+ added some assertions
[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, double* prb, penalty_struct* functions, double* matchmatrix, penalty_struct* qualityScores, double* donor, double* acceptor, bool remove_duplicate_scores, int nr_donor_sites, int* donor_sites, int* max_score_positions, mode currentMode);
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, double* prb, double* chastity, int* s_align, int* e_align, int* m_param, double* alignmentscores, int* max_score_positions, penalty_struct* qparam, mode currentMode);
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 * the idea of the qualityScores array is as follows
58 *
59 * consider a matrix of 24 plifs
60 *
61 * -> row major
62 *
63 */
64
65 class Alignment {
66
67 private:
68 int* splice_align;
69 int* est_align;
70 int* mmatrix_param;
71 double* alignmentscores;
72 struct penalty_struct* qualityScoresAllPaths;
73
74 int dna_len;
75 int est_len;
76 int mlen;
77 int nr_paths;
78
79 int numQualSuppPoints;
80 int totalNumPlifs;
81
82 uint splice_align_size ;
83 uint est_align_size ;
84 uint mmatrix_param_size ;
85 uint alignmentscores_size ;
86 uint qScores_size ;
87
88 INT len;
89 REAL *limits;
90 REAL *penalties;
91 INT max_len;
92 INT min_len;
93 REAL *cache;
94 enum ETransformType transform ;
95 INT id;
96 char * name;
97 INT use_svm;
98
99 public:
100 Alignment(int numQPlifs ,int numq);
101 ~Alignment() {
102 if(splice_align != 0)
103 delete[] splice_align;
104
105 if(est_align != 0)
106 delete[] est_align;
107
108 if(mmatrix_param != 0)
109 delete[] mmatrix_param;
110
111 if(alignmentscores != 0)
112 delete[] alignmentscores;
113
114 if(qualityScoresAllPaths != 0)
115 delete[] qualityScoresAllPaths;
116 }
117
118 void myalign(int nr_paths_p, char* dna, int dna_len_p, char* est,
119 int est_len_p, double* prb, double* chastity, struct penalty_struct h,
120 double* matchmatrix, int mm_len, double* donor, int d_len, double* acceptor,
121 int a_len, struct penalty_struct* qualityScores, bool remove_duplicate_scores,
122 bool print_matrix, bool use_quality_scores);
123
124 void getDNAEST();
125 void getAlignmentResults(int* s_align, int* e_align,
126 int* mmatrix_p, double* alignscores, double* qScores);
127 };
128
129 #endif // _QPALMA_DP_H_
130