SHOGUN
v1.1.0
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The LocalAlignmentString kernel compares two sequences through all possible local alignments between the two sequences.
The implementation is taken from http://www.mloss.org/software/view/40/ and only adjusted to work with shogun.
Definition at line 27 of file LocalAlignmentStringKernel.h.
Public Member Functions | |
CLocalAlignmentStringKernel (int32_t size=0) | |
CLocalAlignmentStringKernel (CStringFeatures< char > *l, CStringFeatures< char > *r, float64_t opening=12, float64_t extension=2) | |
virtual | ~CLocalAlignmentStringKernel () |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual void | cleanup () |
virtual EKernelType | get_kernel_type () |
virtual const char * | get_name () const |
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CStringKernel (int32_t cachesize=0) | |
CStringKernel (CFeatures *l, CFeatures *r) | |
virtual EFeatureClass | get_feature_class () |
virtual EFeatureType | get_feature_type () |
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CKernel () | |
CKernel (int32_t size) | |
CKernel (CFeatures *l, CFeatures *r, int32_t size) | |
virtual | ~CKernel () |
float64_t | kernel (int32_t idx_a, int32_t idx_b) |
SGMatrix< float64_t > | get_kernel_matrix () |
virtual SGVector< float64_t > | get_kernel_col (int32_t j) |
virtual SGVector< float64_t > | get_kernel_row (int32_t i) |
template<class T > | |
SGMatrix< T > | get_kernel_matrix () |
virtual bool | set_normalizer (CKernelNormalizer *normalizer) |
virtual CKernelNormalizer * | get_normalizer () |
virtual bool | init_normalizer () |
void | load (CFile *loader) |
void | save (CFile *writer) |
CFeatures * | get_lhs () |
CFeatures * | get_rhs () |
virtual int32_t | get_num_vec_lhs () |
virtual int32_t | get_num_vec_rhs () |
virtual bool | has_features () |
bool | get_lhs_equals_rhs () |
virtual void | remove_lhs_and_rhs () |
virtual void | remove_lhs () |
virtual void | remove_rhs () |
takes all necessary steps if the rhs is removed from kernel | |
void | set_cache_size (int32_t size) |
int32_t | get_cache_size () |
void | list_kernel () |
bool | has_property (EKernelProperty p) |
virtual void | clear_normal () |
virtual void | add_to_normal (int32_t vector_idx, float64_t weight) |
EOptimizationType | get_optimization_type () |
virtual void | set_optimization_type (EOptimizationType t) |
bool | get_is_initialized () |
virtual bool | init_optimization (int32_t count, int32_t *IDX, float64_t *weights) |
virtual bool | delete_optimization () |
bool | init_optimization_svm (CSVM *svm) |
virtual float64_t | compute_optimized (int32_t vector_idx) |
virtual void | 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) |
float64_t | get_combined_kernel_weight () |
void | set_combined_kernel_weight (float64_t nw) |
virtual int32_t | get_num_subkernels () |
virtual void | compute_by_subkernel (int32_t vector_idx, float64_t *subkernel_contrib) |
virtual const float64_t * | get_subkernel_weights (int32_t &num_weights) |
virtual void | set_subkernel_weights (SGVector< float64_t > weights) |
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CSGObject () | |
CSGObject (const CSGObject &orig) | |
virtual | ~CSGObject () |
virtual bool | is_generic (EPrimitiveType *generic) const |
template<class T > | |
void | set_generic () |
void | unset_generic () |
virtual void | print_serializable (const char *prefix="") |
virtual bool | save_serializable (CSerializableFile *file, const char *prefix="") |
virtual bool | load_serializable (CSerializableFile *file, const char *prefix="") |
void | set_global_io (SGIO *io) |
SGIO * | get_global_io () |
void | set_global_parallel (Parallel *parallel) |
Parallel * | get_global_parallel () |
void | set_global_version (Version *version) |
Version * | get_global_version () |
SGVector< char * > | get_modelsel_names () |
char * | get_modsel_param_descr (const char *param_name) |
index_t | get_modsel_param_index (const char *param_name) |
Protected Member Functions | |
virtual float64_t | compute (int32_t idx_a, int32_t idx_b) |
Protected Attributes | |
bool | initialized |
int32_t * | isAA |
int32_t * | aaIndex |
int32_t | m_opening |
int32_t | m_extension |
int32_t * | scaled_blosum |
Static Protected Attributes | |
static int32_t | logsum_lookup [LOGSUM_TBL] |
static const int32_t | blosum [] |
static const char * | aaList = "ARNDCQEGHILKMFPSTWYV" |
Additional Inherited Members | |
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SGIO * | io |
Parallel * | parallel |
Version * | version |
Parameter * | m_parameters |
Parameter * | m_model_selection_parameters |
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template<class T > | |
static void * | get_kernel_matrix_helper (void *p) |
CLocalAlignmentStringKernel | ( | int32_t | size = 0 | ) |
CLocalAlignmentStringKernel | ( | CStringFeatures< char > * | l, |
CStringFeatures< char > * | r, | ||
float64_t | opening = 12 , |
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float64_t | extension = 2 |
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constructor
l | features of left-hand side |
r | features of right-hand side |
opening | gap opening penalty |
extension | gap extension penalty |
Definition at line 101 of file LocalAlignmentStringKernel.cpp.
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virtual |
Definition at line 113 of file LocalAlignmentStringKernel.cpp.
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virtual |
clean up kernel
Reimplemented from CKernel.
Definition at line 125 of file LocalAlignmentStringKernel.cpp.
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protectedvirtual |
compute kernel function for features a and b idx_{a,b} denote the index of the feature vectors in the corresponding feature object
idx_a | index a |
idx_b | index b |
Implements CKernel.
Definition at line 358 of file LocalAlignmentStringKernel.cpp.
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virtual |
return what type of kernel we are
Implements CStringKernel< char >.
Definition at line 63 of file LocalAlignmentStringKernel.h.
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virtual |
return the kernel's name
Reimplemented from CStringKernel< char >.
Definition at line 72 of file LocalAlignmentStringKernel.h.
initialize kernel
l | features of left-hand side |
r | features of right-hand side |
Reimplemented from CStringKernel< char >.
Definition at line 118 of file LocalAlignmentStringKernel.cpp.
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protected |
correspondance between amino-acid letter and index
Definition at line 133 of file LocalAlignmentStringKernel.h.
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staticprotected |
List of amino acids
Definition at line 147 of file LocalAlignmentStringKernel.h.
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staticprotected |
static blosum
Definition at line 143 of file LocalAlignmentStringKernel.h.
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protected |
if kernel is initialized
Definition at line 128 of file LocalAlignmentStringKernel.h.
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protected |
indicates whether a char is an amino-acid
Definition at line 131 of file LocalAlignmentStringKernel.h.
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staticprotected |
static logsum lookup
Definition at line 141 of file LocalAlignmentStringKernel.h.
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protected |
gap penalty extension
Definition at line 138 of file LocalAlignmentStringKernel.h.
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protected |
gap penalty opening
Definition at line 136 of file LocalAlignmentStringKernel.h.
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protected |
scaled blosum
Definition at line 145 of file LocalAlignmentStringKernel.h.