Definition at line 20 of file LocalAlignmentStringKernel.h.
CLocalAlignmentStringKernel::CLocalAlignmentStringKernel | ( | INT | size | ) |
constructor
size | cache size |
Definition at line 95 of file LocalAlignmentStringKernel.cpp.
CLocalAlignmentStringKernel::CLocalAlignmentStringKernel | ( | CStringFeatures< CHAR > * | l, | |
CStringFeatures< CHAR > * | r | |||
) |
constructor
l | features of left-hand side | |
r | features of right-hand side |
Definition at line 103 of file LocalAlignmentStringKernel.cpp.
CLocalAlignmentStringKernel::~CLocalAlignmentStringKernel | ( | ) | [virtual] |
Definition at line 113 of file LocalAlignmentStringKernel.cpp.
initialize kernel
l | features of left-hand side | |
r | features of right-hand side |
Reimplemented from CStringKernel< ST >.
Definition at line 118 of file LocalAlignmentStringKernel.cpp.
void CLocalAlignmentStringKernel::cleanup | ( | ) | [virtual] |
clean up kernel
Reimplemented from CKernel.
Definition at line 125 of file LocalAlignmentStringKernel.cpp.
virtual bool CLocalAlignmentStringKernel::load_init | ( | FILE * | src | ) | [virtual] |
load kernel init_data
src | file to load from |
Implements CKernel.
Definition at line 54 of file LocalAlignmentStringKernel.h.
virtual bool CLocalAlignmentStringKernel::save_init | ( | FILE * | dest | ) | [virtual] |
save kernel init_data
dest | file to save to |
Implements CKernel.
Definition at line 61 of file LocalAlignmentStringKernel.h.
virtual EKernelType CLocalAlignmentStringKernel::get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CKernel.
Definition at line 67 of file LocalAlignmentStringKernel.h.
virtual const CHAR* CLocalAlignmentStringKernel::get_name | ( | ) | [virtual] |
return the kernel's name
Implements CKernel.
Definition at line 76 of file LocalAlignmentStringKernel.h.
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 351 of file LocalAlignmentStringKernel.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_lhs | ( | ) | [virtual, inherited] |
remove lhs from kernel
Reimplemented in CCombinedKernel, CCommUlongStringKernel, CCommWordStringKernel, CWeightedDegreePositionStringKernel, and CWeightedDegreeStringKernel.
Definition at line 370 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] |
void CKernel::clear_normal | ( | ) | [virtual, inherited] |
for optimizable kernels, i.e. kernels where the weight vector can be computed explicitely (if it fits into memory)
Reimplemented in CCombinedKernel, CCommUlongStringKernel, CCommWordStringKernel, CLinearByteKernel, CLinearKernel, CLinearStringKernel, CLinearWordKernel, CSparseLinearKernel, CWeightedDegreePositionStringKernel, and CWeightedDegreeStringKernel.
Definition at line 578 of file Kernel.cpp.
add vector*factor to 'virtual' normal vector
vector_idx | index | |
weight | weight |
Reimplemented in CCombinedKernel, CCommUlongStringKernel, CCommWordStringKernel, CLinearByteKernel, CLinearKernel, CLinearStringKernel, CLinearWordKernel, CSparseLinearKernel, CWeightedCommWordStringKernel, CWeightedDegreePositionStringKernel, and CWeightedDegreeStringKernel.
Definition at line 573 of file Kernel.cpp.
EOptimizationType CKernel::get_optimization_type | ( | ) | [inherited] |
virtual void CKernel::set_optimization_type | ( | EOptimizationType | t | ) | [virtual, inherited] |
bool CKernel::get_is_initialized | ( | ) | [inherited] |
initialize optimization
count | count | |
IDX | index | |
weights | weights |
Reimplemented in CCombinedKernel, CCommUlongStringKernel, CCommWordStringKernel, CLinearByteKernel, CLinearKernel, CLinearStringKernel, CLinearWordKernel, CSparseLinearKernel, CWeightedDegreePositionStringKernel, and CWeightedDegreeStringKernel.
Definition at line 550 of file Kernel.cpp.
bool CKernel::delete_optimization | ( | ) | [virtual, inherited] |
delete optimization
Reimplemented in CCombinedKernel, CCommUlongStringKernel, CCommWordStringKernel, CLinearByteKernel, CLinearKernel, CLinearStringKernel, CLinearWordKernel, CSparseLinearKernel, CWeightedDegreePositionStringKernel, and CWeightedDegreeStringKernel.
Definition at line 556 of file Kernel.cpp.
bool CKernel::init_optimization_svm | ( | CSVM * | svm | ) | [inherited] |
initialize optimization
svm | svm model |
Definition at line 644 of file Kernel.cpp.
compute optimized
vector_idx | index to compute |
Reimplemented in CCombinedKernel, CCommUlongStringKernel, CCommWordStringKernel, CLinearByteKernel, CLinearKernel, CLinearStringKernel, CLinearWordKernel, CSparseLinearKernel, CWeightedCommWordStringKernel, CWeightedDegreePositionStringKernel, and CWeightedDegreeStringKernel.
Definition at line 562 of file Kernel.cpp.
void CKernel::compute_batch | ( | INT | num_vec, | |
INT * | vec_idx, | |||
DREAL * | target, | |||
INT | num_suppvec, | |||
INT * | IDX, | |||
DREAL * | alphas, | |||
DREAL | factor = 1.0 | |||
) | [virtual, inherited] |
computes output for a batch of examples in an optimized fashion (favorable if kernel supports it, i.e. has KP_BATCHEVALUATION. to the outputvector target (of length num_vec elements) the output for the examples enumerated in vec_idx are added. therefore make sure that it is initialized with ZERO. the following num_suppvec, IDX, alphas arguments are the number of support vectors, their indices and weights
Reimplemented in CCombinedKernel, CWeightedDegreePositionStringKernel, and CWeightedDegreeStringKernel.
Definition at line 568 of file Kernel.cpp.
DREAL CKernel::get_combined_kernel_weight | ( | ) | [inherited] |
void CKernel::set_combined_kernel_weight | ( | double | nw | ) | [inherited] |
INT CKernel::get_num_subkernels | ( | ) | [virtual, inherited] |
get number of subkernels
Reimplemented in CCombinedKernel, CWeightedDegreePositionStringKernel, and CWeightedDegreeStringKernel.
Definition at line 583 of file Kernel.cpp.
void CKernel::compute_by_subkernel | ( | INT | vector_idx, | |
DREAL * | subkernel_contrib | |||
) | [virtual, inherited] |
compute by subkernel
vector_idx | index | |
subkernel_contrib | subkernel contribution |
Reimplemented in CCombinedKernel, CWeightedDegreePositionStringKernel, and CWeightedDegreeStringKernel.
Definition at line 588 of file Kernel.cpp.
get subkernel weights
num_weights | number of weights will be stored here |
Reimplemented in CCombinedKernel, CWeightedDegreePositionStringKernel, and CWeightedDegreeStringKernel.
Definition at line 593 of file Kernel.cpp.
set subkernel weights
weights | subkernel weights | |
num_weights | number of weights |
Reimplemented in CCombinedKernel, CWeightedDegreePositionStringKernel, and CWeightedDegreeStringKernel.
Definition at line 599 of file Kernel.cpp.
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] |
bool CLocalAlignmentStringKernel::initialized [protected] |
if kernel is initialized
Definition at line 127 of file LocalAlignmentStringKernel.h.
int* CLocalAlignmentStringKernel::isAA [protected] |
indicates whether a char is an amino-acid
Definition at line 130 of file LocalAlignmentStringKernel.h.
int* CLocalAlignmentStringKernel::aaIndex [protected] |
correspondance between amino-acid letter and index
Definition at line 132 of file LocalAlignmentStringKernel.h.
int CLocalAlignmentStringKernel::opening [protected] |
gap penalty opening
Definition at line 135 of file LocalAlignmentStringKernel.h.
int CLocalAlignmentStringKernel::extension [protected] |
gap penalty extension
Definition at line 137 of file LocalAlignmentStringKernel.h.
int CLocalAlignmentStringKernel::logsum_lookup [static, protected] |
static logsum lookup
Definition at line 140 of file LocalAlignmentStringKernel.h.
const int CLocalAlignmentStringKernel::blosum [static, protected] |
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}
Definition at line 142 of file LocalAlignmentStringKernel.h.
int* CLocalAlignmentStringKernel::scaled_blosum [protected] |
scaled blosum
Definition at line 144 of file LocalAlignmentStringKernel.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.