\n");
if (motif != NULL)
{
@@ -160,31 +160,31 @@
{
int start = cartInt(cart, "o");
struct dnaSeq *seq = NULL;
struct dnaMotif *motif = loadDnaMotif(item, motifTable);
char *table = tdb->table;
int rowOffset = hOffsetPastBin(database, seqName, table);
char query[256];
struct sqlResult *sr;
char **row;
struct bed *hit = NULL;
struct sqlConnection *conn = hAllocConn(database);
cartWebStart(cart, database, "Regulatory Motif Info");
genericBedClick(conn, tdb, item, start, 6);
-sprintf(query,
+sqlSafef(query, sizeof query,
"select * from %s where name = '%s' and chrom = '%s' and chromStart = %d",
table, item, seqName, start);
sr = sqlGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
hit = bedLoadN(row + rowOffset, 6);
sqlFreeResult(&sr);
if (hit != NULL)
{
seq = hDnaFromSeq(database, hit->chrom, hit->chromStart, hit->chromEnd, dnaLower);
if (hit->strand[0] == '-')
reverseComplement(seq->dna, seq->size);
}
motifHitSection(seq, motif);
@@ -196,34 +196,34 @@
{
struct dyString *query = newDyString(256);
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr = NULL;
char **row;
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
char fullTable[64];
boolean hasBin = FALSE;
char *motifTable = "flyregMotif";
struct dnaMotif *motif = NULL;
boolean isVersion2 = sameString(tdb->table, "flyreg2");
genericHeader(tdb, item);
hFindSplitTable(database, seqName, tdb->table, fullTable, &hasBin);
-dyStringPrintf(query, "select * from %s where chrom = '%s' and ",
+sqlDyStringPrintf(query, "select * from %s where chrom = '%s' and ",
fullTable, seqName);
hAddBinToQuery(start, end, query);
-dyStringPrintf(query, "chromStart = %d and name = '%s'", start, item);
+sqlDyStringPrintf(query, "chromStart = %d and name = '%s'", start, item);
sr = sqlGetResult(conn, query->string);
if ((row = sqlNextRow(sr)) != NULL)
{
struct flyreg2 fr;
if (isVersion2)
flyreg2StaticLoad(row+hasBin, &fr);
else
flyregStaticLoad(row+hasBin, (struct flyreg *)(&fr));
printf("Factor: %s
\n", fr.name);
printf("Target: %s
\n", fr.target);
if (isVersion2)
printf("Footprint ID: %06d
\n", fr.fpid);
printf("PubMed ID: %d
\n", fr.pmid);
@@ -242,31 +242,31 @@
hFreeConn(&conn);
if (motif != NULL)
webNewSection(tdb->longLabel);
printTrackHtml(tdb);
}
static void wrapHgGeneLink(struct sqlConnection *conn, char *name,
char *label, char *geneTable)
/* Wrap label with link to hgGene if possible. */
{
char query[256];
struct sqlResult *sr;
char **row;
int rowOffset = hOffsetPastBin(database, seqName, "sgdGene");
-safef(query, sizeof(query),
+sqlSafef(query, sizeof(query),
"select * from %s where name = '%s'", geneTable, name);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *gp = genePredLoad(row+rowOffset);
printf("name);
printf("&hgg_chrom=%s", gp->chrom);
printf("&hgg_start=%d", gp->txStart);
printf("&hgg_end=%d", gp->txEnd);
printf("\">");
printf("%s", label);
printf("");
}
else
@@ -278,56 +278,56 @@
/* Print anchor to transRegCode details page. */
{
printf("name);
printf("&o=%d", trc->chromStart);
printf("&c=%s", trc->chrom);
printf("\">");
}
static void sacCerHgGeneLinkName(struct sqlConnection *conn, char *name)
/* Wrap link to hgGene if possible around yeast gene name. */
{
char query[256];
char *orf;
-safef(query, sizeof(query),
+sqlSafef(query, sizeof(query),
"select name from sgdToName where value = '%s'", name);
orf = sqlQuickString(conn, query);
if (orf != NULL)
wrapHgGeneLink(conn, orf, name, "sgdGene");
else
printf("%s", name);
freez(&orf);
}
void doTransRegCode(struct trackDb *tdb, char *item, char *motifTable)
/* Display detailed info on a transcriptional regulatory code item. */
{
struct dnaMotif *motif = loadDnaMotif(item, motifTable);
int start = cartInt(cart, "o");
struct dnaSeq *seq = NULL;
char *table = tdb->table;
int rowOffset = hOffsetPastBin(database, seqName, table);
char query[256];
struct sqlResult *sr;
char **row;
struct sqlConnection *conn = hAllocConn(database);
struct transRegCode *trc = NULL;
cartWebStart(cart, database, "Regulatory Code Info");
-sprintf(query,
+sqlSafef(query, sizeof query,
"select * from %s where name = '%s' and chrom = '%s' and chromStart = %d",
table, item, seqName, start);
sr = sqlGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
trc = transRegCodeLoad(row+rowOffset);
sqlFreeResult(&sr);
if (trc != NULL)
{
char strand[2];
seq = hDnaFromSeq(database, trc->chrom, trc->chromStart, trc->chromEnd, dnaLower);
if (seq->size != motif->columnCount)
{
printf("WARNING: seq->size = %d, motif->colCount=%d
\n",
@@ -480,31 +480,31 @@
printf("");
sacCerHgGeneLinkName(conn, tf->name);
printf(" | ");
/* Print stong and weak growth conditions. */
ipPrintInRange(tf->conditionList, 0.0, 0.002, boundHash);
ipPrintInRange(tf->conditionList, 0.002, 0.006, boundHash);
/* Grab list of all conditions tested from database and
* print out ones not in strong or weak as none. */
{
char query[256], **row;
struct sqlResult *sr;
boolean isFirst = TRUE;
boolean gotAny = FALSE;
- safef(query, sizeof(query),
+ sqlSafef(query, sizeof(query),
"select growthCondition from %s where name='%s'",
tfToConditionTable, tf->name);
sr = sqlGetResult(conn, query);
printf("");
while ((row = sqlNextRow(sr)) != NULL)
{
if (!hashLookup(boundHash, row[0]))
{
if (isFirst)
isFirst = FALSE;
else
printf(", ");
printf("%s", row[0]);
gotAny = TRUE;
}
@@ -544,59 +544,59 @@
}
printf(" | ");
}
printf("\n");
hashFree(&boundHash);
}
hTableEnd();
}
void growthConditionSection(struct sqlConnection *conn, char *conditionTable)
/* Print out growth condition information. */
{
struct sqlResult *sr;
char query[256], **row;
webNewSection("Description of Growth Conditions");
-safef(query, sizeof(query), "select * from %s order by name", conditionTable);
+sqlSafef(query, sizeof(query), "select * from %s order by name", conditionTable);
sr = sqlGetResult(conn, query);
printf("");
while ((row = sqlNextRow(sr)) != NULL)
{
struct growthCondition gc;
growthConditionStaticLoad(row, &gc);
printf("- ");
printf("", gc.name);
printf("%s - %s %s\n", gc.name, gc.shortLabel, gc.longLabel);
}
printf("
");
sqlFreeResult(&sr);
}
void doTransRegCodeProbe(struct trackDb *tdb, char *item,
char *codeTable, char *motifTable,
char *tfToConditionTable, char *conditionTable)
/* Display detailed info on a ChIP-chip probe from transRegCode experiments. */
{
char query[256];
struct sqlResult *sr;
char **row;
int rowOffset = hOffsetPastBin(database, seqName, tdb->table);
struct sqlConnection *conn = hAllocConn(database);
struct transRegCodeProbe *probe = NULL;
cartWebStart(cart, database, "ChIP-chip Probe Info");
-safef(query, sizeof(query), "select * from %s where name = '%s'",
+sqlSafef(query, sizeof(query), "select * from %s where name = '%s'",
tdb->table, item);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
probe = transRegCodeProbeLoad(row+rowOffset);
sqlFreeResult(&sr);
if (probe != NULL)
{
struct tfData *tfList = NULL, *tf;
struct hash *tfHash = newHash(0);
struct transRegCode *trc;
int i;
/* Print basic info. */
printf("Name: %s
\n", probe->name);
printPosOnChrom(probe->chrom, probe->chromStart, probe->chromEnd,