d7b8c8436b55a4f08f46a7caae8bf3ab88773f9f
jcasper
  Fri May 17 13:40:41 2019 -0700
Changes in response to code review, refs #23481

diff --git src/hg/lib/hicUi.c src/hg/lib/hicUi.c
index 28133e4..1f43682 100644
--- src/hg/lib/hicUi.c
+++ src/hg/lib/hicUi.c
@@ -1,265 +1,265 @@
 /* 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*));
 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]);
-    sprintWithSiBaseUnit(buffer, sizeof(buffer), value);
+    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("&nbsp;&nbsp;<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("&nbsp;&nbsp;");
 hicUiMaxOptionsMenu(cart, track);
 
 puts("</p><p>");
 hicUiDrawMenu(cart, track);
 puts("&nbsp;&nbsp;");
 hicUiResolutionMenu(cart, track, trackMeta);
 puts("&nbsp;&nbsp;");
 hicUiColorMenu(cart, track);
 cfgEndBox(boxed);
 }