static int releaseSanity(struct gbRelease* release, char *database)
/* Run sanity checks on a release */
{
unsigned orgCats;
int checkedSetCnt = 0;
/* check if native, and/or xeno should be included */
orgCats = getLoadOrgCats(database, release->srcDb, GB_MRNA);
if (orgCats != 0)
{
if (checkRelease(release, database, GB_MRNA, orgCats, NULL))
checkedSetCnt++;
}
orgCats = getLoadOrgCats(database, release->srcDb, GB_EST);
if (orgCats != 0)
{
struct slName* prefixes, *prefix;
boolean checkedSome = FALSE;
if (gOptions.accPrefixRestrict != NULL)
prefixes = newSlName(gOptions.accPrefixRestrict);
else
prefixes = gbReleaseGetAccPrefixes(release, GB_PROCESSED, GB_EST);
for (prefix = prefixes; prefix != NULL; prefix = prefix->next)
{
if (checkRelease(release, database, GB_EST, orgCats, prefix->name))
checkedSome = TRUE;
}
slFreeList(&prefixes);
if (checkedSome)
checkedSetCnt++;
}
return checkedSetCnt;
}
struct gbRelease* loadIndex(char* relName, unsigned types, char* database)
/* load processed section of index for release */
{
struct gbIndex* index = gbIndexNew(database, NULL);
struct gbSelect select;
ZeroVar(&select);
select.release = gbIndexMustFindRelease(index, relName);
if (types & GB_MRNA)
{
select.type = GB_MRNA;
gbReleaseLoadProcessed(&select);
}
if ((types & GB_EST) && (select.release->srcDb == GB_GENBANK))
{
struct slName* prefixes, *prefix;
select.type = GB_EST;
prefixes = gbReleaseGetAccPrefixes(select.release, GB_PROCESSED, GB_EST);
for (prefix = prefixes; prefix != NULL; prefix = prefix->next)
{
select.accPrefix = prefix->name;
gbReleaseLoadProcessed(&select);
}
select.accPrefix = NULL;
slFreeList(&prefixes);
}
return select.release;
}
static void testLoadPrefixes(struct gbSelect* select, unsigned flags,
char* restrictPrefix)
/* do load testing of part of a release */
{
struct slName* prefixes, *prefix;
if (restrictPrefix != NULL)
prefixes = slNameNew(restrictPrefix);
else
prefixes = gbReleaseGetAccPrefixes(select->release, GB_PROCESSED, GB_EST);
for (prefix = prefixes; prefix != NULL; prefix = prefix->next)
{
select->accPrefix = prefix->name;
testLoad(select, flags);
}
slFreeList(&prefixes);
select->accPrefix = NULL;
}
static void getReleasePartitions(struct gbSelect** selectList,
struct gbRelease* release,
unsigned state,
unsigned types,
unsigned orgCats,
char *limitAccPrefix)
/* Get partitions for a release and add to list */
{
if (types & GB_MRNA)
getTypePartitions(selectList, release, GB_MRNA, orgCats, NULL);
if ((types & GB_EST) && (release->srcDb != GB_REFSEQ))
{
struct slName* prefixes, *prefix;
if (limitAccPrefix != NULL)
prefixes = newSlName(limitAccPrefix);
else
prefixes = gbReleaseGetAccPrefixes(release, state, GB_EST);
for (prefix = prefixes; prefix != NULL; prefix = prefix->next)
getTypePartitions(selectList, release, GB_EST, orgCats, prefix->name);
slFreeList(&prefixes);
}
}
