Search Toolkit Book for CAmbigDataBuilder

Encode ambiguities in blast database format. More...

Collaboration diagram for CAmbigDataBuilder:

Public Member Functions
	CAmbigDataBuilder (int sz)
	Constructor. More...

int	Check (int data, int offset)
	Check (and maybe store) a possibly ambiguous letter. More...

void	GetAmbig (string &amb)
	Compute and return the encoded list of ambiguities. More...

void	x_PackNewAmbig (string &amb, const CAmbiguousRegion &r)
	Append the 'new' encoding of one ambiguous region to a string. More...

void	x_PackOldAmbig (string &amb, CAmbiguousRegion &r)
	Append the 'old' encoding of one ambiguous region to a string. More...

Private Member Functions
void	x_AddAmbig (int value, int offset)
	Add an ambiguity letter. More...

int	x_Random (int value)
	Pick a random letter from the set represented by an ambiguity. More...

Private Attributes
int	m_Log2 [16]
	Table mapping 1248 to 0123. More...

int	m_Size
	Size of the input sequence. More...

vector< CAmbiguousRegion >	m_Regions
	Ambiguous regions for the sequence. More...

CRandom	m_Random
	Random number generator. More...

Detailed Description

Encode ambiguities in blast database format.

This class encodes nucleotide ambiguities in blast database format from a series of ambiguous letter values and offsets.

Definition at line 154 of file writedb_convert.cpp.

Constructor & Destructor Documentation

◆ CAmbigDataBuilder()

CAmbigDataBuilder::CAmbigDataBuilder ( int sz )

inline

Constructor.

Parameters

sz	Size of the sequence in letters. [in]

Definition at line 158 of file writedb_convert.cpp.

References i, and m_Log2.

Member Function Documentation

◆ Check()

int CAmbigDataBuilder::Check	(	int	data,
		int	offset
	)

inline

Check (and maybe store) a possibly ambiguous letter.

If the letter is not an ambiguity, this method converts it to Blast-NA2 format, and returns it. If the letter value is an ambiguity, it is added to the list of ambiguities, and a randomly selected letter value is returned. Each ambiguity letter (there are 12 for nucleotide) represents a possiblity between two or more nucleotide bases. The random letter is always selected from the set of these values corresponding to the input ambiguity value.

Parameters

data	Letter value in BlastNA8. [in]
offset	Offset of letter. [in]

Returns: Value to encode as BlastNA2.

Definition at line 186 of file writedb_convert.cpp.

References _ASSERT, data, m_Log2, m_Size, offset, x_AddAmbig(), and x_Random().

Referenced by WriteDB_Ncbi4naToBinary().

◆ GetAmbig()

void CAmbigDataBuilder::GetAmbig ( string & amb )

inline

Compute and return the encoded list of ambiguities.

The list of ambiguous regions is packed in blast database format and returned to the user. If the length of the sequence is larger than 2^24-1, or any of the ambiguous regions is larger than 0xF, the 'new' format of ambiguity is used, which allows for larger ambiguous regions at higher sequence offsets, but requires 8 bytes per ambiguous region instead of four bytes required by the 'old' format.

Parameters

amb	The ambiguity data in blast database format. [out]

Definition at line 238 of file writedb_convert.cpp.

References i, int, m_Regions, m_Size, s_AppendInt4(), x_PackNewAmbig(), and x_PackOldAmbig().

Referenced by WriteDB_Ncbi4naToBinary().

◆ x_AddAmbig()

void CAmbigDataBuilder::x_AddAmbig	(	int	value,
		int	offset
	)

inlineprivate

Add an ambiguity letter.

The internal encoding contains a list of ambiguous ranges. This method adds the given letter at the given offset to the most recent region, if possible, or creates a new region for it.

Parameters

value	Ambiguous letter to add. [in]
offset	Offset at which letter occurs. [in]

Definition at line 349 of file writedb_convert.cpp.

References m_Regions, offset, r(), and rapidjson::value.

Referenced by Check().

◆ x_PackNewAmbig()

void CAmbigDataBuilder::x_PackNewAmbig	(	string &	amb,
		const CAmbiguousRegion &	r
	)

inline

Append the 'new' encoding of one ambiguous region to a string.

Parameters

amb	String encoding of all ambiguous regions. [in\|out]
r	Ambiguous region. [in]

Definition at line 289 of file writedb_convert.cpp.

References _ASSERT, A1, ch0, ch1, r(), and s_AppendInt4().

Referenced by GetAmbig().

◆ x_PackOldAmbig()

void CAmbigDataBuilder::x_PackOldAmbig	(	string &	amb,
		CAmbiguousRegion &	r
	)

inline

Append the 'old' encoding of one ambiguous region to a string.

Parameters

amb	String encoding of all ambiguous regions. [in\|out]
r	Ambiguous region. [in]

Definition at line 317 of file writedb_convert.cpp.

References _ASSERT, A1, ch0, and r().

Referenced by GetAmbig().

◆ x_Random()

int CAmbigDataBuilder::x_Random ( int value )

inlineprivate

Pick a random letter from the set represented by an ambiguity.

This method takes an ambiguous value as input, and returns a letter randomly chosen from the set of letters the ambiguity represents.

Parameters

value An ambiguous letter. [in]

Returns: A non-ambiguous letter.

Definition at line 369 of file writedb_convert.cpp.

References _ASSERT, CRandom::GetRand(), i, m_Random, and rapidjson::value.

Referenced by Check().

Member Data Documentation

◆ m_Log2

int CAmbigDataBuilder::m_Log2[16]

private

Table mapping 1248 to 0123.

Definition at line 415 of file writedb_convert.cpp.

Referenced by CAmbigDataBuilder(), and Check().

◆ m_Random

CRandom CAmbigDataBuilder::m_Random

private

Random number generator.

Definition at line 424 of file writedb_convert.cpp.

Referenced by x_Random().

◆ m_Regions

vector<CAmbiguousRegion> CAmbigDataBuilder::m_Regions

private

Ambiguous regions for the sequence.

Definition at line 421 of file writedb_convert.cpp.

Referenced by GetAmbig(), and x_AddAmbig().

◆ m_Size

int CAmbigDataBuilder::m_Size

private

Size of the input sequence.

Definition at line 418 of file writedb_convert.cpp.

Referenced by Check(), and GetAmbig().

The documentation for this class was generated from the following file:

src/objtools/blast/seqdb_writer/writedb_convert.cpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CAmbigDataBuilder()

Member Function Documentation

◆ Check()

◆ GetAmbig()

◆ x_AddAmbig()

◆ x_PackNewAmbig()

◆ x_PackOldAmbig()

◆ x_Random()

Member Data Documentation

◆ m_Log2

◆ m_Random

◆ m_Regions

◆ m_Size