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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 >:
nvbio::io::SequenceDataEncoder

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 SequenceDataInfoinfo () 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_leninput sequence length
namesequence name
base_pairslist of base pairs
qualitylist of base qualities
quality_encodingquality encoding scheme
truncate_sequence_lentruncate the sequence if longer than this
conversion_flagsconversion 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.


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