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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/vdbread_8hpp_source.html below:

NCBI C++ ToolKit: include/sra/readers/sra/vdbread.hpp Source File

1 #ifndef SRA__READER__SRA__VDBREAD__HPP 2 #define SRA__READER__SRA__VDBREAD__HPP 128 void

x_InitNew(

void

);

156 bool

IsLocalFile()

const

;

161 static bool

IsPlainAccession(

const string

& acc_or_path);

165 static string

ConvertSysPathToPOSIX(

const string

& sys_path);

170 static string

ConvertAccOrSysPathToPOSIX(

const string

& acc_or_path);

173 void

x_Init(

const CVFSManager

& mgr,

const string

& path, EType

type

);

192 void

Commit()

const

;

209 string Resolve

(

const string

& acc)

const

;

217

public CSraRef

226

eDebugInitialize = 3,

233 static int

SetDebugLevel(

int

new_level);

236 string

FindAccPath(

const string

& acc)

const

;

238 string

FindDereferencedAccPath(

const string

& acc_or_path)

const

;

247 string

GetCacheRoot()

const

;

250 void

SetCacheRoot(

const string

& path);

253 void

DeleteCacheOlderThan(

Uint4

days);

256 void

CommitConfig()

const

;

267 CTime

GetTimestamp(

const string

& path)

const

;

269 CTime

GetURLTimestamp(

const string

& url)

const

;

283

public CSraRef

289 CVDB

(

const CVDBMgr

& mgr,

const string

& acc_or_path);

311

public CSraRef

324

EMissing missing = eMissing_Throw);

326 const string

& acc_or_path,

327

EMissing missing = eMissing_Throw);

337 string

GetFullName(

void

)

const

;

351

public CSraRef

363 const char

* index_name,

364

EMissing missing = eMissing_Throw);

374 string

GetFullName(

void

)

const

;

390

public CSraRef

394

: m_RowOpened(

false

)

398

: m_RowOpened(

false

)

416 return

OpenRowRc(row_id) == 0;

418 void

CloseRow(

void

);

460 typedef

pair<TVDBRowId, CRef<CObject> >

TSlot

;

470 template

class

Object>

500

m_Index(kInvalidIndex)

507 Init

(cursor, 0, name,

NULL

, missing);

511 const char

* backup_name =

NULL

514 Init

(cursor, 0, name, backup_name, missing);

517 size_t

element_bit_size,

519 const char

* backup_name =

NULL

522 Init

(cursor, element_bit_size, name, backup_name, missing);

525 bool

IsStatic(

const CVDBCursor

& cursor)

const

;

529

m_Index = kInvalidIndex;

531 void

ResetIfAlwaysEmpty(

const CVDBCursor

& cursor);

553 size_t

element_bit_size,

555 const char

* backup_name,

564 template

size_t

ElementBitSize>

573 const char

* backup_name =

NULL

575

CVDBColumn

(cursor, ElementBitSize, name, backup_name, missing)

582 #define DECLARE_VDB_COLUMN(name) \ 583 CVDBValue::SRef name(TVDBRowId row, CVDBValue::EMissing missing = CVDBValue::eMissing_Throw) const { \ 584 return CVDBValue::SRef(m_Cursor, row, NCBI_NAME2(m_,name), missing); \ 586 CVDBColumn NCBI_NAME2(m_, name) 589 #define DECLARE_VDB_COLUMN_AS(type, name) \ 590 CVDBValueFor<type> name(TVDBRowId row, CVDBValue::EMissing missing = CVDBValue::eMissing_Throw) const { \ 591 return CVDBValueFor<type>(m_Cursor, row, NCBI_NAME2(m_,name), missing); \ 593 CVDBColumnBits<sizeof(type)*8> NCBI_NAME2(m_, name) 596 #define DECLARE_VDB_COLUMN_AS_STRING(name) \ 597 CVDBStringValue name(TVDBRowId row, CVDBValue::EMissing missing = CVDBValue::eMissing_Throw) const { \ 598 return CVDBStringValue(m_Cursor, row, NCBI_NAME2(m_,name), missing); \ 600 CVDBColumnBits<8> NCBI_NAME2(m_, name) 603 #define DECLARE_VDB_COLUMN_AS_4BITS(name) \ 604 CVDBValueFor4Bits name(TVDBRowId row) const { \ 605 return CVDBValueFor4Bits(m_Cursor, row, NCBI_NAME2(m_,name)); \ 607 CVDBColumnBits<4> NCBI_NAME2(m_, name) 610 #define INIT_VDB_COLUMN(name) \ 611 NCBI_NAME2(m_, name)(m_Cursor, #name) 612 #define INIT_VDB_COLUMN_BACKUP(name, backup_name) \ 613 NCBI_NAME2(m_, name)(m_Cursor, #name, #backup_name) 614 #define INIT_VDB_COLUMN_AS(name, type) \ 615 NCBI_NAME2(m_, name)(m_Cursor, "("

#type")"#name)

616 #define INIT_OPTIONAL_VDB_COLUMN(name) \ 617 NCBI_NAME2(m_, name)(m_Cursor, #name, NULL, CVDBColumn::eMissing_Allow) 618 #define INIT_OPTIONAL_VDB_COLUMN_BACKUP(name, backup_name) \ 619 NCBI_NAME2(m_, name)(m_Cursor, #name, #backup_name, CVDBColumn::eMissing_Allow) 620 #define INIT_OPTIONAL_VDB_COLUMN_AS(name, type) \ 621 NCBI_NAME2(m_, name)(m_Cursor, "("

#type")"#name, NULL, CVDBColumn::eMissing_Allow)

622 #define INIT_CONDITIONAL_VDB_COLUMN(name, condition) \ 623 NCBI_NAME2(m_, name)(m_Cursor, (condition)? #name: NULL, NULL, CVDBColumn::eMissing_Allow) 624 #define INIT_CONDITIONAL_VDB_COLUMN_AS(name, type, condition) \ 625 NCBI_NAME2(m_, name)(m_Cursor, (condition)? "("

#type")"#name: NULL, NULL, CVDBColumn::eMissing_Allow)

650

: m_Table(0), m_ColumnName(0), m_Row(0)

659

m_ColumnName =

column

.GetName();

694 const char

* param_name,

const CTempString

& param_value,

699

cursor.

SetParam

(param_name, param_value);

714 return

m_Ref.PrintFullName(

out

);

723

EMissing missing = eMissing_Throw);

725 void

x_ReportIndexOutOfBounds(

size_t

index)

const

;

726 void

x_ReportNotOneValue(

void

)

const

;

729 if

( index >=

size

() ) {

730

x_ReportIndexOutOfBounds(index);

733 void

x_CheckRange(

size_t

pos,

size_t len

)

const

;

736 if

(

size

() != 1 ) {

737

x_ReportNotOneValue();

794 return

x_ValueByRawIndex(index+raw_offset());

798 return Value

(index);

805 return

m_Ref.PrintFullName(

out

);

814 return

sub_index? (v&0xf): (v>>4);

818 return

sub_value(raw_data()[raw_index/2], raw_index%2);

821 void

x_ReportIndexOutOfBounds(

size_t

index)

const

;

824 if

( index >=

size

() ) {

825

x_ReportIndexOutOfBounds(index);

828 void

x_CheckRange(

size_t

pos,

size_t len

)

const

;

893 return

x_ValueByRawIndex(index+raw_offset());

897 return Value

(index);

904 return

m_Ref.PrintFullName(

out

);

913 return

(v>>(6-2*sub_index))&3;

917 return

sub_value(raw_data()[raw_index/4], raw_index%4);

920 void

x_ReportIndexOutOfBounds(

size_t

index)

const

;

923 if

( index >=

size

() ) {

924

x_ReportIndexOutOfBounds(index);

927 void

x_CheckRange(

size_t

pos,

size_t len

)

const

;

967 const char

* param_name,

const CTempString

& param_value,

1019 operator

double(

void

)

const

;

1045 const char

* param_name,

const CTempString

& param_value,

1053 return static_cast<const char

>

(

m_Data

);

1080 #ifndef NCBI_OS_MSWIN

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

CVDBColumnBits(const CVDBCursor &cursor, const char *name, const char *backup_name=NULL, EMissing missing=eMissing_Throw)

CVDBColumn(const CVDBCursor &cursor, const char *name, EMissing missing)

DECLARE_OPERATOR_BOOL(m_Index !=kInvalidIndex)

CVDBColumn(const CVDBCursor &cursor, size_t element_bit_size, const char *name, const char *backup_name=NULL, EMissing missing=eMissing_Throw)

TVDBColumnIdx GetIndex(void) const

const char * GetName(void) const

CVDBColumn(const CVDBCursor &cursor, const char *name, const char *backup_name=NULL, EMissing missing=eMissing_Throw)

TVDBRowIdRange GetRowIdRange(const CVDBCursor &cursor) const

bool RowIsOpened(void) const

CVDBCursor(const CVDBTable &table)

const CVDBTable & GetTable(void) const

void SetParam(const char *name, const CTempString &value) const

bool TryOpenRow(TVDBRowId row_id)

TVDBRowIdRange GetRowIdRange(TVDBColumnIdx column=0) const

CRequestContextUpdater(const CRequestContextUpdater &)=delete

CObject * Get(TVDBRowId row)

CVDBObjectCacheBase(const CVDBObjectCacheBase &)

void Put(CObject *curs, TVDBRowId row)

pair< TVDBRowId, CRef< CObject > > TSlot

void operator=(const CVDBObjectCacheBase &)

void Put(CRef< Object > &ref, TVDBRowId row=0)

CRef< Object > Get(TVDBRowId row=0)

CVDBStringValue(const CVDBCursor &cursor, TVDBRowId row, const CVDBColumn &column, EMissing missing=eMissing_Throw)

CVDBStringValue(const CVDBValue::SRef &ref)

const char * data(void) const

CVDBStringValue(CVDBCursor &cursor, const char *param_name, const CTempString &param_value, const CVDBColumn &column)

CVDBStringValue(const CVDBCursor &cursor, const CVDBColumn &column)

CTempString operator*(void) const

const char * GetName(void) const

const CVDBTable & GetTable(void) const

const CVDB & GetDb(void) const

const string & GetName(void) const

uint32_t size(void) const

TValue x_ValueByRawIndex(size_t raw_index) const

CVDBValueFor2Bits(const CVDBValue::SSaveRef &ref, const char *raw, uint32_t offset, uint32_t sz)

uint32_t raw_offset(void) const

const char * raw_data(void) const

CVDBValueFor2Bits(const CVDBCursor &cursor, TVDBRowId row, const CVDBColumn &column)

CVDBValue::SSaveRef m_Ref

static TValue sub_value(uint8_t v, size_t sub_index)

CNcbiOstream & PrintFullName(CNcbiOstream &out) const

CVDBValueFor2Bits(const CVDBValue::SRef &ref)

TValue operator[](size_t index) const

void x_CheckIndex(size_t index) const

TValue Value(size_t index) const

CVDBValueFor4Bits(const CVDBCursor &cursor, TVDBRowId row, const CVDBColumn &column)

TValue operator[](size_t index) const

TValue x_ValueByRawIndex(size_t raw_index) const

void x_CheckIndex(size_t index) const

uint32_t raw_offset(void) const

CVDBValue::SSaveRef m_Ref

const char * raw_data(void) const

static TValue sub_value(uint8_t v, size_t sub_index)

uint32_t size(void) const

CNcbiOstream & PrintFullName(CNcbiOstream &out) const

TValue Value(size_t index) const

CVDBValueFor4Bits(const CVDBValue::SRef &ref)

CVDBValueFor4Bits(const CVDBValue::SSaveRef &ref, const char *raw, uint32_t offset, uint32_t sz)

CVDBValueFor(const CVDBCursor &cursor, TVDBRowId row, const CVDBColumn &column, EMissing missing=eMissing_Throw)

const_iterator end() const

const TValue & operator*(void) const

CVDBValueFor< TValue > substr(size_t pos, size_t len) const

CVDBValueFor(CVDBCursor &cursor, const char *param_name, const CTempString &param_value, const CVDBColumn &column)

CVDBValueFor(const CVDBCursor &cursor, const CVDBColumn &column)

const TValue & operator[](size_t i) const

CVDBValueFor(const CVDBValue::SRef &ref)

const TValue * const_iterator

const TValue * data() const

const_iterator begin() const

const TValue * operator->(void) const

const TValue & Value(void) const

void x_CheckRange(size_t pos, size_t len) const

CNcbiOstream & PrintFullName(CNcbiOstream &out) const

CVDBValue(const CVDBCursor &cursor, TVDBRowId row, const CVDBColumn &column, EMissing missing=eMissing_Throw)

CVDBValue(const CVDBCursor &cursor, const CVDBColumn &column)

CVDBValue(const SRef &ref)

void x_CheckOneValue(void) const

CVDBValue(const CVDBCursor &cursor, const char *param_name, const CTempString &param_value, const CVDBColumn &column)

void x_CheckIndex(size_t index) const

const string & GetFullName(void) const

const string & GetName(void) const

static string ConvertAccOrSysPathToPOSIX(const string &acc_or_path)

static string ConvertSysPathToPOSIX(const string &sys_path)

CSraRef< const VPath > TParent

CVPath(const VPath *path)

Include a standard set of the NCBI C++ Toolkit most basic headers.

std::ofstream out("events_result.xml")

main entry point for tests

static const char table_name[]

static const char * column

#define NCBI_DEPRECATED_CTOR(decl)

Macro used to mark a constructor as deprecated.

TObjectType * ReleaseOrNull(void)

Release a reference to the object and return a pointer to the object.

uint32_t Uint4

4-byte (32-bit) unsigned integer

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

#define NCBI_SRAREAD_EXPORT

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

const TYPE & Get(const CNamedParameterList *param)

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > T2 value

GenericValue< UTF8<> > Value

GenericValue with UTF8 encoding.

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

@ Resolve

Try to resolve provided seq-ids.

static int GetDebugLevel()

#define row(bind, expected)

SRef(const CVDBCursor &cur, TVDBRowId r, const CVDBColumn &col)

const CVDBColumn & column

const CVDBCursor & cursor

void Set(const CVDBCursor &cursor, TVDBRowId row, const CVDBColumn &column)

const CVDBTable * m_Table

const char * m_ColumnName

DECLARE_SRA_REF_TRAITS(VDBManager, const)

CVDBValueFor< uint16_t > CVDBUInt16Value

pair< TVDBRowId, TVDBRowCount > TVDBRowIdRange

CVDBValueFor< char > CVDBBytesValue

string ToString(const wxRect &rc)

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