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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqdbgimask_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/blast/seqdb_reader/seqdbgimask.cpp Source File

41 #if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION > 550)) && \ 42  (!defined(NCBI_COMPILER_MIPSPRO)) ) 45  const

vector <string> & mask_name)

47

m_MaskNames (mask_name),

49

m_OffsetLease (atlas),

51

m_IndexFile (m_Atlas),

52

m_OffsetFile (m_Atlas)

81  if

(page == -1)

return

;

95

vol =

offset

[pagesize + page * 2];

96

off =

offset

[pagesize + page * 2 + 1];

103  const Int4

* datap = (

const Int4

*)

108

datap = (

const Int4

*)

124  string

ext_i(

".gmi"

);

125  string

ext_o(

".gmo"

);

126  string

ext_d(

".gmd"

);

128  const Int2

bytetest = 0x0011;

129  const char

*ptr = (

const char

*) &bytetest;

130  if

(ptr[0] == 0x11) {

132

ext_i[2] = ext_o[2] = ext_d[2] =

'n'

;

144  if

(! (found_i && found_o)) {

146  "Could not open gi-mask index files."

);

162  "Could not open gi-mask data file."

);

165  for

(

int

vol=0; vol<

m_NumVols

; ++vol) {

169

fnd <<

m_MaskNames

[algo_id] <<

"."

<< vol/10 << vol%10 << ext_d;

175  "Could not open gi-mask data files."

);

195  const char

* ptr =

file

.GetFileDataPtr(lease, begin, end);

202  const int

kFixedFieldBytes = 32;

211  int

fmt_version = header.

ReadInt4

();

213  if

(fmt_version != 1) {

216  "Gi-mask file uses unknown format_version."

);

`Blob' Class for SeqDB (and WriteDB).

Int4 ReadInt4()

Read a 4 byte integer at the pointer (and move the pointer).

void ReferTo(CTempString data)

Refer to an existing memory area.

CTempString ReadString(EStringFormat fmt)

Read string data from the blob (moving the read pointer).

void Init(const string &filename)

Initializes a memory map object.

void GetMaskData(int algo_id, TGi gi, CSeqDB::TSequenceRanges &ranges, CSeqDBLockHold &locked)

Get the mask data for GI.

CSeqDBRawFile m_OffsetFile

Offset file.

const vector< string > m_MaskNames

The set of gi masks found in alias description.

Int4 m_AlgoId

The current used mask id.

void x_ReadFields(void)

Open files and read field data from the atlas.

string m_Desc

The description about the masking algo.

Int4 m_NumIndex

Number of Gi indices.

Int4 m_OffsetSize

Offset size.

static void s_GetFileRange(TIndx begin, TIndx end, CSeqDBRawFile &file, CSeqDBFileMemMap &lease, CBlastDbBlob &blob)

Get a range of the index or data file.

CSeqDBAtlas::TIndx TIndx

File offset type.

CSeqDBAtlas & m_Atlas

Reference to the atlas.

vector< CSeqDBRawFile * > m_DataFile

Data file.

Int4 m_PageSize

Page size.

const Uint4 * m_GiIndex

Mapped Gi index.

void x_VerifyAlgorithmId(int algo_id) const

Verify the algorithm exists. If not, raise an exception.

static const CBlastDbBlob::EStringFormat kStringFmt

Sgring format used by gi mask files.

void x_Open(Int4 algo_id)

Open file for a chosen algo_id.

CSeqDBRawFile m_IndexFile

Index file.

string m_Date

The create date of the GI mask.

CSeqDBGiMask(CSeqDBAtlas &atlas, const vector< string > &mask_name)

Constructor.

CSeqDBFileMemMap m_IndexLease

Index file lease.

const string & GetDesc(int algo_id, CSeqDBLockHold &locked)

Get the mask description for algo id.

vector< CSeqDBFileMemMap * > m_DataLease

Data file lease.

Int4 m_NumGi

Number of Gis.

static bool s_BinarySearch(const T *keys, const int n, const T key, int &idx)

Binary search for value associated with a key.

Int4 m_IndexStart

Start offset (in the index file) of the offset array.

CSeqDBFileMemMap m_OffsetLease

Offset file lease.

Int4 m_NumVols

Number of data volumes.

TIndx GetFileLength() const

Get the length of the file.

bool Open(const CSeqDB_Path &name)

MMap or Open a file.

const char * GetFileDataPtr(CSeqDBFileMemMap &lease, TIndx start, TIndx end) const

Get a pointer to a section of the file.

const string & GetPathS() const

Get the path as a string.

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

#define NCBI_THROW(exception_class, err_code, message)

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

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

string SeqDB_ResolveDbPath(const string &filename)

Resolve a file path using SeqDB's path algorithms.

This file defines several SeqDB utility functions related to byte order and file system portability.

#define SEQDB_FILE_ASSERT(YESNO)

Defines gi-based mask data files.

List of sequence offset ranges.

void append(const void *src, size_type num_elements)

Append extra elements at the end.


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