| 1 | |
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| 2 | const int ph_max_aa = stop; // mussed be 20 |
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| 3 | const int ph_max_paa = unk; // includes virtual aa |
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| 4 | const int ph_resolution = 1000; // max res |
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| 5 | const int ph_max_dist = 10; // max dist |
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| 6 | // stop is first non real AA == 20 |
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| 7 | |
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| 8 | typedef enum { |
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| 9 | universal, ciliate, mito, vertmito, flymito, yeastmito |
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| 10 | } ph_codetype; |
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| 11 | typedef enum { |
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| 12 | none,similarity,kimura,pam,chemical, hall, george |
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| 13 | } ph_cattype; |
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| 14 | |
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| 15 | |
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| 16 | typedef double ph_aa_matrix[ph_max_aa][ph_max_aa]; |
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| 17 | typedef double ph_paa_matrix[ph_max_paa][ph_max_paa]; |
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| 18 | typedef char ph_bool_matrix[ph_max_paa][ph_max_paa]; |
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| 19 | |
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| 20 | class ph_protdist { |
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| 21 | static double pameigs[20]; |
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| 22 | static double pamprobs[20][20]; |
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| 23 | ph_codetype whichcode; |
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| 24 | ph_cattype whichcat; |
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| 25 | |
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| 26 | long spp; // number of species |
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| 27 | long chars; // number of characters |
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| 28 | /* |
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| 29 | * spp = number of species chars = number of sites in actual sequences |
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| 30 | */ |
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| 31 | double freqa, freqc, freqg, freqt, ttratio, xi, xv, ease, fracchange; |
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| 32 | PHENTRY **entries; // link to entries |
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| 33 | aas trans[4][4][4]; |
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| 34 | double pi[20]; |
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| 35 | long cat[ph_max_aa]; |
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| 36 | double eig[ph_max_aa]; |
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| 37 | double exptteig[ph_max_aa]; |
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| 38 | ph_aa_matrix prob, eigvecs; |
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| 39 | ph_paa_matrix *(slopes[ph_resolution*ph_max_dist]); |
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| 40 | // huge cash for many slopes |
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| 41 | ph_paa_matrix *(curves[ph_resolution*ph_max_dist]); |
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| 42 | ph_bool_matrix *(infs[ph_resolution*ph_max_dist]); |
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| 43 | ph_paa_matrix *akt_slopes; |
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| 44 | ph_paa_matrix *akt_curves; |
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| 45 | ph_bool_matrix *akt_infs; |
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| 46 | double weight[2]; // weight akt slope 1 -> linear interpolation |
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| 47 | AP_smatrix *matrix; // link to output matrix |
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| 48 | |
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| 49 | /* Local variables for makedists, propagated globally for c version: */ |
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| 50 | double p, dp, d2p; |
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| 51 | |
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| 52 | |
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| 53 | void cats(ph_cattype wcat); |
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| 54 | void maketrans(); |
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| 55 | void code(); |
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| 56 | void transition(); |
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| 57 | void givens(ph_aa_matrix a,long i,long j,long n,double ctheta,double stheta,GB_BOOL left); |
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| 58 | void coeffs(double x,double y,double *c,double *s,double accuracy); |
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| 59 | void tridiag(ph_aa_matrix a,long n,double accuracy); |
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| 60 | void shiftqr(ph_aa_matrix a, long n, double accuracy); |
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| 61 | void qreigen(ph_aa_matrix prob,long n); |
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| 62 | void pameigen(); |
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| 63 | |
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| 64 | void predict(double tt,long nb1,long nb2); |
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| 65 | int tt_2_pos(double tt); // double to cash index |
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| 66 | double pos_2_tt(int pos); // cash index to pos |
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| 67 | void build_exptteig(double tt); |
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| 68 | void build_predikt_table(int pos); // build akt_slopes akt_curves |
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| 69 | void build_akt_predikt(double tt); // build akt_slopes akt_curves |
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| 70 | |
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| 71 | double predict_slope(int b1,int b2) { |
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| 72 | return akt_slopes[0][b1][b2];}; |
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| 73 | double predict_curve(int b1,int b2) { return |
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| 74 | akt_curves[0][b1][b2];}; |
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| 75 | char predict_infinity(int b1,int b2) { return |
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| 76 | akt_infs[0][b1][b2];}; |
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| 77 | void clean_slopes(); |
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| 78 | |
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| 79 | public: |
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| 80 | ph_protdist(ph_codetype codei, ph_cattype cati, long nentries, PHENTRY **entries, long seq_len, AP_smatrix *matrixi); |
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| 81 | ~ph_protdist(); |
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| 82 | const char *makedists(); // calculate the distance matrix |
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| 83 | }; |
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