BGI/soap_src/soap_builder/extratools.h

   1 #ifndef _EXTRATOOLS_H_
   2 #define _EXTRATOOLS_H_
   3
   4 #include <stdio.h>
   5 #include <stdlib.h>
   6 #include "MiscUtilities.h"
   7 #include "MemManager.h"
   8 #include "TextConverter.h"
   9 #include "Timing.h"
  10 #include "BWT.h"
  11 #include "HSP.h"
  12 #include "Types.h"
  13 #include <fcntl.h>
  14
  15 typedef struct LOOKUPTABLE_TYPE {
  16        unsigned int tableSize;
  17        unsigned int * table;
  18 }LOOKUPTABLE;
  19
  20 typedef struct HASHCELL_TYPE {
  21     unsigned int count;
  22     unsigned int index;
  23 }HASHCELL;
  24
  25 typedef struct HASHITEM_TYPE {
  26     unsigned int l;
  27     unsigned int r;
  28     unsigned int occIndex;
  29 }HASHITEM;
  30
  31 typedef unsigned int OCC;
  32
  33 typedef struct HASHTABLE_TYPE {
  34        unsigned int prime;
  35        unsigned int a;
  36        unsigned int b;
  37        unsigned int tableSize;
  38        HASHCELL * table;
  39        HASHITEM * itemList;
  40        OCC * occList;
  41 }HASHTABLE;
  42
  43
  44
  45 BWT * occBwt;
  46 HASHTABLE * occHashtable;
  47 unsigned int * occCollector;
  48 unsigned int occCollected;
  49
  50 FILE * textPositionFile;
  51 void registerTPFile(FILE * filePtr,unsigned int searchMode);
  52
  53
  54 void registerQIndex(unsigned int queryIndex);
  55 void registerQSection();
  56
  57
  58 void LoadLookupTable(LOOKUPTABLE * lookupTable, const char * fileName, const int tableSize);
  59 void FreeLookupTable(LOOKUPTABLE * lookupTable);
  60 unsigned int LookupSafe(LOOKUPTABLE lookupTable, BWT * bwt,unsigned long long lKey, unsigned long long rKey,unsigned int *l, unsigned int *r);
  61 void LoadHashTable(HASHTABLE * hashTable, const char * fileName);
  62 HASHITEM * HashFind(HASHTABLE * hashTable, unsigned int l,unsigned int r);
  63 void FreeHashTable(HASHTABLE * hashTable);
  64 void RegisterDecoder(BWT * bwt,HASHTABLE * hashTable);
  65
  66 //void OCCClean();
  67 //void OCCProcess(unsigned int l,unsigned int r);
  68 void OCCProcess(unsigned int l,unsigned int r, int chain, unsigned int allele1, unsigned int allele2, HitInfo *hits, unsigned int *numOfHits);
  69
  70 //void CleanDecoder();
  71
  72 double getTextPositionTime();
  73 unsigned int getSARetrieved();
  74 unsigned int getHASHRetrieved();
  75
  76 #endif /*_EXTRATOOLS_H_*/
  77