static void cgDrawItemsCt(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw chromosome graph for customTrack. */
{
cgDrawEither(tg, seqStart, seqEnd, hvg, xOff, yOff, width,
font, color, vis, trackDbRequiredSetting(tg->tdb, "binaryFile"));
}
void doPeakClusters(struct trackDb *tdb, char *item)
/* Display detailed info about a cluster of DNase peaks from other tracks. */
{
int start = cartInt(cart, "o");
char *table = tdb->table;
int rowOffset = hOffsetPastBin(database, seqName, table);
char query[256];
struct sqlResult *sr;
char **row;
struct bed *cluster = NULL;
struct sqlConnection *conn = hAllocConn(database);
cartWebStart(cart, database, "%s item details", tdb->shortLabel);
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)
cluster = bedLoadN(row+rowOffset, 5);
sqlFreeResult(&sr);
if (cluster != NULL)
{
/* Get list of subgroups to display */
char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay");
if (inputTableFieldDisplay != NULL)
{
struct slName *fieldList = stringToSlNames(inputTableFieldDisplay);
char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable");
/* Print out some information about the cluster overall. */
printf("<B>Items in Cluster:</B> %s of %d<BR>\n", cluster->name,
sqlRowCount(conn, sqlCheckIdentifier(inputTrackTable)));
printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score);
printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL);
/* In a new section put up list of hits. */
webNewSection("List of Items in Cluster");
webPrintLinkTableStart();
printClusterTableHeader(fieldList, FALSE, FALSE, TRUE);
printPeakClusterInfo(tdb, cart, conn, inputTrackTable, fieldList, cluster);
}
else
errAbort("Missing required trackDb setting %s for track %s",
"inputTableFieldDisplay", tdb->track);
webPrintLinkTableEnd();
}
printf("<A HREF=\"%s&g=htcListItemsAssayed&table=%s\" TARGET_blank>", hgcPathAndSettings(),
tdb->track);
printf("List all items assayed");
printf("</A><BR>\n");
webNewSection("Track Description");
printTrackHtml(tdb);
hFreeConn(&conn);
}
void retroShowCdnaAli(char *mappedId)
/* Show alignment for accession, mostly ripped off from htcCdnaAli */
{
char *track = cartString(cart, "aliTable");
struct trackDb *tdb = hashMustFindVal(trackHash, track);
char *table = cartString(cart, "table");
int start = cartInt(cart, "o");
struct sqlConnection *conn = hAllocConn(database);
struct sqlConnection *defDbConn = NULL;
struct mappingInfo *mi = mappingInfoNew(conn, table, mappedId);
struct genbankCds cds = getCds(conn, mi);
struct psl *psl;
struct dnaSeq *rnaSeq = NULL;
char *spec = trackDbRequiredSetting(tdb, BASE_COLOR_USE_SEQUENCE);
char *specCopy = cloneString(spec);
char *words[3];
int nwords = chopByWhite(specCopy, words, ArraySize(words));
char acc[512];
/* Print start of HTML. */
writeFramesetType();
puts("<HTML>");
printf("<HEAD>\n<TITLE>%s vs Genomic [%s]</TITLE>\n</HEAD>\n\n", mi->seqId, track);
/* Look up alignment and sequence in database. Always get sequence
* from defaultDb */
psl = loadAlign(conn, mi, start);
if (startsWith("August",mi->geneSet))
safef(acc, sizeof(acc), "aug-%s.T1",mi->seqId);
else
safef(acc, sizeof(acc), "%s",mi->seqId);
// value is: extFile seqTbl extFileTbl
if ((nwords != (int)ArraySize(words)) || !sameString(words[0], "extFile"))
errAbort("invalid %s track setting: %s ", BASE_COLOR_USE_SEQUENCE, spec);
char *seqTable = words[1];
char *extTable = words[2];
rnaSeq = hDnaSeqGet(database, acc, seqTable, extTable);
if (rnaSeq == NULL)
{
char *acc = mi->seqId;
rnaSeq = hExtSeq(database, acc);
if (rnaSeq == NULL)
errAbort("can't get mRNA sequence from %s prefix %s for %s from %s mappedId %s",
database, mi->geneSet, acc, track, mappedId);
}
sqlDisconnect(&defDbConn);
showSomeAlignment(psl, rnaSeq, gftDna, 0, rnaSeq->size, NULL, cds.start, cds.end);
pslFree(&psl);
dnaSeqFree(&rnaSeq);
mappingInfoFree(&mi);
hFreeConn(&conn);
}
static void lookupRetroAliLabels(struct track *tg)
/* This converts the retro ids to labels. */
{
struct sqlConnection *conn = hAllocConn(database);
char *retroInfoTbl = trackDbRequiredSetting(tg->tdb, retroInfoTblSetting);
struct linkedFeatures *lf;
unsigned labelSet = getLabelTypes(tg);
for (lf = tg->items; lf != NULL; lf = lf->next)
getItemLabel(conn, retroInfoTbl, labelSet, lf);
hFreeConn(&conn);
}
static void lookupTransMapLabels(struct track *tg)
/* This converts the transMap ids to labels. */
{
struct sqlConnection *conn = hAllocConn(database);
char *transMapInfoTbl = trackDbRequiredSetting(tg->tdb, transMapInfoTblSetting);
char *transMapGeneTbl = trackDbSetting(tg->tdb, transMapGeneTblSetting);
struct sqlConnection *geneConn = NULL;
if (transMapGeneTbl != NULL)
geneConn = hAllocConnDbTbl(transMapGeneTbl, &transMapGeneTbl, database);
struct linkedFeatures *lf;
unsigned labelSet = getLabelTypes(tg);
for (lf = tg->items; lf != NULL; lf = lf->next)
getItemLabel(conn, transMapInfoTbl, geneConn, transMapGeneTbl, labelSet, lf);
hFreeConn(&geneConn);
hFreeConn(&conn);
}
void doPeakClusterListItemsAssayed()
/* Put up a page that shows all experiments associated with a cluster track. */
{
struct trackDb *clusterTdb = tdbForTableArg();
cartWebStart(cart, database, "List of items assayed in %s", clusterTdb->shortLabel);
struct sqlConnection *conn = hAllocConn(database);
char *inputTableFieldDisplay = trackDbSetting(clusterTdb, "inputTableFieldDisplay");
webPrintLinkTableStart();
if (inputTableFieldDisplay)
{
struct slName *fieldList = stringToSlNames(inputTableFieldDisplay);
printClusterTableHeader(fieldList, FALSE, FALSE, FALSE);
char *inputTrackTable = trackDbRequiredSetting(clusterTdb, "inputTrackTable");
printPeakClusterInfo(clusterTdb, cart, conn, inputTrackTable, fieldList, NULL);
}
else
errAbort("Missing required trackDb setting %s for track %s", "inputTableFieldDisplay",
clusterTdb->track);
webPrintLinkTableEnd();
hFreeConn(&conn);
}
static struct hash* pubsLookupSequences(struct track *tg, struct sqlConnection* conn, char *articleId, bool getSnippet)
/* create a hash with a mapping annotId -> snippet or annotId -> shortSeq for an articleId*/
{
struct dyString *dy = dyStringNew(LARGEBUF);
char *sequenceTable = trackDbRequiredSetting(tg->tdb, "pubsSequenceTable");
// work around sql injection fix problem, suggested by galt
sqlDyStringPrintf(dy, "SELECT annotId, ");
if (getSnippet)
dyStringAppend(dy, "replace(replace(snippet, \"<B>\", \"\\n>>> \"), \"</B>\", \" <<<\\n\")" );
else
dyStringAppend(dy, "concat(substr(sequence,1,4),\"...\",substr(sequence,-4))" );
sqlDyStringPrintf(dy, " FROM %s WHERE articleId='%s' ", sequenceTable, articleId);
// end sql injection fix
struct hash *seqIdHash = sqlQuickHash(conn, dy->string);
//freeMem(sequenceTable); // trackDbRequiredSetting returns a value in a hash, so do not free
freeDyString(&dy);
return seqIdHash;
}
struct genoGraph *getUserGraphs()
/* Get list of all user graphs */
{
struct genoGraph *list = NULL, *gg;
struct customTrack *ct, *ctList = customTracksParseCart(database, cart, NULL, NULL);
for (ct = ctList; ct != NULL; ct = ct->next)
{
struct trackDb *tdb = ct->tdb;
if (sameString(tdb->type, "chromGraph"))
{
AllocVar(gg);
gg->name = tdb->table;
gg->shortLabel = tdb->shortLabel;
gg->longLabel = tdb->longLabel;
gg->binFileName = trackDbRequiredSetting(tdb, "binaryFile");
gg->settings = chromGraphSettingsGet(gg->name, NULL, tdb, cart);
gg->isSubGraph = FALSE;
gg->isComposite = FALSE;
slAddHead(&list, gg);
}
}
slReverse(&list);
return list;
}
void doExpRatio(struct trackDb *tdb, char *item, struct customTrack *ct)
/* Generic expression ratio deatils using microarrayGroups.ra file */
/* and not the expRecord tables. */
{
char *expScale = trackDbRequiredSetting(tdb, "expScale");
char *expStep = trackDbRequiredSetting(tdb, "expStep");
double maxScore = atof(expScale);
double stepSize = atof(expStep);
struct bed *bedList;
char *itemName = cgiUsualString("i2","none");
char *expName = (item == NULL) ? itemName : item;
char *tdbSetting = trackDbSettingOrDefault(tdb, "expColor", "redGreen");
char *colorVal = NULL;
enum expColorType colorScheme;
char colorVarName[256];
safef(colorVarName, sizeof(colorVarName), "%s.color", tdb->track);
colorVal = cartUsualString(cart, colorVarName, tdbSetting);
colorScheme = getExpColorType(colorVal);
if (sameWord(tdb->grp, "cancerGenomics"))
{
/* set global flag */
isCancerGenomicsTrack = TRUE;
}
if (!ct)
{
genericHeader(tdb, itemName);
bedList = loadMsBed(tdb, tdb->table, seqName, winStart, winEnd);
}
else if (ct->dbTrack)
{
genericHeader(tdb, itemName);
printCustomUrl(tdb, itemName, TRUE);
bedList = ctLoadMultScoresBedDb(ct, seqName, winStart, winEnd);
}
else
bedList = bedFilterListInRange(ct->bedList, NULL, seqName, winStart, winEnd);
if (bedList == NULL)
printf("<b>No Expression Data in this Range.</b>\n");
else if (expName && sameString(expName, "zoomInMore"))
printf("<b>Too much data to display in detail in this range.</b>\n");
else
{
struct microarrayGroups *groupings = NULL;
struct maGrouping *combineGroup;
struct hash *erHash = newHash(6);
int i;
if (!ct)
{
groupings = maGetTrackGroupings(database, tdb);
combineGroup = maCombineGroupingFromCart(groupings, cart, tdb->track);
}
else
combineGroup = maGetGroupingFromCt(ct);
maBedClumpGivenGrouping(bedList, combineGroup);
for (i = 0; i < combineGroup->numGroups; i++)
{
/* make stupid exprecord hash.perhaps eventually this won't be needed */
char id[16];
struct expRecord *er = basicExpRecord(combineGroup->names[i], i, 2);
safef(id, sizeof(id), "%d", i);
hashAdd(erHash, id, er);
}
puts("<h2></h2><p>\n");
msBedPrintTable(bedList, erHash, itemName, expName, -1*maxScore, maxScore,
stepSize, 2, msBedDefaultPrintHeader, msBedExpressionPrintRow,
printExprssnColorKey, getColorForExprBed, colorScheme);
hashTraverseEls(erHash, erHashElFree);
hashFree(&erHash);
microarrayGroupsFree(&groupings);
}
puts("<h2></h2><p>\n");
bedFreeList(&bedList);
}
void doFactorSource(struct sqlConnection *conn, struct trackDb *tdb, char *item, int start, int end)
/* Display detailed info about a cluster of TFBS peaks from other tracks. */
{
char extraWhere[256];
safef(extraWhere, sizeof extraWhere, "name='%s'", item);
int rowOffset;
struct sqlResult *sr = hRangeQuery(conn, tdb->table, seqName, start, end, extraWhere, &rowOffset);
char **row = sqlNextRow(sr);
struct factorSource *cluster = NULL;
if (row != NULL)
cluster = factorSourceLoad(row + rowOffset);
sqlFreeResult(&sr);
if (cluster == NULL)
errAbort("Error loading cluster from track %s", tdb->track);
char *sourceTable = trackDbRequiredSetting(tdb, "sourceTable");
char *factorLink = cluster->name;
char *vocab = trackDbSetting(tdb, "controlledVocabulary");
if (vocab != NULL)
{
char *file = cloneFirstWord(vocab);
factorLink = wgEncodeVocabLink(file, "term", factorLink, factorLink, factorLink, "");
}
printf("<B>Factor:</B> %s<BR>\n", factorLink);
printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score);
printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, item);
/* Get list of tracks we'll look through for input. */
char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable");
char query[256];
sqlSafef(query, sizeof(query), "select tableName from %s where factor='%s' order by source",
inputTrackTable,
cluster->name);
/* Next do the lists of hits and misses. We have the hits from the non-zero signals in
* cluster->expScores. We need to figure out the sources actually assayed though
* some other way. We'll do this by one of two techniques. */
char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay");
if (inputTableFieldDisplay != NULL)
{
struct slName *fieldList = stringToSlNames(inputTableFieldDisplay);
char *vocab = trackDbSetting(tdb, "controlledVocabulary");
/* In a new section put up list of hits. */
webNewSection("Assays for %s in Cluster", cluster->name);
webPrintLinkTableStart();
printClusterTableHeader(fieldList, TRUE, FALSE, TRUE);
printFactorSourceTableHits(cluster, conn, sourceTable,
inputTrackTable, fieldList, FALSE, vocab);
webPrintLinkTableEnd();
webNewSectionHeaderStart();
char sectionTitle[128];
safef(sectionTitle,
sizeof(sectionTitle),"Assays for %s Without Hits in Cluster", cluster->name);
jsBeginCollapsibleSectionOldStyle(cart, tdb->track, "cellNoHits", sectionTitle, FALSE);
webNewSectionHeaderEnd();
webPrintLinkTableStart();
printClusterTableHeader(fieldList, TRUE, FALSE, FALSE);
printFactorSourceTableHits(cluster, conn, sourceTable,
inputTrackTable, fieldList, TRUE, vocab);
webPrintLinkTableEnd();
jsEndCollapsibleSection();
}
else
{
errAbort("Missing required trackDb setting %s for track %s",
"inputTableFieldDisplay", tdb->track);
}
webNewSectionHeaderStart();
jsBeginCollapsibleSectionOldStyle(cart, tdb->track, "cellSources", "Cell Abbreviations", FALSE);
webNewSectionHeaderEnd();
hPrintFactorSourceAbbrevTable(conn, tdb);
jsEndCollapsibleSection();
doClusterMotifDetails(conn, tdb, cluster);
}
