7c2d98b2096ecfe0c2a45c4a8b81a0fd41788879
kate
  Wed Jul 5 14:45:11 2017 -0700
Cleanup before merge. refs #15646

diff --git src/hg/hgTracks/gtexEqtlClusterTrack.c src/hg/hgTracks/gtexEqtlClusterTrack.c
index cadd2c8..3d8b872 100644
--- src/hg/hgTracks/gtexEqtlClusterTrack.c
+++ src/hg/hgTracks/gtexEqtlClusterTrack.c
@@ -1,19 +1,20 @@
 /* gtexEqtlClusterTrack - Track of clustered expression QTL's from GTEx */
 
 /* Copyright (C) 2017 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "dystring.h"
 #include "hgTracks.h"
 #include "gtexInfo.h"
 #include "gtexTissue.h"
 #include "gtexUi.h"
 #include "gtexEqtlCluster.h"
 
 struct gtexEqtlClusterTrack
 /* Track info for filtering (maybe later for draw, map) */
 {
     struct gtexTissue *tissues; /*  Tissue names, descriptions */
     struct hash *tissueHash;    /* Tissue info, keyed by UCSC name, filtered by UI */
     double minEffect;           /* Effect size filter (abs value) */
     double minProb;             /* Probability filter */
@@ -73,74 +74,70 @@
 struct gtexEqtlClusterTrack *extras = (struct gtexEqtlClusterTrack *)track->extraUiData;
 for (i=0; i<eqtl->expCount; i++)
     {
     if (hashFindVal(extras->tissueHash, eqtl->expNames[i]))
         {
         maxEffect = fmax(maxEffect, fabs(eqtl->expScores[i]));
         maxProb = fmax(maxProb, fabs(eqtl->expProbs[i]));
         }
     else
         {
         excludeTissue(eqtl, i);
         excluded++;
         }
     }
 // exclude if no tissues match selector
-//uglyf(", excluded: %d, maxEffect: %0.2f (min %0.2f), maxProb: %0.2f (min %0.2f)",
-        //excluded, maxEffect, extras->minEffect, maxProb, extras->minProb);
 if (excluded == eqtl->expCount || 
     // or if variant has no selected tissue where effect size is above cutoff
     maxEffect < extras->minEffect || 
     // or if variant has no selected tissue where probability is above cutoff
     maxProb < extras->minProb)
         return FALSE;
 return TRUE;
 }
 
 static void gtexEqtlClusterLoadItems(struct track *track)
 /* Load items in window and prune those that don't pass filter */
 {
 /* initialize track info */
 struct gtexEqtlClusterTrack *extras;
 AllocVar(extras);
 track->extraUiData = extras;
 
 // filter by gene via SQL
 char cartVar[64];
 safef(cartVar, sizeof cartVar, "%s.%s", track->track, GTEX_EQTL_GENE);
 char *gene = cartNonemptyString(cart, cartVar);
 char *where = NULL;
 if (gene)
     {
     struct dyString *ds = dyStringNew(0);
     sqlDyStringPrintfFrag(ds, "%s = '%s'", GTEX_EQTL_GENE_FIELD, gene); 
     where = dyStringCannibalize(&ds);
     }
 bedLoadItemWhere(track, track->table, where, (ItemLoader)loadOne);
-//uglyf("DEBUG: loaded items: %d\n", slCount(track->items));
 
 safef(cartVar, sizeof cartVar, "%s.%s", track->track, GTEX_EQTL_EFFECT);
 extras->minEffect = fabs(cartUsualDouble(cart, cartVar, GTEX_EFFECT_MIN_DEFAULT));
 safef(cartVar, sizeof cartVar, "%s.%s", track->track, GTEX_EQTL_PROBABILITY);
 extras->minProb = cartUsualDouble(cart, cartVar, 0.0);
 boolean hasTissueFilter = filterTissues(track, extras);
 if (!hasTissueFilter && extras->minEffect == 0.0 && extras->minProb == 0.0)
     return;
 
 // more filtering
 filterItems(track, eqtlIncludeFilter, "include");
-//uglyf(", items after filter: %d\n", slCount(track->items));
 }
 
 static char *gtexEqtlClusterItemName(struct track *track, void *item)
 /* Load all items (and motifs if table is present) in window */
 {
 struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item;
 struct dyString *ds = dyStringNew(0);
 if (eqtl->expCount == 1)
     {
     dyStringPrintf(ds, "%s in %s", eqtl->target, eqtl->expNames[0]);
     }
 else
     {
     int i, included;
     for (i=0, included=0; i<eqtl->expCount; i++)
@@ -172,52 +169,50 @@
     if (maxEffect < 0.0 - cutoff)
         return MG_CYAN;
     return MG_BLUE;
     }
 /* up-regulation displayed as red */
 if (maxEffect > cutoff)
     return MG_MAGENTA;
 return MG_RED;
 }
 
 static void gtexEqtlClusterMapItem(struct track *track, 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 on item and label with list of tissues with colors and effect size */
 {
 char *title = itemName;
-//uglyf("<br>title: %s\n", title);
 if (track->limitedVis != tvDense)
     {
-    // construct list of tissues with colors and effect sizes for mouseover
     struct gtexEqtlCluster *eqtl = (struct gtexEqtlCluster *)item;
+    // Experiment: construct list of tissues with colors and effect sizes for mouseover
     //struct gtexEqtlClusterTrack *extras = (struct gtexEqtlClusterTrack *)track->extraUiData;
     //struct hash *tissueHash = extras->tissueHash;
     struct dyString *ds = dyStringNew(0);
     dyStringPrintf(ds, "%s/%s: ", eqtl->name, eqtl->target);
     int i;
     for (i=0; i<eqtl->expCount; i++)
         {
         if (isExcludedTissue(eqtl, i))
             continue;
         double effect= eqtl->expScores[i];
         dyStringPrintf(ds, "%s(%s%0.2f)%s", eqtl->expNames[i], effect < 0 ? "" : "+", effect, 
                         i < eqtl->expCount - 1 ? ", " : "");
         //struct gtexTissue *tis = (struct gtexTissue *)hashFindVal(tissueHash, eqtl->expNames[i]);
         //unsigned color = tis ? tis->color : 0;       // BLACK
         //char *name = tis ? tis->name : "unknown";
         //#dyStringPrintf(ds,"<tr><td style='color: #%06X;'>*</td><td>%s</td><td>%s%0.2f</td></tr>\n", 
                                 //color, name, effect < 0 ? "" : "+", effect); 
         }
     title = dyStringCannibalize(&ds);
     }
-//uglyf("<br>title2: %s\n", title);
 genericMapItem(track, hvg, item, title, itemName, start, end, x, y, width, height);
 }
 
 void gtexEqtlClusterMethods(struct track *track)
 /* BED5+5 with target, expNames,expScores, expProbs */
 {
 track->loadItems = gtexEqtlClusterLoadItems;
 track->itemName  = gtexEqtlClusterItemName;
 track->itemColor = gtexEqtlClusterItemColor;
 track->mapItem   = gtexEqtlClusterMapItem;
 }