4880079233bb3e037c495199d495bfdb79c99eed
Merge parents 8931b6a 9900ab6
tdreszer
  Mon Nov 21 15:49:43 2011 -0800
Merg-o-rama
diff --cc src/hg/hgTrackUi/hgTrackUi.c
index c45e4f5,405ba0c..ccf56c0
--- src/hg/hgTrackUi/hgTrackUi.c
+++ src/hg/hgTrackUi/hgTrackUi.c
@@@ -2426,140 -2483,171 +2436,142 @@@
              "genome.ucsc.edu", db);
          }
      else
          {
          // TODO: use hTrackUiName()
          printf("<p><b>NOTE</b>: Early access to additional track data may be available on the <a target=_blank href='http://%s/cgi-bin/hgTrackUi?db=%s&g=%s'>Preview Browser</A>.",
              "genome-preview.ucsc.edu", db, tdb->track);
          }
      }
  }
  
  void specificUi(struct trackDb *tdb, struct trackDb *tdbList, struct customTrack *ct, boolean ajax)
  /* Draw track specific parts of UI. */
  {
  char *track = tdb->track;
 -
 -if (sameString(track, "stsMap"))
 -        stsMapUi(tdb);
 +// Ideally check cfgTypeFromTdb()/cfgByCfgType() first, but with all these special cases already in
 +//    place, lets be cautious at this time.
 +// NOTE: Developer, please try to use cfgTypeFromTdb()/cfgByCfgType().
 +
 +boolean boxed = trackDbSettingClosestToHomeOn(tdb, "boxedCfg");
 +// UI precedence:
 +// 1) supers to get them out of the way: they have no controls
 +// 2) special cases based upon track name (developer please avoid)
 +// 3) cfgTypeFromTdb()/cfgByCfgType() <== prefered method
 +// 4) special cases falling through the cracks but based upon type
 +if (tdbIsSuperTrack(tdb))
 +    superTrackUi(tdb, tdbList);
 +else if (sameString(track, "stsMap"))
 +    stsMapUi(tdb);
  else if (sameString(track, "affyTxnPhase2"))
      affyTxnPhase2Ui(tdb);
  else if (sameString(track, "cgapSage"))
      cgapSageUi(tdb);
  else if (sameString(track, "stsMapMouseNew"))
 -        stsMapMouseUi(tdb);
 +    stsMapMouseUi(tdb);
  else if (sameString(track, "stsMapRat"))
 -        stsMapRatUi(tdb);
 +    stsMapRatUi(tdb);
  else if (sameString(track, "snpMap"))
 -        snpMapUi(tdb);
 +    snpMapUi(tdb);
  else if (sameString(track, "snp"))
 -        snpUi(tdb);
 +    snpUi(tdb);
  else if (snpVersion(track) >= 125)
 -	snp125Ui(tdb);
 -else if (sameString(track, "rertyHumanDiversityLd") ||
 -	 startsWith("hapmapLd", track) ||
 -	 sameString(tdb->type, "ld2"))
 -        ldUi(tdb);
 +    snp125Ui(tdb);
 +else if (sameString(track, "rertyHumanDiversityLd")
 +     ||	 startsWith("hapmapLd", track)
 +     ||	 sameString(tdb->type, "ld2"))
 +    ldUi(tdb);
  else if (sameString(track, "cbr_waba"))
 -        cbrWabaUi(tdb);
 +    cbrWabaUi(tdb);
  else if (sameString(track, "fishClones"))
 -        fishClonesUi(tdb);
 +    fishClonesUi(tdb);
  else if (sameString(track, "recombRate"))
 -        recombRateUi(tdb);
 +    recombRateUi(tdb);
  else if (sameString(track, "recombRateRat"))
 -        recombRateRatUi(tdb);
 +    recombRateRatUi(tdb);
  else if (sameString(track, "recombRateMouse"))
 -        recombRateMouseUi(tdb);
 +    recombRateMouseUi(tdb);
  else if (sameString(track, "cghNci60"))
 -        cghNci60Ui(tdb);
 -else if (sameString(track, "xenoRefGene"))
 -        refGeneUI(tdb);
 +    cghNci60Ui(tdb);
 +else if (sameString(track, "xenoRefGene")
 +     ||  sameString(track, "refGene"))
 +    refGeneUI(tdb);
  else if (startsWith("transMapAln", track))
 -        transMapUI(tdb);
 -else if (sameString(track, "refGene"))
 -        refGeneUI(tdb);
 +    transMapUI(tdb);
  else if (sameString(track, "rgdGene2"))
 -        rgdGene2UI(tdb);
 +    rgdGene2UI(tdb);
  else if (sameString(track, "knownGene"))
 -        knownGeneUI(tdb);
 +    knownGeneUI(tdb);
  else if (sameString(track, "omimLocation"))
 -        omimLocationUI(tdb);
 +    omimLocationUI(tdb);
  else if (sameString(track, "omimGene2"))
 -        omimGene2UI(tdb);
 +    omimGene2UI(tdb);
  else if (sameString(track, "omimGene"))
 -        omimGeneUI(tdb);
 +    omimGeneUI(tdb);
  else if (sameString(track, "hg17Kg"))
 -        hg17KgUI(tdb);
 -else if (startsWith("ucscRetro", track) || startsWith("retroMrnaInfo", track))
 -        retroGeneUI(tdb);
 +    hg17KgUI(tdb);
 +else if (startsWith("ucscRetro", track)
 +     ||  startsWith("retroMrnaInfo", track))
 +    retroGeneUI(tdb);
  else if (sameString(track, "ensGeneNonCoding"))
 -        ensemblNonCodingUI(tdb);
 +    ensemblNonCodingUI(tdb);
  else if (sameString(track, "vegaGeneComposite"))
 -        vegaGeneUI(tdb);
 -else if (sameString(track, "all_mrna"))
 -    mrnaUi(tdb, FALSE);
 -else if (sameString(track, "mrna"))
 -    mrnaUi(tdb, FALSE);
 -else if (sameString(track, "splicesP"))
 -    bedUi(tdb, cart, "", FALSE);
 -else if(sameString(track,"FantomCageBedForward") || sameString(track,"FantomCageBedReverse") ||
 -	sameString(track,"FantomCageReadForward") || sameString(track,"FantomCageReadReverse"))
 -    bedUi(tdb, cart, "", FALSE);
 -else if (sameString(track, "all_est"))
 -        mrnaUi(tdb, FALSE);
 -else if (sameString(track, "est"))
 -        mrnaUi(tdb, FALSE);
 -else if (sameString(track, "tightMrna"))
 -        mrnaUi(tdb, FALSE);
 -else if (sameString(track, "tightEst"))
 -        mrnaUi(tdb, FALSE);
 -else if (sameString(track, "intronEst"))
 -        mrnaUi(tdb, FALSE);
 -else if (sameString(track, "xenoMrna"))
 -        mrnaUi(tdb, TRUE);
 -else if (sameString(track, "xenoEst"))
 -        mrnaUi(tdb, TRUE);
 +    vegaGeneUI(tdb);
  else if (sameString(track, "rosetta"))
 -        rosettaUi(tdb);
 +    rosettaUi(tdb);
+ else if (startsWith("t2g", track)) 
+         t2gUi(tdb);
  else if (startsWith("blastDm", track))
 -        blastFBUi(tdb);
 +    blastFBUi(tdb);
  else if (sameString(track, "blastSacCer1SG"))
 -        blastSGUi(tdb);
 -else if (sameString(track, "blastHg17KG") || sameString(track, "blastHg16KG")
 -        || sameString(track, "blastCe3WB") || sameString(track, "blastHg18KG")
 -        || sameString(track, "blatzHg17KG")|| startsWith("mrnaMap", track)|| startsWith("mrnaXeno", track))
 -        blastUi(tdb);
 +    blastSGUi(tdb);
 +else if (sameString(track, "blastHg17KG")
 +     ||  sameString(track, "blastHg16KG")
 +     ||  sameString(track, "blastCe3WB")
 +     ||  sameString(track, "blastHg18KG")
 +     ||  sameString(track, "blatzHg17KG")
 +     ||  startsWith("mrnaMap", track)
 +     ||  startsWith("mrnaXeno", track))
 +    blastUi(tdb);
  else if (sameString(track, "hgPcrResult"))
      pcrResultUi(tdb);
 -else if (startsWith("bedGraph", tdb->type) || startsWith("bigWig", tdb->type))
 -    wigCfgUi(cart,tdb,tdb->track,NULL, FALSE);
 -else if (startsWith("bamWig", tdb->type))
 -    wigCfgUi(cart,tdb,tdb->track,NULL, FALSE);
 -else if (startsWith("wig", tdb->type))
 -        {
 -        if (startsWith("wigMaf", tdb->type))
 -            wigMafCfgUi(cart, tdb, tdb->track, NULL, FALSE, database);
 -        else
 -            wigCfgUi(cart,tdb,tdb->track, NULL, FALSE);
 -        }
 -else if (startsWith("chromGraph", tdb->type))
 -        chromGraphUi(tdb);
 -/* else if (sameString(track, "affyHumanExon")) */
 -/*         affyAllExonUi(tdb); */
  else if (sameString(track, "ancientR"))
 -        ancientRUi(tdb);
 -else if (sameString(track, "zoo") || sameString(track, "zooNew" ))
 -         zooWiggleUi(tdb);
 -else if (sameString(track, "humMusL") ||
 -         sameString( track, "musHumL") ||
 -         sameString( track, "regpotent") ||
 -         sameString( track, "mm3Rn2L" )	 ||
 -         sameString( track, "mm3Hg15L" ) ||
 -         sameString( track, "hg15Mm3L" ))
 -            humMusUi(tdb,7);
 -/* NOTE: type psl xeno <otherDb> tracks use crossSpeciesUi, so
 - * add explicitly here only if track has another type (bed, chain).
 - * For crossSpeciesUi, the
 - * default for chrom coloring is "on", unless track setting
 - * colorChromDefault is set to "off" */
 -else if (startsWith("net", track))
 -    netAlignCfgUi(database, cart, tdb, tdb->track, NULL, FALSE);
 -else if (startsWith("chain", track) || endsWith("chainSelf", track))
 +    ancientRUi(tdb);
 +else if (sameString(track, "zoo")
 +     ||  sameString(track, "zooNew" ))
 +    zooWiggleUi(tdb);
 +else if (sameString(track, "humMusL")
 +     ||  sameString(track, "musHumL")
 +     ||  sameString(track, "regpotent")
 +     ||  sameString(track, "mm3Rn2L" )
 +     ||  sameString(track, "mm3Hg15L" )
 +     ||  sameString(track, "hg15Mm3L" ))
 +    humMusUi(tdb,7);
 +else if (startsWith("chain", track)
 +     || endsWith("chainSelf", track))
      chainColorUi(tdb);
 -else if (sameString(track, "orthoTop4"))
 -    /* still used ?? */
 -    crossSpeciesUi(tdb);
 -else if (sameString(track, "mouseOrtho"))
 -    crossSpeciesUi(tdb);
 -else if (sameString(track, "mouseSyn"))
 -    crossSpeciesUi(tdb);
 +else if (sameString(track, "orthoTop4") // still used ??
 +     ||  sameString(track, "mouseOrtho")
 +     ||  sameString(track, "mouseSyn"))
 +    // NOTE: type psl xeno <otherDb> tracks use crossSpeciesCfgUi, so
 +    // add explicitly here only if track has another type (bed, chain).
 +    // For crossSpeciesCfgUi, the
 +    // default for chrom coloring is "on", unless track setting
 +    // colorChromDefault is set to "off"
 +    crossSpeciesCfgUi(cart,tdb);
  else if (sameString(track, "affyTranscriptome"))
      affyTranscriptomeUi(tdb);
 -
 -else if (startsWith("sample", tdb->type))
 -    genericWiggleUi(tdb,7);
  else if (sameString(track, WIKI_TRACK_TABLE))
      wikiTrackUi(tdb);
  else if (sameString(track, RULER_TRACK_NAME))
      rulerUi(tdb);
  else if (sameString(track, OLIGO_MATCH_TRACK_NAME))
      oligoMatchUi(tdb);
  else if (sameString(track, CUTTERS_TRACK_NAME))
      cutterUi(tdb);
  else if(sameString(track, "affyTransfrags"))
      affyTransfragUi(tdb);
  else if (sameString(track, "gvPos"))
      gvUi(tdb);
  else if (sameString(track, "oreganno"))
      oregannoUi(tdb);
  else if (startsWith("retroposons", track))