| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : di_protdist.hxx // |
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| 4 | // Purpose : // |
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| 5 | // // |
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| 6 | // Institute of Microbiology (Technical University Munich) // |
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| 7 | // http://www.arb-home.de/ // |
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| 8 | // // |
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| 9 | // =============================================================== // |
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| 10 | |
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| 11 | #ifndef DI_PROTDIST_HXX |
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| 12 | #define DI_PROTDIST_HXX |
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| 13 | |
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| 14 | #ifndef AP_SEQ_SIMPLE_PRO_HXX |
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| 15 | #include <AP_seq_simple_pro.hxx> |
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| 16 | #endif |
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| 17 | |
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| 18 | const int DI_MAX_AA = STOP; // must be 20 |
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| 19 | const int DI_MAX_PAA = UNK; // includes virtual aa |
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| 20 | const int DI_RESOLUTION = 1000; // max res |
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| 21 | const int DI_MAX_DIST = 10; // max dist |
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| 22 | |
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| 23 | // stop is first non real AA == 20 |
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| 24 | |
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| 25 | enum di_codetype { UNIVERSAL, CILIATE, MITO, VERTMITO, FLYMITO, YEASTMITO }; |
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| 26 | enum di_cattype { NONE, SIMILARITY, KIMURA, PAM, CHEMICAL, HALL, GEORGE }; |
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| 27 | |
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| 28 | typedef double di_aa_matrix[DI_MAX_AA][DI_MAX_AA]; |
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| 29 | typedef double di_paa_matrix[DI_MAX_PAA][DI_MAX_PAA]; |
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| 30 | typedef char di_bool_matrix[DI_MAX_PAA][DI_MAX_PAA]; |
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| 31 | |
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| 32 | class DI_ENTRY; |
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| 33 | class AP_smatrix; |
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| 34 | |
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| 35 | class di_protdist : virtual Noncopyable { |
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| 36 | static double pameigs[20]; |
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| 37 | static double pamprobs[20][20]; |
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| 38 | |
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| 39 | di_codetype whichcode; |
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| 40 | di_cattype whichcat; |
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| 41 | |
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| 42 | long spp; // number of species |
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| 43 | long chars; // number of characters |
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| 44 | |
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| 45 | // spp = number of species chars = number of sites in actual sequences |
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| 46 | |
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| 47 | double freqa, freqc, freqg, freqt, ttratio, xi, xv, ease, fracchange; |
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| 48 | DI_ENTRY **entries; // link to entries |
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| 49 | aas trans[4][4][4]; |
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| 50 | double pi[20]; |
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| 51 | long cat[DI_MAX_AA]; |
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| 52 | double eig[DI_MAX_AA]; |
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| 53 | double exptteig[DI_MAX_AA]; |
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| 54 | di_aa_matrix prob, eigvecs; |
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| 55 | |
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| 56 | di_paa_matrix *(slopes[DI_RESOLUTION*DI_MAX_DIST]); |
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| 57 | // huge cash for many slopes |
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| 58 | di_paa_matrix *(curves[DI_RESOLUTION*DI_MAX_DIST]); |
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| 59 | di_bool_matrix *(infs[DI_RESOLUTION*DI_MAX_DIST]); |
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| 60 | |
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| 61 | di_paa_matrix *akt_slopes; |
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| 62 | di_paa_matrix *akt_curves; |
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| 63 | di_bool_matrix *akt_infs; |
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| 64 | AP_smatrix *matrix; // link to output matrix |
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| 65 | |
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| 66 | // Local variables for makedists, propagated globally for c version: |
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| 67 | double p, dp, d2p; |
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| 68 | |
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| 69 | void maketrans(); |
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| 70 | void code(); |
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| 71 | void transition(); |
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| 72 | void givens(di_aa_matrix a, long i, long j, long n, double ctheta, double stheta, bool left); |
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| 73 | void coeffs(double x, double y, double *c, double *s, double accuracy); |
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| 74 | void tridiag(di_aa_matrix a, long n, double accuracy); |
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| 75 | void shiftqr(di_aa_matrix a, long n, double accuracy); |
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| 76 | void qreigen(di_aa_matrix prob, long n); |
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| 77 | void pameigen(); |
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| 78 | |
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| 79 | void predict(double tt, long nb1, long nb2); |
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| 80 | int tt_2_pos(double tt); // double to cash index |
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| 81 | double pos_2_tt(int pos); // cash index to pos |
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| 82 | void build_exptteig(double tt); |
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| 83 | void build_predikt_table(int pos); // build akt_slopes akt_curves |
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| 84 | void build_akt_predikt(double tt); // build akt_slopes akt_curves |
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| 85 | |
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| 86 | double predict_slope(int b1, int b2) { return akt_slopes[0][b1][b2]; } |
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| 87 | double predict_curve(int b1, int b2) { return akt_curves[0][b1][b2]; } |
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| 88 | char predict_infinity(int b1, int b2) { return akt_infs[0][b1][b2]; } |
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| 89 | |
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| 90 | void clean_slopes(); |
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| 91 | |
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| 92 | public: |
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| 93 | di_protdist(di_codetype codei, di_cattype cati, long nentries, DI_ENTRY **entries, long seq_len, AP_smatrix *matrixi); |
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| 94 | ~di_protdist(); |
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| 95 | |
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| 96 | GB_ERROR makedists(bool *aborted_flag); // calculate the distance matrix |
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| 97 | }; |
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| 98 | |
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| 99 | #else |
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| 100 | #error di_protdist.hxx included twice |
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| 101 | #endif // DI_PROTDIST_HXX |
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