3003dd8639adc83e45ead18a948ab7e168e9e6cc jcasper Mon May 20 08:11:37 2019 -0700 More changes in response to code review, refs #23481 diff --git src/hg/lib/hicUi.c src/hg/lib/hicUi.c index 1f43682..a615188 100644 --- src/hg/lib/hicUi.c +++ src/hg/lib/hicUi.c @@ -1,265 +1,267 @@ /* hic track controls */ /* Copyright (C) 2019 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "cheapcgi.h" #include "cart.h" #include "hui.h" #include "web.h" #include "trackDb.h" #include "hicUi.h" #include "Cstraw.h" #include "regexHelper.h" #include "obscure.h" char *hicUiFetchNormalization(struct cart *cart, char *track, struct hicMeta *meta) /* Return the current normalization selection, or the default if none * has been selected. Right now this is a hard-coded set specifically for * .hic files, but in the future this list might be dynamically determined by * the contents and format of the Hi-C file. */ { char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_NORMALIZATION); char *selected = cartNonemptyString(cart, cartVar); char *menu[] = {"NONE", "VC", "VC_SQRT", "KR"}; int i, sanityCheck = 0; for (i=0; i<4; i++) { if (sameOk(selected, menu[i])) sanityCheck = 1; } if (!sanityCheck) { selected = menu[0]; } return selected; } void hicUiNormalizationMenu(struct cart *cart, char *track, struct hicMeta *meta) /* Draw a menu to select the normalization method to use. */ { char cartVar[1024]; printf("<b>Score normalization:</b> "); char* selected = hicUiFetchNormalization(cart, track, meta); char *menu[] = {"NONE", "VC", "VC_SQRT", "KR"}; safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_NORMALIZATION); cgiMakeDropList(cartVar, menu, 4, selected); } char *hicUiFetchResolution(struct cart *cart, char *track, struct hicMeta *meta) /* Return the current resolution selection, or the default if none * has been selected. */ { char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_RESOLUTION); char *selected = cartNonemptyString(cart, cartVar); int sanityCheck = sameOk(selected, "Auto"); int i; for (i=0; i<meta->nRes; i++) { if (sameOk(selected, meta->resolutions[i])) sanityCheck = 1; } if (!sanityCheck) selected = "Auto"; return selected; } void hicUiResolutionMenu(struct cart *cart, char *track, struct hicMeta *meta) /* Draw a menu to select which binSize to use for fetching data */ { char cartVar[1024]; char autoscale[10] = "Auto"; printf("<b>Resolution:</b> "); safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_RESOLUTION); -char **menu = calloc(meta->nRes+1, sizeof(char*)); -char **values = calloc(meta->nRes+1, sizeof(char*)); +char **menu = NULL; +AllocArray(menu, meta->nRes+1); +char **values = NULL; +AllocArray(values, meta->nRes+1); menu[0] = autoscale; values[0] = autoscale; int i; for (i=1; i<meta->nRes+1; i++) { char buffer[1024]; long long value = atoll(meta->resolutions[i-1]); sprintWithMetricBaseUnit(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("<b>Draw mode:</b> "); 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("<b>Color:</b> "); safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_COLOR); char* selected = hicUiFetchDrawColor(cart, track); printf("<input type='color' name='%s' value='%s' />\n", cartVar, selected); // Leaving out background color options for now. We'll see if this option is requested. /* printf("<b>Background color:</b> "); safef(cartVar, sizeof(cartVar), "%s.%s", track, HIC_DRAW_BG_COLOR); selected = hicUiFetchBgColor(cart, track); printf("<input type='color' name='%s' value='%s' />\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("<span id='hicMaxText'><b>Maximum:</b></span> "); cgiMakeDoubleVar(cartVar, currentMax, 6); printf(" <b>Auto-scale:</b> "); 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("<p>"); printf("Items are drawn in shades of the chosen color depending on score - scores above the " "chosen maximum are drawn at full intensity.</p><p>\n"); hicUiNormalizationMenu(cart, track, trackMeta); puts(" "); hicUiMaxOptionsMenu(cart, track); puts("</p><p>"); hicUiDrawMenu(cart, track); puts(" "); hicUiResolutionMenu(cart, track, trackMeta); puts(" "); hicUiColorMenu(cart, track); cfgEndBox(boxed); }