Go to the documentation of this file.00001
00002
00003
00004
00005
00006
00007
00008
00009
00010
00011 #ifndef _LOCALALIGNMENTSTRINGKERNEL_H___
00012 #define _LOCALALIGNMENTSTRINGKERNEL_H___
00013
00014 #include <shogun/lib/common.h>
00015 #include <shogun/kernel/string/StringKernel.h>
00016
00017 namespace shogun
00018 {
00019
00021 const int32_t LOGSUM_TBL=10000;
00022
00029 class CLocalAlignmentStringKernel: public CStringKernel<char>
00030 {
00031 public:
00035 CLocalAlignmentStringKernel(int32_t size=0);
00036
00044 CLocalAlignmentStringKernel(
00045 CStringFeatures<char>* l, CStringFeatures<char>* r,
00046 float64_t opening=12, float64_t extension=2);
00047
00048 virtual ~CLocalAlignmentStringKernel();
00049
00056 virtual bool init(CFeatures* l, CFeatures* r);
00057
00059 virtual void cleanup();
00060
00065 virtual EKernelType get_kernel_type()
00066 {
00067 return K_LOCALALIGNMENT;
00068 }
00069
00074 virtual const char* get_name() const
00075 {
00076 return "LocalAlignmentStringKernel";
00077 }
00078
00079 protected:
00088 virtual float64_t compute(int32_t idx_a, int32_t idx_b);
00089
00090
00091 private:
00093 void init_logsum();
00094
00101 int32_t LogSum(int32_t p1, int32_t p2);
00102
00109 float32_t LogSum2(float32_t p1, float32_t p2);
00110
00119 float64_t LAkernelcompute(
00120 int32_t* aaX, int32_t* aaY, int32_t nX, int32_t nY);
00121
00124 void init_static_variables();
00125
00126 void init();
00127
00128 protected:
00130 bool initialized;
00131
00133 int32_t *isAA;
00135 int32_t *aaIndex;
00136
00138 int32_t m_opening;
00140 int32_t m_extension;
00141
00143 static int32_t logsum_lookup[LOGSUM_TBL];
00145 static const int32_t blosum[];
00147 int32_t* scaled_blosum;
00149 static const char* aaList;
00150 };
00151 }
00152 #endif