void test_stList_nullList(CuTest *testCase) { stList *empty = NULL; CuAssertTrue(testCase, stList_length(empty) == 0); stListIterator *it = stList_getIterator(empty); CuAssertTrue(testCase, stList_getNext(it) == NULL); CuAssertTrue(testCase, stList_getPrevious(it) == NULL); stList_destructIterator(it); stList_destruct(empty); }
/* write a malnSet to a MAF file */ void malnSet_writeMaf(struct malnSet *malnSet, char *mafFileName) { malnSet_assert(malnSet); stList *sorted = buildRootSorted(malnSet); FILE *mafFh = mustOpen(mafFileName, "w"); mafWriteStart(mafFh, NULL); stListIterator *iter = stList_getIterator(sorted); struct malnBlk *blk; while ((blk = stList_getNext(iter)) != NULL) { writeBlkToMaf(blk, mafFh); } stList_destructIterator(iter); mafWriteEnd(mafFh); carefulClose(&mafFh); stList_destruct(sorted); }
void test_stList_iterator(CuTest *testCase) { setup(); stListIterator *it = stList_getIterator(list); int64_t i; for(i=0; i<stringNumber; i++) { CuAssertTrue(testCase, stList_getNext(it) == strings[i]); } CuAssertTrue(testCase, stList_getNext(it) == NULL); CuAssertTrue(testCase, stList_getNext(it) == NULL); stListIterator *it2 = stList_copyIterator(it); for(i=0; i<stringNumber; i++) { CuAssertTrue(testCase, stList_getPrevious(it) == strings[stringNumber-1-i]); CuAssertTrue(testCase, stList_getPrevious(it2) == strings[stringNumber-1-i]); } CuAssertTrue(testCase, stList_getPrevious(it) == NULL); CuAssertTrue(testCase, stList_getPrevious(it) == NULL); CuAssertTrue(testCase, stList_getPrevious(it2) == NULL); stList_destructIterator(it); teardown(); }
/* * This builds an adjacency list structure for the the sequences. Every sequence-position * has a column in the hash with which it can be aligned with. */ static stHash *buildAdjacencyList(stList *pairs, int64_t sequenceNumber) { stHash *hash = stHash_construct3((uint64_t (*)(const void *))stIntTuple_hashKey, (int (*)(const void *, const void *))stIntTuple_equalsFn, (void (*)(void *))stIntTuple_destruct, NULL); for(int64_t seq=0; seq<sequenceNumber; seq++) { for(int64_t position=0; position<MAX_SEQUENCE_SIZE; position++) { stIntTuple *seqPos = stIntTuple_construct2( seq, position); stSortedSet *column = stSortedSet_construct3((int (*)(const void *, const void *))stIntTuple_cmpFn, NULL); stSortedSet_insert(column, seqPos); stHash_insert(hash, seqPos, column); } } stListIterator *it = stList_getIterator(pairs); stIntTuple *pair; while((pair = stList_getNext(it)) != NULL) { stIntTuple *seqPos1 = stIntTuple_construct2( stIntTuple_get(pair, 0), stIntTuple_get(pair, 1)); stIntTuple *seqPos2 = stIntTuple_construct2( stIntTuple_get(pair, 2), stIntTuple_get(pair, 3)); stSortedSet *column1 = stHash_search(hash, seqPos1); assert(column1 != NULL); stSortedSet *column2 = stHash_search(hash, seqPos2); assert(column2 != NULL); if(column1 != column2) { //Merge the columns stSortedSetIterator *it2 = stSortedSet_getIterator(column2); stIntTuple *seqPos3; while((seqPos3 = stSortedSet_getNext(it2)) != NULL) { assert(stSortedSet_search(column1, seqPos3) == NULL); stSortedSet_insert(column1, seqPos3); assert(stHash_search(hash, seqPos3) == column2); stHash_insert(hash, seqPos3, column1); assert(stHash_search(hash, seqPos3) == column1); } stSortedSet_destructIterator(it2); stSortedSet_destruct(column2); } //Cleanup loop. stIntTuple_destruct(seqPos1); stIntTuple_destruct(seqPos2); } stList_destructIterator(it); return hash; }
static void cacheSubstringsFromDB(CactusDisk *cactusDisk, stList *substrings) { /* * Caches the given set of substrings in the cactusDisk cache. */ if (cactusDisk->storeSequencesInAFile) { if (cactusDisk->sequencesReadFileHandle == NULL) { if(cactusDisk->sequencesWriteFileHandle != NULL) { fsync(fileno(cactusDisk->sequencesWriteFileHandle)); fclose(cactusDisk->sequencesWriteFileHandle); cactusDisk->sequencesWriteFileHandle = NULL; } cactusDisk->sequencesReadFileHandle = fopen(cactusDisk->absSequencesFileName, "r"); assert(cactusDisk->sequencesReadFileHandle != NULL); } else { assert(cactusDisk->sequencesWriteFileHandle == NULL); } for (int64_t i = 0; i < stList_length(substrings); i++) { Substring *substring = stList_get(substrings, i); char *string = getStringFromDisk(cactusDisk->sequencesReadFileHandle, substring->name, substring->start, substring->length); stCache_setRecord(cactusDisk->stringCache, substring->name, substring->start, substring->length, string); #ifndef NDEBUG int64_t bytesRead; char *string2 = stCache_getRecord(cactusDisk->stringCache, substring->name, substring->start, substring->length, &bytesRead); assert(bytesRead == substring->length); for (int64_t j = 0; j < substring->length; j++) { assert(string2[j] == string[j]); } free(string2); #endif free(string); } } else { stList *getRequests = stList_construct3(0, free); for (int64_t i = 0; i < stList_length(substrings); i++) { Substring *substring = stList_get(substrings, i); int64_t intervalSize = (substring->length + substring->start - 1) / CACTUS_DISK_SEQUENCE_CHUNK_SIZE - substring->start / CACTUS_DISK_SEQUENCE_CHUNK_SIZE + 1; Name shiftedName = substring->name + substring->start / CACTUS_DISK_SEQUENCE_CHUNK_SIZE; for (int64_t j = 0; j < intervalSize; j++) { int64_t *k = st_malloc(sizeof(int64_t)); k[0] = shiftedName + j; stList_append(getRequests, k); } } if (stList_length(getRequests) == 0) { stList_destruct(getRequests); return; } stList *records = NULL; stTry { records = stKVDatabase_bulkGetRecords(cactusDisk->database, getRequests); } stCatch(except) { stThrowNewCause(except, ST_KV_DATABASE_EXCEPTION_ID, "An unknown database error occurred when getting a sequence string"); }stTryEnd ; assert(records != NULL); assert(stList_length(records) == stList_length(getRequests)); stList_destruct(getRequests); stListIterator *recordsIt = stList_getIterator(records); for (int64_t i = 0; i < stList_length(substrings); i++) { Substring *substring = stList_get(substrings, i); int64_t intervalSize = (substring->length + substring->start - 1) / CACTUS_DISK_SEQUENCE_CHUNK_SIZE - substring->start / CACTUS_DISK_SEQUENCE_CHUNK_SIZE + 1; stList *strings = stList_construct(); while (intervalSize-- > 0) { int64_t recordSize; stKVDatabaseBulkResult *result = stList_getNext(recordsIt); assert(result != NULL); char *string = stKVDatabaseBulkResult_getRecord(result, &recordSize); assert(string != NULL); assert(strlen(string) == recordSize - 1); stList_append(strings, string); assert(recordSize <= CACTUS_DISK_SEQUENCE_CHUNK_SIZE + 1); } assert(stList_length(strings) > 0); char *joinedString = stString_join2("", strings); stCache_setRecord(cactusDisk->stringCache, substring->name, (substring->start / CACTUS_DISK_SEQUENCE_CHUNK_SIZE) * CACTUS_DISK_SEQUENCE_CHUNK_SIZE, strlen(joinedString), joinedString); free(joinedString); stList_destruct(strings); } assert(stList_getNext(recordsIt) == NULL); stList_destructIterator(recordsIt); stList_destruct(records); } }