142 lines
3.9 KiB
C++
142 lines
3.9 KiB
C++
#include "headers.h"
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#include "template.h"
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#include "utils.h"
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#include "LoadTimeInitializer.h"
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using namespace std;
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template<class NUMBER>
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NUMBER compute_full_prob(testcase *tc, NUMBER *before_last_log)
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{
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int r, c;
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int ROWS = tc->rslen + 1;
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int COLS = tc->haplen + 1;
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Context<NUMBER> ctx;
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//#define USE_STACK_ALLOCATION 1
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#ifdef USE_STACK_ALLOCATION
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NUMBER M[ROWS][COLS];
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NUMBER X[ROWS][COLS];
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NUMBER Y[ROWS][COLS];
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NUMBER p[ROWS][6];
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#else
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//allocate on heap in way that simulates a 2D array. Having a 2D array instead of
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//a straightforward array of pointers ensures that all data lies 'close' in memory, increasing
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//the chance of being stored together in the cache. Also, prefetchers can learn memory access
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//patterns for 2D arrays, not possible for array of pointers
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//bool locally_allocated = false;
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//NUMBER* common_buffer = 0;
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NUMBER* common_buffer = new NUMBER[3*ROWS*COLS + ROWS*6];
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//unsigned curr_size = sizeof(NUMBER)*(3*ROWS*COLS + ROWS*6);
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//if(true)
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//{
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//common_buffer = new NUMBER[3*ROWS*COLS + ROWS*6];
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//locally_allocated = true;
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//}
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//else
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//common_buffer = (NUMBER*)(g_load_time_initializer.get_buffer());
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//pointers to within the allocated buffer
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NUMBER** common_pointer_buffer = new NUMBER*[4*ROWS];
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NUMBER* ptr = common_buffer;
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unsigned i = 0;
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for(i=0;i<3*ROWS;++i, ptr+=COLS)
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common_pointer_buffer[i] = ptr;
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for(;i<4*ROWS;++i, ptr+=6)
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common_pointer_buffer[i] = ptr;
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NUMBER** M = common_pointer_buffer;
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NUMBER** X = M + ROWS;
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NUMBER** Y = X + ROWS;
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NUMBER** p = Y + ROWS;
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#endif
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p[0][MM] = ctx._(0.0);
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p[0][GapM] = ctx._(0.0);
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p[0][MX] = ctx._(0.0);
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p[0][XX] = ctx._(0.0);
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p[0][MY] = ctx._(0.0);
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p[0][YY] = ctx._(0.0);
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for (r = 1; r < ROWS; r++)
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{
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int _i = tc->i[r-1] & 127;
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int _d = tc->d[r-1] & 127;
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int _c = tc->c[r-1] & 127;
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p[r][MM] = ctx._(1.0) - ctx.ph2pr[(_i + _d) & 127];
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p[r][GapM] = ctx._(1.0) - ctx.ph2pr[_c];
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p[r][MX] = ctx.ph2pr[_i];
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p[r][XX] = ctx.ph2pr[_c];
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p[r][MY] = ctx.ph2pr[_d];
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p[r][YY] = ctx.ph2pr[_c];
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//p[r][MY] = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_d];
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//p[r][YY] = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_c];
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}
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for (c = 0; c < COLS; c++)
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{
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M[0][c] = ctx._(0.0);
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X[0][c] = ctx._(0.0);
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Y[0][c] = ctx.INITIAL_CONSTANT / (tc->haplen);
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}
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for (r = 1; r < ROWS; r++)
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{
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M[r][0] = ctx._(0.0);
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X[r][0] = X[r-1][0] * p[r][XX];
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Y[r][0] = ctx._(0.0);
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}
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NUMBER result = ctx._(0.0);
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for (r = 1; r < ROWS; r++)
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for (c = 1; c < COLS; c++)
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{
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fexcept_t flagp;
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char _rs = tc->rs[r-1];
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char _hap = tc->hap[c-1];
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int _q = tc->q[r-1] & 127;
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NUMBER distm = ctx.ph2pr[_q];
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if (_rs == _hap || _rs == 'N' || _hap == 'N')
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distm = ctx._(1.0) - distm;
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else
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distm = distm/3;
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//feclearexcept(FE_ALL_EXCEPT);
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M[r][c] = distm * (M[r-1][c-1] * p[r][MM] + X[r-1][c-1] * p[r][GapM] + Y[r-1][c-1] * p[r][GapM]);
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//STORE_FP_EXCEPTIONS(flagp, exceptions_array);
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//feclearexcept(FE_ALL_EXCEPT);
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X[r][c] = M[r-1][c] * p[r][MX] + X[r-1][c] * p[r][XX];
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//STORE_FP_EXCEPTIONS(flagp, exceptions_array);
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//feclearexcept(FE_ALL_EXCEPT);
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Y[r][c] = M[r][c-1] * p[r][MY] + Y[r][c-1] * p[r][YY];
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//STORE_FP_EXCEPTIONS(flagp, exceptions_array);
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//CONVERT_AND_PRINT(M[r][c]);
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//CONVERT_AND_PRINT(X[r][c]);
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//CONVERT_AND_PRINT(Y[r][c]);
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}
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for (c = 0; c < COLS; c++)
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{
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result += M[ROWS-1][c] + X[ROWS-1][c];
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}
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if (before_last_log != NULL)
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*before_last_log = result;
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#ifndef USE_STACK_ALLOCATION
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delete common_pointer_buffer;
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//if(locally_allocated)
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delete common_buffer;
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#endif
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return result;
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//return ctx.LOG10(result) - ctx.LOG10_INITIAL_CONSTANT;
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}
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template double compute_full_prob<double>(testcase* tc, double* nextbuf);
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template float compute_full_prob<float>(testcase* tc, float* nextbuf);
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