SNPStringKernel.cpp

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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) 2009 Soeren Sonnenburg
00008  * Copyright (C) 2009 Berlin Institute of Technology
00009  */
00010 
00011 #include "lib/common.h"
00012 #include "lib/io.h"
00013 #include "kernel/SNPStringKernel.h"
00014 #include "kernel/SqrtDiagKernelNormalizer.h"
00015 #include "features/Features.h"
00016 #include "features/StringFeatures.h"
00017 
00018 using namespace shogun;
00019 
00020 CSNPStringKernel::CSNPStringKernel(int32_t size,
00021         int32_t degree, int32_t win_len, bool inhomogene)
00022 : CStringKernel<char>(size),
00023     m_degree(degree), m_win_len(2*win_len), m_inhomogene(inhomogene)
00024 {
00025     m_str_min=NULL;
00026     m_str_maj=NULL;
00027     set_normalizer(new CSqrtDiagKernelNormalizer());
00028 }
00029 
00030 CSNPStringKernel::CSNPStringKernel(
00031     CStringFeatures<char>* l, CStringFeatures<char>* r,
00032     int32_t degree, int32_t win_len, bool inhomogene)
00033 : CStringKernel<char>(10), m_degree(degree), m_win_len(2*win_len),
00034     m_inhomogene(inhomogene)
00035 {
00036     m_str_min=NULL;
00037     m_str_maj=NULL;
00038     set_normalizer(new CSqrtDiagKernelNormalizer());
00039     if (l==r)
00040         obtain_base_strings();
00041     init(l, r);
00042 }
00043 
00044 CSNPStringKernel::~CSNPStringKernel()
00045 {
00046     cleanup();
00047 }
00048 
00049 bool CSNPStringKernel::init(CFeatures* l, CFeatures* r)
00050 {
00051     CStringKernel<char>::init(l, r);
00052     return init_normalizer();
00053 }
00054 
00055 void CSNPStringKernel::cleanup()
00056 {
00057     CKernel::cleanup();
00058     free(m_str_min);
00059     free(m_str_maj);
00060 }
00061 
00062 void CSNPStringKernel::obtain_base_strings()
00063 {
00064     //should only be called on training data
00065     ASSERT(lhs==rhs);
00066 
00067     m_str_len=0;
00068 
00069     for (int32_t i=0; i<num_lhs; i++)
00070     {
00071         int32_t len;
00072         bool free_vec;
00073         char* vec = ((CStringFeatures<char>*) lhs)->get_feature_vector(i, len, free_vec);
00074 
00075         if (m_str_len==0)
00076         {
00077             m_str_len=len;
00078             size_t tlen=(len+1)*sizeof(char);
00079             m_str_min=(char*) malloc(tlen);
00080             m_str_maj=(char*) malloc(tlen);
00081             memset(m_str_min, 0, tlen);
00082             memset(m_str_maj, 0, tlen);
00083         }
00084         else
00085         {
00086             ASSERT(m_str_len==len);
00087         }
00088 
00089         for (int32_t j=0; j<len; j++)
00090         {
00091             // skip sequencing errors
00092             if (vec[j]=='0')
00093                 continue;
00094 
00095             if (m_str_min[j]==0)
00096                 m_str_min[j]=vec[j];
00097             else if (m_str_maj[j]==0 && vec[j]!=m_str_min[j])
00098                 m_str_maj[j]=vec[j];
00099         }
00100 
00101         ((CStringFeatures<char>*) lhs)->free_feature_vector(vec, i, free_vec);
00102     }
00103 
00104     for (int32_t j=0; j<m_str_len; j++)
00105     {
00106         // if only one one symbol occurs use 0
00107         if (m_str_min[j]==0)
00108             m_str_min[j]='0';
00109         if (m_str_maj[j]==0)
00110             m_str_maj[j]='0';
00111 
00112         if (m_str_min[j]>m_str_maj[j])
00113             CMath::swap(m_str_min[j], m_str_maj[j]);
00114     }
00115 }
00116 
00117 float64_t CSNPStringKernel::compute(int32_t idx_a, int32_t idx_b)
00118 {
00119     int32_t alen, blen;
00120     bool free_avec, free_bvec;
00121 
00122     char* avec = ((CStringFeatures<char>*) lhs)->get_feature_vector(idx_a, alen, free_avec);
00123     char* bvec = ((CStringFeatures<char>*) rhs)->get_feature_vector(idx_b, blen, free_bvec);
00124 
00125     ASSERT(alen==blen);
00126     if (alen!=m_str_len)
00127         SG_ERROR("alen (%d) !=m_str_len (%d)\n", alen, m_str_len);
00128     ASSERT(m_str_min);
00129     ASSERT(m_str_maj);
00130 
00131     float64_t total=0;
00132     int32_t inhomogene= (m_inhomogene) ? 1 : 0;
00133 
00134     for (int32_t i = 0; i<alen-1; i+=2)
00135     {
00136         int32_t sumaa=0;
00137         int32_t sumbb=0;
00138         int32_t sumab=0;
00139 
00140         for (int32_t l=0; l<m_win_len && i+l<alen-1; l+=2)
00141         {
00142             char a1=avec[i+l];
00143             char a2=avec[i+l+1];
00144             char b1=bvec[i+l];
00145             char b2=bvec[i+l+1];
00146 
00147             if ((a1!=a2 || a1=='0' || a1=='0') && (b1!=b2 || b1=='0' || b2=='0'))
00148                 sumab++;
00149             else if (a1==a2 && b1==b2)
00150             {
00151                 if (a1!=b1)
00152                     continue;
00153 
00154                 if (a1==m_str_min[i+l])
00155                     sumaa++;
00156                 else if (a1==m_str_maj[i+l])
00157                     sumbb++;
00158                 else
00159                 {
00160                     SG_ERROR("The impossible happened i=%d l=%d a1=%c "
00161                             "a2=%c b1=%c b2=%c min=%c maj=%c\n", i, l, a1,a2, b1,b2, m_str_min[i+l], m_str_maj[i+l]);
00162                 }
00163             }
00164 
00165         }
00166         total+=CMath::pow(float64_t(sumaa+sumbb+sumab+inhomogene),
00167                 (int32_t) m_degree);
00168     }
00169 
00170     ((CStringFeatures<char>*) lhs)->free_feature_vector(avec, idx_a, free_avec);
00171     ((CStringFeatures<char>*) rhs)->free_feature_vector(bvec, idx_b, free_bvec);
00172     return total;
00173 }
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