SHOGUN
v2.0.0
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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/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 /* _LOCALALIGNMENTSTRINGKERNEL_H__ */