src/hg/hgc/hgc.c 1.1573
1.1573 2009/09/23 18:42:19 angie
Fixed compiler warnings from gcc 4.3.3, mostly about system calls whose return values weren't checked and non-literal format strings with no args.
Index: src/hg/hgc/hgc.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/hgc.c,v
retrieving revision 1.1572
retrieving revision 1.1573
diff -b -B -U 4 -r1.1572 -r1.1573
--- src/hg/hgc/hgc.c 21 Sep 2009 23:50:42 -0000 1.1572
+++ src/hg/hgc/hgc.c 23 Sep 2009 18:42:19 -0000 1.1573
@@ -3463,9 +3463,9 @@
genericHeader(tdb, headerItem);
printCustomUrl(tdb, itemForUrl, item == itemForUrl);
if (plus != NULL)
{
- printf(plus);
+ fputs(plus, stdout);
}
if (wordCount > 0)
{
@@ -5286,9 +5286,9 @@
table = "all_mrna";
}
/* Print non-sequence info. */
-cartWebStart(cart, database, acc);
+cartWebStart(cart, database, "%s", acc);
printRnaSpecs(tdb, acc, pslList);
/* Get alignment info. */
@@ -5404,9 +5404,9 @@
void doZfishRHmap(struct trackDb *tdb, char *itemName)
/* Put up Radiation Hybrid map information for Zebrafish */
{
char *dupe, *type, *words[16];
-char title[256], query[256];
+char query[256];
struct sqlResult *sr = NULL;
char **row = NULL;
struct rhMapZfishInfo *rhInfo = NULL;
int wordCount;
@@ -5418,10 +5418,8 @@
dupe = cloneString(tdb->type);
wordCount = chopLine(dupe, words);
genericHeader(tdb, itemName);
-/* Print non-sequence info */
-cartWebStart(cart, database, title);
/* Print out RH map information if available */
if (rhMapInfoExists)
@@ -5840,9 +5838,9 @@
char *secondAcc, *secondAccVer;
char *tmpString;
int first;
-cartWebStart(cart, database, fragName);
+cartWebStart(cart, database, "%s", fragName);
hFindSplitTable(database, seqName, track, splitTable, &hasBin);
sprintf(query, "select * from %s where frag = '%s' and chromStart = %d",
splitTable, fragName, start);
sr = sqlMustGetResult(conn, query);
@@ -6109,9 +6107,9 @@
char **row;
struct clonePos *clone;
int fragCount;
-cartWebStart(cart, database, cloneName);
+cartWebStart(cart, database, "%s", cloneName);
sprintf(query, "select * from %s where name = '%s'", track, cloneName);
selectOneRow(conn, track, query, &sr, &row);
clone = clonePosLoad(row);
sqlFreeResult(&sr);
@@ -7978,10 +7976,9 @@
char supfamURL[512];
printf("<B>Superfamily Link: </B>");
safef(supfamURL, sizeof(supfamURL), "<A HREF=\"%s%s;seqid=%s\" target=_blank>",
tdbSf->url, genomeStr, proteinID);
- printf("%s", supfamURL);
- printf("%s</A><BR>\n", proteinID);
+ printf("%s%s</A><BR>\n", supfamURL, proteinID);
}
}
#endif
}
@@ -8306,10 +8303,9 @@
printf("<B>Superfamily Link: </B>");
sprintf(supfamURL, "<A HREF=\"%s%s;seqid=%s\" target=_blank>",
url, genomeStr, itemName);
- printf("%s", supfamURL);
- printf("%s</A><BR><BR>\n", itemName);
+ printf("%s%s</A><BR><BR>\n", supfamURL, itemName);
}
}
void doSuperfamily(struct trackDb *tdb, char *item, char *itemForUrl)
@@ -8388,10 +8384,9 @@
struct lineFile *lf;
char *line;
int lineSize;
-safef(query, sizeof(query), "%s (%s)", tdb->longLabel, avName);
-cartWebStart(cart, database, query);
+cartWebStart(cart, database, "%s (%s)", tdb->longLabel, avName);
safef(query, sizeof(query), "select * from omimAv where name = '%s'", avName);
sr = sqlGetResult(conn, query);
@@ -9157,9 +9152,9 @@
/* Make sure to escape single quotes for DB parseability */
if (strchr(rnaName, '\''))
sqlRnaName = replaceChars(rnaName, "'", "''");
-cartWebStart(cart, database, tdb->longLabel);
+cartWebStart(cart, database, "%s", tdb->longLabel);
safef(query, sizeof(query), "select * from refLink where mrnaAcc = '%s'", sqlRnaName);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) == NULL)
@@ -10134,9 +10129,9 @@
/* print header */
genericHeader(tdb, acc);
/* Print non-sequence info. */
-cartWebStart(cart, database, acc);
+cartWebStart(cart, database, "%s", acc);
safef(where, sizeof(where), "name = '%s'", acc);
sr = hRangeQuery(conn, track, chrom, start, end, where, &rowOffset);
@@ -11012,9 +11007,9 @@
/* Print heading info including link to NCBI. */
if (tiNum != NULL)
++tiNum;
-cartWebStart(cart, database, itemName);
+cartWebStart(cart, database, "%s", itemName);
printf("<H1>Information on Mouse %s %s</H1>",
(tiNum == NULL ? "Contig" : "Read"), itemName);
/* Print links to NCBI and to sequence. */
@@ -11156,9 +11151,9 @@
char otherString[256];
char *cgiItem = cgiEncode(item);
char *thisOrg = hOrganism(database);
-cartWebStart(cart, database, tdb->longLabel);
+cartWebStart(cart, database, "%s", tdb->longLabel);
printf("<B>%s position:</B> <a target=\"_blank\" href=\"%s?db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\n",
otherOrg, hgTracksName(), otherDb, psl->qName, psl->qStart+1, psl->qEnd,
psl->qName, psl->qStart+1, psl->qEnd);
printf("<B>%s size:</B> %d<BR>\n", otherOrg, psl->qEnd - psl->qStart);
@@ -11195,9 +11190,9 @@
char otherString[256];
char *cgiItem = cgiEncode(item);
char *thisOrg = hOrganism(database);
-cartWebStart(cart, database, tdb->longLabel);
+cartWebStart(cart, database, "%s", tdb->longLabel);
psl = loadPslFromRangePair(tdb->tableName, item);
printf("<B>%s position:</B> <a target=\"_blank\" href=\"%s?db=%s&position=%s%%3A%d-%d\">%s:%d-%d</a><BR>\n",
otherOrg, hgTracksName(), otherDb, psl->qName, psl->qStart+1, psl->qEnd,
psl->qName, psl->qStart+1, psl->qEnd);
@@ -11240,9 +11235,9 @@
char otherString[256];
char *cgiItem = cgiEncode(item);
char *thisOrg = hOrganism(database);
-cartWebStart(cart, database, tdb->longLabel);
+cartWebStart(cart, database, "%s", tdb->longLabel);
psl = loadPslFromRangePair(tdb->tableName, item);
printf("<B>%s position:</B> %s:%d-%d<BR>\n", otherOrg,
psl->qName, psl->qStart+1, psl->qEnd);
printf("<B>%s size:</B> %d<BR>\n", otherOrg, psl->qEnd - psl->qStart);
@@ -11274,9 +11269,9 @@
char anotherString[256];
char *cgiItem = cgiEncode(item);
char *thisOrg = hOrganism(database);
-cartWebStart(cart, database, tdb->longLabel);
+cartWebStart(cart, database, "%s", tdb->longLabel);
psl = loadPslFromRangePair(tdb->tableName, item);
printf("<B>%s position:</B> %s:%d-%d<BR>\n", otherOrg,
psl->qName, psl->qStart+1, psl->qEnd);
printf("<B>%s size:</B> %d<BR>\n", otherOrg, psl->qEnd - psl->qStart);
@@ -11623,9 +11618,9 @@
return;
}
}
freeMem(typeLine);
-cartWebStart(cart, database, itemName);
+cartWebStart(cart, database, "%s", itemName);
printPosOnChrom(chrom,start,end,NULL,FALSE,NULL);
printf("<H1>Information on %s Sequence %s</H1>", otherGenome, itemName);
printf("Get ");
@@ -11666,9 +11661,9 @@
struct psl *pslList = NULL, *psl = NULL;
boolean hasBin = TRUE;
char *table = "refFullAli"; /* Table with the pertinent PSL data */
-cartWebStart(cart, database, itemName);
+cartWebStart(cart, database, "%s", itemName);
printf("<H1>Information on DBTSS Sequence %s</H1>", itemName);
printf("Get ");
printf("<A HREF=\"%s&g=htcExtSeq&c=%s&l=%d&r=%d&i=%s\">",
hgcPathAndSettings(), seqName, winStart, winEnd, itemName);
@@ -11834,9 +11829,9 @@
sqlMarker = replaceChars(marker, "'", "''");
/* Print out non-sequence info */
sprintf(title, "STS Marker %s", marker);
-cartWebStart(cart, database, title);
+cartWebStart(cart, database, "%s", title);
/* Find the instance of the object in the bed table */
sprintf(query, "SELECT * FROM %s WHERE name = '%s' "
"AND chrom = '%s' AND chromStart = %d "
@@ -12155,9 +12150,9 @@
int pslStart;
/* Print out non-sequence info */
sprintf(title, "STS Marker %s", marker);
-cartWebStart(cart, database, title);
+cartWebStart(cart, database, "%s", title);
/* Find the instance of the object in the bed table */
sprintf(query, "SELECT * FROM %s WHERE name = '%s' "
"AND chrom = '%s' AND chromStart = %d "
@@ -12287,9 +12282,9 @@
/* Print out non-sequence info */
sprintf(title, "STS Marker %s\n", marker);
/* sprintf(title, "STS Marker <A HREF=\"http://www.informatics.jax.org/searches/marker_report.cgi?string\%%3AmousemarkerID=%s\" TARGET=_BLANK>%s</A>\n", marker, marker); */
-cartWebStart(cart, database, title);
+cartWebStart(cart, database, "%s", title);
/* Find the instance of the object in the bed table */
sprintf(query, "SELECT * FROM %s WHERE name = '%s' "
"AND chrom = '%s' AND chromStart = %d "
@@ -12464,9 +12459,9 @@
boolean hasBin = FALSE;
/* Print out non-sequence info */
sprintf(title, "STS Marker %s", marker);
-cartWebStart(cart, database, title);
+cartWebStart(cart, database, "%s", title);
/* Find the instance of the object in the bed table */
safef(query, sizeof(query), "name = '%s'", marker);
sr = hRangeQuery(conn, table, seqName, start, end, query, &hasBin);
@@ -12624,9 +12619,9 @@
struct fishClones *fc;
int i;
/* Print out non-sequence info */
-cartWebStart(cart, database, clone);
+cartWebStart(cart, database, "%s", clone);
/* Find the instance of the object in the bed table */
sprintf(query, "SELECT * FROM fishClones WHERE name = '%s' "
@@ -16188,9 +16183,9 @@
table = track;
}
/* Print out non-sequence info */
-cartWebStart(cart, database, title);
+cartWebStart(cart, database, "%s", title);
/* Find the instance of the object in the bed table */
sprintf(query, "SELECT * FROM %s WHERE name = '%s' "
"AND chrom = '%s' AND chromStart = %d "
@@ -16413,9 +16408,9 @@
struct sqlResult *sr;
char **row;
int celeraVersion = 0;
int i = 0;
-cartWebStart(cart, database, tdb->longLabel);
+cartWebStart(cart, database, "%s", tdb->longLabel);
if (sameString(database, "hg15"))
celeraVersion = 3;
else
@@ -16489,24 +16484,24 @@
"(No\\.)?([0-9]+[.,])?[a-zA-Z0-9_]+:[0-9]+ but got %s", origPos);
if (wordCount == 3)
{
*retID = sqlUnsigned(words[0]);
- safef(retChrom, 64, words[1]);
+ safecpy(retChrom, 64, words[1]);
*retPos = sqlUnsigned(words[2]);
}
else
{
*retID = -1;
- safef(retChrom, 64, words[0]);
+ safecpy(retChrom, 64, words[0]);
*retPos = sqlUnsigned(words[1]);
}
}
void doGenomicSuperDups(struct trackDb *tdb, char *dupName)
/* Handle click on genomic dup track. */
{
-cartWebStart(cart, database, tdb->longLabel);
+cartWebStart(cart, database, "%s", tdb->longLabel);
if (cgiVarExists("o"))
{
char *track = tdb->tableName;
@@ -16604,9 +16599,9 @@
struct sqlResult *sr = NULL;
char **row;
/* Print out non-sequence info */
-cartWebStart(cart, database, tissue);
+cartWebStart(cart, database, "%s", tissue);
/* Print general range info */
printf("<H2>UCSF Comparative Genomic Hybridizations - %s</H2>\n", tissue);
printf("<P><HR ALIGN=\"CENTER\"></P>\n<TABLE>\n");
@@ -16658,9 +16653,9 @@
struct mcnBreakpoints *mcnRecord;
/* Print out non-sequence info */
sprintf(title, "MCN Breakpoints - %s",name);
-cartWebStart(cart, database, title);
+cartWebStart(cart, database, "%s", title);
/* Print general range info */
/*printf("<H2>MCN Breakpoints - %s</H2>\n", name);
printf("<P><HR ALIGN=\"CENTER\"></P>");*/
@@ -18600,9 +18595,9 @@
char fullTable[64];
boolean hasBin = FALSE;
char query[1024];
-cartWebStart(cart, database, tdb->longLabel);
+cartWebStart(cart, database, "%s", tdb->longLabel);
genericHeader(tdb, item);
hFindSplitTable(database, seqName, tdb->tableName, fullTable, &hasBin);
safef(query, sizeof(query),
"select * from %s where chrom = '%s' and chromStart = %d and name = '%s'",
@@ -18630,9 +18625,9 @@
char fullTable[64];
boolean hasBin = FALSE;
char query[1024];
-cartWebStart(cart, database, tdb->longLabel);
+cartWebStart(cart, database, "%s", tdb->longLabel);
genericHeader(tdb, item);
hFindSplitTable(database, seqName, tdb->tableName, fullTable, &hasBin);
safef(query, sizeof(query),
"select * from %s where chrom = '%s' and chromStart = %d and name = '%s'",
@@ -19991,9 +19986,9 @@
{
char url[256];
char *accFlag = hashFindVal(thisLink, "acc");
if (accFlag == NULL)
- safef(url, sizeof(url), linktype);
+ safecpy(url, sizeof(url), linktype);
else
{
char *accNum = hashFindVal(thisLink, "accNum");
if (accNum == NULL)
@@ -20887,9 +20882,9 @@
char *chr, *name;
unsigned int chromStart, chromEnd;
boolean blastzAln;
-cartWebStart(cart, database, itemName);
+cartWebStart(cart, database, "%s", itemName);
sprintf(query, "select * from %s where name = '%s'", track, itemName);
selectOneRow(conn, track, query, &sr, &row);
chr = cloneString(row[0]);
chromStart = sqlUnsigned(row[1]);
@@ -22503,9 +22498,9 @@
genericClickHandler(tdb, item, NULL);
}
else
{
- cartWebStart(cart, database, track);
+ cartWebStart(cart, database, "%s", track);
printf("Sorry, clicking there doesn't do anything yet (%s).", track);
}
if (didCartHtmlStart)
cartHtmlEnd();