SHOGUN
v1.1.0
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00001 /* 00002 * This program is free software; you can redistribute it and/or modify 00003 * it under the terms of the GNU General Public License as published by 00004 * the Free Software Foundation; either version 3 of the License, or 00005 * (at your option) any later version. 00006 * 00007 * Written (W) 1999-2009 Soeren Sonnenburg 00008 * Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society 00009 */ 00010 00011 #ifndef _LOCALALIGNMENTSTRINGKERNEL_H___ 00012 #define _LOCALALIGNMENTSTRINGKERNEL_H___ 00013 00014 #include <shogun/lib/common.h> 00015 #include <shogun/kernel/StringKernel.h> 00016 00017 namespace shogun 00018 { 00019 #define LOGSUM_TBL 10000 /* span of the logsum table */ 00020 00027 class CLocalAlignmentStringKernel: public CStringKernel<char> 00028 { 00029 public: 00033 CLocalAlignmentStringKernel(int32_t size=0); 00034 00042 CLocalAlignmentStringKernel( 00043 CStringFeatures<char>* l, CStringFeatures<char>* r, 00044 float64_t opening=12, float64_t extension=2); 00045 00046 virtual ~CLocalAlignmentStringKernel(); 00047 00054 virtual bool init(CFeatures* l, CFeatures* r); 00055 00057 virtual void cleanup(); 00058 00063 virtual EKernelType get_kernel_type() 00064 { 00065 return K_LOCALALIGNMENT; 00066 } 00067 00072 virtual const char* get_name() const 00073 { 00074 return "LocalAlignmentStringKernel"; 00075 } 00076 00077 protected: 00086 virtual float64_t compute(int32_t idx_a, int32_t idx_b); 00087 00088 00089 private: 00091 void init_logsum(); 00092 00099 int32_t LogSum(int32_t p1, int32_t p2); 00100 00107 float32_t LogSum2(float32_t p1, float32_t p2); 00108 00117 float64_t LAkernelcompute( 00118 int32_t* aaX, int32_t* aaY, int32_t nX, int32_t nY); 00119 00122 void init_static_variables(); 00123 00124 void init(); 00125 00126 protected: 00128 bool initialized; 00129 00131 int32_t *isAA; 00133 int32_t *aaIndex; 00134 00136 int32_t m_opening; 00138 int32_t m_extension; 00139 00141 static int32_t logsum_lookup[LOGSUM_TBL]; 00143 static const int32_t blosum[]; 00145 int32_t* scaled_blosum; 00147 static const char* aaList; 00148 }; 00149 } 00150 #endif /* _LOCALALIGNMENTSTRINGKERNEL_H__ */