BGI/soap_src/soap_builder/HSPstatistic.h

   1 /* ==========================================================================
   2  *
   3  * HSPstatistic.h
   4  *
   5  * author: Wong Swee Seong
   6  * date: 30-03-2006
   7  *
   8  * gapped and ungapped extension for string matching
   9  *
  10  * ==========================================================================*/
  11
  12
  13 #ifndef _HSP_statistic_
  14 #define _HSP_statistic_
  15
  16 #ifdef __cplusplus
  17 extern "C" {
  18 #endif
  19
  20 #include <stdint.h>
  21
  22 #define int4 int32_t
  23 #define uint4 uint32_t
  24 #define int8 int64_t
  25 #define uint8 uint64_t
  26 #define int2 int16_t
  27 #define uint2 uint16_t
  28
  29
  30 typedef struct stat__score_block
  31 {
  32   int match, mismatch, gapOpen, gapExt;
  33 } STAT_scoreBlock;
  34
  35 typedef struct stat__Xdropoffs
  36 {
  37   double ungapXdropoff, gapXdropoff, gapXdropoffFinal;
  38 } STAT_Xdropoffs;
  39
  40 void initializeHSPstatistic(uint8 databaseSize, uint8 numOfSequences, uint8 minSeqLength, double *dbCharProb,
  41                                                         uint8 querySize, uint8 numOfContext, double *queryCharProb, int scoringMatrix[16][16]);
  42 void printHSPstatistic(FILE * outFile);
  43 int4 calcUngapCutoffScore();
  44 int4 calcGapCutoffScore();
  45 int4 getUngapXdropoff();
  46 int4 getGapXdropoff();
  47 int4 getGapXdropoffFinal();
  48
  49 int4 stat_ungapNormalized2nominal(double normalizedScore);
  50 double stat_ungapNominal2normalized(int4 nominalScore);
  51 double stat_ungapCalcEvalue(double normalizedScore);
  52 int4 stat_ungapEvalue2nominal(double evalue);
  53 double stat_gapNominal2normalized(int4 nominalScore);
  54 int4 stat_gapNormalized2nominal(double normalizedScore);
  55 double stat_gapCalcEvalue(double normalizedScore);
  56 int4 stat_gapEvalue2nominal(double evalue);
  57
  58 #ifdef __cplusplus
  59 }
  60 #endif
  61
  62 #endif