6ee3fe36febedef865d3cb3fa7e7116b96fd71f1
larrym
  Thu Mar 22 23:09:21 2012 -0700
mark pubsMarker items as bed5 so the article count is correct; fix some indentation
diff --git src/hg/hgTracks/simpleTracks.c src/hg/hgTracks/simpleTracks.c
index 16b6743..5a23e83 100644
--- src/hg/hgTracks/simpleTracks.c
+++ src/hg/hgTracks/simpleTracks.c
@@ -12380,41 +12380,39 @@
 loadSimpleBedAsLinkedFeaturesPerBase(tg);
 //tg->items = simpleBedListToLinkedFeatures(tg->items, tg->bedSize, TRUE, FALSE);
 //if (! (hashFindVal(tdb->settingsHash, "pubsMarkerTable")))
 enum trackVisibility vis = tg->visibility;
 if (vis == tvDense || vis == tvSquish) 
     return;
 
 struct linkedFeatures *lf = NULL;
 for (lf = tg->items; lf != NULL; lf = lf->next)
     lf->extra = lf->name;
 }
 
 char *pubsMarkerItemName(struct track *tg, void *item)
 /* retrieve article count from score field and return.*/
 {
-//struct bed *bed = item;
 struct linkedFeatures *lf = item;
 char newName[64];
 safef(newName, sizeof(newName), "%d articles", (int) lf->score);
 return cloneString(newName);
 }
 
 static void pubsMarkerMapItem(struct track *tg, struct hvGfx *hvg, void *item,
 				char *itemName, char *mapItemName, int start, int end,
 				int x, int y, int width, int height)
-/* use previously saved itemName for the mouseOver */
 {
 struct linkedFeatures *lf = item;
 genericMapItem(tg, hvg, item,
 		    lf->extra, lf->extra, start, end,
 		    x, y, width, height);
 }
 
 static struct hash* pubsLookupSequences(struct track *tg, struct sqlConnection* conn, char* articleId, bool getSnippet)
 /* create a hash with a mapping annotId -> snippet or annotId -> shortSeq for an articleId*/
 {
     char query[LARGEBUF];
     char *sequenceTable = trackDbRequiredSetting(tg->tdb, "pubsSequenceTable");
     char *selectValSql = NULL;
     if (getSnippet)
         selectValSql = "replace(replace(snippet, \"<B>\", \"-->\"), \"</B>\", \"<--\")";
@@ -12501,32 +12499,33 @@
     activatePslTrackIfCgi(tg);
     tg->loadItems = pubsPslLoadItems;
     tg->itemName  = pubsItemName;
     tg->mapItem   = pubsMapItem;
 }
 
 static void pubsBlatMethods(struct track *tg)
 /* publication blat tracks are bed12+2 tracks of sequences in text, mapped with BLAT */
 {
     tg->loadItems = pubsLoadItems;
     tg->itemName  = pubsItemName;
     tg->mapItem   = pubsMapItem;
 }
 
 static void pubsMarkerMethods(struct track *tg)
-/* publication marker tracks are bed4 tracks of genome marker occurences like rsXXXX found in text*/
+/* publication marker tracks are bed5 tracks of genome marker occurences like rsXXXX found in text*/
 {
+tg->bedSize   = 5;
     tg->loadItems= pubsLoadMarkerItem;
     tg->mapItem  = pubsMarkerMapItem;
     tg->itemName = pubsMarkerItemName;
 }
 
 void fillInFromType(struct track *track, struct trackDb *tdb)
 /* Fill in various function pointers in track from type field of tdb. */
 {
 char *typeLine = tdb->type, *words[8], *type;
 int wordCount;
 if (typeLine == NULL)
     return;
 wordCount = chopLine(cloneString(typeLine), words);
 if (wordCount <= 0)
     return;