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TextConverter.c
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#include "config.h"
#ifdef MMX
/*
TextConverter.c Text Converter
This module contains miscellaneous text conversion functions.
Copyright (C) 2004, Wong Chi Kwong.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "TextConverter.h"
#include "MiscUtilities.h"
#include "r250.h"
unsigned int GetWordPackedText(const unsigned int *packedText, const unsigned int index, const unsigned int shift, const unsigned int numberOfBit, const unsigned int vacantBit) {
unsigned int text;
const static unsigned int mask[32] = { 0x00000000, 0x80000000, 0xC0000000, 0xE0000000,
0xF0000000, 0xF8000000, 0xFC000000, 0xFE000000,
0xFF000000, 0xFF800000, 0xFFC00000, 0xFFE00000,
0xFFF00000, 0xFFF80000, 0xFFFC0000, 0xFFFE0000,
0xFFFF0000, 0xFFFF8000, 0xFFFFC000, 0xFFFFE000,
0xFFFFF000, 0xFFFFF800, 0xFFFFFC00, 0xFFFFFE00,
0xFFFFFF00, 0xFFFFFF80, 0xFFFFFFC0, 0xFFFFFFE0,
0xFFFFFFF0, 0xFFFFFFF8, 0xFFFFFFFC, 0xFFFFFFFE };
if (shift > 0) {
// packedText should be allocated with at least 1 Word buffer initialized to zero
#ifdef DNA_ONLY
text = (packedText[index] << shift) | (packedText[index + 1] >> (BITS_IN_WORD - shift));
#else
text = (packedText[index] << shift) | (packedText[index + 1] >> (BITS_IN_WORD - shift) << vacantBit);
#endif
} else {
text = packedText[index];
}
if (numberOfBit < BITS_IN_WORD) {
// Fill unused bit with zero
text &= mask[numberOfBit];
}
return text;
}
unsigned int ReadCharMap(unsigned char *charMap, const char *inputFileName, const unsigned char defaultMapping) {
FILE *inputFile;
char c;
unsigned int v, alphabetSize;
inputFile = (FILE*)fopen64(inputFileName, "r");
if (inputFile == NULL) {
fprintf(stderr, "ReadCharMap() : Cannot open character map!\n");
exit(1);
}
for (v=0; v<CHAR_MAP_SIZE; v++) {
charMap[v] = defaultMapping;
}
alphabetSize = 0;
while (!feof(inputFile)) {
fscanf(inputFile, " %c %u \n", &c, &v);
if (v > CHAR_MAP_SIZE) {
fprintf(stderr, "ReadCharMap() : Invalid charMap!\n");
return 0;
}
charMap[(unsigned int)c] = (unsigned char)v;
if (v > alphabetSize) {
alphabetSize = v;
}
}
fclose(inputFile);
alphabetSize++;
return alphabetSize;
}
void GenerateReverseCharMap(const unsigned char *charMap, unsigned char *reverseCharMap) {
unsigned int i, j;
for (i=0; i<CHAR_MAP_SIZE; i++) {
reverseCharMap[i] = INVALID_CHAR;
for (j=0; j<CHAR_MAP_SIZE; j++) {
if (charMap[j] == i) {
reverseCharMap[i] = (unsigned char)j;
break;
}
}
}
}
unsigned int BitPerWordPackedChar(const unsigned int alphabetSize) {
#ifdef DEBUG
if (alphabetSize < 2) {
fprintf(stderr, "BitPerWordPackedChar() : alphabetSize < 2!\n");
exit(1);
}
#endif
return ceilLog2(alphabetSize);
}
unsigned int TextLengthFromWordPacked(unsigned int wordPackedLength, unsigned int bitPerChar, unsigned int lastWordLength) {
return (wordPackedLength - 1) * (BITS_IN_WORD / bitPerChar) + lastWordLength;
}
unsigned int WordPackedLengthFromText(unsigned int textLength, unsigned int bitPerChar) {
return (textLength + (BITS_IN_WORD / bitPerChar) - 1) / (BITS_IN_WORD / bitPerChar);
}
unsigned int LastWordLength(unsigned int textLength, unsigned int bitPerChar) {
return textLength % (BITS_IN_WORD / bitPerChar);
}
unsigned int BitPerBytePackedChar(const unsigned int alphabetSize) {
unsigned int bitPerChar;
#ifdef DEBUG
if (alphabetSize < 2) {
fprintf(stderr, "BitPerBytePackedChar() : alphabetSize < 2!\n");
exit(1);
}
#endif
bitPerChar = ceilLog2(alphabetSize);
#ifdef DEBUG
if (bitPerChar > BITS_IN_BYTE) {
fprintf(stderr, "BitPerBytePackedChar() : bitPerChar > BITS_IN_BYTE!\n");
exit(1);
}
#endif
// Return the largest number of bit that does not affect packing efficiency
if (BITS_IN_BYTE / (BITS_IN_BYTE / bitPerChar) > bitPerChar) {
bitPerChar = BITS_IN_BYTE / (BITS_IN_BYTE / bitPerChar);
}
return bitPerChar;
}
unsigned int TextLengthFromBytePacked(unsigned int bytePackedLength, unsigned int bitPerChar, unsigned int lastByteLength) {
if (bytePackedLength > ALL_ONE_MASK / (BITS_IN_BYTE / bitPerChar)) {
fprintf(stderr, "TextLengthFromBytePacked(): text length > 2^32!\n");
exit(1);
}
return (bytePackedLength - 1) * (BITS_IN_BYTE / bitPerChar) + lastByteLength;
}
unsigned int BytePackedLengthFromText(unsigned int textLength, unsigned int bitPerChar) {
return (textLength + (BITS_IN_BYTE / bitPerChar) - 1) / (BITS_IN_BYTE / bitPerChar);
}
unsigned char LastByteLength(unsigned int textLength, unsigned int bitPerChar) {
return (unsigned char)(textLength % (BITS_IN_BYTE / bitPerChar));
}
void ConvertTextToWordPacked(const unsigned char *input, unsigned int *output, const unsigned char *charMap, const unsigned int alphabetSize, const unsigned int textLength) {
unsigned int bitPerChar, charPerWord;
unsigned int i, j, k;
unsigned int c;
unsigned int charValue;
bitPerChar = BitPerWordPackedChar(alphabetSize);
charPerWord = BITS_IN_WORD / bitPerChar;
for (i=0; i<textLength/charPerWord; i++) {
c = 0;
j = i * charPerWord;
for (k=0; k<charPerWord; k++) {
charValue = charMap[input[j+k]];
if (charValue >= alphabetSize) {
charValue = 0;
}
c = c | (charValue << (BITS_IN_WORD - (k+1) * bitPerChar));
}
output[i] = c;
}
if (i * charPerWord < textLength) {
c = 0;
j = i * charPerWord;
for (k=0; j+k < textLength; k++) {
charValue = charMap[input[j+k]];
if (charValue >= alphabetSize) {
charValue = 0;
}
c = c | (charValue << (BITS_IN_WORD - (k+1) * bitPerChar));
}
output[i] = c;
}
}
void ConvertTextToBytePacked(const unsigned char *input, unsigned char *output, const unsigned char *charMap, const unsigned int alphabetSize, const unsigned int textLength) {
unsigned int bitPerChar, charPerByte;
unsigned int i, j, k;
unsigned char c;
bitPerChar = BitPerBytePackedChar(alphabetSize);
charPerByte = BITS_IN_BYTE / bitPerChar;
for (i=0; i<textLength/charPerByte; i++) {
c = 0;
j = i * charPerByte;
for (k=0; k<charPerByte; k++) {
c = c | (unsigned char)(charMap[input[j+k]] << (BITS_IN_BYTE - (k+1) * bitPerChar));
}
output[i] = c;
}
if (i * charPerByte < textLength) {
c = 0;
j = i * charPerByte;
for (k=0; j+k < textLength; k++) {
c = c | (unsigned char)(charMap[input[j+k]] << (BITS_IN_BYTE - (k+1) * bitPerChar));
}
output[i] = c;
}
}
void ConvertWordPackedToText(const unsigned int *input, unsigned char *output, const unsigned char *reverseCharMap, const unsigned int alphabetSize, const unsigned int textLength) {
unsigned int bitPerChar, charPerWord;
unsigned int i, j, k;
unsigned int c;
bitPerChar = BitPerWordPackedChar(alphabetSize);
charPerWord = BITS_IN_WORD / bitPerChar;
for (i=0; i<textLength/charPerWord; i++) {
c = input[i];
j = i * charPerWord;
for (k=0; k<charPerWord; k++) {
output[j+k] = reverseCharMap[c >> (BITS_IN_WORD - bitPerChar)];
c <<= bitPerChar;
}
}
if (i * charPerWord < textLength) {
c = input[i];
j = i * charPerWord;
for (k=0; j+k<textLength; k++) {
output[j+k] = reverseCharMap[c >> (BITS_IN_WORD - bitPerChar)];
c <<= bitPerChar;
}
}
}
void ConvertBytePackedToText(const unsigned char *input, unsigned char *output, const unsigned char *reverseCharMap, const unsigned int alphabetSize, const unsigned int textLength) {
unsigned int bitPerChar, charPerByte;
unsigned int i, j, k;
unsigned char c;
bitPerChar = BitPerBytePackedChar(alphabetSize);
charPerByte = BITS_IN_BYTE / bitPerChar;
for (i=0; i<textLength/charPerByte; i++) {
c = input[i];
j = i * charPerByte;
for (k=0; k<charPerByte; k++) {
output[j+k] = reverseCharMap[c >> (BITS_IN_BYTE - bitPerChar)];
c <<= bitPerChar;
}
}
if (i * charPerByte < textLength) {
c = input[i];
j = i * charPerByte;
for (k=0; j+k<textLength; k++) {
output[j+k] = reverseCharMap[c >> (BITS_IN_BYTE - bitPerChar)];
c <<= bitPerChar;
}
}
}
void ConvertBytePackedToCode(const unsigned char *input, unsigned char *output, const unsigned int alphabetSize, const unsigned int textLength) {
unsigned int bitPerChar, charPerByte;
unsigned int i, j, k;
unsigned char c;
bitPerChar = BitPerBytePackedChar(alphabetSize);
charPerByte = BITS_IN_BYTE / bitPerChar;
for (i=0; i<textLength/charPerByte; i++) {
c = input[i];
j = i * charPerByte;
for (k=0; k<charPerByte; k++) {
output[j+k] = c >> (unsigned char)(BITS_IN_BYTE - bitPerChar);
c <<= bitPerChar;
}
}
if (i * charPerByte < textLength) {
c = input[i];
j = i * charPerByte;
for (k=0; j+k<textLength; k++) {
output[j+k] = c >> (unsigned char)(BITS_IN_BYTE - bitPerChar);
c <<= bitPerChar;
}
}
}
void ConvertWordPackedToBytePacked(const unsigned int *input, unsigned char *output, const unsigned int alphabetSize, const unsigned int textLength) {
unsigned int i, j, k;
unsigned int c;
unsigned int bitPerBytePackedChar;
unsigned int bitPerWordPackedChar;
unsigned int charPerWord;
unsigned int charPerByte;
unsigned int bytePerIteration;
unsigned int byteProcessed = 0;
unsigned int wordProcessed = 0;
unsigned int mask, shift;
unsigned int buffer[BITS_IN_WORD];
bitPerBytePackedChar = BitPerBytePackedChar(alphabetSize);
bitPerWordPackedChar = BitPerWordPackedChar(alphabetSize);
charPerWord = BITS_IN_WORD / bitPerBytePackedChar;
charPerByte = BITS_IN_BYTE / bitPerWordPackedChar;
bytePerIteration = charPerWord / charPerByte;
mask = truncateRight(ALL_ONE_MASK, BITS_IN_WORD - bitPerWordPackedChar);
shift = BITS_IN_WORD - bitPerWordPackedChar;
while ((wordProcessed + 1) * charPerWord < textLength) {
c = input[wordProcessed];
for (i=0; i<charPerWord; i++) {
buffer[i] = c >> shift;
c <<= bitPerWordPackedChar;
}
wordProcessed++;
k = 0;
for (i=0; i<bytePerIteration; i++) {
c = 0;
for (j=0; j<charPerByte; j++) {
c |= buffer[k] << (BITS_IN_BYTE - (j+1) * bitPerBytePackedChar);
k++;
}
output[byteProcessed] = (unsigned char)c;
byteProcessed++;
}
}
c = input[wordProcessed];
for (i=0; i < textLength - wordProcessed * charPerWord; i++) {
buffer[i] = c >> shift;
c <<= bitPerWordPackedChar;
}
k = 0;
while (byteProcessed * charPerByte < textLength) {
c = 0;
for (j=0; j < textLength - wordProcessed * charPerWord; j++) {
c |= buffer[k] << (BITS_IN_BYTE - (j+1) * bitPerBytePackedChar);
k++;
}
output[byteProcessed] = (unsigned char)c;
byteProcessed++;
}
}
void ConvertBytePackedToWordPacked(const unsigned char *input, unsigned int *output, const unsigned int alphabetSize, const unsigned int textLength) {
unsigned int i, j, k;
unsigned int c;
unsigned int bitPerBytePackedChar;
unsigned int bitPerWordPackedChar;
unsigned int charPerWord;
unsigned int charPerByte;
unsigned int bytePerIteration;
unsigned int byteProcessed = 0;
unsigned int wordProcessed = 0;
unsigned int mask, shift;
unsigned int buffer[BITS_IN_WORD];
bitPerBytePackedChar = BitPerBytePackedChar(alphabetSize);
bitPerWordPackedChar = BitPerWordPackedChar(alphabetSize);
charPerByte = BITS_IN_BYTE / bitPerBytePackedChar;
charPerWord = BITS_IN_WORD / bitPerWordPackedChar;
bytePerIteration = charPerWord / charPerByte;
mask = truncateRight(ALL_ONE_MASK, BITS_IN_WORD - bitPerWordPackedChar);
shift = BITS_IN_WORD - BITS_IN_BYTE + bitPerBytePackedChar - bitPerWordPackedChar;
while ((wordProcessed + 1) * charPerWord < textLength) {
k = 0;
for (i=0; i<bytePerIteration; i++) {
c = (unsigned int)input[byteProcessed] << shift;
for (j=0; j<charPerByte; j++) {
buffer[k] = c & mask;
c <<= bitPerBytePackedChar;
k++;
}
byteProcessed++;
}
c = 0;
for (i=0; i<charPerWord; i++) {
c |= buffer[i] >> bitPerWordPackedChar * i;
}
output[wordProcessed] = c;
wordProcessed++;
}
k = 0;
for (i=0; i < (textLength - wordProcessed * charPerWord - 1) / charPerByte + 1; i++) {
c = (unsigned int)input[byteProcessed] << shift;
for (j=0; j<charPerByte; j++) {
buffer[k] = c & mask;
c <<= bitPerBytePackedChar;
k++;
}
byteProcessed++;
}
c = 0;
for (i=0; i<textLength - wordProcessed * charPerWord; i++) {
c |= buffer[i] >> bitPerWordPackedChar * i;
}
output[wordProcessed] = c;
}
void ConvertTextToCode(const unsigned char *input, unsigned char *output, const unsigned char *charMap, const unsigned int textLength) {
unsigned int i;
for (i=0; i< textLength; i++) {
output[i] = charMap[input[i]];
}
}
void ConvertCodeToText(const unsigned char *input, unsigned char *output, const unsigned char *reverseCharMap, const unsigned int textLength) {
unsigned int i;
for (i=0; i< textLength; i++) {
output[i] = reverseCharMap[input[i]];
}
}
void PackTextWithAllShift(const unsigned char *input, unsigned int **output, const unsigned char *charMap, const unsigned int alphabetSize, const unsigned int textLength) {
unsigned int bitPerChar;
unsigned int numberOfShift;
unsigned int numberOfWord;
unsigned int shift;
unsigned int i, j;
bitPerChar = BitPerWordPackedChar(alphabetSize);
numberOfShift = BITS_IN_WORD / bitPerChar;
numberOfWord = WordPackedLengthFromText(textLength, bitPerChar);
ConvertTextToWordPacked(input, output[0], charMap, alphabetSize, textLength);
for (i=1; i<numberOfShift; i++) {
shift = i * bitPerChar;
output[i][0] = output[0][0] >> shift;
for (j=1; j<=numberOfWord; j++) {
output[i][j] = (output[0][j] >> shift) | (output[0][j-1] << (BITS_IN_WORD - shift));
}
}
}
unsigned int ReadTextAsWordPacked(const char *inputFileName, const unsigned char *charMap, const unsigned int alphabetSize, unsigned int *targetAddress, const unsigned int maxTextLength) {
FILE *inputFile;
unsigned char *buffer;
unsigned int charPerWord;
unsigned int charRead;
unsigned int charProcessed = 0, wordProcessed = 0;
unsigned int charPerBuffer;
inputFile = (FILE*)fopen64(inputFileName, "rb");
if (inputFile == NULL) {
fprintf(stderr, "ReadTextAsWordPacked() : Cannot open inputFileName!\n");
exit(1);
}
charPerWord = BITS_IN_WORD / BitPerWordPackedChar(alphabetSize);
charPerBuffer = PACKED_BUFFER_SIZE / charPerWord * charPerWord;
buffer = MMUnitAllocate(charPerBuffer);
charRead = (unsigned int)fread(buffer, 1, charPerBuffer, inputFile);
while (charRead > 0 && charProcessed + charRead < maxTextLength) {
ConvertTextToWordPacked(buffer, targetAddress + wordProcessed, charMap, alphabetSize, charRead);
wordProcessed += charRead / charPerWord;
charProcessed += charRead;
charRead = (unsigned int)fread(buffer, 1, charPerBuffer, inputFile);
}
if (charRead > 0 && charProcessed < maxTextLength) {
ConvertTextToWordPacked(buffer, targetAddress + wordProcessed, charMap, alphabetSize, minX(charRead, maxTextLength - charProcessed));
charProcessed += charRead;
}
MMUnitFree(buffer, charPerBuffer);
fclose(inputFile);
return charProcessed;
}
unsigned int ReadBytePackedAsWordPacked(const char *inputFileName, const unsigned int alphabetSize, unsigned int *targetAddress, const unsigned int maxTextLength) {
FILE *inputFile;
unsigned char *buffer1, *buffer2;
unsigned int charPerByte, charPerWord;
unsigned int charPerBuffer, wordPerBuffer;
unsigned int charProcessed = 0, wordProcessed = 0;
unsigned int byteRead, tempByteRead;
unsigned int charInLastBuffer;
unsigned int bufferSize;
inputFile = (FILE*)fopen64(inputFileName, "rb");
if (inputFile == NULL) {
fprintf(stderr, "ReadBytePackedAsWordPacked() : Cannot open inputFileName!\n");
exit(1);
}
charPerByte = BITS_IN_BYTE / BitPerBytePackedChar(alphabetSize);
charPerWord = BITS_IN_WORD / BitPerWordPackedChar(alphabetSize);
bufferSize = PACKED_BUFFER_SIZE / charPerByte / charPerWord * charPerByte * charPerWord;
charPerBuffer = bufferSize * charPerByte;
wordPerBuffer = charPerBuffer / charPerWord;
buffer1 = MMUnitAllocate(bufferSize);
buffer2 = MMUnitAllocate(bufferSize);
byteRead = (unsigned int)fread(buffer1, 1, bufferSize, inputFile);
tempByteRead = (unsigned int)fread(buffer2, 1, bufferSize, inputFile);
while (tempByteRead > 1 && charProcessed + charPerBuffer < maxTextLength) {
ConvertBytePackedToWordPacked(buffer1, targetAddress + wordProcessed, alphabetSize, charPerBuffer);
charProcessed += charPerBuffer;
wordProcessed += wordPerBuffer;
memcpy(buffer1, buffer2, bufferSize);
byteRead = tempByteRead;
tempByteRead = (unsigned int)fread(buffer2, 1, bufferSize, inputFile);
}
if (tempByteRead > 1) {
ConvertBytePackedToWordPacked(buffer1, targetAddress + wordProcessed, alphabetSize, maxTextLength - charProcessed);
charProcessed += charPerBuffer;
} else {
if (tempByteRead == 1) {
charInLastBuffer = charPerBuffer - charPerByte + buffer2[0];
} else {
charInLastBuffer = (byteRead - 2) * charPerByte + buffer1[byteRead - 1];
}
ConvertBytePackedToWordPacked(buffer1, targetAddress + wordProcessed, alphabetSize, minX(maxTextLength - charProcessed, charInLastBuffer));
charProcessed += charInLastBuffer;
}
MMUnitFree(buffer1, bufferSize);
MMUnitFree(buffer2, bufferSize);
fclose(inputFile);
return charProcessed;
}
// Alphabet size of DNA must be 4
void *DNALoadPacked(const char *inputFileName, unsigned int *textLength, const unsigned int convertToWordPacked, const unsigned int trailerBufferInWord) {
FILE *inputFile;
unsigned char tempChar[4];
unsigned int *packedText;
unsigned int packedFileLen;
unsigned char lastByteLength;
unsigned int wordToProcess;
unsigned int i;
unsigned int trailerBufferIn128;
trailerBufferIn128 = (trailerBufferInWord + 3) / 4 * 4;
inputFile = (FILE*)(FILE*)fopen64(inputFileName, "rb");
if (inputFile == NULL) {
fprintf(stderr, "DNALoadPacked() : Cannot open inputFileName!\n");
exit(1);
}
fseek(inputFile, -1, SEEK_END);
packedFileLen = ftell(inputFile);
if ((int)packedFileLen < 0) {
fprintf(stderr, "DNALoadPacked(): Cannot determine file length!\n");
exit(1);
}
fread(&lastByteLength, sizeof(unsigned char), 1, inputFile);
*textLength = (packedFileLen - 1) * 4 + lastByteLength;
wordToProcess = (*textLength + 64 - 1) / 64 * 4 + trailerBufferIn128 * 4; // allocate multiple of 128 bit + trailer buffer
packedText = MMUnitAllocate(wordToProcess * sizeof(unsigned int));
for (i=(*textLength)/16; i<wordToProcess; i++) {
packedText[i] = 0;
}
fseek(inputFile, 0, SEEK_SET);
fread(packedText, 1, packedFileLen, inputFile);
fclose(inputFile);
if (convertToWordPacked) {
for (i=0; i<wordToProcess; i++) {
*(unsigned int*)tempChar = packedText[i];
packedText[i] = (tempChar[0] << 24) | (tempChar[1] << 16) | (tempChar[2] << 8) | tempChar[3];
}
}
return (void*)packedText;
}
void DNAFreePacked(void* packedDNA, const unsigned int textLength, const unsigned int trailerBufferInWord) {
unsigned int trailerBufferIn128;
trailerBufferIn128 = (trailerBufferInWord + 3) / 4 * 4;
MMUnitFree(packedDNA, ((textLength + 64 - 1) / 64 * 4 + trailerBufferIn128 * 4) * sizeof(unsigned int));
}
void SaveText(const char *outputFileName, const unsigned char *text, const unsigned int textLength) {
FILE *outputFile;
outputFile = (FILE*)fopen64(outputFileName, "wb");
if (outputFile == NULL) {
fprintf(stderr, "SaveText() : Cannot open output file!\n");
exit(1);
}
fwrite(text, sizeof(unsigned char), textLength, outputFile);
fclose(outputFile);
}
void SaveBytePacked(const char *outputFileName, const unsigned char *bytePacked, const unsigned int textLength, const unsigned int alphabetSize) {
FILE *outputFile;
unsigned int bitPerChar, charPerByte, bytePackedLen;
unsigned char lastByteLen;
unsigned char zero = 0;
outputFile = (FILE*)fopen64(outputFileName, "wb");
if (outputFile == NULL) {
fprintf(stderr, "SaveBytePacked() : Cannot open output file!\n");
exit(1);
}
bitPerChar = BitPerBytePackedChar(alphabetSize);
charPerByte = BITS_IN_BYTE / bitPerChar;
bytePackedLen = BytePackedLengthFromText(textLength, bitPerChar);
lastByteLen = LastByteLength(textLength, bitPerChar);
fwrite(bytePacked, sizeof(unsigned char), bytePackedLen, outputFile);
if (lastByteLen == 0) {
fwrite(&zero, sizeof(unsigned char), 1, outputFile);
}
fwrite(&lastByteLen, sizeof(unsigned char), 1, outputFile);
fclose(outputFile);
}
void SaveWordPacked(const char *outputFileName, const unsigned int *wordPacked, const unsigned int textLength, const unsigned int alphabetSize) {
FILE *outputFile;
unsigned int bitPerChar, charPerWord, wordPackedLen;
unsigned int lastWordLen;
unsigned int zero = 0;
outputFile = (FILE*)fopen64(outputFileName, "wb");
if (outputFile == NULL) {
fprintf(stderr, "SaveWordPacked() : Cannot open output file!\n");
exit(1);
}
bitPerChar = BitPerWordPackedChar(alphabetSize);
charPerWord = BITS_IN_WORD / bitPerChar;
wordPackedLen = WordPackedLengthFromText(textLength, bitPerChar);
lastWordLen = LastWordLength(textLength, bitPerChar);
fwrite(wordPacked, sizeof(unsigned int), wordPackedLen, outputFile);
if (lastWordLen == 0) {
fwrite(&zero, sizeof(unsigned int), 1, outputFile);
}
fwrite(&lastWordLen, sizeof(unsigned int), 1, outputFile);
fclose(outputFile);
}
FILE *InitialLoadPackedIncFromEnd(const char* inputFileName, unsigned char *packedOutput, const unsigned int alphabetSize,
const unsigned int packedLengthPerLoad, unsigned int *textLength, unsigned int *textLengthForThisLoad) {
FILE *packedFile;
unsigned int len, packedFileLenForThisLoad, packedFileLen;
unsigned char lastByteLength;
unsigned int bitPerChar, charPerWord;
packedFile = (FILE*)fopen64(inputFileName, "rb");
if (packedFile == NULL) {
fprintf(stderr, "InitialLoadPackedIncFromEnd() : Cannot open inputFileName!\n");
exit(1);
}
bitPerChar = BitPerBytePackedChar(alphabetSize);
charPerWord = BITS_IN_WORD / bitPerChar;
fseek(packedFile, -1, SEEK_END);
packedFileLen = ftell(packedFile);
if ((int)packedFileLen < 0) {
fprintf(stderr, "InitialLoadPackedIncFromEnd(): Cannot determine file length!\n");
exit(1);
}
fread(&lastByteLength, sizeof(unsigned char), 1, packedFile);
len = TextLengthFromBytePacked(packedFileLen, bitPerChar, lastByteLength);
if (lastByteLength == 0 && (packedFileLen - 1) % packedLengthPerLoad == 0) {
packedFileLenForThisLoad = 0;
fseek(packedFile, -((int)(2+packedLengthPerLoad)), SEEK_END);
*textLength = len;
*textLengthForThisLoad = 0;
return packedFile;
}
if (packedFileLen % packedLengthPerLoad == 0) {
packedFileLenForThisLoad = packedLengthPerLoad;
} else {
packedFileLenForThisLoad = packedFileLen % packedLengthPerLoad;
}
fseek(packedFile, -1, SEEK_END);
fseek(packedFile, -((int)packedFileLenForThisLoad), SEEK_CUR);
fread(packedOutput, sizeof(unsigned char), packedFileLenForThisLoad, packedFile);
fseek(packedFile, -((int)packedFileLenForThisLoad), SEEK_CUR);
if (packedFileLen > packedFileLenForThisLoad) {
fseek(packedFile, -((int)packedLengthPerLoad), SEEK_CUR);
}
*textLength = len;
*textLengthForThisLoad = TextLengthFromBytePacked(packedFileLenForThisLoad, bitPerChar, lastByteLength);
return packedFile;
}
void LoadPackedIncFromEnd(FILE *packedFile, unsigned char *packedOutput, const unsigned int packedLengthPerLoad) {
fread(packedOutput, sizeof(unsigned char), packedLengthPerLoad, packedFile);
fseek(packedFile, -(2*(int)packedLengthPerLoad), SEEK_CUR);
}
FILE *InitialLoadTextIncFromEnd(const char* inputFileName, unsigned char *textOutput, const unsigned int textLengthPerLoad, unsigned int *textLength, unsigned int *textLengthForThisLoad) {
FILE *textFile;
unsigned int len, textLenForThisLoad;
textFile = (FILE*)fopen64(inputFileName, "rb");
if (textFile == NULL) {
fprintf(stderr, "InitialLoadTextIncFromEnd() : Cannot open inputFileName!\n");
exit(1);
}
fseek(textFile, 0, SEEK_END);
len = ftell(textFile);
if ((int)len < 0) {
fprintf(stderr, "InitialLoadTextIncFromEnd(): Cannot determine file length!\n");
exit(1);
}
textLenForThisLoad = len % textLengthPerLoad;
if (textLenForThisLoad > 0) {
fseek(textFile, -((int)textLenForThisLoad), SEEK_END);
fread(textOutput, sizeof(unsigned char), textLenForThisLoad, textFile);
fseek(textFile, -((int)textLenForThisLoad), SEEK_END);
}
*textLength = len;
*textLengthForThisLoad = textLenForThisLoad;
return textFile;
}
void LoadTextIncFromEnd(FILE *textFile, unsigned char *textOutput, const unsigned int textLengthPerLoad) {
if (ftell(textFile) < (int)textLengthPerLoad) {
fprintf(stderr, "LoadTextIncFromEnd(): file pointer is not correctly placed!\n");
exit(1);
}
fseek(textFile, -((int)textLengthPerLoad), SEEK_CUR);
fread(textOutput, sizeof(unsigned char), textLengthPerLoad, textFile);
fseek(textFile, -((int)textLengthPerLoad), SEEK_CUR);
}
#else
/*
TextConverter.c Text Converter
This module contains miscellaneous text conversion functions.
Copyright (C) 2004, Wong Chi Kwong.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "TextConverter.h"
#include "MiscUtilities.h"
#include "r250.h"
unsigned int GetWordPackedText(const unsigned int *packedText, const unsigned int index, const unsigned int shift, const unsigned int numberOfBit, const unsigned int vacantBit) {
unsigned int text;
const static unsigned int mask[32] = { 0x00000000, 0x80000000, 0xC0000000, 0xE0000000,
0xF0000000, 0xF8000000, 0xFC000000, 0xFE000000,
0xFF000000, 0xFF800000, 0xFFC00000, 0xFFE00000,
0xFFF00000, 0xFFF80000, 0xFFFC0000, 0xFFFE0000,
0xFFFF0000, 0xFFFF8000, 0xFFFFC000, 0xFFFFE000,
0xFFFFF000, 0xFFFFF800, 0xFFFFFC00, 0xFFFFFE00,
0xFFFFFF00, 0xFFFFFF80, 0xFFFFFFC0, 0xFFFFFFE0,
0xFFFFFFF0, 0xFFFFFFF8, 0xFFFFFFFC, 0xFFFFFFFE };
if (shift > 0) {
// packedText should be allocated with at least 1 Word buffer initialized to zero
#ifdef DNA_ONLY
text = (packedText[index] << shift) | (packedText[index + 1] >> (BITS_IN_WORD - shift));
#else
text = (packedText[index] << shift) | (packedText[index + 1] >> (BITS_IN_WORD - shift) << vacantBit);
#endif
} else {
text = packedText[index];
}
if (numberOfBit < BITS_IN_WORD) {
// Fill unused bit with zero
text &= mask[numberOfBit];
}
return text;
}
unsigned int ReadCharMap(unsigned char *charMap, const char *inputFileName, const unsigned char defaultMapping) {
FILE *inputFile;
char c;
unsigned int v, alphabetSize;
inputFile = (FILE*)fopen64(inputFileName, "r");
if (inputFile == NULL) {
fprintf(stderr, "ReadCharMap() : Cannot open character map!\n");
exit(1);
}
for (v=0; v<CHAR_MAP_SIZE; v++) {
charMap[v] = defaultMapping;
}
alphabetSize = 0;
while (!feof(inputFile)) {
fscanf(inputFile, " %c %u \n", &c, &v);
if (v > CHAR_MAP_SIZE) {
fprintf(stderr, "ReadCharMap() : Invalid charMap!\n");
return 0;
}
charMap[(unsigned int)c] = (unsigned char)v;
if (v > alphabetSize) {
alphabetSize = v;
}
}
fclose(inputFile);
alphabetSize++;
return alphabetSize;
}
void GenerateReverseCharMap(const unsigned char *charMap, unsigned char *reverseCharMap) {
unsigned int i, j;
for (i=0; i<CHAR_MAP_SIZE; i++) {
reverseCharMap[i] = INVALID_CHAR;
for (j=0; j<CHAR_MAP_SIZE; j++) {
if (charMap[j] == i) {
reverseCharMap[i] = (unsigned char)j;
break;
}
}
}