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 result_len;
  82       int* DNA_ARRAY;
  83       int* EST_ARRAY;
  84
  85       int numQualSuppPoints;
  86       int numPlifs;
  87       bool use_quality_scores;
  88
  89       uint splice_align_size ;
  90       uint est_align_size ;
  91       uint mmatrix_param_size ;
  92       uint alignmentscores_size ;
  93       uint numPathsPlifs ;
  94
  95       INT len;
  96       REAL *limits;
  97       REAL *penalties;
  98       INT max_len;
  99       INT min_len;
 100       REAL *cache;
 101       enum ETransformType transform ;
 102       INT id;
 103       char * name;
 104       INT use_svm;
 105
 106    public:
 107       Alignment(int numQPlifs ,int numq, bool use_qscores);
 108       ~Alignment() {
 109          if(splice_align != 0)
 110             delete[] splice_align;
 111
 112          if(est_align != 0)
 113             delete[] est_align;
 114
 115          if(mmatrix_param != 0)
 116             delete[] mmatrix_param;
 117
 118          if(alignmentscores != 0)
 119             delete[] alignmentscores;
 120
 121          if(qualityScoresAllPaths != 0)
 122             delete[] qualityScoresAllPaths;
 123       }
 124
 125       void myalign(int nr_paths_p, char* dna, int dna_len_p, char* est,
 126       int est_len_p, double* prb, double* chastity, struct penalty_struct h,
 127       double* matchmatrix, int mm_len, double* donor, int d_len, double* acceptor,
 128       int a_len, struct penalty_struct* qualityScores, bool remove_duplicate_scores,
 129       bool print_matrix);
 130
 131       void getDNAEST();
 132       void getAlignmentResults(int* s_align, int* e_align,
 133       int* mmatrix_p, double* alignscores, double* qScores);
 134
 135       int getResultLength() { return result_len; }
 136       void getAlignmentArrays(int* dna_align, int* est_align);
 137 };
 138
 139 #endif  // _QPALMA_DP_H_