8ea322638d617b5598935df2dc7daf7199064b71
hiram
Wed Feb 10 11:46:16 2016 -0800
code review clean up refs #16795
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index befa85c..5caabba 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -11372,54 +11372,53 @@
printf("%s
\n", summary);
freeMem(summary);
}
htmlHorizontalLine();
return rl;
}
void doNcbiRefSeq(struct trackDb *tdb, char *itemName)
/* Process click on a NCBI RefSeq gene. */
{
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr;
char **row;
char query[256];
-char *sqlRnaName = itemName;
struct ncbiRefSeqLink *nrl;
struct dyString *dy = newDyString(1024);
dyStringPrintf(dy, "%s - %s ", tdb->longLabel, itemName);
struct trackVersion *trackVersion = getTrackVersion(database, "ncbiRefSeq");
if ((trackVersion != NULL) && !isEmpty(trackVersion->version))
dyStringPrintf(dy, "- Release %s\n", trackVersion->version);
cartWebStart(cart, database, "%s", dy->string);
/* get refLink entry */
-sqlSafef(query, sizeof(query), "select * from ncbiRefSeqLink where id = '%s'", sqlRnaName);
+sqlSafef(query, sizeof(query), "select * from ncbiRefSeqLink where id = '%s'", itemName);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) == NULL)
errAbort("Couldn't find %s in ncbiRefSeqLink table.", itemName);
nrl = ncbiRefSeqLinkLoad(row);
sqlFreeResult(&sr);
printf("RefSeq Gene %s
\n", nrl->name);
-printf("RefSeq: RefSeq: %s", nrl->id);
printf(" Status: %s
\n", nrl->status);
printf("Description: %s
\n", nrl->product);
if (differentWord(nrl->gbkey, "n/a"))
{
printf("Molecule type: %s
\n", nrl->gbkey);
}
if (differentWord(nrl->pseudo, "n/a"))
{
printf("Pseudogene: %s
\n", nrl->pseudo);
}
if (differentWord(nrl->source, "n/a"))
{
printf("Source: %s
\n", nrl->source);
}
if (differentWord(nrl->gene_biotype, "n/a"))
@@ -11428,91 +11427,90 @@
}
if (differentWord(nrl->gene_synonym, "n/a"))
{
printf("Synonyms: %s
\n", nrl->gene_synonym);
}
if (differentWord(nrl->ncrna_class, "n/a"))
{
printf("ncRNA class: %s
\n", nrl->ncrna_class);
}
if (differentWord(nrl->note, "n/a"))
{
printf("Other notes: %s
\n", nrl->note);
}
if (differentWord(nrl->omimId, "n/a"))
{
- printf("OMIM: OMIM: %s
\n", nrl->omimId);
}
if (differentWord(nrl->mrnaAcc, "n/a") && differentWord(nrl->mrnaAcc,nrl->id))
{
printf("mRNA: ");
- printf("", nrl->mrnaAcc);
+ printf("", nrl->mrnaAcc);
printf("%s
\n", nrl->mrnaAcc);
}
if (differentWord(nrl->genbank, "n/a") && differentWord(nrl->genbank,nrl->id))
{
printf("Genbank: ");
- printf("", nrl->genbank);
+ printf("", nrl->genbank);
printf("%s
\n", nrl->genbank);
}
if (differentWord(nrl->protAcc, "n/a"))
{
printf("Protein: ");
- printf("", nrl->protAcc);
+ printf("", nrl->protAcc);
printf("%s
\n", nrl->protAcc);
}
if (differentWord(nrl->hgnc, "n/a"))
{
printf("HGNC: ");
- printf("", nrl->hgnc);
+ printf("", nrl->hgnc);
printf("%s
\n", nrl->hgnc);
}
if (differentWord(nrl->locusLinkId, "n/a"))
{
printf("Entrez Gene: ");
- printf("",
+ printf("",
nrl->locusLinkId);
printf("%s
\n", nrl->locusLinkId);
}
if (differentWord(nrl->name,"n/a"))
{
printGeneCards(nrl->name);
if (startsWith("hg", database))
{
printf("AceView: ");
- printf("",
+ printf("",
nrl->name);
printf("%s
\n", nrl->name);
}
}
if ((trackVersion != NULL) && !isEmpty(trackVersion->version))
{
- printf("Annotation Release: %s
", trackVersion->comment, trackVersion->version);
+ printf("Annotation Release: %s
", trackVersion->comment, trackVersion->version);
}
htmlHorizontalLine();
if (differentWord("n/a", nrl->description))
{
printf("Summary of %s
\n%s
\n", nrl->name, nrl->description);
htmlHorizontalLine();
}
-
struct psl *pslList = getAlignments(conn, "ncbiRefSeqPsl", itemName);
// if the itemName isn't found, it might be found as the nrl->mrnaAcc
if (! pslList)
pslList = getAlignments(conn, "ncbiRefSeqPsl", nrl->mrnaAcc);
if (pslList)
{
int start = cartInt(cart, "o");
printf("mRNA/Genomic Alignments
");
printAlignments(pslList, start, "ncbiRefSeqPsl", "ncbiRefSeqPsl", itemName);
}
else
{
printf ("there is NO alignment for %s
\n", itemName);
}