int SocketFree(Socket* socketPointer) { int n = 0; if (socketPointer->masterSocket > 0) { n = close(socketPointer->masterSocket); } MMUnitFree(socketPointer->socketPath, strlen(socketPointer->socketPath + 1)); MMUnitFree(socketPointer, sizeof(Socket)); return n; }
void HSPFree(MMPool *mmPool, HSP *hsp) { if (hsp->packedDNA != NULL) { DNAFreePacked(hsp->packedDNA, hsp->dnaLength); } int i; for(i=0; i<hsp->chrNum; ++i){ MMUnitFree(hsp->chrName[i], (strlen(hsp->chrName[i])+1)*sizeof(char)); } MMUnitFree(hsp->chrName,(hsp->chrNum+1)* sizeof(char *)); MMUnitFree(hsp->blockList, (hsp->numOfBlock+1) * sizeof(ChrBlock)); MMPoolReturn(mmPool, hsp, sizeof(hsp)); }
unsigned int ProcessSearchPattern() { FILE *searchPatternFile; char c; unsigned int i, j, n; searchPatternFile = fopen64(PatternFileName, "r"); if (searchPatternFile == NULL) { fprintf(stderr, "Cannot open search pattern file : %s\n", PatternFileName); exit(1); } j = 0; n = 0; // Find out the size of search pattern while (!feof(searchPatternFile)) { c = (char)fgetc(searchPatternFile); // Find the first comment line while (!feof(searchPatternFile) && c != '>') { c = (char)fgetc(searchPatternFile); } while (!feof(searchPatternFile)) { // Skip comment line while (!feof(searchPatternFile) && c != '\n') { c = (char)fgetc(searchPatternFile); } // Count no. of characters while (!feof(searchPatternFile) && c != '>') { if (c != '\n') { j++; } c = (char)fgetc(searchPatternFile); } // Count no. of patterns n++; } } if (j > searchPatternAllocated) { if (searchPattern != NULL) { MMUnitFree(searchPattern, searchPatternAllocated); } searchPattern = MMUnitAllocate(j); searchPatternAllocated = j; } if (n + 1 > searchPatternPositionAllocated) { if (searchPatternPosition != NULL) { MMUnitFree(searchPatternPosition, searchPatternPositionAllocated); } searchPatternPosition = MMUnitAllocate((n + 1) * sizeof(unsigned int)); searchPatternPositionAllocated = n + 1; } fseek(searchPatternFile, 0, SEEK_SET); j = 0; n = 0; i = 0; searchPatternPosition[0] = 0; // Read pattern into memory while (!feof(searchPatternFile)) { c = (char)fgetc(searchPatternFile); // Find the first comment line while (!feof(searchPatternFile) && c != '>') { c = (char)fgetc(searchPatternFile); } while (!feof(searchPatternFile)) { // Skip comment line while (!feof(searchPatternFile) && c != '\n') { c = (char)fgetc(searchPatternFile); } // Store pattern while (!feof(searchPatternFile) && c != '>') { if (c != '\n') { searchPattern[j] = c; j++; } c = (char)fgetc(searchPatternFile); } // Store pointers to pattern n++; searchPatternPosition[n] = j; } } fclose(searchPatternFile); return n; }
int main(int argc, char** argv) { char c; unsigned int i, j, k; MMPool *mmPool; dictionary *programInput, *ini; char argumentText[11] = "argument:0"; double startTime; double elapsedTime = 0, totalElapsedTime = 0; BWT *bwt; HSP *hsp; unsigned char charMap[256]; unsigned char *convertedKey; unsigned int *packedKey; unsigned int found; unsigned int numberOfPattern, numberOfPatternFound; unsigned int saIndexLeft, saIndexRight; SaIndexGroupNew *saIndexGroup; SaIndexList *tempSaIndex1, *tempSaIndex2; unsigned int numberOfSaIndexGroup; HitList *hitList; unsigned int textPositionMatched, textPositionRetrieved; unsigned long long totalTextPositionMatched, totalTextPositionRetrieved; BWTSaRetrievalStatistics BWTSaRetrievalStatistics; FILE *logFile; init(textPositionRetrieved); // to avoid compiler warning only init(textPositionMatched); // to avoid compiler warning only programInput = ParseInput(argc, argv); ini = ParseIniFile(); ProcessIni(); ValidateIni(); PrintIni(); if (Confirmation == TRUE) { printf("BWT Search. Press Y to go or N to cancel. "); c = (char)getchar(); while (c != 'y' && c != 'Y' && c != 'n' && c!= 'N') { c = (char)getchar(); } if (c == 'n' || c == 'N') { exit(0); } } startTime = setStartTime(); MMMasterInitialize(1, 0, FALSE, NULL); mmPool = MMPoolCreate(PoolSize); // Load Database printf("Loading Database.."); fflush(stdout); bwt = BWTLoad(mmPool, BWTCodeFileName, BWTOccValueFileName, SaValueFileName, NULL, SaIndexFileName, NULL); HSPFillCharMap(charMap); hsp = HSPLoad(mmPool, PackedDNAFileName, AnnotationFileName, AmbiguityFileName, MAX_SEARCH_PATTERN_LENGTH / CHAR_PER_WORD); if (bwt->textLength != hsp->dnaLength) { fprintf(stderr, "BWT-BLAST: Database length inconsistent!\n"); exit(1); } if (LogFileName[0] != '\0') { logFile = fopen64(LogFileName, "w"); if (logFile == NULL) { fprintf(stderr, "Cannot open log file!\n"); exit(1); } } else { logFile = NULL; } packedKey = MMPoolDispatch(mmPool, WordPackedLengthFromText(MAX_SEARCH_PATTERN_LENGTH, BIT_PER_CHAR)); convertedKey = MMPoolDispatch(mmPool, MAX_SEARCH_PATTERN_LENGTH); saIndexGroup = MMUnitAllocate(MaxNumberOfHitGroups * sizeof(SaIndexGroup)); hitList = MMUnitAllocate(MaxNumberOfTextPosition * sizeof(HitList)); tempSaIndex1 = MMUnitAllocate(MaxNumberOfTextPosition * sizeof(SaIndexList)); tempSaIndex2 = MMUnitAllocate(MaxNumberOfTextPosition * sizeof(SaIndexList)); elapsedTime = getElapsedTime(startTime) - totalElapsedTime; printf("Elapsed time = "); printElapsedTime(stdout, FALSE, FALSE, TRUE, 4, elapsedTime); totalElapsedTime += elapsedTime; printf("\n"); // Process search pattern files for (i=1; i<=NumberOfSearchPatternFile; i++) { argumentText[9] = '0' + (char)(i + 2); iniparser_copystring(programInput, argumentText, PatternFileName, PatternFileName, MAX_FILENAME_LEN); printf("Loading search pattern : %s\n", PatternFileName); numberOfPattern = ProcessSearchPattern(); printf("Finished loading search pattern.\n"); elapsedTime = getElapsedTime(startTime) - totalElapsedTime; printf("Elapsed time = "); printElapsedTime(stdout, FALSE, FALSE, TRUE, 4, elapsedTime); totalElapsedTime += elapsedTime; printf("\n"); if (LogFileName[0] != '\0') { fprintf(logFile, "Searching for pattern : %s\n", PatternFileName); } if (SABinarySearch == TRUE) { printf("Start forward search with SA index.\n"); if (LogFileName[0] != '\0') { fprintf(logFile, "Forward search with SA index.\n"); } numberOfPatternFound = 0; totalTextPositionMatched = 0; totalTextPositionRetrieved = 0; BWTInitializeSaRetrievalStatistics(&BWTSaRetrievalStatistics); for (j=0; j<numberOfPattern; j++) { //ConvertTextToWordPacked(searchPattern + searchPatternPosition[j], packedKey, charMap, ALPHABET_SIZE, // searchPatternPosition[j+1] - searchPatternPosition[j]); //found = BWTForwardSearchSaIndex(packedKey, searchPatternPosition[j+1] - searchPatternPosition[j], // bwt, hsp->packedDNA, &saIndexLeft, &saIndexRight); ConvertTextToCode(searchPattern + searchPatternPosition[j], convertedKey, charMap, searchPatternPosition[j+1] - searchPatternPosition[j]); found = BWTSaBinarySearch(convertedKey, searchPatternPosition[j+1] - searchPatternPosition[j], bwt, hsp->packedDNA, &saIndexLeft, &saIndexRight, packedKey); if (found) { numberOfPatternFound++; textPositionMatched = saIndexRight - saIndexLeft + 1; totalTextPositionMatched += textPositionMatched; if (FindTextPosition) { saIndexGroup->startSaIndex = saIndexLeft; if (textPositionMatched <= MaxNumberOfTextPosition) { saIndexGroup->numOfMatch = textPositionMatched; } else { saIndexGroup->numOfMatch = MaxNumberOfTextPosition; printf("Max no of text positions reached! Only %u out of %u text positions retrieved.\n", MaxNumberOfTextPosition, textPositionMatched); } saIndexGroup->posQuery = 0; saIndexGroup->info = 0; textPositionRetrieved = BWTTextPosition(bwt, saIndexGroup, 1, hitList, tempSaIndex1, tempSaIndex2, &BWTSaRetrievalStatistics, FALSE); totalTextPositionRetrieved += textPositionRetrieved; } } if (LogFileName[0] != '\0') { if (found) { fprintf(logFile, "Pattern number %u found. SA Index from %u to %u. ", j + 1, saIndexLeft, saIndexRight); if (FindTextPosition) { fprintf(logFile, "%u matches of %u located. ", textPositionRetrieved, textPositionMatched); for (k=0; k<textPositionRetrieved; k++) { fprintf(logFile, "%u ", hitList[k].posText); } } } else { fprintf(logFile, "Pattern number %u not found.", j + 1); } fprintf(logFile, "\n"); } } printf("Finished forward search with SA index.\n"); printf("%u patterns out of %u found. %llu of %llu matches located.\n", numberOfPatternFound, numberOfPattern, totalTextPositionRetrieved, totalTextPositionMatched); if (FindTextPosition) { printf("Hits: BWT/Cached/Diag/Dup : %u/%u/%u/%u\n", BWTSaRetrievalStatistics.bwtSaRetrieved, BWTSaRetrievalStatistics.cachedSaRetrieved, BWTSaRetrievalStatistics.saDiagonalLinked, BWTSaRetrievalStatistics.saDuplicated); } elapsedTime = getElapsedTime(startTime) - totalElapsedTime; printf("Elapsed time = "); printElapsedTime(stdout, FALSE, FALSE, TRUE, 4, elapsedTime); totalElapsedTime += elapsedTime; printf("\n"); if (LogFileName[0] != '\0') { fprintf(logFile, "Finished forward search with SA index.\n"); fprintf(logFile, "%u patterns out of %u found. %llu of %llu matches located.\n", numberOfPatternFound, numberOfPattern, totalTextPositionRetrieved, totalTextPositionMatched); if (FindTextPosition) { fprintf(logFile, "Hits: BWT/Cached/Diag/Dup : %u/%u/%u/%u\n", BWTSaRetrievalStatistics.bwtSaRetrieved, BWTSaRetrievalStatistics.cachedSaRetrieved, BWTSaRetrievalStatistics.saDiagonalLinked, BWTSaRetrievalStatistics.saDuplicated); } fprintf(logFile, "Elapsed time = "); printElapsedTime(logFile, FALSE, FALSE, TRUE, 4, elapsedTime); fprintf(logFile, "\n"); } } if (BackwardSearch == TRUE) { printf("Start backward search.\n"); if (LogFileName[0] != '\0') { fprintf(logFile, "Backward search.\n"); } numberOfPatternFound = 0; totalTextPositionMatched = 0; totalTextPositionRetrieved = 0; BWTInitializeSaRetrievalStatistics(&BWTSaRetrievalStatistics); for (j=0; j<numberOfPattern; j++) { ConvertTextToCode(searchPattern + searchPatternPosition[j], convertedKey, charMap, searchPatternPosition[j+1] - searchPatternPosition[j]); found = BWTBackwardSearch(convertedKey, searchPatternPosition[j+1] - searchPatternPosition[j], bwt, &saIndexLeft, &saIndexRight); if (found) { numberOfPatternFound++; textPositionMatched = saIndexRight - saIndexLeft + 1; totalTextPositionMatched += textPositionMatched; if (FindTextPosition) { saIndexGroup->startSaIndex = saIndexLeft; if (textPositionMatched <= MaxNumberOfTextPosition) { saIndexGroup->numOfMatch = textPositionMatched; } else { saIndexGroup->numOfMatch = MaxNumberOfTextPosition; printf("Max no of text positions reached! Only %u out of %u text positions retrieved.\n", MaxNumberOfTextPosition, textPositionMatched); } saIndexGroup->posQuery = 0; saIndexGroup->info = 0; textPositionRetrieved = BWTTextPosition(bwt, saIndexGroup, 1, hitList, tempSaIndex1, tempSaIndex2, &BWTSaRetrievalStatistics, FALSE); totalTextPositionRetrieved += textPositionRetrieved; } } if (LogFileName[0] != '\0') { if (found) { fprintf(logFile, "Pattern number %u found. SA Index from %u to %u. Total %u occurrences ", j + 1, saIndexLeft, saIndexRight, saIndexRight - saIndexLeft + 1); if (FindTextPosition) { fprintf(logFile, "%u matches of %u located. ", textPositionRetrieved, textPositionMatched); for (k=0; k<textPositionRetrieved; k++) { fprintf(logFile, "%u ", hitList[k].posText); } } } else { fprintf(logFile, "Pattern number %u not found.", j + 1); } fprintf(logFile, "\n"); } } printf("Finished backward search.\n"); printf("%u patterns out of %u found. %llu of %llu matches located.\n", numberOfPatternFound, numberOfPattern, totalTextPositionRetrieved, totalTextPositionMatched); if (FindTextPosition) { printf("Hits: BWT/Cached/Diag/Dup : %u/%u/%u/%u\n", BWTSaRetrievalStatistics.bwtSaRetrieved, BWTSaRetrievalStatistics.cachedSaRetrieved, BWTSaRetrievalStatistics.saDiagonalLinked, BWTSaRetrievalStatistics.saDuplicated); } elapsedTime = getElapsedTime(startTime) - totalElapsedTime; printf("Elapsed time = "); printElapsedTime(stdout, FALSE, FALSE, TRUE, 4, elapsedTime); totalElapsedTime += elapsedTime; printf("\n"); if (LogFileName[0] != '\0') { fprintf(logFile, "Finished backward search.\n"); fprintf(logFile, "%u patterns out of %u found. %llu of %llu matches located.\n", numberOfPatternFound, numberOfPattern, totalTextPositionRetrieved, totalTextPositionMatched); if (FindTextPosition) { fprintf(logFile, "Hits: BWT/Cached/Diag/Dup : %u/%u/%u/%u\n", BWTSaRetrievalStatistics.bwtSaRetrieved, BWTSaRetrievalStatistics.cachedSaRetrieved, BWTSaRetrievalStatistics.saDiagonalLinked, BWTSaRetrievalStatistics.saDuplicated); } fprintf(logFile, "Elapsed time = "); printElapsedTime(logFile, FALSE, FALSE, TRUE, 4, elapsedTime); fprintf(logFile, "\n"); } } if (BackwardSearchCheck == TRUE) { printf("Start backward search with text.\n"); if (LogFileName[0] != '\0') { fprintf(logFile, "Backward search with text.\n"); } numberOfPatternFound = 0; totalTextPositionMatched = 0; totalTextPositionRetrieved = 0; BWTInitializeSaRetrievalStatistics(&BWTSaRetrievalStatistics); for (j=0; j<numberOfPattern; j++) { ConvertTextToCode(searchPattern + searchPatternPosition[j], convertedKey, charMap, searchPatternPosition[j+1] - searchPatternPosition[j]); ConvertTextToWordPacked(searchPattern + searchPatternPosition[j], packedKey, charMap, ALPHABET_SIZE, searchPatternPosition[j+1] - searchPatternPosition[j]); found = BWTBackwardSearchCheckWithText(convertedKey, packedKey, searchPatternPosition[j+1] - searchPatternPosition[j], bwt, hsp->packedDNA, TextCheckCostFactor, MaxNumberOfTextPosition, hitList, &saIndexLeft, &saIndexRight); if (found) { numberOfPatternFound++; textPositionMatched = saIndexRight - saIndexLeft + 1; totalTextPositionMatched += textPositionMatched; // Find text position if text check not used if (FindTextPosition && saIndexLeft != 0) { saIndexGroup->startSaIndex = saIndexLeft; if (textPositionMatched <= MaxNumberOfTextPosition) { saIndexGroup->numOfMatch = textPositionMatched; } else { saIndexGroup->numOfMatch = MaxNumberOfTextPosition; printf("Max no of text positions reached! Only %u out of %u text positions retrieved.\n", MaxNumberOfTextPosition, textPositionMatched); } saIndexGroup->posQuery = 0; saIndexGroup->info = 0; textPositionRetrieved = BWTTextPosition(bwt, saIndexGroup, 1, hitList, tempSaIndex1, tempSaIndex2, &BWTSaRetrievalStatistics, FALSE); totalTextPositionRetrieved += textPositionRetrieved; } else { textPositionRetrieved = textPositionMatched; totalTextPositionRetrieved += textPositionRetrieved; } } if (LogFileName[0] != '\0') { if (found) { fprintf(logFile, "Pattern number %u found. ", j + 1); if (FindTextPosition) { fprintf(logFile, "%u matches of %u located. ", textPositionRetrieved, textPositionMatched); for (k=0; k<textPositionRetrieved; k++) { fprintf(logFile, "%u ", hitList[k].posText); } } } else { fprintf(logFile, "Pattern number %u not found.", j + 1); } fprintf(logFile, "\n"); } } printf("Finished backward search with text.\n"); printf("%u patterns out of %u found. %llu of %llu matches located.\n", numberOfPatternFound, numberOfPattern, totalTextPositionRetrieved, totalTextPositionMatched); if (FindTextPosition) { printf("Hits: BWT/Cached/Diag/Dup : %u/%u/%u/%u\n", BWTSaRetrievalStatistics.bwtSaRetrieved, BWTSaRetrievalStatistics.cachedSaRetrieved, BWTSaRetrievalStatistics.saDiagonalLinked, BWTSaRetrievalStatistics.saDuplicated); } elapsedTime = getElapsedTime(startTime) - totalElapsedTime; printf("Elapsed time = "); printElapsedTime(stdout, FALSE, FALSE, TRUE, 4, elapsedTime); totalElapsedTime += elapsedTime; printf("\n"); if (LogFileName[0] != '\0') { fprintf(logFile, "Finished backward search with text.\n"); fprintf(logFile, "%u patterns out of %u found. %llu of %llu matches located.\n", numberOfPatternFound, numberOfPattern, totalTextPositionRetrieved, totalTextPositionMatched); if (FindTextPosition) { fprintf(logFile, "Hits: BWT/Cached/Diag/Dup : %u/%u/%u/%u\n", BWTSaRetrievalStatistics.bwtSaRetrieved, BWTSaRetrievalStatistics.cachedSaRetrieved, BWTSaRetrievalStatistics.saDiagonalLinked, BWTSaRetrievalStatistics.saDuplicated); } fprintf(logFile, "Elapsed time = "); printElapsedTime(logFile, FALSE, FALSE, TRUE, 4, elapsedTime); fprintf(logFile, "\n"); } } if (HammingDistSearch == TRUE) { printf("Start hamming distance %u approximate match.\n", MaxErrorAllowed); if (LogFileName[0] != '\0') { fprintf(logFile, "Hamming distance %u approximate match.\n", MaxErrorAllowed); } numberOfPatternFound = 0; totalTextPositionMatched = 0; totalTextPositionRetrieved = 0; BWTInitializeSaRetrievalStatistics(&BWTSaRetrievalStatistics); for (j=0; j<numberOfPattern; j++) { ConvertTextToCode(searchPattern + searchPatternPosition[j], convertedKey, charMap, searchPatternPosition[j+1] - searchPatternPosition[j]); numberOfSaIndexGroup = BWTHammingDistMatchOld(convertedKey, searchPatternPosition[j+1] - searchPatternPosition[j], bwt, MaxErrorAllowed, saIndexGroup, MaxNumberOfHitGroups, 0, 0); if (numberOfSaIndexGroup) { numberOfPatternFound++; textPositionMatched = 0; for (k=0; k<numberOfSaIndexGroup; k++) { textPositionMatched += saIndexGroup[k].numOfMatch; } if (textPositionMatched > MaxNumberOfTextPosition) { textPositionMatched = 0; for (k=0; k<numberOfSaIndexGroup && textPositionMatched < MaxNumberOfTextPosition; k++) { textPositionMatched += saIndexGroup[k].numOfMatch; } numberOfSaIndexGroup = k - 1; saIndexGroup[numberOfSaIndexGroup].numOfMatch -= textPositionMatched - MaxNumberOfTextPosition; for (; k<numberOfSaIndexGroup; k++) { textPositionMatched += saIndexGroup[k].numOfMatch; } printf("Max no of text positions reached! Only %u out of %u text positions retrieved.\n", MaxNumberOfTextPosition, textPositionMatched); } totalTextPositionMatched += textPositionMatched; if (FindTextPosition) { textPositionRetrieved = BWTTextPosition(bwt, saIndexGroup, numberOfSaIndexGroup, hitList, tempSaIndex1, tempSaIndex2, &BWTSaRetrievalStatistics, FALSE); totalTextPositionRetrieved += textPositionRetrieved; } } if (LogFileName[0] != '\0') { if (numberOfSaIndexGroup) { fprintf(logFile, "Pattern number %u found. %u matches", j + 1, textPositionMatched); if (FindTextPosition) { fprintf(logFile, "%u matches of %u located. ", textPositionRetrieved, textPositionMatched); for (k=0; k<textPositionRetrieved; k++) { fprintf(logFile, "%u ", hitList[k].posText); } } } else { fprintf(logFile, "Pattern number %u not found.", j + 1); } fprintf(logFile, "\n"); } } printf("Finished hamming distance search.\n"); printf("%u patterns out of %u found. %llu of %llu matches located.\n", numberOfPatternFound, numberOfPattern, totalTextPositionRetrieved, totalTextPositionMatched); if (FindTextPosition) { printf("Hits: BWT/Cached/Diag/Dup : %u/%u/%u/%u\n", BWTSaRetrievalStatistics.bwtSaRetrieved, BWTSaRetrievalStatistics.cachedSaRetrieved, BWTSaRetrievalStatistics.saDiagonalLinked, BWTSaRetrievalStatistics.saDuplicated); } elapsedTime = getElapsedTime(startTime) - totalElapsedTime; printf("Elapsed time = "); printElapsedTime(stdout, FALSE, FALSE, TRUE, 4, elapsedTime); totalElapsedTime += elapsedTime; printf("\n"); if (LogFileName[0] != '\0') { fprintf(logFile, "Finished hamming distance search.\n"); fprintf(logFile, "%u patterns out of %u found. %llu of %llu matches located.\n", numberOfPatternFound, numberOfPattern, totalTextPositionRetrieved, totalTextPositionMatched); if (FindTextPosition) { fprintf(logFile, "Hits: BWT/Cached/Diag/Dup : %u/%u/%u/%u\n", BWTSaRetrievalStatistics.bwtSaRetrieved, BWTSaRetrievalStatistics.cachedSaRetrieved, BWTSaRetrievalStatistics.saDiagonalLinked, BWTSaRetrievalStatistics.saDuplicated); } fprintf(logFile, "Elapsed time = "); printElapsedTime(logFile, FALSE, FALSE, TRUE, 4, elapsedTime); fprintf(logFile, "\n"); } } if (EditDistSearch == TRUE) { printf("Start edit distance %u approximate match.\n", MaxErrorAllowed); if (LogFileName[0] != '\0') { fprintf(logFile, "Edit distance %u approximate match.\n", MaxErrorAllowed); } numberOfPatternFound = 0; totalTextPositionMatched = 0; totalTextPositionRetrieved = 0; BWTInitializeSaRetrievalStatistics(&BWTSaRetrievalStatistics); for (j=0; j<numberOfPattern; j++) { ConvertTextToCode(searchPattern + searchPatternPosition[j], convertedKey, charMap, searchPatternPosition[j+1] - searchPatternPosition[j]); numberOfSaIndexGroup = BWTEditDistMatchOld(convertedKey, searchPatternPosition[j+1] - searchPatternPosition[j], bwt, MaxErrorAllowed, (SaIndexGroupWithLengthError*)saIndexGroup, MaxNumberOfHitGroups); if (numberOfSaIndexGroup > MaxNumberOfHitGroups) { fprintf(stderr, "numberOfSaIndexGroup > MaxNumberOfHitGroups!\n"); } if (numberOfSaIndexGroup) { numberOfPatternFound++; textPositionMatched = 0; for (k=0; k<numberOfSaIndexGroup; k++) { textPositionMatched += saIndexGroup[k].numOfMatch; } if (textPositionMatched > MaxNumberOfTextPosition) { textPositionMatched = 0; for (k=0; k<numberOfSaIndexGroup && textPositionMatched < MaxNumberOfTextPosition; k++) { textPositionMatched += saIndexGroup[k].numOfMatch; } numberOfSaIndexGroup = k - 1; saIndexGroup[numberOfSaIndexGroup].numOfMatch -= textPositionMatched - MaxNumberOfTextPosition; for (; k<numberOfSaIndexGroup; k++) { textPositionMatched += saIndexGroup[k].numOfMatch; } printf("Max no of text positions reached! Only %u out of %u text positions retrieved.\n", MaxNumberOfTextPosition, textPositionMatched); } totalTextPositionMatched += textPositionMatched; if (FindTextPosition) { textPositionRetrieved = BWTTextPosition(bwt, saIndexGroup, numberOfSaIndexGroup, hitList, tempSaIndex1, tempSaIndex2, &BWTSaRetrievalStatistics, FALSE); totalTextPositionRetrieved += textPositionRetrieved; } } if (LogFileName[0] != '\0') { if (numberOfSaIndexGroup) { fprintf(logFile, "Pattern number %u found. %u matches. ", j + 1, textPositionMatched); if (FindTextPosition) { fprintf(logFile, "%u matches of %u located. ", textPositionRetrieved, textPositionMatched); for (k=0; k<textPositionRetrieved; k++) { fprintf(logFile, "%u ", hitList[k].posText); } } } else { fprintf(logFile, "Pattern number %u not found.", j + 1); } fprintf(logFile, "\n"); } } printf("Finished edit distance search.\n"); printf("%u patterns out of %u found. %llu of %llu matches located.\n", numberOfPatternFound, numberOfPattern, totalTextPositionRetrieved, totalTextPositionMatched); if (FindTextPosition) { printf("Hits: BWT/Cached/Diag/Dup : %u/%u/%u/%u\n", BWTSaRetrievalStatistics.bwtSaRetrieved, BWTSaRetrievalStatistics.cachedSaRetrieved, BWTSaRetrievalStatistics.saDiagonalLinked, BWTSaRetrievalStatistics.saDuplicated); } elapsedTime = getElapsedTime(startTime) - totalElapsedTime; printf("Elapsed time = "); printElapsedTime(stdout, FALSE, FALSE, TRUE, 4, elapsedTime); totalElapsedTime += elapsedTime; printf("\n"); if (LogFileName[0] != '\0') { fprintf(logFile, "Finished edit distance search.\n"); fprintf(logFile, "%u patterns out of %u found. %llu of %llu matches located.\n", numberOfPatternFound, numberOfPattern, totalTextPositionRetrieved, totalTextPositionMatched); if (FindTextPosition) { fprintf(logFile, "Hits: BWT/Cached/Diag/Dup : %u/%u/%u/%u\n", BWTSaRetrievalStatistics.bwtSaRetrieved, BWTSaRetrievalStatistics.cachedSaRetrieved, BWTSaRetrievalStatistics.saDiagonalLinked, BWTSaRetrievalStatistics.saDuplicated); } fprintf(logFile, "Elapsed time = "); printElapsedTime(logFile, FALSE, FALSE, TRUE, 4, elapsedTime); fprintf(logFile, "\n"); } } } MMPoolReturn(mmPool, packedKey, WordPackedLengthFromText(MAX_SEARCH_PATTERN_LENGTH, BIT_PER_CHAR)); MMPoolReturn(mmPool, convertedKey, MAX_SEARCH_PATTERN_LENGTH); HSPFree(mmPool, hsp, MAX_SEARCH_PATTERN_LENGTH / CHAR_PER_WORD); BWTFree(mmPool, bwt); if (searchPattern != NULL) { MMUnitFree(searchPattern, searchPatternAllocated); } if (searchPatternPosition != NULL) { MMUnitFree(searchPatternPosition, searchPatternPositionAllocated); } MMUnitFree(saIndexGroup, MaxNumberOfHitGroups * sizeof(unsigned int)); MMUnitFree(hitList, MaxNumberOfTextPosition * sizeof(unsigned int)); MMPoolFree(mmPool); iniparser_freedict(programInput); iniparser_freedict(ini); return 0; }
int main(int argc, char** argv) { unsigned int* __restrict address; unsigned int* __restrict memory; unsigned int i, j; unsigned int t=0; unsigned int numberOfMemoryLocation; dictionary *programInput; double startTime; double elapsedTime = 0, totalElapsedTime = 0; double initializationTime, experimentTime; programInput = ParseInput(argc, argv); ValidateParameters(); // Initialize memory manager MMMasterInitialize(0, 0, FALSE, NULL); numberOfMemoryLocation = MemorySize / sizeof(int); // Allocate memory address = MMUnitAllocate((NumberOfAccess + 8) * sizeof(unsigned int)); memory = MMUnitAllocate((numberOfMemoryLocation + 32) * sizeof(unsigned int)); // Set random seed r250_init(getRandomSeed()); // Set start time startTime = setStartTime(); printf("Initialize memory pointers with random values.."); for (i=0; i<numberOfMemoryLocation + 32; i++) { memory[i] = r250(); } // Initialize address and memory for (i=0; i<NumberOfAccess + 8; i++) { address[i] = (r250() % numberOfMemoryLocation) / 4 * 4; } printf("finished.\n"); elapsedTime = getElapsedTime(startTime) - totalElapsedTime; totalElapsedTime += elapsedTime; initializationTime = elapsedTime; // Test memory speed for read if (ReadWrite[0] == 'R' || ReadWrite[0] == 'r') { for (i=0; i<NumberOfIteration; i++) { for (j=0; j<NumberOfAccess; j++) { t += memory[address[j]]; } } } // Test memory speed for write if (ReadWrite[0] == 'W' || ReadWrite[0] == 'w') { for (i=0; i<NumberOfIteration; i++) { for (j=0; j<NumberOfAccess; j++) { memory[address[j]] += address[j]; } } } elapsedTime = getElapsedTime(startTime) - totalElapsedTime; totalElapsedTime += elapsedTime; experimentTime = elapsedTime; // So that compiler does not remove code for variables t and r if (t==0) { printf("\n"); } printf("Experiment completed.\n"); printf("Initialization time = "); printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, initializationTime); printf("Experiment time = "); printElapsedTime(stdout, FALSE, FALSE, TRUE, 2, experimentTime); MMUnitFree(address, (NumberOfAccess + 8) * sizeof(unsigned int)); MMUnitFree(memory, (numberOfMemoryLocation + 32) * sizeof(unsigned int)); iniparser_freedict(programInput); return 0; }