nRes+1; i++)
+ {
+ char buffer[1024];
+ long long value = atoll(meta->resolutions[i-1]);
+ sprintWithSiBaseUnit(buffer, sizeof(buffer), value);
+ menu[i] = cloneString(buffer);
+ values[i] = cloneString(meta->resolutions[i-1]);
+ }
+char *selected = hicUiFetchResolution(cart, track, meta);
+cgiMakeDropListWithVals(cartVar, menu, values, meta->nRes+1, selected);
+free(menu);
+}
+
+
+char *hicUiFetchDrawMode(struct cart *cart, char *track)
+/* Return the current draw mode selection, or the default if none
+ * has been selected. */
+{
+char cartVar[1024];
+safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_MODE);
+char* selected = cartNonemptyString(cart, cartVar);
+if ( !sameOk(selected, HIC_DRAW_MODE_SQUARE) &&
+ !sameOk(selected, HIC_DRAW_MODE_ARC) &&
+ !sameOk(selected, HIC_DRAW_MODE_TRIANGLE) )
+ {
+ selected = HIC_DRAW_MODE_DEFAULT;
+ }
+return selected;
+}
+
+
+void hicUiDrawMenu(struct cart *cart, char *track)
+/* Draw the list of draw mode options for Hi-C tracks. Square is the
+ * standard square-shaped heatmap with the chromosome position axis on
+ * a diagonal from top left to bottom right. Triangle is the top half
+ * of that square, after rotating it 45 degrees to have the position
+ * axis lie horizontally. Arc draws arcs between related positions,
+ * but skips over self-relations. */
+{
+char cartVar[1024];
+printf("Draw mode: ");
+safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_MODE);
+char *menu[] = {HIC_DRAW_MODE_SQUARE, HIC_DRAW_MODE_TRIANGLE, HIC_DRAW_MODE_ARC};
+char* selected = hicUiFetchDrawMode(cart, track);
+cgiMakeDropList(cartVar, menu, 3, selected);
+}
+
+
+char *hicUiFetchDrawColor(struct cart *cart, char *track)
+/* Retrieve the HTML hex code for the color to draw the
+ * track values in (e.g., #00ffa1) */
+{
+char cartVar[1024];
+safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_COLOR);
+char* selected = cartNonemptyString(cart, cartVar);
+if (selected == NULL)
+ selected = HIC_DRAW_COLOR_DEFAULT;
+const char *colorExpr ="^#[0-9a-fA-F]{6}$";
+if (!regexMatch(selected, colorExpr))
+ {
+ selected = HIC_DRAW_COLOR_DEFAULT;
+ }
+return selected;
+}
+
+char *hicUiFetchBgColor(struct cart *cart, char *track)
+/* Retrieve the HTML hex code of the background color for the
+ * track. This is the color associated with scores at or close to 0. */
+{
+char cartVar[1024];
+safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_BG_COLOR);
+char* selected = cartNonemptyString(cart, cartVar);
+if (selected == NULL)
+ selected = HIC_DRAW_BG_COLOR_DEFAULT;
+const char *colorExpr ="^#[0-9a-fA-F]{6}$";
+if (!regexMatch(selected, colorExpr))
+ {
+ selected = HIC_DRAW_BG_COLOR_DEFAULT;
+ }
+return selected;
+}
+
+double hicUiFetchMaxValue(struct cart *cart, char *track)
+/* Retrieve the score value at which the draw color reaches its
+ * its maximum intensity. Any scores above this value will
+ * share that same draw color. */
+{
+char cartVar[1024];
+safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_MAX_VALUE);
+return cartUsualDouble(cart, cartVar, HIC_DRAW_MAX_VALUE_DEFAULT);
+}
+
+
+void hicUiAddAutoScaleJS(struct cart *cart, char *track)
+/* Write out a bit of javascript to associate checking/unchecking the autoscale
+ * checkbox with deactivating/activating (respectively) the maximum score
+ * input. */
+{
+struct dyString *new = dyStringNew(0);
+dyStringPrintf(new, "$('input[name=\"%s.%s\"]')[0].onclick = function() {", track, HIC_DRAW_AUTOSCALE);
+dyStringPrintf(new, "if (this.checked) {$('input[name=\"%s.%s\"]')[0].disabled = true; $('span#hicMaxText').css('color', 'gray');}", track, HIC_DRAW_MAX_VALUE);
+dyStringPrintf(new, "else {$('input[name=\"%s.%s\"]')[0].disabled = false; $('span#hicMaxText').css('color', '');} };\n", track, HIC_DRAW_MAX_VALUE);
+dyStringPrintf(new, "if ($('input[name=\"%s.%s\"]')[0].checked) {$('input[name=\"%s.%s\"]')[0].disabled = true; $('span#hicMaxText').css('color', 'gray');}\n",
+ track, HIC_DRAW_AUTOSCALE, track, HIC_DRAW_MAX_VALUE);
+jsInline(dyStringContents(new));
+dyStringFree(&new);
+}
+
+boolean hicUiFetchAutoScale(struct cart *cart, char *track)
+/* Returns whether the track is configured to automatically scale its color range
+ * depending on the scores present in the window, or if it should stick to a
+ * gradient based on the user's selected maximum value. */
+{
+char cartVar[1024];
+safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_AUTOSCALE);
+return cartUsualBoolean(cart, cartVar, TRUE);
+}
+
+
+void hicUiColorMenu(struct cart *cart, char *track)
+/* Draw the menu inputs associated with selecting draw colors for the track. */
+{
+char cartVar[1024];
+printf("Color: ");
+safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_COLOR);
+char* selected = hicUiFetchDrawColor(cart, track);
+printf("\n", cartVar, selected);
+
+// Leaving out background color options for now. We'll see if this option is requested.
+/*
+printf("Background color: ");
+safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_BG_COLOR);
+selected = hicUiFetchBgColor(cart, track);
+printf("\n", cartVar, selected);
+*/
+}
+
+void hicUiMaxOptionsMenu(struct cart *cart, char *track)
+/* Draw the menu inputs associated with selecting whether the track should automatically
+ * scale its color gradient based on the scores present in the view window, or whether it
+ * should stick to a gradient based on a user-selected maximum score. */
+{
+char cartVar[1024];
+safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_MAX_VALUE);
+double currentMax = hicUiFetchMaxValue(cart, track);
+printf("Maximum: ");
+cgiMakeDoubleVar(cartVar, currentMax, 6);
+
+printf(" Auto-scale: ");
+safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_AUTOSCALE);
+boolean autoscaleChecked = hicUiFetchAutoScale(cart, track);
+cgiMakeCheckBox(cartVar, autoscaleChecked);
+
+hicUiAddAutoScaleJS(cart, track);
+}
+
+void hicCfgUi(char *database, struct cart *cart, struct trackDb *tdb, char *track,
+ char *title, boolean boxed)
+/* Draw the list of track configuration options for Hi-C tracks */
+{
+
+boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
+char *filename = trackDbSetting(tdb, "bigDataUrl");
+if (filename == NULL)
+ errAbort("Error: no bigDataUrl provided in trackDb for hic track %s", tdb->track);
+struct hicMeta *trackMeta;
+char *errMsg = hicLoadHeader(filename, &trackMeta);
+if (errMsg != NULL)
+ errAbort("Error retrieving file info: %s", errMsg);
+
+puts("");
+printf("Items are drawn in shades of the chosen color depending on score - scores above the "
+ "chosen maximum are drawn at full intensity.
\n");
+hicUiNormalizationMenu(cart, track, trackMeta);
+puts(" ");
+hicUiMaxOptionsMenu(cart, track);
+
+puts("
");
+hicUiDrawMenu(cart, track);
+puts(" ");
+hicUiResolutionMenu(cart, track, trackMeta);
+puts(" ");
+hicUiColorMenu(cart, track);
+cfgEndBox(boxed);
+}