+ extended evaluation function to return positionwise deviations
[qpalma.git] / dyn_prog / 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 void fassert(bool exp,int line, char* file);
36 #define FA(expr) (fassert(expr,__LINE__,__FILE__))
37
38 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);
39
40 extern void print_align(Pre_score* matrix, int length_est, int length_dna, Align_pair* vektor, int result_length, int print_matrix);
41
42
43 /*
44 * The function myalign calculates a new alignment given the scoring scheme
45 * Its input arguments are:
46 *
47 * num_path(id) -> an integer specifying which alignment has to be done
48 * dna ->
49 * est ->
50 * h ->
51 * mmatrix ->
52 * donor ->
53 * acceptor ->
54 * remove_duplicate_scores -> a boolean
55 * print_matrix -> a boolean
56 *
57 * [SpliceAlign, EstAlign, weightMatch, Gesamtscores, dnaest] = myalign_local(...
58 *
59 * the idea of the qualityScores array is as follows
60 *
61 * consider a matrix of 24 plifs
62 *
63 * -> row major
64 *
65 */
66
67 class Alignment {
68
69 private:
70 int* splice_align;
71 int* est_align;
72 int* mmatrix_param;
73 double* alignmentscores;
74 struct penalty_struct** qualityScoresAllPaths;
75
76 int dna_len;
77 int est_len;
78 int mlen;
79 int nr_paths;
80
81 int numQualSuppPoints;
82 int numPlifs;
83 bool use_quality_scores;
84
85 uint splice_align_size ;
86 uint est_align_size ;
87 uint mmatrix_param_size ;
88 uint alignmentscores_size ;
89 uint numPathsPlifs ;
90
91 INT len;
92 REAL *limits;
93 REAL *penalties;
94 INT max_len;
95 INT min_len;
96 REAL *cache;
97 enum ETransformType transform ;
98 INT id;
99 char * name;
100 INT use_svm;
101
102 public:
103 Alignment(int numQPlifs ,int numq, bool use_qscores);
104 ~Alignment() {
105 if(splice_align != 0)
106 delete[] splice_align;
107
108 if(est_align != 0)
109 delete[] est_align;
110
111 if(mmatrix_param != 0)
112 delete[] mmatrix_param;
113
114 if(alignmentscores != 0)
115 delete[] alignmentscores;
116
117 if(qualityScoresAllPaths != 0)
118 delete[] qualityScoresAllPaths;
119 }
120
121 void myalign(int nr_paths_p, char* dna, int dna_len_p, char* est,
122 int est_len_p, double* prb, double* chastity, struct penalty_struct h,
123 double* matchmatrix, int mm_len, double* donor, int d_len, double* acceptor,
124 int a_len, struct penalty_struct* qualityScores, bool remove_duplicate_scores,
125 bool print_matrix);
126
127 void getDNAEST();
128 void getAlignmentResults(int* s_align, int* e_align,
129 int* mmatrix_p, double* alignscores, double* qScores);
130 };
131
132 #endif // _QPALMA_DP_H_