struct gbRelease* gbIndexNewestRelease(struct gbIndex* index,
unsigned state, unsigned srcDb,
unsigned types, char* limitAccPrefix)
/* find the newest release that is either processed or aligned (based on
* state) for the specified srcDb */
{
struct gbRelease* release = index->rels[gbSrcDbIdx(srcDb)];
if (srcDb == GB_REFSEQ)
{
types &= GB_MRNA; /* only mRNAs for refseq */
if (types == 0)
return NULL; /* no types left */
}
/* Find the first with at least one aligned index. Note that incomplete
* alignments will not cause data lose here, if a partation (equal to a
* *.alidx file is complete, but others aren't, only it will be processed.
*/
while (release != NULL)
{
if (types & GB_MRNA)
{
if (gbReleaseHasData(release, state, GB_MRNA, limitAccPrefix))
return release;
}
if (types & GB_EST)
{
if (gbReleaseHasData(release, state, GB_EST, limitAccPrefix))
return release;
}
release = release->next;
}
return NULL; /* didn't find one */
}
static struct gbRelease* newestReleaseWithAligns(struct gbIndex* index,
char* database, unsigned srcDb)
/* find the newest release for srcDb that has alignements */
{
/* can't look at update objects, since they haven't been loaded */
struct gbRelease* release;
char alIdxPat[PATH_LEN];
safef(alIdxPat, sizeof(alIdxPat), "*.%s", ALIDX_EXT);
for (release = index->rels[gbSrcDbIdx(srcDb)]; release != NULL;
release = release->next)
{
char relDir[PATH_LEN];
struct slName* idxFiles;
safef(relDir, sizeof(relDir), "%s/%s/%s/%s", GB_ALIGNED_DIR, release->name,
database, GB_FULL_UPDATE);
idxFiles = listDir(relDir, alIdxPat);
if (idxFiles != NULL)
{
slFreeList(&idxFiles);
verbose(1, "checking %s for %s\n", release->name, database);
return release;
}
}
return NULL;
}
struct gbIndex* gbIndexNew(char *database, char* gbRoot)
/* Construct a new gbIndex object, finding all of the release directories. If
* aligned objects are to be accessed database should be specified. If gbRoot
* is not null, it should be the path to the root directory. Otherwise
* the current directory is assumed.*/
{
struct gbIndex* index;
AllocVar(index);
if (gbRoot == NULL)
gbRoot = ".";
index->gbRoot = cloneString(gbRoot);
if (database != NULL)
index->genome = gbGenomeNew(database);
index->rels[gbSrcDbIdx(GB_GENBANK)] = findReleases(index, GB_GENBANK);
index->rels[gbSrcDbIdx(GB_REFSEQ)] = findReleases(index, GB_REFSEQ);
return index;
}
