fd8e1e948258bfd0bb55364281883d0032516e9e
max
  Fri Apr 13 17:37:44 2012 -0700
removed some comments
diff --git src/hg/hgTracks/simpleTracks.c src/hg/hgTracks/simpleTracks.c
index c262455..23fc049 100644
--- src/hg/hgTracks/simpleTracks.c
+++ src/hg/hgTracks/simpleTracks.c
@@ -12227,31 +12227,31 @@
 static void pubsAddExtra(struct track* tg, struct linkedFeatures* lf)
 /* add authorYear and title to linkedFeatures->extra */
 {
 char *articleTable = trackDbSettingClosestToHome(tg->tdb, "pubsArticleTable");
 if(isEmpty(articleTable))
     return;
 if (lf->extra != NULL)
     return;
 
 struct sqlConnection *conn = hAllocConn(database);
 struct pubsExtra* extra = pubsMakeExtra(articleTable, conn, lf);
 lf->extra = extra;
 hFreeConn(&conn);
 }
 
-static void pubsLoadKeywordYearItems(struct track *tg)
+static void pubsBlatLoadItems(struct track *tg)
 /* load items that fulfill keyword and year filter */
 {
 struct sqlConnection *conn = hAllocConn(database);
 char *keywords = cartOptionalStringClosestToHome(cart, tg->tdb, FALSE, "pubsKeywords");
 char *yearFilter = cartOptionalStringClosestToHome(cart, tg->tdb, FALSE, "pubsYear");
 char *articleTable = pubsArticleTable(tg);
 
 if(yearFilter == NULL || sameWord(yearFilter, "anytime"))
     yearFilter = NULL;
 
 if(isNotEmpty(keywords))
     keywords = makeMysqlMatchStr(sqlEscapeString(keywords));
 
 if(isEmpty(yearFilter) && isEmpty(keywords))
     {
@@ -12465,76 +12465,79 @@
     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 */
 {
-tg->loadItems = pubsLoadKeywordYearItems;
+bedMethods(tg);
+tg->loadItems = pubsBlatLoadItems;
 tg->itemName  = pubsItemName;
 tg->mapItem   = pubsMapItem;
 }
 
 static void pubsMarkerMethods(struct track *tg)
 /* publication marker tracks are bed5 tracks of genome marker occurences like rsXXXX found in text*/
 {
+bedMethods(tg);
 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;
 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: registerTrackHandler cannot do wildcards
-    // I think this is the only way to a similar behaviour
+    // 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);
     }
 /*
 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);
@@ -13280,37 +13283,34 @@
 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);
-
-/* publications track */
-// FIXME: need a way to register based on pattern, see fillInFromType
 registerTrackHandler("pubsBlat", pubsBlatMethods);
 registerTrackHandler("pubsBlatPsl", pubsBlatPslMethods);
-registerTrackHandler("pubsDevBlat", pubsBlatMethods); // pubs testing tracks
-registerTrackHandler("pubsDevBlatPsl", 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);