ARB
di_protdist.hxx
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1 // =============================================================== //
2 // //
3 // File : di_protdist.hxx //
4 // Purpose : //
5 // //
6 // Institute of Microbiology (Technical University Munich) //
7 // http://www.arb-home.de/ //
8 // //
9 // =============================================================== //
10 
11 #ifndef DI_PROTDIST_HXX
12 #define DI_PROTDIST_HXX
13 
14 #ifndef AP_SEQ_SIMPLE_PRO_HXX
15 #include <AP_seq_simple_pro.hxx>
16 #endif
17 
18 const int DI_MAX_AA = STOP; // must be 20
19 const int DI_MAX_PAA = UNK; // includes virtual aa
20 const int DI_RESOLUTION = 1000; // max res
21 const int DI_MAX_DIST = 10; // max dist
22 
23 // stop is first non real AA == 20
24 
27 
28 typedef double di_aa_matrix[DI_MAX_AA][DI_MAX_AA];
31 
32 class DI_ENTRY;
33 class AP_smatrix;
34 
35 class di_protdist : virtual Noncopyable {
36  static double pameigs[20];
37  static double pamprobs[20][20];
38 
39  di_codetype whichcode;
40  di_cattype whichcat;
41 
42  long spp; // number of species
43  long chars; // number of characters
44 
45  // spp = number of species chars = number of sites in actual sequences
46 
47  double freqa, freqc, freqg, freqt, ttratio, xi, xv, ease, fracchange;
48  DI_ENTRY **entries; // link to entries
49  aas trans[4][4][4];
50  double pi[20];
51  long cat[DI_MAX_AA];
52  double eig[DI_MAX_AA];
53  double exptteig[DI_MAX_AA];
54  di_aa_matrix prob, eigvecs;
55 
56  di_paa_matrix *slopes[DI_RESOLUTION*DI_MAX_DIST];
57  // huge cash for many slopes
58  di_paa_matrix *curves[DI_RESOLUTION*DI_MAX_DIST];
59  di_bool_matrix *infs[DI_RESOLUTION*DI_MAX_DIST];
60 
61  di_paa_matrix *akt_slopes;
62  di_paa_matrix *akt_curves;
63  di_bool_matrix *akt_infs;
64  AP_smatrix *matrix; // link to output matrix
65 
66  // Local variables for makedists, propagated globally for c version:
67  double p, dp, d2p;
68 
69  void maketrans();
70  void code();
71  void transition();
72  void givens(di_aa_matrix a, long i, long j, long n, double ctheta, double stheta, bool left);
73  void coeffs(double x, double y, double *c, double *s, double accuracy);
74  void tridiag(di_aa_matrix a, long n, double accuracy);
75  void shiftqr(di_aa_matrix a, long n, double accuracy);
76  void qreigen(di_aa_matrix prob, long n);
77  void pameigen();
78 
79  void predict(double tt, long nb1, long nb2);
80  int tt_2_pos(double tt); // double to cash index
81  double pos_2_tt(int pos); // cash index to pos
82  void build_exptteig(double tt);
83  void build_predikt_table(int pos); // build akt_slopes akt_curves
84  void build_akt_predikt(double tt); // build akt_slopes akt_curves
85 
86  double predict_slope(int b1, int b2) { return akt_slopes[0][b1][b2]; }
87  double predict_curve(int b1, int b2) { return akt_curves[0][b1][b2]; }
88  char predict_infinity(int b1, int b2) { return akt_infs[0][b1][b2]; }
89 
90  void clean_slopes();
91 
92 public:
93  di_protdist(di_codetype codei, di_cattype cati, long nentries, DI_ENTRY **entries, long seq_len, AP_smatrix *matrixi);
94  ~di_protdist();
95 
96  GB_ERROR makedists(bool *aborted_flag); // calculate the distance matrix
97 };
98 
99 #else
100 #error di_protdist.hxx included twice
101 #endif // DI_PROTDIST_HXX
static char * y[maxsp+1]
double di_aa_matrix[DI_MAX_AA][DI_MAX_AA]
Definition: di_protdist.hxx:28
const int DI_MAX_DIST
Definition: di_protdist.hxx:21
di_protdist(di_codetype codei, di_cattype cati, long nentries, DI_ENTRY **entries, long seq_len, AP_smatrix *matrixi)
char di_bool_matrix[DI_MAX_PAA][DI_MAX_PAA]
Definition: di_protdist.hxx:30
const int DI_RESOLUTION
Definition: di_protdist.hxx:20
di_codetype
Definition: di_protdist.hxx:25
Definition: di_matr.hxx:75
di_cattype
Definition: di_protdist.hxx:26
const int DI_MAX_AA
Definition: di_protdist.hxx:18
GB_ERROR makedists(bool *aborted_flag)
double di_paa_matrix[DI_MAX_PAA][DI_MAX_PAA]
Definition: di_protdist.hxx:29
const int DI_MAX_PAA
Definition: di_protdist.hxx:19
GB_write_int const char s
Definition: AW_awar.cxx:156