src/hg/hgTracks/hgTracks.c 1.1648
1.1648 2010/05/18 19:01:16 kent
Adding parent field to struct track, and filling it in for composite and container subtracks. For supertracks, the existing parent finding at the track (as opposed to trackDb) level is buried enough this is difficult, so putting this off until the mythical day when supertracks are refactored out. Making mrna searches open mrna track in hg19, and in general improving search auto-opening when track and table name are different.
Index: src/hg/hgTracks/hgTracks.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/hgTracks.c,v
retrieving revision 1.1647
retrieving revision 1.1648
diff -b -B -U 1000000 -r1.1647 -r1.1648
--- src/hg/hgTracks/hgTracks.c 11 May 2010 01:43:27 -0000 1.1647
+++ src/hg/hgTracks/hgTracks.c 18 May 2010 19:01:16 -0000 1.1648
@@ -1,5654 +1,5676 @@
/* hgTracks - Human Genome browser main cgi script. */
#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"
static char const rcsid[] = "$Id$";
/* 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? */
#ifndef IMAGEv2_DRAG_REORDER
boolean withPriorityOverride = FALSE; /* Display priority for each track to allow reordering */
#endif//ndef IMAGEv2_DRAG_REORDER
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"
};
static long enteredMainTime = 0; /* time at beginning of main() */
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)
{
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);
#ifndef IMAGEv2_DRAG_REORDER
if (withPriorityOverride)
{
safef(pname, sizeof(pname), "%s.priority",tdb->parent->track);
cartRemove(cart, pname);
}
#endif//ndef IMAGEv2_DRAG_REORDER
}
track->visibility = tdb->visibility;
cartRemove(cart, track->track);
/* set the track priority back to the default value */
#ifndef IMAGEv2_DRAG_REORDER
if (withPriorityOverride)
{
safef(pname, sizeof(pname), "%s.priority",track->track);
cartRemove(cart, pname);
track->priority = track->defaultPriority;
}
#endif//ndef IMAGEv2_DRAG_REORDER
}
else
{
/* 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
{
/* regular track */
if (changeVis == tdb->visibility)
/* remove if setting to default vis */
cartRemove(cart, track->track);
else
cartSetString(cart, track->track,
hStringFromTv(changeVis));
track->visibility = changeVis;
}
}
}
}
}
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)
{
char title[256];
safef(title,sizeof(title),"%s controls", shortLabel);
struct imgSlice *curSlice = imgTrackSliceGetByType(curImgTrack,stButton);
if(curSlice)
sliceAddLink(curSlice,url,title);
}
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");
}
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 (isWithCenterLabels(track))
y += fontHeight;
if (tdbIsComposite(track->tdb))
{
struct track *subtrack;
for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack) && isWithCenterLabels(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
{
trashDirFile(ideoTn, "hgtIdeo", "hgtIdeo", ".gif");
hvg = hvGfxOpenGif(ideoWidth, ideoHeight, ideoTn->forCgi, FALSE);
}
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 (isWithCenterLabels(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 (isWithCenterLabels(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 arrowWidth = insideHeight;
int arrowButtonWidth = arrowWidth + 2 * NEXT_ITEM_ARROW_BUFFER;
int rightButtonX = insideX + insideWidth - 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, insideX + NEXT_ITEM_ARROW_BUFFER, y, arrowWidth, arrowWidth, labelColor, fillColor, FALSE);
safef(buttonText, ArraySize(buttonText), "hgt.prevItem=%s", track->track);
mapBoxReinvoke(hvg, insideX, y + 1, arrowButtonWidth, insideHeight, NULL,
NULL, 0, 0, (revCmplDisp ? "Next item" : "Prev item"), buttonText);
mapBoxToggleVis(hvg, insideX + arrowButtonWidth, y + 1, insideWidth - (2 * arrowButtonWidth),
insideHeight, (theImgBox ? track : parentTrack));
safef(buttonText, ArraySize(buttonText), "hgt.nextItem=%s", track->track);
mapBoxReinvoke(hvg, insideX + insideWidth - 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)
{
#ifdef FLAT_TRACK_LIST
if(isWithCenterLabels(track))
#endif//def FLAT_TRACK_LIST
{
int trackPastTabX = (withLeftLabels ? trackTabWidth : 0);
int trackPastTabWidth = tl.picWidth - trackPastTabX;
int fontHeight = mgFontLineHeight(font);
int insideHeight = fontHeight-1;
boolean toggleDone = FALSE;
Color labelColor = (track->labelColor ?
track->labelColor : track->ixColor);
hvGfxTextCentered(hvg, insideX, y+1, insideWidth, insideHeight,
labelColor, font, track->longLabel);
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 (isWithCenterLabels(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 (isWithCenterLabels(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 pixWidth = tl.picWidth;
int fontHeight = mgFontLineHeight(font);
int tHeight = trackPlusLabelHeight(track, fontHeight);
Color labelColor = (track->labelColor ? track->labelColor : track->ixColor);
if (track->limitedVis == tvPack)
{ /*XXX This needs to be looked at, no example yet*/
hvGfxSetClip(hvg, gfxBorder+trackTabWidth+1, y,
pixWidth-2*gfxBorder-trackTabWidth-1, track->height);
track->drawLeftLabels(track, winStart, winEnd,
hvg, leftLabelX, y, leftLabelWidth, tHeight,
isWithCenterLabels(track), font, labelColor,
track->limitedVis);
}
else
{
hvGfxSetClip(hvg, leftLabelX, y, leftLabelWidth, tHeight);
/* when the limitedVis == tvPack is correct above,
* this should be outside this else clause
*/
track->drawLeftLabels(track, winStart, winEnd,
hvg, leftLabelX, y, leftLabelWidth, tHeight,
isWithCenterLabels(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 (isWithCenterLabels(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 (isWithCenterLabels(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 (isWithCenterLabels(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. */
{
enum trackVisibility vis = subtrack->limitedVis == tvHide ?
subtrack->visibility :
tvMin(subtrack->visibility,subtrack->limitedVis);
struct trackDb *tdb = subtrack->tdb;
if(tdbIsCompositeChild(tdb))
{
char *viewName = NULL;
if (subgroupFind(tdb,"view",&viewName))
{
struct trackDb *parent = trackDbCompositeParent(tdb);
assert(parent != NULL);
int len = strlen(parent->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", parent->track,viewName);
char * fromParent = cartOptionalString(cart, ddName);
if(fromParent)
vis = hTvFromString(fromParent);
else
vis = visCompositeViewDefault(parent,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]);
}
#ifdef FLAT_TRACK_LIST
struct flatTracks *flatTracks = NULL;
struct flatTracks *flatTrack = NULL;
#endif//def FLAT_TRACK_LIST
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;
}
if (track->limitedVis != tvHide)
{
if (tdbIsComposite(track->tdb))
{
struct track *subtrack;
for (subtrack = track->subtracks; subtrack != NULL;
subtrack = subtrack->next)
{
if (!isSubtrackVisible(subtrack))
continue;
if (!subtrack->limitedVisSet)
{
subtrack->visibility = track->visibility;
subtrack->limitedVis = track->limitedVis;
subtrack->limitedVisSet = TRUE;
}
// 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);
}
}
#ifdef FLAT_TRACK_LIST
subtrack->hasUi = track->hasUi;
flatTracksAdd(&flatTracks,subtrack,cart);
pixHeight += trackPlusLabelHeight(subtrack, fontHeight);
#endif//def FLAT_TRACK_LIST
}
}
#ifdef FLAT_TRACK_LIST
else
flatTracksAdd(&flatTracks,track,cart);
#endif//def FLAT_TRACK_LIST
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;
}
else
#ifdef FLAT_TRACK_LIST
if (!tdbIsComposite(track->tdb))
#endif//def FLAT_TRACK_LIST
pixHeight += trackPlusLabelHeight(track, fontHeight);
}
}
#ifdef FLAT_TRACK_LIST
flatTracksSort(&flatTracks); // Now we should have a perfectly good flat track list!
#endif//def FLAT_TRACK_LIST
imagePixelHeight = pixHeight;
if (psOutput)
{
hvg = hvGfxOpenPostScript(pixWidth, pixHeight, psOutput);
hvgSide = hvg; // Always only one image
}
else
{
#ifdef USE_PNG
trashDirFile(&gifTn, "hgt", "hgt", ".png");
#ifdef IMAGEv2_BG_IMAGE
hvg = hvGfxOpenPng(pixWidth, pixHeight, gifTn.forCgi, (theImgBox!=NULL?TRUE:FALSE)); // transparent when BG is defined
#else//ifndef IMAGEv2_BG_IMAGE
hvg = hvGfxOpenPng(pixWidth, pixHeight, gifTn.forCgi, FALSE);
#endif//ndef IMAGEv2_BG_IMAGE
#else //ifndef
trashDirFile(&gifTn, "hgt", "hgt", ".gif");
hvg = hvGfxOpenGif(pixWidth, pixHeight, gifTn.forCgi, FALSE);
#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, FALSE);
#else //ifndef
trashDirFile(&gifTnSide, "hgt", "side", ".gif");
hvgSide = hvGfxOpenGif(pixWidth, pixHeight, gifTnSide.forCgi, FALSE);
#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
}
#ifdef FLAT_TRACK_LIST
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
#else//ifndef FLAT_TRACK_LIST
for (track = trackList; track != NULL; track = track->next)
{
#endif//ndef FLAT_TRACK_LIST
if (track->limitedVis != tvHide)
{
#ifdef FLAT_TRACK_LIST
int order = flatTrack->order;
#else//ifndef FLAT_TRACK_LIST
char var[256];
safef(var,sizeof(var),"%s_%s",track->tdb->track,IMG_ORDER_VAR);
int order = cartUsualInt(cart, var,IMG_ANYORDER);
#endif//ndef FLAT_TRACK_LIST
curImgTrack = imgBoxTrackFindOrAdd(theImgBox,track->tdb,NULL,track->limitedVis,isWithCenterLabels(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);
#ifdef FLAT_TRACK_LIST
curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stButton,NULL,NULL,sliceWidth[stButton],sliceHeight,sliceOffsetX[stButton],sliceOffsetY); // flatTracksButton is all html, no jpg
#else//ifndef FLAT_TRACK_LIST
curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stButton,theSideImg,NULL,sliceWidth[stButton],sliceHeight,sliceOffsetX[stButton],sliceOffsetY);
#endif//ndef FLAT_TRACK_LIST
}
drawGrayButtonBox(hvgSide, trackTabX, y, trackTabWidth, height, TRUE);
mapBoxTrackUi(hvgSide, trackTabX, y, trackTabWidth, height,
RULER_TRACK_NAME, RULER_TRACK_LABEL, "ruler");
y += height + 1;
}
#ifdef FLAT_TRACK_LIST
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
#else//ifndef FLAT_TRACK_LIST
for (track = trackList; track != NULL; track = track->next)
{
#endif//ndef FLAT_TRACK_LIST
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);
#ifdef FLAT_TRACK_LIST
curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stButton,NULL,NULL,sliceWidth[stButton],sliceHeight,sliceOffsetX[stButton],sliceOffsetY); // flatTracksButton is all html, no jpg
#else//ifndef FLAT_TRACK_LIST
curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stButton,theSideImg,NULL,sliceWidth[stButton],sliceHeight,sliceOffsetX[stButton],sliceOffsetY);
#endif//ndef FLAT_TRACK_LIST
}
if (track->hasUi)
{
if(tdbIsCompositeChild(track->tdb))
{
struct trackDb *parent = trackDbCompositeParent(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;
}
#ifdef FLAT_TRACK_LIST
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
#else//ifndef FLAT_TRACK_LIST
for (track = trackList; track != NULL; track = track->next)
{
#endif//ndef FLAT_TRACK_LIST
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
}
#ifndef FLAT_TRACK_LIST
if (trackIsCompositeWithSubtracks(track))
{
struct track *subtrack;
if (isWithCenterLabels(track))
y += fontHeight;
for (subtrack = track->subtracks; subtrack != NULL;subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack))
y = doLeftLabels(subtrack, hvgSide, font, y);
//if (track->limitedVis == tvDense)
//track->nextItemButtonable = FALSE;
}
track->nextItemButtonable = FALSE; // Composites are not NextItemButtonable (but subtracks may be)
}
else
#endif//ndef FLAT_TRACK_LIST
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 defined(IMAGEv2_BG_IMAGE) && defined(USE_PNG)
if(theImgBox)
{
struct tempName gifBg;
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, FALSE);
imgBoxImageAdd(theImgBox,gifBg.forHtml,NULL,pixWidth, pixHeight,TRUE); // Adds BG image
}
#endif //defined(IMAGEv2_BG_IMAGE) && defined(USE_PNG)
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;
#ifdef FLAT_TRACK_LIST
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
#else//ifndef FLAT_TRACK_LIST
for (track = trackList; track != NULL; track = track->next)
{
#endif//ndef FLAT_TRACK_LIST
if (track->limitedVis == tvHide)
continue;
if(theImgBox)
{
//if (isWithCenterLabels(track)) // NOTE: Since track may not have centerlabel but subtrack may (How?), then must always make this slice!
// center label slice of tracks
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
}
#ifndef FLAT_TRACK_LIST
if (trackIsCompositeWithSubtracks(track)) //TODO: Change when tracks->subtracks are always set for composite
{
if (isWithCenterLabels(track))
y = doCenterLabels(track, track, hvg, font, y) - track->height; /* subtrack heights tallied below: */
if(theImgBox)
{
// Special case: data slice of tracks
sliceHeight = trackPlusLabelHeight(track, fontHeight) - fontHeight;
sliceOffsetY = y;
curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stData,theOneImg,NULL,sliceWidth[stData],sliceHeight,sliceOffsetX[stData],sliceOffsetY);
curMap = sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot
}
struct track *subtrack;
for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack))
{
if (isWithCenterLabels(subtrack))
y = doCenterLabels(subtrack, track, hvg, font, y);
else
y += subtrack->totalHeight(subtrack,subtrack->limitedVis);
}
}
}
else
#endif//ndef FLAT_TRACK_LIST
y = doCenterLabels(track, track, hvg, font, y);
}
hvGfxUnclip(hvg);
}
/* Draw tracks. */
{
long lastTime = 0;
y = yAfterRuler;
if (measureTiming)
lastTime = clock1000();
#ifdef FLAT_TRACK_LIST
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
#else//ifndef FLAT_TRACK_LIST
for (track = trackList; track != NULL; track = track->next)
{
#endif//ndef FLAT_TRACK_LIST
if (track->limitedVis == tvHide)
continue;
int centerLabelHeight = (isWithCenterLabels(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
}
}
#ifndef FLAT_TRACK_LIST
if (trackIsCompositeWithSubtracks(track)) //TODO: Change when tracks->subtracks are always set for composite
{
struct track *subtrack;
if (isWithCenterLabels(track))
y += fontHeight;
for (subtrack = track->subtracks; subtrack != NULL;subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack))
y = doDrawItems(subtrack, hvg, font, y, &lastTime);
}
}
else
#endif//ndef FLAT_TRACK_LIST
y = doDrawItems(track, hvg, font, y, &lastTime);
#if defined(IMAGEv2_DRAG_REORDER) && defined(FLAT_TRACK_LIST)
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
#endif// defined(IMAGEv2_DRAG_REORDER) && defined(FLAT_TRACK_LIST)
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;
#ifdef FLAT_TRACK_LIST
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
#else//ifndef FLAT_TRACK_LIST
for (track = trackList; track != NULL; track = track->next)
{
#endif//ndef FLAT_TRACK_LIST
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
}
#ifndef FLAT_TRACK_LIST
if (trackIsCompositeWithSubtracks(track)) //TODO: Change when tracks->subtracks are always set for composite
{
struct track *subtrack;
if (isWithCenterLabels(track))
y += fontHeight;
for (subtrack = track->subtracks; subtrack != NULL;subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack))
{
if (subtrack->drawLeftLabels != NULL)
y = doOwnLeftLabels(subtrack, hvgSide, font, y);
else
y += trackPlusLabelHeight(subtrack, fontHeight);
}
}
}
else
#endif//ndef FLAT_TRACK_LIST
{
if (track->drawLeftLabels != NULL)
y = doOwnLeftLabels(track, hvgSide, font, y);
else
y += trackPlusLabelHeight(track, fontHeight);
}
}
}
/* Make map background. */
y = yAfterRuler;
#ifdef FLAT_TRACK_LIST
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
#else//ifndef FLAT_TRACK_LIST
for (track = trackList; track != NULL; track = track->next)
{
#endif//ndef FLAT_TRACK_LIST
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");
}
#ifdef FLAT_TRACK_LIST
flatTracksFree(&flatTracks);
#endif//def FLAT_TRACK_LIST
}
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 loadFromTrackDb(struct track **pTrackList)
/* Load tracks from database, consulting handler list. */
{
struct trackDb *tdb, *next, *tdbList = NULL;
struct track *track;
TrackHandler handler;
char *trackNameFilter = cartOptionalString(cart, "hgt.trackNameFilter");
if(trackNameFilter == NULL)
tdbList = hTrackDb(database, chromName);
else
tdbList = hTrackDbForTrack(database, trackNameFilter);
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);
}
}
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;
}
#ifdef USE_BAM
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"));
}
#endif//def USE_BAM
else if (sameString(type, "makeItems"))
{
tg = trackFromTrackDb(tdb);
makeItemsMethods(tg);
tg->nextItemButtonable = TRUE;
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 **pGroupList)
/* 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 = *pGroupList; 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(pGroupList, tg);
}
}
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);
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=\"2\"><TR>\n");
hPrintf("<TD ALIGN=CENTER><A HREF=\"../index.html?org=%s&db=%s&%s=%u\" class=\"topbar\">Home</A></TD>",
orgEnc, database, cartSessionVarName(), cartSessionId(cart));
if (hIsGisaidServer())
{
/* disable hgGateway for gisaid for now */
//hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgGateway?org=%s&db=%s\" class=\"topbar\">Sequence View Gateway</A></TD>", orgEnc, database);
hPrintf(
"<TD ALIGN=CENTER><A HREF=\"../cgi-bin/gisaidTable?gisaidTable.do.advFilter=filter+%c28now+on%c29&fromProg=hgTracks&%s=%u\" class=\"topbar\">%s</A></TD>",
'%', '%',
cartSessionVarName(),
cartSessionId(cart),
"Select Subjects");
}
else
if (hIsGsidServer())
{
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgGateway?org=%s&db=%s\" class=\"topbar\">Sequence View Gateway</A></TD>", orgEnc, database);
hPrintf(
"<TD ALIGN=CENTER><A HREF=\"../cgi-bin/gsidTable?gsidTable.do.advFilter=filter+%c28now+on%c29&fromProg=hgTracks\" class=\"topbar\">%s</A></TD>",
'%', '%', "Select Subjects");
}
else
{
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgGateway?org=%s&db=%s&%s=%u\" class=\"topbar\">Genomes</A></TD>", orgEnc, database, cartSessionVarName(), cartSessionId(cart));
}
if (gotBlat)
{
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgBlat?%s\" class=\"topbar\">Blat</A></TD>", uiVars->string);
}
if (hIsGisaidServer())
{
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/gisaidTable?db=%s&%s=%u\" class=\"topbar\">%s</A></TD>",
database,
cartSessionVarName(),
cartSessionId(cart),
"Table View");
}
else if (hIsGsidServer())
{
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/gsidTable?db=%s\" class=\"topbar\">%s</A></TD>",
database, "Table View");
}
else
{
/* disable TB for CGB servers */
if (!hIsCgbServer())
{
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgTables?db=%s&position=%s:%d-%d&%s=%u\" class=\"topbar\">%s</A></TD>",
database, chromName, winStart+1, winEnd,
cartSessionVarName(),
cartSessionId(cart),
"Tables");
}
}
if (hgNearOk(database))
{
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgNear?%s\" class=\"topbar\">%s</A></TD>",
uiVars->string, "Gene Sorter");
}
if (hgPcrOk(database))
{
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgPcr?%s\" class=\"topbar\">PCR</A></TD>", uiVars->string);
}
hPrintf("<TD ALIGN=CENTER><A HREF=\"%s&o=%d&g=getDna&i=mixed&c=%s&l=%d&r=%d&db=%s&%s\" class=\"topbar\">"
" %s </A></TD>", hgcNameAndSettings(),
winStart, chromName, winStart, winEnd, database, uiVars->string, "DNA");
/* disable Convert function for CGB servers for the time being */
if (!hIsCgbServer())
if (liftOverChainForDb(database) != NULL)
{
hPrintf("<TD ALIGN=CENTER><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></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 (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"))
{
hPuts("<TD ALIGN=CENTER>");
printEnsemblAnchor(database, NULL, chromName, winStart, winEnd);
hPrintf("%s</A></TD>", "Ensembl");
}
else if (sameWord(database,"hg18"))
{
hPuts("<TD ALIGN=CENTER>");
printEnsemblAnchor(database, "ncbi36", chromName, winStart, winEnd);
hPrintf("%s</A></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;
hPuts("<TD ALIGN=CENTER>");
printEnsemblAnchor(database, archive, ctgItem->contig,
ctgStart, ctgEnd);
hPrintf("%s</A></TD>", "Ensembl");
}
}
ctgPosFree(&ctgItem); // the one we maybe used
}
}
else
{
hPuts("<TD ALIGN=CENTER>");
printEnsemblAnchor(database, archive, chromName, winStart, winEnd);
hPrintf("%s</A></TD>", "Ensembl");
}
}
}
/* Print NCBI MapView anchor */
if (sameString(database, "hg18"))
{
hPrintf("<TD ALIGN=CENTER><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></TD>", "NCBI");
}
if (sameString(database, "hg19"))
{
hPrintf("<TD ALIGN=CENTER><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></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></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></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></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></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></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></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></TD>", "NCBI");
}
if (startsWith("oryLat", database))
{
hPrintf("<TD ALIGN=CENTER><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></TD>",
skipChr(chromName), winStart+1, winEnd, "UTGB");
}
if (sameString(database, "cb3"))
{
hPrintf("<TD ALIGN=CENTER><A HREF=\"http://www.wormbase.org/db/seq/gbrowse/briggsae?name=%s:%d-%d\" TARGET=_blank class=\"topbar\">%s</A></TD>",
skipChr(chromName), winStart+1, winEnd, "WormBase");
}
if (sameString(database, "ce4"))
{
hPrintf("<TD ALIGN=CENTER><A HREF=\"http://ws170.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d\" TARGET=_blank class=\"topbar\">%s</A></TD>",
skipChr(chromName), winStart+1, winEnd, "WormBase");
}
if (sameString(database, "ce2"))
{
hPrintf("<TD ALIGN=CENTER><A HREF=\"http://ws120.wormbase.org/db/seq/gbrowse/wormbase?name=%s:%d-%d\" TARGET=_blank class=\"topbar\">%s</A></TD>",
skipChr(chromName), winStart+1, winEnd, "WormBase");
}
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgTracks?%s=%u&hgt.psOutput=on\" id='pdfLink' class=\"topbar\">%s</A></TD>\n",cartSessionVarName(),
cartSessionId(cart), "PDF/PS");
if (wikiLinkEnabled())
{
printf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgSession?%s=%u"
"&hgS_doMainPage=1\" class=\"topbar\">Session</A></TD>",
cartSessionVarName(), cartSessionId(cart));
}
if (hIsGisaidServer())
{
//hPrintf("<TD ALIGN=CENTER><A HREF=\"/goldenPath/help/gisaidTutorial.html#SequenceView\" TARGET=_blank class=\"topbar\">%s</A></TD>\n", "Help");
hPrintf("<TD ALIGN=CENTER><A HREF=\"../cgi-bin/hgNotYet\" TARGET=_blank class=\"topbar\">%s</A></TD>\n", "Help");
}
else
if (hIsGsidServer())
{
hPrintf("<TD ALIGN=CENTER><A HREF=\"/goldenPath/help/gsidTutorial.html#SequenceView\" TARGET=_blank class=\"topbar\">%s</A></TD>\n", "Help");
}
else
{
hPrintf("<TD ALIGN=CENTER><A HREF=\"../goldenPath/help/hgTracksHelp.html\" TARGET=_blank class=\"topbar\">%s</A></TD>\n", "Help");
}
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;
#ifndef IMAGEv2_DRAG_REORDER
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);
}
#endif//ndef IMAGEv2_DRAG_REORDER
/* 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)
{
#ifndef IMAGEv2_DRAG_REORDER
/* 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;
}
#endif//ndef IMAGEv2_DRAG_REORDER
/* 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);
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->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;
}
}
#ifdef CONTEXT_MENU
static void trackJson(struct dyString *trackDbJson, struct track *track, int count)
{
// add entry for given track to the trackDbJson string
if(count)
dyStringAppend(trackDbJson, "\n,");
dyStringPrintf(trackDbJson, "\t%s: {", track->track);
if(tdbIsSuperTrackChild(track->tdb) || tdbIsCompositeChild(track->tdb))
dyStringPrintf(trackDbJson, "\n\t\tparentTrack: '%s',", track->tdb->parent->track);
dyStringPrintf(trackDbJson, "\n\t\tshortLabel: '%s',\n\t\tlongLabel: '%s',\n\t\tcanPack: %d,\n\t\tvisibility: %d\n\t}",
javaScriptLiteralEncode(track->shortLabel), javaScriptLiteralEncode(track->longLabel), track->canPack, track->limitedVis);
}
#endif
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);
}
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;
#ifdef CONTEXT_MENU
struct dyString *trackDbJson = newDyString(1000);
int trackDbJsonCount = 1;
dyStringPrintf(trackDbJson, "<script>var trackDbJson = {\nruler: {shortLabel: 'ruler', longLabel: 'Base Position Controls', canPack: 0, visibility: %d}", rulerMode);
#endif
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 */
#ifdef IMAGEv2_DRAG_REORDER
// honor defaultImgOrder
if(cgiVarExists("hgt.defaultImgOrder"))
{
char wildCard[32];
safef(wildCard,sizeof(wildCard),"*_%s",IMG_ORDER_VAR);
cartRemoveLike(cart, wildCard);
}
#endif//def IMAGEv2_DRAG_REORDER
/* 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)
{
// 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;
}
#ifdef CONTEXT_MENU
trackJson(trackDbJson, track, trackDbJsonCount++);
if (trackIsCompositeWithSubtracks(track))
{
struct track *subtrack;
for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
// isSubtrackVisible is causing a problem in panTro2
if (isSubtrackVisible(subtrack))
trackJson(trackDbJson, subtrack, trackDbJsonCount++);
}
}
#endif
}
}
#ifdef CONTEXT_MENU
dyStringAppend(trackDbJson, "}\n</script>\n");
if(!trackImgOnly)
hPrintf(dyStringContents(trackDbJson));
#endif
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 (!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(" <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</EM></B></A></FONT>\n");
if (survey && differentWord(survey, "off"))
hPrintf(" <FONT SIZE=3><A STYLE=\"background-color:yellow;\" HREF=\"%s\" TARGET=_BLANK><EM><B>%s</EM></B></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% to the left'><<<</a>\n");
hPrintf("<td width='30' align='left'><a href='?hgt.left2=1' title='move 47.5% to the left'><<</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% to the left'><</a>\n");
hPrintf("<td> </td>\n"); // Without 'width=' this cell expand to table with, forcing other cells to the sides.
hPrintf("<td width='80' align='left'><a href='?hgt.in3=1' title='zoom in 10x'>>>> <<<</a>\n");
hPrintf("<td width='60' align='left'><a href='?hgt.in2=1' title='zoom in 3x'>>> <<</a>\n");
hPrintf("<td width='40' align='left'><a href='?hgt.in1=1' title='zoom in 1.5x'>> <</a>\n");
hPrintf("<td width='40' align='left'><a href='?hgt.inBase=1' title='zoom in to base range'><i>base</i></a>\n");
hPrintf("<td> </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'>< ></a>\n");
hPrintf("<td width='60' align='right'><a href='?hgt.out2=1' title='zoom out 3x'><< >></a>\n");
hPrintf("<td width='80' align='right'><a href='?hgt.out3=1' title='zoom out 10x'><<< >>></a>\n");
hPrintf("<td> </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% to the right'>></a>\n");
hPrintf("<td width='30' align='right'><a href='?hgt.right2=1' title='move 47.5% to the right'>>></a>\n");
hPrintf("<td width='40' align='right'><a href='?hgt.right3=1' title='move 95% to the right'>>>></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);
hPrintf("<TD COLSPAN=6 ALIGN=left NOWRAP>");
hPrintf("move start<BR>");
#ifdef USE_NAVIGATION_LINKS
hPrintf("<a href='?hgt.dinkLL=1' title='move window start position to the left'><</a>\n");
hTextVar("dinkL", cartUsualString(cart, "dinkL", "2.0"), 3);
hPrintf("<a href='?hgt.dinkLR=1' title='move window start position to the right'>></a>\n");
#else//ifndef USE_NAVIGATION_LINKS
hButton("hgt.dinkLL", " < ");
hTextVar("dinkL", cartUsualString(cart, "dinkL", "2.0"), 3);
hButton("hgt.dinkLR", " > ");
#endif//ndef USE_NAVIGATION_LINKS
hPrintf("</TD>");
hPrintf("<td width='30'> </td>\n");
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. ");
#ifdef IMAGEv2_DRAG_REORDER
hWrites("Click side bars for track options. ");
hWrites("Drag side bars or labels up or down to reorder tracks. ");
#else//ifndef IMAGEv2_DRAG_REORDER
hWrites("Click gray/blue bars on left for track options and descriptions. ");
#endif//ndef IMAGEv2_DRAG_REORDER
#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>");
hPrintf("<td width='30'> </td>\n");
hPrintf("<TD COLSPAN=6 ALIGN=right NOWRAP>");
hPrintf("move end<BR>");
#ifdef USE_NAVIGATION_LINKS
hPrintf("<a href='?hgt.dinkRL=1' title='move window end position to the left'><</a>\n");
hTextVar("dinkR", cartUsualString(cart, "dinkR", "2.0"), 3);
hPrintf("<a href='?hgt.dinkRR=1' title='move window end position to the right'>></a>\n");
#else//ifndef USE_NAVIGATION_LINKS
hButton("hgt.dinkRL", " < ");
hTextVar("dinkR", cartUsualString(cart, "dinkR", "2.0"), 3);
hButton("hgt.dinkRR", " > ");
#endif//ndef USE_NAVIGATION_LINKS
hPrintf("</TD></TR></TABLE>\n");
// smallBreak();
/* Display bottom control panel. */
hButton("hgt.reset", "default tracks");
#ifdef IMAGEv2_DRAG_REORDER
hPrintf(" ");
hButton("hgt.defaultImgOrder", "default order");
#endif//def IMAGEv2_DRAG_REORDER
// if (showTrackControls) - always show "hide all", Hiram 2008-06-26
{
hPrintf(" ");
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(" ");
}
#ifdef TRACK_SEARCH
hPrintf("<input type='submit' name='%s' value='find tracks'>", searchTracks);
hPrintf(" ");
#endif
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> ",
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, "\"", """);
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(" %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");
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");
}
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 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);
}
}
-if (NULL != hgp && NULL != hgp->tableList && NULL != hgp->tableList->name)
- {
- char *trackName = hgp->tableList->name;
- char *parent = hGetParent(database, trackName); // This only works for a composite track (not superTrack)
- if (parent) // TODO: Therefore I wonder about the need for this code.
- trackName = cloneString(parent);
- char *vis = cartOptionalString(cart, trackName);
- if (vis == NULL || differentString(vis, "full"))
- cartSetString(cart, trackName, hTrackOpenVis(database, trackName));
- }
-
/* 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. */
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);
}
#ifndef IMAGEv2_DRAG_REORDER
withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE);
#endif//ndef IMAGEv2_DRAG_REORDER
insideX = trackOffsetX();
insideWidth = tl.picWidth-gfxBorder-insideX;
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(" ");
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(" ");
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 ");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
puts("Length (bp) including gaps ");
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 ???
}
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
#ifdef CONTEXT_MENU
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");
jsIncludeFile("jquery-ui.js", NULL);
jsIncludeFile("jquery.contextmenu.js", NULL);
hPrintf("<div id='hgTrackUiDialog' style='display: none'></div>");
// 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
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))
{
cartRemove(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");
}
/* Other than submit and Submit all these vars should start with hgt.
* to avoid weeding things out of other program's namespaces.
* Because the browser is a central program, most of it's cart
* variables are not hgt. qualified. It's a good idea if other
* program's unique variables be qualified with a prefix though. */
char *excludeVars[] = { "submit", "Submit", "hgt.reset",
"hgt.in1", "hgt.in2", "hgt.in3", "hgt.inBase",
"hgt.out1", "hgt.out2", "hgt.out3",
"hgt.left1", "hgt.left2", "hgt.left3",
"hgt.right1", "hgt.right2", "hgt.right3",
"hgt.dinkLL", "hgt.dinkLR", "hgt.dinkRL", "hgt.dinkRR",
"hgt.tui", "hgt.hideAll", "hgt.visAllFromCt",
"hgt.psOutput", "hideControls", "hgt.toggleRevCmplDisp",
"hgt.chromName", "hgt.winStart", "hgt.winEnd", "hgt.newWinWidth",
"hgt.insideX", "hgt.rulerClickHeight", "hgt.dragSelection", "hgt.revCmplDisp",
"hgt.collapseGroups", "hgt.expandGroups", "hgt.suggest",
"hgt.jump", "hgt.refresh",
#ifdef CONTEXT_MENU
"hgt.trackImgOnly", "hgt.ideogramToo", "hgt.trackNameFilter",
#endif
#ifdef TRACK_SEARCH
searchTracks,
#endif
NULL };
int main(int argc, char *argv[])
{
enteredMainTime = clock1000();
uglyTime(NULL);
browserName = (hIsPrivateHost() ? "Test Browser" : "Genome Browser");
organization = "UCSC";
/* change title if this is for GSID */
browserName = (hIsGsidServer() ? "Sequence View" : browserName);
organization = (hIsGsidServer() ? "GSID" : organization);
organization = (hIsGisaidServer() ? "GISAID" : organization);
/* Push very early error handling - this is just
* for the benefit of the cgiVarExists, which
* somehow can't be moved effectively into doMiddle. */
htmlPushEarlyHandlers();
cgiSpoof(&argc, argv);
htmlSetBackground(hBackgroundImage());
htmlSetStyle("<LINK REL=\"STYLESHEET\" HREF=\"../style/HGStyle.css\" TYPE=\"text/css\">\n");
oldVars = hashNew(10);
if (hIsGsidServer())
cartHtmlShell("GSID Sequence View", doMiddle, hUserCookie(), excludeVars, oldVars);
else
cartHtmlShell("UCSC Genome Browser v"CGI_VERSION, doMiddle, hUserCookie(), excludeVars, oldVars);
if (measureTiming)
{
fprintf(stdout, "Overall total time: %ld millis<BR>\n",
clock1000() - enteredMainTime);
}
return 0;
}