void wormCdnaUncache()
/* Tear down structure for reading cDNAs. */
{
snofClose(&cdnaSnof);
carefulClose(&cdnaFa);
freez(&cdnaDir);
}
struct xaAli *getOneXaAli(char *organism, char *xaName)
/* Return a single named xaAli for organism. */
{
char ixFileName[512];
char dataFileName[512];
char *xDir;
struct snof *snof;
long offset;
FILE *f;
struct xaAli *xa;
xDir = wormXenoDir();
sprintf(ixFileName, "%s%s/all", xDir, organism);
sprintf(dataFileName, "%s%s/all%s", xDir, organism, xaAlignSuffix());
snof = snofMustOpen(ixFileName);
if (!snofFindOffset(snof, xaName, &offset))
errAbort("Couldn't find %s", xaName);
snofClose(&snof);
f = xaOpenVerify(dataFileName);
fseek(f, offset, SEEK_SET);
xa = xaReadNext(f, FALSE);
fclose(f);
return xa;
}
struct snof *snofOpen(char *indexName)
/* Open up the index file. Returns NULL if there's any problem. */
{
struct snof *snof;
int sigBuf[4];
FILE *f;
char fileName[512];
if (!makeSnofName(fileName, indexName))
return NULL;
if ((snof = needMem(sizeof(*snof))) == NULL)
return NULL;
if ((snof->file = f = fopen(fileName, "rb")) == NULL)
{
freeMem(snof);
return NULL;
}
if ((fread(sigBuf, sizeof(sigBuf), 1, f)) != 1)
{
snofClose(&snof);
return NULL;
}
if (!isSnofSig(&sigBuf))
{
snofClose(&snof);
return NULL;
}
if ((fread(&snof->maxNameSize, sizeof(snof->maxNameSize), 1, f)) != 1)
{
snofClose(&snof);
return NULL;
}
snof->headSize = ftell(f);
snof->itemSize = snof->maxNameSize + sizeof(unsigned);
if ((snof->first = needMem(5*snof->itemSize)) == NULL)
{
snofClose(&snof);
return NULL;
}
snof->last = snof->first + snof->itemSize;
snof->less = snof->last + snof->itemSize;
snof->mid = snof->less + snof->itemSize;
snof->more = snof->mid + snof->itemSize;
if (fread(snof->first, snof->itemSize, 1, f) != 1)
{
snofClose(&snof);
return NULL;
}
fseek(f, -snof->itemSize, SEEK_END);
snof->endIx = (ftell(f)-snof->headSize)/snof->itemSize;
if (fread(snof->last, snof->itemSize, 1, f) != 1)
{
snofClose(&snof);
return NULL;
}
return snof;
}
void wormUncacheSomeGdf(struct wormGdfCache *cache)
/* Uncache some gene prediction set. */
{
snofClose(&cache->snof);
carefulClose(&cache->file);
}
