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NCBI C++ ToolKit: src/objtools/blast/blastdb_format/blastdb_formatter.cpp Source File

);

vector<string> data2write;

data2write.push_back(dbmeta.

());

data2write.push_back(dbmeta.

());

os <<

<< *fmt <<

;

+

.size();

data2write_size = accumulate(data2write.begin(), data2write.end(),

retval.reserve(

.size() + data2write_size -

(data2write.size() * 2));

retval.append(data2write[

]);

Definition of a customizable BLAST DB information formatter interface.

string m_FmtSpec

The output format specification.

vector< SIZE_TYPE > m_ReplOffsets

Vector of offsets where the replacements will take place.

string Write(const SSeqDBInitInfo &db_init_info)

Extracts the BLAST database information for the requested BLAST DB according to the output format spe...

string x_Replacer(const vector< string > &data2write) const

Replace format specifiers for the data contained in data2write.

CBlastDbFormatter(const string &fmt_spec)

Constructor.

vector< char > m_ReplacementTypes

Defines invalid user input exceptions.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

Uint8 GetTotalLength() const

Returns the sum of the lengths of all available sequences.

static string ESeqType2String(ESeqType type)

Converts a CSeqDB sequence type into a human readable string.

Int8 GetDiskUsage() const

Retrieve the disk usage in bytes for this BLAST database.

string GetTitle() const

Returns the database title.

int GetNumSeqs() const

Returns the number of sequences available.

string GetDate() const

Returns the construction date of the database.

EBlastDbVersion GetBlastDbVersion() const

Return blast db version.

#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.

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.

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.

NCBI_NS_STD::string::size_type SIZE_TYPE

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string UInt8ToString(Uint8 value, TNumToStringFlags flags=0, int base=10)

Convert UInt8 to string.

Structure to define basic information to initialize a BLAST DB.

string m_BlastDbName

The BLAST DB name.

CRef< CSeqDB > InitSeqDb() const

Create a new CSeqDB instance from this object.

CSeqDB::ESeqType m_MoleculeType

The molecule type.

Auxiliary functor to compute the length of a string (shamlessly copied from seq_writer....

SIZE_TYPE operator()(SIZE_TYPE a, const string &b) const

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