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) 2010 Soeren Sonnenburg 00008 * Copyright (C) 2010 Berlin Institute of Technology 00009 */ 00010 00011 #ifndef _SPARSESPATIALSAMPLESTRINGKERNEL_H___ 00012 #define _SPARSESPATIALSAMPLESTRINGKERNEL_H___ 00013 00014 #include <shogun/lib/common.h> 00015 #include <shogun/kernel/StringKernel.h> 00016 00017 namespace shogun 00018 { 00020 struct SSKFeatures 00021 { 00023 int *features; 00025 int *group; 00027 int n; 00028 }; 00029 00034 class CSparseSpatialSampleStringKernel: public CStringKernel<char> 00035 { 00036 public: 00039 CSparseSpatialSampleStringKernel(); 00040 00046 CSparseSpatialSampleStringKernel(CStringFeatures<char>* l, CStringFeatures<char>* r); 00047 00048 virtual ~CSparseSpatialSampleStringKernel(); 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_SPARSESPATIALSAMPLE; 00068 } 00069 00073 void set_d(int32_t max_distance) 00074 { 00075 ASSERT(d>0); 00076 d=max_distance; 00077 } 00078 00080 int32_t get_d() 00081 { 00082 return d; 00083 } 00084 00088 void set_t(int32_t sequence_length) 00089 { 00090 ASSERT(t==2 || t==3); 00091 t=sequence_length; 00092 } 00093 00095 int32_t get_t() 00096 { 00097 return t; 00098 } 00099 00104 virtual const char* get_name() const { return "SparseSpatialSampleStringKernel"; } 00105 00106 protected: 00115 virtual float64_t compute(int32_t idx_a, int32_t idx_b); 00116 00124 SSKFeatures *extractTriple(int **S, int *len, int nStr, int d1, int d2); 00131 SSKFeatures *extractDouble(int **S, int *len, int nStr, int d1); 00136 void compute_double(int32_t idx_a, int32_t idx_b); 00141 void compute_triple(int32_t idx_a, int32_t idx_b); 00148 int* cntsrtna(int *sx, int k, int r, int na); 00157 void countAndUpdate(int *outK, int *sx, int *g, int k, int r, int nStr); 00158 00159 protected: 00162 int32_t t; 00163 00166 int32_t d; 00167 00169 bool isVerbose; 00170 }; 00171 } 00172 #endif /* _SPARSESPATIALSAMPLESTRINGKERNEL_H___ */