Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes

CStringFeatures< ST > Class Template Reference


Detailed Description

template<class ST>
class shogun::CStringFeatures< ST >

Template class StringFeatures implements a list of strings.

As this class is a template the underlying storage type is quite arbitrary and not limited to character strings, but could also be sequences of floating point numbers etc. Strings differ from matrices (cf. CSimpleFeatures) in a way that the dimensionality of the feature vectors (i.e. the strings) is not fixed; it may vary between strings.

Most string kernels require StringFeatures but a number of them actually requires strings to have same length.

When preprocessors are attached to string features they may shorten the string, but are not allowed to return strings longer than max_string_length, as some algorithms depend on this.

Also note that string features cannot currently be computed on-the-fly.

Definition at line 127 of file StringFeatures.h.

Inheritance diagram for CStringFeatures< ST >:
Inheritance graph
[legend]

List of all members.

Public Member Functions

 CStringFeatures ()
 CStringFeatures (EAlphabet alpha)
 CStringFeatures (T_STRING< ST > *p_features, int32_t p_num_vectors, int32_t p_max_string_length, EAlphabet alpha)
 CStringFeatures (T_STRING< ST > *p_features, int32_t p_num_vectors, int32_t p_max_string_length, CAlphabet *alpha)
 CStringFeatures (CAlphabet *alpha)
 CStringFeatures (const CStringFeatures &orig)
 CStringFeatures (CFile *loader, EAlphabet alpha=DNA)
virtual ~CStringFeatures ()
virtual void cleanup ()
virtual void cleanup_feature_vector (int32_t num)
virtual EFeatureClass get_feature_class ()
virtual EFeatureType get_feature_type ()
CAlphabetget_alphabet ()
virtual CFeaturesduplicate () const
void get_feature_vector (ST **dst, int32_t *len, int32_t num)
void set_feature_vector (ST *src, int32_t len, int32_t num)
void enable_on_the_fly_preprocessing ()
void disable_on_the_fly_preprocessing ()
ST * get_feature_vector (int32_t num, int32_t &len, bool &dofree)
CStringFeatures< ST > * get_transposed ()
T_STRING< ST > * get_transposed (int32_t &num_feat, int32_t &num_vec)
void free_feature_vector (ST *feat_vec, int32_t num, bool dofree)
virtual ST get_feature (int32_t vec_num, int32_t feat_num)
virtual int32_t get_vector_length (int32_t vec_num)
virtual int32_t get_max_vector_length ()
virtual int32_t get_num_vectors ()
floatmax_t get_num_symbols ()
floatmax_t get_max_num_symbols ()
floatmax_t get_original_num_symbols ()
int32_t get_order ()
ST get_masked_symbols (ST symbol, uint8_t mask)
ST shift_offset (ST offset, int32_t amount)
ST shift_symbol (ST symbol, int32_t amount)
virtual void load (CFile *loader)
void load_ascii_file (char *fname, bool remap_to_bin=true, EAlphabet ascii_alphabet=DNA, EAlphabet binary_alphabet=RAWDNA)
bool load_fasta_file (const char *fname, bool ignore_invalid=false)
bool load_fastq_file (const char *fname, bool ignore_invalid=false, bool bitremap_in_single_string=false)
bool load_from_directory (char *dirname)
bool set_features (T_STRING< ST > *p_features, int32_t p_num_vectors, int32_t p_max_string_length)
bool append_features (CStringFeatures< ST > *sf)
bool append_features (T_STRING< ST > *p_features, int32_t p_num_vectors, int32_t p_max_string_length)
virtual T_STRING< ST > * get_features (int32_t &num_str, int32_t &max_str_len)
virtual T_STRING< ST > * copy_features (int32_t &num_str, int32_t &max_str_len)
virtual void get_features (T_STRING< ST > **dst, int32_t *num_str)
virtual void save (CFile *writer)
virtual bool load_compressed (char *src, bool decompress)
virtual bool save_compressed (char *dest, E_COMPRESSION_TYPE compression, int level)
virtual int32_t get_size ()
virtual bool apply_preproc (bool force_preprocessing=false)
int32_t obtain_by_sliding_window (int32_t window_size, int32_t step_size, int32_t skip=0)
int32_t obtain_by_position_list (int32_t window_size, CDynamicArray< int32_t > *positions, int32_t skip=0)
bool obtain_from_char (CStringFeatures< char > *sf, int32_t start, int32_t p_order, int32_t gap, bool rev)
template<class CT >
bool obtain_from_char_features (CStringFeatures< CT > *sf, int32_t start, int32_t p_order, int32_t gap, bool rev)
bool have_same_length (int32_t len=-1)
void embed_features (int32_t p_order)
void compute_symbol_mask_table (int64_t max_val)
void unembed_word (ST word, uint8_t *seq, int32_t len)
ST embed_word (ST *seq, int32_t len)
void determine_maximum_string_length ()
virtual void set_feature_vector (int32_t num, ST *string, int32_t len)
virtual void get_histogram (float64_t **hist, int32_t *rows, int32_t *cols, bool normalize=true)
virtual void create_random (float64_t *hist, int32_t rows, int32_t cols, int32_t num_vec)
virtual const char * get_name () const

Static Public Member Functions

static ST * get_zero_terminated_string_copy (T_STRING< ST > str)

Protected Member Functions

virtual ST * compute_feature_vector (int32_t num, int32_t &len)

Protected Attributes

CAlphabetalphabet
 alphabet
int32_t num_vectors
 number of string vectors
T_STRING< ST > * features
 this contains the array of features.
ST * single_string
 true when single string / created by sliding window
int32_t length_of_single_string
 length of prior single string
int32_t max_string_length
 length of longest string
floatmax_t num_symbols
 number of used symbols
floatmax_t original_num_symbols
 original number of used symbols (before higher order mapping)
int32_t order
 order used in higher order mapping
ST * symbol_mask_table
 order used in higher order mapping
bool preprocess_on_get
 preprocess on-the-fly?
CCache< ST > * feature_cache

Constructor & Destructor Documentation

CStringFeatures (  ) 

default constructor

Definition at line 133 of file StringFeatures.h.

CStringFeatures ( EAlphabet  alpha  ) 

constructor

Parameters:
alpha alphabet (type) to use for string features

Definition at line 144 of file StringFeatures.h.

CStringFeatures ( T_STRING< ST > *  p_features,
int32_t  p_num_vectors,
int32_t  p_max_string_length,
EAlphabet  alpha 
)

constructor

Parameters:
p_features new features
p_num_vectors number of vectors
p_max_string_length maximum string length
alpha alphabet (type) to use for string features

Definition at line 163 of file StringFeatures.h.

CStringFeatures ( T_STRING< ST > *  p_features,
int32_t  p_num_vectors,
int32_t  p_max_string_length,
CAlphabet alpha 
)

constructor

Parameters:
p_features new features
p_num_vectors number of vectors
p_max_string_length maximum string length
alpha an actual alphabet

Definition at line 184 of file StringFeatures.h.

CStringFeatures ( CAlphabet alpha  ) 

constructor

Parameters:
alpha alphabet to use for string features

Definition at line 202 of file StringFeatures.h.

CStringFeatures ( const CStringFeatures< ST > &  orig  ) 

copy constructor

Definition at line 216 of file StringFeatures.h.

CStringFeatures ( CFile loader,
EAlphabet  alpha = DNA 
)

constructor

Parameters:
loader File object via which to load data
alpha alphabet (type) to use for string features

Definition at line 256 of file StringFeatures.h.

virtual ~CStringFeatures (  )  [virtual]

Definition at line 268 of file StringFeatures.h.


Member Function Documentation

bool append_features ( CStringFeatures< ST > *  sf  ) 

append features

Parameters:
sf features to append
Returns:
if setting was successful

Definition at line 1113 of file StringFeatures.h.

bool append_features ( T_STRING< ST > *  p_features,
int32_t  p_num_vectors,
int32_t  p_max_string_length 
)

append features

Parameters:
p_features features to append
p_num_vectors number of vectors
p_max_string_length maximum string length

note that p_features will be delete[]'d on success

Returns:
if setting was successful

Definition at line 1139 of file StringFeatures.h.

virtual bool apply_preproc ( bool  force_preprocessing = false  )  [virtual]

apply preprocessor

Parameters:
force_preprocessing if preprocssing shall be forced
Returns:
if applying was successful

Definition at line 1411 of file StringFeatures.h.

virtual void cleanup (  )  [virtual]

cleanup string features

Reimplemented in CStringFileFeatures< ST >.

Definition at line 276 of file StringFeatures.h.

virtual void cleanup_feature_vector ( int32_t  num  )  [virtual]

cleanup a single feature vector

Reimplemented in CStringFileFeatures< ST >.

Definition at line 306 of file StringFeatures.h.

virtual ST* compute_feature_vector ( int32_t  num,
int32_t &  len 
) [protected, virtual]

compute feature vector for sample num if target is set the vector is written to target len is returned by reference

default implementation returns

Parameters:
num which vector
len length of vector
Returns:
feature vector

Definition at line 1926 of file StringFeatures.h.

void compute_symbol_mask_table ( int64_t  max_val  ) 

compute symbol mask table

required to access bit-based symbols

Definition at line 1724 of file StringFeatures.h.

virtual T_STRING<ST>* copy_features ( int32_t &  num_str,
int32_t &  max_str_len 
) [virtual]

copy_features

Parameters:
num_str number of strings (returned)
max_str_len maximal string length (returned)
Returns:
string features

Definition at line 1208 of file StringFeatures.h.

virtual void create_random ( float64_t hist,
int32_t  rows,
int32_t  cols,
int32_t  num_vec 
) [virtual]

create some random strings based on normalized histogram

Definition at line 1879 of file StringFeatures.h.

void determine_maximum_string_length (  ) 

determine new maximum string length

Definition at line 1790 of file StringFeatures.h.

void disable_on_the_fly_preprocessing (  ) 

call this to disable on the fly feature preprocessing on get_feature_vector. Useful when you manually apply preprocessors.

Definition at line 410 of file StringFeatures.h.

virtual CFeatures* duplicate (  )  const [virtual]

duplicate feature object

Returns:
feature object

Implements CFeatures.

Definition at line 343 of file StringFeatures.h.

void embed_features ( int32_t  p_order  ) 

embed string features in bit representation in-place

Definition at line 1669 of file StringFeatures.h.

ST embed_word ( ST *  seq,
int32_t  len 
)

embed a single word

Parameters:
seq sequence of size len in a bitfield
len 

Definition at line 1775 of file StringFeatures.h.

void enable_on_the_fly_preprocessing (  ) 

call this to preprocess string features upon get_feature_vector

Definition at line 402 of file StringFeatures.h.

void free_feature_vector ( ST *  feat_vec,
int32_t  num,
bool  dofree 
)

free feature vector

Parameters:
feat_vec feature vector to free
num index in feature cache
dofree if vector should be really deleted

Definition at line 519 of file StringFeatures.h.

CAlphabet* get_alphabet (  ) 

get alphabet used in string features

Returns:
alphabet

Definition at line 333 of file StringFeatures.h.

virtual ST get_feature ( int32_t  vec_num,
int32_t  feat_num 
) [virtual]

get feature

Parameters:
vec_num which vector
feat_num which feature
Returns:
feature

Definition at line 534 of file StringFeatures.h.

virtual EFeatureClass get_feature_class (  )  [virtual]

get feature class

Returns:
feature class STRING

Implements CFeatures.

Definition at line 321 of file StringFeatures.h.

virtual EFeatureType get_feature_type (  )  [virtual]

get feature type

Returns:
templated feature type

Implements CFeatures.

Definition at line 327 of file StringFeatures.h.

ST* get_feature_vector ( int32_t  num,
int32_t &  len,
bool &  dofree 
)

get feature vector for sample num

Parameters:
num index of feature vector
len length is returned by reference
dofree whether returned vector must be freed by caller via free_feature_vector
Returns:
feature vector for sample num

Definition at line 423 of file StringFeatures.h.

void get_feature_vector ( ST **  dst,
int32_t *  len,
int32_t  num 
)

get string for selected example num

Parameters:
dst destination where vector will be stored
len number of features in vector
num index of the string

Definition at line 354 of file StringFeatures.h.

virtual T_STRING<ST>* get_features ( int32_t &  num_str,
int32_t &  max_str_len 
) [virtual]

get_features

Parameters:
num_str number of strings (returned)
max_str_len maximal string length (returned)
Returns:
string features

Definition at line 1195 of file StringFeatures.h.

virtual void get_features ( T_STRING< ST > **  dst,
int32_t *  num_str 
) [virtual]

get_features (swig compatible)

Parameters:
dst string features (returned)
num_str number of strings (returned)

Definition at line 1235 of file StringFeatures.h.

virtual void get_histogram ( float64_t **  hist,
int32_t *  rows,
int32_t *  cols,
bool  normalize = true 
) [virtual]

compute histogram over strings

Definition at line 1834 of file StringFeatures.h.

ST get_masked_symbols ( ST  symbol,
uint8_t  mask 
)

a higher order mapped symbol will be shaped such that the symbols specified by bits in the mask will be returned.

Parameters:
symbol symbol to mask
mask mask to apply
Returns:
masked symbol

Definition at line 613 of file StringFeatures.h.

floatmax_t get_max_num_symbols (  ) 

get maximum number of symbols

Note: floatmax_t sounds weird, but int64_t is not long enough (and there is no int128_t type)

Returns:
maximum number of symbols

Definition at line 590 of file StringFeatures.h.

virtual int32_t get_max_vector_length (  )  [virtual]

get maximum vector length

Returns:
maximum vector/string length

Definition at line 564 of file StringFeatures.h.

virtual const char* get_name (  )  const [virtual]
Returns:
object name

Implements CSGObject.

Definition at line 1912 of file StringFeatures.h.

floatmax_t get_num_symbols (  ) 

get number of symbols

Note: floatmax_t sounds weird, but LONG is not long enough

Returns:
number of symbols

Definition at line 581 of file StringFeatures.h.

virtual int32_t get_num_vectors (  )  [virtual]

get number of vectors

Returns:
number of vectors

Implements CFeatures.

Definition at line 573 of file StringFeatures.h.

int32_t get_order (  ) 

order used for higher order mapping

Returns:
order

Definition at line 604 of file StringFeatures.h.

floatmax_t get_original_num_symbols (  ) 

number of symbols before higher order mapping

Returns:
original number of symbols

Definition at line 598 of file StringFeatures.h.

virtual int32_t get_size (  )  [virtual]

get memory footprint of one feature

Returns:
memory footprint of one feature

Implements CFeatures.

Definition at line 1404 of file StringFeatures.h.

T_STRING<ST>* get_transposed ( int32_t &  num_feat,
int32_t &  num_vec 
)

compute and return the transpose of string features matrix which will be prepocessed. num_feat, num_vectors are returned by reference caller has to clean up

note that strings all have to have same length

Parameters:
num_feat number of features in matrix
num_vec number of vectors in matrix
Returns:
transposed string features

Definition at line 482 of file StringFeatures.h.

CStringFeatures<ST>* get_transposed (  ) 

get a transposed copy of the features

Returns:
transposed copy

Definition at line 462 of file StringFeatures.h.

virtual int32_t get_vector_length ( int32_t  vec_num  )  [virtual]

get vector length

Parameters:
vec_num which vector
Returns:
length of vector

Definition at line 551 of file StringFeatures.h.

static ST* get_zero_terminated_string_copy ( T_STRING< ST >  str  )  [static]

get a zero terminated copy of the string

Parameters:
str the string to copy
Returns:
zero terminated copy of str

note that this function is only sensible for character strings

Definition at line 1805 of file StringFeatures.h.

bool have_same_length ( int32_t  len = -1  ) 

check if length of each vector in this feature object equals the given length.

Parameters:
len vector length to check against
Returns:
if length of each vector in this feature object equals the given length.

Definition at line 1647 of file StringFeatures.h.

virtual void load ( CFile loader  )  [virtual]

load features from file

Parameters:
loader File object via which to load data

Reimplemented from CFeatures.

void load_ascii_file ( char *  fname,
bool  remap_to_bin = true,
EAlphabet  ascii_alphabet = DNA,
EAlphabet  binary_alphabet = RAWDNA 
)

load ascii line-based string features from file

Parameters:
fname filename to load from
remap_to_bin if translation to other binary alphabet should be performed
ascii_alphabet src alphabet
binary_alphabet alphabet to translate to

Definition at line 657 of file StringFeatures.h.

virtual bool load_compressed ( char *  src,
bool  decompress 
) [virtual]

load compressed features from file

Parameters:
src filename to load from
decompress whether to decompress on loading
Returns:
if loading was successful

Definition at line 1255 of file StringFeatures.h.

bool load_fasta_file ( const char *  fname,
bool  ignore_invalid = false 
)

load fasta file as string features

Parameters:
fname filename to load from
ignore_invalid if set to true, characters other than A,C,G,T are converted to A
Returns:
if loading was successful

Definition at line 796 of file StringFeatures.h.

bool load_fastq_file ( const char *  fname,
bool  ignore_invalid = false,
bool  bitremap_in_single_string = false 
)

load fastq file as string features

Parameters:
fname filename to load from
ignore_invalid if set to true, characters other than A,C,G,T are converted to A
bitremap_in_single_string if set to true, do binary embedding of symbols
Returns:
if loading was successful

Definition at line 895 of file StringFeatures.h.

bool load_from_directory ( char *  dirname  ) 

load features from directory

Parameters:
dirname directory name to load from
Returns:
if loading was successful

Definition at line 1000 of file StringFeatures.h.

int32_t obtain_by_position_list ( int32_t  window_size,
CDynamicArray< int32_t > *  positions,
int32_t  skip = 0 
)

extracts windows of size window_size from first string using the positions in list

Parameters:
window_size window size
positions positions
skip skip
Returns:
something inty

Definition at line 1486 of file StringFeatures.h.

int32_t obtain_by_sliding_window ( int32_t  window_size,
int32_t  step_size,
int32_t  skip = 0 
)

slides a window of size window_size over the current single string step_size is the amount by which the window is shifted. creates (string_len-window_size)/step_size many feature obj if skip is nonzero, skip the first 'skip' characters of each string

Parameters:
window_size window size
step_size step size
skip skip
Returns:
something inty

Definition at line 1444 of file StringFeatures.h.

bool obtain_from_char ( CStringFeatures< char > *  sf,
int32_t  start,
int32_t  p_order,
int32_t  gap,
bool  rev 
)

obtain string features from char features

wrapper for template method

Parameters:
sf string features
start start
p_order order
gap gap
rev reverse
Returns:
if obtaining was successful

Definition at line 1551 of file StringFeatures.h.

bool obtain_from_char_features ( CStringFeatures< CT > *  sf,
int32_t  start,
int32_t  p_order,
int32_t  gap,
bool  rev 
)

template obtain from char features

Parameters:
sf string features
start start
p_order order
gap gap
rev reverse
Returns:
if obtaining was successful

Definition at line 1566 of file StringFeatures.h.

virtual void save ( CFile writer  )  [virtual]

save features to file

Parameters:
writer File object via which to save data

Reimplemented from CFeatures.

virtual bool save_compressed ( char *  dest,
E_COMPRESSION_TYPE  compression,
int  level 
) [virtual]

save compressed features to file

Parameters:
dest filename to save to
compression compressor to use
level compression level to use (1-9)
Returns:
if saving was successful

Definition at line 1342 of file StringFeatures.h.

void set_feature_vector ( ST *  src,
int32_t  len,
int32_t  num 
)

set string for selected example num

Parameters:
src destination where vector will be stored
len number of features in vector
num index of the string

Definition at line 379 of file StringFeatures.h.

virtual void set_feature_vector ( int32_t  num,
ST *  string,
int32_t  len 
) [virtual]

set feature vector for sample num

Parameters:
num index of feature vector
string string with the feature vector's content
len length of the string

Definition at line 1820 of file StringFeatures.h.

bool set_features ( T_STRING< ST > *  p_features,
int32_t  p_num_vectors,
int32_t  p_max_string_length 
)

set features

Parameters:
p_features new features
p_num_vectors number of vectors
p_max_string_length maximum string length
Returns:
if setting was successful

Definition at line 1074 of file StringFeatures.h.

ST shift_offset ( ST  offset,
int32_t  amount 
)

shift offset to the left by amount

Parameters:
offset offset to shift
amount amount to shift the offset
Returns:
shifted offset

Definition at line 625 of file StringFeatures.h.

ST shift_symbol ( ST  symbol,
int32_t  amount 
)

shift symbol to the right by amount (taking care of custom symbol sizes)

Parameters:
symbol symbol to shift
amount amount to shift the symbol
Returns:
shifted symbol

Definition at line 637 of file StringFeatures.h.

void unembed_word ( ST  word,
uint8_t *  seq,
int32_t  len 
)

remap bit-based word to character sequence

Parameters:
word word to remap
seq sequence of size len that remapped characters are written to
len length of sequence and word

Definition at line 1754 of file StringFeatures.h.


Member Data Documentation

CAlphabet* alphabet [protected]

alphabet

Definition at line 2026 of file StringFeatures.h.

CCache<ST>* feature_cache [protected]

feature cache

Definition at line 2059 of file StringFeatures.h.

T_STRING<ST>* features [protected]

this contains the array of features.

Definition at line 2032 of file StringFeatures.h.

int32_t length_of_single_string [protected]

length of prior single string

Definition at line 2038 of file StringFeatures.h.

int32_t max_string_length [protected]

length of longest string

Definition at line 2041 of file StringFeatures.h.

floatmax_t num_symbols [protected]

number of used symbols

Definition at line 2044 of file StringFeatures.h.

int32_t num_vectors [protected]

number of string vectors

Definition at line 2029 of file StringFeatures.h.

int32_t order [protected]

order used in higher order mapping

Definition at line 2050 of file StringFeatures.h.

original number of used symbols (before higher order mapping)

Definition at line 2047 of file StringFeatures.h.

bool preprocess_on_get [protected]

preprocess on-the-fly?

Definition at line 2056 of file StringFeatures.h.

ST* single_string [protected]

true when single string / created by sliding window

Definition at line 2035 of file StringFeatures.h.

ST* symbol_mask_table [protected]

order used in higher order mapping

Definition at line 2053 of file StringFeatures.h.


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