static struct genePos *xyzAdvFilter(struct column *col,
struct sqlConnection *conn, struct genePos *list)
/* Do advanced filter on xyz type column. */
{
char *term = advFilterVal(col, "term");
if (term != NULL)
{
/* Construct a hash of all genes that pass filter. */
struct hash *passHash = newHash(17);
char query[1000];
char **row;
struct sqlResult *sr;
sqlSafef(query, sizeof(query), "select %s from %s where %s='%s'",
col->keyField, col->table, col->valField, term);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
hashAdd(passHash, row[0], NULL);
sqlFreeResult(&sr);
/* Remove non-passing genes. */
list = weedUnlessInHash(list, passHash);
hashFree(&passHash);
}
return list;
}
static struct genePos *wildAssociationFilter(
struct slName *wildList, boolean orLogic,
struct column *col, struct sqlConnection *conn, struct genePos *list)
/* Handle relatively slow filtering when there is a wildcard present. */
{
struct assocGroup *ag = assocGroupNew(16);
struct genePos *gp;
struct hash *passHash = newHash(16); /* Hash of items passing filter. */
int assocCount = 0;
struct sqlResult *sr;
char **row;
/* Build up associations. */
sr = sqlGetResult(conn, col->queryFull);
while ((row = sqlNextRow(sr)) != NULL)
{
++assocCount;
assocGroupAdd(ag, row[0],row[1]);
}
sqlFreeResult(&sr);
/* Look for matching associations and put them on newList. */
for (gp = list; gp != NULL; gp = gp->next)
{
char *key = (col->protKey
? (kgVersion == KG_III ? lookupProtein(conn, gp->name) : gp->protein)
: gp->name);
struct assocList *al = hashFindVal(ag->listHash, key);
if (al != NULL)
{
if (wildList == NULL || wildMatchRefs(wildList, al->list, orLogic))
hashAdd(passHash, gp->name, gp);
}
}
list = weedUnlessInHash(list, passHash);
hashFree(&passHash);
assocGroupFree(&ag);
return list;
}
static struct genePos *pfamAdvFilter(struct column *col,
struct sqlConnection *defaultConn, struct genePos *list)
/* Do advanced filter on for pfam. */
{
char *terms = advFilterVal(col, "terms");
if (terms != NULL)
{
struct sqlConnection *conn = sqlConnect(col->protDb);
char query[256];
struct sqlResult *sr;
struct dyString *dy = newDyString(1024);
char **row;
boolean orLogic = advFilterOrLogic(col, "logic", TRUE);
struct slName *term, *termList = stringToSlNames(terms);
struct hash *passHash = newHash(17);
struct hash *prevHash = NULL;
struct genePos *gp;
/* Build up hash of all genes. */
struct hash *geneHash = newHash(18);
for (gp = list; gp != NULL; gp = gp->next)
hashAdd(geneHash, gp->name, gp);
for (term = termList; term != NULL; term = term->next)
{
/* Build up a list of IDs of descriptions that match term. */
struct slName *idList = NULL, *id;
if (isPfamId(term->name))
{
idList = slNameNew(term->name);
}
else
{
char *sqlWild = sqlLikeFromWild(term->name);
sqlSafef(query, sizeof(query),
"select pfamAC from pfamDesc where description like '%s'",
sqlWild);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
id = slNameNew(row[0]);
slAddHead(&idList, id);
}
sqlFreeResult(&sr);
}
if (idList != NULL)
{
/* Build up query that includes all IDs. */
dyStringClear(dy);
sqlDyStringPrintf(dy, "select name from %s where ", col->table);
sqlDyStringPrintf(dy, "value='%s'", idList->name);
for (id = idList->next; id != NULL; id = id->next)
sqlDyStringPrintf(dy, "or value='%s'", id->name);
/* Execute query and put matchers into hash. */
sr = sqlGetResult(defaultConn, dy->string);
while ((row = sqlNextRow(sr)) != NULL)
{
gp = hashFindVal(geneHash, row[0]);
if (gp != NULL)
{
char *name = gp->name;
if (prevHash == NULL || hashLookup(prevHash, name) != NULL)
hashStore(passHash, name);
}
}
sqlFreeResult(&sr);
slFreeList(&idList);
}
if (!orLogic)
{
hashFree(&prevHash);
if (term->next != NULL)
{
prevHash = passHash;
passHash = newHash(17);
}
}
}
list = weedUnlessInHash(list, passHash);
hashFree(&prevHash);
hashFree(&passHash);
dyStringFree(&dy);
sqlDisconnect(&conn);
}
return list;
}
static struct genePos *tameAssociationFilter(
struct slName *termList, boolean orLogic,
struct column *col, struct sqlConnection *conn, struct genePos *list)
/* Handle filtering when there are no wildcards present. */
{
struct sqlResult *sr;
char **row;
struct slName *term;
struct hash *passHash = newHash(17);
struct hash *protHash = NULL;
struct hash *prevHash = NULL;
struct genePos *gp;
int protCount = 0, termCount = 0, matchRow = 0, keyRow = 0;
/* Make up protein-keyed hash if need be. */
if (col->protKey)
{
protHash = newHash(17);
for (gp = list; gp != NULL; gp = gp->next)
{
hashAdd(protHash, gp->protein, gp->name);
++protCount;
}
}
for (term = termList; term != NULL; term = term->next)
{
char query[1024];
safef(query, sizeof(query), col->invQueryOne, term->name);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
char *key = row[0];
++matchRow;
if (protHash != NULL)
key = hashFindVal(protHash, key);
if (key != NULL)
{
++keyRow;
if (prevHash == NULL || hashLookup(prevHash, key) != NULL)
{
hashStore(passHash, key);
}
}
}
if (!orLogic)
{
hashFree(&prevHash);
if (term->next != NULL)
{
prevHash = passHash;
passHash = newHash(17);
}
}
sqlFreeResult(&sr);
++termCount;
}
list = weedUnlessInHash(list, passHash);
hashFree(&prevHash);
freeHash(&protHash);
freeHash(&passHash);
return list;
}
