1 | const int DI_ML_RESOLUTION = 1000; // max res |
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2 | const int DI_ML_MAX_DIST = 10; // max dist |
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3 | const int DI_ML_MAX_MAT_SIZE = 16; |
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4 | |
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5 | |
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6 | typedef double di_ml_matrix[DI_ML_MAX_MAT_SIZE][DI_ML_MAX_MAT_SIZE]; |
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7 | typedef double di_pml_matrix[DI_ML_MAX_MAT_SIZE][DI_ML_MAX_MAT_SIZE]; |
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8 | typedef char di_bool_matrix[DI_ML_MAX_MAT_SIZE][DI_ML_MAX_MAT_SIZE]; |
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9 | |
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10 | class di_mldist { |
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11 | long spp; // number of species |
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12 | long chars; // number of characters |
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13 | long n_states; // << DI_ML_MAX_MAT_SIZE |
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14 | |
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15 | /* |
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16 | * spp = number of species chars = number of sites in actual sequences |
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17 | */ |
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18 | |
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19 | double fracchange; |
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20 | DI_ENTRY **entries; // link to entries |
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21 | double pi[20]; |
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22 | |
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23 | double eig[DI_ML_MAX_MAT_SIZE]; |
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24 | double exptteig[DI_ML_MAX_MAT_SIZE]; |
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25 | di_ml_matrix prob, eigvecs; |
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26 | |
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27 | di_pml_matrix *(slopes[DI_ML_RESOLUTION*DI_ML_MAX_DIST]); |
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28 | // huge cash for many slopes |
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29 | di_pml_matrix *(curves[DI_ML_RESOLUTION*DI_ML_MAX_DIST]); |
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30 | di_bool_matrix *(infs[DI_ML_RESOLUTION*DI_ML_MAX_DIST]); |
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31 | |
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32 | di_pml_matrix *akt_slopes; |
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33 | di_pml_matrix *akt_curves; |
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34 | di_bool_matrix *akt_infs; |
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35 | double weight[2]; // weight akt slope 1 -> linear interpolation |
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36 | AP_smatrix *matrix; // link to output matrix |
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37 | |
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38 | /* Local variables for makedists, propagated globally for c version: */ |
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39 | double p, dp, d2p; |
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40 | |
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41 | |
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42 | void givens(di_ml_matrix a,long i,long j,long n,double ctheta,double stheta,GB_BOOL left); |
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43 | void coeffs(double x,double y,double *c,double *s,double accuracy); |
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44 | void tridiag(di_ml_matrix a,long n,double accuracy); |
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45 | void shiftqr(di_ml_matrix a, long n, double accuracy); |
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46 | void qreigen(di_ml_matrix prob,long n); |
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47 | |
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48 | void predict(double tt,long nb1,long nb2); |
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49 | int tt_2_pos(double tt); // double to cash index |
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50 | double pos_2_tt(int pos); // cash index to pos |
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51 | void build_exptteig(double tt); |
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52 | void build_predikt_table(int pos); // build akt_slopes akt_curves |
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53 | void build_akt_predikt(double tt); // build akt_slopes akt_curves |
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54 | |
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55 | double predict_slope(int b1,int b2) { return akt_slopes[0][b1][b2]; } |
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56 | double predict_curve(int b1,int b2) { return akt_curves[0][b1][b2]; } |
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57 | char predict_infinity(int b1,int b2) { return akt_infs[0][b1][b2]; } |
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58 | void clean_slopes(); |
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59 | |
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60 | public: |
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61 | di_mldist(long nentries, DI_ENTRY **entries, long seq_len, AP_smatrix *matrixi); |
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62 | ~di_mldist(); |
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63 | |
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64 | const char *makedists(); // calculate the distance matrix |
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65 | }; |
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