f7d7d19f5160b5553f500ce99a2e47621cb7c2dc
kate
  Wed Jul 22 18:15:17 2015 -0700
1. Fix pack problem.  2. Fix map box in dense/squish. refs #15645

diff --git src/hg/hgTracks/gtexTracks.c src/hg/hgTracks/gtexTracks.c
index d54fb51..ba91a5a 100644
--- src/hg/hgTracks/gtexTracks.c
+++ src/hg/hgTracks/gtexTracks.c
@@ -212,31 +212,32 @@
 struct rgbColor lineColor = {.r=0};
 int lineColorIx = hvGfxFindColorIx(hvg, lineColor.r, lineColor.g, lineColor.b);
 int heightPer = tg->heightPer;
 
 int graphX = gtexGraphX(geneBed);
 if (graphX < 0)
     return;
 // x1 is at left of graph
 int x1 = xOff + graphX;
 
 // yZero is at bottom of graph
 int yZero = gtexGraphHeight() + y - 1;
 
 // draw faint line under graph to delineate extent when bars are missing (tissue w/ 0 expression)
 Color lightGray = MAKECOLOR_32(0xD1, 0xD1, 0xD1);
-hvGfxBox(hvg, x1, yZero+1, gtexGraphWidth(geneBed), 1, lightGray);
+int graphWidth = gtexGraphWidth(geneBed);
+hvGfxBox(hvg, x1, yZero+1, graphWidth, 1, lightGray);
 
 //uglyf("DRAW: xOff=%d, x1=%d, y=%d, yZero=%d<br>", xOff, x1, y, yZero);
 
 int barWidth = gtexBarWidth();
 int graphPadding = gtexGraphPadding();
 char *colorScheme = cartUsualStringClosestToHome(cart, tg->tdb, FALSE, GTEX_COLORS, 
                         GTEX_COLORS_DEFAULT);
 struct rgbColor *colors;
 if (sameString(colorScheme, GTEX_COLORS_GTEX))
     {
     // retrieve from table
     // TODO: cache this
     colors = getGtexTissueColors();
     }
 else
@@ -262,75 +263,69 @@
     //int height = yZero - yMedian + 1;
     int height = yZero - yMedian;
     // TODO: adjust yGene instead of yMedian+1 to get gene track distance as desired
     //if (i ==0) uglyf("DRAW: expScore=%.2f, maxExp=%.2f, graphHeight=%d, y=%d<br>", expScore, maxExp, gtexGraphHeight(), y);
     //if (i ==0) uglyf("DRAW: yZero=%d, yMedian=%d, height=%d<br>", yZero, yMedian, height);
     if (graphPadding == 0 || sameString(colorScheme, GTEX_COLORS_GTEX))
         hvGfxBox(hvg, x1, yMedian+1, barWidth, height, fillColorIx);
     else
         hvGfxOutlinedBox(hvg, x1, yMedian+1, barWidth, height, fillColorIx, lineColorIx);
     x1 = x1 + barWidth + graphPadding;
     }
 
 // mark gene extent
 int yGene = yZero + gtexGeneMargin() - 1;
 
-#ifdef NO_GENE
-// underline
-int start = max(geneBed->chromStart, winStart);
-int end = min(geneBed->chromEnd, winEnd);
-if (start > end)
-    return;
-int xStart = round((start - winStart) * scale)+xOff;
-int width = round((end-start)*scale);
-hvGfxBox(hvg, xStart, yGene, width, gtexGeneHeight(), lineColorIx);
-//uglyf("DRAW: xStart=%d, yGene=%d, width=%d, height=%d<br> ", xStart, yGene, width, gtexGeneHeight());
-#endif
-
 // load & draw gene model
 
 char query[1024];
 char **row;
 sqlSafef(query, sizeof query, "select * from gtexGeneModel where name='%s'", geneBed->geneId);
 struct sqlConnection *conn = hAllocConn(database);
 if (conn == NULL)
     return;
 //uglyf("query: %s<br>", query);
 struct sqlResult *sr = sqlGetResult(conn, query);
 struct genePred *geneModel = NULL;
 if (sr != NULL)
     {
     if ((row = sqlNextRow(sr)) != NULL)
         geneModel = genePredLoad(row);
     sqlFreeResult(&sr);
     }
 if (geneModel == NULL)
     return;
 struct linkedFeatures *lf = linkedFeaturesFromGenePred(tg, geneModel, FALSE);
 tg->heightPer = gtexGeneHeight()+1;
 lf->filterColor = statusColor;
 linkedFeaturesDrawAt(tg, lf, hvg, xOff, yGene, scale, font, color, tvSquish);
 tg->heightPer = heightPer;
 hFreeConn(&conn);
 }
 
 static void gtexGeneMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, 
                         char *mapItemName, int start, int end, int x, int y, int width, int height)
-/* Create a map box for each tissue (bar in the graph) */
+/* Create a map box for each tissue (bar in the graph) or a single map for squish/dense modes */
 {
 //uglyf("map item: itemName=%s, mapItemName=%s, start=%d, end=%d, x=%d, y=%d, width=%d, height=%d, insideX=%d<br>",
         //itemName, mapItemName, start, end, x, y, width, height, insideX);
+
+if (tg->visibility == tvDense || tg->visibility == tvSquish)
+    {
+    genericMapItem(tg, hvg, item, itemName, itemName, start, end, x, y, width, height);
+    }
+
 struct gtexTissue *tissues = getGtexTissues();
 struct gtexTissue *tissue = NULL;
 struct gtexGeneBed *gtex = item;
 int barWidth = gtexBarWidth();
 int padding = gtexGraphPadding();
 double maxExp = ((struct gtexGeneExtras *)tg->extraUiData)->maxExp;
 
 int graphX = gtexGraphX((struct gtexGeneBed *)item);
 if (graphX < 0)
     return;
 // x1 is at left of graph
 int x1 = insideX + graphX;
 
 int i = 0;
 int yZero = gtexGraphHeight() + y - 1;
@@ -355,46 +350,58 @@
 }
 
 static void gtexGeneLoadItems(struct track *track)
 {
 bedLoadItem(track, track->table, (ItemLoader)loadGtexGeneBed);
 double maxExp = 0.0;
 int i;
 struct gtexGeneBed *geneBed;
 for (geneBed = track->items; geneBed != NULL; geneBed = geneBed->next)
     for (i=0; i<geneBed->expCount; i++)
         maxExp = (geneBed->expScores[i] > maxExp ? geneBed->expScores[i] : maxExp);
 struct gtexGeneExtras *extras;
 AllocVar(extras);
 extras->maxExp = maxExp;
 track->extraUiData = extras;
+
 }
 
 static int gtexGeneItemHeight(struct track *track, void *item)
 {
 if ((item == NULL) || (track->visibility == tvSquish) || (track->visibility == tvDense))
     return 0;
 return gtexGraphHeight() + + gtexGeneMargin() + gtexGeneHeight();
 }
 
 static int gtexTotalHeight(struct track *track, enum trackVisibility vis)
 /* Figure out total height of track */
 {
 int height;
 if (track->visibility == tvSquish || track->visibility == tvDense)
     height = 10;
 else 
     height = gtexGraphHeight() + gtexGeneMargin() + gtexGeneHeight();
 return tgFixedTotalHeightOptionalOverflow(track, vis, height, height, FALSE);
 }
 
+static int gtexGeneItemEnd(struct track *track, void *item)
+/* Return end chromosome coordinate of item, including graph */
+{
+struct gtexGeneBed *geneBed = (struct gtexGeneBed *)item;
+double scale = scaleForWindow(insideWidth, winStart, winEnd);
+int graphWidth = gtexGraphWidth(geneBed);
+return max(geneBed->chromEnd, max(winStart, geneBed->chromStart) + graphWidth/scale);
+}
+
+
 void gtexGeneMethods(struct track *track)
 {
 track->drawItemAt = gtexGeneDrawAt;
 track->loadItems = gtexGeneLoadItems;
 track->mapItem = gtexGeneMapItem;
 track->itemHeight = gtexGeneItemHeight;
+track->itemEnd = gtexGeneItemEnd;
 track->totalHeight = gtexTotalHeight;
 }