sim4.h

Go to the documentation of this file.

#ifndef SIM4_H
#define SIM4_H
#include <iostream.h>

/* $Id: sim4.h,v 1.1.1.1 2007-07-13 03:44:06 kzhou Exp $ */

#define  DEFAULT_NUM_I     3       
#define  DIST_CUTOFF       3
#define  DEFAULT_MIN_COV   .8

#define  MININT           -99999
#define  MIN_INTRON        30
#define  MAX_INTRON        20000
#define  MAX_GRINIT        500
#define  MAX_INTERNAL_GAP  50   /* 50 */
#define  LL                60

#define  DEFAULT_DRANGE    10
#define  DEFAULT_WEIGHT    100
#define  DEFAULT_W         15
#define  DEFAULT_X         12    
#define  DEFAULT_K         18
#define  DEFAULT_C         16
#define  P                 .2 

#define  min(x,y)        ((x>y) ? (y):(x))
#define  max(x,y)        ((x<y) ? (y):(x))
#define  START_SIG       ((G_score >= abs(C_score)) ? "GT" : "CT") 
#define  END_SIG         ((G_score >= abs(C_score)) ? "AG" : "AC")

#define  MATCH           1
#define  MISMATCH       -5
#define  L               8

#define  DELETE          1
#define  INSERT          2
#define  SUBSTITUTE      3
#define  INTRON          4
#define  O_INTRON        5

enum { FALSE = 0, TRUE = 1};
enum { INIT = 0, PERM = 1, TEMP = 2};
enum comparisonType { EST_GEN = 1, GEN_EST = 2 };  //kemin zhou
//EST can be either 5' or 3'!!!
enum { FWD = 0, BWD = 1, BOTH = 2 };
enum { OK = 0, FREE_START = 1, FREE_END = 2, FREE_BOTH_ENDS = 3};

/* data structures */

/* used in select_path() */
typedef struct msp {
        int len, pos1, pos2;
        int score;
        int Score;
        int  prev;
        struct msp *next_msp;
} *Msp_ptr;

class exon
{
        public:
                exon();
                friend ostream& operator<<(ostream &os, const exon& ex);
                bool isEmpty() const { return length == 0; }
                int sumLength(int matchCut=90) const;
                //get the total matching length with 90% default cut
      int  from1, from2, to1, to2;
      int  min_diag, max_diag;
      int  match;               //percent 0-100%
      char ori;                 //C E G N  ?
      int  length;              //length of the matches region
      int  flag;
      int  ematches;
      int  edist;  //what is this?
      Msp_ptr msps;
      exon *next_exon;
};
typedef exon  *Exon_ptr;

typedef struct intron {
        int from1, from2, to1, to2;
        int  length;
        char orientation;
        struct intron *next_intron;
} *Intron_ptr, Intron;

typedef struct exon   Exon;

typedef struct coordinates {
        int pos1;
        int pos2;
}  coords;

/* used only in the alignment stage */
class edit_script 
{
        public:
          char op_type;   /* SUB, INS, or DEL */
     int num;        /* Number of operations */
     edit_script *next;
};

class edit_script_list 
{
        public:
                edit_script_list();
                friend ostream& operator<<(ostream &os, const edit_script_list &esl);
      int   offset1, offset2;
      int   len1, len2;  //length of each match
      int    score;  //total number of INS, DEL, SUB
      edit_script *script;
      edit_script_list *next_script;
};

struct edit {
        struct edit *link;            /* previous edit instruction */
        char   type[2];
        int    accumulation;
        char   op;                    /* INSERT, DELETE or INTRON */
        int    line1;                 /* line number in file1 */
        int    line2;                 /* line number in file2 */
};

typedef  void  *Pointer;

typedef  struct ValNode {
         Pointer      data;
         struct ValNode *next;
} *ValNodePtr;

typedef int signal_t[4][4];

typedef struct spliced {
   int xs, xe, ys, ye, score;
   char type;
   struct spliced *next;
} splice_t;

class sim4_stats 
{
        public:
        sim4_stats();
        friend ostream &operator<<(ostream &os, const sim4_stats &ss);
        //for testing purpose
   int internal;
        int icoverage; //siez of the match
        int mult;      //I don't know what is it
        int nmatches;  //number of identical bases in icoverage
   double fcoverage;  //fraction of coverage icoverage/cDNA.len
        // or nmatch/cDNA.len
        double marginals;
};
typedef sim4_stats sim4_stats_t;

class sim4Args {
        public:
   int ali_flag, 
                poly_flag, // 0 display PolyA or T in alignment
                acc_flag,  //N Request an additional search for small 
                //marginal exons (N=1) guided by the splice_site 
                //recognition signals.  default is 0
                reverse,  // 0 plus strand, 1 - strand, 2 both
                DRANGE,
                weight,
                cutoff; 
   bool set_K, set_C;
   int W, K, C, X, B, CDS_from, CDS_to;
   char *S;  //stores the CDS S=123..2000 text info
        //may not be needed
        void getArg(int agc, char *agv[]);
        sim4Args();
        ~sim4Args();
};


#endif