.

TRegisterInfo GetRegisterInfo(void)

static void RegisterInObjectManager(CObjectManager &om, CLoaderMaker_Base &loader_maker, CObjectManager::EIsDefault is_default, CObjectManager::TPriority priority)

Register the loader only if the name is not yet registered in the object manager.

virtual TBlobVersion GetBlobVersion(const TBlobId &id)

virtual void GetChunks(const TChunkSet &chunks)

virtual TTSE_LockSet GetExternalRecords(const CBioseq_Info &bioseq)

Request from a datasource set of blobs with external annotations.

vector< TChunk > TChunkSet

virtual void GetChunk(TChunk chunk_info)

virtual TBlobId GetBlobId(const CSeq_id_Handle &idh)

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

static void NCBI_EntryPointImpl(TDriverInfoList &info_list, EEntryPointRequest method)

Entry point implementation.

string GetParam(const string &driver_name, const TPluginManagerParamTree *params, const string &param_name, bool mandatory, const string &default_value) const

Utility function to get an element of parameter tree Throws an exception when mandatory parameter is ...

list< SDriverInfo > TDriverInfoList

List of driver information.

EEntryPointRequest

Actions performed by the entry point.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

const TTreeType * FindNode(const TKeyType &key, TNodeSearchMode sflag=eImmediateAndTop) const

Search for node.

@ e_Hist

hist field of seq-inst object

@ e_Fuzz

fuzz field of seq-inst object

@ e_Mol

mol field of seq-inst object

@ e_Length

length field of seq-inst object

@ e_Seq_data

seq-data field of seq-inst object

@ e_Topology

topology field of seq-inst object

@ e_Repr

repr field of seq-inst object

@ e_Strand

strand field of seq-inst object

@ e_Ext

extr field of seq-inst object

@ e_Inst

whole seq-inst object

@ e_Remove_seqentry

Remove a seq entry from bioseq-set.

@ e_Add_descr

Add descriptors to an object.

@ e_Attach_seqentry

Attach a seq entry to bioseq-set.

@ e_Add_desc

Add a descriptor ot an object.

@ e_not_set

No variant selected.

@ e_Attach_seq

Attach a bioseq to seq entry.

@ e_Remove_id

Remove a seq-id from bioseq.

@ e_Reset_seqentry

Detach an object from seq entry.

@ e_Attach_annot

Add a compelte annotation.

@ e_Reset_setattr

Reset bioseq-set's attribute.

@ e_Reset_ids

Reset ids field of bioseq.

@ e_Add_annot

Add an annotaion object.

@ e_Remove_desc

Remove a descripor from an object.

@ e_Set_descr

Set an objects's descriptors.

@ e_Remove_annot

Remove an annotation object.

@ e_Change_setattr

Change bioseq-set's attribure.

@ e_Attach_set

Attach a bioseq-set to seq entry.

@ e_Replace_annot

Replace an annotation object.

@ e_Add_id

Add a new seq-id to bioseq.

@ e_Reset_descr

Reset an objects's descriptors.

@ e_Reset_seqattr

Reset bioseq's attribute.

@ e_Change_seqattr

Change bioseq's attribure.

@ e_Feat

otherwise use an annot object

@ eWhat_strand

strand field of seq-inst object

@ eWhat_repr

repr field of seq-inst object

@ eWhat_mol

mol field of seq-inst object

@ eWhat_ext

extr field of seq-inst object

@ eWhat_length

length field of seq-inst object

@ eWhat_hist

hist field of seq-inst object

@ eWhat_fuzz

fuzz field of seq-inst object

@ eWhat_topology

topology field of seq-inst object

@ eWhat_seq_data

seq-data field of seq-inst object

@ eWhat_inst

whole seq-inst object

@ e_Descr

If an annotation does not have any objects,.

list< CRef< CSeqdesc > > Tdata

ERepr

representation class

const Tdata & Get(void) const

Get the member data.

ETopology

topology of molecule

EMol

molecule class in living organism

EStrand

strandedness in living organism

CSeq_entry_Info & GetSeq_entry(CTSE_Info &tse, const CBioObjectId &id)

CBioseq_Info & GetBioseq(CTSE_Info &tse, const CBioObjectId &id)

CBioseq_set_Info & GetBioseq_set(CTSE_Info &tse, const CBioObjectId &id)

const string kDataLoader_Patcher_DriverName("dlpatcher")

void x_ApplyCmd(CTSE_Info &tse, const CSeqEdit_Cmd_AddId &cmd)

static CBioObjectId s_Convert(const CSeqEdit_Id &id)

static void x_MakeRemove(CTSE_Info &tse, const CSeq_entry_Info &info, const CAnnotName &name, const T &old_value)

void DataLoaders_Register_Patcher(void)

CBioseq_Base_Info & GetBase(CTSE_Info &tse, const CBioObjectId &id)

static void x_MakeReplace(CTSE_Info &tse, const CSeq_entry_Info &info, const CAnnotName &name, const T &old_value, const T &new_value)

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

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

const string kCFParam_DLP_EditsDBEngine

const string kCFParam_DLP_DataLoader

const string kCFParam_DLP_EditSaver

Helper classes and templates to implement plugins.

CRef< objects::CObjectManager > om

CRef< CDataLoader > m_DataLoader

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