106 lines
3.9 KiB
C
106 lines
3.9 KiB
C
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/*
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BWTConstruct.h BWT-Index Construction
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This module constructs BWT and auxiliary data structures.
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Copyright (C) 2004, Wong Chi Kwong.
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This program is free software; you can redistribute it and/or
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modify it under the terms of the GNU General Public License
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as published by the Free Software Foundation; either version 2
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of the License, or (at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program; if not, write to the Free Software
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Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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*/
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#ifndef BWT_GEN_H
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#define BWT_GEN_H
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#define ALPHABET_SIZE 4
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#define BIT_PER_CHAR 2
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#define CHAR_PER_WORD 16
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#define CHAR_PER_BYTE 4
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#define BITS_IN_WORD 32
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#define BITS_IN_BYTE 8
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#define BYTES_IN_WORD 4
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#define ALL_ONE_MASK 0xFFFFFFFF
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#define DNA_OCC_CNT_TABLE_SIZE_IN_WORD 65536
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#define BITS_PER_OCC_VALUE 16
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#define OCC_VALUE_PER_WORD 2
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#define OCC_INTERVAL 256
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#define OCC_INTERVAL_MAJOR 65536
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#define TRUE 1
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#define FALSE 0
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#define BWTINC_INSERT_SORT_NUM_ITEM 7
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#define average(value1, value2) ( ((value1) & (value2)) + ((value1) ^ (value2)) / 2 )
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#define min(value1, value2) ( ((value1) < (value2)) ? (value1) : (value2) )
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#define max(value1, value2) ( ((value1) > (value2)) ? (value1) : (value2) )
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#define med3(a, b, c) ( a<b ? (b<c ? b : a<c ? c : a) : (b>c ? b : a>c ? c : a))
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#define swap(a, b, t); t = a; a = b; b = t;
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#define truncateLeft(value, offset) ( (value) << (offset) >> (offset) )
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#define truncateRight(value, offset) ( (value) >> (offset) << (offset) )
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#define DNA_OCC_SUM_EXCEPTION(sum) ((sum & 0xfefefeff) == 0)
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typedef struct SaIndexRange {
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unsigned int startSaIndex;
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unsigned int endSaIndex;
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} SaIndexRange;
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typedef struct BWT {
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unsigned int textLength; // length of the text
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unsigned int saInterval; // interval between two SA values stored explicitly
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unsigned int inverseSaInterval; // interval between two inverse SA stored explicitly
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unsigned int inverseSa0; // SA-1[0]
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unsigned int *cumulativeFreq; // cumulative frequency
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unsigned int *bwtCode; // BWT code
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unsigned int *occValue; // Occurrence values stored explicitly
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unsigned int *occValueMajor; // Occurrence values stored explicitly
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unsigned int *saValue; // SA values stored explicitly
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unsigned int *inverseSa; // Inverse SA stored explicitly
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SaIndexRange *saIndexRange; // SA index range
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int saIndexRangeNumOfChar; // Number of characters indexed in SA index range
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unsigned int *saValueOnBoundary; // Pre-calculated frequently referred data
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unsigned int *decodeTable; // For decoding BWT by table lookup
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unsigned int decodeTableGenerated; // == TRUE if decode table is generated on load and will be freed
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unsigned int bwtSizeInWord; // Temporary variable to hold the memory allocated
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unsigned int occSizeInWord; // Temporary variable to hold the memory allocated
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unsigned int occMajorSizeInWord; // Temporary variable to hold the memory allocated
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unsigned int saValueSize; // Temporary variable to hold the memory allocated
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unsigned int inverseSaSize; // Temporary variable to hold the memory allocated
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unsigned int saIndexRangeSize; // Temporary variable to hold the memory allocated
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} BWT;
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typedef struct BWTInc {
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BWT *bwt;
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unsigned int numberOfIterationDone;
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unsigned int *cumulativeCountInCurrentBuild;
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unsigned int availableWord;
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unsigned int targetTextLength;
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float targetNBit;
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unsigned int buildSize;
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unsigned int initialMaxBuildSize;
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unsigned int incMaxBuildSize;
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unsigned int firstCharInLastIteration;
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unsigned int *workingMemory;
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unsigned int *packedText;
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unsigned char *textBuffer;
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unsigned int *packedShift;
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} BWTInc;
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#endif
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