, which is
// not a real MySQL db). Use the conn's db for hTableExists/startsWith
// checks so we don't abort on "Unknown database".
char *srcDb = sqlGetDatabase(conn);
int ver = gbCdnaGetVersion(conn, rl->mrnaAcc);
char *cdsCmpl = NULL;
printf("\n");
@@ -13173,31 +13186,31 @@
if (stat != NULL)
printf(" Status: %s", stat);
}
puts("
");
char *desc = gbCdnaGetDescription(conn, rl->mrnaAcc);
if (desc != NULL)
{
printf("Description: ");
htmlTextOut(desc);
printf("
\n");
}
if (isXeno)
prRefGeneXenoInfo(conn, rl);
else
- printCcdsForSrcDb(conn, rl->mrnaAcc);
+ printCcdsForSrcDb(conn, tdb, rl->mrnaAcc);
cdsCmpl = getRefSeqCdsCompleteness(conn, sqlRnaName);
if (cdsCmpl != NULL)
{
printf("CDS: %s
", cdsCmpl);
}
if (rl->omimId != 0)
{
printf("OMIM: omimId);
printf("\" TARGET=_blank>%d
\n", rl->omimId);
}
if (rl->locusLinkId != 0)
{
printf("Entrez Gene: ");
@@ -13280,61 +13293,61 @@
}
sqlFreeResult(&sr);
}
if (startsWith("hg", srcDb))
{
printf("\n");
printf("AceView: ");
printf("",
rl->name);
printf("%s
\n", rl->name);
}
prGRShortRefGene(conn, rl->name);
}
-void prKnownGeneInfo(struct sqlConnection *conn, char *rnaName,
+void prKnownGeneInfo(struct sqlConnection *conn, struct trackDb *tdb, char *rnaName,
char *sqlRnaName, struct refLink *rl)
/* print basic details information and links for a Known Gene */
{
struct sqlResult *sr;
char **row;
char query[256];
int ver = gbCdnaGetVersion(conn, rl->mrnaAcc);
char *cdsCmpl = NULL;
printf(" | \n");
printf("Known Gene %s\n", rl->name);
printf("KnownGene: mrnaAcc);
if (ver > 0)
printf("\" TARGET=_blank>%s.%d", rl->mrnaAcc, ver);
else
printf("\" TARGET=_blank>%s", rl->mrnaAcc);
fflush(stdout);
puts("
");
char *desc = gbCdnaGetDescription(conn, rl->mrnaAcc);
if (desc != NULL)
{
printf("Description: ");
htmlTextOut(desc);
printf("
\n");
}
-printCcdsForSrcDb(conn, rl->mrnaAcc);
+printCcdsForSrcDb(conn, tdb, rl->mrnaAcc);
cdsCmpl = getRefSeqCdsCompleteness(conn, sqlRnaName);
if (cdsCmpl != NULL)
{
printf("CDS: %s
", cdsCmpl);
}
if (rl->omimId != 0)
{
printf("OMIM: omimId);
printf("\" TARGET=_blank>%d
\n", rl->omimId);
}
if (rl->locusLinkId != 0)
{
printf("Entrez Gene: ");
@@ -13398,31 +13411,31 @@
errAbort("Couldn't find %s in %s table - this accession may no longer be available.",
rnaName, refLinkTable);
rl = refLinkLoad(row);
sqlFreeResult(&sr);
}
else
{
rlR.name = strdup(kgId);
rlR.mrnaAcc = strdup(kgId);
rlR.locusLinkId = 0;
rl = &rlR;
}
cartWebStart(cart, database, "Known Gene");
printf("\n\n");
-prKnownGeneInfo(conn, rnaName, sqlRnaName, rl);
+prKnownGeneInfo(conn, tdb, rnaName, sqlRnaName, rl);
printf(" \n \n");
/* optional summary text */
summary = getRefSeqSummary(conn, kgId);
if (summary != NULL)
{
htmlHorizontalLine();
printf("Summary of %s\n", kgId);
printf("%s \n", summary);
freeMem(summary);
}
htmlHorizontalLine();
/* print alignments that track was based on */
@@ -13489,31 +13502,31 @@
else
{
sqlSafef(query, sizeof(query), "select * from %s r, %s g where mrnaAcc = '%s' and r.mrnaAcc=g.acc and g.version='%s'", refLinkTable,gbCdnaInfoTable, sqlRnaName, version);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) == NULL)
{
sqlFreeResult(&sr);
return NULL;
}
rl = refLinkLoad(row);
sqlFreeResult(&sr);
}
/* print the first section with info */
printf("\n\n");
-prRefGeneInfo(conn, rnaName, sqlRnaName, rl, isXeno);
+prRefGeneInfo(conn, tdb, rnaName, sqlRnaName, rl, isXeno);
addGeneExtra(rl->name); /* adds columns if extra info is available */
printf(" \n \n");
/* optional summary text */
summary = getRefSeqSummary(conn, sqlRnaName);
if (summary != NULL)
{
htmlHorizontalLine();
printf("Summary of %s\n", rl->name);
printf("%s \n", summary);
freeMem(summary);
}
htmlHorizontalLine();
|