UI kernel.
Definition at line 24 of file GUIKernel.h.
Public Member Functions | |
CGUIKernel () | |
CGUIKernel (CSGInterface *interface) | |
~CGUIKernel () | |
CKernel * | get_kernel () |
bool | set_normalization (char *normalization, float64_t c=0.0, float64_t r=0.0) |
bool | set_kernel (CKernel *kern) |
bool | add_kernel (CKernel *kern, float64_t weight=1) |
bool | del_last_kernel () |
bool | init_kernel (const char *target) |
bool | init_kernel_optimization () |
bool | delete_kernel_optimization () |
bool | save_kernel (char *filename) |
bool | clean_kernel () |
bool | resize_kernel_cache (int32_t size) |
bool | set_optimization_type (char *opt_type) |
bool | precompute_subkernels () |
bool | is_initialized () |
CKernel * | create_oligo (int32_t size, int32_t k, float64_t width) |
CKernel * | create_diag (int32_t size=10, float64_t diag=1) |
CKernel * | create_const (int32_t size=10, float64_t c=1) |
CKernel * | create_custom (float64_t *kmatrix, int32_t num_feat, int32_t num_vec, bool source_is_diag, bool dest_is_diag) |
CKernel * | create_gaussianshift (int32_t size=10, float64_t width=1, int32_t max_shift=0, int32_t shift_step=1) |
CKernel * | create_sparsegaussian (int32_t size=10, float64_t width=1) |
CKernel * | create_gaussian (int32_t size=10, float64_t width=1) |
CKernel * | create_sigmoid (int32_t size=10, float64_t gamma=0.01, float64_t coef0=0) |
CKernel * | create_tppk (int32_t size, float64_t *km, int32_t rows, int32_t cols) |
CKernel * | create_sparsepoly (int32_t size=10, int32_t degree=2, bool inhomogene=false, bool normalize=true) |
CKernel * | create_poly (int32_t size=10, int32_t degree=2, bool inhomogene=false, bool normalize=true) |
CKernel * | create_wavelet (int32_t size=10, float64_t Wdilation=5.0, float64_t Wtranslation=2.0) |
CKernel * | create_localityimprovedstring (int32_t size=10, int32_t length=3, int32_t inner_degree=3, int32_t outer_degree=1, EKernelType ktype=K_LOCALITYIMPROVED) |
CKernel * | create_weighteddegreestring (int32_t size=10, int32_t order=3, int32_t max_mismatch=1, bool use_normalization=true, int32_t mkl_stepsize=1, bool block_computation=true, int32_t single_degree=-1) |
CKernel * | create_weighteddegreepositionstring (int32_t size=10, int32_t order=3, int32_t max_mismatch=1, int32_t length=0, int32_t center=0, float64_t step=1) |
CKernel * | create_weighteddegreepositionstring3 (int32_t size=10, int32_t order=3, int32_t max_mismatch=1, int32_t *shifts=NULL, int32_t length=0, int32_t mkl_stepsize=1, float64_t *position_weights=NULL) |
CKernel * | create_weighteddegreepositionstring2 (int32_t size=10, int32_t order=3, int32_t max_mismatch=1, int32_t *shifts=NULL, int32_t length=0, bool use_normalization=true) |
CKernel * | create_weighteddegreerbf (int32_t size=10, int32_t degree=1, int32_t nof_properties=1, float64_t width=1) |
CKernel * | create_spectrummismatchrbf (int32_t size=10, float64_t *AA_matrix=NULL, int32_t nr=128, int32_t nc=128, int32_t max_mismatch=1, int32_t degree=1, float64_t width=1) |
CKernel * | create_localalignmentstring (int32_t size=10) |
CKernel * | create_fixeddegreestring (int32_t size=10, int32_t d=3) |
CKernel * | create_chi2 (int32_t size=10, float64_t width=1) |
CKernel * | create_commstring (int32_t size=10, bool use_sign=false, char *norm_str=NULL, EKernelType ktype=K_WEIGHTEDCOMMWORDSTRING) |
CKernel * | create_matchwordstring (int32_t size=10, int32_t d=3, bool normalize=true) |
CKernel * | create_polymatchstring (int32_t size=10, int32_t degree=2, bool inhomogene=false, bool normalize=true) |
CKernel * | create_polymatchwordstring (int32_t size=10, int32_t degree=2, bool inhomogene=false, bool normalize=true) |
CKernel * | create_salzbergword (int32_t size=10) |
CKernel * | create_histogramword (int32_t size=10) |
CKernel * | create_linearbyte (int32_t size=10, float64_t scale=-1) |
CKernel * | create_linearword (int32_t size=10, float64_t scale=-1) |
CKernel * | create_linearstring (int32_t size=10, float64_t scale=-1) |
CKernel * | create_linear (int32_t size=10, float64_t scale=-1) |
CKernel * | create_sparselinear (int32_t size=10, float64_t scale=-1) |
CKernel * | create_distance (int32_t size=10, float64_t width=1) |
CKernel * | create_combined (int32_t size=10, bool append_subkernel_weights=false) |
virtual const char * | get_name () const |
Protected Attributes | |
CKernel * | kernel |
CSGInterface * | ui |
bool | initialized |
CGUIKernel | ( | ) |
constructor
Definition at line 28 of file GUIKernel.h.
CGUIKernel | ( | CSGInterface * | interface | ) |
~CGUIKernel | ( | ) |
destructor
Definition at line 71 of file GUIKernel.cpp.
add kernel to a Combined kernel, creating one if necessary
Definition at line 867 of file GUIKernel.cpp.
bool clean_kernel | ( | ) |
clean/r kernel
Definition at line 920 of file GUIKernel.cpp.
create a new Chi2 kernel
Definition at line 432 of file GUIKernel.cpp.
CKernel * create_combined | ( | int32_t | size = 10 , |
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bool | append_subkernel_weights = false | |||
) |
create a new Combined kernel
Definition at line 633 of file GUIKernel.cpp.
CKernel * create_commstring | ( | int32_t | size = 10 , |
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bool | use_sign = false , |
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char * | norm_str = NULL , |
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EKernelType | ktype = K_WEIGHTEDCOMMWORDSTRING | |||
) |
create a new WeightedCommWord/CommWord/CommULongString kernel
Definition at line 443 of file GUIKernel.cpp.
create a new Const kernel
Definition at line 100 of file GUIKernel.cpp.
CKernel * create_custom | ( | float64_t * | kmatrix, | |
int32_t | num_feat, | |||
int32_t | num_vec, | |||
bool | source_is_diag, | |||
bool | dest_is_diag | |||
) |
create a new Custom kernel
Definition at line 113 of file GUIKernel.cpp.
create a new Diag kernel
Definition at line 89 of file GUIKernel.cpp.
create a new Distance kernel
Definition at line 618 of file GUIKernel.cpp.
CKernel * create_fixeddegreestring | ( | int32_t | size = 10 , |
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int32_t | d = 3 | |||
) |
create a new FixedDegreeString kernel
Definition at line 421 of file GUIKernel.cpp.
create a new Gaussian kernel
Definition at line 158 of file GUIKernel.cpp.
CKernel * create_gaussianshift | ( | int32_t | size = 10 , |
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float64_t | width = 1 , |
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int32_t | max_shift = 0 , |
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int32_t | shift_step = 1 | |||
) |
create a new GaussianShift kernel
Definition at line 135 of file GUIKernel.cpp.
CKernel * create_histogramword | ( | int32_t | size = 10 |
) |
create a new HistogramWord kernel
Definition at line 536 of file GUIKernel.cpp.
create a new Linear kernel
Definition at line 584 of file GUIKernel.cpp.
create a new LinearByte kernel
Definition at line 552 of file GUIKernel.cpp.
create a new LinearString kernel
Definition at line 572 of file GUIKernel.cpp.
create a new LinearWord kernel
Definition at line 562 of file GUIKernel.cpp.
CKernel * create_localalignmentstring | ( | int32_t | size = 10 |
) |
create a new LocalAlignmentString kernel
Definition at line 410 of file GUIKernel.cpp.
CKernel * create_localityimprovedstring | ( | int32_t | size = 10 , |
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int32_t | length = 3 , |
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int32_t | inner_degree = 3 , |
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int32_t | outer_degree = 1 , |
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EKernelType | ktype = K_LOCALITYIMPROVED | |||
) |
create a new (Simple)LocalityImprovedString kernel
Definition at line 213 of file GUIKernel.cpp.
CKernel * create_matchwordstring | ( | int32_t | size = 10 , |
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int32_t | d = 3 , |
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bool | normalize = true | |||
) |
create a new MatchWordString kernel
Definition at line 475 of file GUIKernel.cpp.
create Oligo kernel
Definition at line 81 of file GUIKernel.cpp.
CKernel * create_poly | ( | int32_t | size = 10 , |
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int32_t | degree = 2 , |
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bool | inhomogene = false , |
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bool | normalize = true | |||
) |
create a new Poly kernel
Definition at line 202 of file GUIKernel.cpp.
CKernel * create_polymatchstring | ( | int32_t | size = 10 , |
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int32_t | degree = 2 , |
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bool | inhomogene = false , |
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bool | normalize = true | |||
) |
create a new PolyMatchString kernel
Definition at line 486 of file GUIKernel.cpp.
CKernel * create_polymatchwordstring | ( | int32_t | size = 10 , |
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int32_t | degree = 2 , |
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bool | inhomogene = false , |
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bool | normalize = true | |||
) |
create a new PolyMatchWordString kernel
Definition at line 497 of file GUIKernel.cpp.
CKernel * create_salzbergword | ( | int32_t | size = 10 |
) |
create a new SalzbergWord kernel
Definition at line 508 of file GUIKernel.cpp.
create a new Sigmoid kernel
Definition at line 169 of file GUIKernel.cpp.
create a new SparseGaussian kernel
Definition at line 147 of file GUIKernel.cpp.
create a new SparseLinear kernel
Definition at line 595 of file GUIKernel.cpp.
CKernel * create_sparsepoly | ( | int32_t | size = 10 , |
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int32_t | degree = 2 , |
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bool | inhomogene = false , |
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bool | normalize = true | |||
) |
create a new SparsePoly kernel
Definition at line 191 of file GUIKernel.cpp.
CKernel * create_spectrummismatchrbf | ( | int32_t | size = 10 , |
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float64_t * | AA_matrix = NULL , |
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int32_t | nr = 128 , |
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int32_t | nc = 128 , |
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int32_t | max_mismatch = 1 , |
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int32_t | degree = 1 , |
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float64_t | width = 1 | |||
) |
create a new SpectrumMismatchRBF kernel
Definition at line 396 of file GUIKernel.cpp.
create a new TPP kernel
Definition at line 606 of file GUIKernel.cpp.
CKernel * create_wavelet | ( | int32_t | size = 10 , |
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float64_t | Wdilation = 5.0 , |
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float64_t | Wtranslation = 2.0 | |||
) |
create new Wavelet kernel
Definition at line 180 of file GUIKernel.cpp.
CKernel * create_weighteddegreepositionstring | ( | int32_t | size = 10 , |
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int32_t | order = 3 , |
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int32_t | max_mismatch = 1 , |
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int32_t | length = 0 , |
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int32_t | center = 0 , |
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float64_t | step = 1 | |||
) |
create a new WeightedDegreePositionString kernel
Definition at line 278 of file GUIKernel.cpp.
CKernel * create_weighteddegreepositionstring2 | ( | int32_t | size = 10 , |
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int32_t | order = 3 , |
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int32_t | max_mismatch = 1 , |
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int32_t * | shifts = NULL , |
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int32_t | length = 0 , |
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bool | use_normalization = true | |||
) |
create a new WeightedDegreePositionString2
Definition at line 337 of file GUIKernel.cpp.
CKernel * create_weighteddegreepositionstring3 | ( | int32_t | size = 10 , |
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int32_t | order = 3 , |
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int32_t | max_mismatch = 1 , |
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int32_t * | shifts = NULL , |
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int32_t | length = 0 , |
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int32_t | mkl_stepsize = 1 , |
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float64_t * | position_weights = NULL | |||
) |
create a new WeightedDegreePositionString3
Definition at line 313 of file GUIKernel.cpp.
CKernel * create_weighteddegreerbf | ( | int32_t | size = 10 , |
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int32_t | degree = 1 , |
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int32_t | nof_properties = 1 , |
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float64_t | width = 1 | |||
) |
create a new WeightedDegreeRBF kernel
Definition at line 385 of file GUIKernel.cpp.
CKernel * create_weighteddegreestring | ( | int32_t | size = 10 , |
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int32_t | order = 3 , |
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int32_t | max_mismatch = 1 , |
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bool | use_normalization = true , |
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int32_t | mkl_stepsize = 1 , |
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bool | block_computation = true , |
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int32_t | single_degree = -1 | |||
) |
create a new WeightedDegreeString kernel
Definition at line 238 of file GUIKernel.cpp.
bool del_last_kernel | ( | ) |
delete last kernel in combined kernel
Definition at line 903 of file GUIKernel.cpp.
bool delete_kernel_optimization | ( | ) |
delete kernel optimization
Definition at line 754 of file GUIKernel.cpp.
CKernel * get_kernel | ( | ) |
get active kernel
Definition at line 76 of file GUIKernel.cpp.
virtual const char* get_name | ( | void | ) | const [virtual] |
bool init_kernel | ( | const char * | target | ) |
initialize kernel
Definition at line 763 of file GUIKernel.cpp.
bool init_kernel_optimization | ( | ) |
initialize kernel optimization
Definition at line 721 of file GUIKernel.cpp.
bool is_initialized | ( | ) |
check if kernel is initialized
Definition at line 68 of file GUIKernel.h.
bool precompute_subkernels | ( | ) |
precompute subkernels
Definition at line 966 of file GUIKernel.cpp.
bool resize_kernel_cache | ( | int32_t | size | ) |
resize kernel cache
Definition at line 928 of file GUIKernel.cpp.
bool save_kernel | ( | char * | filename | ) |
save kernel (matrix) to file
Definition at line 843 of file GUIKernel.cpp.
bool set_kernel | ( | CKernel * | kern | ) |
set active kernel
Definition at line 705 of file GUIKernel.cpp.
set normalization
Definition at line 645 of file GUIKernel.cpp.
bool set_optimization_type | ( | char * | opt_type | ) |
set optimization type
Definition at line 938 of file GUIKernel.cpp.
bool initialized [protected] |
initialized
Definition at line 180 of file GUIKernel.h.
kernel
Definition at line 176 of file GUIKernel.h.
CSGInterface* ui [protected] |
ui
Definition at line 178 of file GUIKernel.h.