common.h File Reference

Go to the source code of this file.

Standard Types

Definition of Platform independent Types

enum  EMessageType {
  M_DEBUG, M_INFO, M_NOTICE, M_WARN,
  M_ERROR, M_CRITICAL, M_ALERT, M_EMERGENCY,
  M_MESSAGEONLY
}
enum  EOptimizationType { FASTBUTMEMHUNGRY, SLOWBUTMEMEFFICIENT }
enum  ENormalizationType {
  NO_NORMALIZATION, SQRT_NORMALIZATION, FULL_NORMALIZATION, SQRTLEN_NORMALIZATION,
  LEN_NORMALIZATION, SQLEN_NORMALIZATION
}
enum  EWDKernType {
  E_WD = 0, E_EXTERNAL = 1, E_BLOCK_CONST = 2, E_BLOCK_LINEAR = 3,
  E_BLOCK_SQPOLY = 4, E_BLOCK_CUBICPOLY = 5, E_BLOCK_EXP = 6, E_BLOCK_LOG = 7,
  E_BLOCK_EXTERNAL = 8
}
enum  EKernelType {
  K_UNKNOWN = 0, K_LINEAR = 10, K_SPARSELINEAR = 11, K_POLY = 20,
  K_GAUSSIAN = 30, K_SPARSEGAUSSIAN = 31, K_GAUSSIANSHIFT = 32, K_HISTOGRAM = 40,
  K_SALZBERG = 41, K_LOCALITYIMPROVED = 50, K_SIMPLELOCALITYIMPROVED = 60, K_FIXEDDEGREE = 70,
  K_WEIGHTEDDEGREE = 80, K_WEIGHTEDDEGREEPOS = 81, K_WEIGHTEDCOMMWORDSTRING = 90, K_POLYMATCH = 100,
  K_ALIGNMENT = 110, K_COMMWORDSTRING = 120, K_COMMULONGSTRING = 121, K_COMBINED = 140,
  K_AUC = 150, K_CUSTOM = 160, K_SIGMOID = 170, K_CHI2 = 180,
  K_DIAG = 190, K_CONST = 200, K_MINDYGRAM = 210, K_DISTANCE = 220,
  K_LOCALALIGNMENT = 230, K_PYRAMIDCHI2 = 240
}
enum  EClassifierType {
  CT_NONE = 0, CT_LIGHT = 10, CT_LIBSVM = 20, CT_LIBSVMONECLASS = 30,
  CT_LIBSVMMULTICLASS = 40, CT_MPD = 50, CT_GPBT = 60, CT_CPLEXSVM = 70,
  CT_PERCEPTRON = 80, CT_KERNELPERCEPTRON = 90, CT_LDA = 100, CT_LPM = 110,
  CT_LPBOOST = 120, CT_KNN = 130, CT_SVMLIN = 140, CT_KRR = 150,
  CT_GNPPSVM = 160, CT_GMNPSVM = 170, CT_SUBGRADIENTSVM = 180, CT_SUBGRADIENTLPM = 190,
  CT_SVMPERF = 200, CT_LIBSVR = 210, CT_SVRLIGHT = 220, CT_LIBLINEAR = 230,
  CT_KMEANS = 240, CT_HIERARCHICAL = 250, CT_SVMOCAS = 260, CT_WDSVMOCAS = 270,
  CT_SVMSGD = 280
}
enum  EDistanceType {
  D_UNKNOWN = 0, D_MINKOWSKI = 10, D_MANHATTAN = 20, D_CANBERRA = 30,
  D_CHEBYSHEW = 40, D_GEODESIC = 50, D_JENSEN = 60, D_MANHATTANWORD = 70,
  D_HAMMINGWORD = 80, D_CANBERRAWORD = 90, D_SPARSEEUCLIDIAN = 100, D_EUCLIDIAN = 110
}
enum  ERegressionType { RT_NONE = 0, RT_LIGHT = 10, RT_LIBSVM = 20 }
enum  EPreProcType {
  P_UNKNOWN = 0, P_NORMONE = 10, P_LOGPLUSONE = 20, P_SORTWORDSTRING = 30,
  P_SORTULONGSTRING = 40, P_SORTWORD = 50, P_PRUNEVARSUBMEAN = 60
}
enum  EKernelProperty { KP_NONE = 0, KP_LINADD = 1, KP_KERNCOMBINATION = 2, KP_BATCHEVALUATION = 4 }
enum  EFeatureType {
  F_UNKNOWN = 0, F_CHAR = 10, F_BYTE = 20, F_SHORT = 30,
  F_WORD = 40, F_INT = 50, F_UINT = 60, F_LONG = 70,
  F_ULONG = 80, F_SHORTREAL = 90, F_DREAL = 100, F_LONGREAL = 110,
  F_ANY = 1000
}
enum  EFeatureClass {
  C_UNKNOWN = 0, C_SIMPLE = 10, C_SPARSE = 20, C_STRING = 30,
  C_COMBINED = 40, C_ANY = 50, C_MINDYGRAM = 60
}
enum  E_ALPHABET {
  DNA = 0, RAWDNA = 1, RNA = 2, PROTEIN = 3,
  ALPHANUM = 5, CUBE = 6, RAWBYTE = 7, IUPAC_NUCLEIC_ACID = 8,
  IUPAC_AMINO_ACID = 9, NONE = 10, UNKNOWN = 11
}
 Alphabet of charfeatures/observations. More...
typedef char CHAR
 Type CHAR.
typedef CHARP_CHAR
typedef unsigned char BYTE
 Type BYTE.
typedef BYTEP_BYTE
typedef short int SHORT
 Type SHORT is 2 bytes in size.
typedef SHORTP_SHORT
typedef unsigned short int WORD
 Type WORD is 2 bytes in size.
typedef WORDP_WORD
typedef int INT
 Type INT is 4 bytes in size.
typedef INTP_INT
typedef unsigned int UINT
 Type INT is 4 bytes in size.
typedef UINTP_UINT
typedef int64_t LONG
 Type LONG is 8 bytes in size.
typedef LONGP_LONG
typedef uint64_t ULONG
 Type ULONG is 8 bytes in size.
typedef ULONGP_ULONG
typedef float SHORTREAL
 Type SHORTREAL is 4 bytes in size.
typedef SHORTREALP_SHORTREAL
typedef double DREAL
 Type DREAL is 8 bytes in size.
typedef DREALP_DREAL
typedef long double LONGREAL
 Type LONGREAL is 16 bytes in size.
typedef LONGREALP_LONGREAL
typedef DREAL KERNELCACHE_ELEM
typedef LONG KERNELCACHE_IDX

Defines

#define RANDOM_MAX   2147483647


Define Documentation

#define RANDOM_MAX   2147483647

Definition at line 30 of file common.h.


Typedef Documentation

typedef unsigned char BYTE

Type BYTE.

Definition at line 45 of file common.h.

typedef char CHAR

Type CHAR.

Definition at line 41 of file common.h.

typedef double DREAL

Type DREAL is 8 bytes in size.

Definition at line 87 of file common.h.

typedef int INT

Type INT is 4 bytes in size.

Definition at line 57 of file common.h.

Definition at line 97 of file common.h.

Definition at line 100 of file common.h.

typedef int64_t LONG

Type LONG is 8 bytes in size.

Definition at line 67 of file common.h.

typedef long double LONGREAL

Type LONGREAL is 16 bytes in size.

Definition at line 91 of file common.h.

typedef BYTE* P_BYTE

Definition at line 46 of file common.h.

typedef CHAR* P_CHAR

Definition at line 42 of file common.h.

typedef DREAL* P_DREAL

Definition at line 88 of file common.h.

typedef INT* P_INT

Definition at line 58 of file common.h.

typedef LONG* P_LONG

Definition at line 71 of file common.h.

typedef LONGREAL* P_LONGREAL

Definition at line 92 of file common.h.

typedef SHORT* P_SHORT

Definition at line 50 of file common.h.

Definition at line 84 of file common.h.

typedef UINT* P_UINT

Definition at line 62 of file common.h.

typedef ULONG* P_ULONG

Definition at line 80 of file common.h.

typedef WORD* P_WORD

Definition at line 54 of file common.h.

typedef short int SHORT

Type SHORT is 2 bytes in size.

Definition at line 49 of file common.h.

typedef float SHORTREAL

Type SHORTREAL is 4 bytes in size.

Definition at line 83 of file common.h.

typedef unsigned int UINT

Type INT is 4 bytes in size.

Definition at line 61 of file common.h.

typedef uint64_t ULONG

Type ULONG is 8 bytes in size.

Definition at line 76 of file common.h.

typedef unsigned short int WORD

Type WORD is 2 bytes in size.

Definition at line 53 of file common.h.


Enumeration Type Documentation

enum E_ALPHABET

Alphabet of charfeatures/observations.

Enumerator:
DNA  DNA - letters A,C,G,T,*,N,n.
RAWDNA  RAWDNA - letters 0,1,2,3.
RNA  RNA - letters A,C,G,U,*,N,n.
PROTEIN  PROTEIN - letters a-z.
ALPHANUM  ALPHANUM - [0-9a-z].
CUBE  CUBE - [1-6].
RAWBYTE  RAW BYTE - [0-255].
IUPAC_NUCLEIC_ACID  IUPAC_NUCLEIC_ACID.
IUPAC_AMINO_ACID  IUPAC_AMINO_ACID.
NONE  NONE - type has no alphabet.
UNKNOWN  unknown alphabet

Definition at line 286 of file common.h.

Enumerator:
CT_NONE 
CT_LIGHT 
CT_LIBSVM 
CT_LIBSVMONECLASS 
CT_LIBSVMMULTICLASS 
CT_MPD 
CT_GPBT 
CT_CPLEXSVM 
CT_PERCEPTRON 
CT_KERNELPERCEPTRON 
CT_LDA 
CT_LPM 
CT_LPBOOST 
CT_KNN 
CT_SVMLIN 
CT_KRR 
CT_GNPPSVM 
CT_GMNPSVM 
CT_SUBGRADIENTSVM 
CT_SUBGRADIENTLPM 
CT_SVMPERF 
CT_LIBSVR 
CT_SVRLIGHT 
CT_LIBLINEAR 
CT_KMEANS 
CT_HIERARCHICAL 
CT_SVMOCAS 
CT_WDSVMOCAS 
CT_SVMSGD 

Definition at line 182 of file common.h.

Enumerator:
D_UNKNOWN 
D_MINKOWSKI 
D_MANHATTAN 
D_CANBERRA 
D_CHEBYSHEW 
D_GEODESIC 
D_JENSEN 
D_MANHATTANWORD 
D_HAMMINGWORD 
D_CANBERRAWORD 
D_SPARSEEUCLIDIAN 
D_EUCLIDIAN 

Definition at line 215 of file common.h.

Enumerator:
C_UNKNOWN 
C_SIMPLE 
C_SPARSE 
C_STRING 
C_COMBINED 
C_ANY 
C_MINDYGRAM 

Definition at line 274 of file common.h.

Enumerator:
F_UNKNOWN 
F_CHAR 
F_BYTE 
F_SHORT 
F_WORD 
F_INT 
F_UINT 
F_LONG 
F_ULONG 
F_SHORTREAL 
F_DREAL 
F_LONGREAL 
F_ANY 

Definition at line 257 of file common.h.

Enumerator:
KP_NONE 
KP_LINADD 
KP_KERNCOMBINATION 
KP_BATCHEVALUATION 

Definition at line 249 of file common.h.

Enumerator:
K_UNKNOWN 
K_LINEAR 
K_SPARSELINEAR 
K_POLY 
K_GAUSSIAN 
K_SPARSEGAUSSIAN 
K_GAUSSIANSHIFT 
K_HISTOGRAM 
K_SALZBERG 
K_LOCALITYIMPROVED 
K_SIMPLELOCALITYIMPROVED 
K_FIXEDDEGREE 
K_WEIGHTEDDEGREE 
K_WEIGHTEDDEGREEPOS 
K_WEIGHTEDCOMMWORDSTRING 
K_POLYMATCH 
K_ALIGNMENT 
K_COMMWORDSTRING 
K_COMMULONGSTRING 
K_COMBINED 
K_AUC 
K_CUSTOM 
K_SIGMOID 
K_CHI2 
K_DIAG 
K_CONST 
K_MINDYGRAM 
K_DISTANCE 
K_LOCALALIGNMENT 
K_PYRAMIDCHI2 

Definition at line 148 of file common.h.

The io libs output [DEBUG] etc in front of every message 'higher' messages filter output depending on the loglevel, i.e. CRITICAL messages will print all M_CRITICAL TO M_EMERGENCY messages to

Enumerator:
M_DEBUG 
M_INFO 
M_NOTICE 
M_WARN 
M_ERROR 
M_CRITICAL 
M_ALERT 
M_EMERGENCY 
M_MESSAGEONLY 

Definition at line 105 of file common.h.

Enumerator:
NO_NORMALIZATION 
SQRT_NORMALIZATION 
FULL_NORMALIZATION 
SQRTLEN_NORMALIZATION 
LEN_NORMALIZATION 
SQLEN_NORMALIZATION 

Definition at line 124 of file common.h.

Enumerator:
FASTBUTMEMHUNGRY 
SLOWBUTMEMEFFICIENT 

Definition at line 118 of file common.h.

Enumerator:
P_UNKNOWN 
P_NORMONE 
P_LOGPLUSONE 
P_SORTWORDSTRING 
P_SORTULONGSTRING 
P_SORTWORD 
P_PRUNEVARSUBMEAN 

Definition at line 238 of file common.h.

Enumerator:
RT_NONE 
RT_LIGHT 
RT_LIBSVM 

Definition at line 231 of file common.h.

Enumerator:
E_WD 
E_EXTERNAL 
E_BLOCK_CONST 
E_BLOCK_LINEAR 
E_BLOCK_SQPOLY 
E_BLOCK_CUBICPOLY 
E_BLOCK_EXP 
E_BLOCK_LOG 
E_BLOCK_EXTERNAL 

Definition at line 134 of file common.h.


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