+ started to add quality scoring function to C code
[qpalma.git] / QPalmaDP / qpalma_dp.h
1 #ifndef _QPALMA_DP_H_
2 #define _QPALMA_DP_H_
3
4 #include "penalty_info.h"
5
6 struct ArrayElem { //24B
7 double score;
8 int prev_j;
9 int prev_i;
10 int prev_matrix_no;
11 bool isSplice;
12 } ;
13
14 struct pre_score { //24B
15 double value; //8
16 int prev_i; //4
17 int prev_j; //4
18 int prev_matrix_no;//4
19 bool issplice;//4
20 };
21
22 typedef struct pre_score Pre_score;
23
24 typedef struct Align_pair { //24B
25 double value ;
26 bool issplice;
27 int previ,prevj ;
28 char est_char;
29 char dna_char;
30 };
31
32 void fill_matrix (int nr_paths, Pre_score* matrices[], int len_est, int len_dna, char* est, char* dna, penalty_struct* functions, double* matchmatrix, double* donor, double* acceptor, bool remove_duplicate_scores, int nr_donor_sites, int* donor_sites, int* max_score_positions);
33
34 int check_char(char base);
35
36 bool result_align (Pre_score* matrices[], int matrixnr, int i, int j, int* result_length_ptr, char* est, char* dna, int* s_align, int* e_align, int* m_param, double* alignmentscores, int* max_score_positions );
37
38 extern void print_align(Pre_score* matrix, int length_est, int length_dna, Align_pair* vektor, int result_length, int print_matrix);
39
40
41 /*
42 * The function myalign calculates a new alignment given the scoring scheme
43 * Its input arguments are:
44 *
45 * num_path(id) -> an integer specifying which alignment has to be done
46 * dna ->
47 * est ->
48 * h ->
49 * mmatrix ->
50 * donor ->
51 * acceptor ->
52 * remove_duplicate_scores -> a boolean
53 * print_matrix -> a boolean
54 *
55 * [SpliceAlign, EstAlign, weightMatch, Gesamtscores, dnaest] = myalign_local(...
56 */
57
58 class Alignment {
59
60 private:
61 int* splice_align;
62 int* est_align;
63 int* mmatrix_param;
64 double* alignmentscores;
65 double* qualityMatrix;
66
67 int dna_len;
68 int est_len;
69 int mlen;
70 int nr_paths;
71
72 struct penalty_struct* matching_plifs;
73
74 INT len;
75 REAL *limits;
76 REAL *penalties;
77 INT max_len;
78 INT min_len;
79 REAL *cache;
80 enum ETransformType transform ;
81 INT id;
82 char * name;
83 INT use_svm;
84
85 public:
86 Alignment();
87 ~Alignment() {
88 if(splice_align != 0)
89 delete[] splice_align;
90
91 if(est_align != 0)
92 delete[] est_align;
93
94 if(mmatrix_param != 0)
95 delete[] mmatrix_param;
96
97 if(alignmentscores != 0)
98 delete[] alignmentscores;
99
100 if(qualityMatrix != 0)
101 delete[] qualityMatrix;
102 }
103
104 void myalign(int nr_paths_p, char* dna, int dna_len_p, char* est,
105 int est_len_p, struct penalty_struct h, double* matchmatrix, int mm_len,
106 double* donor, int d_len, double* acceptor, int a_len,
107 bool remove_duplicate_scores, bool print_matrix);
108
109 void setMatchPlifs(struct penalty_struct match_plifs,int idx);
110
111 void penSetLength(int l) { len = l; }
112 void penSetLimits(REAL* lts) {
113 limits = new REAL[len];
114 for(int i=0; i<len; i++)
115 limits[i] = lts[i];
116 }
117
118 void setQualityMatrix(double* qMat, int length);
119 void getDNAEST();
120 void getAlignmentResults(int* s_align, int* e_align,
121 int* mmatrix_p, double* alignscores);
122 };
123
124 #endif // _QPALMA_DP_H_
125