void testMetaSequence_serialisation(CuTest* testCase) {
cactusMetaSequenceTestSetup();
int64_t i;
Name name = metaSequence_getName(metaSequence);
CuAssertTrue(testCase, cactusDisk_getMetaSequence(cactusDisk, name) == metaSequence);
void *vA = binaryRepresentation_makeBinaryRepresentation(metaSequence,
(void (*)(void *, void (*)(const void *, size_t, size_t)))metaSequence_writeBinaryRepresentation, &i);
CuAssertTrue(testCase, i > 0);
metaSequence_destruct(metaSequence);
CuAssertTrue(testCase, cactusDisk_getMetaSequence(cactusDisk, name) == NULL);
void *vA2 = vA;
metaSequence = metaSequence_loadFromBinaryRepresentation(&vA2, cactusDisk);
CuAssertTrue(testCase, name == metaSequence_getName(metaSequence));
CuAssertStrEquals(testCase, headerString, metaSequence_getHeader(metaSequence));
CuAssertTrue(testCase, cactusDisk_getMetaSequence(cactusDisk, name) == metaSequence);
cactusDisk_write(cactusDisk);
metaSequence_destruct(metaSequence);
CuAssertTrue(testCase, cactusDisk_getMetaSequence(cactusDisk, name) != NULL);
metaSequence = cactusDisk_getMetaSequence(cactusDisk, name);
nestedTest = 1;
testMetaSequence_getName(testCase);
testMetaSequence_getStart(testCase);
testMetaSequence_getLength(testCase);
testMetaSequence_getEventName(testCase);
testMetaSequence_getString(testCase);
testMetaSequence_getHeader(testCase);
testMetaSequence_isTrivialSequence(testCase);
nestedTest = 0;
cactusMetaSequenceTestTeardown();
}
void metaSequence_writeBinaryRepresentation(MetaSequence *metaSequence,
void (*writeFn)(const void * ptr, size_t size, size_t count)) {
binaryRepresentation_writeElementType(CODE_META_SEQUENCE, writeFn);
binaryRepresentation_writeName(metaSequence_getName(metaSequence), writeFn);
binaryRepresentation_writeInteger(metaSequence_getStart(metaSequence), writeFn);
binaryRepresentation_writeInteger(metaSequence_getLength(metaSequence), writeFn);
binaryRepresentation_writeName(metaSequence_getEventName(metaSequence), writeFn);
binaryRepresentation_writeName(metaSequence->stringName, writeFn);
binaryRepresentation_writeString(metaSequence_getHeader(metaSequence), writeFn);
binaryRepresentation_writeBool(metaSequence_isTrivialSequence(metaSequence), writeFn);
}
int main(int argc, char *argv[])
{
char *cactusDiskString = NULL;
stKVDatabaseConf *kvDatabaseConf;
CactusDisk *cactusDisk;
Flower *flower;
Flower_SequenceIterator *flowerIt;
Sequence *sequence;
struct option longopts[] = { {"cactusDisk", required_argument, NULL, 'c' },
{0, 0, 0, 0} };
int flag;
while((flag = getopt_long(argc, argv, "", longopts, NULL)) != -1) {
switch(flag) {
case 'c':
cactusDiskString = stString_copy(optarg);
break;
case '?':
default:
usage();
return 1;
}
}
if (cactusDiskString == NULL) {
st_errAbort("--cactusDisk option must be provided");
}
kvDatabaseConf = stKVDatabaseConf_constructFromString(cactusDiskString);
cactusDisk = cactusDisk_construct(kvDatabaseConf, 0);
// Get top-level flower.
flower = cactusDisk_getFlower(cactusDisk, 0);
flowerIt = flower_getSequenceIterator(flower);
while((sequence = flower_getNextSequence(flowerIt)) != NULL) {
MetaSequence *metaSequence = sequence_getMetaSequence(sequence);
const char *header;
char *firstToken, *newHeader;
stList *tokens;
// Strip the ID token from the header (should be the first
// |-separated token) and complain if there isn't one.
header = metaSequence_getHeader(metaSequence);
tokens = fastaDecodeHeader(header);
assert(stList_length(tokens) > 1);
firstToken = stList_removeFirst(tokens);
assert(!strncmp(firstToken, "id=", 3));
free(firstToken);
newHeader = fastaEncodeHeader(tokens);
metaSequence_setHeader(metaSequence, newHeader);
}
cactusDisk_write(cactusDisk);
}
const char *sequence_getHeader(Sequence *sequence) {
return metaSequence_getHeader(sequence->metaSequence);
}
void testMetaSequence_getHeader(CuTest* testCase) {
cactusMetaSequenceTestSetup();
CuAssertStrEquals(testCase, headerString, metaSequence_getHeader(metaSequence));
cactusMetaSequenceTestTeardown();
}
