Public Member Functions | Protected Member Functions | Protected Attributes

CRegulatoryModulesStringKernel Class Reference


Detailed Description

The Regulaty Modules kernel, based on the WD kernel, as published in Schultheiss et al., Bioinformatics (2009) on regulatory sequences.

Definition at line 25 of file RegulatoryModulesStringKernel.h.

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

Public Member Functions

 CRegulatoryModulesStringKernel (void)
 CRegulatoryModulesStringKernel (int32_t size, float64_t width, int32_t degree, int32_t shift, int32_t window)
 CRegulatoryModulesStringKernel (CStringFeatures< char > *lstr, CStringFeatures< char > *rstr, CSimpleFeatures< uint16_t > *lpos, CSimpleFeatures< uint16_t > *rpos, float64_t width, int32_t degree, int32_t shift, int32_t window, int32_t size=10)
virtual ~CRegulatoryModulesStringKernel ()
virtual bool init (CFeatures *l, CFeatures *r)
virtual EKernelType get_kernel_type ()
virtual const char * get_name () const
void set_motif_positions (CSimpleFeatures< uint16_t > *positions_lhs, CSimpleFeatures< uint16_t > *positions_rhs)

Protected Member Functions

virtual float64_t compute (int32_t idx_a, int32_t idx_b)
float64_t compute_wds (char *avec, char *bvec, int32_t len)
void set_wd_weights ()

Protected Attributes

float64_t width
int32_t degree
int32_t shift
int32_t window
CSimpleFeatures< uint16_t > * motif_positions_lhs
CSimpleFeatures< uint16_t > * motif_positions_rhs
float64_tposition_weights
float64_tweights

Constructor & Destructor Documentation

default constructor

Definition at line 19 of file RegulatoryModulesStringKernel.cpp.

CRegulatoryModulesStringKernel ( int32_t  size,
float64_t  width,
int32_t  degree,
int32_t  shift,
int32_t  window 
)

constructor

Parameters:
size cache size
width width of gaussian kernel
degree degree of wds kernel
shift shift of wds kernel
window size of window around motifs to compute wds kernels on

Definition at line 28 of file RegulatoryModulesStringKernel.cpp.

CRegulatoryModulesStringKernel ( CStringFeatures< char > *  lstr,
CStringFeatures< char > *  rstr,
CSimpleFeatures< uint16_t > *  lpos,
CSimpleFeatures< uint16_t > *  rpos,
float64_t  width,
int32_t  degree,
int32_t  shift,
int32_t  window,
int32_t  size = 10 
)

constructor

Parameters:
lstr string features of left-hand side
rstr string features of right-hand side
lpos motif positions on lhs
rpos motif positions on rhs
width width of gaussian kernel
degree degree of wds kernel
shift shift of wds kernel
window size of window around motifs to compute wds kernels on
size cache size

Definition at line 35 of file RegulatoryModulesStringKernel.cpp.

~CRegulatoryModulesStringKernel (  )  [virtual]

default destructor

Definition at line 45 of file RegulatoryModulesStringKernel.cpp.


Member Function Documentation

float64_t compute ( int32_t  idx_a,
int32_t  idx_b 
) [protected, virtual]

compute kernel function for features a and b idx_{a,b} denote the index of the feature vectors in the corresponding feature object

Parameters:
idx_a index a
idx_b index b
Returns:
computed kernel function at indices a,b

Implements CKernel.

Definition at line 84 of file RegulatoryModulesStringKernel.cpp.

float64_t compute_wds ( char *  avec,
char *  bvec,
int32_t  len 
) [protected]

compute WDS kernel for features a and b

Parameters:
avec vector a
bvec vector b
len length of string
Returns:
computed kernel function

Definition at line 133 of file RegulatoryModulesStringKernel.cpp.

virtual EKernelType get_kernel_type (  )  [virtual]

return what type of kernel we are

Returns:
kernel type

Implements CStringKernel< char >.

Definition at line 72 of file RegulatoryModulesStringKernel.h.

virtual const char* get_name ( void   )  const [virtual]

return the kernel's name

Returns:
name Regulatory Modules

Reimplemented from CStringKernel< char >.

Definition at line 78 of file RegulatoryModulesStringKernel.h.

bool init ( CFeatures l,
CFeatures r 
) [virtual]

initialize kernel

Parameters:
l features of left-hand side
r features of right-hand side
Returns:
if initializing was successful

Reimplemented from CStringKernel< char >.

Definition at line 51 of file RegulatoryModulesStringKernel.cpp.

void set_motif_positions ( CSimpleFeatures< uint16_t > *  positions_lhs,
CSimpleFeatures< uint16_t > *  positions_rhs 
)

set motif positions

Parameters:
positions_lhs motif positions on lhs
positions_rhs motif positions on rhs

Definition at line 68 of file RegulatoryModulesStringKernel.cpp.

void set_wd_weights (  )  [protected]

set standard weighted degree kernel weighting

Definition at line 198 of file RegulatoryModulesStringKernel.cpp.


Member Data Documentation

int32_t degree [protected]

degree of Weighted Degree kernel part

Definition at line 117 of file RegulatoryModulesStringKernel.h.

CSimpleFeatures<uint16_t>* motif_positions_lhs [protected]

Matrix of motif positions from sequences left-hand side

Definition at line 125 of file RegulatoryModulesStringKernel.h.

CSimpleFeatures<uint16_t>* motif_positions_rhs [protected]

Matrix of motif positions from sequences right-hand side

Definition at line 128 of file RegulatoryModulesStringKernel.h.

scaling weights in window

Definition at line 131 of file RegulatoryModulesStringKernel.h.

int32_t shift [protected]

shift of Weighted Degree with Shifts kernel part

Definition at line 119 of file RegulatoryModulesStringKernel.h.

float64_t* weights [protected]

weights of WD kernel

Definition at line 134 of file RegulatoryModulesStringKernel.h.

float64_t width [protected]

width of Gaussian kernel part

Definition at line 114 of file RegulatoryModulesStringKernel.h.

int32_t window [protected]

size of window around motifs

Definition at line 122 of file RegulatoryModulesStringKernel.h.


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