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NCBI C++ ToolKit: src/objtools/lds2/lds2.cpp Source File

* annot_name,

BeginBlob(

);

ResetBlob(

);

m_CurBlobPos = m_LastBlobPos + pos;

m_IsGBBioseqSet =

;

m_IsGBBioseqSet;

m_Manager.GetSeqAlignGroupSize();

(*m_Ids)[it.GetSeq_id_Handle()].range.CombineWith(it.GetRange());

(*m_Ids)[it.GetSeq_id_Handle()].range.CombineWith(it.GetRange());

(*m_Ids)[it.GetSeq_id_Handle()].range.CombineWith(it.GetRange());

(

.GetMemberInfo()->GetId().GetName() ==

) {

(

.GetMemberInfo()->GetId().GetName() ==

) {

(

.GetMemberInfo()->GetId().GetName() ==

) {

m_CurFileId(file_id),

m_IsGBBioseqSet(

)

( blob_type ) {

(eIndexerError,

);

(

= 0;

< num_types;

++) {

(

.size() == 1 ) {

(

= 0;

< num_types;

++) {

<<

+

, bioseq_ids_hook, objstr.get());

id_hook, annot_desc_hook, annot_type_hook);

, bioseq_set_hook, objstr.get());

, bioseq_set_hook, objstr.get());

, bioseq_set_hook, objstr.get());

objstr->Skip(type_info);

* annot_name,

annot->

= annot_type;

annot->

= *annot_name;

: m_GBReleaseMode(eGB_Ignore),

m_DupIdMode(eDuplicate_Store),

m_ErrorMode(eError_Report),

m_SeqAlignGroupSize(0)

( sub.

() ) {

handler_name = url_it->second;

+ url_it->second);

+ url_it->second);

= h_it->second.GetPointerOrNull();

(db_info.

!= 0) {

( file_info.

() ) {

+ *it);

+ *it);

(db_info.

== 0) {

file_info.

= db_info.

;

(file_info != db_info) {

+

.name +

);

parsed_entries = 0;

(

.format ) {

( !

->eof() ) {

+

<<

(parsed_entries == 0) {

( !

.AtEOF() ) {

( !se->

() ) {

( !

.AtEOF() ) {

<<

.name);

(parsed_entries == 0) {

+

.name);

<<

.name);

(parsed_entries > 0) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Checksum and hash calculation classes.

Implementation of ILineReader for IReader.

Base class for reading FASTA sequences.

EFormat

The formats are checked in the same order as declared here.

@ eBinaryASN

Binary ASN.1.

@ eGZip

GNU zip compressed file.

@ eFasta

FASTA format sequence record, CFastaReader.

static EFormat Format(const string &path, EOnError onerror=eDefault)

Guess file format.

~CLDS2_AnnotDesc_Hook(void)

virtual void SkipObject(CObjectIStream &in, const CObjectTypeInfo &info)

const string & GetName(void) const

CLDS2_AnnotDesc_Hook(void)

~CLDS2_AnnotType_Hook(void)

CLDS2_AnnotType_Hook(void)

virtual void SkipObject(CObjectIStream &in, const CObjectTypeInfo &info)

SLDS2_Annot::TIdMap * m_Ids

void ResetAnnot(SLDS2_Annot::TIdMap *ids)

const string & GetType(void) const

CLDS2_ObjectParser & m_Parser

SLDS2_Annot::TIdMap m_IdMap

CLDS2_AnnotDesc_Hook & m_DescHook

CLDS2_Annot_Hook(CLDS2_ObjectParser &parser, CLDS2_Seq_id_Hook &id_hook, CLDS2_AnnotDesc_Hook &desc_hook, CLDS2_AnnotType_Hook &type_hook)

CLDS2_Seq_id_Hook & m_IdHook

virtual void SkipObject(CObjectIStream &in, const CObjectTypeInfo &info)

CLDS2_AnnotType_Hook & m_TypeHook

CLDS2_ObjectParser & m_Parser

virtual void SkipClassMember(CObjectIStream &in, const CObjectTypeInfoMI &info)

CLDS2_Seq_id_Hook & m_IdHook

CLDS2_BioseqIds_Hook(CLDS2_ObjectParser &parser, CLDS2_Seq_id_Hook &id_hook)

virtual void SkipClassMember(CObjectIStream &in, const CObjectTypeInfoMI &info)

CLDS2_BioseqSet_Hook(CLDS2_ObjectParser &parser)

CLDS2_ObjectParser & m_Parser

CBioseq_set::EClass m_Class

Int8 AddAnnot(SLDS2_Annot &annot)

Add annotation, return the new annot id.

Int8 AddBlob(Int8 file_id, SLDS2_Blob::EBlobType blob_type, Int8 file_pos)

Add blob, return the new blob id.

void GetFileNames(TStringSet &files) const

Get all known file names.

void Open(EAccessMode mode=eWrite)

Open LDS2 database. If the database does not exist, throws exception.

void AddFile(SLDS2_File &info)

Add new file record. On success file_info.id is not zero.

void BeginUpdate(void)

Start update transaction.

const string & GetDbFile(void) const

Get database file name.

vector< AutoPtr< SLDS2_Annot > > TLDS2Annots

void DeleteFile(const string &file_name)

Delete file and all related entries from the database.

void UpdateFile(SLDS2_File &info)

Update info for the known file. The 'id' of the info will change.

Int8 GetBioseqId(const CSeq_id_Handle &idh) const

Check if the db contains a bioseq with the given id.

void Create(void)

Create the database.

void EndUpdate(void)

End update transaction, commit the changes.

SLDS2_File GetFileInfo(const string &file_name) const

Get complete file info.

Int8 AddBioseq(Int8 blob_id, const TSeqIdSet &ids)

Add bioseq, return the new bioseq id.

Class for managing LDS2 database and related data files.

@ eError_Throw

Throw exceptions on errors.

@ eError_Report

Print error messages, but do not fail (default).

SLDS2_File x_GetFileInfo(const string &file_name, CRef< CLDS2_UrlHandler_Base > &handler)

THandlersByUrl m_HandlersByUrl

@ eGB_Force

Split all top-level bioseq-sets into seq-entries.

@ eGB_Ignore

Do not split bioseq-sets (default)

void AddDataDir(const string &data_dir, EDirMode mode=eDir_Recurse)

Add data directory.

void RegisterUrlHandler(CLDS2_UrlHandler_Base *handler)

Register a URL handler.

EDuplicateIdMode GetDuplicateIdMode(void) const

CLDS2_Manager(const string &db_file)

Create LDS2 manager for the specified db file.

void ResetData(void)

Remove all data from the database.

virtual ~CLDS2_Manager(void)

CLDS2_UrlHandler_Base * x_GetUrlHandler(const SLDS2_File &file_info)

void AddDataFile(const string &data_file)

Add new data file to the list.

void UpdateData(void)

Rescan all indexed files, check for modifications, update the database.

void AddDataUrl(const string &url, const string &handler_name)

Add a URL.

bool x_IsGZipFile(const SLDS2_File &file_info)

EDirMode

Directory parsing mode while indexing files.

@ eDir_Recurse

Automatically scan sub-directories (default).

CFastaReader::TFlags m_FastaFlags

CRef< CLDS2_Database > m_Db

void x_ParseFile(const SLDS2_File &info, CLDS2_UrlHandler_Base &handler)

void SetDbFile(const string &db_file)

Select new database.

@ eDuplicate_Skip

Ignore bioseqs with duplicate ids, store just the first one.

@ eDuplicate_Store

Store all bioseqs regardless of seq-id conflicts (defalut).

CLDS2_ObjectParser(CLDS2_Manager &mgr, Int8 file_id, TFormat format, CNcbiIstream &in, CLDS2_Database &db)

void SetBlobOffset(Int8 pos)

int GetSeqAlignGroupSize(void) const

vector< AutoPtr< SBioseqInfo > > TBioseqs

SLDS2_Blob::EBlobType m_LastBlobType

void AddBioseq(const TSeqIdSet &ids)

SLDS2_Blob::EBlobType x_GetBlobType(void)

void SetGBBioseqSet(bool value)

CLDS2_Database::TLDS2Annots TAnnots

CLDS2_Manager & m_Manager

ESerialDataFormat m_Format

static TTypeInfo sx_GetObjectTypeInfo(SLDS2_Blob::EBlobType blob_type)

bool ParseNext(SLDS2_Blob::EBlobType blob_type=SLDS2_Blob::eUnknown)

SLDS2_Blob::EBlobType m_BlobType

void EndBlob(SLDS2_Blob::EBlobType blob_type)

bool GetSplitBioseqSet(void) const

~CLDS2_ObjectParser(void)

void AddAnnot(SLDS2_Annot::EType annot_type, const string *annot_name, const SLDS2_Annot::TIdMap &ids)

SLDS2_File::TFormat TFormat

virtual void SkipObject(CObjectIStream &in, const CObjectTypeInfo &info)

CLDS2_ObjectParser & m_Parser

CLDS2_SeqEntry_Hook(CLDS2_ObjectParser &parser)

void operator=(const CGuard &)

CLDS2_Seq_id_Hook & m_Hook

CGuard(CLDS2_Seq_id_Hook &hook, TSeqIdSet &ids)

virtual void SkipObject(CObjectIStream &in, const CObjectTypeInfo &info)

stack< TSeqIdSet * > TIdStack

void PushSet(TSeqIdSet &ids)

Base class for URL handler.

Default handler for local files - registered automatically by LDS2 manager and data loader.

static const string s_GetHandlerName(void)

Handler for GZip local files. Not registered by default.

static const string s_GetHandlerName(void)

Helper class: installs hooks in constructor, and uninstalls in destructor.

CRange< TSeqPos > GetSeqRange(TDim row) const

GetSeqRange NB: On a Spliced-seg, in case the product-type is protein, these only return the amin par...

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

namespace ncbi::objects::

Root class for all serialization exceptions.

Skip hook for data member of a containing object (eg, SEQUENCE)

Skip hook for a standalone object.

CTypeInfo class contains all information about C++ types (both basic and classes): members and layout...

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

void(*)(CSeq_entry_Handle seh, IWorkbench *wb, const CSerialObject &obj) handler

static const struct type types[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

void Error(CExceptionArgs_Base &args)

void Warning(CExceptionArgs_Base &args)

TEntries GetEntries(const string &mask=kEmptyStr, TGetEntriesFlags flags=0) const

Get directory entries based on the specified "mask".

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

virtual bool Exists(void) const

Check the entry existence.

bool IsDir(EFollowLinks follow=eFollowLinks) const

Check whether a directory entry is a directory.

bool IsFile(EFollowLinks follow=eFollowLinks) const

Check whether a directory entry is a file.

const string & GetPath(void) const

Get entry path.

@ fIgnoreRecursive

Suppress "self recursive" elements (the directories "." and "..").

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

virtual CRef< CSeq_entry > ReadOneSeq(ILineErrorListener *pMessageListener=nullptr)

Read a single effective sequence, which may turn out to be a segmented set.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

string AsString(void) const

static TTypeInfo GetTypeInfo(void)

void DefaultSkip(CObjectIStream &stream, const CObjectTypeInfoMI &member)

pair< TObjectPtr, TTypeInfo > ObjectInfo(C &obj)

const CEnumeratedTypeValues & GetEnumeratedTypeValues(void) const

Get a set of possible values of enumeration.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

void DefaultRead(CObjectIStream &in, const CObjectInfo &object)

Default read.

void DefaultSkip(CObjectIStream &in, const CObjectTypeInfo &type)

Default skip.

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

int64_t Int8

8-byte (64-bit) signed integer

static TThisType GetWhole(void)

#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.

Int8 NcbiStreamposToInt8(NCBI_NS_STD::char_traits< char >::pos_type stream_pos)

Convert stream position to 64-bit int.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

TDim GetDim(void) const

Get the Dim member data.

bool IsSetDim(void) const

dimensionality Check if a value has been assigned to Dim data member.

const TLocation & GetLocation(void) const

Get the Location member data.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

const TLoc & GetLoc(void) const

Get the Loc member data.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

@ eClass_genbank

converted genbank

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

const TName & GetName(void) const

Get the variant data.

bool IsName(void) const

Check if variant Name is selected.

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

static bool IsSupportedFormat(CFormatGuess::EFormat format)

static const SLDS2_Blob::EBlobType kExpectedBlobTypes[]

#define LDS2_THROW(errcode, message)

const GenericPointer< typename T::ValueType > T2 value

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

std::istream & in(std::istream &in_, double &x_)

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

#define row(bind, expected)

Info about seq-id used in an annotation.

EBlobType

Top-level object types.

@ eBioseq_set_element

Used for indexing individual seq-entries from a top-level bioseq-set.

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