COligoKernel Member List

This is the complete list of members for COligoKernel, including all inherited members.

add_to_normal(int32_t vector_idx, float64_t weight)CKernel [virtual]
cache_sizeCKernel [protected]
CKernel(int32_t size)CKernel
CKernel(CFeatures *l, CFeatures *r, int32_t size)CKernel
cleanup()CKernel [virtual]
clear_normal()CKernel [virtual]
COligoKernel(int32_t cache_size, int32_t k, float64_t width)COligoKernel
combined_kernel_weightCKernel [protected]
compute(int32_t x, int32_t y)COligoKernel [virtual]
compute_batch(int32_t num_vec, int32_t *vec_idx, float64_t *target, int32_t num_suppvec, int32_t *IDX, float64_t *alphas, float64_t factor=1.0)CKernel [virtual]
compute_by_subkernel(int32_t vector_idx, float64_t *subkernel_contrib)CKernel [virtual]
compute_optimized(int32_t vector_idx)CKernel [virtual]
CSGObject()CSGObject
CSGObject(const CSGObject &orig)CSGObject
CStringKernel(int32_t cachesize)CStringKernel< char >
CStringKernel(CFeatures *l, CFeatures *r)CStringKernel< char >
delete_optimization()CKernel [virtual]
encodeOligo(const std::string &sequence, uint32_t k_mer_length, const std::string &allowed_characters, std::vector< std::pair< int32_t, float64_t > > &values)COligoKernel [protected, static]
get_cache_size()CKernel
get_combined_kernel_weight()CKernel
get_feature_class()CStringKernel< char > [virtual]
get_feature_type()CStringKernel< char > [virtual]
get_is_initialized()CKernel
get_kernel_matrix(float64_t **dst, int32_t *m, int32_t *n)CKernel
get_kernel_matrix_real(int32_t &m, int32_t &n, float64_t *target)CKernel [virtual]
get_kernel_matrix_shortreal(int32_t &m, int32_t &n, float32_t *target)CKernel [virtual]
get_kernel_type()COligoKernel [virtual]
get_lhs()CKernel
get_name()COligoKernel [virtual]
get_normalizer()CKernel [virtual]
get_num_subkernels()CKernel [virtual]
get_num_vec_lhs()CKernel
get_num_vec_rhs()CKernel
get_optimization_type()CKernel
get_rhs()CKernel
get_subkernel_weights(int32_t &num_weights)CKernel [virtual]
getExpFunctionCache(float64_t sigma, uint32_t sequence_length, std::vector< float64_t > &cache)COligoKernel [protected, static]
getSequences(const std::vector< std::string > &sequences, uint32_t k_mer_length, const std::string &allowed_characters, std::vector< std::vector< std::pair< int32_t, float64_t > > > &encoded_sequences)COligoKernel [protected, static]
has_features()CKernel
has_property(EKernelProperty p)CKernel
init(CFeatures *l, CFeatures *r)COligoKernel [virtual]
init_normalizer()CKernel [virtual]
init_optimization(int32_t count, int32_t *IDX, float64_t *weights)CKernel [virtual]
init_optimization_svm(CSVM *svm)CKernel
ioCSGObject
kCOligoKernel [protected]
kernel(int32_t idx_a, int32_t idx_b)CKernel
kernel_matrixCKernel [protected]
kernelOligo(const std::vector< std::pair< int32_t, float64_t > > &x, const std::vector< std::pair< int32_t, float64_t > > &y, float64_t sigma_square)COligoKernel [protected, static]
kernelOligoFast(const std::vector< std::pair< int32_t, float64_t > > &x, const std::vector< std::pair< int32_t, float64_t > > &y, const std::vector< float64_t > &exp_cache, int32_t max_distance=-1)COligoKernel [protected, static]
lhsCKernel [protected]
lhs_equals_rhs()CKernel
list_kernel()CKernel
load(char *fname)CKernel
load_init(FILE *)COligoKernel [virtual]
normalizerCKernel [protected]
opt_typeCKernel [protected]
optimization_initializedCKernel [protected]
parallelCSGObject
propertiesCKernel [protected]
ref()CSGObject
ref_count() const CSGObject
remove_lhs()CKernel [virtual]
remove_lhs_and_rhs()CKernel [virtual]
remove_rhs()CKernel [virtual]
rhsCKernel [protected]
save(char *fname)CKernel
save_init(FILE *)COligoKernel [virtual]
set_cache_size(int32_t size)CKernel
set_combined_kernel_weight(float64_t nw)CKernel
set_is_initialized(bool p_init)CKernel [protected]
set_normalizer(CKernelNormalizer *normalizer)CKernel [virtual]
set_optimization_type(EOptimizationType t)CKernel [virtual]
set_property(EKernelProperty p)CKernel [protected]
set_subkernel_weights(float64_t *weights, int32_t num_weights)CKernel [virtual]
unref()CSGObject
unset_property(EKernelProperty p)CKernel [protected]
versionCSGObject
widthCOligoKernel [protected]
~CKernel()CKernel [virtual]
~COligoKernel()COligoKernel
~CSGObject()CSGObject [virtual]


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