BGI/soap_src/soap_builder/MiscUtilities.h

   1 /*
   2
   3    MiscUtilities.h              Miscellaneous Utilities
   4
   5    This module contains miscellaneous utility functions.
   6
   7
   8    Copyright (C) 2004, Wong Chi Kwong.
   9
  10    This program is free software; you can redistribute it and/or
  11    modify it under the terms of the GNU General Public License
  12    as published by the Free Software Foundation; either version 2
  13    of the License, or (at your option) any later version.
  14
  15    This program is distributed in the hope that it will be useful,
  16    but WITHOUT ANY WARRANTY; without even the implied warranty of
  17    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  18    GNU General Public License for more details.
  19
  20    You should have received a copy of the GNU General Public License
  21    along with this program; if not, write to the Free Software
  22    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
  23
  24 */
  25
  26 #ifndef __MISC_UTILITIES_H__
  27 #define __MISC_UTILITIES_H__
  28
  29 #include "TypeNLimit.h"
  30 #include "stdio.h"
  31
  32 #define init(variable)                                                  variable = 0;   // this is for avoiding compiler warning
  33                                                                                                                                 // disable it if compiler becomes smarter!
  34
  35 #define truncateRight(value, offset)                    ( (value) >> (offset) << (offset) )
  36 #define truncateLeft(value, offset)                             ( (value) << (offset) >> (offset) )
  37 // alignBoundary must be power of 2
  38 #define nextAlignedBoundary(offset, alignBoundary)      ( ((offset) + (alignBoundary) - 1) & (- (alignBoundary)) )
  39 #define lastAlignedBoundary(offset, alignBoundary)              ( (offset) & (- (alignBoundary)) )
  40 #define average(value1, value2)                                 ( ((value1) & (value2)) + ((value1) ^ (value2)) / 2 )
  41 #define min(value1, value2)                                             ( ((value1) < (value2)) ? (value1) : (value2) )
  42 #define max(value1, value2)                                             ( ((value1) > (value2)) ? (value1) : (value2) )
  43 #define med3(a, b, c)                                                   ( a<b ? (b<c ? b : a<c ? c : a) : (b>c ? b : a>c ? c : a))
  44 #define med3Index(key, ia, ib, ic)                              ( key[ia]<key[ib] ? (key[ib]<key[ic] ? ib : key[ia]<key[ic] ? ic : ia) : (key[ib]>key[ic] ? ib : key[ia]>key[ic] ? ic : ia))
  45 #define swap(a, b, t);                                                  t = a; a = b; b = t;
  46
  47 void Dust(const unsigned int len, unsigned char *pattern, const unsigned int level, const unsigned int window, const unsigned int word);
  48
  49 void LimitCodeGenerateCodeTable(const unsigned int limit, unsigned int** codeValue, unsigned int** codeLength);
  50
  51 int QSortUnsignedIntOrder(const void *data, const int index1, const int index2);
  52 void QSort(void* __restrict data, const int numData, const int dataWidth, int (*QSortComp)(const void*, const int, const int) );
  53
  54 unsigned int checkDuplicate(int *input, const unsigned int numItem, const int minValue, const int maxValue, char* text);
  55 unsigned int leadingZero(const unsigned int input);
  56 unsigned int ceilLog2(const unsigned int input);
  57 unsigned int floorLog2(const unsigned int input);
  58 unsigned int power(const unsigned int base, const unsigned int power);
  59 void formatVALAsBinary(const unsigned int input, char* output, unsigned int bitGroup);
  60 unsigned int getRandomSeed();
  61
  62 void ConvertBytePackedDNAToWordPacked(const unsigned char *input, unsigned int *output, const unsigned int textLength);
  63
  64
  65 unsigned int reverseBit(unsigned int x);
  66 void initializeVAL(unsigned int *startAddr, const unsigned int length, const unsigned int initValue);
  67 void initializeCHAR(unsigned char *startAddr, const unsigned int length, const unsigned char initValue);
  68 unsigned int numberOfMatchInVAL(unsigned int *startAddr, const unsigned int length, const unsigned int searchValue);
  69 unsigned int numberOfMatchInCHAR(unsigned char *startAddr, const unsigned int length, const unsigned char searchValue);
  70
  71 void bitCopyNoDestOffset(unsigned int *destinationAddress, const unsigned int *sourceAddress,
  72                                                         int sourceBitOffset, int copyLengthInBit);
  73 void bitCopyNoDestBitOffset(unsigned int *destinationAddress, int destinationWordOffset,
  74                                                         const unsigned int *sourceAddress, int sourceWordOffset,
  75                                                         int sourceBitOffset, int copyLengthInBit);
  76 unsigned int bitCopy(unsigned int *destinationAddress, int destinationWordOffset, int destinationBitOffset,
  77                          const unsigned int *sourceAddress, int sourceBitOffset, int copyLengthInBit);
  78
  79 unsigned int nextPrime(const unsigned int number);
  80 unsigned int popCount(const unsigned int bitVector);
  81
  82 #endif
  83