b9992412e4108b145204db612e185001b92c83a6
max
  Fri Apr 13 18:00:36 2012 -0700
going back to initial state
diff --git src/hg/hgTracks/simpleTracks.c src/hg/hgTracks/simpleTracks.c
index 23fc049..bdfffe2 100644
--- src/hg/hgTracks/simpleTracks.c
+++ src/hg/hgTracks/simpleTracks.c
@@ -12465,31 +12465,30 @@
     struct pubsExtra *extra = needMem(sizeof(struct pubsExtra));
     extra->mouseOver=snip;
     extra->label=shortSeq;
     lfList->extra = extra;
     }
 sqlFreeResult(&sr);
 slReverse(&lfList);
 slSort(&lfList, linkedFeaturesCmp);
 tg->items = lfList;
 hFreeConn(&conn);
 }
 
 static void pubsBlatPslMethods(struct track *tg)
 /* a track that shows only the indiv matches for one single article */
 {
-//pslMethods(tg, NULL, 0, NULL);
 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 */
 {
 bedMethods(tg);
 tg->loadItems = pubsBlatLoadItems;
 tg->itemName  = pubsItemName;
 tg->mapItem   = pubsMapItem;
 }
 
@@ -12516,30 +12515,32 @@
 type = words[0];
 
 #ifndef GBROWSE
 if (sameWord(type, "bed"))
     {
     complexBedMethods(track, tdb, FALSE, wordCount, words);
     /* bed.h includes genePred.h so should be able to use these trackDb
        settings. */
     if (trackDbSetting(track->tdb, GENEPRED_CLASS_TBL) !=NULL)
         track->itemColor = genePredItemClassColor;
 
     // FIXME: this is in the wrong function, but needs to stay as long as 
     // registerTrackHandler does not accept wildcards
     if (startsWith("pubs", track->track) && stringIn("Marker", track->track))
         pubsMarkerMethods(track);
+    if (startsWith("pubs", track->track) && stringIn("Blat", track->track))
+        pubsBlatMethods(track);
     }
 /*
 else if (sameWord(type, "bedLogR"))
     {
     wordCount++;
     words[1] = "9";
     complexBedMethods(track, tdb, FALSE, wordCount, words);
     //track->bedSize = 10;
     }
     */
 else if (sameWord(type, "bigBed"))
     {
     bigBedMethods(track, tdb, wordCount, words);
     if (trackShouldUseAjaxRetrieval(track))
         track->loadItems = dontLoadItems;
@@ -12575,30 +12576,32 @@
     track->loadItems = loadGenePred;
     track->colorShades = NULL;
     if (track->itemAttrTbl != NULL)
         track->itemColor = genePredItemAttrColor;
     else if (trackDbSetting(track->tdb, GENEPRED_CLASS_TBL) !=NULL)
         track->itemColor = genePredItemClassColor;
     }
 else if (sameWord(type, "logo"))
     {
     logoMethods(track, tdb, wordCount, words);
     }
 #endif /* GBROWSE */
 else if (sameWord(type, "psl"))
     {
     pslMethods(track, tdb, wordCount, words);
+    if (startsWith("pubs", track->track))
+        pubsBlatPslMethods(track);
     }
 else if (sameWord(type, "snake"))
     {
     snakeMethods(track, tdb, wordCount, words);
     }
 else if (sameWord(type, "chain"))
     {
     chainMethods(track, tdb, wordCount, words);
     }
 else if (sameWord(type, "netAlign"))
     {
     netMethods(track);
     }
 else if (sameWord(type, "maf"))
     {
@@ -13283,34 +13286,30 @@
 registerTrackHandler("encode_tba23EvoFold", rnaSecStrMethods);
 registerTrackHandler("encodeEvoFold", rnaSecStrMethods);
 registerTrackHandler("rnafold", rnaSecStrMethods);
 registerTrackHandler("mcFolds", rnaSecStrMethods);
 registerTrackHandler("rnaEditFolds", rnaSecStrMethods);
 registerTrackHandler("altSpliceFolds", rnaSecStrMethods);
 registerTrackHandler("chimpSimpleDiff", chimpSimpleDiffMethods);
 registerTrackHandler("tfbsCons", tfbsConsMethods);
 registerTrackHandler("tfbsConsSites", tfbsConsSitesMethods);
 registerTrackHandler("pscreen", simpleBedTriangleMethods);
 registerTrackHandler("dless", dlessMethods);
 registerTrackHandler("jaxAllele", jaxAlleleMethods);
 registerTrackHandler("jaxPhenotype", jaxPhenotypeMethods);
 registerTrackHandler("jaxAlleleLift", jaxAlleleMethods);
 registerTrackHandler("jaxPhenotypeLift", jaxPhenotypeMethods);
-registerTrackHandler("pubsBlat", pubsBlatMethods);
-registerTrackHandler("pubsBlatPsl", pubsBlatPslMethods);
-registerTrackHandler("pubsDevBlat", pubsBlatMethods); // pubs testing track
-registerTrackHandler("pubsDevBlatPsl", pubsBlatPslMethods); // pubs testing track
 
 /* ENCODE related */
 registerTrackHandlerOnFamily("wgEncodeGencode", gencodeGeneMethods);
 registerTrackHandlerOnFamily("wgEncodeSangerGencode", gencodeGeneMethods);
 // one per gencode version, after V7 when it was substantially changed
 // FIXME: this is hacky, need a way to register based on pattern
 registerTrackHandlerOnFamily("wgEncodeGencodeV3", gencodeGeneMethods);
 registerTrackHandlerOnFamily("wgEncodeGencodeV4", gencodeGeneMethods);
 registerTrackHandlerOnFamily("wgEncodeGencodeV7", gencodeGeneMethods);
 registerTrackHandlerOnFamily("wgEncodeGencodeV8", gencodeGeneMethods);
 registerTrackHandlerOnFamily("wgEncodeGencodeV9", gencodeGeneMethods);
 registerTrackHandlerOnFamily("wgEncodeGencodeV10", gencodeGeneMethods);
 registerTrackHandlerOnFamily("wgEncodeGencodeV11", gencodeGeneMethods);
 registerTrackHandlerOnFamily("wgEncodeGencodeV12", gencodeGeneMethods);
 registerTrackHandlerOnFamily("wgEncodeGencodeV13", gencodeGeneMethods);