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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqdbtax_8cpp_source.html below:

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

38 #define NCBI_USE_ERRCODE_X Objtools_SeqDBTax 126

: m_AllTaxidCount(0),

150 Uint4

data_start = (4 +

156 if

(idx_file_len < (data_start +

sizeof

(

CSeqDBTaxId

))) {

170 const unsigned

TAX_DB_MAGIC_NUMBER = 0x8739;

175 ERR_POST

(

"Error: Tax database file has wrong magic number."

);

184 int

taxid_array_size =

int

((idx_file_len - data_start)/

sizeof

(

CSeqDBTaxId

));

190

") entries but file has room for ("

<< taxid_array_size

221 if

(

.IsMissingTaxInfo())

return false

;

224 Int4

high_index =

.GetTaxidCount() - 1;

226 const char

* Data =

.GetDataPtr();

231 if

((tax_id < low_taxid) || (tax_id > high_taxid))

234 Int4

new_index = (low_index+high_index)/2;

235 Int4

old_index = new_index;

240 if

(tax_id < curr_taxid) {

241

high_index = new_index;

242

}

else if

(tax_id > curr_taxid){

243

low_index = new_index;

248

new_index = (low_index+high_index)/2;

249 if

(new_index == old_index) {

250 if

(tax_id > curr_taxid) {

255

old_index = new_index;

258 if

(tax_id == Index[new_index].

GetTaxId

()) {

259 info

.taxid = tax_id;

261 Uint4

begin_data(Index[new_index].GetOffset());

264 if

(new_index == high_index) {

266

end_data =

Uint4

(

.GetDataFileSize());

268 if

(end_data < begin_data) {

270 ERR_POST

(

"Error: Offset error at end of taxdb file."

);

274

end_data = (Index[new_index+1].

GetOffset

());

277 const char

* start_ptr = &Data[begin_data];

288 if

(rc1 && rc2 && rc3 &&

buffer

.Size()) {

Uint4 m_Offset

The offset of the start of the taxonomy data.

Int4 GetOffset() const

Return the offset field (in host order)

TTaxId GetTaxId() const

Return the taxonomic identifier field (in host order)

Uint4 m_Taxid

The taxonomic identifier.

CSeqDBTaxId(const CSeqDBTaxId &)

This structure should not be copy constructed.

CSeqDBTaxId()

Constructor.

static bool GetTaxNames(TTaxId tax_id, SSeqDBTaxInfo &info)

Get the taxonomy names for a given tax id.

void GetString(string &s) const

Return the data by assigning it to a string.

const char * GetDataPtr()

bool m_MissingDB

Indicator if tax db files are missing.

unique_ptr< CMemoryFile > m_IndexFileMap

Memory map of the index file.

const Int4 GetTaxidCount()

const CSeqDBTaxId * GetIndexPtr()

unique_ptr< CMemoryFile > m_DataFileMap

string m_IndexFN

The filename of the taxonomic db index file.

string m_DataFN

The filename of the taxnomoic db data file.

Int4 m_AllTaxidCount

Total number of taxids in the database.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define TAX_ID_FROM(T, value)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

Int8 GetLength(void) const

Get size of file.

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

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.

unsigned int

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

string SeqDB_ResolveDbPath(const string &filename)

Resolve a file path using SeqDB's path algorithms.

bool SeqDB_SplitString(CSeqDB_Substring &buffer, CSeqDB_Substring &front, char delim)

Parse a prefix from a substring.

T SeqDB_GetStdOrd(const T *stdord_obj)

Read a network order integer value.

Defines database volume access classes.

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