Definition at line 22 of file WeightedDegreePositionStringKernel.h.
CWeightedDegreePositionStringKernel::CWeightedDegreePositionStringKernel | ( | INT | size, | |
INT | degree, | |||
INT | max_mismatch = 0 , |
|||
bool | use_norm = true , |
|||
INT | mkl_stepsize = 1 | |||
) |
constructor
size | cache size | |
degree | degree | |
max_mismatch | maximum mismatch | |
use_norm | if normalization shall be used | |
mkl_stepsize | MKL stepsize |
Definition at line 47 of file WeightedDegreePositionStringKernel.cpp.
CWeightedDegreePositionStringKernel::CWeightedDegreePositionStringKernel | ( | INT | size, | |
DREAL * | weights, | |||
INT | degree, | |||
INT | max_mismatch, | |||
INT * | shift, | |||
INT | shift_len, | |||
bool | use_norm = true , |
|||
INT | mkl_stepsize = 1 | |||
) |
constructor
size | cache size | |
weights | weights | |
degree | degree | |
max_mismatch | maximum mismatch | |
shift | position shifts | |
shift_len | number of shifts | |
use_norm | if normalization shall be used | |
mkl_stepsize | MKL stepsize |
Definition at line 65 of file WeightedDegreePositionStringKernel.cpp.
CWeightedDegreePositionStringKernel::CWeightedDegreePositionStringKernel | ( | CStringFeatures< CHAR > * | l, | |
CStringFeatures< CHAR > * | r, | |||
INT | degree | |||
) |
constructor
l | features of left-hand side | |
r | features of right-hand side | |
degree | degree |
Definition at line 87 of file WeightedDegreePositionStringKernel.cpp.
CWeightedDegreePositionStringKernel::~CWeightedDegreePositionStringKernel | ( | ) | [virtual] |
Definition at line 108 of file WeightedDegreePositionStringKernel.cpp.
initialize kernel
l | features of left-hand side | |
r | features of right-hand side |
Reimplemented from CStringKernel< ST >.
Definition at line 166 of file WeightedDegreePositionStringKernel.cpp.
void CWeightedDegreePositionStringKernel::cleanup | ( | ) | [virtual] |
clean up kernel
Reimplemented from CKernel.
Definition at line 229 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::load_init | ( | FILE * | src | ) | [virtual] |
load kernel init_data
src | file to load from |
Implements CKernel.
Definition at line 250 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::save_init | ( | FILE * | dest | ) | [virtual] |
save kernel init_data
dest | file to save to |
Implements CKernel.
Definition at line 255 of file WeightedDegreePositionStringKernel.cpp.
virtual EKernelType CWeightedDegreePositionStringKernel::get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CKernel.
Definition at line 92 of file WeightedDegreePositionStringKernel.h.
virtual const CHAR* CWeightedDegreePositionStringKernel::get_name | ( | ) | [virtual] |
return the kernel's name
Implements CKernel.
Definition at line 98 of file WeightedDegreePositionStringKernel.h.
virtual bool CWeightedDegreePositionStringKernel::init_optimization | ( | INT | p_count, | |
INT * | IDX, | |||
DREAL * | alphas | |||
) | [virtual] |
initialize optimization
p_count | count | |
IDX | index | |
alphas | alphas |
Reimplemented from CKernel.
Definition at line 107 of file WeightedDegreePositionStringKernel.h.
bool CWeightedDegreePositionStringKernel::init_optimization | ( | INT | count, | |
INT * | IDX, | |||
DREAL * | alphas, | |||
INT | tree_num, | |||
INT | upto_tree = -1 | |||
) | [virtual] |
initialize optimization do initialization for tree_num up to upto_tree, use tree_num=-1 to construct all trees
count | count | |
IDX | IDX | |
alphas | alphas | |
tree_num | which tree | |
upto_tree | up to this tree |
Definition at line 260 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::delete_optimization | ( | ) | [virtual] |
delete optimization
Reimplemented from CKernel.
Definition at line 305 of file WeightedDegreePositionStringKernel.cpp.
compute optimized
idx | index to compute |
Reimplemented from CKernel.
Definition at line 137 of file WeightedDegreePositionStringKernel.h.
void * CWeightedDegreePositionStringKernel::compute_batch_helper | ( | void * | p | ) | [static] |
helper for compute batch
p | thread parameter |
Definition at line 1211 of file WeightedDegreePositionStringKernel.cpp.
void CWeightedDegreePositionStringKernel::compute_batch | ( | INT | num_vec, | |
INT * | vec_idx, | |||
DREAL * | target, | |||
INT | num_suppvec, | |||
INT * | IDX, | |||
DREAL * | alphas, | |||
DREAL | factor = 1.0 | |||
) | [virtual] |
compute batch
num_vec | number of vectors | |
vec_idx | vector index | |
target | target | |
num_suppvec | number of support vectors | |
IDX | IDX | |
alphas | alphas | |
factor | factor |
Reimplemented from CKernel.
Definition at line 1256 of file WeightedDegreePositionStringKernel.cpp.
virtual void CWeightedDegreePositionStringKernel::clear_normal | ( | ) | [virtual] |
clear normal subkernel functionality
Reimplemented from CKernel.
Definition at line 167 of file WeightedDegreePositionStringKernel.h.
add to normal
idx | where to add | |
weight | what to add |
Reimplemented from CKernel.
Definition at line 193 of file WeightedDegreePositionStringKernel.h.
virtual INT CWeightedDegreePositionStringKernel::get_num_subkernels | ( | ) | [virtual] |
get number of subkernels
Reimplemented from CKernel.
Definition at line 203 of file WeightedDegreePositionStringKernel.h.
void CWeightedDegreePositionStringKernel::compute_by_subkernel | ( | INT | idx, | |
DREAL * | subkernel_contrib | |||
) | [virtual] |
compute by subkernel
idx | index | |
subkernel_contrib | subkernel contribution |
Reimplemented from CKernel.
Definition at line 217 of file WeightedDegreePositionStringKernel.h.
const DREAL* CWeightedDegreePositionStringKernel::get_subkernel_weights | ( | INT & | num_weights | ) | [virtual] |
get subkernel weights
num_weights | number of weights will be stored here |
Reimplemented from CKernel.
Definition at line 233 of file WeightedDegreePositionStringKernel.h.
void CWeightedDegreePositionStringKernel::set_subkernel_weights | ( | DREAL * | weights2, | |
INT | num_weights2 | |||
) | [virtual] |
set subkernel weights
weights2 | weights | |
num_weights2 | number of weights |
Reimplemented from CKernel.
Definition at line 255 of file WeightedDegreePositionStringKernel.h.
compute abs weights
len | len |
Definition at line 807 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::is_tree_initialized | ( | ) |
check if tree is initialized
Definition at line 296 of file WeightedDegreePositionStringKernel.h.
INT CWeightedDegreePositionStringKernel::get_max_mismatch | ( | ) |
get maximum mismatch
Definition at line 302 of file WeightedDegreePositionStringKernel.h.
INT CWeightedDegreePositionStringKernel::get_degree | ( | ) |
DREAL CWeightedDegreePositionStringKernel::get_normalization_const | ( | ) |
get normalization constant
Definition at line 314 of file WeightedDegreePositionStringKernel.h.
get degree weights
d | degree weights will be stored here | |
len | number of degree weights will be stored here |
Definition at line 321 of file WeightedDegreePositionStringKernel.h.
get weights
num_weights | number of weights will be stored here |
Definition at line 333 of file WeightedDegreePositionStringKernel.h.
get position weights
len | number of position weights will be stored here |
Definition at line 352 of file WeightedDegreePositionStringKernel.h.
set shifts
shifts | new shifts | |
len | number of shifts |
Definition at line 812 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::set_weights | ( | DREAL * | weights, | |
INT | d, | |||
INT | len = 0 | |||
) | [virtual] |
set weights
weights | new weights | |
d | degree | |
len | number of weights |
Definition at line 874 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::set_wd_weights | ( | ) | [virtual] |
set wd weights
Definition at line 836 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::set_position_weights | ( | DREAL * | position_weights, | |
INT | len = 0 | |||
) | [virtual] |
set position weights
position_weights | new position weights | |
len | number of position weights |
Definition at line 896 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::set_position_weights_lhs | ( | DREAL * | pws, | |
INT | len, | |||
INT | num | |||
) |
set position weights for left-hand side
pws | new position weights | |
len | len | |
num | num |
Definition at line 929 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::set_position_weights_rhs | ( | DREAL * | pws, | |
INT | len, | |||
INT | num | |||
) |
set position weights for right-hand side
pws | new position weights | |
len | len | |
num | num |
Definition at line 971 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::init_block_weights | ( | ) |
initialize block weights
Definition at line 1182 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::init_block_weights_from_wd | ( | ) |
initialize block weights from weighted degree
Definition at line 1021 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::init_block_weights_from_wd_external | ( | ) |
initialize block weights from external weighted degree
Definition at line 1039 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::init_block_weights_const | ( | ) |
initialize block weights constant
Definition at line 1067 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::init_block_weights_linear | ( | ) |
initialize block weights linear
Definition at line 1081 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::init_block_weights_sqpoly | ( | ) |
initialize block weights squared polynomial
Definition at line 1095 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::init_block_weights_cubicpoly | ( | ) |
initialize block weights cubic polynomial
Definition at line 1112 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::init_block_weights_exp | ( | ) |
initialize block weights exponential
Definition at line 1129 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::init_block_weights_log | ( | ) |
initialize block weights logarithmic
Definition at line 1146 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::init_block_weights_external | ( | ) |
initialize block weights external
Definition at line 1163 of file WeightedDegreePositionStringKernel.cpp.
bool CWeightedDegreePositionStringKernel::delete_position_weights | ( | ) |
delete position weights
Definition at line 469 of file WeightedDegreePositionStringKernel.h.
bool CWeightedDegreePositionStringKernel::delete_position_weights_lhs | ( | ) |
delete position weights left-hand side
Definition at line 475 of file WeightedDegreePositionStringKernel.h.
bool CWeightedDegreePositionStringKernel::delete_position_weights_rhs | ( | ) |
delete position weights right-hand side
Definition at line 481 of file WeightedDegreePositionStringKernel.h.
bool CWeightedDegreePositionStringKernel::get_use_normalization | ( | ) |
check if normalization is used
Definition at line 487 of file WeightedDegreePositionStringKernel.h.
compute by tree
idx | index |
Definition at line 740 of file WeightedDegreePositionStringKernel.cpp.
void CWeightedDegreePositionStringKernel::compute_by_tree | ( | INT | idx, | |
DREAL * | LevelContrib | |||
) | [virtual] |
compute by tree
idx | index | |
LevelContrib | level contribution |
Definition at line 776 of file WeightedDegreePositionStringKernel.cpp.
DREAL * CWeightedDegreePositionStringKernel::compute_scoring | ( | INT | max_degree, | |
INT & | num_feat, | |||
INT & | num_sym, | |||
DREAL * | target, | |||
INT | num_suppvec, | |||
INT * | IDX, | |||
DREAL * | weights | |||
) |
compute positional scoring function, which assigns a weight per position, per symbol in the sequence
max_degree | maximum degree | |
num_feat | number of features | |
num_sym | number of symbols | |
target | target | |
num_suppvec | number of support vectors | |
IDX | IDX | |
weights | weights |
Definition at line 1364 of file WeightedDegreePositionStringKernel.cpp.
CHAR * CWeightedDegreePositionStringKernel::compute_consensus | ( | INT & | num_feat, | |
INT | num_suppvec, | |||
INT * | IDX, | |||
DREAL * | alphas | |||
) |
compute consensus string
num_feat | number of features | |
num_suppvec | number of support vectors | |
IDX | IDX | |
alphas | alphas |
Definition at line 1518 of file WeightedDegreePositionStringKernel.cpp.
DREAL * CWeightedDegreePositionStringKernel::extract_w | ( | INT | max_degree, | |
INT & | num_feat, | |||
INT & | num_sym, | |||
DREAL * | w_result, | |||
INT | num_suppvec, | |||
INT * | IDX, | |||
DREAL * | alphas | |||
) |
extract w
max_degree | maximum degree | |
num_feat | number of features | |
num_sym | number of symbols | |
w_result | w | |
num_suppvec | number of support vectors | |
IDX | IDX | |
alphas | alphas |
Definition at line 1634 of file WeightedDegreePositionStringKernel.cpp.
DREAL * CWeightedDegreePositionStringKernel::compute_POIM | ( | INT | max_degree, | |
INT & | num_feat, | |||
INT & | num_sym, | |||
DREAL * | poim_result, | |||
INT | num_suppvec, | |||
INT * | IDX, | |||
DREAL * | alphas, | |||
DREAL * | distrib | |||
) |
compute POIM
max_degree | maximum degree | |
num_feat | number of features | |
num_sym | number of symbols | |
poim_result | poim | |
num_suppvec | number of support vectors | |
IDX | IDX | |
alphas | alphas | |
distrib | distribution |
Definition at line 1695 of file WeightedDegreePositionStringKernel.cpp.
void CWeightedDegreePositionStringKernel::prepare_POIM2 | ( | DREAL * | distrib, | |
INT | num_sym, | |||
INT | num_feat | |||
) |
prepare POIM2
num_feat | number of features | |
num_sym | number of symbols | |
distrib | distribution |
Definition at line 1828 of file WeightedDegreePositionStringKernel.cpp.
compute POIM2
max_degree | maximum degree | |
svm | SVM |
Definition at line 1839 of file WeightedDegreePositionStringKernel.cpp.
get POIM2
poim | POIMs (returned) | |
result_len | (returned) |
Definition at line 1873 of file WeightedDegreePositionStringKernel.cpp.
void CWeightedDegreePositionStringKernel::cleanup_POIM2 | ( | ) |
void CWeightedDegreePositionStringKernel::create_empty_tries | ( | ) | [protected] |
create emtpy tries
Definition at line 147 of file WeightedDegreePositionStringKernel.cpp.
void CWeightedDegreePositionStringKernel::add_example_to_tree | ( | INT | idx, | |
DREAL | weight | |||
) | [protected, virtual] |
add example to tree
idx | index | |
weight | weight |
Definition at line 639 of file WeightedDegreePositionStringKernel.cpp.
void CWeightedDegreePositionStringKernel::add_example_to_single_tree | ( | INT | idx, | |
DREAL | weight, | |||
INT | tree_num | |||
) | [protected] |
add example to single tree
idx | index | |
weight | weight | |
tree_num | which tree |
Definition at line 690 of file WeightedDegreePositionStringKernel.cpp.
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 610 of file WeightedDegreePositionStringKernel.cpp.
DREAL CWeightedDegreePositionStringKernel::compute_with_mismatch | ( | CHAR * | avec, | |
INT | alen, | |||
CHAR * | bvec, | |||
INT | blen | |||
) | [protected] |
compute with mismatch
avec | vector a | |
alen | length of vector a | |
bvec | vector b | |
blen | length of vector b |
Definition at line 330 of file WeightedDegreePositionStringKernel.cpp.
DREAL CWeightedDegreePositionStringKernel::compute_without_mismatch | ( | CHAR * | avec, | |
INT | alen, | |||
CHAR * | bvec, | |||
INT | blen | |||
) | [protected] |
compute without mismatch
avec | vector a | |
alen | length of vector a | |
bvec | vector b | |
blen | length of vector b |
Definition at line 408 of file WeightedDegreePositionStringKernel.cpp.
DREAL CWeightedDegreePositionStringKernel::compute_without_mismatch_matrix | ( | CHAR * | avec, | |
INT | alen, | |||
CHAR * | bvec, | |||
INT | blen | |||
) | [protected] |
compute without mismatch matrix
avec | vector a | |
alen | length of vector a | |
bvec | vector b | |
blen | length of vector b |
Definition at line 471 of file WeightedDegreePositionStringKernel.cpp.
DREAL CWeightedDegreePositionStringKernel::compute_without_mismatch_position_weights | ( | CHAR * | avec, | |
DREAL * | posweights_lhs, | |||
INT | alen, | |||
CHAR * | bvec, | |||
DREAL * | posweights_rhs, | |||
INT | blen | |||
) | [protected] |
compute without mismatch position weights
avec | vector a | |
posweights_lhs | position weights left-hand side | |
alen | length of vector a | |
bvec | vector b | |
posweights_rhs | position weights right-hand side | |
blen | length of vector b |
Definition at line 533 of file WeightedDegreePositionStringKernel.cpp.
void CWeightedDegreePositionStringKernel::remove_lhs | ( | ) | [protected, virtual] |
remove lhs from kernel
Reimplemented from CKernel.
Definition at line 135 of file WeightedDegreePositionStringKernel.cpp.
virtual EFeatureClass CStringKernel< ST >::get_feature_class | ( | ) | [virtual, inherited] |
return feature class the kernel can deal with
Implements CKernel.
Definition at line 63 of file StringKernel.h.
virtual EFeatureType CStringKernel< ST >::get_feature_type | ( | ) | [virtual, inherited] |
return feature type the kernel can deal with
Implements CKernel.
Reimplemented in CCommUlongStringKernel, CCommWordStringKernel, and CWeightedCommWordStringKernel.
EFeatureType CStringKernel< DREAL >::get_feature_type | ( | ) | [virtual, inherited] |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Reimplemented in CCommUlongStringKernel, CCommWordStringKernel, and CWeightedCommWordStringKernel.
Definition at line 72 of file StringKernel.h.
EFeatureType CStringKernel< ULONG >::get_feature_type | ( | ) | [virtual, inherited] |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Reimplemented in CCommUlongStringKernel, CCommWordStringKernel, and CWeightedCommWordStringKernel.
Definition at line 74 of file StringKernel.h.
EFeatureType CStringKernel< INT >::get_feature_type | ( | ) | [virtual, inherited] |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Reimplemented in CCommUlongStringKernel, CCommWordStringKernel, and CWeightedCommWordStringKernel.
Definition at line 76 of file StringKernel.h.
EFeatureType CStringKernel< WORD >::get_feature_type | ( | ) | [virtual, inherited] |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Reimplemented in CCommUlongStringKernel, CCommWordStringKernel, and CWeightedCommWordStringKernel.
Definition at line 78 of file StringKernel.h.
EFeatureType CStringKernel< SHORT >::get_feature_type | ( | ) | [virtual, inherited] |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Reimplemented in CCommUlongStringKernel, CCommWordStringKernel, and CWeightedCommWordStringKernel.
Definition at line 80 of file StringKernel.h.
EFeatureType CStringKernel< BYTE >::get_feature_type | ( | ) | [virtual, inherited] |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Reimplemented in CCommUlongStringKernel, CCommWordStringKernel, and CWeightedCommWordStringKernel.
Definition at line 82 of file StringKernel.h.
EFeatureType CStringKernel< CHAR >::get_feature_type | ( | ) | [virtual, inherited] |
return feature type the kernel can deal with
abstract base method
Implements CKernel.
Reimplemented in CCommUlongStringKernel, CCommWordStringKernel, and CWeightedCommWordStringKernel.
Definition at line 84 of file StringKernel.h.
get kernel matrix
dst | destination where matrix will be stored | |
m | dimension m of matrix | |
n | dimension n of matrix |
Definition at line 79 of file Kernel.cpp.
get kernel matrix real
m | dimension m of matrix | |
n | dimension n of matrix | |
target | the kernel matrix |
Definition at line 216 of file Kernel.cpp.
SHORTREAL * CKernel::get_kernel_matrix_shortreal | ( | int & | m, | |
int & | n, | |||
SHORTREAL * | target | |||
) | [virtual, inherited] |
get kernel matrix shortreal
m | dimension m of matrix | |
n | dimension n of matrix | |
target | target for kernel matrix |
Reimplemented in CCustomKernel.
Definition at line 146 of file Kernel.cpp.
bool CKernel::load | ( | CHAR * | fname | ) | [inherited] |
load the kernel matrix
fname | filename to load from |
Definition at line 322 of file Kernel.cpp.
bool CKernel::save | ( | CHAR * | fname | ) | [inherited] |
save kernel matrix
fname | filename to save to |
Definition at line 327 of file Kernel.cpp.
CFeatures* CKernel::get_lhs | ( | ) | [inherited] |
CFeatures* CKernel::get_rhs | ( | ) | [inherited] |
INT CKernel::get_num_vec_lhs | ( | ) | [inherited] |
INT CKernel::get_num_vec_rhs | ( | ) | [inherited] |
bool CKernel::has_features | ( | ) | [inherited] |
void CKernel::remove_lhs_and_rhs | ( | ) | [virtual, inherited] |
remove lhs and rhs from kernel
Definition at line 358 of file Kernel.cpp.
void CKernel::remove_rhs | ( | ) | [virtual, inherited] |
takes all necessary steps if the rhs is removed from kernel
remove rhs from kernel
Reimplemented in CCombinedKernel, CCommUlongStringKernel, and CCommWordStringKernel.
Definition at line 379 of file Kernel.cpp.
void CKernel::set_cache_size | ( | INT | size | ) | [inherited] |
int CKernel::get_cache_size | ( | ) | [inherited] |
void CKernel::list_kernel | ( | ) | [inherited] |
list kernel
Definition at line 389 of file Kernel.cpp.
bool CKernel::has_property | ( | EKernelProperty | p | ) | [inherited] |
EOptimizationType CKernel::get_optimization_type | ( | ) | [inherited] |
virtual void CKernel::set_optimization_type | ( | EOptimizationType | t | ) | [virtual, inherited] |
bool CKernel::get_is_initialized | ( | ) | [inherited] |
bool CKernel::init_optimization_svm | ( | CSVM * | svm | ) | [inherited] |
initialize optimization
svm | svm model |
Definition at line 644 of file Kernel.cpp.
DREAL CKernel::get_combined_kernel_weight | ( | ) | [inherited] |
void CKernel::set_combined_kernel_weight | ( | double | nw | ) | [inherited] |
bool CKernel::get_precompute_matrix | ( | ) | [inherited] |
bool CKernel::get_precompute_subkernel_matrix | ( | ) | [inherited] |
virtual void CKernel::set_precompute_matrix | ( | bool | flag, | |
bool | subkernel_flag | |||
) | [virtual, inherited] |
set precompute matrix
flag | flag | |
subkernel_flag | subkernel flag |
Reimplemented in CCombinedKernel.
void CKernel::set_property | ( | EKernelProperty | p | ) | [protected, inherited] |
void CKernel::unset_property | ( | EKernelProperty | p | ) | [protected, inherited] |
void CKernel::set_is_initialized | ( | bool | p_init | ) | [protected, inherited] |
void CKernel::do_precompute_matrix | ( | ) | [protected, inherited] |
DREAL* CWeightedDegreePositionStringKernel::weights [protected] |
weights
Definition at line 665 of file WeightedDegreePositionStringKernel.h.
position weights
Definition at line 667 of file WeightedDegreePositionStringKernel.h.
position weights left-hand side
Definition at line 669 of file WeightedDegreePositionStringKernel.h.
position weights right-hand side
Definition at line 671 of file WeightedDegreePositionStringKernel.h.
bool* CWeightedDegreePositionStringKernel::position_mask [protected] |
position mask
Definition at line 673 of file WeightedDegreePositionStringKernel.h.
DREAL* CWeightedDegreePositionStringKernel::weights_buffer [protected] |
weights buffer
Definition at line 676 of file WeightedDegreePositionStringKernel.h.
INT CWeightedDegreePositionStringKernel::mkl_stepsize [protected] |
MKL stepsize
Definition at line 678 of file WeightedDegreePositionStringKernel.h.
INT CWeightedDegreePositionStringKernel::degree [protected] |
degree
Definition at line 681 of file WeightedDegreePositionStringKernel.h.
INT CWeightedDegreePositionStringKernel::length [protected] |
length
Definition at line 683 of file WeightedDegreePositionStringKernel.h.
INT CWeightedDegreePositionStringKernel::max_mismatch [protected] |
maximum mismatch
Definition at line 686 of file WeightedDegreePositionStringKernel.h.
INT CWeightedDegreePositionStringKernel::seq_length [protected] |
length of sequence
Definition at line 688 of file WeightedDegreePositionStringKernel.h.
INT* CWeightedDegreePositionStringKernel::shift [protected] |
shifts
Definition at line 691 of file WeightedDegreePositionStringKernel.h.
INT CWeightedDegreePositionStringKernel::shift_len [protected] |
length of shifts
Definition at line 693 of file WeightedDegreePositionStringKernel.h.
INT CWeightedDegreePositionStringKernel::max_shift [protected] |
maximum shift
Definition at line 695 of file WeightedDegreePositionStringKernel.h.
bool CWeightedDegreePositionStringKernel::initialized [protected] |
if kernel is initialized
Definition at line 698 of file WeightedDegreePositionStringKernel.h.
bool CWeightedDegreePositionStringKernel::use_normalization [protected] |
if normalization is used
Definition at line 700 of file WeightedDegreePositionStringKernel.h.
bool CWeightedDegreePositionStringKernel::block_computation [protected] |
if block computation is used
Definition at line 702 of file WeightedDegreePositionStringKernel.h.
normalization constant
Definition at line 705 of file WeightedDegreePositionStringKernel.h.
number of external block weights
Definition at line 708 of file WeightedDegreePositionStringKernel.h.
external block weights
Definition at line 710 of file WeightedDegreePositionStringKernel.h.
DREAL* CWeightedDegreePositionStringKernel::block_weights [protected] |
(internal) block weights
Definition at line 713 of file WeightedDegreePositionStringKernel.h.
EWDKernType CWeightedDegreePositionStringKernel::type [protected] |
WeightedDegree kernel type
Definition at line 715 of file WeightedDegreePositionStringKernel.h.
INT CWeightedDegreePositionStringKernel::which_degree [protected] |
which degree
Definition at line 717 of file WeightedDegreePositionStringKernel.h.
CTrie<DNATrie> CWeightedDegreePositionStringKernel::tries [protected] |
tries
Definition at line 720 of file WeightedDegreePositionStringKernel.h.
CTrie<POIMTrie> CWeightedDegreePositionStringKernel::poim_tries [protected] |
POIM tries
Definition at line 722 of file WeightedDegreePositionStringKernel.h.
bool CWeightedDegreePositionStringKernel::tree_initialized [protected] |
if tree is initialized
Definition at line 725 of file WeightedDegreePositionStringKernel.h.
bool CWeightedDegreePositionStringKernel::use_poim_tries [protected] |
makes add_example_to_tree (ONLY!) use POIMTrie
Definition at line 727 of file WeightedDegreePositionStringKernel.h.
DREAL* CWeightedDegreePositionStringKernel::m_poim_distrib [protected] |
temporary memory for the interface to the poim functions
Definition at line 730 of file WeightedDegreePositionStringKernel.h.
DREAL* CWeightedDegreePositionStringKernel::m_poim [protected] |
temporary memory for the interface to the poim functions
Definition at line 732 of file WeightedDegreePositionStringKernel.h.
number of symbols
Definition at line 735 of file WeightedDegreePositionStringKernel.h.
length of string (==num_feat)
Definition at line 737 of file WeightedDegreePositionStringKernel.h.
total size of poim array
Definition at line 739 of file WeightedDegreePositionStringKernel.h.
CAlphabet* CWeightedDegreePositionStringKernel::alphabet [protected] |
alphabet of features
Definition at line 742 of file WeightedDegreePositionStringKernel.h.
INT CKernel::cache_size [protected, inherited] |
KERNELCACHE_ELEM* CKernel::kernel_matrix [protected, inherited] |
SHORTREAL* CKernel::precomputed_matrix [protected, inherited] |
bool CKernel::precompute_subkernel_matrix [protected, inherited] |
bool CKernel::precompute_matrix [protected, inherited] |
CFeatures* CKernel::lhs [protected, inherited] |
CFeatures* CKernel::rhs [protected, inherited] |
DREAL CKernel::combined_kernel_weight [protected, inherited] |
bool CKernel::optimization_initialized [protected, inherited] |
EOptimizationType CKernel::opt_type [protected, inherited] |
ULONG CKernel::properties [protected, inherited] |
CParallel CSGObject::parallel [static, inherited] |
Definition at line 105 of file SGObject.h.
CIO CSGObject::io [static, inherited] |
Definition at line 106 of file SGObject.h.
CVersion CSGObject::version [static, inherited] |
Definition at line 107 of file SGObject.h.