struct subjInfo *intAdvFilter(struct column *col,
struct sqlConnection *conn, struct subjInfo *list)
/* Do advanced filter on string in main table. */
{
char *minString = advFilterVal(col, "min");
char *maxString = advFilterVal(col, "max");
if (minString || maxString)
{
int min = minString ? sqlSigned(minString) : 0;
int max = maxString ? sqlSigned(maxString) : 0;
struct subjInfo *newList = NULL, *next, *si;
for (si = list; si != NULL; si = next)
{
char *cell = col->cellVal(col, si, conn);
int val = sqlSigned(cell);
freez(&cell);
next = si->next;
if (!((minString && (val < min)) || (maxString && (val > max))))
{
slAddHead(&newList, si);
}
}
slReverse(&newList);
list = newList;
}
return list;
}
struct subjInfo *doubleAdvFilter(struct column *col,
struct sqlConnection *conn, struct subjInfo *list)
/* Do advanced filter on string in main table. */
{
char *minString = advFilterVal(col, "min");
char *maxString = advFilterVal(col, "max");
if (minString || maxString)
{
double min = minString ? sqlDouble(minString) : 0.0;
double max = maxString ? sqlDouble(maxString) : 0.0;
struct subjInfo *newList = NULL, *next, *si;
for (si = list; si != NULL; si = next)
{
char *cell = col->cellVal(col, si, conn);
boolean invalid = sameString(cell,".");
double val = invalid ? 0.0 : sqlDouble(cell);
freez(&cell);
next = si->next;
if (!invalid && !((minString && (val < min)) || (maxString && (val > max))))
{
slAddHead(&newList, si);
}
}
slReverse(&newList);
list = newList;
}
return list;
}
static struct genePos *genePredPosAdvFilter(struct column *col,
struct sqlConnection *conn, struct genePos *list)
/* Do advanced filter on position. */
{
char *chrom = advFilterVal(col, "chr");
char *startString = advFilterVal(col, "start");
char *endString = advFilterVal(col, "end");
if (chrom != NULL)
{
struct genePos *newList = NULL, *gp, *next;
for (gp = list; gp != NULL; gp = next)
{
next = gp->next;
if (sameWord(chrom, gp->chrom))
{
slAddHead(&newList, gp);
}
}
slReverse(&newList);
list = newList;
}
if (startString != NULL)
{
int start = atoi(startString)-1;
struct genePos *newList = NULL, *gp, *next;
for (gp = list; gp != NULL; gp = next)
{
next = gp->next;
if (gp->end > start)
{
slAddHead(&newList, gp);
}
}
slReverse(&newList);
list = newList;
}
if (endString != NULL)
{
int end = atoi(endString);
struct genePos *newList = NULL, *gp, *next;
for (gp = list; gp != NULL; gp = next)
{
next = gp->next;
if (gp->start < end)
{
slAddHead(&newList, gp);
}
}
slReverse(&newList);
list = newList;
}
return list;
}
void refineFilterOn(struct column *colList)
/* Consult cart to see if filtering is on/off. */
{
char *val;
struct column *col;
for (col = colList; col != NULL; col = col->next)
{
val = advFilterVal(col,"max");
if (val != NULL)
col->filterOn = TRUE; //sameString(val, "1");
val = advFilterVal(col,"wild");
if (val != NULL)
col->filterOn = TRUE; //sameString(val, "1");
}
}
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 char *keyFileName(struct column *col)
/* Return key file name for this column. Return
* NULL if no key file. */
{
char *fileName = advFilterVal(col, "keyFile");
if (fileName == NULL)
return NULL;
if (!fileExists(fileName))
{
cartRemove(cart, advFilterName(col, "keyFile"));
return NULL;
}
return fileName;
}
static struct genePos *associationAdvFilter(struct column *col,
struct sqlConnection *conn, struct genePos *list)
/* Do advanced filter on position. */
{
char *terms = advFilterVal(col, "terms");
if (terms != NULL)
{
boolean orLogic = advFilterOrLogic(col, "logic", TRUE);
struct slName *termList = stringToSlNames(terms);
if (anyWild(terms))
list = wildAssociationFilter(termList, orLogic, col, conn, list);
else
list = tameAssociationFilter(termList, orLogic, col, conn, list);
}
return list;
}
struct subjInfo *stringAdvFilter(struct column *col,
struct sqlConnection *conn, struct subjInfo *list)
/* Do advanced filter on string in main table. */
{
char *wild = advFilterVal(col, "wild");
struct hash *keyHash = keyFileHash(col);
if (keyHash != NULL)
{
struct subjInfo *newList = NULL, *next, *si;
for (si = list; si != NULL; si = next)
{
char *cell = col->cellVal(col, si, conn);
next = si->next;
if (hashLookupUpperCase(keyHash, cell))
{
slAddHead(&newList, si);
}
freez(&cell);
}
slReverse(&newList);
list = newList;
}
if (wild != NULL)
{
boolean orLogic = advFilterOrLogic(col, "logic", TRUE);
struct subjInfo *newList = NULL, *next, *si;
struct slName *wildList = stringToSlNames(wild);
for (si = list; si != NULL; si = next)
{
char *cell = col->cellVal(col, si, conn);
next = si->next;
if (wildMatchList(cell, wildList, orLogic))
{
slAddHead(&newList, si);
}
freez(&cell);
}
slReverse(&newList);
list = newList;
}
hashFree(&keyHash);
return list;
}
void lookupAdvFilterControls(struct column *col, struct sqlConnection *conn)
/* Print out controls for advanced filter on lookup column. */
{
char *fileName = advFilterVal(col, "keyFile");
hPrintf("%s search (including * and ? wildcards):", col->shortLabel);
advFilterRemakeTextVar(col, "wild", 18);
hPrintf("<BR>\n");
hPrintf("Include if ");
advFilterAnyAllMenu(col, "logic", TRUE);
hPrintf("words in search term match.<BR>");
if (!columnSetting(col, "noKeys", NULL))
{
hPrintf("Limit to items (no wildcards) in list: ");
advFilterKeyPasteButton(col);
hPrintf(" ");
advFilterKeyUploadButton(col);
hPrintf(" ");
if (fileName != NULL)
{
if (fileExists(fileName))
{
int count = countQuotedWordsInFile(fileName);
advFilterKeyClearButton(col);
hPrintf("<BR>\n");
if (count == 1)
hPrintf("(There is currently 1 item in the list.)");
else
hPrintf("(There are currently %d items in the list.)", count);
}
else
{
cartRemove(cart, advFilterName(col, "keyFile"));
}
}
}
if (col->filterDropDown)
showListOfFilterValues(col, conn);
}
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;
}
