SVMINT j;	for(j=0;j<new_examples_size;j++){	  (new_rows[new_pos])[j] = (rows[old_pos])[j];	};	delete [](rows[old_pos]);	new_last_used[new_pos] = last_used[old_pos];	new_index[new_pos] = index[old_pos];	new_pos++;      }      else{	if(rows[old_pos] != 0){	  delete [](rows[old_pos]);	};      };      old_pos++;    };    while(new_pos < cache_size){      new_rows[new_pos] = 0; //new SVMFLOAT[new_examples_size];      new_last_used[new_pos] = 0;      new_index[new_pos] = new_examples_size;      new_pos++;    };    while(old_pos < old_cache_size){      if(rows[old_pos] != 0){	delete [](rows[old_pos]);      };      old_pos++;    };    delete []rows;    rows = new_rows;    delete []last_used;    last_used = new_last_used;    delete []index;    index = new_index;    examples_size = new_examples_size;  };};void kernel_c::compute_row(const SVMINT i, SVMFLOAT* myrow){  // place row i in row  svm_example x = the_examples->get_example(i);  svm_example y;  SVMINT k;  for(k=0;k<examples_size;k++){    y = the_examples->get_example(k);    myrow[k] = calculate_K(x,y);  };};SVMFLOAT* kernel_c::get_row(const SVMINT i){  // lookup row in cache or compute  SVMINT low=0;  SVMINT high=cache_size;  SVMINT pos=0;  SVMINT j;  // binary search for i in [low,high]  high = lookup(i);  if(high==cache_size){    pos = high-1;  }  else{    pos=high;  };  if((index[pos] != i) || (last_used[pos] == 0)){    // cache miss    SVMINT k;    if(index[pos] == i){      low = pos;    }    else{      SVMINT min_time = last_used[cache_size-1];  // empty entries are at the end      low=cache_size-1;      for(k=0;k<cache_size;k++){	// search for last recently used element	if(last_used[k] < min_time){	  min_time = last_used[k];	  low = k;	};      };    };        // delete low, calculate row i, place in high    SVMFLOAT* a_row = rows[low];    if(high<=low){      for(j=low;j>high;j--){	rows[j] = rows[j-1];	index[j] = index[j-1];	last_used[j] = last_used[j-1];      };    }    else{      for(j=low;j<high-1;j++){	rows[j] = rows[j+1];	index[j] = index[j+1];	last_used[j] = last_used[j+1];      };      high--;    };    pos=high;    if(0 == a_row){      a_row = new SVMFLOAT[examples_size];    };    rows[high] = a_row;    compute_row(i,a_row);    index[high]=i;  };  counter++;  last_used[pos] = counter;  return(rows[pos]);};void kernel_c::input(istream& data_stream){  throw read_exception("ERROR: Attempt to read in abstract kernel.");};void kernel_c::output(ostream& data_stream) const{  data_stream<<"Abstract kernel"<<endl;};istream& operator >> (istream& data_stream, kernel_c& the_kernel){  the_kernel.input(data_stream);  //  throw read_exception("ERROR: Attempt to read in abstract kernel.");  return data_stream;};ostream& operator << (ostream& data_stream, kernel_c& the_kernel){  the_kernel.output(data_stream);  //  data_stream<<"Abstract kernel"<<endl;  return data_stream;};/* * * The following kernels are defined * - kernel_dot_c: inner product * - kernel_pol_c: polynomial * - kernel_radial_c: radial basis function * plus: * - kernel_user_c: user defined kernel 1 * - kernel_user2_c: user defined kernel 2 * *//* * * kernel_dot_c * */SVMFLOAT kernel_dot_c::calculate_K(const svm_example x, const svm_example y){  SVMFLOAT result = innerproduct(x,y);  return(result);};void kernel_dot_c::input(istream& data_stream){  // read comments until next @, throw error at parameters  char next = data_stream.peek();  if(next == EOF){     // set stream to eof    next = data_stream.get();   };  char* s = new char[MAXCHAR];  while((! data_stream.eof()) && (next != '@')){    if((next != '#') && (next != '\n')){      // trying to read in parameter      cout<<"WARNING: Parameters for dot kernel are ignored."<<endl;    };    data_stream.getline(s,MAXCHAR);    next = data_stream.peek();    if(next == EOF){       // set stream to eof      next = data_stream.get();     };  };  delete []s;};void kernel_dot_c::output(ostream& data_stream) const{  data_stream<<"type dot"<<endl;};/* * * kernel_lin_dot_c * */SVMFLOAT kernel_lin_dot_c::calculate_K(const svm_example x, const svm_example y){  SVMFLOAT result = a*innerproduct(x,y)+b;  return(result);};void kernel_lin_dot_c::input(istream& data_stream){  // read comments and parameters until next @  char next = data_stream.peek();  if(next == EOF){     // set stream to eof    next = data_stream.get();   };  a=1;   b=0;  char* s = new char[MAXCHAR];  while((! data_stream.eof()) && (next != '@')){    if('#' == next){      // ignore comment      data_stream.getline(s,MAXCHAR);    }    else if('\n' == next){      // ignore line-end      next = data_stream.get();    }    else{      // trying to read in parameter      data_stream >> s;      if(0 == strcmp("a",s)){	data_stream >> a;      }      if(0 == strcmp("b",s)){	data_stream >> b;      }      else{	cout<<"Ignoring unknown parameter: "<<s<<endl;      };      data_stream.getline(s,MAXCHAR);    };    next = data_stream.peek();    if(next == EOF){       // set stream to eof      next = data_stream.get();     };  };  delete []s;};void kernel_lin_dot_c::output(ostream& data_stream) const{  data_stream<<"type dot"<<endl;  data_stream<<"a "<<a<<endl;  data_stream<<"b "<<b<<endl;};/* * * kernel_polynomial_c * */SVMFLOAT kernel_polynomial_c::calculate_K(const svm_example x, const svm_example y){  SVMFLOAT prod=1+innerproduct(x,y);  SVMFLOAT result=1;  SVMINT i;  for(i=0;i<degree;i++) result *= prod;  return (result);};void kernel_polynomial_c::input(istream& data_stream){  // read comments and parameters until next @  char next = data_stream.peek();  if(next == EOF){     // set stream to eof    next = data_stream.get();   };  int ok=0;  char* s = new char[MAXCHAR];  while((! data_stream.eof()) && (next != '@')){    if('#' == next){      // ignore comment      data_stream.getline(s,MAXCHAR);    }    else if('\n' == next){      // ignore line-end      next = data_stream.get();    }    else{      // trying to read in parameter      data_stream >> s;      if(0 == strcmp("degree",s)){	data_stream >> degree;	ok = 1;      }      else{	cout<<"Ignoring unknown parameter: "<<s<<endl;      };      data_stream.getline(s,MAXCHAR);    };    next = data_stream.peek();    if(next == EOF){       // set stream to eof      next = data_stream.get();     };  };  if(! ok){    throw read_exception("The parameters did not contain a valid description of a polynomial kernel.");  };  delete []s;};void kernel_polynomial_c::output(ostream& data_stream) const{  data_stream<<"type polynomial"<<endl;  data_stream<<"degree "<<degree<<endl;};/* * * kernel_radial_c * */SVMFLOAT kernel_radial_c::calculate_K(const svm_example x, const svm_example y){  return exp(-gamma*norm2(x,y));};void kernel_radial_c::input(istream& data_stream){  // read comments and parameters until next @  char next = data_stream.peek();  if(next == EOF){     // set stream to eof    next = data_stream.get();   };  int ok=0;  char* s = new char[MAXCHAR];  while((! data_stream.eof()) && (next != '@')){    if('#' == next){      // ignore comment      data_stream.getline(s,MAXCHAR);    }    else if('\n' == next){      // ignore line-end      next = data_stream.get();    }    else{      // trying to read in parameter      data_stream >> s;      if(0 == strcmp("gamma",s)){	data_stream >> gamma;	if(gamma <= 0){	  throw read_exception("ERROR: Gamma must be > 0.");	};	ok = 1;      }      else{	cout<<"Ignoring unknown parameter: "<<s<<endl;      };      data_stream.getline(s,MAXCHAR);    };    next = data_stream.peek();    if(next == EOF){       // set stream to eof      next = data_stream.get();     };  };  if(! ok){    throw read_exception("The parameters did not contain a valid description of a radial kernel.");  };  delete []s;};void kernel_radial_c::output(ostream& data_stream) const{  data_stream<<"type radial"<<endl;  data_stream<<"gamma "<<gamma<<endl;};/* * * kernel_neural_c * */SVMFLOAT kernel_neural_c::calculate_K(const svm_example x, const svm_example y){  return tanh(a*innerproduct(x,y)+b);};void kernel_neural_c::input(istream& data_stream){  // read comments and parameters until next @  char next = data_stream.peek();  if(next == EOF){     // set stream to eof    next = data_stream.get();   };  a=1;   b=1;  char* s = new char[MAXCHAR];  while((! data_stream.eof()) && (next != '@')){    if('#' == next){      // ignore comment      data_stream.getline(s,MAXCHAR);    }    else if('\n' == next){      // ignore line-end      next = data_stream.get();    }    else{      // trying to read in parameter      data_stream >> s;      if(0 == strcmp("a",s)){	data_stream >> a;      }      else if(0 == strcmp("b",s)){	data_stream >> b;      }      else{	cout<<"Ignoring unknown parameter: "<<s<<endl;      };      data_stream.getline(s,MAXCHAR);    };    next = data_stream.peek();    if(next == EOF){       // set stream to eof      next = data_stream.get();     };  };  delete []s;};void kernel_neural_c::output(ostream& data_stream) const{  data_stream<<"type neural"<<endl;  data_stream<<"a "<<a<<endl;  data_stream<<"b "<<b<<endl;};/* * * kernel_anova_c * */SVMFLOAT kernel_anova_c::calculate_K(const svm_example x, const svm_example y){  SVMFLOAT result=0;  SVMINT length_x = x.length;  SVMINT length_y = y.length;  svm_attrib* att_x = x.example;  svm_attrib* att_y = y.example;  SVMINT pos_x=0;  SVMINT pos_y=0;  SVMINT zeros=dim;  SVMFLOAT diff;  while((pos_x < length_x) && (pos_y < length_y)){    if(att_x[pos_x].index == att_y[pos_y].index){      diff = att_x[pos_x++].att-att_y[pos_y++].att;      result += exp(-gamma*(diff*diff));    }    else if(att_x[pos_x].index < att_y[pos_y].index){      diff = att_x[pos_x++].att;      result += exp(-gamma*(diff*diff));    }    else{      diff = att_y[pos_y++].att;      result += exp(-gamma*(diff*diff));    };    zeros--;  };  while(pos_x < length_x){    diff = att_x[pos_x++].att;    result += exp(-gamma*(diff*diff));    zeros--;  };  while(pos_y < length_y){    diff = att_y[pos_y++].att;    result += exp(-gamma*(diff*diff));    zeros--;  };  result += (SVMFLOAT)zeros;  SVMFLOAT result2=1;  SVMINT i;  for(i=0;i<degree;i++){    result2 *= result;  };  return result2;};void kernel_anova_c::input(istream& data_stream){  // read comments and parameters until next @  char next = data_stream.peek();  if(next == EOF){     // set stream to eof    next = data_stream.get();   };  int ok_gamma=0;  int ok_degree=0;  char* s = new char[MAXCHAR];  while((! data_stream.eof()) && (next != '@')){    if('#' == next){      // ignore comment      data_stream.getline(s,MAXCHAR);    }    else if('\n' == next){      // ignore line-end      next = data_stream.get();    }    else{      // trying to read in parameter      data_stream >> s;      if(0 == strcmp("gamma",s)){	data_stream >> gamma;	ok_gamma = 1;      }      else if(0 == strcmp("degree",s)){	data_stream >> degree;	ok_degree = 1;      }      else{	cout<<"Ignoring unknown parameter: "<<s<<endl;      };      data_stream.getline(s,MAXCHAR);    };    next = data_stream.peek();    if(next == EOF){       // set stream to eof      next = data_stream.get();     };  };  if((!ok_gamma) || (!ok_degree)){    throw read_exception("The parameters did not contain a valid description of an anova kernel.");  };  delete []s;};void kernel_anova_c::output(ostream& data_stream) const{  data_stream<<"type anova"<<endl;  data_stream<<"gamma "<<gamma<<endl;  data_stream<<"degree "<<degree<<endl;};/* * * kernel_exponential_c * */ SVMFLOAT kernel_exponential_c::calculate_K(const svm_example x, const svm_example y){  SVMFLOAT result=0;  SVMINT length_x = x.length;  SVMINT length_y = y.length;  svm_attrib* att_x = x.example;  svm_attrib* att_y = y.example;  SVMINT pos_x=0;  SVMINT pos_y=0;  SVMINT i=0;  SVMFLOAT mylambda=1;  while((pos_x < length_x) && (pos_y < length_y)){    if(att_x[pos_x].index == att_y[pos_y].index){      for(;i<att_x[pos_x].index;i++) mylambda *= lambda;