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Public Member Functions | Protected Attributes
CGUIKernel Class Reference

Detailed Description

UI kernel.

Definition at line 24 of file GUIKernel.h.

Inheritance diagram for CGUIKernel:
Inheritance graph
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List of all members.

Public Member Functions

 CGUIKernel ()
 CGUIKernel (CSGInterface *interface)
 ~CGUIKernel ()
CKernelget_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 set_optimization_type (char *opt_type)
bool precompute_subkernels ()
bool is_initialized ()
CKernelcreate_oligo (int32_t size, int32_t k, float64_t width)
CKernelcreate_diag (int32_t size=10, float64_t diag=1)
CKernelcreate_const (int32_t size=10, float64_t c=1)
CKernelcreate_custom (float64_t *kmatrix, int32_t num_feat, int32_t num_vec, bool source_is_diag, bool dest_is_diag)
CKernelcreate_gaussianshift (int32_t size=10, float64_t width=1, int32_t max_shift=0, int32_t shift_step=1)
CKernelcreate_sparsegaussian (int32_t size=10, float64_t width=1)
CKernelcreate_gaussian (int32_t size=10, float64_t width=1)
CKernelcreate_sigmoid (int32_t size=10, float64_t gamma=0.01, float64_t coef0=0)
CKernelcreate_tppk (int32_t size, float64_t *km, int32_t rows, int32_t cols)
CKernelcreate_sparsepoly (int32_t size=10, int32_t degree=2, bool inhomogene=false, bool normalize=true)
CKernelcreate_poly (int32_t size=10, int32_t degree=2, bool inhomogene=false, bool normalize=true)
CKernelcreate_wavelet (int32_t size=10, float64_t Wdilation=5.0, float64_t Wtranslation=2.0)
CKernelcreate_localityimprovedstring (int32_t size=10, int32_t length=3, int32_t inner_degree=3, int32_t outer_degree=1, EKernelType ktype=K_LOCALITYIMPROVED)
CKernelcreate_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)
CKernelcreate_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)
CKernelcreate_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)
CKernelcreate_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)
CKernelcreate_weighteddegreerbf (int32_t size=10, int32_t degree=1, int32_t nof_properties=1, float64_t width=1)
CKernelcreate_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)
CKernelcreate_localalignmentstring (int32_t size=10)
CKernelcreate_fixeddegreestring (int32_t size=10, int32_t d=3)
CKernelcreate_chi2 (int32_t size=10, float64_t width=1)
CKernelcreate_commstring (int32_t size=10, bool use_sign=false, char *norm_str=NULL, EKernelType ktype=K_WEIGHTEDCOMMWORDSTRING)
CKernelcreate_matchwordstring (int32_t size=10, int32_t d=3, bool normalize=true)
CKernelcreate_polymatchstring (int32_t size=10, int32_t degree=2, bool inhomogene=false, bool normalize=true)
CKernelcreate_polymatchwordstring (int32_t size=10, int32_t degree=2, bool inhomogene=false, bool normalize=true)
CKernelcreate_salzbergword (int32_t size=10)
CKernelcreate_histogramword (int32_t size=10)
CKernelcreate_linearbyte (int32_t size=10, float64_t scale=-1)
CKernelcreate_linearword (int32_t size=10, float64_t scale=-1)
CKernelcreate_linearstring (int32_t size=10, float64_t scale=-1)
CKernelcreate_linear (int32_t size=10, float64_t scale=-1)
CKernelcreate_sparselinear (int32_t size=10, float64_t scale=-1)
CKernelcreate_distance (int32_t size=10, float64_t width=1)
CKernelcreate_combined (int32_t size=10, bool append_subkernel_weights=false)
virtual const char * get_name () const

Protected Attributes

CKernelkernel
CSGInterface * ui
bool initialized

Constructor & Destructor Documentation

constructor

Definition at line 28 of file GUIKernel.h.

CGUIKernel ( CSGInterface *  interface)

constructor

Parameters:
interface

Definition at line 65 of file GUIKernel.cpp.

~CGUIKernel ( )

destructor

Definition at line 71 of file GUIKernel.cpp.


Member Function Documentation

bool add_kernel ( CKernel kern,
float64_t  weight = 1 
)

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.

CKernel * create_chi2 ( int32_t  size = 10,
float64_t  width = 1 
)

create a new Chi2 kernel

Definition at line 432 of file GUIKernel.cpp.

CKernel * create_combined ( int32_t  size = 10,
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,
bool  use_sign = false,
char *  norm_str = NULL,
EKernelType  ktype = K_WEIGHTEDCOMMWORDSTRING 
)

create a new WeightedCommWord/CommWord/CommULongString kernel

Definition at line 443 of file GUIKernel.cpp.

CKernel * create_const ( int32_t  size = 10,
float64_t  c = 1 
)

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.

CKernel * create_diag ( int32_t  size = 10,
float64_t  diag = 1 
)

create a new Diag kernel

Definition at line 89 of file GUIKernel.cpp.

CKernel * create_distance ( int32_t  size = 10,
float64_t  width = 1 
)

create a new Distance kernel

Definition at line 618 of file GUIKernel.cpp.

CKernel * create_fixeddegreestring ( int32_t  size = 10,
int32_t  d = 3 
)

create a new FixedDegreeString kernel

Definition at line 421 of file GUIKernel.cpp.

CKernel * create_gaussian ( int32_t  size = 10,
float64_t  width = 1 
)

create a new Gaussian kernel

Definition at line 158 of file GUIKernel.cpp.

CKernel * create_gaussianshift ( int32_t  size = 10,
float64_t  width = 1,
int32_t  max_shift = 0,
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.

CKernel * create_linear ( int32_t  size = 10,
float64_t  scale = -1 
)

create a new Linear kernel

Definition at line 584 of file GUIKernel.cpp.

CKernel * create_linearbyte ( int32_t  size = 10,
float64_t  scale = -1 
)

create a new LinearByte kernel

Definition at line 552 of file GUIKernel.cpp.

CKernel * create_linearstring ( int32_t  size = 10,
float64_t  scale = -1 
)

create a new LinearString kernel

Definition at line 572 of file GUIKernel.cpp.

CKernel * create_linearword ( int32_t  size = 10,
float64_t  scale = -1 
)

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,
int32_t  length = 3,
int32_t  inner_degree = 3,
int32_t  outer_degree = 1,
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,
int32_t  d = 3,
bool  normalize = true 
)

create a new MatchWordString kernel

Definition at line 475 of file GUIKernel.cpp.

CKernel * create_oligo ( int32_t  size,
int32_t  k,
float64_t  width 
)

create Oligo kernel

Definition at line 81 of file GUIKernel.cpp.

CKernel * create_poly ( int32_t  size = 10,
int32_t  degree = 2,
bool  inhomogene = false,
bool  normalize = true 
)

create a new Poly kernel

Definition at line 202 of file GUIKernel.cpp.

CKernel * create_polymatchstring ( int32_t  size = 10,
int32_t  degree = 2,
bool  inhomogene = false,
bool  normalize = true 
)

create a new PolyMatchString kernel

Definition at line 486 of file GUIKernel.cpp.

CKernel * create_polymatchwordstring ( int32_t  size = 10,
int32_t  degree = 2,
bool  inhomogene = false,
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.

CKernel * create_sigmoid ( int32_t  size = 10,
float64_t  gamma = 0.01,
float64_t  coef0 = 0 
)

create a new Sigmoid kernel

Definition at line 169 of file GUIKernel.cpp.

CKernel * create_sparsegaussian ( int32_t  size = 10,
float64_t  width = 1 
)

create a new SparseGaussian kernel

Definition at line 147 of file GUIKernel.cpp.

CKernel * create_sparselinear ( int32_t  size = 10,
float64_t  scale = -1 
)

create a new SparseLinear kernel

Definition at line 595 of file GUIKernel.cpp.

CKernel * create_sparsepoly ( int32_t  size = 10,
int32_t  degree = 2,
bool  inhomogene = false,
bool  normalize = true 
)

create a new SparsePoly kernel

Definition at line 191 of file GUIKernel.cpp.

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 
)

create a new SpectrumMismatchRBF kernel

Definition at line 396 of file GUIKernel.cpp.

CKernel * create_tppk ( int32_t  size,
float64_t km,
int32_t  rows,
int32_t  cols 
)

create a new TPP kernel

Definition at line 606 of file GUIKernel.cpp.

CKernel * create_wavelet ( int32_t  size = 10,
float64_t  Wdilation = 5.0,
float64_t  Wtranslation = 2.0 
)

create new Wavelet kernel

Definition at line 180 of file GUIKernel.cpp.

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 
)

create a new WeightedDegreePositionString kernel

Definition at line 278 of file GUIKernel.cpp.

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 
)

create a new WeightedDegreePositionString2

Definition at line 337 of file GUIKernel.cpp.

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 
)

create a new WeightedDegreePositionString3

Definition at line 313 of file GUIKernel.cpp.

CKernel * create_weighteddegreerbf ( int32_t  size = 10,
int32_t  degree = 1,
int32_t  nof_properties = 1,
float64_t  width = 1 
)

create a new WeightedDegreeRBF kernel

Definition at line 385 of file GUIKernel.cpp.

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 
)

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.

delete kernel optimization

Definition at line 754 of file GUIKernel.cpp.

get active kernel

Definition at line 76 of file GUIKernel.cpp.

virtual const char* get_name ( ) const [virtual]
Returns:
object name

Implements CSGObject.

Definition at line 169 of file GUIKernel.h.

bool init_kernel ( const char *  target)

initialize kernel

Definition at line 763 of file GUIKernel.cpp.

initialize kernel optimization

Definition at line 721 of file GUIKernel.cpp.

bool is_initialized ( )

check if kernel is initialized

Definition at line 65 of file GUIKernel.h.

precompute subkernels

Definition at line 957 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.

bool set_normalization ( char *  normalization,
float64_t  c = 0.0,
float64_t  r = 0.0 
)

set normalization

Definition at line 645 of file GUIKernel.cpp.

bool set_optimization_type ( char *  opt_type)

set optimization type

Definition at line 929 of file GUIKernel.cpp.


Member Data Documentation

bool initialized [protected]

initialized

Definition at line 177 of file GUIKernel.h.

CKernel* kernel [protected]

kernel

Definition at line 173 of file GUIKernel.h.

CSGInterface* ui [protected]

ui

Definition at line 175 of file GUIKernel.h.


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