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 "lib/common.h" 00015 #include "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); 00034 00040 CLocalAlignmentStringKernel( 00041 CStringFeatures<char>* l, CStringFeatures<char>* r); 00042 00043 virtual ~CLocalAlignmentStringKernel(); 00044 00051 virtual bool init(CFeatures* l, CFeatures* r); 00052 00054 virtual void cleanup(); 00055 00060 virtual EKernelType get_kernel_type() 00061 { 00062 return K_LOCALALIGNMENT; 00063 } 00064 00069 virtual const char* get_name() const { return "LocalAlignment"; } 00070 00071 private: 00073 void init_logsum(); 00074 00081 int32_t LogSum(int32_t p1, int32_t p2); 00082 00089 float32_t LogSum2(float32_t p1, float32_t p2); 00090 00092 void initialize(); 00093 00102 float64_t LAkernelcompute( 00103 int32_t* aaX, int32_t* aaY, int32_t nX, int32_t nY); 00104 00105 protected: 00114 virtual float64_t compute(int32_t idx_a, int32_t idx_b); 00115 00116 protected: 00118 bool initialized; 00119 00121 int32_t *isAA; 00123 int32_t *aaIndex; 00124 00126 int32_t opening; 00128 int32_t extension; 00129 00131 static int32_t logsum_lookup[LOGSUM_TBL]; 00133 static const int32_t blosum[]; 00135 int32_t* scaled_blosum; 00137 static const char* aaList; 00138 }; 00139 } 00140 #endif /* _LOCALALIGNMENTSTRINGKERNEL_H__ */