d781bc31ad6c4a86a3b8e1f0e78827a08c544128
tdreszer
  Fri Oct 1 11:05:56 2010 -0700
Fixing git mess (I hope) created from an accidental 'git add .'
diff --git src/hg/hgTracks/hgTracks.c.old src/hg/hgTracks/hgTracks.c.old
deleted file mode 100644
index f68887d..0000000
--- src/hg/hgTracks/hgTracks.c.old
+++ /dev/null
@@ -1,5646 +0,0 @@
-/* hgTracks - the original, and still the largest module for the UCSC Human Genome
- * Browser main cgi script.  Currently contains most of the track framework, though
- * there's quite a bit of other framework type code in simpleTracks.c.  The main
- * routine got moved to create a new entry point to the bulk of the code for the
- * hgRenderTracks web service.  See mainMain.c for the main used by the hgTracks CGI. */
-
-#include "common.h"
-#include "hCommon.h"
-#include "linefile.h"
-#include "portable.h"
-#include "memalloc.h"
-#include "localmem.h"
-#include "obscure.h"
-#include "dystring.h"
-#include "hash.h"
-#include "jksql.h"
-#include "gfxPoly.h"
-#include "memgfx.h"
-#include "hvGfx.h"
-#include "psGfx.h"
-#include "cheapcgi.h"
-#include "hPrint.h"
-#include "htmshell.h"
-#include "cart.h"
-#include "hdb.h"
-#include "hui.h"
-#include "hgFind.h"
-#include "hgTracks.h"
-#include "trashDir.h"
-#include "grp.h"
-#include "versionInfo.h"
-#include "web.h"
-#include "cds.h"
-#include "cutterTrack.h"
-#include "wikiTrack.h"
-#include "ctgPos.h"
-#include "bed.h"
-#include "bigBed.h"
-#include "bigWig.h"
-#include "bedCart.h"
-#include "customTrack.h"
-#include "cytoBand.h"
-#include "ensFace.h"
-#include "liftOver.h"
-#include "pcrResult.h"
-#include "wikiLink.h"
-#include "jsHelper.h"
-#include "mafTrack.h"
-#include "hgConfig.h"
-#include "encode.h"
-#include "agpFrag.h"
-#include "imageV2.h"
-#include "suggest.h"
-#include "searchTracks.h"
-
-static char const rcsid[] = "$Id: doMiddle.c,v 1.1651 2010/06/11 17:53:06 larrym Exp $";
-
-/* These variables persist from one incarnation of this program to the
- * next - living mostly in the cart. */
-boolean baseShowPos;           /* TRUE if should display full position at top of base track */
-boolean baseShowAsm;           /* TRUE if should display assembly info at top of base track */
-boolean baseShowScaleBar;      /* TRUE if should display scale bar at very top of base track */
-boolean baseShowRuler;         /* TRUE if should display the basic ruler in the base track (default) */
-char *baseTitle = NULL;        /* Title it should display top of base track (optional)*/
-static char *userSeqString = NULL;  /* User sequence .fa/.psl file. */
-
-/* These variables are set by getPositionFromCustomTracks() at the very
- * beginning of tracksDisplay(), and then used by loadCustomTracks(). */
-char *ctFileName = NULL;    /* Custom track file. */
-struct customTrack *ctList = NULL;  /* Custom tracks. */
-boolean hasCustomTracks = FALSE;  /* whether any custom tracks are for this db*/
-struct slName *browserLines = NULL; /* Custom track "browser" lines. */
-
-boolean withNextItemArrows = FALSE; /* Display next feature (gene) navigation buttons near center labels? */
-boolean withPriorityOverride = FALSE;   /* Display priority for each track to allow reordering */
-
-int gfxBorder = hgDefaultGfxBorder; /* Width of graphics border. */
-int guidelineSpacing = 12;  /* Pixels between guidelines. */
-
-boolean withIdeogram = TRUE;            /* Display chromosome ideogram? */
-
-int rulerMode = tvHide;         /* on, off, full */
-
-char *rulerMenu[] =
-/* dropdown for ruler visibility */
-    {
-    "hide",
-    "dense",
-    "full"
-    };
-
-char *protDbName;               /* Name of proteome database for this genome. */
-#define MAX_CONTROL_COLUMNS 6
-#define LOW 1
-#define MEDIUM 2
-#define BRIGHT 3
-#define MAXCHAINS 50000000
-boolean hgDebug = FALSE;      /* Activate debugging code. Set to true by hgDebug=on in command line*/
-int imagePixelHeight = 0;
-boolean dragZooming = TRUE;
-struct hash *oldVars = NULL;
-
-boolean hideControls = FALSE;		/* Hide all controls? */
-boolean trackImgOnly = FALSE;           /* caller wants just the track image and track table html */
-boolean ideogramToo =  FALSE;           /* caller wants the ideoGram (when requesting just one track) */
-
-/* Structure returned from findGenomePos.
- * We use this to to expand any tracks to full
- * that were found to contain the searched-upon
- * position string */
-struct hgPositions *hgp = NULL;
-
-
-/* Other global variables. */
-struct group *groupList = NULL;    /* List of all tracks. */
-char *browserName;              /* Test or public browser */
-char *organization;             /* UCSC */
-
-
-struct track *trackFindByName(struct track *tracks, char *trackName)
-/* find a track in tracks by name, recursively searching subtracks */
-{
-struct track *track;
-for (track = tracks; track != NULL; track = track->next)
-    {
-    if (sameString(track->track, trackName))
-        return track;
-    else if (track->subtracks != NULL)
-        {
-        struct track *st = trackFindByName(track->subtracks, trackName);
-        if (st != NULL)
-            return st;
-        }
-    }
-return NULL;
-}
-
-int tgCmpPriority(const void *va, const void *vb)
-/* Compare to sort based on priority; use shortLabel as secondary sort key. */
-{
-const struct track *a = *((struct track **)va);
-const struct track *b = *((struct track **)vb);
-float dif = a->group->priority - b->group->priority;
-
-if (dif == 0)
-    dif = a->priority - b->priority;
-if (dif < 0)
-   return -1;
-else if (dif == 0.0)
-    /* secondary sort on label */
-    return strcasecmp(a->shortLabel, b->shortLabel);
-else
-   return 1;
-}
-
-int trackRefCmpPriority(const void *va, const void *vb)
-/* Compare based on priority. */
-{
-const struct trackRef *a = *((struct trackRef **)va);
-const struct trackRef *b = *((struct trackRef **)vb);
-return tgCmpPriority(&a->track, &b->track);
-}
-
-int gCmpPriority(const void *va, const void *vb)
-/* Compare groups based on priority. */
-{
-const struct group *a = *((struct group **)va);
-const struct group *b = *((struct group **)vb);
-float dif = a->priority - b->priority;
-
-if (dif == 0)
-    return 0;
-if (dif < 0)
-   return -1;
-else if (dif == 0.0)
-   return 0;
-else
-   return 1;
-}
-
-void changeTrackVis(struct group *groupList, char *groupTarget, int changeVis)
-/* Change track visibilities. If groupTarget is
- * NULL then set visibility for tracks in all groups.  Otherwise,
- * just set it for the given group.  If vis is -2, then visibility is
- * unchanged.  If -1 then set visibility to default, otherwise it should
- * be tvHide, tvDense, etc.
- * If we are going back to default visibility, then reset the track
- * ordering also. */
-{
-struct group *group;
-if (changeVis == -2)
-    return;
-for (group = groupList; group != NULL; group = group->next)
-    {
-    struct trackRef *tr;
-    if (groupTarget == NULL || sameString(group->name,groupTarget))
-        {
-        static char pname[512];
-        /* if default vis then reset group priority */
-        if (changeVis == -1)
-            group->priority = group->defaultPriority;
-    for (tr = group->trackList; tr != NULL; tr = tr->next)
-        {
-        struct track *track = tr->track;
-	struct trackDb *tdb = track->tdb;
-        if (changeVis == -1) // to default
-                {
-                if(tdbIsComposite(tdb))
-                    {
-                    safef(pname, sizeof(pname),"%s.*",track->track); //to remove all settings associated with this composite!
-                    cartRemoveLike(cart,pname);
-                    struct track *subTrack;
-                    for(subTrack = track->subtracks;subTrack != NULL; subTrack = subTrack->next)
-                        {
-                        subTrack->visibility = tdb->visibility;
-                        cartRemove(cart, subTrack->track);
-                        }
-                    }
-
-                /* restore defaults */
-                if (tdbIsSuperTrackChild(tdb) || tdbIsCompositeChild(tdb))
-                    {
-                    assert(tdb->parent != NULL && tdb->parent->track);
-                    cartRemove(cart, tdb->parent->track);
-                    if (withPriorityOverride)
-                        {
-                        safef(pname, sizeof(pname), "%s.priority",tdb->parent->track);
-                        cartRemove(cart, pname);
-                        }
-                    }
-
-                track->visibility = tdb->visibility;
-                cartRemove(cart, track->track);
-
-                /* set the track priority back to the default value */
-                if (withPriorityOverride)
-                    {
-                    safef(pname, sizeof(pname), "%s.priority",track->track);
-                    cartRemove(cart, pname);
-                    track->priority = track->defaultPriority;
-                    }
-                }
-            else // to changeVis value (Usually tvHide)
-                {
-                /* change to specified visibility */
-                if (tdbIsSuperTrackChild(tdb))
-                    {
-                    assert(tdb->parent != NULL);
-                    /* Leave supertrack members alone -- only change parent */
-                    struct trackDb *parentTdb = tdb->parent;
-                    if ((changeVis == tvHide && !parentTdb->isShow) ||
-                        (changeVis != tvHide && parentTdb->isShow))
-                        {
-                        /* remove if setting to default vis */
-                        cartRemove(cart, parentTdb->track);
-                        }
-                    else
-                        cartSetString(cart, parentTdb->track,
-                                    changeVis == tvHide ? "hide" : "show");
-                    }
-                else // Not super  child
-                    {
-                    if (changeVis == tdb->visibility)
-                        /* remove if setting to default vis */
-                        cartRemove(cart, track->track);
-                    else
-                        cartSetString(cart, track->track, hStringFromTv(changeVis));
-                    track->visibility = changeVis;
-                    }
-
-                #ifdef SUBTRACKS_HAVE_VIS
-                // Whether super child or not, if its a composite, then handle the children
-                if (tdbIsComposite(tdb))
-                    {
-                    struct track *subtrack;
-                    for(subtrack=track->subtracks;subtrack!=NULL;subtrack=subtrack->next)
-                        {
-                        if (changeVis == tvHide)
-                            cartRemove(cart, subtrack->track); // Since subtrack level vis is an override, simply remove it to hide it
-                        else
-                            cartSetString(cart, subtrack->track, hStringFromTv(changeVis));
-                        subtrack->visibility = changeVis;
-                        }
-                    }
-                #endif///def SUBTRACKS_HAVE_VIS
-                }
-            }
-        }
-    }
-slSort(&groupList, gCmpPriority);
-}
-
-int trackOffsetX()
-/* Return x offset where track display proper begins. */
-{
-int x = gfxBorder;
-if (withLeftLabels)
-    x += tl.leftLabelWidth + gfxBorder;
-return x;
-}
-
-
-static void mapBoxTrackUi(struct hvGfx *hvg, int x, int y, int width,
-              int height, char *name, char *shortLabel, char *id)
-/* Print out image map rectangle that invokes hgTrackUi. */
-{
-x = hvGfxAdjXW(hvg, x, width);
-char *url = trackUrl(name, chromName);
-
-if(theImgBox && curImgTrack)
-    {
-    struct imgSlice *curSlice = imgTrackSliceGetByType(curImgTrack,stButton);
-    if(curSlice)
-        sliceAddLink(curSlice,url,shortLabel);
-    }
-else
-    {
-    hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", x, y, x+width, y+height);
-    hPrintf("HREF=\"%s\"", url);
-    mapStatusMessage("%s controls", shortLabel);
-    hPrintf(">\n");
-    }
-freeMem(url);
-}
-
-static void mapBoxToggleComplement(struct hvGfx *hvg, int x, int y, int width, int height,
-    struct track *toggleGroup, char *chrom,
-    int start, int end, char *message)
-/*print out a box along the DNA bases that toggles a cart variable
- * "complement" to complement the DNA bases at the top by the ruler*/
-{
-struct dyString *ui = uiStateUrlPart(toggleGroup);
-x = hvGfxAdjXW(hvg, x, width);
-if(theImgBox && curImgTrack)
-    {
-    char link[512];
-    safef(link,sizeof(link),"%s?complement_%s=%d&%s",
-        hgTracksName(), database, !cartUsualBooleanDb(cart, database, COMPLEMENT_BASES_VAR, FALSE),ui->string);
-    imgTrackAddMapItem(curImgTrack,link,(char *)(message != NULL?message:NULL),x, y, x+width, y+height, NULL);
-    }
-else
-    {
-    hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", x, y, x+width, y+height);
-    hPrintf("HREF=\"%s?complement_%s=%d",
-        hgTracksName(), database, !cartUsualBooleanDb(cart, database, COMPLEMENT_BASES_VAR, FALSE));
-    hPrintf("&%s\"", ui->string);
-    freeDyString(&ui);
-    if (message != NULL)
-        mapStatusMessage("%s", message);
-    hPrintf(">\n");
-    }
-}
-
-char *trackUrl(char *mapName, char *chromName)
-/* Return hgTrackUi url; chromName is optional. */
-{
-char *encodedMapName = cgiEncode(mapName);
-char buf[2048];
-if(chromName == NULL)
-    safef(buf, sizeof(buf), "%s?%s=%u&g=%s", hgTrackUiName(), cartSessionVarName(), cartSessionId(cart), encodedMapName);
-else
-    safef(buf, sizeof(buf), "%s?%s=%u&c=%s&g=%s", hgTrackUiName(), cartSessionVarName(), cartSessionId(cart), chromName, encodedMapName);
-freeMem(encodedMapName);
-return(cloneString(buf));
-}
-
-void smallBreak()
-/* Draw small horizontal break */
-{
-hPrintf("<FONT SIZE=1><BR></FONT>\n");
-}
-
-static int trackPlusLabelHeight(struct track *track, int fontHeight)
-/* Return the sum of heights of items in this track (or subtrack as it may be)
- * and the center label(s) above the items (if any). */
-{
-int y = track->totalHeight(track, limitVisibility(track));
-if (isCenterLabelIncluded(track))
-    y += fontHeight;
-if (tdbIsComposite(track->tdb))
-    {
-    struct track *subtrack;
-    for (subtrack = track->subtracks;  subtrack != NULL; subtrack = subtrack->next)
-        {
-        if (isSubtrackVisible(subtrack) &&  isCenterLabelIncluded(subtrack))
-            y += fontHeight;
-        }
-    }
-return y;
-}
-
-void drawColoredButtonBox(struct hvGfx *hvg, int x, int y, int w, int h,
-                                int enabled, Color shades[])
-/* draw button box, providing shades of the desired button color */
-{
-int light = shades[1], mid = shades[2], dark = shades[4];
-if (enabled)
-    {
-    hvGfxBox(hvg, x, y, w, 1, light);
-    hvGfxBox(hvg, x, y+1, 1, h-1, light);
-    hvGfxBox(hvg, x+1, y+1, w-2, h-2, mid);
-    hvGfxBox(hvg, x+1, y+h-1, w-1, 1, dark);
-    hvGfxBox(hvg, x+w-1, y+1, 1, h-1, dark);
-    }
-else                /* try to make the button look as if
-                 * it is already depressed */
-    {
-    hvGfxBox(hvg, x, y, w, 1, dark);
-    hvGfxBox(hvg, x, y+1, 1, h-1, dark);
-    hvGfxBox(hvg, x+1, y+1, w-2, h-2, light);
-    hvGfxBox(hvg, x+1, y+h-1, w-1, 1, light);
-    hvGfxBox(hvg, x+w-1, y+1, 1, h-1, light);
-    }
-}
-
-void drawGrayButtonBox(struct hvGfx *hvg, int x, int y, int w, int h, int enabled)
-/* Draw a gray min-raised looking button. */
-{
-    drawColoredButtonBox(hvg, x, y, w, h, enabled, shadesOfGray);
-}
-
-void drawBlueButtonBox(struct hvGfx *hvg, int x, int y, int w, int h, int enabled)
-/* Draw a blue min-raised looking button. */
-{
-    drawColoredButtonBox(hvg, x, y, w, h, enabled, shadesOfSea);
-}
-
-void drawButtonBox(struct hvGfx *hvg, int x, int y, int w, int h, int enabled)
-/* Draw a standard (gray) min-raised looking button. */
-{
-    drawGrayButtonBox(hvg, x, y, w, h, enabled);
-}
-
-void beforeFirstPeriod( char *str )
-{
-char *t = rindex( str, '.' );
-
-if( t == NULL )
-    return;
-else
-    str[strlen(str) - strlen(t)] = '\0';
-}
-
-static void drawBases(struct hvGfx *hvg, int x, int y, int width, int height,
-                        Color color, MgFont *font, boolean complementSeq,
-                        struct dnaSeq *thisSeq)
-/* Draw evenly spaced bases. */
-{
-struct dnaSeq *seq;
-
-if (thisSeq == NULL)
-    seq = hDnaFromSeq(database, chromName, winStart, winEnd, dnaUpper);
-else
-    seq = thisSeq;
-
-if (complementSeq)
-    complement(seq->dna, seq->size);
-spreadBasesString(hvg, x, y, width, height, color, font,
-                                seq->dna, seq->size, FALSE);
-
-if (thisSeq == NULL)
-    freeDnaSeq(&seq);
-}
-
-void drawComplementArrow( struct hvGfx *hvg, int x, int y,
-                                int width, int height, MgFont *font)
-/* Draw arrow and create clickbox for complementing ruler bases */
-{
-boolean baseCmpl = cartUsualBooleanDb(cart, database, COMPLEMENT_BASES_VAR, FALSE);
-// reverse arrow when base complement doesn't match display
-char *text =  (baseCmpl == revCmplDisp) ? "--->" : "<---";
-hvGfxTextRight(hvg, x, y, width, height, MG_BLACK, font, text);
-mapBoxToggleComplement(hvg, x, y, width, height, NULL, chromName, winStart, winEnd,
-                       "complement bases");
-}
-
-struct track *chromIdeoTrack(struct track *trackList)
-/* Find chromosome ideogram track */
-{
-struct track *track;
-for(track = trackList; track != NULL; track = track->next)
-    {
-    if(sameString(track->track, "cytoBandIdeo"))
-	{
-	if (hTableExists(database, track->table))
-	    return track;
-	else
-	    return NULL;
-	}
-    }
-return NULL;
-}
-
-void removeTrackFromGroup(struct track *track)
-/* Remove track from group it is part of. */
-{
-struct trackRef *tr = NULL;
-for(tr = track->group->trackList; tr != NULL; tr = tr->next)
-    {
-    if(tr->track == track)
-	{
-	slRemoveEl(&track->group->trackList, tr);
-	break;
-	}
-    }
-}
-
-
-void fillInStartEndBands(struct track *ideoTrack, char *startBand, char *endBand, int buffSize)
-/* Loop through the bands and fill in the one that the current window starts
-   on and ends on. */
-{
-struct cytoBand *cb = NULL, *cbList = ideoTrack->items;
-for(cb = cbList; cb != NULL; cb = cb->next)
-    {
-    /* If the start or end is encompassed by this band fill
-       it in. */
-    if(winStart >= cb->chromStart &&
-       winStart <= cb->chromEnd)
-	{
-	safef(startBand, buffSize, "%s", cb->name);
-	}
-    /* End is > rather than >= due to odditiy in the
-       cytoband track where the starts and ends of two
-       bands overlaps by one. */
-    if(winEnd > cb->chromStart &&
-       winEnd <= cb->chromEnd)
-	{
-	safef(endBand, buffSize, "%s", cb->name);
-	}
-    }
-}
-
-void makeChromIdeoImage(struct track **pTrackList, char *psOutput,
-                        struct tempName *ideoTn)
-/* Make an ideogram image of the chromsome and our position in it.  If the
- * ideoTn parameter is not NULL, it is filled in if the ideogram is created. */
-{
-struct track *ideoTrack = NULL;
-MgFont *font = tl.font;
-char *mapName = "ideoMap";
-struct hvGfx *hvg;
-boolean doIdeo = TRUE;
-boolean ideogramAvail = FALSE;
-int ideoWidth = round(.8 *tl.picWidth);
-int ideoHeight = 0;
-int textWidth = 0;
-struct tempName gifTn;
-if (ideoTn == NULL)
-    ideoTn = &gifTn;   // not returning value
-
-ideoTrack = chromIdeoTrack(*pTrackList);
-
-/* If no ideogram don't draw. */
-if(ideoTrack == NULL)
-    doIdeo = FALSE;
-else if(trackImgOnly && !ideogramToo)
-    {
-    doIdeo = FALSE;
-    }
-else
-    {
-    ideogramAvail = TRUE;
-    /* Remove the track from the group and track list. */
-    removeTrackFromGroup(ideoTrack);
-    slRemoveEl(pTrackList, ideoTrack);
-
-    /* Fix for hide all button hiding the ideogram as well. */
-    if(withIdeogram && ideoTrack->items == NULL)
-	{
-	ideoTrack->visibility = tvDense;
-	ideoTrack->loadItems(ideoTrack);
-	}
-    limitVisibility(ideoTrack);
-
-    /* If hidden don't draw. */
-    if(ideoTrack->limitedVis == tvHide || !withIdeogram)
-        doIdeo = FALSE;
-    }
-if(doIdeo)
-    {
-    char startBand[16];
-    char endBand[16];
-    char title[32];
-    startBand[0] = endBand[0] = '\0';
-    fillInStartEndBands(ideoTrack, startBand, endBand, sizeof(startBand));
-    /* Start up client side map. */
-    if (!psOutput)
-        hPrintf("<MAP Name=%s>\n", mapName);
-    /* Draw the ideogram. */
-    ideoHeight = gfxBorder + ideoTrack->height;
-    if (psOutput)
-        {
-        trashDirFile(ideoTn, "hgtIdeo", "hgtIdeo", ".ps");
-        hvg = hvGfxOpenPostScript(ideoWidth, ideoHeight, ideoTn->forCgi);
-        }
-    else
-        {
-#ifdef USE_PNG
-        trashDirFile(ideoTn, "hgtIdeo", "hgtIdeo", ".png");
-        hvg = hvGfxOpenPng(ideoWidth, ideoHeight, ideoTn->forCgi, FALSE);
-#else
-        trashDirFile(ideoTn, "hgtIdeo", "hgtIdeo", ".gif");
-        hvg = hvGfxOpenGif(ideoWidth, ideoHeight, ideoTn->forCgi, FALSE);
-#endif
-        }
-    hvg->rc = revCmplDisp;
-    initColors(hvg);
-    ideoTrack->ixColor = hvGfxFindRgb(hvg, &ideoTrack->color);
-    ideoTrack->ixAltColor = hvGfxFindRgb(hvg, &ideoTrack->altColor);
-    hvGfxSetClip(hvg, 0, gfxBorder, ideoWidth, ideoTrack->height);
-    if(sameString(startBand, endBand))
-        safef(title, sizeof(title), "%s (%s)", chromName, startBand);
-    else
-        safef(title, sizeof(title), "%s (%s-%s)", chromName, startBand, endBand);
-    textWidth = mgFontStringWidth(font, title);
-    hvGfxTextCentered(hvg, 2, gfxBorder, textWidth, ideoTrack->height, MG_BLACK, font, title);
-    ideoTrack->drawItems(ideoTrack, winStart, winEnd, hvg, textWidth+4, gfxBorder, ideoWidth-textWidth-4,
-             font, ideoTrack->ixColor, ideoTrack->limitedVis);
-    hvGfxUnclip(hvg);
-    /* Save out picture and tell html file about it. */
-    hvGfxClose(&hvg);
-    /* Finish map. */
-    if (!psOutput)
-        hPrintf("</MAP>\n");
-    }
-hPrintf("<TABLE BORDER=0 CELLPADDING=0>");
-if (doIdeo && !psOutput)
-    {
-    hPrintf("<TR><TD HEIGHT=5></TD></TR>");
-    hPrintf("<TR><TD><IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s id='chrom'>",
-        ideoTn->forHtml, ideoWidth, ideoHeight, mapName);
-    hPrintf("</TD></TR>");
-    hPrintf("<TR><TD HEIGHT=5></TD></TR></TABLE>\n");
-    }
-else
-    hPrintf("<TR><TD HEIGHT=10></TD></TR></TABLE>\n");
-if(ideoTrack != NULL)
-    {
-    ideoTrack->limitedVisSet = TRUE;
-    ideoTrack->limitedVis = tvHide; /* Don't draw in main gif. */
-    }
-}
-
-char *pcrResultMapItemName(struct track *tg, void *item)
-/* Stitch accession and display name back together (if necessary). */
-{
-struct linkedFeatures *lf = item;
-return pcrResultItemAccName(lf->name, lf->extra);
-}
-
-void pcrResultLoad(struct track *tg)
-/* Load locations of primer matches into linkedFeatures items. */
-{
-char *pslFileName, *primerFileName;
-struct targetDb *target;
-if (! pcrResultParseCart(database, cart, &pslFileName, &primerFileName, &target))
-    return;
-
-/* Don't free psl -- used in drawing phase by baseColor code. */
-struct psl *pslList = pslLoadAll(pslFileName), *psl;
-struct linkedFeatures *itemList = NULL;
-if (target != NULL)
-    {
-    int rowOffset = hOffsetPastBin(database, chromName, target->pslTable);
-    struct sqlConnection *conn = hAllocConn(database);
-    struct sqlResult *sr;
-    char **row;
-    char query[2048];
-    struct psl *tpsl;
-    for (tpsl = pslList;  tpsl != NULL;  tpsl = tpsl->next)
-	{
-	char *itemAcc = pcrResultItemAccession(tpsl->tName);
-	char *itemName = pcrResultItemName(tpsl->tName);
-	/* Query target->pslTable to get target-to-genomic mapping: */
-	safef(query, sizeof(query), "select * from %s where qName = '%s'",
-	      target->pslTable, itemAcc);
-	sr = sqlGetResult(conn, query);
-	while ((row = sqlNextRow(sr)) != NULL)
-	    {
-	    struct psl *gpsl = pslLoad(row+rowOffset);
-	    if (sameString(gpsl->tName, chromName) && gpsl->tStart < winEnd && gpsl->tEnd > winStart)
-		{
-		struct psl *trimmed = pslTrimToQueryRange(gpsl, tpsl->tStart,
-				      tpsl->tEnd);
-		struct linkedFeatures *lf;
-		char *targetStyle = cartUsualString(cart,
-		     PCR_RESULT_TARGET_STYLE, PCR_RESULT_TARGET_STYLE_DEFAULT);
-		if (sameString(targetStyle, PCR_RESULT_TARGET_STYLE_TALL))
-		    {
-		    lf = lfFromPslx(gpsl, 1, FALSE, FALSE, tg);
-		    lf->tallStart = trimmed->tStart;
-		    lf->tallEnd = trimmed->tEnd;
-		    }
-		else
-		    {
-		    lf = lfFromPslx(trimmed, 1, FALSE, FALSE, tg);
-		    }
-		lf->name = cloneString(itemAcc);
-		char extraInfo[512];
-		safef(extraInfo, sizeof(extraInfo), "%s|%d|%d",
-		      (itemName ? itemName : ""), tpsl->tStart, tpsl->tEnd);
-		lf->extra = cloneString(extraInfo);
-		slAddHead(&itemList, lf);
-		}
-	    }
-	}
-    hFreeConn(&conn);
-    }
-else
-    for (psl = pslList;  psl != NULL;  psl = psl->next)
-    if (sameString(psl->tName, chromName) && psl->tStart < winEnd && psl->tEnd > winStart)
-        {
-        struct linkedFeatures *lf =
-        lfFromPslx(psl, 1, FALSE, FALSE, tg);
-        lf->name = cloneString("");
-        lf->extra = cloneString("");
-        slAddHead(&itemList, lf);
-        }
-slSort(&itemList, linkedFeaturesCmp);
-tg->items = itemList;
-}
-
-char *pcrResultTrackItemName(struct track *tg, void *item)
-/* If lf->extra is non-empty, return it (display name for item).
- * Otherwise default to item name. */
-{
-struct linkedFeatures *lf = item;
-char *extra = (char *)lf->extra;
-if (isNotEmpty(extra))
-    {
-    static char displayName[512];
-    safecpy(displayName, sizeof(displayName), extra);
-    char *ptr = strchr(displayName, '|');
-    if (ptr != NULL)
-	*ptr = '\0';
-    if (isNotEmpty(displayName))
-	return displayName;
-    }
-return lf->name;
-}
-
-struct track *pcrResultTg()
-/* Make track of hgPcr results (alignments of user's submitted primers). */
-{
-struct trackDb *tdb = pcrResultFakeTdb();
-struct track *tg = trackFromTrackDb(tdb);
-tg->loadItems = pcrResultLoad;
-tg->itemName = pcrResultTrackItemName;
-tg->mapItemName = pcrResultMapItemName;
-tg->exonArrows = TRUE;
-tg->hasUi = TRUE;
-return tg;
-}
-
-struct track *linkedFeaturesTg()
-/* Return generic track for linked features. */
-{
-struct track *tg = trackNew();
-linkedFeaturesMethods(tg);
-tg->colorShades = shadesOfGray;
-return tg;
-}
-
-void setTgDarkLightColors(struct track *tg, int r, int g, int b)
-/* Set track color to r,g,b.  Set altColor to a lighter version
- * of the same. */
-{
-tg->colorShades = NULL;
-tg->color.r = r;
-tg->color.g = g;
-tg->color.b = b;
-tg->altColor.r = (r+255)/2;
-tg->altColor.g = (g+255)/2;
-tg->altColor.b = (b+255)/2;
-}
-
-void parseSs(char *ss, char **retPsl, char **retFa)
-/* Parse out ss variable into components. */
-{
-static char buf[1024];
-char *words[2];
-int wordCount;
-
-safecpy(buf, sizeof(buf), ss);
-wordCount = chopLine(buf, words);
-if (wordCount < 2)
-    errAbort("Badly formated ss variable");
-*retPsl = words[0];
-*retFa = words[1];
-}
-
-boolean ssFilesExist(char *ss)
-/* Return TRUE if both files in ss exist. */
-{
-char *faFileName, *pslFileName;
-parseSs(ss, &pslFileName, &faFileName);
-return fileExists(pslFileName) && fileExists(faFileName);
-}
-
-void loadUserPsl(struct track *tg)
-/* Load up hgBlat results from table into track items. */
-{
-char *ss = userSeqString;
-char buf2[3*512];
-char *faFileName, *pslFileName;
-struct lineFile *f;
-struct psl *psl;
-struct linkedFeatures *lfList = NULL, *lf;
-enum gfType qt, tt;
-int sizeMul = 1;
-
-parseSs(ss, &pslFileName, &faFileName);
-pslxFileOpen(pslFileName, &qt, &tt, &f);
-if (qt == gftProt)
-    {
-    setTgDarkLightColors(tg, 0, 80, 150);
-    tg->colorShades = NULL;
-    sizeMul = 3;
-    }
-tg->itemName = linkedFeaturesName;
-while ((psl = pslNext(f)) != NULL)
-    {
-    if (sameString(psl->tName, chromName) && psl->tStart < winEnd && psl->tEnd > winStart)
-	{
-	lf = lfFromPslx(psl, sizeMul, TRUE, FALSE, tg);
-	sprintf(buf2, "%s %s", ss, psl->qName);
-	lf->extra = cloneString(buf2);
-	slAddHead(&lfList, lf);
-	/* Don't free psl -- used in drawing phase by baseColor code. */
-	}
-    else
-	pslFree(&psl);
-    }
-slSort(&lfList, linkedFeaturesCmpStart);
-lineFileClose(&f);
-tg->items = lfList;
-}
-
-static void addUserSeqBaseAndIndelSettings(struct trackDb *tdb)
-/* If user sequence is a dna or rna alignment, add settings to enable
- * base-level differences and indel display. */
-{
-enum gfType qt, tt;
-struct lineFile *lf;
-char *faFileName, *pslFileName;
-parseSs(userSeqString, &pslFileName, &faFileName);
-pslxFileOpen(pslFileName, &qt, &tt, &lf);
-lineFileClose(&lf);
-if (qt != gftProt)
-    {
-    if (tdb->settingsHash == NULL)
-	tdb->settingsHash = hashNew(0);
-    hashAdd(tdb->settingsHash, BASE_COLOR_DEFAULT, cloneString("diffBases"));
-    hashAdd(tdb->settingsHash, BASE_COLOR_USE_SEQUENCE, cloneString("ss"));
-    hashAdd(tdb->settingsHash, SHOW_DIFF_BASES_ALL_SCALES, cloneString("."));
-    hashAdd(tdb->settingsHash, INDEL_DOUBLE_INSERT, cloneString("on"));
-    hashAdd(tdb->settingsHash, INDEL_QUERY_INSERT, cloneString("on"));
-    hashAdd(tdb->settingsHash, INDEL_POLY_A, cloneString("on"));
-    }
-}
-
-struct track *userPslTg()
-/* Make track of user pasted sequence. */
-{
-struct track *tg = linkedFeaturesTg();
-struct trackDb *tdb;
-tg->track = "hgUserPsl";
-tg->table = tg->track;
-tg->canPack = TRUE;
-tg->visibility = tvPack;
-tg->longLabel = "Your Sequence from Blat Search";
-tg->shortLabel = "Blat Sequence";
-tg->loadItems = loadUserPsl;
-tg->mapItemName = lfMapNameFromExtra;
-tg->priority = 100;
-tg->defaultPriority = tg->priority;
-tg->groupName = "map";
-tg->defaultGroupName = cloneString(tg->groupName);
-tg->exonArrows = TRUE;
-
-/* better to create the tdb first, then use trackFromTrackDb */
-AllocVar(tdb);
-tdb->track = cloneString(tg->track);
-tdb->table = cloneString(tg->table);
-tdb->visibility = tg->visibility;
-tdb->shortLabel = cloneString(tg->shortLabel);
-tdb->longLabel = cloneString(tg->longLabel);
-tdb->grp = cloneString(tg->groupName);
-tdb->priority = tg->priority;
-tdb->type = cloneString("psl");
-trackDbPolish(tdb);
-addUserSeqBaseAndIndelSettings(tdb);
-tg->tdb = tdb;
-return tg;
-}
-
-char *oligoMatchSeq()
-/* Return sequence for oligo matching. */
-{
-char *s = cartOptionalString(cart, oligoMatchVar);
-if (s != NULL)
-    {
-    int len;
-    tolowers(s);
-    dnaFilter(s, s);
-    len = strlen(s);
-    if (len < 2)
-       s = NULL;
-    }
-if (s == NULL)
-    s = cloneString(oligoMatchDefault);
-return s;
-}
-
-char *oligoMatchName(struct track *tg, void *item)
-/* Return name for oligo, which is just the base position. */
-{
-struct bed *bed = item;
-static char buf[22];
-buf[0] = bed->strand[0];
-sprintLongWithCommas(buf+1, bed->chromStart+1);
-return buf;
-}
-
-char *dnaInWindow()
-/* This returns the DNA in the window, all in lower case. */
-{
-static struct dnaSeq *seq = NULL;
-if (seq == NULL)
-    seq = hDnaFromSeq(database, chromName, winStart, winEnd, dnaLower);
-return seq->dna;
-}
-
-
-void oligoMatchLoad(struct track *tg)
-/* Create track of perfect matches to oligo on either strand. */
-{
-char *dna = dnaInWindow();
-char *fOligo = oligoMatchSeq();
-int oligoSize = strlen(fOligo);
-char *rOligo = cloneString(fOligo);
-char *rMatch = NULL, *fMatch = NULL;
-struct bed *bedList = NULL, *bed;
-char strand;
-int count = 0, maxCount = 1000000;
-
-if (oligoSize >= 2)
-    {
-    fMatch = stringIn(fOligo, dna);
-    reverseComplement(rOligo, oligoSize);
-    if (sameString(rOligo, fOligo))
-        rOligo = NULL;
-    else
-    rMatch = stringIn(rOligo, dna);
-    for (;;)
-        {
-	char *oneMatch = NULL;
-	if (rMatch == NULL)
-	    {
-	    if (fMatch == NULL)
-		break;
-	    else
-		{
-		oneMatch = fMatch;
-		fMatch = stringIn(fOligo, fMatch+1);
-		strand = '+';
-		}
-	    }
-	else if (fMatch == NULL)
-	    {
-	    oneMatch = rMatch;
-	    rMatch = stringIn(rOligo, rMatch+1);
-	    strand = '-';
-	    }
-	else if (rMatch < fMatch)
-	    {
-	    oneMatch = rMatch;
-	    rMatch = stringIn(rOligo, rMatch+1);
-	    strand = '-';
-	    }
-	else
-	    {
-	    oneMatch = fMatch;
-	    fMatch = stringIn(fOligo, fMatch+1);
-	    strand = '+';
-	    }
-	if (count < maxCount)
-	    {
-	    ++count;
-	    AllocVar(bed);
-	    bed->chromStart = winStart + (oneMatch - dna);
-	    bed->chromEnd = bed->chromStart + oligoSize;
-	    bed->strand[0] = strand;
-	    slAddHead(&bedList, bed);
-	    }
-	else
-	    break;
-	}
-    slReverse(&bedList);
-    if (count < maxCount)
-	tg->items = bedList;
-    else
-        warn("More than %d items in %s, suppressing display", maxCount, tg->shortLabel);
-    }
-}
-
-struct track *oligoMatchTg()
-/* Make track of perfect matches to oligomer. */
-{
-struct track *tg = trackNew();
-char *oligo = oligoMatchSeq();
-int oligoSize = strlen(oligo);
-char *medOligo = cloneString(oligo);
-static char longLabel[80];
-struct trackDb *tdb;
-
-/* Generate abbreviated strings. */
-if (oligoSize >= 30)
-    {
-    memset(medOligo + 30-3, '.', 3);
-    medOligo[30] = 0;
-    }
-touppers(medOligo);
-
-bedMethods(tg);
-tg->track = "oligoMatch";
-tg->table = tg->track;
-tg->canPack = TRUE;
-tg->visibility = tvHide;
-tg->hasUi = TRUE;
-tg->shortLabel = cloneString(OLIGO_MATCH_TRACK_LABEL);
-safef(longLabel, sizeof(longLabel),
-    "Perfect Matches to Short Sequence (%s)", medOligo);
-tg->longLabel = longLabel;
-tg->loadItems = oligoMatchLoad;
-tg->itemName = oligoMatchName;
-tg->mapItemName = oligoMatchName;
-tg->priority = 99;
-tg->defaultPriority = tg->priority;
-tg->groupName = "map";
-tg->defaultGroupName = cloneString(tg->groupName);
-
-AllocVar(tdb);
-tdb->track = cloneString(tg->track);
-tdb->table = cloneString(tg->table);
-tdb->visibility = tg->visibility;
-tdb->shortLabel = cloneString(tg->shortLabel);
-tdb->longLabel = cloneString(tg->longLabel);
-tdb->grp = cloneString(tg->groupName);
-tdb->priority = tg->priority;
-trackDbPolish(tdb);
-tg->tdb = tdb;
-return tg;
-}
-
-static int doLeftLabels(struct track *track, struct hvGfx *hvg, MgFont *font,
-                                int y)
-/* Draw left labels.  Return y coord. */
-{
-struct slList *prev = NULL;
-
-/* for sample tracks */
-double minRangeCutoff, maxRangeCutoff;
-double minRange, maxRange;
-double min0, max0;
-char minRangeStr[32];
-char maxRangeStr[32];
-
-int ymin, ymax;
-int start;
-int newy;
-char o4[256];
-char o5[256];
-struct slList *item;
-enum trackVisibility vis = track->limitedVis;
-enum trackVisibility savedVis = vis;
-Color labelColor = (track->labelColor ?
-                        track->labelColor : track->ixColor);
-int fontHeight = mgFontLineHeight(font);
-int tHeight = trackPlusLabelHeight(track, fontHeight);
-if (vis == tvHide)
-    return y;
-
-/*  if a track can do its own left labels, do them after drawItems */
-if (track->drawLeftLabels != NULL)
-    return y + tHeight;
-
-/*  Wiggle tracks depend upon clipping.  They are reporting
- *  totalHeight artifically high by 1 so this will leave a
- *  blank area one pixel high below the track.
- */
-if (sameString("wig",track->tdb->type) || sameString("bedGraph",track->tdb->type))
-    hvGfxSetClip(hvg, leftLabelX, y, leftLabelWidth, tHeight-1);
-else
-    hvGfxSetClip(hvg, leftLabelX, y, leftLabelWidth, tHeight);
-
-minRange = 0.0;
-safef( o4, sizeof(o4),"%s.min.cutoff", track->track);
-safef( o5, sizeof(o5),"%s.max.cutoff", track->track);
-minRangeCutoff = max( atof(cartUsualString(cart,o4,"0.0"))-0.1,
-                                track->minRange );
-maxRangeCutoff = min( atof(cartUsualString(cart,o5,"1000.0"))+0.1,
-                                track->maxRange);
-if( sameString( track->table, "humMusL" ) ||
-    sameString( track->table, "musHumL" ) ||
-    sameString( track->table, "mm3Rn2L" ) ||
-    sameString( track->table, "hg15Mm3L" ) ||
-    sameString( track->table, "mm3Hg15L" ) ||
-    sameString( track->table, "regpotent" ) ||
-    sameString( track->table, "HMRConservation" )  )
-    {
-    int binCount = round(1.0/track->scaleRange);
-    minRange = whichSampleBin( minRangeCutoff, track->minRange, track->maxRange, binCount );
-    maxRange = whichSampleBin( maxRangeCutoff, track->minRange, track->maxRange ,binCount );
-    min0 = whichSampleNum( minRange, track->minRange,track->maxRange, binCount );
-    max0 = whichSampleNum( maxRange, track->minRange, track->maxRange, binCount );
-    sprintf( minRangeStr, " "  );
-    sprintf( maxRangeStr, " " );
-    if( vis == tvFull && track->heightPer >= 74  )
-        {
-        samplePrintYAxisLabel( hvg, y+5, track, "1.0", min0, max0 );
-        samplePrintYAxisLabel( hvg, y+5, track, "2.0", min0, max0 );
-        samplePrintYAxisLabel( hvg, y+5, track, "3.0", min0, max0 );
-        samplePrintYAxisLabel( hvg, y+5, track, "4.0", min0, max0 );
-        samplePrintYAxisLabel( hvg, y+5, track, "5.0", min0, max0 );
-        samplePrintYAxisLabel( hvg, y+5, track, "6.0", min0, max0 );
-        }
-    }
-else
-    {
-    sprintf( minRangeStr, "%d", (int)round(minRangeCutoff));
-    sprintf( maxRangeStr, "%d", (int)round(maxRangeCutoff));
-    }
-/* special label handling for wigMaf type tracks -- they
-   display a left label in pack mode.  To use the full mode
-   labeling, temporarily set visibility to full.
-   Restore savedVis later */
-if (startsWith("wigMaf", track->tdb->type) || startsWith("maf", track->tdb->type))
-    vis = tvFull;
-
-switch (vis)
-    {
-    case tvHide:
-        break;  /* Do nothing; */
-    case tvPack:
-    case tvSquish:
-	y += tHeight;
-        break;
-    case tvFull:
-        if (isCenterLabelIncluded(track))
-            y += fontHeight;
-        start = 1;
-
-        if( track->subType == lfSubSample && track->items == NULL )
-            y += track->height;
-
-        for (item = track->items; item != NULL; item = item->next)
-            {
-            char *rootName;
-            char *name = track->itemName(track, item);
-            int itemHeight = track->itemHeight(track, item);
-            newy = y;
-
-            if (track->itemLabelColor != NULL)
-                labelColor = track->itemLabelColor(track, item, hvg);
-
-            /* Do some fancy stuff for sample tracks.
-             * Draw y-value limits for 'sample' tracks. */
-            if (track->subType == lfSubSample )
-                {
-                if( prev == NULL )
-                    newy += itemHeight;
-                else
-                    newy += sampleUpdateY(name,
-                            track->itemName(track, prev), itemHeight);
-                if( newy == y )
-                    continue;
-
-                if( track->heightPer > (3 * fontHeight ) )
-                    {
-                    ymax = y - (track->heightPer / 2) + (fontHeight / 2);
-                    ymin = y + (track->heightPer / 2) - (fontHeight / 2);
-                    hvGfxTextRight(hvg, leftLabelX, ymin, leftLabelWidth-1,
-                                itemHeight, track->ixAltColor,
-                                font, minRangeStr );
-                    hvGfxTextRight(hvg, leftLabelX, ymax, leftLabelWidth-1,
-                                itemHeight, track->ixAltColor,
-                                font, maxRangeStr );
-                    }
-                prev = item;
-
-                rootName = cloneString( name );
-                beforeFirstPeriod( rootName );
-                if( sameString( track->table, "humMusL" ) ||
-                         sameString( track->table, "hg15Mm3L" ))
-                    hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1,
-                             itemHeight, track->ixColor, font, "Mouse Cons");
-                else if( sameString( track->table, "musHumL" ) ||
-                         sameString( track->table, "mm3Hg15L"))
-                    hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1,
-                                itemHeight, track->ixColor, font, "Human Cons");
-                else if( sameString( track->table, "mm3Rn2L" ))
-                    hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1,
-                                itemHeight, track->ixColor, font, "Rat Cons");
-                else
-                    hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1,
-                                itemHeight, track->ixColor, font, rootName );
-                freeMem( rootName );
-                start = 0;
-                y = newy;
-                }
-            else
-                {
-                /* standard item labeling */
-		if (highlightItem(track, item))
-		    {
-		    int nameWidth = mgFontStringWidth(font, name);
-		    int boxStart = leftLabelX + leftLabelWidth - 2 - nameWidth;
-		    hvGfxBox(hvg, boxStart, y, nameWidth+1, itemHeight - 1,
-		      labelColor);
-		    hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth-1,
-			itemHeight, MG_WHITE, font, name);
-		    }
-		else
-		    hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1,
-			itemHeight, labelColor, font, name);
-		y += itemHeight;
-		}
-            }
-        break;
-    case tvDense:
-
-        if (isCenterLabelIncluded(track))
-            y += fontHeight;
-
-        /*draw y-value limits for 'sample' tracks.
-         * (always puts 0-100% range)*/
-        if( track->subType == lfSubSample &&
-                track->heightPer > (3 * fontHeight ) )
-            {
-            ymax = y - (track->heightPer / 2) + (fontHeight / 2);
-            ymin = y + (track->heightPer / 2) - (fontHeight / 2);
-            hvGfxTextRight(hvg, leftLabelX, ymin,
-                        leftLabelWidth-1, track->lineHeight,
-                        track->ixAltColor, font, minRangeStr );
-            hvGfxTextRight(hvg, leftLabelX, ymax,
-                        leftLabelWidth-1, track->lineHeight,
-                        track->ixAltColor, font, maxRangeStr );
-            }
-        hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth-1,
-                    track->lineHeight, labelColor, font,
-                    track->shortLabel);
-        y += track->height;
-        break;
-    }
-/* NOTE: might want to just restore savedVis here for all track types,
-   but I'm being cautious... */
-if (sameString(track->tdb->type, "wigMaf"))
-    vis = savedVis;
-hvGfxUnclip(hvg);
-return y;
-}
-
-static void doLabelNextItemButtons(struct track *track, struct track *parentTrack, struct hvGfx *hvg, MgFont *font, int y,
-                  int trackPastTabX, int trackPastTabWidth, int fontHeight,
-                  int insideHeight, Color labelColor)
-/* If the track allows label next-item buttons (next gene), draw them. */
-/* The button will cause hgTracks to run again with the additional CGI */
-/* vars nextItem=trackName or prevItem=trackName, which will then  */
-/* signal the browser to find the next thing on the track before it */
-/* does anything else. */
-{
-int portWidth = insideWidth;
-int portX = insideX;
-#ifdef IMAGEv2_DRAG_SCROLL
-// If a portal was established, then set the portal dimensions
-int portalStart,chromStart;
-double basesPerPixel;
-if (imgBoxPortalDimensions(theImgBox,&chromStart,NULL,NULL,NULL,&portalStart,NULL,&portWidth,&basesPerPixel))
-    {
-    portX = (int)((portalStart - chromStart) / basesPerPixel);
-    portX += gfxBorder;
-    if (withLeftLabels)
-        portX += tl.leftLabelWidth + gfxBorder;
-    portWidth = portWidth-gfxBorder-insideX;
-    }
-#endif//def IMAGEv2_DRAG_SCROLL
-int arrowWidth = insideHeight;
-int arrowButtonWidth = arrowWidth + 2 * NEXT_ITEM_ARROW_BUFFER;
-int rightButtonX = portX + portWidth - arrowButtonWidth - 1;
-char buttonText[256];
-Color fillColor = lightGrayIndex();
-labelColor = blackIndex();
-hvGfxNextItemButton(hvg, rightButtonX + NEXT_ITEM_ARROW_BUFFER, y, arrowWidth, arrowWidth, labelColor, fillColor, TRUE);
-hvGfxNextItemButton(hvg, portX + NEXT_ITEM_ARROW_BUFFER, y, arrowWidth, arrowWidth, labelColor, fillColor, FALSE);
-safef(buttonText, ArraySize(buttonText), "hgt.prevItem=%s", track->track);
-mapBoxReinvoke(hvg, portX, y + 1, arrowButtonWidth, insideHeight, NULL,
-           NULL, 0, 0, (revCmplDisp ? "Next item" : "Prev item"), buttonText);
-mapBoxToggleVis(hvg, portX + arrowButtonWidth, y + 1, portWidth - (2 * arrowButtonWidth),
-                insideHeight, (theImgBox ? track : parentTrack));
-safef(buttonText, ArraySize(buttonText), "hgt.nextItem=%s", track->track);
-mapBoxReinvoke(hvg, portX + portWidth - arrowButtonWidth, y + 1, arrowButtonWidth, insideHeight, NULL,
-           NULL, 0, 0, (revCmplDisp ? "Prev item" : "Next item"), buttonText);
-}
-
-static int doCenterLabels(struct track *track, struct track *parentTrack,
-                                struct hvGfx *hvg, MgFont *font, int y)
-/* Draw center labels.  Return y coord */
-{
-if (track->limitedVis != tvHide)
-    {
-    if (isCenterLabelIncluded(track))
-        {
-        int trackPastTabX = (withLeftLabels ? trackTabWidth : 0);
-        int trackPastTabWidth = tl.picWidth - trackPastTabX;
-        int fontHeight = mgFontLineHeight(font);
-        int insideHeight = fontHeight-1;
-	boolean toggleDone = FALSE;
-        char *label = track->longLabel;
-        if (isCenterLabelConditional(track))
-            label = track->tdb->parent->longLabel;
-        Color labelColor = (track->labelColor ?
-                            track->labelColor : track->ixColor);
-        hvGfxTextCentered(hvg, insideX, y+1, insideWidth, insideHeight,
-                            labelColor, font, label);
-        if (track->nextItemButtonable && track->nextPrevItem && !tdbIsComposite(track->tdb))
-            {
-            if (withNextItemArrows || trackDbSettingOn(track->tdb, "nextItemButton"))
-                {
-                doLabelNextItemButtons(track, parentTrack, hvg, font, y, trackPastTabX,
-                        trackPastTabWidth, fontHeight, insideHeight, labelColor);
-                toggleDone = TRUE;
-                }
-            }
-        if (!toggleDone)
-            mapBoxToggleVis(hvg, trackPastTabX, y+1,trackPastTabWidth, insideHeight,
-                            (theImgBox ? track : parentTrack));
-        y += fontHeight;
-        }
-    y += track->totalHeight(track, track->limitedVis);
-    }
-return y;
-}
-
-static int doDrawItems(struct track *track, struct hvGfx *hvg, MgFont *font,
-                                    int y, long *lastTime)
-/* Draw track items.  Return y coord */
-{
-int fontHeight = mgFontLineHeight(font);
-int pixWidth = tl.picWidth;
-if (isCenterLabelIncluded(track))
-    y += fontHeight;
-if (track->limitedVis == tvPack)
-    {
-    hvGfxSetClip(hvg, gfxBorder+trackTabWidth+1, y,
-        pixWidth-2*gfxBorder-trackTabWidth-1, track->height);
-    }
-else
-    hvGfxSetClip(hvg, insideX, y, insideWidth, track->height);
-track->drawItems(track, winStart, winEnd, hvg, insideX, y, insideWidth,
-                 font, track->ixColor, track->limitedVis);
-if (measureTiming && lastTime)
-    {
-    long thisTime = clock1000();
-    track->drawTime = thisTime - *lastTime;
-    *lastTime = thisTime;
-    }
-hvGfxUnclip(hvg);
-y += track->totalHeight(track, track->limitedVis);
-return y;
-}
-
-static int doMapItems(struct track *track, struct hvGfx *hvg, int fontHeight, int y)
-/* Draw map boxes around track items */
-{
-char *type = track->tdb->type;
-int newy;
-int trackPastTabX = (withLeftLabels ? trackTabWidth : 0);
-int trackPastTabWidth = tl.picWidth - trackPastTabX;
-int start = 1;
-struct slList *item;
-boolean isWig = (sameString("wig", type) || startsWith("wig ", type) ||
-        startsWith("bedGraph", type));
-
-if (isCenterLabelIncluded(track))
-    y += fontHeight;
-if (track->mapsSelf)
-    {
-    return y+track->height;
-    }
-if (track->subType == lfSubSample && track->items == NULL)
-     y += track->lineHeight;
-
-/* override doMapItems for hapmapLd track */
-/* does not scale with subtracks right now, so this is commented out until it can be fixed
-if (startsWith("hapmapLd",track->table))
-    {
-    y += round((double)(scaleForPixels(insideWidth)*insideWidth/2));
-    return y;
-    }
-*/
-for (item = track->items; item != NULL; item = item->next)
-    {
-    int height = track->itemHeight(track, item);
-
-    /*wiggle tracks don't always increment height (y-value) here*/
-    if( track->subType == lfSubSample )
-        {
-        newy = y;
-        if( !start && item->next != NULL  )
-            {
-            newy += sampleUpdateY( track->itemName(track, item),
-                             track->itemName(track, item->next),
-                             height );
-            }
-        else if( item->next != NULL || start )
-            newy += height;
-        start = 0;
-        y = newy;
-        }
-    else
-        {
-	if (track->mapItem == NULL)
-	    track->mapItem = genericMapItem;
-        if (!track->mapsSelf)
-            {
-	    track->mapItem(track, hvg, item, track->itemName(track, item),
-                           track->mapItemName(track, item),
-                           track->itemStart(track, item),
-                           track->itemEnd(track, item), trackPastTabX,
-                           y, trackPastTabWidth,height);
-            }
-        y += height;
-        }
-    }
-/* Wiggle track's ->height is actually one less than what it returns from
- * totalHeight()... I think the least disruptive way to account for this
- * (and not touch Ryan Weber's Sample stuff) is to just correct here if
- * we see wiggle or bedGraph: */
-if (isWig)
-    y++;
-return y;
-}
-
-static int doOwnLeftLabels(struct track *track, struct hvGfx *hvg,
-                                                MgFont *font, int y)
-/* Track draws it own, custom left labels */
-{
-int fontHeight = mgFontLineHeight(font);
-int tHeight = trackPlusLabelHeight(track, fontHeight);
-Color labelColor = (track->labelColor ? track->labelColor : track->ixColor);
-hvGfxSetClip(hvg, leftLabelX, y, leftLabelWidth, tHeight);
-track->drawLeftLabels(track, winStart, winEnd,
-		      hvg, leftLabelX, y, leftLabelWidth, tHeight,
-		      isCenterLabelIncluded(track), font, labelColor,
-		      track->limitedVis);
-hvGfxUnclip(hvg);
-y += tHeight;
-return y;
-}
-
-// defined below:
-static int getMaxWindowToDraw(struct trackDb *tdb);
-
-int doTrackMap(struct track *track, struct hvGfx *hvg, int y, int fontHeight,
-           int trackPastTabX, int trackPastTabWidth)
-/* Write out the map for this track. Return the new offset. */
-{
-int mapHeight = 0;
-switch (track->limitedVis)
-    {
-    case tvPack:
-    case tvSquish:
-        y += trackPlusLabelHeight(track, fontHeight);
-        break;
-    case tvFull:
-        if (!nextItemCompatible(track))
-            {
-            if (trackIsCompositeWithSubtracks(track))  //TODO: Change when tracks->subtracks are always set for composite
-                {
-                if (isCenterLabelIncluded(track))
-                    y += fontHeight;
-                struct track *subtrack;
-                for (subtrack = track->subtracks;  subtrack != NULL;subtrack = subtrack->next)
-                    {
-                    if (isSubtrackVisible(subtrack))
-                        {
-                        if(subtrack->limitedVis == tvFull)
-                            y = doMapItems(subtrack, hvg, fontHeight, y);
-                        else
-                            {
-                            if (isCenterLabelIncluded(subtrack))
-                                y += fontHeight;
-                            if(theImgBox && subtrack->limitedVis == tvDense)
-                                mapBoxToggleVis(hvg, trackPastTabX, y, trackPastTabWidth, track->lineHeight, subtrack);
-                            y += subtrack->totalHeight(subtrack, subtrack->limitedVis);
-                            }
-                        }
-                    }
-                }
-            else
-		y = doMapItems(track, hvg, fontHeight, y);
-            }
-        else
-            y += trackPlusLabelHeight(track, fontHeight);
-        break;
-    case tvDense:
-        if (isCenterLabelIncluded(track))
-            y += fontHeight;
-        if (tdbIsComposite(track->tdb))
-            mapHeight = track->height;
-        else
-            mapHeight = track->lineHeight;
-        int maxWinToDraw = getMaxWindowToDraw(track->tdb);
-        if (maxWinToDraw <= 1 || (winEnd - winStart) <= maxWinToDraw)
-            mapBoxToggleVis(hvg, trackPastTabX, y, trackPastTabWidth, mapHeight, track);
-        y += mapHeight;
-        break;
-    case tvHide:
-    default:
-        break;  /* Do nothing; */
-    }
-return y;
-}
-
-int computeScaleBar(int numBases, char scaleText[], int scaleTextSize)
-/* Do some scalebar calculations and return the number of bases the scalebar will span. */
-{
-char *baseWord = "bases";
-int scaleBases = 0;
-int scaleBasesTextNum = 0;
-int numFigs = (int)log10(numBases);
-int frontNum = (int)(numBases/pow(10,numFigs));
-if (frontNum == 1)
-    {
-    numFigs--;
-    scaleBases = 5 * pow(10, numFigs);
-    scaleBasesTextNum = 5 * pow(10, numFigs % 3);
-    }
-else if ((frontNum > 1) && (frontNum <= 4))
-    {
-    scaleBases = pow(10, numFigs);
-    scaleBasesTextNum = pow(10, numFigs % 3);
-    }
-else if (frontNum > 4)
-    {
-    scaleBases = 2 * pow(10, numFigs);
-    scaleBasesTextNum = 2 * pow(10, numFigs % 3);
-    }
-if ((numFigs >= 3) && (numFigs < 6))
-    baseWord = "kb";
-else if ((numFigs >= 6) && (numFigs < 9))
-    baseWord = "Mb";
-safef(scaleText, scaleTextSize, "%d %s", scaleBasesTextNum, baseWord);
-return scaleBases;
-}
-
-enum trackVisibility limitedVisFromComposite(struct track *subtrack)
-/* returns the subtrack visibility which may be limited by composite with multi-view dropdowns. */
-{
-#ifdef SUBTRACKS_HAVE_VIS
-if (tdbIsCompositeChild(subtrack->tdb))
-    {
-    if (fourStateVisible(subtrackFourStateChecked(subtrack->tdb,cart))) // Don't need all 4 states here.  Visible=checked&&enabled
-        {
-        char *var = cartOptionalString(cart, subtrack->track);
-        if (var)
-            {
-            subtrack->visibility = hTvFromString(var);
-
-            if (subtrack->limitedVisSet)
-                subtrack->limitedVis = tvMin(subtrack->visibility,subtrack->limitedVis);
-            else
-                {
-                if (subtrack->visibility != tvHide && slCount(subtrack->items) == 0)
-                    subtrack->loadItems(subtrack);
-
-                limitVisibility(subtrack);
-                }
-            return hTvFromString(var);
-            }
-        }
-    else
-        return tvHide;
-    }
-#endif///def SUBTRACKS_HAVE_VIS
-
-enum trackVisibility vis = subtrack->limitedVis == tvHide ?
-                           subtrack->visibility :
-                           tvMin(subtrack->visibility,subtrack->limitedVis);
-struct trackDb *tdb = subtrack->tdb;
-if(tdbIsCompositeChild(tdb))
-    {
-    struct trackDb *parentTdb = tdbGetComposite(tdb);
-    assert(parentTdb != NULL);
-
-    char *viewName = NULL;
-    if (subgroupFind(tdb,"view",&viewName))
-	{
-        int len = strlen(parentTdb->track) + strlen(viewName) + 10;
-
-	// Create the view dropdown var name.  This needs to have the view name surrounded by dots
-	// in the middle for the javascript to work.
-	char ddName[len];
-        safef(ddName,len,"%s.%s.vis", parentTdb->track,viewName);
-        char * fromParent = cartOptionalString(cart, ddName);
-        if(fromParent)
-            vis = tvMin(vis,hTvFromString(fromParent));
-        else
-            vis = tvMin(vis,visCompositeViewDefault(parentTdb,viewName));
-        subgroupFree(&viewName);
-	}
-    }
-return vis;
-}
-
-static int makeRulerZoomBoxes(struct hvGfx *hvg, struct cart *cart, int winStart,int winEnd,
-	int insideWidth,int seqBaseCount,int rulerClickY,int rulerClickHeight)
-/* Make hit boxes that will zoom program around ruler. */
-{
-int boxes = 30;
-int winWidth = winEnd - winStart;
-int newWinWidth = winWidth;
-int i, ws, we = 0, ps, pe = 0;
-int mid, ns, ne;
-double wScale = (double)winWidth/boxes;
-double pScale = (double)insideWidth/boxes;
-char message[32];
-char *zoomType = cartCgiUsualString(cart, RULER_BASE_ZOOM_VAR, ZOOM_3X);
-
-safef(message, sizeof(message), "%s zoom", zoomType);
-if (sameString(zoomType, ZOOM_1PT5X))
-    newWinWidth = winWidth/1.5;
-else if (sameString(zoomType, ZOOM_3X))
-    newWinWidth = winWidth/3;
-else if (sameString(zoomType, ZOOM_10X))
-    newWinWidth = winWidth/10;
-else if (sameString(zoomType, ZOOM_BASE))
-    newWinWidth = insideWidth/tl.mWidth;
-else
-    errAbort("invalid zoom type %s", zoomType);
-
-if (newWinWidth < 1)
-    newWinWidth = 1;
-
-for (i=1; i<=boxes; ++i)
-    {
-    ps = pe;
-    ws = we;
-    pe = round(pScale*i);
-    we = round(wScale*i);
-    mid = (ws + we)/2 + winStart;
-    ns = mid-newWinWidth/2;
-    ne = ns + newWinWidth;
-    if (ns < 0)
-        {
-        ns = 0;
-        ne -= ns;
-        }
-    if (ne > seqBaseCount)
-        {
-        ns -= (ne - seqBaseCount);
-        ne = seqBaseCount;
-        }
-    if(!dragZooming)
-        {
-        mapBoxJumpTo(hvg, ps+insideX,rulerClickY,pe-ps,rulerClickHeight,
-                        chromName, ns, ne, message);
-        }
-    }
-return newWinWidth;
-}
-
-static int doDrawRuler(struct hvGfx *hvg,int *newWinWidth,int *rulerClickHeight,
-	int rulerHeight, int yAfterRuler, int yAfterBases, MgFont *font,
-	int fontHeight,boolean rulerCds)
-/* draws the ruler. */
-{
-int scaleBarPad = 2;
-int scaleBarHeight = fontHeight;
-int scaleBarTotalHeight = fontHeight + 2 * scaleBarPad;
-int titleHeight = fontHeight;
-int baseHeight = fontHeight;
-//int yAfterBases = yAfterRuler;
-int showPosHeight = fontHeight;
-int codonHeight = fontHeight;
-struct dnaSeq *seq = NULL;
-int rulerClickY = 0;
-*rulerClickHeight = rulerHeight;
-
-int y = rulerClickY;
-hvGfxSetClip(hvg, insideX, y, insideWidth, yAfterRuler-y+1);
-int relNumOff = winStart;
-
-if (baseTitle)
-    {
-    hvGfxTextCentered(hvg, insideX, y, insideWidth, titleHeight,MG_BLACK, font, baseTitle);
-    *rulerClickHeight += titleHeight;
-    y += titleHeight;
-    }
-if (baseShowPos||baseShowAsm)
-    {
-    char txt[256];
-    char numBuf[SMALLBUF];
-    char *freezeName = NULL;
-    freezeName = hFreezeFromDb(database);
-    sprintLongWithCommas(numBuf, winEnd-winStart);
-    if(freezeName == NULL)
-	freezeName = "Unknown";
-    if (baseShowPos&&baseShowAsm)
-	safef(txt,sizeof(txt),"%s %s   %s (%s bp)",organism,
-		freezeName, addCommasToPos(database, position), numBuf);
-    else if (baseShowPos)
-	safef(txt,sizeof(txt),"%s (%s bp)",addCommasToPos(database, position),numBuf);
-    else
-	safef(txt,sizeof(txt),"%s %s",organism,freezeName);
-    hvGfxTextCentered(hvg, insideX, y, insideWidth, showPosHeight,MG_BLACK, font, txt);
-    *rulerClickHeight += showPosHeight;
-    freez(&freezeName);
-    y += showPosHeight;
-    }
-if (baseShowScaleBar)
-    {
-    char scaleText[32];
-    int numBases = winEnd-winStart;
-    int scaleBases = computeScaleBar(numBases, scaleText, sizeof(scaleText));
-    int scalePixels = (int)((double)insideWidth*scaleBases/numBases);
-    int scaleBarX = insideX + (int)(((double)insideWidth-scalePixels)/2);
-    int scaleBarEndX = scaleBarX + scalePixels;
-    int scaleBarY = y + 0.5 * scaleBarTotalHeight;
-    *rulerClickHeight += scaleBarTotalHeight;
-    hvGfxTextRight(hvg, insideX, y + scaleBarPad,
-	    (scaleBarX-2)-insideX, scaleBarHeight, MG_BLACK, font, scaleText);
-    hvGfxLine(hvg, scaleBarX, scaleBarY, scaleBarEndX, scaleBarY, MG_BLACK);
-    hvGfxLine(hvg, scaleBarX, y+scaleBarPad, scaleBarX,
-	    y+scaleBarTotalHeight-scaleBarPad, MG_BLACK);
-    hvGfxLine(hvg, scaleBarEndX, y+scaleBarPad, scaleBarEndX,
-	    y+scaleBarTotalHeight-scaleBarPad, MG_BLACK);
-    y += scaleBarTotalHeight;
-    }
-if (baseShowRuler)
-    {
-    hvGfxDrawRulerBumpText(hvg, insideX, y, rulerHeight, insideWidth, MG_BLACK,
-		font, relNumOff, winBaseCount, 0, 1);
-    }
-*newWinWidth = makeRulerZoomBoxes(hvg, cart,winStart,winEnd,insideWidth,seqBaseCount,rulerClickY,*rulerClickHeight);
-
-if (zoomedToBaseLevel || rulerCds)
-    {
-    Color baseColor = MG_BLACK;
-    int start, end, chromSize;
-    struct dnaSeq *extraSeq;
-    /* extraSeq has extra leading & trailing bases
-    * for translation in to amino acids */
-    boolean complementRulerBases =
-	    cartUsualBooleanDb(cart, database, COMPLEMENT_BASES_VAR, FALSE);
-    // gray bases if not matching the direction of display
-    if (complementRulerBases != revCmplDisp)
-	baseColor = MG_GRAY;
-
-    /* get sequence, with leading & trailing 3 bases
-     * used for amino acid translation */
-    start = max(winStart - 3, 0);
-    chromSize = hChromSize(database, chromName);
-    end = min(winEnd + 3, chromSize);
-    extraSeq = hDnaFromSeq(database, chromName, start, end, dnaUpper);
-    if (start != winStart - 3 || end != winEnd + 3)
-	{
-	/* at chromosome boundaries, pad with N's to assure
-	 * leading & trailing 3 bases */
-	char header[4] = "NNN", trailer[4] = "NNN";
-	int size = winEnd - winStart + 6;
-	char *padded = (char *)needMem(size+1);
-	header[max(3 - winStart, 0)] = 0;
-	trailer[max(winEnd - chromSize + 3, 0)] = 0;
-	safef(padded, size+1, "%s%s%s", header, extraSeq->dna, trailer);
-	extraSeq = newDnaSeq(padded, strlen(padded), extraSeq->name);
-	}
-
-    /* for drawing bases, must clip off leading and trailing 3 bases */
-    seq = cloneDnaSeq(extraSeq);
-    seq = newDnaSeq(seq->dna+3, seq->size-6, seq->name);
-
-    if (zoomedToBaseLevel)
-	drawBases(hvg, insideX, y+rulerHeight, insideWidth, baseHeight,
-	    baseColor, font, complementRulerBases, seq);
-
-    /* set up clickable area to toggle ruler visibility */
-	{
-	char newRulerVis[100];
-	safef(newRulerVis, 100, "%s=%s", RULER_TRACK_NAME,
-		     rulerMode == tvFull ?
-			    rulerMenu[tvDense] :
-			    rulerMenu[tvFull]);
-	mapBoxReinvoke(hvg, insideX, y+rulerHeight, insideWidth,baseHeight,
-	    NULL, NULL, 0, 0, "", newRulerVis);
-	}
-    if (rulerCds)
-	{
-	/* display codons */
-	int frame;
-	int firstFrame = 0;
-	int mod;            // for determining frame ordering on display
-	struct simpleFeature *sfList;
-	double scale = scaleForWindow(insideWidth, winStart, winEnd);
-
-	/* WARNING: tricky code to assure that an amino acid
-	 * stays in the same frame line on the browser during panning.
-	 * There may be a simpler way... */
-	if (complementRulerBases)
-	    mod = (chromSize - winEnd) % 3;
-	else
-	    mod = winStart % 3;
-	if (mod == 0)
-	    firstFrame = 0;
-	else if (mod == 1)
-	    firstFrame = 2;
-	else if (mod == 2)
-	    firstFrame = 1;
-
-	y = yAfterBases;
-	if (complementRulerBases)
-	    reverseComplement(extraSeq->dna, extraSeq->size);
-	for (frame = 0; frame < 3; frame++, y += codonHeight)
-	    {
-	    /* reference frame to start of chromosome */
-	    int refFrame = (firstFrame + frame) % 3;
-
-	    /* create list of codons in the specified coding frame */
-	    sfList = baseColorCodonsFromDna(refFrame, winStart, winEnd,
-					 extraSeq, complementRulerBases);
-	    /* draw the codons in the list, with alternating colors */
-	    baseColorDrawRulerCodons(hvg, sfList, scale, insideX, y,
-				codonHeight, font, winStart, MAXPIXELS,
-				zoomedToCodonLevel);
-	    }
-	}
-    }
-hvGfxUnclip(hvg);
-return y;
-}
-
-static void rAddToTrackHash(struct hash *trackHash, struct track *trackList)
-/* Add list and any children of list to hash. */
-{
-struct track *track;
-for (track = trackList; track != NULL; track = track->next)
-    {
-    hashAddUnique(trackHash, track->track, track);
-    rAddToTrackHash(trackHash, track->subtracks);
-    }
-}
-
-static void makeGlobalTrackHash(struct track *trackList)
-/* Start a global track hash. */
-{
-trackHash = newHash(8);
-rAddToTrackHash(trackHash, trackList);
-}
-
-
-void makeActiveImage(struct track *trackList, char *psOutput)
-/* Make image and image map. */
-{
-struct track *track;
-MgFont *font = tl.font;
-struct hvGfx *hvg;
-struct tempName gifTn;
-char *mapName = "map";
-int fontHeight = mgFontLineHeight(font);
-int trackPastTabX = (withLeftLabels ? trackTabWidth : 0);
-int trackTabX = gfxBorder;
-int trackPastTabWidth = tl.picWidth - trackPastTabX;
-int pixWidth, pixHeight;
-int y=0;
-int titleHeight = fontHeight;
-int scaleBarPad = 2;
-int scaleBarHeight = fontHeight;
-int scaleBarTotalHeight = fontHeight + 2 * scaleBarPad;
-int showPosHeight = fontHeight;
-int rulerHeight = fontHeight;
-int baseHeight = fontHeight;
-int basePositionHeight = rulerHeight;
-int codonHeight = fontHeight;
-int rulerTranslationHeight = codonHeight * 3;        // 3 frames
-int yAfterRuler = gfxBorder;
-int yAfterBases = yAfterRuler;  // differs if base-level translation shown
-boolean rulerCds = zoomedToCdsColorLevel;
-int rulerClickHeight = 0;
-int newWinWidth = 0;
-
-/* Figure out dimensions and allocate drawing space. */
-pixWidth = tl.picWidth;
-
-leftLabelX = gfxBorder;
-leftLabelWidth = insideX - gfxBorder*3;
-
-struct image *theOneImg  = NULL; // No need to be global, only the map needs to be global
-struct image *theSideImg = NULL; // Because dragScroll drags off end of image, the side label gets seen. Therefore we need 2 images!!
-struct hvGfx *hvgSide = NULL;    // Strategy an extra pointer to a side image that can be built if needed
-//struct imgTrack *curImgTrack = NULL; // Make this global for now to avoid huge rewrite
-struct imgSlice *curSlice    = NULL; // No need to be global, only the map needs to be global
-struct mapSet   *curMap      = NULL; // Make this global for now to avoid huge rewrite
-// Set up imgBox dimensions
-int sliceWidth[stMaxSliceTypes]; // Just being explicit
-int sliceOffsetX[stMaxSliceTypes];
-int sliceHeight        = 0;
-int sliceOffsetY       = 0;
-char *rulerTtl = NULL;
-if(theImgBox)
-// theImgBox is a global for now to avoid huge rewrite of hgTracks.  It is started
-// prior to this in doTrackForm()
-    {
-    rulerTtl = (dragZooming?"drag select or click to zoom":"click to zoom 3x");
-    hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
-    hPrintf("<input type='hidden' name='c' value='%s'>\n", chromName);
-    hPrintf("<input type='hidden' name='l' value='%d'>\n", winStart);
-    hPrintf("<input type='hidden' name='r' value='%d'>\n", winEnd);
-    hPrintf("<input type='hidden' name='pix' value='%d'>\n", tl.picWidth);
-    #ifdef IMAGEv2_DRAG_SCROLL
-    // If a portal was established, then set the global dimensions to the entire image size
-    if(imgBoxPortalDimensions(theImgBox,&winStart,&winEnd,&(tl.picWidth),NULL,NULL,NULL,NULL,NULL))
-        {
-        pixWidth = tl.picWidth;
-        winBaseCount = winEnd - winStart;
-        insideWidth = tl.picWidth-gfxBorder-insideX;
-        }
-    #endif//def IMAGEv2_DRAG_SCROLL
-    memset((char *)sliceWidth,  0,sizeof(sliceWidth));
-    memset((char *)sliceOffsetX,0,sizeof(sliceOffsetX));
-    if (withLeftLabels)
-        {
-        sliceWidth[stButton]   = trackTabWidth + 1;
-        sliceWidth[stSide]     = leftLabelWidth - sliceWidth[stButton] + 2;
-        sliceOffsetX[stSide]   = (revCmplDisp? (tl.picWidth - sliceWidth[stSide] - sliceWidth[stButton]) : sliceWidth[stButton]);
-        sliceOffsetX[stButton] = (revCmplDisp? (tl.picWidth - sliceWidth[stButton]) : 0);
-        }
-    sliceOffsetX[stData] = (revCmplDisp?0:sliceWidth[stSide] + sliceWidth[stButton]);
-    sliceWidth[stData]   = tl.picWidth - (sliceWidth[stSide] + sliceWidth[stButton]);
-    }
-struct flatTracks *flatTracks = NULL;
-struct flatTracks *flatTrack = NULL;
-
-if (rulerMode != tvFull)
-    {
-    rulerCds = FALSE;
-    }
-
-/* Figure out height of each visible track. */
-pixHeight = gfxBorder;
-if (rulerMode != tvHide)
-    {
-    if (!baseShowRuler && !baseTitle && !baseShowPos && !baseShowAsm && !baseShowScaleBar && !zoomedToBaseLevel && !rulerCds)
-        {
-        warn("Can't turn everything off in base position track.  Turning ruler back on");
-        baseShowRuler = TRUE;
-        cartSetBoolean(cart, BASE_SHOWRULER, TRUE);
-        }
-
-    if (baseTitle)
-        basePositionHeight += titleHeight;
-
-    if (baseShowPos||baseShowAsm)
-        basePositionHeight += showPosHeight;
-
-    if (baseShowScaleBar)
-        basePositionHeight += scaleBarTotalHeight;
-
-    if (!baseShowRuler)
-        {
-        basePositionHeight -= rulerHeight;
-        rulerHeight = 0;
-        }
-
-    if (zoomedToBaseLevel)
-        basePositionHeight += baseHeight;
-
-    yAfterRuler += basePositionHeight;
-    yAfterBases = yAfterRuler;
-    pixHeight += basePositionHeight;
-    if (rulerCds)
-        {
-        yAfterRuler += rulerTranslationHeight;
-        pixHeight += rulerTranslationHeight;
-        }
-    }
-
-boolean safeHeight = TRUE;
-/* firefox on Linux worked almost up to 34,000 at the default 620 width */
-#define maxSafeHeight   32000
-/* Hash tracks/subtracks, limit visibility and calculate total image height: */
-for (track = trackList; track != NULL; track = track->next)
-    {
-    limitVisibility(track);
-    if (!safeHeight)
-        {
-        track->limitedVis = tvHide;
-        track->limitedVisSet = TRUE;
-        continue;
-        }
-#ifndef SUBTRACKS_HAVE_VIS
-    if (track->limitedVis != tvHide)
-#endif///ndef SUBTRACKS_HAVE_VIS
-        {
-        if (tdbIsComposite(track->tdb))
-            {
-            struct track *subtrack;
-            for (subtrack = track->subtracks; subtrack != NULL;
-                         subtrack = subtrack->next)
-                {
-                if (!isSubtrackVisible(subtrack))
-                    continue;
-
-                // If the composite track has "view" based drop downs, set visibility based upon those
-                enum trackVisibility vis = limitedVisFromComposite(subtrack);
-                if(subtrack->visibility != vis)
-                    {
-                    subtrack->visibility = vis;
-                    if (subtrack->limitedVisSet)
-                        {
-                        subtrack->limitedVis = tvMin(vis, subtrack->limitedVis);
-                        }
-                    else
-                        {
-                        subtrack->limitedVis = tvMin(vis,subtrack->visibility);
-                        subtrack->limitedVisSet = (subtrack->limitedVis != tvHide && subtrack->visibility != subtrack->limitedVis);
-                        }
-                    }
-                if (!subtrack->limitedVisSet && track->limitedVisSet)
-                    {
-                    subtrack->visibility = track->visibility;
-                    subtrack->limitedVis = track->limitedVis;
-                    subtrack->limitedVisSet = track->limitedVisSet;
-                    }
-
-                #ifdef SUBTRACKS_HAVE_VIS
-                if (subtrack->limitedVis != tvHide)
-                #endif///def SUBTRACKS_HAVE_VIS
-                    {
-                    subtrack->hasUi = track->hasUi;
-                    flatTracksAdd(&flatTracks,subtrack,cart);
-                    }
-                }
-            }
-        else
-            #ifdef SUBTRACKS_HAVE_VIS
-            if (track->limitedVis != tvHide)
-            #endif///def SUBTRACKS_HAVE_VIS
-                flatTracksAdd(&flatTracks,track,cart);
-        if (maxSafeHeight < (pixHeight+trackPlusLabelHeight(track,fontHeight)))
-            {
-            char numBuf[SMALLBUF];
-            sprintLongWithCommas(numBuf, maxSafeHeight);
-            printf("warning: image is over %s pixels high at "
-                "track '%s',<BR>remaining tracks set to hide "
-                "for this view.<BR>\n", numBuf, track->tdb->shortLabel);
-            safeHeight = FALSE;
-            track->limitedVis = tvHide;
-            track->limitedVisSet = TRUE;
-            }
-        }
-    }
-flatTracksSort(&flatTracks); // Now we should have a perfectly good flat track list!
-struct track *prevTrack = NULL;
-for (flatTrack = flatTracks,prevTrack=NULL; flatTrack != NULL; flatTrack = flatTrack->next)
-    {
-    track = flatTrack->track;
-    if (maxSafeHeight < (pixHeight+trackPlusLabelHeight(track,fontHeight)))
-        {
-        char numBuf[SMALLBUF];
-        sprintLongWithCommas(numBuf, maxSafeHeight);
-        printf("warning: image is over %s pixels high at "
-            "track '%s',<BR>remaining tracks set to hide "
-            "for this view.<BR>\n", numBuf, track->tdb->shortLabel);
-        safeHeight = FALSE;
-        track->limitedVis = tvHide;
-        track->limitedVisSet = TRUE;
-        }
-    if (track->limitedVis != tvHide)
-        {
-        track->prevTrack = prevTrack; // Important for keeping track of conditional center labels!
-        pixHeight += trackPlusLabelHeight(track, fontHeight);
-        prevTrack = track;
-        }
-    }
-
-imagePixelHeight = pixHeight;
-if (psOutput)
-    {
-    hvg = hvGfxOpenPostScript(pixWidth, pixHeight, psOutput);
-    hvgSide = hvg; // Always only one image
-    }
-else
-    {
-    boolean transparentImage = FALSE;
-    if (theImgBox!=NULL)
-        transparentImage = TRUE;   // transparent because BG (blue ruler lines) is separate image
-
-#ifdef USE_PNG
-    trashDirFile(&gifTn, "hgt", "hgt", ".png");
-    hvg = hvGfxOpenPng(pixWidth, pixHeight, gifTn.forCgi, transparentImage);
-#else //ifndef
-    trashDirFile(&gifTn, "hgt", "hgt", ".gif");
-    hvg = hvGfxOpenGif(pixWidth, pixHeight, gifTn.forCgi, transparentImage);
-#endif //ndef USE_PNG
-
-    if(theImgBox)
-        {
-        // Adds one single image for all tracks (COULD: build the track by track images)
-        theOneImg = imgBoxImageAdd(theImgBox,gifTn.forHtml,NULL,pixWidth, pixHeight,FALSE);
-        theSideImg = theOneImg; // Unlkess this is overwritten below, there is a single image
-        }
-    hvgSide = hvg; // Unlkess this is overwritten below, there is a single image
-
-    if (theImgBox && theImgBox->showPortal && withLeftLabels)
-        {
-        // TODO: It would be great to make the images smaller, but keeping both the same full size for now
-        struct tempName gifTnSide;
-        #ifdef USE_PNG
-            trashDirFile(&gifTnSide, "hgt", "side", ".png");
-            hvgSide = hvGfxOpenPng(pixWidth, pixHeight, gifTnSide.forCgi, transparentImage);
-        #else //ifndef
-            trashDirFile(&gifTnSide, "hgt", "side", ".gif");
-            hvgSide = hvGfxOpenGif(pixWidth, pixHeight, gifTnSide.forCgi, transparentImage);
-        #endif //ndef USE_PNG
-
-        // Also add the side image
-        theSideImg = imgBoxImageAdd(theImgBox,gifTnSide.forHtml,NULL,pixWidth, pixHeight,FALSE);
-        hvgSide->rc = revCmplDisp;
-        initColors(hvgSide);
-        }
-    }
-hvg->rc = revCmplDisp;
-initColors(hvg);
-
-/* Start up client side map. */
-hPrintf("<MAP id='map' Name=%s>\n", mapName);
-
-/* Find colors to draw in. */
-findTrackColors(hvg, trackList);
-
-// Good to go ahead and add all imgTracks regardless of buttons, left label, centerLabel, etc.
-if(theImgBox)
-    {
-    if (rulerMode != tvHide)
-        {
-        curImgTrack = imgBoxTrackFindOrAdd(theImgBox,NULL,RULER_TRACK_NAME,rulerMode,FALSE,IMG_FIXEDPOS); // No tdb, no centerlabel, not reorderable
-        }
-
-    for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
-        {
-        track = flatTrack->track;
-        if (track->limitedVis != tvHide)
-            {
-            #ifdef SUBTRACKS_HAVE_VIS
-            if(track->labelColor == track->ixColor && track->ixColor == 0)
-                track->ixColor = hvGfxFindRgb(hvg, &track->color);
-            #endif//def SUBTRACKS_HAVE_VIS
-            int order = flatTrack->order;
-            curImgTrack = imgBoxTrackFindOrAdd(theImgBox,track->tdb,NULL,track->limitedVis,isCenterLabelIncluded(track),order);
-            }
-        }
-    }
-
-
-/* Draw mini-buttons. */
-if (withLeftLabels && psOutput == NULL)
-    {
-    int butOff;
-    boolean grayButtonGroup = FALSE;
-    struct group *lastGroup = NULL;
-    y = gfxBorder;
-    if (rulerMode != tvHide)
-        {
-        /* draw button for Base Position pseudo-track */
-        int height = basePositionHeight;
-        if (rulerCds)
-            height += rulerTranslationHeight;
-        if(theImgBox)
-            {
-            // Mini-buttons (side label slice) for ruler
-            sliceHeight      = height + 1;
-            sliceOffsetY     = 0;
-            curImgTrack = imgBoxTrackFind(theImgBox,NULL,RULER_TRACK_NAME);
-            curSlice    = imgTrackSliceUpdateOrAdd(curImgTrack,stButton,NULL,NULL,sliceWidth[stButton],sliceHeight,sliceOffsetX[stButton],sliceOffsetY); // flatTracksButton is all html, no jpg
-            }
-        drawGrayButtonBox(hvgSide, trackTabX, y, trackTabWidth, height, TRUE);
-        mapBoxTrackUi(hvgSide, trackTabX, y, trackTabWidth, height,
-              RULER_TRACK_NAME, RULER_TRACK_LABEL, "ruler");
-        y += height + 1;
-        }
-
-    for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
-        {
-        track = flatTrack->track;
-        int h, yStart = y, yEnd;
-        if (track->limitedVis != tvHide)
-            {
-        y += trackPlusLabelHeight(track, fontHeight);
-        yEnd = y;
-        h = yEnd - yStart - 1;
-
-        /* alternate button colors for track groups*/
-        if (track->group != lastGroup)
-            grayButtonGroup = !grayButtonGroup;
-        lastGroup = track->group;
-        if (grayButtonGroup)
-            drawGrayButtonBox(hvgSide, trackTabX, yStart, trackTabWidth,
-                        h, track->hasUi);
-        else
-            drawBlueButtonBox(hvgSide, trackTabX, yStart, trackTabWidth,
-                        h, track->hasUi);
-        if(theImgBox)
-            {
-            // Mini-buttons (side label slice) for tracks
-            sliceHeight      = yEnd - yStart;
-            sliceOffsetY     = yStart - 1;
-            curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL);
-            curSlice    = imgTrackSliceUpdateOrAdd(curImgTrack,stButton,NULL,NULL,sliceWidth[stButton],sliceHeight,sliceOffsetX[stButton],sliceOffsetY); // flatTracksButton is all html, no jpg
-            }
-        if (track->hasUi)
-            {
-            if(tdbIsCompositeChild(track->tdb))
-                {
-                struct trackDb *parent = tdbGetComposite(track->tdb);
-                mapBoxTrackUi(hvgSide, trackTabX, yStart, trackTabWidth, (yEnd - yStart - 1),
-                    parent->track, parent->shortLabel, track->track);
-                }
-            else
-                mapBoxTrackUi(hvgSide, trackTabX, yStart, trackTabWidth, h, track->track, track->shortLabel, track->track);
-            }
-        }
-        }
-    butOff = trackTabX + trackTabWidth;
-    leftLabelX += butOff;
-    leftLabelWidth -= butOff;
-    }
-
-if (withLeftLabels)
-    {
-    Color lightRed = hvGfxFindColorIx(hvgSide, 255, 180, 180);
-
-    hvGfxBox(hvgSide, leftLabelX + leftLabelWidth, 0,
-        gfxBorder, pixHeight, lightRed);
-    y = gfxBorder;
-    if (rulerMode != tvHide)
-        {
-        if(theImgBox)
-            {
-            // side label slice for ruler
-            sliceHeight      = basePositionHeight + (rulerCds ? rulerTranslationHeight : 0) + 1;
-            sliceOffsetY     = 0;
-            curImgTrack = imgBoxTrackFind(theImgBox,NULL,RULER_TRACK_NAME);
-            curSlice    = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL,sliceWidth[stSide],sliceHeight,sliceOffsetX[stSide],sliceOffsetY);
-            curMap      = sliceMapFindOrStart(curSlice,RULER_TRACK_NAME,NULL); // No common linkRoot
-            }
-        if (baseTitle)
-            {
-            hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, titleHeight,
-                MG_BLACK, font, WIN_TITLE_LABEL);
-            y += titleHeight;
-            }
-        if (baseShowPos||baseShowAsm)
-            {
-            hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, showPosHeight,
-                MG_BLACK, font, WIN_POS_LABEL);
-            y += showPosHeight;
-            }
-        if (baseShowScaleBar)
-            {
-            y += scaleBarPad;
-            hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, scaleBarHeight,
-                MG_BLACK, font, SCALE_BAR_LABEL);
-            y += scaleBarHeight + scaleBarPad;
-            }
-        if (baseShowRuler)
-            {
-            char rulerLabel[SMALLBUF];
-            char *shortChromName = cloneString(chromName);
-            safef(rulerLabel,ArraySize(rulerLabel),":%s",shortChromName);
-            int labelWidth = mgFontStringWidth(font,rulerLabel);
-            while ((labelWidth > 0) && (labelWidth > leftLabelWidth))
-                {
-                int len = strlen(shortChromName);
-                shortChromName[len-1] = 0;
-                safef(rulerLabel,ArraySize(rulerLabel),":%s",shortChromName);
-                labelWidth = mgFontStringWidth(font,rulerLabel);
-                }
-            if (hvgSide->rc)
-            safef(rulerLabel,ArraySize(rulerLabel),":%s",shortChromName);
-            else
-                safef(rulerLabel,ArraySize(rulerLabel),"%s:",shortChromName);
-            hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, rulerHeight,
-                MG_BLACK, font, rulerLabel);
-            y += rulerHeight;
-            freeMem(shortChromName);
-            }
-        if (zoomedToBaseLevel || rulerCds)
-            {
-            /* disable complement toggle for HIV because HIV is single stranded RNA */
-            if (!hIsGsidServer())
-                    drawComplementArrow(hvgSide,leftLabelX, y,
-                                        leftLabelWidth-1, baseHeight, font);
-            if (zoomedToBaseLevel)
-                y += baseHeight;
-            }
-            if (rulerCds)
-                y += rulerTranslationHeight;
-        }
-    for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
-        {
-        track = flatTrack->track;
-        if (track->limitedVis == tvHide)
-            continue;
-         if(theImgBox)
-            {
-            // side label slice for tracks
-            sliceHeight      = trackPlusLabelHeight(track, fontHeight);
-            sliceOffsetY     = y;
-            curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL);
-            curSlice    = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL,sliceWidth[stSide],sliceHeight,sliceOffsetX[stSide],sliceOffsetY);
-            curMap      = sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot
-            }
-        y = doLeftLabels(track, hvgSide, font, y);
-        }
-    }
-else
-    {
-    leftLabelX = leftLabelWidth = 0;
-    }
-
-/* Draw guidelines. */
-if (withGuidelines)
-    {
-    //if(theImgBox)
-        // TODO: We should be making transparent data images and a separate background img for guidelines.
-        // This will allow the guidelines to dragscroll while the center labels are static.
-        // NOTE: The background image could easily be a reusable file, based upon zoom level and width.  Height could propbaby easily be stretched.
-        // struct image *bgImg = imgBoxImageAdd(theImgBox,gifBg.forHtml,
-        //    (char *)(dragZooming?"click or drag mouse in base position track to zoom in" : NULL),
-        //    pixWidth, pixHeight,FALSE);
-    struct hvGfx *bgImg = hvg; // Default to the one image
-    if(theImgBox)
-        {
-        struct tempName gifBg;
-        #ifdef USE_PNG
-        trashDirFile(&gifBg, "hgt", "bg", ".png");  // TODO: We could have a few static files by (pixHeight*pixWidth)  And I doubt pixHeight is needed!
-        bgImg = hvGfxOpenPng(pixWidth, pixHeight, gifBg.forCgi, TRUE);
-        #else //ifndef
-        trashDirFile(&gifBg, "hgt", "bg", ".gif");
-        bgImg = hvGfxOpenGif(pixWidth, pixHeight, gifBg.forCgi, TRUE);
-        #endif //ndef USE_PNG
-        bgImg->rc = revCmplDisp;
-        imgBoxImageAdd(theImgBox,gifBg.forHtml,NULL,pixWidth, pixHeight,TRUE); // Adds BG image
-        }
-    int height = pixHeight - 2*gfxBorder;
-    int x;
-    Color lightBlue = hvGfxFindRgb(bgImg, &guidelineColor);
-
-    hvGfxSetClip(bgImg, insideX, gfxBorder, insideWidth, height);
-    y = gfxBorder;
-
-    for (x = insideX+guidelineSpacing-1; x<pixWidth; x += guidelineSpacing)
-        hvGfxBox(bgImg, x, y, 1, height, lightBlue);
-    hvGfxUnclip(bgImg);
-    if(bgImg != hvg)
-        hvGfxClose(&bgImg);
-    }
-
-/* Show ruler at top. */
-if (rulerMode != tvHide)
-    {
-    if(theImgBox)
-        {
-        // data slice for ruler
-        sliceHeight      = basePositionHeight + (rulerCds ? rulerTranslationHeight : 0) + 1;
-        sliceOffsetY     = 0;
-        curImgTrack = imgBoxTrackFind(theImgBox,NULL,RULER_TRACK_NAME);
-        curSlice    = imgTrackSliceUpdateOrAdd(curImgTrack,stData,theOneImg,rulerTtl,sliceWidth[stData],sliceHeight,sliceOffsetX[stData],sliceOffsetY);
-        curMap      = sliceMapFindOrStart(curSlice,RULER_TRACK_NAME,NULL); // No common linkRoot
-        }
-    y = doDrawRuler(hvg,&newWinWidth,&rulerClickHeight,rulerHeight,yAfterRuler,yAfterBases,font,fontHeight,rulerCds);
-    }
-
-/* Draw center labels. */
-if (withCenterLabels)
-    {
-    hvGfxSetClip(hvg, insideX, gfxBorder, insideWidth, pixHeight - 2*gfxBorder);
-    y = yAfterRuler;
-    for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
-        {
-        track = flatTrack->track;
-        if (track->limitedVis == tvHide)
-            continue;
-
-        if(theImgBox)
-            {
-            // center label slice of tracks Must always make, even if the centerLabel is empty
-            sliceHeight      = fontHeight;
-            sliceOffsetY     = y;
-            curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL);
-            curSlice    = imgTrackSliceUpdateOrAdd(curImgTrack,stCenter,theOneImg,NULL,sliceWidth[stData],sliceHeight,sliceOffsetX[stData],sliceOffsetY);
-            curMap      = sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot
-            if (isCenterLabelConditional(track))
-                imgTrackUpdateCenterLabelSeen(curImgTrack,isCenterLabelConditionallySeen(track)?clNowSeen:clNotSeen);
-            }
-        y = doCenterLabels(track, track, hvg, font, y);
-        }
-    hvGfxUnclip(hvg);
-    }
-
-/* Draw tracks. */
-    {
-    long lastTime = 0;
-    y = yAfterRuler;
-    if (measureTiming)
-        lastTime = clock1000();
-    for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
-        {
-        track = flatTrack->track;
-        if (track->limitedVis == tvHide)
-                continue;
-
-        int centerLabelHeight = (isCenterLabelIncluded(track) ? fontHeight : 0);
-        int yStart = y + centerLabelHeight;
-        int yEnd   = y + trackPlusLabelHeight(track, fontHeight);
-        if(theImgBox)
-            {
-            // data slice of tracks
-            sliceOffsetY     = yStart;
-            sliceHeight      = yEnd - yStart - 1;
-            curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL);
-            if(sliceHeight > 0)
-                {
-                curSlice    = imgTrackSliceUpdateOrAdd(curImgTrack,stData,theOneImg,NULL,sliceWidth[stData],sliceHeight,sliceOffsetX[stData],sliceOffsetY);
-                curMap      = sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot
-                }
-            }
-        y = doDrawItems(track, hvg, font, y, &lastTime);
-
-        if (theImgBox && track->limitedVis == tvDense && tdbIsCompositeChild(track->tdb))
-            mapBoxToggleVis(hvg, 0, yStart,tl.picWidth, sliceHeight,track); // Strange mabBoxToggleLogic handles reverse complement itself so x=0, width=tl.picWidth
-
-        if(yEnd!=y)
-            warn("Slice height does not add up.  Expecting %d != %d actual",yEnd - yStart - 1,y-yStart);
-        }
-    y++;
-    }
-/* if a track can draw its left labels, now is the time since it
- *  knows what exactly happened during drawItems
- */
-if (withLeftLabels)
-    {
-    y = yAfterRuler;
-    for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
-        {
-        track = flatTrack->track;
-        if (track->limitedVis == tvHide)
-                continue;
-        if(theImgBox)
-            {
-            // side label slice of tracks
-            sliceHeight      = trackPlusLabelHeight(track, fontHeight);
-            sliceOffsetY     = y;
-            curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL);
-            curSlice    = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL,sliceWidth[stSide],sliceHeight,sliceOffsetX[stSide],sliceOffsetY);
-            curMap      = sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot
-            }
-
-        if (track->drawLeftLabels != NULL)
-            y = doOwnLeftLabels(track, hvgSide, font, y);
-        else
-            y += trackPlusLabelHeight(track, fontHeight);
-        }
-    }
-
-
-/* Make map background. */
-y = yAfterRuler;
-for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
-    {
-    track = flatTrack->track;
-    if (track->limitedVis != tvHide)
-        {
-        if(theImgBox)
-            {
-            // Set imgTrack in case any map items will be set
-            sliceHeight      = trackPlusLabelHeight(track, fontHeight);
-            sliceOffsetY     = y;
-            curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL);
-            }
-        y = doTrackMap(track, hvg, y, fontHeight, trackPastTabX, trackPastTabWidth);
-        }
-    }
-
-/* Finish map. */
-hPrintf("</MAP>\n");
-
-hPrintf("<input type='hidden' id='hgt.dragSelection' name='dragSelection' value='%d'>\n", dragZooming ? 1 : 0);
-if(rulerClickHeight)
-    {
-    hPrintf("<input type='hidden' id='hgt.rulerClickHeight' name='rulerClickHeight' value='%d'>\n", rulerClickHeight);
-    }
-if(newWinWidth)
-    {
-    hPrintf("<input type='hidden' id='hgt.newWinWidth' name='newWinWidth' value='%d'>\n", newWinWidth);
-    }
-
-/* Save out picture and tell html file about it. */
-if(hvgSide != hvg)
-    hvGfxClose(&hvgSide);
-hvGfxClose(&hvg);
-if(theImgBox)
-    {
-    imageBoxDraw(theImgBox);
-    #ifdef IMAGEv2_DRAG_SCROLL
-    // If a portal was established, then set the global dimensions back to the portal size
-    if(imgBoxPortalDimensions(theImgBox,NULL,NULL,NULL,NULL,&winStart,&winEnd,&(tl.picWidth),NULL))
-        {
-        pixWidth = tl.picWidth;
-        winBaseCount = winEnd - winStart;
-        insideWidth = tl.picWidth-gfxBorder-insideX;
-        }
-    #endif//def IMAGEv2_DRAG_SCROLL
-    imgBoxFree(&theImgBox);
-    }
-else
-    {
-    char *titleAttr = dragZooming ? "title='click or drag mouse in base position track to zoom in'" : "";
-    hPrintf("<IMG SRC='%s' BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s %s id='trackMap'",
-        gifTn.forHtml, pixWidth, pixHeight, mapName, titleAttr);
-    hPrintf("><BR>\n");
-    }
-flatTracksFree(&flatTracks);
-}
-
-static void printEnsemblAnchor(char *database, char* archive,
-    char *chrName, int start, int end)
-/* Print anchor to Ensembl display on same window. */
-{
-char *scientificName = hScientificName(database);
-char *dir = ensOrgNameFromScientificName(scientificName);
-struct dyString *ensUrl;
-char *name;
-int localStart, localEnd;
-
-name = chrName;
-
-if (sameWord(scientificName, "Takifugu rubripes"))
-    {
-    /* for Fugu, must give scaffold, not chr coordinates */
-    /* Also, must give "chrom" as "scaffold_N", name below. */
-    if (differentWord(chromName,"chrM") &&
-    !hScaffoldPos(database, chromName, winStart, winEnd,
-                        &name, &localStart, &localEnd))
-        /* position doesn't appear on Ensembl browser.
-         * Ensembl doesn't show scaffolds < 2K */
-        return;
-    }
-else if (sameWord(scientificName, "Gasterosteus aculeatus"))
-    {
-    if (differentWord("chrM", chrName))
-    {
-    char *fixupName = replaceChars(chrName, "chr", "group");
-    name = fixupName;
-    }
-    }
-else if (sameWord(scientificName, "Ciona intestinalis"))
-    {
-    if (stringIn("chr0", chrName))
-	{
-	char *fixupName = replaceChars(chrName, "chr0", "chr");
-	name = fixupName;
-	}
-    }
-else if (sameWord(scientificName, "Saccharomyces cerevisiae"))
-    {
-    if (stringIn("2micron", chrName))
-	{
-	char *fixupName = replaceChars(chrName, "2micron", "2-micron");
-	name = fixupName;
-	}
-    }
-
-if (sameWord(chrName, "chrM"))
-    name = "chrMt";
-localStart = start;
-localEnd = end + 1; // Ensembl base-1 display coordinates
-ensUrl = ensContigViewUrl(database, dir, name, seqBaseCount, localStart, localEnd, archive);
-hPrintf("<A HREF=\"%s\" TARGET=_blank class=\"topbar\">", ensUrl->string);
-/* NOTE: you can not freeMem(dir) because sometimes it is a literal
- * constant */
-freeMem(scientificName);
-dyStringFree(&ensUrl);
-}
-
-void makeHgGenomeTrackVisible(struct track *track)
-/* This turns on a track clicked from hgGenome, even if it was previously */
-/* hidden manually and there are cart vars to support that. */
-{
-struct hashEl *hels;
-struct hashEl *hel;
-char prefix[SMALLBUF];
-/* First check if the click was from hgGenome.  If not, leave. */
-/* get the names of the tracks in the cart */
-safef(prefix, sizeof(prefix), "%s_", hggGraphPrefix);
-hels = cartFindPrefix(cart, prefix);
-/* loop through them and compare them to the track passed into this */
-/* function. */
-for (hel = hels; hel != NULL; hel = hel->next)
-    {
-    struct trackDb *subtrack;
-    char *subtrackName = hel->val;
-    /* check non-subtrack. */
-    if (sameString(track->tdb->track, subtrackName))
-	{
-	track->visibility = tvFull;
-	track->tdb->visibility = tvFull;
-	cartSetString(cart, track->tdb->track, "full");
-	}
-    else if (track->tdb->subtracks != NULL)
-	{
-	struct slRef *tdbRef, *tdbRefList = trackDbListGetRefsToDescendants(track->tdb->subtracks);
-	for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
-	    {
-	    subtrack = tdbRef->val;
-	    if (sameString(subtrack->track, subtrackName))
-		{
-		char selName[SMALLBUF];
-		track->visibility = tvFull;
-		cartSetString(cart, track->tdb->track, "full");
-		track->tdb->visibility = tvFull;
-		subtrack->visibility = tvFull;
-		safef(selName, sizeof(selName), "%s_sel", subtrackName);
-		cartSetBoolean(cart, selName, TRUE);
-		}
-	    }
-	slFreeList(&tdbRefList);
-	}
-    }
-hashElFreeList(&hels);
-}
-
-struct sqlConnection *remoteTrackConnection(struct track *tg)
-/* Get a connection to remote database as specified in remoteSql settings... */
-{
-if (!tg->isRemoteSql)
-    {
-    internalErr();
-    return NULL;
-    }
-else
-    {
-    return sqlConnectRemote(tg->remoteSqlHost, tg->remoteSqlUser, tg->remoteSqlPassword,
-        tg->remoteSqlDatabase);
-    }
-}
-
-void addTdbListToTrackList(struct trackDb *tdbList, char *trackNameFilter,
-	struct track **pTrackList)
-/* Convert a list of trackDb's to tracks, and append these to trackList. */
-{
-struct trackDb *tdb, *next;
-struct track *track;
-TrackHandler handler;
-tdbSortPrioritiesFromCart(cart, &tdbList);
-for (tdb = tdbList; tdb != NULL; tdb = next)
-    {
-    next = tdb->next;
-    if(trackNameFilter != NULL && strcmp(trackNameFilter, tdb->track))
-        // suppress loading & display of all tracks except for the one passed in via trackNameFilter
-        continue;
-    track = trackFromTrackDb(tdb);
-    track->hasUi = TRUE;
-    if (slCount(tdb->subtracks) != 0)
-        {
-        tdbSortPrioritiesFromCart(cart, &(tdb->subtracks));
-	if (trackDbLocalSetting(tdb, "compositeTrack"))
-	    makeCompositeTrack(track, tdb);
-	else if (trackDbLocalSetting(tdb, "container"))
-	    makeContainerTrack(track, tdb);
-        }
-    else
-        {
-        handler = lookupTrackHandler(tdb->table);
-        if (handler != NULL)
-            handler(track);
-        }
-    if (cgiVarExists("hgGenomeClick"))
-	makeHgGenomeTrackVisible(track);
-    if (track->loadItems == NULL)
-        warn("No load handler for %s; possible missing trackDb `type' or `subTrack' attribute", tdb->track);
-    else if (track->drawItems == NULL)
-        warn("No draw handler for %s", tdb->track);
-    else
-        slAddHead(pTrackList, track);
-    }
-}
-
-void loadFromTrackDb(struct track **pTrackList)
-/* Load tracks from database, consulting handler list. */
-{
-char *trackNameFilter = cartOptionalString(cart, "hgt.trackNameFilter");
-struct trackDb *tdbList;
-if(trackNameFilter == NULL)
-    tdbList = hTrackDb(database, chromName);
-else
-    tdbList = hTrackDbForTrack(database, trackNameFilter);
-addTdbListToTrackList(tdbList, trackNameFilter, pTrackList);
-}
-
-static int getScoreFilter(char *trackName)
-/* check for score filter configuration setting */
-{
-char optionScoreStr[256];
-
-safef(optionScoreStr, sizeof(optionScoreStr), "%s.scoreFilter", trackName);
-return cartUsualInt(cart, optionScoreStr, 0);
-}
-
-void ctLoadSimpleBed(struct track *tg)
-/* Load the items in one custom track - just move beds in
- * window... */
-{
-struct customTrack *ct = tg->customPt;
-struct bed *bed, *nextBed, *list = NULL;
-int scoreFilter = getScoreFilter(ct->tdb->track);
-
-if (ct->dbTrack)
-    {
-    int fieldCount = ct->fieldCount;
-    int rowOffset;
-    char **row;
-    struct sqlConnection *conn =
-        hAllocConn(CUSTOM_TRASH);
-    struct sqlResult *sr = NULL;
-
-    sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd,
-             NULL, &rowOffset);
-    while ((row = sqlNextRow(sr)) != NULL)
-	{
-	bed = bedLoadN(row+rowOffset, fieldCount);
-	    if (scoreFilter && bed->score < scoreFilter)
-		continue;
-	slAddHead(&list, bed);
-	}
-    hFreeConn(&conn);
-    }
-else
-    {
-    for (bed = ct->bedList; bed != NULL; bed = nextBed)
-	{
-	nextBed = bed->next;
-	if (bed->chromStart < winEnd && bed->chromEnd > winStart
-		&& sameString(chromName, bed->chrom))
-	    {
-	    if (scoreFilter && bed->score < scoreFilter)
-		continue;
-	    slAddHead(&list, bed);
-	    }
-	}
-    }
-slSort(&list, bedCmp);
-tg->items = list;
-}
-
-void ctLoadBed9(struct track *tg)
-/* Convert bed info in window to linked feature. */
-{
-struct customTrack *ct = tg->customPt;
-struct bed *bed;
-struct linkedFeatures *lfList = NULL, *lf;
-boolean useItemRgb = FALSE;
-int scoreFilter = getScoreFilter(ct->tdb->track);
-
-useItemRgb = bedItemRgb(ct->tdb);
-
-if (ct->dbTrack)
-    {
-    int rowOffset;
-    char **row;
-    struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
-    struct sqlResult *sr = NULL;
-
-    sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd,
-             NULL, &rowOffset);
-    while ((row = sqlNextRow(sr)) != NULL)
-	{
-	bed = bedLoadN(row+rowOffset, 9);
-	if (scoreFilter && bed->score < scoreFilter)
-	    continue;
-	bed8To12(bed);
-	lf = lfFromBed(bed);
-	if (useItemRgb)
-	    {
-	    lf->extra = (void *)USE_ITEM_RGB;   /* signal for coloring */
-	    lf->filterColor=bed->itemRgb;
-	    }
-	slAddHead(&lfList, lf);
-	}
-    hFreeConn(&conn);
-    }
-else
-    {
-    for (bed = ct->bedList; bed != NULL; bed = bed->next)
-	{
-        if (scoreFilter && bed->score < scoreFilter)
-            continue;
-	if (bed->chromStart < winEnd && bed->chromEnd > winStart
-		&& sameString(chromName, bed->chrom))
-	    {
-	    bed8To12(bed);
-	    lf = lfFromBed(bed);
-	    if (useItemRgb)
-		{
-		lf->extra = (void *)USE_ITEM_RGB;   /* signal for coloring */
-		lf->filterColor=bed->itemRgb;
-		}
-	    slAddHead(&lfList, lf);
-	    }
-	}
-    }
-slReverse(&lfList);
-slSort(&lfList, linkedFeaturesCmp);
-tg->items = lfList;
-}
-
-
-void ctLoadBed8(struct track *tg)
-/* Convert bed info in window to linked feature. */
-{
-struct customTrack *ct = tg->customPt;
-struct bed *bed;
-struct linkedFeatures *lfList = NULL, *lf;
-int scoreFilter = getScoreFilter(ct->tdb->track);
-
-if (ct->dbTrack)
-    {
-    int fieldCount = ct->fieldCount;
-    int rowOffset;
-    char **row;
-    struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
-    struct sqlResult *sr = NULL;
-
-    sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd,
-             NULL, &rowOffset);
-    while ((row = sqlNextRow(sr)) != NULL)
-	{
-	bed = bedLoadN(row+rowOffset, fieldCount);
-	    if (scoreFilter && bed->score < scoreFilter)
-		continue;
-	bed8To12(bed);
-	lf = lfFromBed(bed);
-	slAddHead(&lfList, lf);
-	}
-    hFreeConn(&conn);
-    }
-else
-    {
-    for (bed = ct->bedList; bed != NULL; bed = bed->next)
-	{
-	if (scoreFilter && bed->score < scoreFilter)
-	    continue;
-	if (bed->chromStart < winEnd && bed->chromEnd > winStart
-		&& sameString(chromName, bed->chrom))
-	    {
-	    bed8To12(bed);
-	    lf = lfFromBed(bed);
-	    slAddHead(&lfList, lf);
-	    }
-	}
-    }
-slReverse(&lfList);
-slSort(&lfList, linkedFeaturesCmp);
-tg->items = lfList;
-}
-
-void ctLoadGappedBed(struct track *tg)
-/* Convert bed info in window to linked feature. */
-{
-struct customTrack *ct = tg->customPt;
-struct bed *bed;
-struct linkedFeatures *lfList = NULL, *lf;
-boolean useItemRgb = FALSE;
-int scoreFilter = getScoreFilter(ct->tdb->track);
-
-useItemRgb = bedItemRgb(ct->tdb);
-
-if (ct->dbTrack)
-    {
-    int fieldCount = ct->fieldCount;
-    int rowOffset;
-    char **row;
-    struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
-    struct sqlResult *sr = NULL;
-
-    sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd,
-             NULL, &rowOffset);
-    while ((row = sqlNextRow(sr)) != NULL)
-	{
-	bed = bedLoadN(row+rowOffset, fieldCount);
-	lf = lfFromBed(bed);
-	    if (scoreFilter && bed->score < scoreFilter)
-		continue;
-	if (useItemRgb)
-	    {
-	    lf->extra = (void *)USE_ITEM_RGB;   /* signal for coloring */
-	    lf->filterColor=bed->itemRgb;
-	    }
-	slAddHead(&lfList, lf);
-	}
-    hFreeConn(&conn);
-    }
-else
-    {
-    for (bed = ct->bedList; bed != NULL; bed = bed->next)
-	{
-        if (scoreFilter && bed->score < scoreFilter)
-            continue;
-	if (bed->chromStart < winEnd && bed->chromEnd > winStart
-		&& sameString(chromName, bed->chrom))
-	    {
-	    lf = lfFromBed(bed);
-	    if (useItemRgb)
-		{
-		lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */
-		lf->filterColor=bed->itemRgb;
-		}
-	    slAddHead(&lfList, lf);
-	    }
-	}
-    }
-slReverse(&lfList);
-slSort(&lfList, linkedFeaturesCmp);
-tg->items = lfList;
-}
-
-void ctLoadColoredExon(struct track *tg)
-/* Convert bed info in window to linked features series for custom track. */
-{
-struct customTrack *ct = tg->customPt;
-struct bed *bed;
-struct linkedFeaturesSeries *lfsList = NULL, *lfs;
-if (ct->dbTrack)
-    {
-    int fieldCount = ct->fieldCount;
-    int rowOffset;
-    char **row;
-    struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
-    struct sqlResult *sr = NULL;
-    sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd,
-             NULL, &rowOffset);
-    while ((row = sqlNextRow(sr)) != NULL)
-	{
-	bed = bedLoadN(row+rowOffset, fieldCount);
-	lfs = lfsFromColoredExonBed(bed);
-	slAddHead(&lfsList, lfs);
-	}
-    hFreeConn(&conn);
-    }
-else
-    {
-    for (bed = ct->bedList; bed != NULL; bed = bed->next)
-	{
-	if (bed->chromStart < winEnd && bed->chromEnd > winStart
-		&& sameString(chromName, bed->chrom))
-	    {
-	    lfs = lfsFromColoredExonBed(bed);
-	    slAddHead(&lfsList, lfs);
-	    }
-	}
-    }
-slReverse(&lfsList);
-slSort(&lfsList, linkedFeaturesSeriesCmp);
-tg->items = lfsList;
-}
-
-char *ctMapItemName(struct track *tg, void *item)
-/* Return composite item name for custom tracks. */
-{
-char *itemName = tg->itemName(tg, item);
-static char buf[256];
-if (strlen(itemName) > 0)
-  sprintf(buf, "%s %s", ctFileName, itemName);
-else
-  sprintf(buf, "%s NoItemName", ctFileName);
-return buf;
-}
-
-
-void coloredExonMethodsFromCt(struct track *tg)
-/* same as coloredExonMethods but different loader. */
-{
-linkedFeaturesSeriesMethods(tg);
-tg->loadItems = ctLoadColoredExon;
-tg->canPack = TRUE;
-}
-
-struct track *newCustomTrack(struct customTrack *ct)
-/* Make up a new custom track. */
-{
-struct track *tg = NULL;
-struct trackDb *tdb = ct->tdb;
-boolean useItemRgb = FALSE;
-char *typeOrig = tdb->type;
-char *typeDupe = cloneString(typeOrig);
-char *typeParam = typeDupe;
-char *type = nextWord(&typeParam);
-
-if (ct->dbTrack)
-    {
-    // make sure we can connect
-    struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
-    hFreeConn(&conn);
-    }
-
-useItemRgb = bedItemRgb(tdb);
-
-if (sameString(type, "maf"))
-    {
-    tg = trackFromTrackDb(tdb);
-    tg->canPack = TRUE;
-
-    wigMafMethods(tg, tdb, 0, NULL);
-    if (!ct->dbTrack)
-    errAbort("custom maf tracks must be in database");
-
-    struct mafPriv *mp;
-    AllocVar(mp);
-    mp->ct = ct;
-
-    tg->customPt = mp;
-    tg->nextItemButtonable = FALSE;
-    }
-else if (sameString(type, "wig"))
-    {
-    tg = trackFromTrackDb(tdb);
-    if (ct->dbTrack)
-    tg->loadItems = wigLoadItems;
-    else
-    tg->loadItems = ctWigLoadItems;
-    tg->customPt = ct;
-    tg->nextItemButtonable = FALSE;
-    }
-else if (sameString(type, "bigWig"))
-    {
-    tg = trackFromTrackDb(tdb);
-    tg->bbiFile = ct->bbiFile;
-    tg->nextItemButtonable = FALSE;
-    }
-else if (sameString(type, "bigBed"))
-    {
-    struct bbiFile *bbi = ct->bbiFile;
-
-    /* Find field counts, and from that revise the tdb->type to be more complete. */
-    char extra = (bbi->fieldCount > bbi->definedFieldCount ? '+' : '.');
-    char typeBuf[64];
-    safef(typeBuf, sizeof(typeBuf), "bigBed %d %c", bbi->definedFieldCount, extra);
-    tdb->type = cloneString(typeBuf);
-
-    /* Finish wrapping track around tdb. */
-    tg = trackFromTrackDb(tdb);
-    tg->bbiFile = bbi;
-    tg->nextItemButtonable = FALSE;
-    }
-else if (sameString(type, "bedGraph"))
-    {
-    tg = trackFromTrackDb(tdb);
-    tg->canPack = FALSE;
-    tg->customPt = ct;
-    ct->wigFile = ctFileName;
-    tg->mapItemName = ctMapItemName;
-    tg->nextItemButtonable = FALSE;
-    }
-else if (sameString(type, "bed"))
-    {
-    tg = trackFromTrackDb(tdb);
-    if (ct->fieldCount < 8)
-	{
-	tg->loadItems = ctLoadSimpleBed;
-	}
-    else if (useItemRgb && ct->fieldCount == 9)
-	{
-	tg->loadItems = ctLoadBed9;
-	}
-    else if (ct->fieldCount < 12)
-	{
-	tg->loadItems = ctLoadBed8;
-	}
-    else if (ct->fieldCount == 15)
-	{
-	char *theType = trackDbSetting(tdb, "type");
-	if (theType && sameString(theType, "expRatio"))
-	    {
-	    tg = trackFromTrackDb(tdb);
-	    expRatioMethodsFromCt(tg);
-	    }
-	else
-	    tg->loadItems = ctLoadGappedBed;
-	}
-    else
-	{
-	tg->loadItems = ctLoadGappedBed;
-	}
-    tg->mapItemName = ctMapItemName;
-    tg->canPack = TRUE;
-    tg->nextItemButtonable = TRUE;
-    tg->customPt = ct;
-    }
-else if (sameString(type, "chromGraph"))
-    {
-    tdb->type = NULL;   /* Swap out type for the moment. */
-    tg = trackFromTrackDb(tdb);
-    chromGraphMethodsCt(tg);
-    tg->nextItemButtonable = FALSE;
-    tdb->type = typeOrig;
-    }
-else if (sameString(type, "array"))
-    {
-    tg = trackFromTrackDb(tdb);
-    expRatioMethodsFromCt(tg);
-    tg->nextItemButtonable = TRUE;
-    tg->customPt = ct;
-    }
-else if (sameString(type, "coloredExon"))
-    {
-    tg = trackFromTrackDb(tdb);
-    coloredExonMethodsFromCt(tg);
-    tg->nextItemButtonable = TRUE;
-    tg->customPt = ct;
-    }
-else if (sameString(type, "encodePeak"))
-    {
-    tg = trackFromTrackDb(tdb);
-    encodePeakMethodsCt(tg);
-    tg->nextItemButtonable = TRUE;
-    tg->customPt = ct;
-    }
-else if (sameString(type, "bam"))
-    {
-    tg = trackFromTrackDb(tdb);
-    tg->customPt = ct;
-    bamMethods(tg);
-    tg->mapItemName = ctMapItemName;
-    hashAdd(tdb->settingsHash, BASE_COLOR_USE_SEQUENCE, cloneString("lfExtra"));
-    hashAdd(tdb->settingsHash, BASE_COLOR_DEFAULT, cloneString("diffBases"));
-    hashAdd(tdb->settingsHash, SHOW_DIFF_BASES_ALL_SCALES, cloneString("."));
-    hashAdd(tdb->settingsHash, INDEL_DOUBLE_INSERT, cloneString("on"));
-    hashAdd(tdb->settingsHash, INDEL_QUERY_INSERT, cloneString("on"));
-    hashAdd(tdb->settingsHash, INDEL_POLY_A, cloneString("on"));
-    hashAdd(tdb->settingsHash, "showDiffBasesMaxZoom", cloneString("100"));
-    }
-else if (sameString(type, "makeItems"))
-    {
-    tg = trackFromTrackDb(tdb);
-    makeItemsMethods(tg);
-    tg->nextItemButtonable = TRUE;
-    tg->customPt = ct;
-    }
-else if (sameString(type, "bedDetail"))
-    {
-    tg = trackFromTrackDb(tdb);
-    bedDetailCtMethods(tg, ct);
-    tg->mapItemName = ctMapItemName; /* must be here to see ctMapItemName */
-    }
-else if (sameString(type, "pgSnp"))
-    {
-    tg = trackFromTrackDb(tdb);
-    pgSnpCtMethods(tg);
-    //tg->mapItemName = ctMapItemName;
-    tg->customPt = ct;
-    }
-else
-    {
-    errAbort("Unrecognized custom track type %s", type);
-    }
-if (!ct->dbTrack)
-    tg->nextItemButtonable = FALSE;
-tg->hasUi = TRUE;
-freez(&typeDupe);
-return tg;
-}
-
-char *getPositionFromCustomTracks()
-/* Parses custom track data to get the position variable
- * return - The first chromosome position variable found in the
- * custom track data.  */
-{
-char *pos = NULL;
-struct slName *bl = NULL;
-
-ctList = customTracksParseCart(database, cart, &browserLines, &ctFileName);
-
-for (bl = browserLines; bl != NULL; bl = bl->next)
-    {
-    char *words[96];
-    int wordCount;
-    char *dupe = cloneString(bl->name);
-
-    wordCount = chopLine(dupe, words);
-    if (wordCount >= 3)
-        {
-        char *command = words[1];
-        if (sameString(command, "position"))
-            pos = cloneString(words[2]);
-        }
-    freez(&dupe);
-    if (pos != NULL)
-        break;
-    }
-return pos;
-}
-
-void loadCustomTracks(struct track **pTrackList)
-/* Load up custom tracks and append to list. */
-{
-struct customTrack *ct;
-struct track *tg;
-struct slName *bl;
-
-/* build up browser lines from cart variables set by hgCustom */
-char *visAll = cartCgiUsualString(cart, "hgt.visAllFromCt", NULL);
-if (visAll)
-    {
-    char buf[SMALLBUF];
-    safef(buf, sizeof buf, "browser %s %s", visAll, "all");
-    slAddTail(&browserLines, slNameNew(buf));
-    }
-struct hashEl *visEl;
-struct hashEl *visList = cartFindPrefix(cart, "hgtct.");
-for (visEl = visList; visEl != NULL; visEl = visEl->next)
-    {
-    char buf[256];
-    safef(buf, sizeof buf, "browser %s %s", cartString(cart, visEl->name),
-                chopPrefix(cloneString(visEl->name)));
-    slAddTail(&browserLines, slNameNew(buf));
-    cartRemove(cart, visEl->name);
-    }
-hashElFreeList(&visList);
-
-/* The loading is now handled by getPositionFromCustomTracks(). */
-/* Process browser commands in custom track. */
-for (bl = browserLines; bl != NULL; bl = bl->next)
-    {
-    char *words[96];
-    int wordCount;
-
-    wordCount = chopLine(bl->name, words);
-    if (wordCount > 1)
-        {
-	char *command = words[1];
-	if (sameString(command, "hide")
-            || sameString(command, "dense")
-            || sameString(command, "pack")
-            || sameString(command, "squish")
-            || sameString(command, "full"))
-	    {
-	    if (wordCount > 2)
-		{
-		int i;
-		for (i=2; i<wordCount; ++i)
-		    {
-		    char *s = words[i];
-		    struct track *tg;
-		    boolean toAll = sameWord(s, "all");
-		    for (tg = *pTrackList; tg != NULL; tg = tg->next)
-			{
-			if (toAll || sameString(s, tg->track))
-			    {
-			    if (hTvFromString(command) == tg->tdb->visibility)
-				/* remove if setting to default vis */
-				cartRemove(cart, tg->track);
-			    else
-				cartSetString(cart, tg->track, command);
-			    /* hide or show supertrack enclosing this track */
-			    if (tdbIsSuperTrackChild(tg->tdb))
-				{
-				assert(tg->tdb->parentName != NULL);
-				cartSetString(cart, tg->tdb->parentName,
-					    (sameString(command, "hide") ?
-						"hide" : "show"));
-				}
-			    }
-			}
-		    }
-		}
-	    }
-	else if (sameString(command, "position"))
-	    {
-	    if (wordCount < 3)
-		errAbort("Expecting 3 words in browser position line");
-	    if (!hgIsChromRange(database, words[2]))
-		errAbort("browser position needs to be in chrN:123-456 format");
-	    hgParseChromRange(database, words[2], &chromName, &winStart, &winEnd);
-
-		/*Fix a start window of -1 that is returned when a custom track position
-		  begins at 0
-		*/
-		if (winStart < 0)
-		    {
-		    winStart = 0;
-		    }
-	    }
-	else if (sameString(command, "pix"))
-	    {
-	    if (wordCount != 3)
-		errAbort("Expecting 3 words in pix line");
-	    trackLayoutSetPicWidth(&tl, words[2]);
-	    }
-	}
-    }
-for (ct = ctList; ct != NULL; ct = ct->next)
-    {
-    hasCustomTracks = TRUE;
-    tg = newCustomTrack(ct);
-    slAddHead(pTrackList, tg);
-    }
-}
-
-void addTracksFromDataHub(char *hubUrl, struct track **pTrackList)
-/* Load up stuff from data hub and append to list. The hubUrl points to
- * a trackDb.ra format file.  */
-{
-/* Squirrel away hub directory for later. */
-char hubDir[PATH_LEN];
-splitPath(hubUrl, hubDir, NULL, NULL);
-
-/* Load trackDb.ra file and make it into proper trackDb tree */
-struct trackDb *tdb, *tdbList = trackDbFromRa(hubUrl);
-for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
-     {
-     trackDbFieldsFromSettings(tdb);
-     trackDbPolish(tdb);
-     }
-trackDbLinkUpGenerations(tdbList);
-addTdbListToTrackList(tdbList, NULL, pTrackList);
-}
-
-void loadDataHubs(struct track **pTrackList)
-/* Load up stuff from data hubs and append to list. */
-{
-char *dataHubs = cloneString(cartUsualString(cart, "dataHubs", NULL));
-if (dataHubs == NULL)
-    return;
-int hubCount = chopByWhite(dataHubs, NULL, 10);
-char *hubArrays[hubCount];
-chopByWhite(dataHubs, hubArrays, hubCount);
-int i;
-for (i = 0; i<hubCount; ++i)
-    {
-    addTracksFromDataHub(hubArrays[i], pTrackList);
-    }
-}
-
-boolean restrictionEnzymesOk()
-/* Check to see if it's OK to do restriction enzymes. */
-{
-return (hTableExists("hgFixed", "cutters") &&
-    hTableExists("hgFixed", "rebaseRefs") &&
-    hTableExists("hgFixed", "rebaseCompanies"));
-}
-
-void fr2ScaffoldEnsemblLink(char *archive)
-/* print out Ensembl link to appropriate scaffold there */
-{
-struct sqlConnection *conn = hAllocConn(database);
-struct sqlResult *sr = NULL;
-char **row = NULL;
-char query[256];
-safef(query, sizeof(query),
-"select * from chrUn_gold where chrom = '%s' and chromStart<%u and chromEnd>%u",
-chromName, winEnd, winStart);
-sr = sqlGetResult(conn, query);
-
-int itemCount = 0;
-struct agpFrag *agpItem = NULL;
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    agpFragFree(&agpItem);  // if there is a second one
-    agpItem = agpFragLoad(row+1);
-    ++itemCount;
-    if (itemCount > 1)
-	break;
-    }
-sqlFreeResult(&sr);
-hFreeConn(&conn);
-if (1 == itemCount)
-    {   // verify *entirely* within single contig
-    if ((winEnd <= agpItem->chromEnd) &&
-	(winStart >= agpItem->chromStart))
-	{
-	int agpStart = winStart - agpItem->chromStart;
-	int agpEnd = agpStart + winEnd - winStart;
-	hPuts("<TD ALIGN=CENTER>");
-	printEnsemblAnchor(database, archive, agpItem->frag,
-	agpStart, agpEnd);
-	hPrintf("%s</A></TD>", "Ensembl");
-	}
-    }
-agpFragFree(&agpItem);  // the one we maybe used
-}
-
-void hotLinks()
-/* Put up the hot links bar. */
-{
-boolean gotBlat = hIsBlatIndexedDatabase(database);
-struct dyString *uiVars = uiStateUrlPart(NULL);
-char *orgEnc = cgiEncode(organism);
-boolean psOutput = cgiVarExists("hgt.psOutput");
-
-hPrintf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#000000\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"1\"><TR><TD>\n");
-hPrintf("<TABLE WIDTH=\"100%%\" BGCOLOR=\"#2636D1\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"0\"><TR>\n");
-hPrintf("<TD><TABLE BORDER=\"0\"><TR>\n");
-hPrintf("<TD ALIGN=CENTER><A HREF=\"../index.html?org=%s&db=%s&%s=%u\" class=\"topbar\">Home</A>&nbsp;&nbsp;</TD>",
-    orgEnc, database, cartSessionVarName(), cartSessionId(cart));
-
-if (hIsGisaidServer())
-    {
-    /* disable hgGateway for gisaid for now */
-    //hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"../cgi-bin/hgGateway?org=%s&db=%s\" class=\"topbar\">Sequence View Gateway</A>&nbsp;&nbsp;</TD>", orgEnc, database);
-    hPrintf(
-    "<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"../cgi-bin/gisaidTable?gisaidTable.do.advFilter=filter+%c28now+on%c29&fromProg=hgTracks&%s=%u\" class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>",
-    '%', '%',
-    cartSessionVarName(),
-    cartSessionId(cart),
-    "Select Subjects");
-    }
-else
-if (hIsGsidServer())
-    {
-    hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"../cgi-bin/hgGateway?org=%s&db=%s\" class=\"topbar\">Sequence View Gateway</A>&nbsp;&nbsp;</TD>", orgEnc, database);
-    hPrintf(
-    "<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"../cgi-bin/gsidTable?gsidTable.do.advFilter=filter+%c28now+on%c29&fromProg=hgTracks\" class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>",
-    '%', '%', "Select Subjects");
-    }
-else
-    {
-    hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"../cgi-bin/hgGateway?org=%s&db=%s&%s=%u\" class=\"topbar\">Genomes</A>&nbsp;&nbsp;</TD>", orgEnc, database, cartSessionVarName(), cartSessionId(cart));
-    }
-if (psOutput)
-    {
-    hPrintf("<TD ALIGN=CENTER nowrap>&nbsp;&nbsp;<A HREF=\"../cgi-bin/hgTracks?hgTracksConfigPage=notSetorg=%s&db=%s&%s=%u\" class='topbar'>Genome Browser</A>&nbsp;&nbsp;</TD>", orgEnc, database, cartSessionVarName(), cartSessionId(cart));
-    }
-if (gotBlat)
-    {
-    hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"../cgi-bin/hgBlat?%s\" class=\"topbar\">Blat</A>&nbsp;&nbsp;</TD>", uiVars->string);
-    }
-if (hIsGisaidServer())
-    {
-    hPrintf("<TD ALIGN=CENTER nowrap>&nbsp;&nbsp;<A HREF=\"../cgi-bin/gisaidTable?db=%s&%s=%u\" class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>",
-       database,
-       cartSessionVarName(),
-       cartSessionId(cart),
-       "Table View");
-    }
-else if (hIsGsidServer())
-    {
-    hPrintf("<TD ALIGN=CENTER nowrap>&nbsp;&nbsp;<A HREF=\"../cgi-bin/gsidTable?db=%s\" class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>",
-       database, "Table View");
-    }
-else
-    {
-    /* disable TB for CGB servers */
-    if (!hIsCgbServer())
-	{
-	    hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"../cgi-bin/hgTables?db=%s&position=%s:%d-%d&%s=%u\" class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>",
-	    database, chromName, winStart+1, winEnd,
-	cartSessionVarName(),
-	    cartSessionId(cart),
-	"Tables");
-	}
-    }
-
-if (hgNearOk(database))
-    {
-    hPrintf("<TD ALIGN=CENTER nowrap>&nbsp;&nbsp;<A HREF=\"../cgi-bin/hgNear?%s\" class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>",
-                 uiVars->string, "Gene Sorter");
-    }
-if (hgPcrOk(database))
-    {
-    hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"../cgi-bin/hgPcr?%s\" class=\"topbar\">PCR</A>&nbsp;&nbsp;</TD>", uiVars->string);
-    }
-if (!psOutput)
-    {
-    hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"%s&o=%d&g=getDna&i=mixed&c=%s&l=%d&r=%d&db=%s&%s\" class=\"topbar\">"
-        " %s </A>&nbsp;&nbsp;</TD>",  hgcNameAndSettings(),
-        winStart, chromName, winStart, winEnd, database, uiVars->string, "DNA");
-    }
-
-if (!psOutput)
-    {
-    /* disable Convert function for CGB servers for the time being */
-    if (!hIsCgbServer())
-    if (liftOverChainForDb(database) != NULL)
-        {
-        hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"");
-        hPrintf("../cgi-bin/hgConvert?%s&db=%s&position=%s:%d-%d",
-            uiVars->string, database, chromName, winStart+1, winEnd);
-        hPrintf("\" class=\"topbar\">Convert</A>&nbsp;&nbsp;</TD>");
-        }
-    }
-
-/* see if hgFixed.trackVersion exists */
-boolean trackVersionExists = hTableExists("hgFixed", "trackVersion");
-char ensVersionString[256];
-char ensDateReference[256];
-ensVersionString[0] = 0;
-ensDateReference[0] = 0;
-if (trackVersionExists)
-    {
-    struct sqlConnection *conn = hAllocConn("hgFixed");
-    char query[256];
-    safef(query, sizeof(query), "select version,dateReference from hgFixed.trackVersion where db = '%s' order by updateTime DESC limit 1", database);
-    struct sqlResult *sr = sqlGetResult(conn, query);
-    char **row;
-
-    while ((row = sqlNextRow(sr)) != NULL)
-        {
-        safef(ensVersionString, sizeof(ensVersionString), "Ensembl %s",
-                row[0]);
-        safef(ensDateReference, sizeof(ensDateReference), "%s",
-                row[1]);
-        }
-    sqlFreeResult(&sr);
-    hFreeConn(&conn);
-    }
-
-if (!psOutput)
-    {
-    if (differentWord(database,"susScr2"))
-        {
-        /* Print Ensembl anchor for latest assembly of organisms we have
-        * supported by Ensembl == if versionString from trackVersion exists */
-        if (sameWord(database,"hg19"))
-            {
-            hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;");
-            printEnsemblAnchor(database, NULL, chromName, winStart, winEnd);
-            hPrintf("%s</A>&nbsp;&nbsp;</TD>", "Ensembl");
-            }
-        else if (sameWord(database,"hg18"))
-            {
-            hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;");
-            printEnsemblAnchor(database, "ncbi36", chromName, winStart, winEnd);
-            hPrintf("%s</A>&nbsp;&nbsp;</TD>", "Ensembl");
-            }
-        else if (ensVersionString[0])
-            {
-            char *archive = NULL;
-            if (ensDateReference[0] && differentWord("current", ensDateReference))
-                archive = cloneString(ensDateReference);
-            /*  Can we perhaps map from a UCSC random chrom to an Ensembl contig ? */
-            if (sameWord(database,"oryCun2") || isUnknownChrom(database, chromName))
-                {
-                //	which table to check
-                char *ctgPos = "ctgPos";
-                if (sameWord(database,"oryCun2"))
-                    ctgPos = "ctgPos2";
-
-                if (sameWord(database,"fr2"))
-                    fr2ScaffoldEnsemblLink(archive);
-                else if (hTableExists(database, ctgPos))
-                    /* see if we are entirely within a single contig */
-                    {
-                    struct sqlConnection *conn = hAllocConn(database);
-                    struct sqlResult *sr = NULL;
-                    char **row = NULL;
-                    char query[256];
-                    safef(query, sizeof(query),
-            "select * from %s where chrom = '%s' and chromStart<%u and chromEnd>%u",
-                    ctgPos, chromName, winEnd, winStart);
-                    sr = sqlGetResult(conn, query);
-
-                    int itemCount = 0;
-                    struct ctgPos *ctgItem = NULL;
-                    while ((row = sqlNextRow(sr)) != NULL)
-                        {
-                        ctgPosFree(&ctgItem);   // if there is a second one
-                        ctgItem = ctgPosLoad(row);
-                        ++itemCount;
-                        if (itemCount > 1)
-                            break;
-                        }
-                    sqlFreeResult(&sr);
-                    hFreeConn(&conn);
-                    if (1 == itemCount)
-                        {   // verify *entirely* within single contig
-                        if ((winEnd <= ctgItem->chromEnd) &&
-                            (winStart >= ctgItem->chromStart))
-                            {
-                            int ctgStart = winStart - ctgItem->chromStart;
-                            int ctgEnd = ctgStart + winEnd - winStart;
-                            hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;");
-                            printEnsemblAnchor(database, archive, ctgItem->contig,
-                            ctgStart, ctgEnd);
-                            hPrintf("%s</A>&nbsp;&nbsp;</TD>", "Ensembl");
-                            }
-                        }
-                    ctgPosFree(&ctgItem);   // the one we maybe used
-                    }
-                }
-            else
-                {
-                hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;");
-                printEnsemblAnchor(database, archive, chromName, winStart, winEnd);
-                hPrintf("%s</A>&nbsp;&nbsp;</TD>", "Ensembl");
-                }
-            }
-        }
-    }
-
-if (!psOutput)
-    {
-    /* Print NCBI MapView anchor */
-    if (sameString(database, "hg18"))
-        {
-        hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&CHR=%s&BEG=%d&END=%d&build=36\" TARGET=_blank class=\"topbar\">",
-            skipChr(chromName), winStart+1, winEnd);
-        hPrintf("%s</A>&nbsp;&nbsp;</TD>", "NCBI");
-        }
-    if (sameString(database, "hg19"))
-        {
-        hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9606&CHR=%s&BEG=%d&END=%d&build=37\" TARGET=_blank class=\"topbar\">",
-            skipChr(chromName), winStart+1, winEnd);
-        hPrintf("%s</A>&nbsp;&nbsp;</TD>", "NCBI");
-        }
-    if (sameString(database, "mm8"))
-        {
-        hPrintf("<TD ALIGN=CENTER>");
-        hPrintf("<A HREF=\"http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=10090&CHR=%s&BEG=%d&END=%d\" TARGET=_blank class=\"topbar\">",
-            skipChr(chromName), winStart+1, winEnd);
-        hPrintf("%s</A>&nbsp;&nbsp;</TD>", "NCBI");
-        }
-    if (sameString(database, "danRer2"))
-        {
-        hPrintf("<TD ALIGN=CENTER>");
-        hPrintf("<A HREF=\"http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=7955&CHR=%s&BEG=%d&END=%d\" TARGET=_blank class=\"topbar\">",
-            skipChr(chromName), winStart+1, winEnd);
-        hPrintf("%s</A>&nbsp;&nbsp;</TD>", "NCBI");
-        }
-    if (sameString(database, "galGal3"))
-        {
-        hPrintf("<TD ALIGN=CENTER>");
-        hPrintf("<A HREF=\"http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9031&CHR=%s&BEG=%d&END=%d\" TARGET=_blank class=\"topbar\">",
-            skipChr(chromName), winStart+1, winEnd);
-        hPrintf("%s</A>&nbsp;&nbsp;</TD>", "NCBI");
-        }
-    if (sameString(database, "canFam2"))
-        {
-        hPrintf("<TD ALIGN=CENTER>");
-        hPrintf("<A HREF=\"http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9615&CHR=%s&BEG=%d&END=%d\" TARGET=_blank class=\"topbar\">",
-            skipChr(chromName), winStart+1, winEnd);
-        hPrintf("%s</A>&nbsp;&nbsp;</TD>", "NCBI");
-        }
-    if (sameString(database, "rheMac2"))
-        {
-        hPrintf("<TD ALIGN=CENTER>");
-        hPrintf("<A HREF=\"http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9544&CHR=%s&BEG=%d&END=%d\" TARGET=_blank class=\"topbar\">",
-            skipChr(chromName), winStart+1, winEnd);
-        hPrintf("%s</A>&nbsp;&nbsp;</TD>", "NCBI");
-        }
-    if (sameString(database, "panTro2"))
-        {
-        hPrintf("<TD ALIGN=CENTER>");
-        hPrintf("<A HREF=\"http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=9598&CHR=%s&BEG=%d&END=%d\" TARGET=_blank class=\"topbar\">",
-            skipChr(chromName), winStart+1, winEnd);
-        hPrintf("%s</A>&nbsp;&nbsp;</TD>", "NCBI");
-        }
-    if (sameString(database, "anoGam1"))
-        {
-        hPrintf("<TD ALIGN=CENTER>");
-        hPrintf("<A HREF=\"http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?taxid=7165&CHR=%s&BEG=%d&END=%d\" TARGET=_blank class=\"topbar\">",
-            skipChr(chromName), winStart+1, winEnd);
-        hPrintf("%s</A>&nbsp;&nbsp;</TD>", "NCBI");
-        }
-    if (startsWith("oryLat", database))
-        {
-        hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"http://medaka.utgenome.org/browser_ens_jump.php?revision=version1.0&chr=chromosome%s&start=%d&end=%d\" TARGET=_blank class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>",
-            skipChr(chromName), winStart+1, winEnd, "UTGB");
-        }
-    if (sameString(database, "cb3"))
-        {
-        hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"http://www.wormbase.org/db/seq/gbrowse/briggsae?name=%s:%d-%d\" TARGET=_blank class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>",
-            skipChr(chromName), winStart+1, winEnd, "WormBase");
-        }
-    if (sameString(database, "ce4"))
-        {
-        hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"http://ws170.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d\" TARGET=_blank class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>",
-            skipChr(chromName), winStart+1, winEnd, "WormBase");
-        }
-    if (sameString(database, "ce2"))
-        {
-        hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"http://ws120.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d\" TARGET=_blank class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>",
-            skipChr(chromName), winStart+1, winEnd, "WormBase");
-        }
-    }
-
-if (!psOutput)
-    {
-    hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"../cgi-bin/hgTracks?%s=%u&hgt.psOutput=on\" id='pdfLink' class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>",cartSessionVarName(),
-        cartSessionId(cart), "PDF/PS");
-    }
-
-if (!psOutput)
-    {
-    if (wikiLinkEnabled())
-        {
-        printf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"../cgi-bin/hgSession?%s=%u"
-        "&hgS_doMainPage=1\" class=\"topbar\">Session</A>&nbsp;&nbsp;</TD>",
-        cartSessionVarName(), cartSessionId(cart));
-        }
-    }
-if (hIsGisaidServer())
-    {
-    //hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"/goldenPath/help/gisaidTutorial.html#SequenceView\" TARGET=_blank class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>\n", "Help");
-    hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"../cgi-bin/hgNotYet\" TARGET=_blank class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>\n", "Help");
-    }
-else
-if (hIsGsidServer())
-    {
-    hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"/goldenPath/help/gsidTutorial.html#SequenceView\" TARGET=_blank class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>\n", "Help");
-    }
-else
-    {
-    hPrintf("<TD ALIGN=CENTER>&nbsp;&nbsp;<A HREF=\"../goldenPath/help/hgTracksHelp.html\" TARGET=_blank class=\"topbar\">%s</A>&nbsp;&nbsp;</TD>\n", "Help");
-    }
-hPuts("<TD colspan=20>&nbsp;</TD></TR></TABLE></TD>");
-hPuts("</TR></TABLE>");
-hPuts("</TD></TR></TABLE>\n");
-}
-
-static void setSuperTrackHasVisibleMembers(struct trackDb *tdb)
-/* Determine if any member tracks are visible -- currently
- * recording this in the parent's visibility setting */
-{
-tdb->visibility = tvDense;
-}
-
-boolean superTrackHasVisibleMembers(struct trackDb *tdb)
-/* Determine if any member tracks are visible -- currently
- * recording this in the parent's visibility setting */
-{
-if (!tdbIsSuper(tdb))
-    return FALSE;
-return (tdb->visibility != tvHide);
-}
-
-static void groupTracks(struct track **pTrackList, struct group **pGroupList,
-                                int vis)
-/* Make up groups and assign tracks to groups.
- * If vis is -1, restore default groups to tracks. */
-{
-struct group *unknown = NULL;
-struct group *group, *list = NULL;
-struct hash *hash = newHash(8);
-struct track *track;
-struct trackRef *tr;
-struct grp* grps = hLoadGrps(database);
-struct grp *grp;
-
-/* build group objects from database. */
-for (grp = grps; grp != NULL; grp = grp->next)
-    {
-    /* deal with group reordering */
-    float priority = grp->priority;
-    if (withPriorityOverride)
-        {
-        char cartVar[512];
-        safef(cartVar, sizeof(cartVar), "%s.priority",grp->name);
-        if (vis != -1)
-            priority = (float)cartUsualDouble(cart, cartVar, grp->priority);
-        if (priority == grp->priority)
-            cartRemove(cart, cartVar);
-        }
-    /* create group object; add to list and hash */
-    AllocVar(group);
-    group->name = cloneString(grp->name);
-    group->label = cloneString(grp->label);
-    group->defaultPriority = grp->priority;
-    group->priority = priority;
-    group->defaultIsClosed = grp->defaultIsClosed;
-    slAddHead(&list, group);
-    hashAdd(hash, grp->name, group);
-    }
-grpFreeList(&grps);
-
-/* Loop through tracks and fill in their groups.
- * If necessary make up an unknown group. */
-for (track = *pTrackList; track != NULL; track = track->next)
-    {
-    /* handle track reordering feature -- change group assigned to track */
-    if (withPriorityOverride)
-        {
-        char *groupName = NULL;
-        char cartVar[256];
-
-        /* belt and suspenders -- accomodate inconsistent track/trackDb
-         * creation.  Note -- with code cleanup, these default variables
-         * could be retired, and the tdb versions used as defaults */
-        if (!track->defaultGroupName)
-            {
-            if (track->tdb && track->tdb->grp)
-                track->defaultGroupName = cloneString(track->tdb->grp);
-            else
-                track->defaultGroupName = cloneString("other");
-            }
-        if (tdbIsSuperTrackChild(track->tdb))
-            {
-            assert(track->tdb->parentName != NULL);
-            /* supertrack member must be in same group as its super */
-            /* determine supertrack group */
-            safef(cartVar, sizeof(cartVar), "%s.group",track->tdb->parentName);
-            groupName = cloneString(                                              //1
-                    cartUsualString(cart, cartVar, track->tdb->parent->grp));
-            track->tdb->parent->grp = cloneString(groupName);                     //2
-            }
-        else
-            {
-            /* get group */
-            safef(cartVar, sizeof(cartVar), "%s.group",track->track);
-            groupName = cloneString(                                              //1
-                    cartUsualString(cart, cartVar, track->defaultGroupName));
-            }
-        if (vis == -1)
-            groupName = track->defaultGroupName;                                  //0
-        track->groupName = cloneString(groupName);  // wasting a few clones!      //3
-        if (sameString(groupName, track->defaultGroupName))
-            cartRemove(cart, cartVar);
-
-        /* get priority */
-        safef(cartVar, sizeof(cartVar), "%s.priority",track->track);
-        float priority = (float)cartUsualDouble(cart, cartVar,
-                                                    track->defaultPriority);
-        /* remove cart variables that are the same as the trackDb settings */
-/*  UGLY - add me back when tdb->priority is no longer pre-clobbered by cart var value
-        if (priority == track->defaultPriority)
-            cartRemove(cart, cartVar);
-*/
-        track->priority = priority;
-        }
-
-    /* assign group object to track */
-    if (track->groupName == NULL)
-        group = NULL;
-    else
-	group = hashFindVal(hash, track->groupName);
-    if (group == NULL)
-        {
-	if (unknown == NULL)
-	    {
-	    AllocVar(unknown);
-	    unknown->name = cloneString("other");
-	    unknown->label = cloneString("other");
-	    unknown->priority = 1000000;
-	    slAddHead(&list, unknown);
-	    }
-	group = unknown;
-	}
-    track->group = group;
-    }
-
-/* Sort tracks by combined group/track priority, and
- * then add references to track to group. */
-slSort(pTrackList, tgCmpPriority);
-for (track = *pTrackList; track != NULL; track = track->next)
-    {
-    AllocVar(tr);
-    tr->track = track;
-    slAddHead(&track->group->trackList, tr);
-    }
-
-/* Straighten things out, clean up, and go home. */
-for (group = list; group != NULL; group = group->next)
-    slReverse(&group->trackList);
-slSort(&list, gCmpPriority);
-hashFree(&hash);
-*pGroupList = list;
-}
-
-void groupTrackListAddSuper(struct cart *cart, struct group *group)
-/* Construct a new track list that includes supertracks, sort by priority,
- * and determine if supertracks have visible members.
- * Replace the group track list with this new list.
- * Shared by hgTracks and configure page to expand track list,
- * in contexts where no track display functions (which don't understand
- * supertracks) are invoked. */
-{
-struct trackRef *newList = NULL, *tr, *ref;
-struct hash *superHash = hashNew(8);
-
-if (!group || !group->trackList)
-    return;
-for (tr = group->trackList; tr != NULL; tr = tr->next)
-    {
-    struct track *track = tr->track;
-    AllocVar(ref);
-    ref->track = track;
-    slAddHead(&newList, ref);
-    if (tdbIsSuperTrackChild(track->tdb))
-        {
-        assert(track->tdb->parentName != NULL);
-        if (hTvFromString(cartUsualString(cart, track->track,
-                        hStringFromTv(track->tdb->visibility))) != tvHide)
-            setSuperTrackHasVisibleMembers(track->tdb->parent);
-        if (hashLookup(superHash, track->tdb->parentName))
-            /* ignore supertrack if it's already been handled */
-            continue;
-        /* create track and reference for the supertrack */
-        struct track *superTrack = trackFromTrackDb(track->tdb->parent);
-        superTrack->hasUi = TRUE;
-        superTrack->group = group;
-        superTrack->groupName = cloneString(group->name);
-        superTrack->defaultGroupName = cloneString(group->name);
-
-        /* handle track reordering */
-        char cartVar[256];
-        safef(cartVar, sizeof(cartVar), "%s.priority",track->tdb->parentName);
-        float priority = (float)cartUsualDouble(cart, cartVar,
-                                        track->tdb->parent->priority);
-        /* remove cart variables that are the same as the trackDb settings */
-        if (priority == track->tdb->parent->priority)
-            cartRemove(cart, cartVar);
-        superTrack->priority = priority;
-
-        AllocVar(ref);
-        ref->track = superTrack;
-        slAddHead(&newList, ref);
-        hashAdd(superHash, track->tdb->parentName, track->tdb->parent);
-        }
-    }
-slSort(&newList, trackRefCmpPriority);
-hashFree(&superHash);
-/* we could free the old track list here, but it's a trivial amount of mem */
-group->trackList = newList;
-}
-
-void topButton(char *var, char *label)
-/* create a 3 or 4-char wide button for top line of display.
- * 3 chars wide for odd-length labels, 4 for even length.
- * Pad with spaces so label is centered */
-{
-char paddedLabel[5] = "    ";
-int len = strlen(label);
-if (len > 4)
-    {
-    /* truncate */
-    /* or maybe errabort ? */
-    label[3] = 0;
-    len = 4;
-    }
-if (len % 2 != 0)
-    paddedLabel[3] = 0;
-if (len == strlen(paddedLabel))
-    strcpy(paddedLabel, label);
-else
-    {
-    int i;
-    for (i=0; i<len; i++)
-        paddedLabel[i+1] = label[i];
-    }
-hButton(var, paddedLabel);
-}
-
-void limitSuperTrackVis(struct track *track)
-/* Limit track visibility by supertrack parent */
-{
-if(tdbIsSuperTrackChild(track->tdb))
-    {
-    assert(track->tdb->parent != NULL);
-    if (sameString("hide", cartUsualString(cart, track->tdb->parent->track,
-                                    track->tdb->parent->isShow ? "show" : "hide")))
-        track->visibility = tvHide;
-    }
-}
-
-struct track *rFindTrackWithTable(char *tableName, struct track *trackList)
-/* Recursively search through track list looking for first one that matches table. */
-{
-struct track *track;
-for (track = trackList; track != NULL; track = track->next)
-    {
-    if (sameString(tableName, track->table))
-         return track;
-    struct track *subTrack = rFindTrackWithTable(tableName, track->subtracks);
-    if (subTrack != NULL)
-         return subTrack;
-    }
-return NULL;
-}
-
-static void setSearchedTrackToPackOrFull(struct track *trackList)
-/* Open track associated with search position if any.   Also open its parents
- * if any.  At the moment parents include composites but not supertracks. */
-{
-if (NULL != hgp && NULL != hgp->tableList && NULL != hgp->tableList->name)
-    {
-    char *tableName = hgp->tableList->name;
-    struct track *matchTrack = rFindTrackWithTable(tableName, trackList);
-    if (matchTrack != NULL)
-	{
-	struct track *track;
-	for (track = matchTrack; track != NULL; track = track->parent)
-	    cartSetString(cart, track->track, hCarefulTrackOpenVis(database, track->track));
-	}
-    }
-}
-
-
-struct track *getTrackList( struct group **pGroupList, int vis)
-/* Return list of all tracks, organizing by groups.
- * If vis is -1, restore default groups to tracks.
- * Shared by hgTracks and configure page. */
-{
-struct track *track, *trackList = NULL;
-registerTrackHandlers();
-/* Load regular tracks, blatted tracks, and custom tracks.
- * Best to load custom last. */
-loadFromTrackDb(&trackList);
-if (pcrResultParseCart(database, cart, NULL, NULL, NULL))
-    slSafeAddHead(&trackList, pcrResultTg());
-if (userSeqString != NULL) slSafeAddHead(&trackList, userPslTg());
-slSafeAddHead(&trackList, oligoMatchTg());
-if (restrictionEnzymesOk())
-    {
-    slSafeAddHead(&trackList, cuttersTg());
-    }
-if (wikiTrackEnabled(database, NULL))
-    addWikiTrack(&trackList);
-#ifdef SOON
-loadDataHubs(&trackList);
-#endif /* SOON */
-loadCustomTracks(&trackList);
-groupTracks(&trackList, pGroupList, vis);
-setSearchedTrackToPackOrFull(trackList);
-if (cgiOptionalString( "hideTracks"))
-    changeTrackVis(groupList, NULL, tvHide);
-
-/* Get visibility values if any from ui. */
-for (track = trackList; track != NULL; track = track->next)
-    {
-    char *s = cartOptionalString(cart, track->track);
-    if (cgiOptionalString("hideTracks"))
-	{
-	s = cgiOptionalString(track->track);
-	if (s != NULL && (hTvFromString(s) != track->tdb->visibility))
-	    {
-	    cartSetString(cart, track->track, s);
-	    }
-	}
-    if (s != NULL && !track->limitedVisSet)
-	track->visibility = hTvFromString(s);
-    if (tdbIsComposite(track->tdb) && track->visibility != tvHide)
-	{
-	struct trackDb *parent = track->tdb->parent;
-	char *parentShow = NULL;
-	if (parent)
-	    parentShow = cartUsualString(cart, parent->track,
-			 parent->isShow ? "show" : "hide");
-	if (!parent || sameString(parentShow, "show"))
-	    compositeTrackVis(track);
-	}
-    }
-if (measureTiming)
-    uglyTime("getTrackList");
-return trackList;
-}
-
-void doNextPrevItem(boolean goNext, char *trackName)
-/* In case a next item arrow was clicked on a track, change */
-/* position (i.e. winStart, winEnd, etc.) based on what track it was */
-{
-struct track *track = trackFindByName(trackList, trackName);
-if ((track != NULL) && (track->nextPrevItem != NULL))
-    track->nextPrevItem(track, goNext);
-}
-
-char *collapseGroupVar(char *name)
-/* Construct cart variable name for collapsing group */
-{
-static char varName[256];
-safef(varName, sizeof(varName),
-        "%s%s_%s_%s", "hgt", "group", name, "close");
-return (cloneString(varName));
-}
-
-boolean isCollapsedGroup(struct group *grp)
-/* Determine if group is collapsed */
-{
-return cartUsualInt(cart, collapseGroupVar(grp->name), grp->defaultIsClosed);
-}
-
-void collapseGroupGoodies(boolean isOpen, boolean wantSmallImage,
-                                char **img, char **indicator, char **otherState)
-/* Get image, char representation of image, and 'otherState' (1 or 0)
- * for a group, based on whether it is collapsed, and whether we want
- * larger or smaller image for collapse box */
-{
-if (otherState)
-    *otherState = (isOpen ? "1" : "0");
-if (indicator)
-    *indicator = (isOpen ? "-" : "+");
-if (img)
-    {
-    if (wantSmallImage)
-        *img = (isOpen ? "../images/remove_sm.gif" : "../images/add_sm.gif");
-    else
-        *img = (isOpen ? "../images/remove.gif" : "../images/add.gif");
-    }
-}
-
-void collapseGroup(char *name, boolean doCollapse)
-/* Set cart variable to cause group to collapse */
-{
-cartSetBoolean(cart, collapseGroupVar(name), doCollapse);
-}
-
-void myControlGridStartCell(struct controlGrid *cg, boolean isOpen, char *id)
-/* Start a new cell in control grid; support Javascript open/collapsing by including id's in tr's.
-   id is used as id prefix (a counter is added to make id's unique). */
-{
-static int counter = 1;
-if (cg->columnIx == cg->columns)
-    controlGridEndRow(cg);
-if (!cg->rowOpen)
-    {
-#if 0
-    /* This is unnecessary, b/c we can just use a blank display attribute to show the element rather
-       than figuring out what the browser specific string is to turn on display of the tr;
-       however, we may want to put in browser specific strings in the future, so I'm leaving this
-       code in as a reference. */
-    char *ua = getenv("HTTP_USER_AGENT");
-    char *display = ua && stringIn("MSIE", ua) ? "block" : "table-row";
-#endif
-    // use counter to ensure unique tr id's (prefix is used to find tr's in javascript).
-    printf("<tr %sid='%s-%d'>", isOpen ? "" : "style='display: none' ", id, counter++);
-    cg->rowOpen = TRUE;
-    }
-if (cg->align)
-    printf("<td align=%s>", cg->align);
-else
-    printf("<td>");
-}
-
-static void pruneRedundantCartVis(struct track *trackList)
-/* When the config page or track form has been submitted, there usually
- * are many track visibility cart variables that have not been changed
- * from the default.  To keep down cart bloat, prune those out before we
- * save the cart.  changeTrackVis does this too, but this is for the
- * more common case where track visibilities are tweaked. */
-{
-struct track *track;
-if (measureTiming)
-    uglyTime("Done with trackForm");
-for (track = trackList; track != NULL; track = track->next)
-    {
-    char *cartVis = cartOptionalString(cart, track->track);
-    if (cartVis != NULL && hTvFromString(cartVis) == track->tdb->visibility)
-    cartRemove(cart, track->track);
-    }
-if (measureTiming)
-    {
-    uglyTime("Pruned redundant vis from cart");
-    }
-}
-
-static int getMaxWindowToDraw(struct trackDb *tdb)
-/* If trackDb setting maxWindowToDraw exists and is a sensible size, return it, else 0. */
-{
-if (tdb == NULL)
-    return 0;
-char *maxWinToDraw = trackDbSettingClosestToHome(tdb, "maxWindowToDraw");
-if (isNotEmpty(maxWinToDraw))
-    {
-    unsigned maxWTD = sqlUnsigned(maxWinToDraw);
-    if (maxWTD > 1)
-    return maxWTD;
-    }
-return 0;
-}
-
-static void drawMaxWindowWarning(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg,
-                 int xOff, int yOff, int width, MgFont *font, Color color,
-                 enum trackVisibility vis)
-/* This is a stub drawItems handler to be swapped in for the usual drawItems when the window
- * size is larger than the threshold specified by trackDb setting maxWindowToDraw. */
-{
-int maxWinToDraw = getMaxWindowToDraw(tg->tdb);
-char commafied[256];
-sprintLongWithCommas(commafied, maxWinToDraw);
-char message[512];
-safef(message, sizeof(message), "zoom in to <= %s bases to view items", commafied);
-Color yellow = hvGfxFindRgb(hvg, &undefinedYellowColor);
-hvGfxBox(hvg, xOff, yOff, width, tg->heightPer, yellow);
-hvGfxTextCentered(hvg, xOff, yOff, width, tg->heightPer, MG_BLACK, font, message);
-}
-
-static void dontLoadItems(struct track *tg)
-/* No-op loadItems when we aren't going to try. */
-{
-}
-
-static void checkMaxWindowToDraw(struct track *tg)
-/* If (winEnd - winStart) > trackDb setting maxWindowToDraw, force track to a dense line
- * that will ask the user to zoom in closer to see track items and return TRUE so caller
- * can skip loading items. */
-{
-int maxWinToDraw = getMaxWindowToDraw(tg->tdb);
-if (tdbIsComposite(tg->tdb))
-    {
-    struct track *subtrack;
-    for (subtrack = tg->subtracks;  subtrack != NULL;  subtrack = subtrack->next)
-	{
-	if (!isSubtrackVisible(subtrack))
-	    continue;
-	maxWinToDraw = getMaxWindowToDraw(subtrack->tdb);
-	if (maxWinToDraw > 1 && (winEnd - winStart) > maxWinToDraw)
-	    {
-	    subtrack->loadItems = dontLoadItems;
-	    subtrack->drawItems = drawMaxWindowWarning;
-	    subtrack->limitedVis = tvDense;
-	    subtrack->limitedVisSet = TRUE;
-	    }
-	}
-    }
-else if (maxWinToDraw > 1 && (winEnd - winStart) > maxWinToDraw)
-    {
-    tg->loadItems = dontLoadItems;
-    tg->drawItems = drawMaxWindowWarning;
-    tg->limitedVis = tvDense;
-    tg->limitedVisSet = TRUE;
-    }
-}
-
-void printTrackInitJavascript(struct track *trackList)
-{
-hPrintf("<input type='hidden' id='%s' name='%s' value=''>\n", hgtJsCommand, hgtJsCommand);
-hPrintf("<script type='text/javascript'>\n");
-hPrintf( "function hgTracksInitTracks()\n{\n");
-
-struct track *track;
-for (track = trackList; track != NULL; track = track->next)
-    {
-    if (startsWithWord("makeItems", track->tdb->type) )
-        hPrintf("setUpMakeItemsDrag(\"%s\");\n", track->track);
-    }
-
-hPrintf( "}\n");
-hPrintf("</script>\n");
-}
-
-void jsCommandDispatch(char *command, struct track *trackList)
-/* Dispatch a command sent to us from some javaScript event.
- * This gets executed after the track list is built, but before
- * the track->loadItems methods are called.  */
-{
-if (startsWithWord("makeItems", command))
-    makeItemsJsCommand(command, trackList, trackHash);
-else
-    warn("Unrecognized jsCommand %s", command);
-}
-
-#ifdef SUBTRACKS_HAVE_VIS
-static void parentChildCartCleanup(struct track *trackList,struct cart *newCart,struct hash *oldVars)
-/* When composite/view settings changes, remove subtrack specific vis
-   When superTrackChild is found and selected, shape superTrack to match. */
-{
-struct track *track = trackList;
-for (;track != NULL; track = track->next)
-    {
-    if (tdbIsMultiTrack(track->tdb))
-        if(cartTdbTreeMatchSubtrackVis(cart,track->tdb)) // Note, this is done for found multi-track kids but composites are only straightened up in hgTrackUi
-            track->visibility = tdbVisLimitedByAncestry(cart,track->tdb,FALSE);
-
-    if (cartTdbTreeCleanupOverrides(track->tdb,newCart,oldVars))
-        { // Need to update track visibility
-        if (tdbIsSuperTrackChild(track->tdb))
-            {
-            // Unfortunately, since supertracks are not in trackList, this occurs on superChildren,
-            // So now we need to find the supertrack and take changed cart values of its children
-            struct slRef *childRef;
-            for(childRef = track->tdb->parent->children;childRef != NULL;childRef = childRef->next)
-                {
-                struct trackDb * childTdb = childRef->val;
-                struct track *child = hashFindVal(trackHash, childTdb->track);
-                char *cartVis = cartOptionalString(cart,child->track);
-                if (cartVis)
-                    child->visibility = hTvFromString(cartVis);
-                }
-            }
-        }
-    }
-}
-#endif///def SUBTRACKS_HAVE_VIS
-
-void doTrackForm(char *psOutput, struct tempName *ideoTn)
-/* Make the tracks display form with the zoom/scroll buttons and the active
- * image.  If the ideoTn parameter is not NULL, it is filled in if the
- * ideogram is created.  */
-{
-struct group *group;
-struct track *track;
-char *freezeName = NULL;
-boolean hideAll = cgiVarExists("hgt.hideAll");
-boolean defaultTracks = cgiVarExists("hgt.reset");
-boolean showedRuler = FALSE;
-boolean showTrackControls = cartUsualBoolean(cart, "trackControlsOnMain", TRUE);
-long thisTime = 0, lastTime = 0;
-char *clearButtonJavascript;
-
-basesPerPixel = ((float)winBaseCount) / ((float)insideWidth);
-zoomedToBaseLevel = (winBaseCount <= insideWidth / tl.mWidth);
-zoomedToCodonLevel = (ceil(winBaseCount/3) * tl.mWidth) <= insideWidth;
-zoomedToCdsColorLevel = (winBaseCount <= insideWidth*3);
-
-if (psOutput != NULL)
-   {
-   hPrintDisable();
-   hideControls = TRUE;
-   withNextItemArrows = FALSE;
-   withNextExonArrows = FALSE;
-   hgFindMatches = NULL;
-   }
-
-/* Tell browser where to go when they click on image. */
-hPrintf("<FORM ACTION=\"%s\" NAME=\"TrackHeaderForm\" id=\"TrackHeaderForm\" METHOD=\"GET\">\n\n", hgTracksName());
-hPrintf("<input type='hidden' id='hgt.insideX' name='insideX' value='%d'>\n", insideX);
-hPrintf("<input type='hidden' id='hgt.revCmplDisp' name='revCmplDisp' value='%d'>\n", revCmplDisp);
-if (!psOutput) cartSaveSession(cart);
-clearButtonJavascript = "document.TrackHeaderForm.position.value=''; document.getElementById('suggest').value='';";
-
-/* See if want to include sequence search results. */
-userSeqString = cartOptionalString(cart, "ss");
-if (userSeqString && !ssFilesExist(userSeqString))
-    {
-    userSeqString = NULL;
-    cartRemove(cart, "ss");
-    }
-if (!hideControls)
-    hideControls = cartUsualBoolean(cart, "hideControls", FALSE);
-if (measureTiming)
-    uglyTime("Time before getTrackList");
-trackList = getTrackList(&groupList, defaultTracks ? -1 : -2);
-makeGlobalTrackHash(trackList);
-#ifdef SOON
-if (measureTiming)
-    uglyTime("getTrackList");
-#endif /* SOON */
-
-// honor defaultImgOrder
-if(cgiVarExists("hgt.defaultImgOrder"))
-    {
-    char wildCard[32];
-    safef(wildCard,sizeof(wildCard),"*_%s",IMG_ORDER_VAR);
-    cartRemoveLike(cart, wildCard);
-    }
-#ifdef SUBTRACKS_HAVE_VIS
-parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated
-#endif///def SUBTRACKS_HAVE_VIS
-
-/* Honor hideAll and visAll variables */
-if (hideAll || defaultTracks)
-    {
-    int vis = (hideAll ? tvHide : -1);
-    changeTrackVis(groupList, NULL, vis);
-    }
-
-/* Before loading items, deal with the next/prev item arrow buttons if pressed. */
-if (cgiVarExists("hgt.nextItem"))
-    doNextPrevItem(TRUE, cgiUsualString("hgt.nextItem", NULL));
-else if (cgiVarExists("hgt.prevItem"))
-    doNextPrevItem(FALSE, cgiUsualString("hgt.prevItem", NULL));
-
-if(advancedJavascriptFeaturesEnabled(cart) && !psOutput && !cgiVarExists("hgt.imageV1"))
-    {
-    // Start an imagebox (global for now to avoid huge rewrite of hgTracks)
-    // Set up imgBox dimensions
-    int sideSliceWidth  = 0;   // Just being explicit
-    if (withLeftLabels)
-        sideSliceWidth   = (insideX - gfxBorder*3) + 2;
-    theImgBox = imgBoxStart(database,chromName,winStart,winEnd,(!revCmplDisp),sideSliceWidth,tl.picWidth);
-    #ifdef IMAGEv2_DRAG_SCROLL
-    // Define a portal with a default expansion size, then set the global dimensions to the full image size
-    if(imgBoxPortalDefine(theImgBox,&winStart,&winEnd,&(tl.picWidth),0))
-        {
-        winBaseCount = winEnd - winStart;
-        insideWidth = tl.picWidth-gfxBorder-insideX;
-        }
-    #endif//def IMAGEv2_DRAG_SCROLL
-    }
-
-char *jsCommand = cartCgiUsualString(cart, hgtJsCommand, "");
-if (!isEmpty(jsCommand))
-   {
-   cartRemove(cart, hgtJsCommand);
-   jsCommandDispatch(jsCommand, trackList);
-   }
-
-/* Tell tracks to load their items. */
-for (track = trackList; track != NULL; track = track->next)
-    {
-    /* adjust track visibility based on supertrack just before load loop */
-    if (tdbIsSuperTrackChild(track->tdb))
-        limitSuperTrackVis(track);
-
-    /* remove cart priority variables if they are set
-       to the default values in the trackDb */
-    if(!hTrackOnChrom(track->tdb, chromName))
-	{
-	track->limitedVis = tvHide;
-	track->limitedVisSet = TRUE;
-	}
-    else if (track->visibility != tvHide)
-	{
-	if (measureTiming)
-	    lastTime = clock1000();
-	checkMaxWindowToDraw(track);
-	track->loadItems(track);
-
-	if (measureTiming)
-	    {
-	    thisTime = clock1000();
-	    track->loadTime = thisTime - lastTime;
-	    }
-	}
-    }
-
-printTrackInitJavascript(trackList);
-
-/* Generate two lists of hidden variables for track group visibility.  Kludgy,
-   but required b/c we have two different navigation forms on this page, but
-   we want open/close changes in the bottom form to be submitted even if the user
-   submits via the top form. */
-struct dyString *trackGroupsHidden1 = newDyString(1000);
-struct dyString *trackGroupsHidden2 = newDyString(1000);
-for (group = groupList; group != NULL; group = group->next)
-    {
-    if (group->trackList != NULL)
-        {
-        int looper;
-        for(looper=1;looper<=2;looper++)
-            {
-            boolean isOpen = !isCollapsedGroup(group);
-            char buf[1000];
-            safef(buf, sizeof(buf), "<input type='hidden' name=\"%s\" id=\"%s_%d\" value=\"%s\">\n", collapseGroupVar(group->name), collapseGroupVar(group->name), looper, isOpen ? "0" : "1");
-            dyStringAppend(looper == 1 ? trackGroupsHidden1 : trackGroupsHidden2, buf);
-            }
-        }
-    }
-
-#ifdef IMAGEv2_DRAG_SCROLL
-if(theImgBox)
-    {
-    // If a portal was established, then set the global dimensions back to the portal size
-    if(imgBoxPortalDimensions(theImgBox,NULL,NULL,NULL,NULL,&winStart,&winEnd,&(tl.picWidth),NULL))
-        {
-        winBaseCount = winEnd - winStart;
-        insideWidth = tl.picWidth-gfxBorder-insideX;
-        }
-    }
-#endif//def IMAGEv2_DRAG_SCROLL
-/* Center everything from now on. */
-hPrintf("<CENTER>\n");
-
-if(trackImgOnly)
-    {
-    makeActiveImage(trackList, psOutput);
-    fflush(stdout);
-    return;  // bail out b/c we are done
-    }
-
-
-if (!hideControls)
-    {
-    /* set white-space to nowrap to prevent buttons from wrapping when screen is
-     * narrow */
-    hPrintf("<DIV STYLE=\"white-space:nowrap;\">\n");
-    hotLinks();
-
-    /* Show title . */
-    freezeName = hFreezeFromDb(database);
-    if(freezeName == NULL)
-    freezeName = "Unknown";
-    hPrintf("<FONT SIZE=5><B>");
-    if (startsWith("zoo",database) )
-	{
-	hPrintf("%s %s on %s June 2002 Assembly %s target1",
-	    organization, browserName, organism, freezeName);
-	}
-    else
-	{
-	if (sameString(organism, "Archaea"))
-	    {
-	    hPrintf("%s %s on Archaeon %s Assembly",
-		organization, browserName, freezeName);
-	    }
-	else
-	    {
-	    if (stringIn(database, freezeName))
-		hPrintf("%s %s on %s %s Assembly",
-			organization, browserName, organism, freezeName);
-	    else
-		hPrintf("%s %s on %s %s Assembly (%s)",
-			organization, browserName, organism, freezeName, database);
-	    }
-	}
-    hPrintf("</B></FONT><BR>\n");
-
-    /* This is a clear submit button that browsers will use by default when enter is pressed in position box. */
-    hPrintf("<INPUT TYPE=IMAGE BORDER=0 NAME=\"hgt.dummyEnterButton\" src=\"../images/DOT.gif\">");
-    /* Put up scroll and zoom controls. */
-#ifndef USE_NAVIGATION_LINKS
-    hWrites("move ");
-    hButtonWithMsg("hgt.left3", "<<<", "move 95% to the left");
-    hButtonWithMsg("hgt.left2", " <<", "move 47.5% to the left");
-    hButtonWithMsg("hgt.left1", " < ", "move 10% to the left");
-    hButtonWithMsg("hgt.right1", " > ", "move 10% to the right");
-    hButtonWithMsg("hgt.right2", ">> ", "move 47.5% to the right");
-    hButtonWithMsg("hgt.right3", ">>>", "move 95% to the right");
-    hWrites(" zoom in ");
-    /* use button maker that determines padding, so we can share constants */
-    topButton("hgt.in1", ZOOM_1PT5X);
-    topButton("hgt.in2", ZOOM_3X);
-    topButton("hgt.in3", ZOOM_10X);
-    topButton("hgt.inBase", ZOOM_BASE);
-    hWrites(" zoom out ");
-    topButton("hgt.out1", ZOOM_1PT5X);
-    topButton("hgt.out2", ZOOM_3X);
-    topButton("hgt.out3", ZOOM_10X);
-    hWrites("<BR>\n");
-#endif//ndef USE_NAVIGATION_LINKS
-
-    if (showTrackControls)
-	{
-	/* Break into a second form so that zooming and scrolling
-	 * can be done with a 'GET' so that user can back up from details
-	 * page without Internet Explorer popping up an annoying dialog.
-	 * Do rest of page as a 'POST' so that the ultra-long URL from
-	 * all the track controls doesn't break things.  IE URL limit
-	 * is 2000 bytes, but some firewalls impose a ~1000 byte limit.
-	 * As a side effect of breaking up the page into two forms
-	 * we need to repeat the position in a hidden variable here
-	 * so that zoom/scrolling always has current position to work
-	 * from. */
-	hPrintf("<INPUT TYPE=HIDDEN id='positionHidden' NAME=\"position\" "
-	    "VALUE=\"%s:%d-%d\">", chromName, winStart+1, winEnd);
-	    hPrintf("\n%s", trackGroupsHidden1->string);
-	hPrintf("</CENTER></FORM>\n");
-	hPrintf("<FORM ACTION=\"%s\" NAME=\"TrackForm\" id=\"TrackForm\" METHOD=\"POST\">\n\n", hgTracksName());
-	    hPrintf("%s", trackGroupsHidden2->string);
-	    freeDyString(&trackGroupsHidden1);
-	    freeDyString(&trackGroupsHidden2);
-	if (!psOutput) cartSaveSession(cart);   /* Put up hgsid= as hidden variable. */
-	clearButtonJavascript = "document.TrackForm.position.value=''; document.getElementById('suggest').value='';";
-	hPrintf("<CENTER>");
-	}
-
-
-    /* Make line that says position. */
-	{
-	char buf[256];
-	char *survey = cfgOptionEnv("HGDB_SURVEY", "survey");
-	char *surveyLabel = cfgOptionEnv("HGDB_SURVEY_LABEL", "surveyLabel");
-	    char *javascript = "onchange=\"document.location = '/cgi-bin/hgTracks?db=' + document.TrackForm.db.options[document.TrackForm.db.selectedIndex].value;\"";
-	    if (containsStringNoCase(database, "zoo"))
-		{
-		hPuts("Organism ");
-		printAssemblyListHtmlExtra(database, javascript);
-		}
-
-	sprintf(buf, "%s:%d-%d", chromName, winStart+1, winEnd);
-	position = cloneString(buf);
-	hWrites("position/search ");
-	hTextVar("position", addCommasToPos(database, position), 30);
-	sprintLongWithCommas(buf, winEnd - winStart);
-	if(dragZooming && assemblySupportsGeneSuggest(database))
-            hWrites(" <a title='click for help on gene search box' target='_blank' href='../goldenPath/help/geneSearchBox.html'>gene</a> <input type='text' size='8' name='hgt.suggest' id='suggest'>\n");
-	hWrites(" ");
-	hButtonWithOnClick("hgt.jump", "jump", NULL, "jumpButtonOnClick()");
-	hOnClickButton(clearButtonJavascript,"clear");
-	hPrintf(" size <span id='size'>%s</span> bp. ", buf);
-	hWrites(" ");
-	hButton("hgTracksConfigPage", "configure");
-        //hPrintf("&nbsp;&nbsp;<FONT SIZE=3><A STYLE=\"text-decoration:none; padding:2px; background-color:yellow; border:solid 1px\" HREF=\"http://www.surveymonkey.com/s.asp?u=881163743177\" TARGET=_BLANK><EM><B>Your feedback</B></EM></A></FONT>\n");
-	if (survey && differentWord(survey, "off"))
-	    hPrintf("&nbsp;&nbsp;<FONT SIZE=3><A STYLE=\"background-color:yellow;\" HREF=\"%s\" TARGET=_BLANK><EM><B>%s</B></EM></A></FONT>\n", survey, surveyLabel ? surveyLabel : "Take survey");
-	// info for drag selection javascript
-	hPrintf("<input type='hidden' id='hgt.winStart' name='winStart' value='%d'>\n", winStart);
-	hPrintf("<input type='hidden' id='hgt.winEnd' name='winEnd' value='%d'>\n", winEnd);
-	hPrintf("<input type='hidden' id='hgt.chromName' name='chromName' value='%s'>\n", chromName);
-
-	hPutc('\n');
-
-	}
-    }
-
-/* Make chromsome ideogram gif and map. */
-makeChromIdeoImage(&trackList, psOutput, ideoTn);
-
-#ifdef USE_NAVIGATION_LINKS
-    hPrintf("<TABLE BORDER=0 CELLPADDING=0 width='%d'><tr style='font-size:small;'>\n",tl.picWidth);//min(tl.picWidth, 800));
-    hPrintf("<td width='40' align='left'><a href='?hgt.left3=1' title='move 95&#37; to the left'>&lt;&lt;&lt;</a>\n");
-    hPrintf("<td width='30' align='left'><a href='?hgt.left2=1' title='move 47.5&#37; to the left'>&lt;&lt;</a>\n");
-    #ifdef IMAGEv2_DRAG_SCROLL
-    if(!advancedJavascriptFeaturesEnabled(cart))
-    #endif//def IMAGEv2_DRAG_SCROLL
-        hPrintf("<td width='20' align='left'><a href='?hgt.left1=1' title='move 10&#37; to the left'>&lt;</a>\n");
-
-    hPrintf("<td>&nbsp;</td>\n"); // Without 'width=' this cell expand to table with, forcing other cells to the sides.
-    hPrintf("<td width='40' align='left'><a href='?hgt.in1=1' title='zoom in 1.5x'>&gt;&nbsp;&lt;</a>\n");
-    hPrintf("<td width='60' align='left'><a href='?hgt.in2=1' title='zoom in 3x'>&gt;&gt;&nbsp;&lt;&lt;</a>\n");
-    hPrintf("<td width='80' align='left'><a href='?hgt.in3=1' title='zoom in 10x'>&gt;&gt;&gt;&nbsp;&lt;&lt;&lt;</a>\n");
-    hPrintf("<td width='40' align='left'><a href='?hgt.inBase=1' title='zoom in to base range'>&gt;<i>base</i>&lt;</a>\n");
-
-    hPrintf("<td>&nbsp;</td>\n"); // Without 'width=' this cell expand to table with, forcing other cells to the sides.
-    hPrintf("<td width='40' align='right'><a href='?hgt.out1=1' title='zoom out 1.5x'>&lt;&nbsp;&gt;</a>\n");
-    hPrintf("<td width='60' align='right'><a href='?hgt.out2=1' title='zoom out 3x'>&lt;&lt;&nbsp;&gt;&gt;</a>\n");
-    hPrintf("<td width='80' align='right'><a href='?hgt.out3=1' title='zoom out 10x'>&lt;&lt;&lt;&nbsp;&gt;&gt;&gt;</a>\n");
-        hPrintf("<td>&nbsp;</td>\n"); // Without 'width=' this cell expand to table with, forcing other cells to the sides.
-    #ifdef IMAGEv2_DRAG_SCROLL
-    if(!advancedJavascriptFeaturesEnabled(cart))
-    #endif//ndef IMAGEv2_DRAG_SCROLL
-        hPrintf("<td width='20' align='right'><a href='?hgt.right1=1' title='move 10&#37; to the right'>&gt;</a>\n");
-
-    hPrintf("<td width='30' align='right'><a href='?hgt.right2=1' title='move 47.5&#37; to the right'>&gt;&gt;</a>\n");
-    hPrintf("<td width='40' align='right'><a href='?hgt.right3=1' title='move 95&#37; to the right'>&gt;&gt;&gt;</a>\n");
-    hPrintf("</tr></table>\n");
-#endif//def USE_NAVIGATION_LINKS
-
-/* Make clickable image and map. */
-makeActiveImage(trackList, psOutput);
-fflush(stdout);
-
-if(trackImgOnly)
-    // bail out b/c we are done
-    return;
-
-if (!hideControls)
-    {
-    struct controlGrid *cg = NULL;
-
-    /* note a trick of WIDTH=27 going on here.  The 6,15,6 widths following
-     * go along with this trick */
-    hPrintf("<TABLE BORDER=0 CELLSPACING=1 CELLPADDING=1 WIDTH=%d COLS=%d><TR>\n",
-        tl.picWidth, 27);
-#ifndef USE_NAVIGATION_LINKS
-    hPrintf("<TD COLSPAN=6 ALIGN=left NOWRAP>");
-    hPrintf("move start<BR>");
-    hButton("hgt.dinkLL", " < ");
-    hTextVar("dinkL", cartUsualString(cart, "dinkL", "2.0"), 3);
-    hButton("hgt.dinkLR", " > ");
-    hPrintf("</TD>");
-    hPrintf("<td width='30'>&nbsp;</td>\n");
-#endif//ndef USE_NAVIGATION_LINKS
-    hPrintf("<TD COLSPAN=15 style=\"white-space:normal\">"); // allow this text to wrap
-    hWrites("Click on a feature for details. ");
-    hWrites(dragZooming ? "Click or drag in the base position track to zoom in. " : "Click on base position to zoom in around cursor. ");
-    hWrites("Click side bars for track options. ");
-    hWrites("Drag side bars or labels up or down to reorder tracks. ");
-#ifdef IMAGEv2_DRAG_SCROLL
-    hWrites("Drag tracks left or right to new position. ");
-#endif//def IMAGEv2_DRAG_SCROLL
-//#if !defined(IMAGEv2_DRAG_SCROLL) && !defined(USE_NAVIGATION_LINKS)
-    hPrintf("</TD>");
-#ifndef USE_NAVIGATION_LINKS
-    hPrintf("<td width='30'>&nbsp;</td>\n");
-    hPrintf("<TD COLSPAN=6 ALIGN=right NOWRAP>");
-    hPrintf("move end<BR>");
-    hButton("hgt.dinkRL", " < ");
-    hTextVar("dinkR", cartUsualString(cart, "dinkR", "2.0"), 3);
-    hButton("hgt.dinkRR", " > ");
-    hPrintf("</TD>");
-#endif//ndef USE_NAVIGATION_LINKS
-    hPrintf("</TR></TABLE>\n");
-    // smallBreak();
-
-    /* Display bottom control panel. */
-
-#ifdef TRACK_SEARCH
-    if(isSearchTracksSupported(database))
-        {
-        hPrintf("<input type='submit' name='%s' value='find tracks'>", searchTracks);
-        hPrintf(" ");
-        }
-#endif
-    hButton("hgt.reset", "default tracks");
-	hPrintf("&nbsp;");
-    hButton("hgt.defaultImgOrder", "default order");
-    // if (showTrackControls)  - always show "hide all", Hiram 2008-06-26
-	{
-	hPrintf("&nbsp;");
-	hButton("hgt.hideAll", "hide all");
-	}
-
-    hPrintf(" ");
-    hOnClickButton("document.customTrackForm.submit();return false;",
-                        hasCustomTracks ?
-                            CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL);
-
-    hPrintf(" ");
-    hButton("hgTracksConfigPage", "configure");
-    hPrintf(" ");
-
-    if (!hIsGsidServer())
-	{
-        hButton("hgt.toggleRevCmplDisp", "reverse");
-        hPrintf(" ");
-	}
-
-    hButton("hgt.refresh", "refresh");
-
-    hPrintf("<BR>\n");
-
-    if( chromosomeColorsMade )
-        {
-        hPrintf("<B>Chromosome Color Key:</B><BR> ");
-        hPrintf("<IMG SRC = \"../images/new_colorchrom.gif\" BORDER=1 WIDTH=596 HEIGHT=18 ><BR>\n");
-        }
-
-    if (showTrackControls)
-	{
-	/* Display viewing options for each track. */
-	/* Chuck: This is going to be wrapped in a table so that
-	 * the controls don't wrap around randomly */
-	hPrintf("<table border=0 cellspacing=1 cellpadding=1 width=%d>\n", CONTROL_TABLE_WIDTH);
-	hPrintf("<tr><td align='left'>\n");
-
-	hButtonWithOnClick("hgt.collapseGroups", "collapse all", "collapse all track groups", "return setAllTrackGroupVisibility(false)");
-	hPrintf("</td>");
-
-	hPrintf("<td colspan='%d' align='CENTER' nowrap>"
-	   "Use drop-down controls below and press refresh to alter tracks "
-	   "displayed.<BR>"
-	   "Tracks with lots of items will automatically be displayed in "
-	   "more compact modes.</td>\n", MAX_CONTROL_COLUMNS - 2);
-
-	hPrintf("<td align='right'>");
-	hButtonWithOnClick("hgt.expandGroups", "expand all", "expand all track groups", "return setAllTrackGroupVisibility(true)");
-	hPrintf("</td></tr>");
-
-	if (!hIsGsidServer())
-	    {
-	    cg = startControlGrid(MAX_CONTROL_COLUMNS, "left");
-	    }
-	else
-	    {
-	    /* 4 cols fit GSID's display better */
-	    cg = startControlGrid(4, "left");
-	    }
-	boolean isFirstNotCtGroup = TRUE;
-	for (group = groupList; group != NULL; group = group->next)
-	    {
-	    if (group->trackList == NULL)
-		continue;
-
-	    struct trackRef *tr;
-
-	    /* check if group section should be displayed */
-	    char *otherState;
-	    char *indicator;
-	    char *indicatorImg;
-	    boolean isOpen = !isCollapsedGroup(group);
-	    collapseGroupGoodies(isOpen, TRUE, &indicatorImg,
-				    &indicator, &otherState);
-	    hPrintf("<TR>");
-	    cg->rowOpen = TRUE;
-	    if (!hIsGsidServer())
-		{
-		hPrintf("<th align=\"left\" colspan=%d BGCOLOR=#536ED3>",
-		    MAX_CONTROL_COLUMNS);
-		}
-	    else
-		{
-		hPrintf("<th align=\"left\" colspan=%d BGCOLOR=#536ED3>",
-		    MAX_CONTROL_COLUMNS-1);
-		}
-	    hPrintf("<table width='100%%'><tr><td align='left'>");
-	    hPrintf("\n<A NAME=\"%sGroup\"></A>",group->name);
-	    hPrintf("<A HREF=\"%s?%s&%s=%s#%sGroup\" class='bigBlue'><IMG height='18' width='18' onclick=\"return toggleTrackGroupVisibility(this, '%s');\" id=\"%s_button\" src=\"%s\" alt=\"%s\" class='bigBlue'></A>&nbsp;&nbsp;",
-		    hgTracksName(), cartSidUrlString(cart),
-		    collapseGroupVar(group->name),
-		    otherState, group->name,
-		    group->name, group->name, indicatorImg, indicator);
-	    hPrintf("</td><td align='center' width='100%%'>\n");
-	    hPrintf("<B>%s</B>", wrapWhiteFont(group->label));
-	    hPrintf("</td><td align='right'>\n");
-	    hPrintf("<input type='submit' name='hgt.refresh' value='refresh'>\n");
-	    hPrintf("</td></tr></table></th>\n");
-	    controlGridEndRow(cg);
-
-	    /* First track group that is not custom track group gets ruler,
-	     * unless it's collapsed. */
-	    if (!showedRuler && isFirstNotCtGroup &&
-			differentString(group->name, "user"))
-		{
-		char *url = trackUrl(RULER_TRACK_NAME, chromName);
-		showedRuler = TRUE;
-		myControlGridStartCell(cg, isOpen, group->name);
-		hPrintf("<A HREF=\"%s\">", url);
-		hPrintf(" %s<BR> ", RULER_TRACK_LABEL);
-		hPrintf("</A>");
-		hDropListClassWithStyle("ruler", rulerMenu,
-			sizeof(rulerMenu)/sizeof(char *), rulerMenu[rulerMode],
-			rulerMode == tvHide ? "hiddenText" : "normalText",
-			TV_DROPDOWN_STYLE);
-		controlGridEndCell(cg);
-		freeMem(url);
-		}
-	    if (differentString(group->name, "user"))
-		isFirstNotCtGroup = FALSE;
-
-	    /* Add supertracks to  track list, sort by priority and
-	     * determine if they have visible member tracks */
-	    groupTrackListAddSuper(cart, group);
-
-	    /* Display track controls */
-	    for (tr = group->trackList; tr != NULL; tr = tr->next)
-		{
-		struct track *track = tr->track;
-		if (tdbIsSuperTrackChild(track->tdb))
-		    /* don't display supertrack members */
-		    continue;
-		myControlGridStartCell(cg, isOpen, group->name);
-		if (track->hasUi)
-		    {
-		    char *url = trackUrl(track->track, chromName);
-		    char *longLabel = replaceChars(track->longLabel, "\"", "&quot;");
-		    if(trackDbSetting(track->tdb, "wgEncode") != NULL)
-			hPrintf("<a title='encode project' href='../ENCODE'><img height='16' width='16' src='../images/encodeThumbnail.jpg'></a>\n");
-		    hPrintf("<A HREF=\"%s\" title=\"%s\">", url, longLabel);
-		    freeMem(url);
-		    freeMem(longLabel);
-		    }
-		hPrintf(" %s", track->shortLabel);
-		if (tdbIsSuper(track->tdb))
-		    hPrintf("...");
-		hPrintf("<BR> ");
-		if (track->hasUi)
-		    hPrintf("</A>");
-
-		if (hTrackOnChrom(track->tdb, chromName))
-		    {
-		    if (tdbIsSuper(track->tdb))
-			superTrackDropDown(cart, track->tdb,
-					    superTrackHasVisibleMembers(track->tdb));
-		    else
-			{
-			/* check for option of limiting visibility to one mode */
-			hTvDropDownClassVisOnly(track->track, track->visibility,
-				    track->canPack, (track->visibility == tvHide) ?
-				    "hiddenText" : "normalText",
-				    trackDbSetting(track->tdb, "onlyVisibility"));
-			}
-		    }
-		else
-		    /* If track is not on this chrom print an informational
-		    message for the user. */
-		    hPrintf("[No data-%s]", chromName);
-		controlGridEndCell(cg);
-		}
-	    /* now finish out the table */
-	    if (group->next != NULL)
-		controlGridEndRow(cg);
-	    }
-	endControlGrid(&cg);
-	}
-
-    if (measureTiming)
-	{
-	hPrintf("track, load time, draw time, total<BR>\n");
-	for (track = trackList; track != NULL; track = track->next)
-	    {
-	    if (track->visibility == tvHide)
-		    continue;
-	    if (trackIsCompositeWithSubtracks(track))  //TODO: Change when tracks->subtracks are always set for composite
-		{
-		struct track *subtrack;
-		for (subtrack = track->subtracks; subtrack != NULL;
-						    subtrack = subtrack->next)
-		    if (isSubtrackVisible(subtrack))
-			hPrintf("%s, %d, %d, %d<BR>\n", subtrack->shortLabel,
-				subtrack->loadTime, subtrack->drawTime,
-		subtrack->loadTime + subtrack->drawTime);
-		}
-	    else
-		{
-		hPrintf("%s, %d, %d, %d<BR>\n",
-		    track->shortLabel, track->loadTime, track->drawTime,
-		    track->loadTime + track->drawTime);
-		if (startsWith("wigMaf", track->tdb->type))
-		  if (track->subtracks)
-		      if (track->subtracks->loadTime)
-			 hPrintf("&nbsp; &nbsp; %s wiggle, load %d<BR>\n",
-			    track->shortLabel, track->subtracks->loadTime);
-		}
-	    }
-	}
-    hPrintf("</DIV>\n");
-    }
-if (showTrackControls)
-    hButton("hgt.refresh", "refresh");
-hPrintf("</CENTER>\n");
-
-#ifdef SLOW
-/* We'll rely on the end of program to do the cleanup.
- * It turns out that the 'free' routine on Linux is
- * quite slow.  For chromosome level views the browser
- * spends about 1/3 of it's time doing the cleanup
- * below if it's enabled.  Since we really don't
- * need to reclaim this memory at this point I'm
- * taking this out.  Please don't delete the code though.
- * I'll like to keep it for testing now and then. -jk. */
-
-/* Clean up. */
-for (track = trackList; track != NULL; track = track->next)
-    {
-    if (track->visibility != tvHide)
-	{
-	if (track->freeItems != NULL)
-	    track->freeItems(track);
-	lmCleanup(&track->lm);
-	}
-    }
-#endif /* SLOW */
-hPrintf("</FORM>\n");
-
-/* hidden form for custom tracks CGI */
-hPrintf("<FORM ACTION='%s' NAME='customTrackForm'>", hgCustomName());
-cartSaveSession(cart);
-hPrintf("</FORM>\n");
-
-pruneRedundantCartVis(trackList);
-}
-
-static void toggleRevCmplDisp()
-/* toggle the reverse complement display mode */
-{
-// forces complement bases to match display
-revCmplDisp = !revCmplDisp;
-cartSetBooleanDb(cart, database, REV_CMPL_DISP, revCmplDisp);
-cartSetBooleanDb(cart, database, COMPLEMENT_BASES_VAR, revCmplDisp);
-}
-
-void zoomToSize(int newSize)
-/* Zoom so that center stays in same place,
- * but window is new size.  If necessary move
- * center a little bit to keep it from going past
- * edges. */
-{
-int center = ((long long int)winStart + (long long int)winEnd)/2;
-if (center < 0)
-    errAbort("zoomToSize: error computing center: %d = (%d + %d)/2\n",
-    center, winStart, winEnd);
-if (newSize > seqBaseCount)
-    newSize = seqBaseCount;
-winStart = center - newSize/2;
-winEnd = winStart + newSize;
-if (winStart <= 0)
-    {
-    winStart = 0;
-    winEnd = newSize;
-    }
-else if (winEnd > seqBaseCount)
-    {
-    winEnd = seqBaseCount;
-    winStart = winEnd - newSize;
-    }
-winBaseCount = winEnd - winStart;
-}
-
-void zoomAroundCenter(double amount)
-/* Set ends so as to zoom around center by scaling amount. */
-{
-double newSizeDbl = (winBaseCount*amount + 0.5);
-int newSize;
-if (newSizeDbl > seqBaseCount)
-    newSize = seqBaseCount;
-else if (newSizeDbl < 1.0)
-    newSize = 1;
-else
-    newSize = (int)newSizeDbl;
-zoomToSize(newSize);
-}
-
-void zoomToBaseLevel()
-/* Set things so that it's zoomed to base level. */
-{
-zoomToSize(insideWidth/tl.mWidth);
-if (rulerMode == tvHide)
-    cartSetString(cart, "ruler", "dense");
-}
-
-void relativeScroll(double amount)
-/* Scroll percentage of visible window. */
-{
-int offset;
-int newStart, newEnd;
-if (revCmplDisp)
-    amount = -amount;
-offset = (int)(amount * winBaseCount);
-/* Make sure don't scroll of ends. */
-newStart = winStart + offset;
-newEnd = winEnd + offset;
-if (newStart < 0)
-    offset = -winStart;
-else if (newEnd > seqBaseCount)
-    offset = seqBaseCount - winEnd;
-
-/* Move window. */
-winStart += offset;
-winEnd += offset;
-}
-
-void dinkWindow(boolean start, int dinkAmount)
-/* Move one end or other of window a little. */
-{
-if (revCmplDisp)
-    {
-    start = !start;
-    dinkAmount = -dinkAmount;
-    }
-if (start)
-   {
-   winStart += dinkAmount;
-   if (winStart < 0) winStart = 0;
-   }
-else
-   {
-   winEnd += dinkAmount;
-   if (winEnd > seqBaseCount)
-       winEnd = seqBaseCount;
-   }
-}
-
-int dinkSize(char *var)
-/* Return size to dink. */
-{
-char *stringVal = cartOptionalString(cart, var);
-double x;
-int insideX = trackOffsetX(); /* The global versions of these are not yet set */
-int insideWidth = tl.picWidth-gfxBorder-insideX;
-double guideBases = (double)guidelineSpacing * (double)(winEnd - winStart)
-    / ((double)insideWidth);
-
-if (stringVal == NULL || !isdigit(stringVal[0]))
-    {
-    stringVal = "1";
-    cartSetString(cart, var, stringVal);
-    }
-x = atof(stringVal);
-int ret = round(x*guideBases);
-
-return (ret == 0) ? 1 : ret;
-}
-
-void handlePostscript()
-/* Deal with Postscript output. */
-{
-struct tempName psTn, ideoPsTn;
-char *pdfFile = NULL, *ideoPdfFile = NULL;
-ZeroVar(&ideoPsTn);
-trashDirFile(&psTn, "hgt", "hgt", ".eps");
-
-hotLinks();
-printf("<H1>PostScript/PDF Output</H1>\n");
-printf("PostScript images can be printed at high resolution "
-       "and edited by many drawing programs such as Adobe "
-       "Illustrator.");
-doTrackForm(psTn.forCgi, &ideoPsTn);
-
-// postscript
-printf("<UL>\n");
-printf("<LI><A HREF=\"%s\">Click here</A> "
-       "to download the current browser graphic in PostScript.  ", psTn.forCgi);
-if (strlen(ideoPsTn.forCgi))
-    printf("<LI><A HREF=\"%s\">Click here</A> "
-           "to download the current chromosome ideogram in PostScript.  ", ideoPsTn.forCgi);
-printf("</UL>\n");
-
-pdfFile = convertEpsToPdf(psTn.forCgi);
-if (strlen(ideoPsTn.forCgi))
-    ideoPdfFile = convertEpsToPdf(ideoPsTn.forCgi);
-if(pdfFile != NULL)
-    {
-    printf("<BR>PDF can be viewed with Adobe Acrobat Reader.\n");
-    printf("<UL>\n");
-    printf("<LI><A TARGET=_blank HREF=\"%s\">Click here</A> "
-       "to download the current browser graphic in PDF.", pdfFile);
-    if (ideoPdfFile != NULL)
-        printf("<LI><A TARGET=_blank HREF=\"%s\">Click here</A> "
-               "to download the current chromosome ideogram in PDF.", ideoPdfFile);
-    printf("</UL>\n");
-    freez(&pdfFile);
-    freez(&ideoPdfFile);
-    }
-else
-    printf("<BR><BR>PDF format not available");
-
-    #define RETURN_BUTTON "<FORM ACTION='../cgi-bin/hgTracks' NAME='TrackHeaderForm' id='TrackHeaderForm' METHOD='GET'><INPUT TYPE=SUBMIT ID='ChangeToNameToSetSomething' VALUE='Return to Browser'></FORM>"
-    printf(RETURN_BUTTON);
-}
-
-boolean isGenome(char *pos)
-/* Return TRUE if pos is genome. */
-{
-pos = trimSpaces(pos);
-return(sameWord(pos, "genome") || sameWord(pos, "hgBatch"));
-}
-
-void setRulerMode()
-/* Set the rulerMode variable from cart. */
-{
-char *s = cartUsualString(cart, RULER_TRACK_NAME, "dense");
-if (sameWord(s, "full") || sameWord(s, "on"))
-    rulerMode = tvFull;
-else if (sameWord(s, "dense"))
-    rulerMode = tvDense;
-else
-    rulerMode = tvHide;
-}
-
-void setLayoutGlobals()
-/* Figure out basic dimensions of display.  */
-{
-withIdeogram = cartUsualBoolean(cart, "ideogram", TRUE);
-withLeftLabels = cartUsualBoolean(cart, "leftLabels", TRUE);
-withCenterLabels = cartUsualBoolean(cart, "centerLabels", TRUE);
-withGuidelines = cartUsualBoolean(cart, "guidelines", TRUE);
-withNextItemArrows = cartUsualBoolean(cart, "nextItemArrows", FALSE);
-withNextExonArrows = cartUsualBoolean(cart, "nextExonArrows", TRUE);
-if (!hIsGsidServer())
-    {
-    revCmplDisp = cartUsualBooleanDb(cart, database, REV_CMPL_DISP, FALSE);
-    }
-withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE);
-insideX = trackOffsetX();
-insideWidth = tl.picWidth-gfxBorder-insideX;
-
-}
-
-void tracksDisplay()
-/* Put up main tracks display. This routine handles zooming and
- * scrolling. */
-{
-char newPos[256];
-char *defaultPosition = hDefaultPos(database);
-char titleVar[256];
-position = getPositionFromCustomTracks();
-if (NULL == position)
-    {
-    position = cloneString(cartUsualString(cart, "position", NULL));
-    }
-
-/* default if not set at all, as would happen if it came from a URL with no
- * position. Otherwise tell them to go back to the gateway. Also recognize
- * "default" as specifying the default position. */
-if (((position == NULL) || sameString(position, "default"))
-    && (defaultPosition != NULL))
-    position = cloneString(defaultPosition);
-if (sameString(position, ""))
-    {
-    hUserAbort("Please go back and enter a coordinate rangeor a search term in the \"position\" field.<br>For example: chr22:20100000-20200000.\n");
-    }
-
-chromName = NULL;
-winStart = 0;
-if (isGenome(position) || NULL ==
-    (hgp = findGenomePos(database, position, &chromName, &winStart, &winEnd, cart)))
-    {
-    if (winStart == 0)  /* number of positions found */
-        {
-        freeMem(position);
-        position = cloneString(cartUsualString(cart, "lastPosition", defaultPosition));
-        hgp = findGenomePos(database, position, &chromName, &winStart, &winEnd,cart);
-        if(hgp != NULL && position != defaultPosition)
-            cartSetString(cart, "position", position);
-        }
-    }
-
-/* After position is found set up hash of matches that should
-   be drawn with names highlighted for easy identification. */
-createHgFindMatchHash();
-
-/* This means that no single result was found
-I.e., multiple results may have been found and are printed out prior to this code*/
-if (NULL == chromName)
-    {
-    return;
-    }
-
-seqBaseCount = hChromSize(database, chromName);
-winBaseCount = winEnd - winStart;
-
-/* Figure out basic dimensions of display.  This
- * needs to be done early for the sake of the
- * zooming and dinking routines. */
-setLayoutGlobals();
-
-baseShowPos = cartUsualBoolean(cart, BASE_SHOWPOS, FALSE);
-baseShowAsm = cartUsualBoolean(cart, BASE_SHOWASM, FALSE);
-baseShowScaleBar = cartUsualBoolean(cart, BASE_SCALE_BAR, TRUE);
-baseShowRuler = cartUsualBoolean(cart, BASE_SHOWRULER, TRUE);
-safef(titleVar,sizeof(titleVar),"%s_%s", BASE_TITLE, database);
-baseTitle = cartUsualString(cart, titleVar, "");
-if (sameString(baseTitle, ""))
-    baseTitle = NULL;
-
-if  (cgiVarExists("hgt.toggleRevCmplDisp"))
-    toggleRevCmplDisp();
-setRulerMode();
-
-/* Do zoom/scroll if they hit it. */
-if (cgiVarExists("hgt.left3"))
-    relativeScroll(-0.95);
-else if (cgiVarExists("hgt.left2"))
-    relativeScroll(-0.475);
-else if (cgiVarExists("hgt.left1"))
-    relativeScroll(-0.1);
-else if (cgiVarExists("hgt.right1"))
-    relativeScroll(0.1);
-else if (cgiVarExists("hgt.right2"))
-    relativeScroll(0.475);
-else if (cgiVarExists("hgt.right3"))
-    relativeScroll(0.95);
-else if (cgiVarExists("hgt.inBase"))
-    zoomToBaseLevel();
-else if (cgiVarExists("hgt.in3"))
-    zoomAroundCenter(1.0/10.0);
-else if (cgiVarExists("hgt.in2"))
-    zoomAroundCenter(1.0/3.0);
-else if (cgiVarExists("hgt.in1"))
-    zoomAroundCenter(1.0/1.5);
-else if (cgiVarExists("hgt.out1"))
-    zoomAroundCenter(1.5);
-else if (cgiVarExists("hgt.out2"))
-    zoomAroundCenter(3.0);
-else if (cgiVarExists("hgt.out3"))
-    zoomAroundCenter(10.0);
-else if (cgiVarExists("hgt.dinkLL"))
-    dinkWindow(TRUE, -dinkSize("dinkL"));
-else if (cgiVarExists("hgt.dinkLR"))
-    dinkWindow(TRUE, dinkSize("dinkL"));
-else if (cgiVarExists("hgt.dinkRL"))
-    dinkWindow(FALSE, -dinkSize("dinkR"));
-else if (cgiVarExists("hgt.dinkRR"))
-    dinkWindow(FALSE, dinkSize("dinkR"));
-
-/* Clip chromosomal position to fit. */
-if (winEnd < winStart)
-    {
-    int temp = winEnd;
-    winEnd = winStart;
-    winStart = temp;
-    }
-else if (winStart == winEnd)
-    {
-    winStart -= 1;
-    winEnd += 1;
-    }
-
-if (winStart < 0)
-    {
-    winStart = 0;
-    }
-
-if (winEnd > seqBaseCount)
-    {
-    winEnd = seqBaseCount;
-    }
-
-if (winStart > seqBaseCount)
-    {
-    winStart = seqBaseCount - 1000;
-    }
-
-winBaseCount = winEnd - winStart;
-if (winBaseCount <= 0)
-    hUserAbort("Window out of range on %s", chromName);
-/* Save computed position in cart. */
-sprintf(newPos, "%s:%d-%d", chromName, winStart+1, winEnd);
-cartSetString(cart, "org", organism);
-cartSetString(cart, "db", database);
-cartSetString(cart, "position", newPos);
-if (cgiVarExists("hgt.psOutput"))
-    handlePostscript();
-else
-    doTrackForm(NULL, NULL);
-}
-
-void chromInfoTotalRow(int count, long long total)
-/* Make table row with total number of sequences and size from chromInfo. */
-{
-cgiSimpleTableRowStart();
-cgiSimpleTableFieldStart();
-printf("Total: %d", count);
-cgiTableFieldEnd();
-cgiSimpleTableFieldStart();
-printLongWithCommas(stdout, total);
-cgiTableFieldEnd();
-cgiTableRowEnd();
-}
-
-void chromInfoRowsChrom()
-/* Make table rows of chromosomal chromInfo name & size, sorted by name. */
-{
-struct slName *chromList = hAllChromNames(database);
-struct slName *chromPtr = NULL;
-long long total = 0;
-
-slSort(&chromList, chrSlNameCmp);
-for (chromPtr = chromList;  chromPtr != NULL;  chromPtr = chromPtr->next)
-    {
-    unsigned size = hChromSize(database, chromPtr->name);
-    cgiSimpleTableRowStart();
-    cgiSimpleTableFieldStart();
-    printf("<A HREF=\"%s?%s=%u&position=%s\">%s</A>",
-       hgTracksName(), cartSessionVarName(), cartSessionId(cart),
-       chromPtr->name, chromPtr->name);
-    cgiTableFieldEnd();
-    cgiTableFieldStartAlignRight();
-    printLongWithCommas(stdout, size);
-    puts("&nbsp;&nbsp;");
-    cgiTableFieldEnd();
-    cgiTableRowEnd();
-    total += size;
-    }
-chromInfoTotalRow(slCount(chromList), total);
-slFreeList(&chromList);
-}
-
-void chromInfoRowsNonChrom(int limit)
-/* Make table rows of non-chromosomal chromInfo name & size, sorted by size. */
-{
-struct sqlConnection *conn = hAllocConn(database);
-struct sqlResult *sr = NULL;
-char **row = NULL;
-long long total = 0;
-char query[512];
-char msg1[512], msg2[512];
-int seqCount = 0;
-boolean truncating;
-
-seqCount = sqlQuickNum(conn, "select count(*) from chromInfo");
-truncating = (limit > 0) && (seqCount > limit);
-
-if (!truncating)
-    {
-    sr = sqlGetResult(conn, "select chrom,size from chromInfo order by size desc");
-    }
-else
-    {
-
-    safef(query, sizeof(query), "select chrom,size from chromInfo order by size desc limit %d", limit);
-    sr = sqlGetResult(conn, query);
-    }
-
-while ((row = sqlNextRow(sr)) != NULL)
-    {
-    unsigned size = sqlUnsigned(row[1]);
-    cgiSimpleTableRowStart();
-    cgiSimpleTableFieldStart();
-    printf("<A HREF=\"%s?%s=%u&position=%s\">%s</A>",
-       hgTracksName(), cartSessionVarName(), cartSessionId(cart),
-       row[0], row[0]);
-    cgiTableFieldEnd();
-    cgiTableFieldStartAlignRight();
-    printLongWithCommas(stdout, size);
-    puts("&nbsp;&nbsp;");
-    cgiTableFieldEnd();
-    cgiTableRowEnd();
-    total += size;
-    }
-if (!truncating)
-    {
-    chromInfoTotalRow(seqCount, total);
-    }
-else
-    {
-    safef(msg1, sizeof(msg1), "Limit reached");
-    safef(msg2, sizeof(msg2), "%d rows displayed", limit);
-    cgiSimpleTableRowStart();
-    cgiSimpleTableFieldStart();
-    puts(msg1);
-    cgiTableFieldEnd();
-    cgiSimpleTableFieldStart();
-    puts(msg2);
-    cgiTableFieldEnd();
-    sqlFreeResult(&sr);
-    safef(query, sizeof(query), "select count(*),sum(size) from chromInfo");
-    sr = sqlGetResult(conn, query);
-    if ((row = sqlNextRow(sr)) != NULL)
-	{
-	unsigned scafCount = sqlUnsigned(row[0]);
-	unsigned totalSize = sqlUnsigned(row[1]);
-	cgiTableRowEnd();
-	safef(msg1, sizeof(msg1), "contig/scaffold<BR>count:");
-	safef(msg2, sizeof(msg2), "total size:");
-	cgiSimpleTableRowStart();
-	cgiSimpleTableFieldStart();
-	puts(msg1);
-	cgiTableFieldEnd();
-	cgiSimpleTableFieldStart();
-	puts(msg2);
-	cgiTableFieldEnd();
-	cgiTableRowEnd();
-	cgiSimpleTableRowStart();
-	cgiSimpleTableFieldStart();
-	printLongWithCommas(stdout, scafCount);
-	cgiTableFieldEnd();
-	cgiSimpleTableFieldStart();
-	printLongWithCommas(stdout, totalSize);
-	cgiTableFieldEnd();
-	}
-    cgiTableRowEnd();
-    }
-sqlFreeResult(&sr);
-hFreeConn(&conn);
-}
-
-void chromInfoPage()
-/* Show list of chromosomes (or scaffolds, etc) on which this db is based. */
-{
-char *position = cartUsualString(cart, "position", hDefaultPos(database));
-char *defaultChrom = hDefaultChrom(database);
-char *freeze = hFreezeFromDb(database);
-struct dyString *title = dyStringNew(512);
-if (stringIn(database, freeze))
-    dyStringPrintf(title, "%s %s Browser Sequences",
-		   hOrganism(database), freeze);
-else
-    dyStringPrintf(title, "%s %s (%s) Browser Sequences",
-		   hOrganism(database), freeze, database);
-webStartWrapperDetailedNoArgs(cart, database, "", title->string, FALSE, FALSE, FALSE, FALSE);
-printf("<FORM ACTION=\"%s\" NAME=\"posForm\" METHOD=GET>\n", hgTracksName());
-cartSaveSession(cart);
-
-puts("Enter a position, or click on a sequence name to view the entire "
-     "sequence in the genome browser.<P>");
-puts("position ");
-hTextVar("position", addCommasToPos(database, position), 30);
-cgiMakeButton("Submit", "submit");
-puts("<P>");
-
-hTableStart();
-cgiSimpleTableRowStart();
-cgiSimpleTableFieldStart();
-puts("Sequence name &nbsp;");
-cgiTableFieldEnd();
-cgiSimpleTableFieldStart();
-puts("Length (bp) including gaps &nbsp;");
-cgiTableFieldEnd();
-cgiTableRowEnd();
-
-if ((startsWith("chr", defaultChrom) || startsWith("Group", defaultChrom)) &&
-    hChromCount(database) < 100)
-    chromInfoRowsChrom();
-else
-    chromInfoRowsNonChrom(1000);
-
-hTableEnd();
-
-hgPositionsHelpHtml(organism, database);
-puts("</FORM>");
-dyStringFree(&title);
-webEndSectionTables();
-}
-
-
-void resetVars()
-/* Reset vars except for position and database. */
-{
-static char *except[] = {"db", "position", NULL};
-char *cookieName = hUserCookie();
-int sessionId = cgiUsualInt(cartSessionVarName(), 0);
-char *hguidString = findCookieData(cookieName);
-int userId = (hguidString == NULL ? 0 : atoi(hguidString));
-struct cart *oldCart = cartNew(userId, sessionId, NULL, NULL);
-cartRemoveExcept(oldCart, except);
-cartCheckout(&oldCart);
-cgiVarExcludeExcept(except);
-}
-
-void doMiddle(struct cart *theCart)
-/* Print the body of an html file.   */
-{
-char *debugTmp = NULL;
-/* Uncomment this to see parameters for debugging. */
-/* struct dyString *state = NULL; */
-/* Initialize layout and database. */
-cart = theCart;
-
-/* #if 1 this to see parameters for debugging. */
-/* Be careful though, it breaks if custom track
- * is more than 4k */
-#if  0
-state = cgiUrlString();
-printf("State: %s\n", state->string);
-#endif
-getDbAndGenome(cart, &database, &organism, oldVars);
-
-protDbName = hPdbFromGdb(database);
-debugTmp = cartUsualString(cart, "hgDebug", "off");
-if(sameString(debugTmp, "on"))
-    hgDebug = TRUE;
-else
-    hgDebug = FALSE;
-
-if (hIsGisaidServer())
-    {
-    validateGisaidUser(cart);
-    }
-
-setUdcCacheDir();
-
-initTl();
-measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));
-
-char *configPageCall = cartCgiUsualString(cart, "hgTracksConfigPage", "notSet");
-
-dragZooming = advancedJavascriptFeaturesEnabled(cart);
-
-/* Do main display. */
-
-if (cartUsualBoolean(cart, "hgt.trackImgOnly", FALSE))
-    {
-    trackImgOnly = TRUE;
-    ideogramToo = cartUsualBoolean(cart, "hgt.ideogramToo", FALSE);
-    hideControls = TRUE;
-    withNextItemArrows = FALSE;
-    withNextExonArrows = FALSE;
-    hgFindMatches = NULL;     // XXXX necessary ???
-    }
-
-hWrites(commonCssStyles());
-jsIncludeFile("jquery.js", NULL);
-jsIncludeFile("utils.js", NULL);
-if(dragZooming)
-    {
-    jsIncludeFile("jquery.imgareaselect.js", NULL);
-    jsIncludeFile("ajax.js", NULL);
-    hPrintf("<link href='../style/autocomplete.css' rel='stylesheet' type='text/css' />\n");
-    jsIncludeFile("jquery.autocomplete.js", NULL);
-    jsIncludeFile("autocomplete.js", NULL);
-    }
-jsIncludeFile("hgTracks.js", NULL);
-
-#ifdef LOWELAB
-jsIncludeFile("lowetooltip.js", NULL);
-#endif
-
-#if defined(CONTEXT_MENU) || defined(TRACK_SEARCH)
-hPrintf("<link href='../style/jquery.contextmenu.css' rel='stylesheet' type='text/css' />\n");
-hPrintf("<link href='../style/jquery-ui.css' rel='stylesheet' type='text/css' />\n");
-#ifdef CONTEXT_MENU
-jsIncludeFile("jquery.contextmenu.js", NULL);
-#endif/// def CONTEXT_MENU
-jsIncludeFile("jquery-ui.js", NULL);
-
-//if (!trackImgOnly)
-    {
-hPrintf("<div id='hgTrackUiDialog' style='display: none'></div>\n");
-// XXXX stole this and '.hidden' from bioInt.css - needs work
-hPrintf("<div id='warning' class='ui-state-error ui-corner-all hidden' style='font-size: 0.75em; display: none;' onclick='$(this).hide();'><p><span class='ui-icon ui-icon-alert' style='float: left; margin-right: 0.3em;'></span><strong></strong><span id='warningText'></span> (click to hide)</p></div>\n");
-    }
-#endif/// defined(CONTEXT_MENU) || defined(TRACK_SEARCH)
-if (cartVarExists(cart, "chromInfoPage"))
-    {
-    cartRemove(cart, "chromInfoPage");
-    chromInfoPage();
-    }
-else if (sameWord(configPageCall, "configure") ||
-    sameWord(configPageCall, "configure tracks and display"))
-    {
-    cartRemove(cart, "hgTracksConfigPage");
-    configPage();
-    }
-else if (cartVarExists(cart, configHideAll))
-    {
-    cartRemove(cart, configHideAll);
-    configPageSetTrackVis(tvHide);
-    }
-else if (cartVarExists(cart, configShowAll))
-    {
-    cartRemove(cart, configShowAll);
-    configPageSetTrackVis(tvDense);
-    }
-else if (cartVarExists(cart, configDefaultAll))
-    {
-    cartRemove(cart, configDefaultAll);
-    configPageSetTrackVis(-1);
-    }
-else if (cartVarExists(cart, configHideAllGroups))
-    {
-    cartRemove(cart, configHideAllGroups);
-    struct grp *grp = NULL, *grps = hLoadGrps(database);
-    for (grp = grps; grp != NULL; grp = grp->next)
-        collapseGroup(grp->name, TRUE);
-    configPageSetTrackVis(-2);
-    }
-else if (cartVarExists(cart, configShowAllGroups))
-    {
-    cartRemove(cart, configShowAllGroups);
-    struct grp *grp = NULL, *grps = hLoadGrps(database);
-    for (grp = grps; grp != NULL; grp = grp->next)
-        collapseGroup(grp->name, FALSE);
-    configPageSetTrackVis(-2);
-    }
-else if (cartVarExists(cart, configHideEncodeGroups))
-    {
-    /* currently not used */
-    cartRemove(cart, configHideEncodeGroups);
-    struct grp *grp = NULL, *grps = hLoadGrps(database);
-    for (grp = grps; grp != NULL; grp = grp->next)
-        if (startsWith("encode", grp->name))
-            collapseGroup(grp->name, TRUE);
-    configPageSetTrackVis(-2);
-    }
-else if (cartVarExists(cart, configShowEncodeGroups))
-    {
-    /* currently not used */
-    cartRemove(cart, configShowEncodeGroups);
-    struct grp *grp = NULL, *grps = hLoadGrps(database);
-    for (grp = grps; grp != NULL; grp = grp->next)
-        if (startsWith("encode", grp->name))
-            collapseGroup(grp->name, FALSE);
-    configPageSetTrackVis(-2);
-    }
-#ifdef TRACK_SEARCH
-else if (cartVarExists(cart, searchTracks))
-    {
-    doSearchTracks(groupList);
-    }
-#endif
-else
-    {
-    tracksDisplay();
-    }
-}
-
-void doDown(struct cart *cart)
-{
-printf("<H2>The Browser is Being Updated</H2>\n");
-printf("The browser is currently unavailable.  We are in the process of\n");
-printf("updating the database and the display software with a number of\n");
-printf("new tracks, including some gene predictions.  Please try again tomorrow.\n");
-}
-