3fd4131517e0d224eb271e312c9fda6419e1872d
kate
  Tue Mar 13 15:51:59 2018 -0700
1. Add support for spectrum setting. 2. Allow dot for empty field. 3. Show multiple items on details page if they overlap. 4. Some cleanup of map boxes. refs #17512

diff --git src/hg/hgTracks/interactTrack.c src/hg/hgTracks/interactTrack.c
index 23c2982..cda8b05 100644
--- src/hg/hgTracks/interactTrack.c
+++ src/hg/hgTracks/interactTrack.c
@@ -14,69 +14,79 @@
 /* calculate height of all the interactions being displayed */
 {
 if ( tg->visibility == tvDense)
     return  tl.fontHeight;
 int min, max, deflt, current; 
 cartTdbFetchMinMaxPixels(cart, tg->tdb, 
                                 INTERACT_MINHEIGHT, INTERACT_MAXHEIGHT, atoi(INTERACT_DEFHEIGHT),
                                 &min, &max, &deflt, &current);
 return tg->height = current;
 }
 
 static Color interactItemColor(struct track *tg, void *item, struct hvGfx *hvg)
 /* Return color to draw an interaction */
 {
 struct interact *inter = item;
+if (tg->colorShades)
+    return tg->colorShades[grayInRange(inter->score, 0, 1000)];
 
 struct rgbColor itemRgb;
 // There must be a better way...
 itemRgb.r = (inter->color & 0xff0000) >> 16;
 itemRgb.g = (inter->color & 0xff00) >> 8;
 itemRgb.b = inter->color & 0xff;
 return hvGfxFindColorIx(hvg, itemRgb.r, itemRgb.g, itemRgb.b);
 }
 
 void interactLoadItems(struct track *tg)
 /* Load all interact items in region */
 {
 loadSimpleBedWithLoader(tg, (bedItemLoader)interactLoad);
 
 if (tg->limitedVisSet)
     {
     // too many items to display
     // borrowed behaviors in bamTrack and vcfTrack
     // TODO BRANEY: make this behavior generic for bigBeds
     // (bigBedSelectRange)
     tg->drawItems = bigDrawWarning;
     tg->networkErrMsg = "Too many items in display (zoom in)"; 
     tg->totalHeight = bigWarnTotalHeight;
     return;
 }
 
-// filters
+// filter and grayscale adjustment on score
 char buf[1024];
 safef(buf, sizeof buf, "%s.%s", tg->tdb->track, INTERACT_MINSCORE);
 int minScore = cartUsualInt(cart, buf, INTERACT_DEFMINSCORE);
+int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMin", "0"));
+int scoreMax = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "scoreMax", "1000"));
 struct interact *inter, *next, *filteredItems = NULL;
 for (inter = tg->items; inter; inter = next)
     {
     next = inter->next;
     if (inter->score < minScore)
         continue;
+    if (tg->colorShades)
+        {
+        struct bed *bed = (struct bed *)inter;
+        adjustBedScoreGrayLevel(tg->tdb, bed, scoreMin, scoreMax);
+        }
     slAddHead(&filteredItems, inter);
     }
 slReverse(&filteredItems);
+// consider sorting by score/value so highest scored items draw last (on top)
 tg->items = filteredItems;
 }
 
 static void interactDrawItems(struct track *tg, int seqStart, int seqEnd,
         struct hvGfx *hvg, int xOff, int yOff, int width, 
         MgFont *font, Color color, enum trackVisibility vis)
 /* Draw a list of interact structures. */
 {
 #define DRAW_LINE       0
 #define DRAW_CURVE      1
 #define DRAW_ELLIPSE    2
 
 int draw = DRAW_LINE;
 if (vis != tvDense)
     {
@@ -155,31 +165,31 @@
             sprintLongWithCommas(buf, inter->chromEnd - inter->chromStart);
             dyStringPrintf(ds, "%s bp", buf);
             }
         }
     else
         dyStringPrintf(ds, "%s", inter->name);
     if (inter->score)
         dyStringPrintf(ds, " %d", inter->score);
     if (inter->value != 0.0)
         dyStringPrintf(ds, " %0.2f", inter->value);
     char *statusBuf = dyStringCannibalize(&ds);
 
     color = interactItemColor(tg, inter, hvg);
     if (vis == tvDense && interactOtherChrom(inter) && color == MG_BLACK)
         color = MG_MAGENTA;
-    int peakColor = (color == MG_BLACK) ? MG_MAGENTA : MG_GRAY;
+    int peakColor = (color == MG_BLACK || tg->colorShades) ? MG_MAGENTA : MG_GRAY;
     
     // TODO: simplify by using start/end instead of center and width
     // This is a holdover from longRange track implementation
     unsigned lowStart, lowEnd, highStart, highEnd;
     if (otherChrom)
         {
         lowStart = highStart = inter->chromStart;
         lowEnd = highEnd = inter->chromEnd;
         }
     else if (inter->sourceStart < inter->targetStart)
         {
         lowStart = inter->sourceStart;
         lowEnd = inter->sourceEnd;
         highStart = inter->targetStart;
         highEnd = inter->targetEnd;
@@ -297,109 +307,95 @@
                 hvGfxDottedLine(hvg, ex, yOff, ex, peak, color, TRUE);
             else
                 hvGfxLine(hvg, ex, yOff, ex, peak, color);
             }
         }
     if (tg->visibility == tvFull)
         {
         char *nameBuf = NULL;
         if (sOnScreen)
             {
             /* add mapbox to lower region */
             nameBuf = (inter->chromStart == inter->sourceStart ?      
                             inter->sourceName : inter->targetName);
             if (isEmptyTextField(nameBuf))
                 nameBuf = statusBuf;
-            int xMap = sx-1;
-            int yMap = yOff;
-            int w = 3;
-            int h = 1;
-            hvGfxBox(hvg, xMap, yMap, w, h, peakColor);
-            hvGfxBox(hvg, xMap, yMap+1, w, h-2, MG_WHITE);
+            hvGfxBox(hvg, sx-1, yOff, 3, 1, peakColor);
+            hvGfxBox(hvg, sx, yOff, 1, 1, MG_WHITE);
             mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, 
-                               sx + sFootWidth, yOff, sFootWidth * 2, 4,
+                               sx - sFootWidth, yOff, sFootWidth * 2, 3,
                                tg->track, itemBuf, nameBuf, NULL, TRUE, NULL);
 
             }
         if (eOnScreen)
             {
             /* add mapbox to upper region */
             nameBuf = (inter->chromEnd == inter->targetEnd ?      
                             inter->targetName : inter->sourceName);
             if (isEmptyTextField(nameBuf))
                 nameBuf = statusBuf;
-            int xMap = ex-1;
-            int yMap = yOff;
-            int w = 3;
-            int h = 1;
-            hvGfxBox(hvg, xMap, yMap, w, h, peakColor);
-            hvGfxBox(hvg, xMap, yMap+1, w, h-2, MG_WHITE);
+            hvGfxBox(hvg, ex-1, yOff, 3, 1, peakColor);
+            hvGfxBox(hvg, ex, yOff, 1, 1, MG_WHITE);
             mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, 
-                            ex + eFootWidth, yOff, eFootWidth * 2, 4,
+                            ex - eFootWidth, yOff, eFootWidth * 2, 3,
                             tg->track, itemBuf, nameBuf, NULL, TRUE, NULL);
             }
         if (sOnScreen && eOnScreen && draw != DRAW_LINE)
             {
             boolean isDashed = (inter->sourceStart > inter->targetStart);
             if (draw == DRAW_CURVE)
                 {
                 int peakX = ((ex - sx + 1) / 2) + sx;
-                int peakY = peak + 30;
+                int peakY = peak + 30; // admittedly a hack (obscure how to define ypeak of curve)
                 int maxY = hvGfxCurve(hvg, sx, yOff, peakX, peakY, ex, yOff, color, isDashed);
                 // curve drawer does not use peakY as expected, so it returns actual max Y used
                 // draw map box on peak
-                int w = 3;
-                int h = 1;
-                hvGfxBox(hvg, peakX-1, maxY, w, h, peakColor);
-                hvGfxBox(hvg, peakX, maxY, w-2, h, MG_WHITE);
-                mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, peakX, maxY, w, h,
+                hvGfxBox(hvg, peakX-1, maxY, 3, 1, peakColor);
+                hvGfxBox(hvg, peakX, maxY, 1, 1, MG_WHITE);
+                mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, peakX, maxY, 3, 1,
                                tg->track, itemBuf, nameBuf, NULL, TRUE, NULL);
                 }
             else if (draw == DRAW_ELLIPSE)
                 {
                 int yLeft = yOff + peakHeight;
                 int yTop = yOff - peakHeight;
                 hvGfxEllipseDraw(hvg, sx, yLeft, ex, yTop, color, ELLIPSE_BOTTOM, isDashed);
                 // draw map box on peak
                 int maxY = peakHeight + yOff;
                 int peakX = ((ex - sx + 1) / 2) + sx;
-                int w = 3;
-                int h = 1;
-                hvGfxBox(hvg, peakX-1, maxY, w, h, peakColor);
-                hvGfxBox(hvg, peakX, maxY, w-2, h, MG_WHITE);
-                mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, peakX, maxY, w, h,
+                hvGfxBox(hvg, peakX-1, maxY, 3, 1, peakColor);
+                hvGfxBox(hvg, peakX, maxY, 1, 1, MG_WHITE);
+                mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, peakX, maxY, 3, 1,
                                tg->track, itemBuf, nameBuf, NULL, TRUE, NULL);
                 }
             }
         else
             {
             // draw link horizontal line between regions
             unsigned ePeak = eOnScreen ? ex : xOff + width;
             unsigned sPeak = sOnScreen ? sx : xOff;
             if (inter->sourceStart > inter->targetStart && isDirectional)
                 hvGfxDottedLine(hvg, sPeak, peak, ePeak, peak, color, TRUE);
             else
                 hvGfxLine(hvg, sPeak, peak, ePeak, peak, color);
 
             // map box on mid-point of horizontal line
             int xMap = sPeak + (double)(ePeak-sPeak)/2;
             int yMap = peak-1;
-            int w = 1;
-            int h = 3;
-            hvGfxBox(hvg, xMap, yMap, w, h, peakColor);
-            hvGfxBox(hvg, xMap, yMap+1, w, h-2, MG_WHITE);
-            mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, xMap, yMap, w, h,
+            hvGfxBox(hvg, xMap, peak-1, 1, 3, peakColor);
+            hvGfxBox(hvg, xMap, peak, 1, 1, MG_WHITE);
+            mapBoxHgcOrHgGene(hvg, inter->chromStart, inter->chromEnd, xMap-1, yMap, 3, 3,
                                tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
             }
         }
     }
 }
 
 void interactDrawLeftLabels(struct track *tg, int seqStart, int seqEnd,
     struct hvGfx *hvg, int xOff, int yOff, int width, int height,
     boolean withCenterLabels, MgFont *font,
     Color color, enum trackVisibility vis)
 /* Override default */
 {
 }
 
 void interactMethods(struct track *tg)