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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/writedb__isam_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/blast/seqdb_writer/writedb_isam.cpp Source File

extn[0] = protein ?

:

;

extn[2] = is_index ?

:

;

m_DataFile (datafile),

isam_version = 1;

max_line_size = 0;

);

key_off.reserve(nsamples);

output_count = 0;

element, prev_elem;

element[0] = char(0);

(iter != end_iter) {

prev_elem.swap(element);

(prev_elem == element) {

key_off.push_back((

) key_buffer.size());

key_buffer.append(element.data(), element.length()-1);

key_buffer.append(NUL);

key_off.push_back((

) key_buffer.size());

key_off_start =

+ (nsamples + 1) * 8;

(

= 0;

< key_off.size();

++) {

(

= 0;

<

;

++) {

(prevp && (*prevp == elem)) {

(

= 0;

<

;

++) {

(prevp && (*prevp == elem)) {

);

sz = sprintf(

,

, (

)

);

& seqid = **iter;

(seqid.

()) {

& seqid = **iter;

& seqid = **iter;

(seqid.

()) {

(objid.

()) {

(! mol.

()) {

);

short_id(full_id, 4);

(short_id[4] ==

)

(

.size() !=

.size())

(

.CanGetAccession()) {

acc =

.GetAccession();

(

.CanGetName()) {

(! acc.

()) {

ver =

.CanGetVersion() ?

.GetVersion() : 0;

(ver && acc.

()) {

memcpy(

, sbuf, sz);

(

= 0;

< sz;

++) {

sz += sprintf(

+ sz,

, oid);

(acc.

() && ver) {

sz = acc.

();

sz += sprintf(

+ sz,

, ver);

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

CWriteDB_IndexFile class.

Uint8 m_MaxFileSize

Maximum file size in bytes.

unsigned int WriteInt4(int data)

Write an Int4 (in bigendian order) to the file.

bool m_Created

True if the file has already been opened.

const string & GetFilename() const

Get the current filename for this file.

virtual void RenameFileIndex(unsigned int num_digits)

void Create()

Create and open the file.

void Close()

Close the file, flushing any remaining data to disk.

unsigned int Write(const CTempString &data)

Write contents of a string to the file.

virtual void RenameSingle()

Rename this file, disincluding the volume index.

unsigned int WriteInt8(Int8 data)

Write an Int8 (in bigendian order) to the file.

~CWriteDB_IsamData()

Destructor.

CWriteDB_IsamData(EIsamType itype, const string &dbname, bool protein, int index, Uint8 max_file_size)

Constructor for an ISAM data file.

void x_Flush()

This should flush any unwritten data to disk.

CWriteDB_IsamIndex class.

void x_AddLocal(int oid, const CSeq_id &seqid)

Add a 'local' type Seq-id.

void AddPig(int oid, int pig)

Set PIG for a protein sequence.

@ eKeyDelim

Byte indicating end of key.

@ eIsamNumericType

Numeric ISAM file with Int4 key.

@ eMaxStringLine

Maximum line size for string.

@ eRecordDelim

Byte indicating end of data.

@ eIsamStringType

String ISAM file.

@ eIsamNumericLong

Numeric ISAM file with Int8 key.

@ eKeyOffset

Offset of the key offset table.

void x_AddTraceIds(int oid, const TIdList &idlist)

Store GIs found in Seq-id list.

bool m_UseInt8

Use an Int8 table for numeric IDs.

void AddHash(int oid, int hash)

Set a sequence's hash value.

void x_AddString(int oid, const CTempString &s, int ver)

Add an accession with a version.

bool CanFit(int num)

Tests whether there is room for a given number of IDs.

void x_AddStringData(int oid, const CTempString &s)

Add a string to the string table.

void x_AddStringIds(int oid, const TIdList &idlist)

Compute and store string IDs from Seq-ids.

bool Empty() const

Tests whether the index file is empty (has no entries).

void x_AddPatent(int oid, const CSeq_id &seqid)

Add a 'patent' type Seq-id.

Uint8 m_DataFileSize

Accumulated size of data file.

EIsamType m_Type

Type of identifier indexed here.

CRef< CWriteDB_IsamData > m_DataFile

The data file associated with this index file.

void x_AddPdb(int oid, const CSeq_id &seqid)

Add the index strings for the specified PDB identifier.

void x_Flush()

Flush index data in preparation for Close().

void x_AddTextId(int oid, const CTextseq_id &id)

Add a text ID.

void x_AddGis(int oid, const TIdList &idlist)

Store GIs found in Seq-id list.

CWriteDB_IsamIndex(EIsamType itype, const string &dbname, bool protein, int index, CRef< CWriteDB_IsamData > datafile, bool sparse, Int8 max_file_size=0)

Constructor for an ISAM index file.

vector< SIdOid > m_NumberTable

Sorted list of numbers.

void AddIds(int oid, const TIdList &ids)

Add sequence IDs to the index file.

CWriteDB_PackedSemiTree m_StringSort

Sorted list of strings.

int m_Oid

OID being to which seqid strings are being added.

vector< CRef< CSeq_id > > TIdList

Type used for lists of sequence identifiers.

int m_PageSize

Ratio of samples to data records.

~CWriteDB_IsamIndex()

Destructor.

void x_FlushStringIndex()

Flush index data for a string ISAM file.

void x_WriteHeader()

Write the ISAM index header to disk.

void x_Free()

Free no longer needed array and string memory.

set< string > m_OidStringData

Keep track of string seqids associated with current value of m_Oid.

bool m_Sparse

If true, fewer strings are used.

void x_FlushNumericIndex()

Flush index data for a numeric ISAM file.

void x_AddStdString(int oid, const string &s)

Add a string to the string table.

int m_BytesPerElem

Byte (over)estimate per Seq-id.

void AddHash(int oid, int hash)

Set a sequence's hash value.

~CWriteDB_Isam()

Destructor.

CRef< CWriteDB_IsamData > m_DFile

Data file, contains one record for each key/oid pair.

bool CanFit(int num)

Tests whether there is room for a given number of IDs.

CRef< CWriteDB_IsamIndex > m_IFile

Index file, contains meta data and samples of the key/oid pairs.

void ListFiles(vector< string > &files) const

List Filenames.

vector< CRef< CSeq_id > > TIdList

Type used for lists of sequence identifiers.

CWriteDB_Isam(EIsamType itype, const string &dbname, bool protein, int index, Uint8 max_file_size, bool sparse)

Constructor for an ISAM index file.

void AddPig(int oid, int pig)

Set PIG for a protein sequence.

void AddIds(int oid, const TIdList &ids)

Add sequence IDs to the index file.

void RenameSingle()

Rename files to single-volume names.

void Close()

Flush data to disk and close all associated files.

void RenameFileIndex(unsigned int num_digits)

Class providing iteration over string data.

void Get(string &data)

Get the string pointed to by this iterator.

void Insert(const char *x, int L)

Insert string data into the container.

Iterator End()

Get an iterator to the end of this collection.

void Sort()

Sort all contained data.

int Size() const

Return the number of contained entries.

void Clear()

Clear all objects from this container.

Iterator Begin()

Get an iterator to the beginning of this collection.

iterator_bool insert(const value_type &val)

#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.

const TPrim & Get(void) const

const string AsFastaString(void) const

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

void Reset(void)

Reset reference object.

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static Int8 StringToInt8(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to Int8.

static int strncasecmp(const char *s1, const char *s2, size_t n)

Case-insensitive comparison of two zero-terminated strings, narrowed to the specified number of chara...

const char * data(void) const

Return a pointer to the array represented.

bool empty(void) const

Return true if the represented string is empty (i.e., the length is zero)

size_type size(void) const

Return the length of the represented array.

bool IsStr(void) const

Check if variant Str is selected.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsId(void) const

Check if variant Id is selected.

bool CanGetTag(void) const

Check if it is safe to call GetTag method.

const TDb & GetDb(void) const

Get the Db member data.

const TStr & GetStr(void) const

Get the variant data.

TId GetId(void) const

Get the variant data.

const TPdb & GetPdb(void) const

Get the variant data.

bool IsGeneral(void) const

Check if variant General is selected.

E_Choice Which(void) const

Which variant is currently selected.

bool CanGetMol(void) const

Check if it is safe to call GetMol method.

TGi GetGi(void) const

Get the variant data.

const TMol & GetMol(void) const

Get the Mol member data.

const TLocal & GetLocal(void) const

Get the variant data.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

unsigned int

A callback function used to compare two keys in a database.

constexpr auto sort(_Init &&init)

#define row(bind, expected)

Element type for numeric tables.

int oid() const

Return the oid.

Int8 id() const

Return the numeric identifier.

Data conversion tools for CWriteDB and associated code.

Defines exception class for WriteDB.

int s_DivideRoundUp(int value, int blocksize)

Divide by a number, rounding up to a whole integer.

bool s_NoCaseEqual(CTempString &a, CTempString &b)

Compare two strings, ignoring case.

USING_SCOPE(std)

Import C++ std namespace.

static string s_IsamExtension(EWriteDBIsamType itype, bool protein, bool is_index)

Compute the file extension for an ISAM file.

Code for database isam construction.

EWriteDBIsamType

Type of ISAM index.

@ eAcc

Accession (string) Index.

@ ePig

Protein Identifier Group.

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