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 resize_kernel_cache (int32_t size)
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

CGUIKernel (  ) 

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.

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]
Returns:
object name

Implements CSGObject.

Definition at line 172 of file GUIKernel.h.

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.

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 938 of file GUIKernel.cpp.


Member Data Documentation

bool initialized [protected]

initialized

Definition at line 180 of file GUIKernel.h.

CKernel* kernel [protected]

kernel

Definition at line 176 of file GUIKernel.h.

CSGInterface* ui [protected]

ui

Definition at line 178 of file GUIKernel.h.


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