![\"%s\"](\"../images/%s\")
\n"
#define DEF_BUTTON_JS "setCheckBoxesThatContain('%s',true,false,'%s','','%s');" \
"setCheckBoxesThatContain('%s',false,false,'%s','_defOff','%s');"
@@ -3938,106 +3939,123 @@
printf(" value='%s'",name);
if (filterBy->styleFollows)
{
char *styler = label + strlen(label)+1;
if (*styler != '\0')
{
if (*styler == '#') // Legacy: just the color that follows
printf(" style='color: %s;'",styler);
else
printf(" style='%s'",styler);
}
}
printf(">%s\n",label);
}
+static boolean filterByColumnIsMultiple(struct cart *cart, struct trackDb *tdb, char *column)
+{
+char settingString[4096];
+safef(settingString, sizeof settingString, "%s%s", column, FILTER_TYPE_NAME);
+char *setting = cartOrTdbString(cart, tdb, settingString, NULL);
+if (setting == NULL)
+ {
+ safef(settingString, sizeof settingString, "%s.%s", column, FILTER_TYPE_NAME);
+ setting = cartOrTdbString(cart, tdb, settingString, FILTERBY_MULTIPLE_LIST_AND);
+ }
+return (sameString(setting, FILTERBY_MULTIPLE) ||
+ sameString(setting, FILTERBY_MULTIPLE_LIST_OR) ||
+ sameString(setting, FILTERBY_MULTIPLE_LIST_AND));
+}
+
void filterBySetCfgUiGuts(struct cart *cart, struct trackDb *tdb,
filterBy_t *filterBySet, boolean onOneLine,
char *filterTypeTitle, char *selectIdPrefix, char *allLabel, char *prefix)
// Does the UI for a list of filterBy structure for either filterBy or highlightBy controls
{
if (filterBySet == NULL)
return;
#define FILTERBY_HELP_LINK "| ");
char selectStatement[4096];
- if (isMultiple)
+ if (filterByColumnIsMultiple(cart, tdb, filterBy->column))
safef(selectStatement, sizeof selectStatement, " (select multiple items - %s)", FILTERBY_HELP_LINK);
else
selectStatement[0] = 0;
if(count == 1)
printf("%s by %s%s",filterTypeTitle,filterBy->title,selectStatement);
else
printf("%s",filterBy->title);
- printf(" \n"); - - if (isMultiple && tdbIsBigBed(tdb)) + puts(" | ");
+ }
+puts("
| "); + if (filterByColumnIsMultiple(cart, tdb, filterBy->column) && tdbIsBigBed(tdb)) + { + char settingString[4096]; + safef(settingString, sizeof settingString, "%s%s", filterBy->column, FILTER_TYPE_NAME); + char *setting = cartOrTdbString(cart, tdb, settingString, FILTERBY_MULTIPLE_LIST_AND); char cartSettingString[4096]; safef(cartSettingString, sizeof cartSettingString, "%s.%s", prefix, settingString); printf(" "); } - // TODO: columnCount (Number of filterBoxes per row) should be configurable through tdb setting - + puts(" | "); + } +puts("
| "); // value is always "All", even if label is different, to simplify javascript code int valIx = 0; - if (isMultiple) + if (filterByColumnIsMultiple(cart, tdb, filterBy->column)) { printf( " | "); + } puts("
"); +} + +static struct trackDb *tdbOrAncestorByName(struct trackDb *tdb, char *name) +/* For reasons Angie cannot fathom, if a composite or view is passed to cfgByCfgType then + * cfgByCfgType passes a leaf subtrack to its callees like bigDbSnpCfgUi. That is why we + * see so many calls to isNameAtParentLevel, which returns true if the tdb was originally + * at the composite or view level, which we can only tell by comparing with the original track name. + * labelMakeCheckBox, called by many handlers in hgTrackUi that must be always top-level + * (or have a special handler that bypasses cfgByCfgType like refSeqComposite), + * is blissfully unaware of this. It uses the same tdb for looking in cart ClosestToHome + * and for making the HTML element's cart var name, trusting that the correct tdb has been + * handed to it. + * So in order for a callee of cfgByCfgType to call labelMakeCheckBox with the correct tdb, + * we need to walk back up comparing name like isNameAtParentLevel does. + * If name doesn't match tdb or any of its ancestors then this returns NULL. */ +{ +struct trackDb *correctTdb; +for (correctTdb = tdb; correctTdb != NULL; correctTdb = correctTdb->parent) + if (startsWithWordByDelimiter(correctTdb->track, '.', name)) + return correctTdb; +return NULL; +} + +void bigDbSnpCfgUi(char *db, struct cart *cart, struct trackDb *leafTdb, char *name, char *title, + boolean boxed) +/* UI for bigDbSnp a.k.a. "dbSNP 2.0". */ +{ +boxed = cfgBeginBoxAndTitle(leafTdb, boxed, title); +freqSourceSelect(cart, leafTdb, name); +puts("
"); +puts("Label:"); +struct trackDb *correctTdb = tdbOrAncestorByName(leafTdb, name); +labelMakeCheckBox(cart, correctTdb, "rsId", "rs# identifier", TRUE); +labelMakeCheckBox(cart, correctTdb, "refAlt", "reference/alternate allele", TRUE); +labelMakeCheckBox(cart, correctTdb, "majMin", "major/minor allele", FALSE); +labelMakeCheckBox(cart, correctTdb, "maf", "MAF if available", FALSE); +labelMakeCheckBox(cart, correctTdb, "func", "Most severe functional impact on gene if any", FALSE); +puts("
"); +scoreCfgUi(db, cart, leafTdb, name, "", 0, FALSE); +puts("
"); +puts("Minimum MAF:"); +boolean parentLevel = isNameAtParentLevel(leafTdb, name); +double minMaf = cartUsualDoubleClosestToHome(cart, leafTdb, parentLevel, "minMaf", 0.0); +char cartVar[1024]; +safef(cartVar, sizeof cartVar, "%s.minMaf", name); +cgiMakeDoubleVarWithLimits(cartVar, minMaf, "MAF", 0, 0.0, 0.5); +puts("range: 0.0 - 0.5"); +cfgEndBox(boxed); +} + void cfgByCfgType(eCfgType cType,char *db, struct cart *cart, struct trackDb *tdb,char *prefix, char *title, boolean boxed) // Methods for putting up type specific cfgs used by composites/subtracks in hui.c { // When only one subtrack, then show it's cfg settings instead of composite/view level settings // This simplifies the UI where hgTrackUi won't have 2 levels of cfg, // while hgTracks still supports rightClick cfg of the subtrack. if (configurableByAjax(tdb,cType) > 0) // Only if subtrack's configurable by ajax do we { // consider this option if (tdbIsComposite(tdb) // called for the composite && !isCustomComposite(tdb) && !tdbIsCompositeView(tdb->subtracks) // and there is no view level && slCount(tdb->subtracks) == 1) // and there is only one subtrack { @@ -4354,30 +4455,32 @@ case cfgLong: longRangeCfgUi(cart, tdb, prefix, title, boxed); break; case cfgSnake: snakeCfgUi(cart, tdb, prefix, title, boxed); break; case cfgPsl: pslCfgUi(db,cart,tdb,prefix,title,boxed); break; case cfgBarChart: barChartCfgUi(db,cart,tdb,prefix,title,boxed); break; case cfgInteract: interactCfgUi(db,cart,tdb,prefix,title,boxed); break; case cfgLollipop: lollyCfgUi(db,cart,tdb,prefix,title,boxed); scoreCfgUi(db, cart,tdb,prefix,title,1000,boxed); break; case cfgHic: hicCfgUi(db,cart,tdb,prefix,title,boxed); break; + case cfgBigDbSnp: bigDbSnpCfgUi(db, cart, tdb, prefix, title, boxed); + break; default: warn("Track type is not known to multi-view composites. type is: %d ", cType); break; } } char *encodeRestrictionDate(char *db,struct trackDb *trackDb,boolean excludePast) // Create a string for ENCODE restriction date of this track // if return is not null, then free it after use { if (!trackDb) return NULL; char *date = NULL; @@ -8893,38 +8996,34 @@ if (isCustomTrack(tdb->track)) { if (ct) { conn = hAllocConn(CUSTOM_TRASH); tableName = ct->dbTableName; } } else if (startsWith("big", tdb->type)) { char *tableName = hTableForTrack(database, tdb->table); struct sqlConnection *conn = hAllocConnTrack(database, tdb); char *bbiFileName = bbiNameFromSettingOrTable(tdb, conn, tableName); hFreeConn(&conn); struct bbiFile *bbi = NULL; - if (startsWith("bigBed", tdb->type) || sameString("bigBarChart", tdb->type) - || sameString("bigMaf", tdb->type) || sameString("bigPsl", tdb->type) - || sameString("bigChain", tdb->type) || sameString("bigGenePred", tdb->type) - || startsWith("bigLolly", tdb->type) - || sameString("bigInteract", tdb->type)) - bbi = bigBedFileOpen(bbiFileName); - else if (startsWith("bigWig", tdb->type)) + if (startsWith("bigWig", tdb->type)) bbi = bigWigFileOpen(bbiFileName); + else + bbi = bigBedFileOpen(bbiFileName); time_t timep = 0; if (bbi) { timep = bbiUpdateTime(bbi); bbiFileClose(&bbi); } printBbiUpdateTime(&timep); } else { tableName = hTableForTrack(database, tdb->table); conn = hAllocConnTrack(database, tdb); } if (tableName) {