nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET > Struct Template Reference

Detailed description

template< Alphabet SEQUENCE_ALPHABET>
struct nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >

Concrete class to encode a host-side SequenceData object.

Definition at line 270 of file sequence_encoder.cpp.

Inheritance diagram for nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >:

Public Methods
	SequenceDataEncoderImpl (SequenceDataHost *data, bool append=false)
void	reserve (const uint32 n_sequences, const uint32 n_bps)
void	begin_batch (void)
void	push_back (const uint32 in_sequence_len, const char *name, const uint8 *base_pairs, const uint8 *quality, const QualityEncoding quality_encoding, const uint32 max_sequence_len, const uint32 trim3, const uint32 trim5, const StrandOp conversion_flags)
void	end_batch (void)
const SequenceDataInfo *	info () const
Public Methods inherited from nvbio::io::SequenceDataEncoder
	SequenceDataEncoder (const Alphabet alphabet)
virtual	~SequenceDataEncoder ()
Alphabet	alphabet () const

Static Public Members
static const uint32	SEQUENCE_BITS = SequenceDataTraits<SEQUENCE_ALPHABET>::SEQUENCE_BITS
static const bool	SEQUENCE_BIG_ENDIAN = SequenceDataTraits<SEQUENCE_ALPHABET>::SEQUENCE_BIG_ENDIAN
static const uint32	SEQUENCE_SYMBOLS_PER_WORD = SequenceDataTraits<SEQUENCE_ALPHABET>::SEQUENCE_SYMBOLS_PER_WORD

Additional Inherited Members
Public Types inherited from nvbio::io::SequenceDataEncoder
enum	StrandOp { NO_OP = 0x0000, REVERSE_OP = 0x0001, COMPLEMENT_OP = 0x0002, REVERSE_COMPLEMENT_OP = 0x0003 }

Constructor & Destructor Documentation

template<Alphabet SEQUENCE_ALPHABET>

nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >::SequenceDataEncoderImpl ( SequenceDataHost *  data, bool  append = false  )

inline

constructor

Definition at line 279 of file sequence_encoder.cpp.

Member Function Documentation

template<Alphabet SEQUENCE_ALPHABET>

void nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >::begin_batch ( void  )

inlinevirtual

signals that the batch is to begin

Reimplemented from nvbio::io::SequenceDataEncoder.

Definition at line 296 of file sequence_encoder.cpp.

template<Alphabet SEQUENCE_ALPHABET>

void nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >::end_batch ( void  )

inlinevirtual

signals that the batch is complete

Reimplemented from nvbio::io::SequenceDataEncoder.

Definition at line 406 of file sequence_encoder.cpp.

template<Alphabet SEQUENCE_ALPHABET>

const SequenceDataInfo* nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >::info ( ) const

inlinevirtual

return the sequence data info

Reimplemented from nvbio::io::SequenceDataEncoder.

Definition at line 415 of file sequence_encoder.cpp.

template<Alphabet SEQUENCE_ALPHABET>

void nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >::push_back ( const uint32  in_sequence_len, const char *  name, const uint8 *  base_pairs, const uint8 *  quality, const QualityEncoding  quality_encoding, const uint32  max_sequence_len, const uint32  trim3, const uint32  trim5, const StrandOp  conversion_flags  )

inlinevirtual

add a sequence to the end of this batch

Parameters

sequence_len	input sequence length
name	sequence name
base_pairs	list of base pairs
quality	list of base qualities
quality_encoding	quality encoding scheme
truncate_sequence_len	truncate the sequence if longer than this
conversion_flags	conversion operators applied to the strand

Reimplemented from nvbio::io::SequenceDataEncoder.

Definition at line 331 of file sequence_encoder.cpp.

template<Alphabet SEQUENCE_ALPHABET>

void nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >::reserve ( const uint32  n_sequences, const uint32  n_bps  )

inlinevirtual

reserve enough storage for a given number of sequences and bps

Reimplemented from nvbio::io::SequenceDataEncoder.

Definition at line 286 of file sequence_encoder.cpp.

Member Data Documentation

template<Alphabet SEQUENCE_ALPHABET>

const bool nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >::SEQUENCE_BIG_ENDIAN = SequenceDataTraits<SEQUENCE_ALPHABET>::SEQUENCE_BIG_ENDIAN

static

Definition at line 274 of file sequence_encoder.cpp.

template<Alphabet SEQUENCE_ALPHABET>

const uint32 nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >::SEQUENCE_BITS = SequenceDataTraits<SEQUENCE_ALPHABET>::SEQUENCE_BITS

static

Definition at line 273 of file sequence_encoder.cpp.

template<Alphabet SEQUENCE_ALPHABET>

const uint32 nvbio::io::SequenceDataEncoderImpl< SEQUENCE_ALPHABET >::SEQUENCE_SYMBOLS_PER_WORD = SequenceDataTraits<SEQUENCE_ALPHABET>::SEQUENCE_SYMBOLS_PER_WORD

static

Definition at line 275 of file sequence_encoder.cpp.

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

• E:/git/nvbio/nvbio/io/sequence/sequence_encoder.cpp