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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/writedb__volume_8cpp_source.html below:

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

m_OidMasks (oid_masks),

&

,

& binhdr,

(! (seq.size() && binhdr.size())) {

);

overfull =

;

num = (

)idlist.size();

(

blob_i = 0; blob_i < (

) blobs.size(); blob_i++) {

(!

[blob_i / 2]->CanFit(blobs[blob_i]->Size())) {

(

&& overfull) {

pair<set<string>::iterator,

> rv;

((rv.second ==

) && (!(*iter)->IsLocal())) {

<<

<< endl <<

<< endl;

<<

<< endl

off_hdr(0), off_seq(0), off_amb(0);

& seqid = **iter;

(seqid.

()) {

gi = seqid.

();

model_id_count = 0;

(model_id_count == num_accs) {

(

col_i = 0; col_i < (

)

.size(); col_i++) {

(col_i * 2 < (

) blobs.size());

(col_i == maskcol_id) {

[col_i]->AddBlob(*blobs[col_i * 2], *blobs[col_i * 2 + 1]);

[col_i]->AddBlob(*blobs[col_i * 2]);

(**iter).RenameSingle();

= index_filename.find_last_of(

);

(**iter).RenameFileIndex(num_digits);

(**iter).ListFiles(files,

);

extn(

?

:

);

);

extn[1] =

[col_id];

(mbo) new_col->AddByteOrder(

,

(

j = 0; j <

; j++) {

(mbo) new_col->AddBlob(blank, blank);

new_col->AddBlob(blank);

&

)

((col_id < 0) || (col_id >= (

)

.size())) {

);

m_Type(mask_type), m_TotalOids(0), m_Map(

), m_MapSize(0) { }

= (size_t) ((num_oids - 1U) / BITWIDTH + 1U);

BITSHIFT = 3;

BITMASK = (1U << BITSHIFT) - 1U;

= *oid >> BITSHIFT;

ncbi::TMaskedQueryRegions mask

`Blob' Class for SeqDB (and WriteDB).

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

CWriteDB_IndexFile class.

unsigned int WriteInt4(int data)

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

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.

static string MakeShortName(const string &base, int index)

Construct the short name for a volume.

unsigned int Write(const CTempString &data)

Write contents of a string to the file.

virtual void RenameSingle()

Rename this file, disincluding the volume index.

This class builds the volume index file (pin or nin).

void AddSequence(int length, unsigned int hdr, unsigned int seq)

Add a sequence to a protein index file (pin).

bool CanFit()

Returns true if another sequence can fit into the file.

void AddHash(int oid, int hash)

Set a sequence's hash value.

bool CanFit(int num)

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

void ListFiles(vector< string > &files) const

List Filenames.

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)

void x_CreateBitMap(int num_oids)

void x_Flush()

This should flush any unwritten data to disk.

void Close(int total_oids)

Total num of oids in db or vol.

CWriteDB_OidList(const string &dbname, bool protein, int index, Uint8 max_fsize, EOidMaskType mask_type)

vector< uint32_t > m_OidList

bool CanFit(int size, int letters)

Returns true if the specified amount of data would fit.

void AddSequence(const string &sequence, unsigned int &offset, int length)

Add a protein sequence to this file.

~CWriteDB_Volume()

Destructor.

Uint8 m_OidMasks

Oid masks.

vector< CRef< CSeq_id > > TIdList

Type used for lists of identifiers.

void RenameSingle()

Rename all volumes files to single-volume names.

void AddColumnMetaData(int col_id, const string &key, const string &value)

Add meta data to a column.

void RenameFileIndex(unsigned int num_digits)

set< string > m_IdSet

Included Seq_ids.

CRef< CWriteDB_Isam > m_PigIsam

PIG index (ppi+ppd, protein only).

CRef< CWriteDB_OidList > m_ExModelList

string m_VolName

Database name plus version (if used).

CRef< CWriteDB_HeaderFile > m_Hdr

Header file (phr / nhr).

CWriteDB_Volume(const string &dbname, bool protein, const string &title, const string &date, int index, Uint8 max_file_size, Uint8 max_letters, EIndexType indices, EBlastDbVersion dbver=eBDB_Version5, Uint8 oid_masks=EOidMaskType::fNone)

Build a database volume.

const int & GetOID() const

Get the current OID of the volume.

bool m_Open

True if user can still append sequences.

vector< CRef< CBlastDbBlob > > TBlobList

Type used for lists of identifiers.

CRef< CWriteDB_Isam > m_HashIsam

Hash index (phi+phd or nhi+nhd).

CRef< CWriteDB_Isam > m_AccIsam

Accession index (psi+psd / nsi+nsd).

CRef< CWriteDB_Isam > m_TraceIsam

Trace ID index (pti+ptd or nti+ntd).

EBlastDbVersion m_DbVersion

Blast DB version.

int m_OID

Next assigned OID.

int CreateColumn(const string &title, const TColumnMeta &meta, Uint8 max_sz, bool mbo=true)

Create a new database column.

int m_Index

Index of this volume (1 based).

bool WriteSequence(const string &seq, const string &ambig, const string &binhdr, const TIdList &ids, int pig, int hash, const TBlobList &blobs, int maskcol_id=-1)

Add a sequence to this volume.

CRef< CWriteDB_Isam > m_GiIsam

GI index (pni+pnd / nni+nnd).

CRef< CWriteDB_GiIndex > m_GiIndex

OID->GI lookup (pgx or ngx).

CRef< CWriteDB_SequenceFile > m_Seq

Sequence file (psq / nsq).

bool m_Protein

True for protein; false for nucleotide.

int x_FindNuclLength(const string &seq)

Compute base-length of compressed nucleotide sequence.

EIndexType m_Indices

Indices are sparse, full, or disabled.

void Close()

Close the volume.

CRef< CWriteDB_IndexFile > m_Idx

Index file (pin / nin).

string m_DbName

Base name of the database.

vector< CRef< CWriteDB_Column > > m_Columns

Database columns.

void ListFiles(vector< string > &files) const

List all files associated with this volume.

EIndexType

Whether and what kind of indices to build.

@ eAddHash

Add an index from sequence hash to OID.

@ eSparseIndex

Use only simple accessions in the string index.

@ eNoIndex

Build a database without any indices.

@ eAddTrace

OR this in to add an index for trace IDs.

iterator_bool insert(const value_type &val)

#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 LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_THROW(exception_class, err_code, message)

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

void Info(CExceptionArgs_Base &args)

@ fLabel_UpperCase

Upper case label, with special encoding for PDB chain-ids.

@ fLabel_Default

default options - always show the version

@ eDefault

default is to show type + content

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

int32_t Int4

4-byte (32-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.

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

unsigned int

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

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

const string SeqDB_GetOidMaskFileExt(bool db_is_protein, EOidMaskType t)

EBlastDbVersion

BLAST database version.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static bool ambig(char c)

Defines exception class for WriteDB.

int WriteDB_FindSequenceLength(bool protein, const string &seq)

Compute length of sequence from raw packing.

@ eAcc

Accession (string) Index.

@ ePig

Protein Identifier Group.

USING_SCOPE(std)

Include C++ std library symbols.

Code for database volume construction.

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