static void orderFieldsInTable(struct tableJoiner *tj)
/* Rearrange order of fields in tj->fieldList so that
* they are the same as the order in the database. */
{
struct sqlConnection *conn = hAllocConn(tj->database);
char *splitTable = chromTable(conn, tj->table);
struct hash *fieldHash = hashNew(0);
struct slName *field, *fieldList = sqlListFields(conn, splitTable);
struct joinerDtf *dtf, *newList = NULL;
/* Build up hash of field names. */
for (dtf = tj->fieldList; dtf != NULL; dtf = dtf->next)
hashAdd(fieldHash, dtf->field, dtf);
hFreeConn(&conn);
/* Build up new list in correct order. */
for (field = fieldList; field != NULL; field = field->next)
{
dtf = hashFindVal(fieldHash, field->name);
if (dtf != NULL)
{
slAddHead(&newList, dtf);
}
}
slFreeList(&fieldList);
slReverse(&newList);
tj->fieldList = newList;
freez(&splitTable);
}
static void showTableFieldsDb(char *db, char *rootTable, boolean withGetButton)
/* Put up a little html table with a check box, name, and hopefully
* a description for each field in SQL rootTable. */
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConn(db);
struct trackDb *tdb = findTdbForTable(db, curTrack, rootTable, ctLookupName);
struct asObject *asObj = asForTable(conn, rootTable);
boolean showItemRgb = FALSE;
showItemRgb=bedItemRgb(tdb); /* should we expect itemRgb instead of "reserved" */
struct slName *fieldList;
if (isBigBed(database, rootTable, curTrack, ctLookupName))
fieldList = bigBedGetFields(rootTable, conn);
else if (isBamTable(rootTable))
fieldList = bamGetFields();
else if (isVcfTable(rootTable, NULL))
fieldList = vcfGetFields();
else
{
char *table = chromTable(conn, rootTable);
fieldList = sqlListFields(conn, table);
freez(&table);
}
showTableFieldsOnList(db, rootTable, asObj, fieldList, showItemRgb, withGetButton);
hFreeConn(&conn);
}
void makeDbOrderedCommaFieldList(struct sqlConnection *conn,
char *table, struct joinerDtf *dtfList, struct dyString *dy)
/* Assumes that dtfList all points to same table. This will return
* a comma-separated field list in the same order as the fields are
* in database. */
{
char *split = chromTable(conn, table);
struct slName *fieldList = sqlListFields(conn, split);
makeOrderedCommaFieldList(fieldList, dtfList, dy);
slFreeList(&fieldList);
freez(&split);
}
long long gapsInRegion(struct sqlConnection *conn, struct region *regionList,
int limit)
/* Return count of gaps in all regions to limit number of regions,
* limit=0 == no limit, do them all
*/
{
long long gapBases = 0;
char *splitTable = chromTable(conn, "gap");
int regionCount = 0;
if (sqlTableExists(conn, splitTable))
{
struct region *region;
for (region = regionList;
(region != NULL) && (!(limit && (regionCount >= limit)));
region = region->next, ++regionCount)
{
int rowOffset;
char **row;
struct agpGap gap;
struct sqlResult *sr = hRangeQuery(conn, "gap",
region->chrom, region->start, region->end,
NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
agpGapStaticLoad(row + rowOffset, &gap);
if (gap.chromStart < region->start) gap.chromStart = region->start;
if (gap.chromEnd > region->end) gap.chromEnd = region->end;
gapBases += gap.chromEnd - gap.chromStart;
}
sqlFreeResult(&sr);
}
}
freez(&splitTable);
return gapBases;
}
static void filterControlsForTableDb(char *db, char *rootTable)
/* Put up filter controls for a single database table. */
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(db))
conn = hAllocConn(db);
char *table = chromTable(conn, rootTable);
struct trackDb *tdb = findTdbForTable(db, curTrack, rootTable, ctLookupName);
boolean isSmallWig = isWiggle(db, table);
boolean isBigWig = tdb ? tdbIsBigWig(tdb) : isBigWigTable(table);
boolean isWig = isSmallWig || isBigWig;
boolean isBedGr = tdb ? tdbIsBedGraph(tdb) : isBedGraph(rootTable);
boolean isBb = tdb ? tdbIsBigBed(tdb) : isBigBed(database, table, curTrack, ctLookupName);
boolean isBam = tdb ? tdbIsBam(tdb) : isBamTable(rootTable);
boolean isVcf = tdb ? tdbIsVcf(tdb) : isVcfTable(rootTable, NULL);
int bedGraphColumn = 5; /* default score column */
if (isBedGr)
{
int wordCount;
char *words[8];
char *typeLine = cloneString(tdb->type);
wordCount = chopLine(typeLine,words);
if (wordCount > 1)
bedGraphColumn = sqlUnsigned(words[1]);
freez(&typeLine);
}
if (isWig)
{
hPrintf("<TABLE BORDER=0>\n");
if ((tdb != NULL) && (tdb->type != NULL))
{
double min, max;
wiggleMinMax(tdb,&min,&max);
numericFilterWithLimits(db, rootTable, filterDataValueVar,filterDataValueVar,min,max,"");
hPrintf("<TR><TD COLSPAN=3 ALIGN=RIGHT> (dataValue range: [%g:%g]) "
"</TD></TR></TABLE>\n", min, max);
}
else
{
numericFilter(db, rootTable, filterDataValueVar,filterDataValueVar, "");
hPrintf("</TABLE>\n");
}
}
else
{
struct sqlFieldType *ftList;
if (isBb)
ftList = bigBedListFieldsAndTypes(tdb, conn);
else if (isBam)
ftList = bamListFieldsAndTypes();
else if (isVcf)
ftList = vcfListFieldsAndTypes();
else
ftList = sqlListFieldsAndTypes(conn, table);
printSqlFieldListAsControlTable(ftList, db, rootTable, tdb, isBedGr);
}
/* Printf free-form query row. */
if (!(isWig||isBedGr||isBam||isVcf))
{
char *name;
hPrintf("<TABLE BORDER=0><TR><TD>\n");
name = filterFieldVarName(db, rootTable, "", filterRawLogicVar);
cgiMakeDropList(name, logOpMenu, logOpMenuSize,
cartUsualString(cart, name, logOpMenu[0]));
hPrintf(" Free-form query: ");
name = filterFieldVarName(db, rootTable, "", filterRawQueryVar);
char *val = cartUsualString(cart, name, "");
// escape double quotes to avoid HTML parse trouble in the text input.
val = htmlEncodeText(val, FALSE);
cgiMakeTextVar(name, val, 50);
hPrintf("</TD></TR></TABLE>\n");
}
if (isWig||isBedGr||isBam||isVcf)
{
char *name;
hPrintf("<TABLE BORDER=0><TR><TD> Limit data output to: \n");
name = filterFieldVarName(db, rootTable, "_", filterMaxOutputVar);
cgiMakeDropList(name, maxOutMenu, maxOutMenuSize,
cartUsualString(cart, name, maxOutMenu[0]));
hPrintf(" lines</TD></TR></TABLE>\n");
}
freez(&table);
hFreeConn(&conn);
hPrintf("<BR>\n");
cgiMakeButton(hgtaDoFilterSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
}
