SHOGUN v0.9.0
|
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=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 { return "LocalAlignment"; } 00073 00074 protected: 00083 virtual float64_t compute(int32_t idx_a, int32_t idx_b); 00084 00085 00086 private: 00088 void init_logsum(); 00089 00096 int32_t LogSum(int32_t p1, int32_t p2); 00097 00104 float32_t LogSum2(float32_t p1, float32_t p2); 00105 00114 float64_t LAkernelcompute( 00115 int32_t* aaX, int32_t* aaY, int32_t nX, int32_t nY); 00116 00119 void init_static_variables(); 00120 00121 void init(); 00122 00123 protected: 00125 bool initialized; 00126 00128 int32_t *isAA; 00130 int32_t *aaIndex; 00131 00133 int32_t m_opening; 00135 int32_t m_extension; 00136 00138 static int32_t logsum_lookup[LOGSUM_TBL]; 00140 static const int32_t blosum[]; 00142 int32_t* scaled_blosum; 00144 static const char* aaList; 00145 }; 00146 } 00147 #endif /* _LOCALALIGNMENTSTRINGKERNEL_H__ */