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CLocalAlignmentStringKernel Class Reference

Detailed Description

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.

Inheritance diagram for CLocalAlignmentStringKernel:
Inheritance graph
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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
- Public Member Functions inherited from CStringKernel< char >
 CStringKernel (int32_t cachesize=0)
 CStringKernel (CFeatures *l, CFeatures *r)
virtual EFeatureClass get_feature_class ()
virtual EFeatureType get_feature_type ()
- Public Member Functions inherited from CKernel
 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_tget_kernel_matrix ()
virtual SGVector< float64_tget_kernel_col (int32_t j)
virtual SGVector< float64_tget_kernel_row (int32_t i)
template<class T >
SGMatrix< T > get_kernel_matrix ()
virtual bool set_normalizer (CKernelNormalizer *normalizer)
virtual CKernelNormalizerget_normalizer ()
virtual bool init_normalizer ()
void load (CFile *loader)
void save (CFile *writer)
CFeaturesget_lhs ()
CFeaturesget_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_tget_subkernel_weights (int32_t &num_weights)
virtual void set_subkernel_weights (SGVector< float64_t > weights)
- Public Member Functions inherited from CSGObject
 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)
SGIOget_global_io ()
void set_global_parallel (Parallel *parallel)
Parallelget_global_parallel ()
void set_global_version (Version *version)
Versionget_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

- Public Attributes inherited from CSGObject
SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
- Static Protected Member Functions inherited from CKernel
template<class T >
static void * get_kernel_matrix_helper (void *p)

Constructor & Destructor Documentation

CLocalAlignmentStringKernel ( int32_t  size = 0)

constructor

Parameters
sizecache size

Definition at line 94 of file LocalAlignmentStringKernel.cpp.

CLocalAlignmentStringKernel ( CStringFeatures< char > *  l,
CStringFeatures< char > *  r,
float64_t  opening = 12,
float64_t  extension = 2 
)

constructor

Parameters
lfeatures of left-hand side
rfeatures of right-hand side
openinggap opening penalty
extensiongap extension penalty

Definition at line 101 of file LocalAlignmentStringKernel.cpp.

Definition at line 113 of file LocalAlignmentStringKernel.cpp.

Member Function Documentation

void cleanup ( )
virtual

clean up kernel

Reimplemented from CKernel.

Definition at line 125 of file LocalAlignmentStringKernel.cpp.

float64_t compute ( int32_t  idx_a,
int32_t  idx_b 
)
protectedvirtual

compute kernel function for features a and b idx_{a,b} denote the index of the feature vectors in the corresponding feature object

Parameters
idx_aindex a
idx_bindex b
Returns
computed kernel function at indices a,b

Implements CKernel.

Definition at line 358 of file LocalAlignmentStringKernel.cpp.

virtual EKernelType get_kernel_type ( )
virtual

return what type of kernel we are

Returns
kernel type LOCALALIGNMENT

Implements CStringKernel< char >.

Definition at line 63 of file LocalAlignmentStringKernel.h.

virtual const char* get_name ( ) const
virtual

return the kernel's name

Returns
name LocalAlignment

Reimplemented from CStringKernel< char >.

Definition at line 72 of file LocalAlignmentStringKernel.h.

bool init ( CFeatures l,
CFeatures r 
)
virtual

initialize kernel

Parameters
lfeatures of left-hand side
rfeatures of right-hand side
Returns
if initializing was successful

Reimplemented from CStringKernel< char >.

Definition at line 118 of file LocalAlignmentStringKernel.cpp.

Member Data Documentation

int32_t* aaIndex
protected

correspondance between amino-acid letter and index

Definition at line 133 of file LocalAlignmentStringKernel.h.

const char * aaList = "ARNDCQEGHILKMFPSTWYV"
staticprotected

List of amino acids

Definition at line 147 of file LocalAlignmentStringKernel.h.

const int32_t blosum
staticprotected
Initial value:
{
6,
-2, 8,
-2, -1, 9,
-3, -2, 2, 9,
-1, -5, -4, -5, 13,
-1, 1, 0, 0, -4, 8,
-1, 0, 0, 2, -5, 3, 7,
0, -3, -1, -2, -4, -3, -3, 8,
-2, 0, 1, -2, -4, 1, 0, -3, 11,
-2, -5, -5, -5, -2, -4, -5, -6, -5, 6,
-2, -3, -5, -5, -2, -3, -4, -5, -4, 2, 6,
-1, 3, 0, -1, -5, 2, 1, -2, -1, -4, -4, 7,
-1, -2, -3, -5, -2, -1, -3, -4, -2, 2, 3, -2, 8,
-3, -4, -5, -5, -4, -5, -5, -5, -2, 0, 1, -5, 0, 9,
-1, -3, -3, -2, -4, -2, -2, -3, -3, -4, -4, -2, -4, -5, 11,
2, -1, 1, 0, -1, 0, 0, 0, -1, -4, -4, 0, -2, -4, -1, 6,
0, -2, 0, -2, -1, -1, -1, -2, -3, -1, -2, -1, -1, -3, -2, 2, 7,
-4, -4, -6, -6, -3, -3, -4, -4, -4, -4, -2, -4, -2, 1, -6, -4, -4, 16,
-3, -3, -3, -5, -4, -2, -3, -5, 3, -2, -2, -3, -1, 4, -4, -3, -2, 3, 10,
0, -4, -4, -5, -1, -3, -4, -5, -5, 4, 1, -3, 1, -1, -4, -2, 0, -4, -2, 6}

static blosum

Definition at line 143 of file LocalAlignmentStringKernel.h.

bool initialized
protected

if kernel is initialized

Definition at line 128 of file LocalAlignmentStringKernel.h.

int32_t* isAA
protected

indicates whether a char is an amino-acid

Definition at line 131 of file LocalAlignmentStringKernel.h.

int32_t logsum_lookup
staticprotected

static logsum lookup

Definition at line 141 of file LocalAlignmentStringKernel.h.

int32_t m_extension
protected

gap penalty extension

Definition at line 138 of file LocalAlignmentStringKernel.h.

int32_t m_opening
protected

gap penalty opening

Definition at line 136 of file LocalAlignmentStringKernel.h.

int32_t* scaled_blosum
protected

scaled blosum

Definition at line 145 of file LocalAlignmentStringKernel.h.


The documentation for this class was generated from the following files:

SHOGUN Machine Learning Toolbox - Documentation