static struct mappingInfo *mappingInfoNew(struct sqlConnection *conn,
char *tbl, char *mappedId)
/* load mapping info for a mapped gene */
{
struct mappingInfo *mi;
int preLen;
char *suffix = containsStringNoCase(tbl,"Info");
int suffixLen = 4;
AllocVar(mi);
if (startsWith("retroAnc", tbl))
safef(mi->tblPre, sizeof(mi->tblPre), "retroAnc");
else if (startsWith("retroOld", tbl))
safef(mi->tblPre, sizeof(mi->tblPre), "retroOld");
else if (startsWith("retro", tbl))
safef(mi->tblPre, sizeof(mi->tblPre), "retro");
else
{
safef(mi->tblPre, sizeof(mi->tblPre), "ucsc");
suffix = containsStringNoCase(tbl,"Ali");
suffixLen = 3;
}
if (suffix != NULL)
{
suffix +=suffixLen;
safef(mi->suffix,ID_BUFSZ,"%s",suffix);
}
preLen = strlen(mi->tblPre);
if (startsWith("retroAugust", tbl))
safef(mi->geneSet, sizeof(mi->geneSet), "August");
else if (startsWith("retro", tbl))
safef(mi->geneSet, sizeof(mi->geneSet), "Mrna");
else
safef(mi->geneSet, sizeof(mi->geneSet), "Retro");
if (suffix != NULL && strlen(suffix) > 0)
mi->pg = sqlQueryObjs(conn, (sqlLoadFunc)ucscRetroInfoLoad, sqlQueryMust|sqlQuerySingle,
"select * from %s%sInfo%s where name='%s'", mi->tblPre, mi->geneSet, suffix,
mappedId);
else
{
mi->pg = sqlQueryObjs(conn, (sqlLoadFunc)ucscRetroInfoLoad, sqlQueryMust|sqlQuerySingle,
"select * from %s%sInfo where name='%s'", mi->tblPre, mi->geneSet,
mappedId);
}
parseSrcId(mi);
getGenbankInfo(conn, mi);
return mi;
}
static void chimeraxGen(struct sqlConnection *conn,
char *pdbId, char *where,
char *primarySnpId,
char *outName)
/* Generate a chimerax file for the given PDB, optionally coloring
* primarySnpId differently. The where arguments specifies which entries to
* obtain from the lsSnpPdb table.
*/
{
FILE *xfh = chimeraxBegin(outName);
fprintf(xfh, "\ndisplayPdb(\"%s\", (", pdbId);
struct lsSnpPdb *pdbSnp, *pdbSnps = NULL;
if (sqlTableExists(conn, "lsSnpPdb"))
pdbSnps = sqlQueryObjs(conn, (sqlLoadFunc)lsSnpPdbLoad, sqlQueryMulti,
"SELECT * FROM lsSnpPdb WHERE %-s", where);
for (pdbSnp = pdbSnps; pdbSnp != NULL; pdbSnp = pdbSnp->next)
prSnp(xfh, pdbSnp, primarySnpId);
lsSnpPdbFreeList(&pdbSnps);
fprintf(xfh, "))\n");
chimeraxEnd(&xfh);
}
struct transMapGene *transMapGeneQuery(struct sqlConnection *geneConn,
char *table, char *srcDb, char *srcId)
/* load a single transMapSrc object for an srcDb and srcId from a table,
* or return NULL if not found */
{
/* geneId field was added after original table definition. Return empty string
* in query for legacy tables. */
if (sqlFieldIndex(geneConn, table, "geneId") >= 0)
return sqlQueryObjs(geneConn, (sqlLoadFunc)transMapGeneLoad,
sqlQuerySingle,
"SELECT %-s FROM %s WHERE (db=\"%s\") and (id = \"%s\")",
transMapGeneCommaSepFieldNames, table, srcDb, srcId);
else
return sqlQueryObjs(geneConn, (sqlLoadFunc)transMapGeneLoad,
sqlQuerySingle,
"SELECT %-s,\"\" FROM %s WHERE (db=\"%s\") and (id = \"%s\")",
transMapGeneCommaSepFieldNames4, table, srcDb, srcId);
}
struct transMapSrc *transMapSrcQuery(struct sqlConnection *srcConn,
char *table, char *srcDb, char *srcId)
/* load a single transMapSrc object for an srcDb and srcId from a table,
* or error if not found */
{
return sqlQueryObjs(srcConn, (sqlLoadFunc)transMapSrcLoad,
sqlQueryMust|sqlQuerySingle,
"SELECT * FROM %s WHERE (db=\"%s\") and (id = \"%s\")",
table, srcDb, srcId);
}
struct transMapGene *transMapGeneQuery(struct sqlConnection *geneConn,
char *table, char *srcDb, char *srcId)
/* load a single transMapSrc object for an srcDb and srcId from a table,
* or return NULL if not found */
{
return sqlQueryObjs(geneConn, (sqlLoadFunc)transMapGeneLoad,
sqlQuerySingle,
"SELECT * FROM %s WHERE (db=\"%s\") and (id = \"%s\")",
table, srcDb, srcId);
}
static void prMiscDiffs(struct sqlConnection *conn, char *acc)
/* print any gbMiscDiff rows for the accession */
{
struct gbMiscDiff *gmds = NULL, *gmd;
if (sqlTableExists(conn, "gbMiscDiff"))
gmds = sqlQueryObjs(conn, (sqlLoadFunc)gbMiscDiffLoad, sqlQueryMulti,
"select * from gbMiscDiff where acc=\"%s\"", acc);
webNewSection("NCBI Clone Validation");
if (gmds != NULL)
{
unsigned miscDiffFlds = getMiscDiffFields(gmds);
webPrintLinkTableStart();
prMiscDiffHdr(miscDiffFlds);
for (gmd = gmds; gmd != NULL; gmd = gmd->next)
prMiscDiff(gmd, miscDiffFlds);
webPrintLinkTableEnd();
}
else
printf("<EM>No clone discrepancies annotated</EM><BR><BR>\n");
}
static void writePublicNotesHtml(struct sqlConnection *conn, char *ccdsId)
/* write public notes if available */
{
struct ccdsNotes *ccdsNotes = NULL;
if (sqlTableExists(conn, "ccdsNotes"))
ccdsNotes = sqlQueryObjs(conn, (sqlLoadFunc)ccdsNotesLoad, sqlQueryMulti,
"select * from ccdsNotes where ccds = \"%s\" order by createDate", ccdsId);
if (ccdsNotes != NULL)
{
htmlHorizontalLine();
printf("<H3>Annotator Notes</H3>\n");
printf("<TABLE class=\"hgcCcds\">\n");
printf("<THEAD>\n");
printf("<TR><TH>Date<TH>Note</TR>\n");
printf("</THEAD><TBODY>\n");
struct ccdsNotes *note;
for (note = ccdsNotes; note != NULL; note = note->next)
printf("<TR><TD style=\"white-space: nowrap;\">%s<TD>%s</TR>", note->createDate, note->note);
printf("</TBODY></TABLE>\n");
}
}
