src/hg/hgTracks/hgTracks.c 1.1570
1.1570 2009/06/10 18:47:09 kuhn
turned on scalebar by default
Index: src/hg/hgTracks/hgTracks.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/hgTracks.c,v
retrieving revision 1.1569
retrieving revision 1.1570
diff -b -B -U 1000000 -r1.1569 -r1.1570
--- src/hg/hgTracks/hgTracks.c 5 Jun 2009 17:14:02 -0000 1.1569
+++ src/hg/hgTracks/hgTracks.c 10 Jun 2009 18:47:09 -0000 1.1570
@@ -1,4796 +1,4796 @@
/* 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 "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"
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? */
boolean withPriorityOverride = FALSE; /* Display priority for each track to allow reordering */
int gfxBorder = hgDefaultGfxBorder; /* Width of graphics border. */
int guidelineSpacing = 12; /* Pixels between guidelines. */
boolean withIdeogram = TRUE; /* Display chromosome ideogram? */
int rulerMode = tvHide; /* on, off, full */
char *rulerMenu[] =
/* dropdown for ruler visibility */
{
"hide",
"dense",
"full"
};
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? */
/* 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 or MGC */
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->mapName, 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->mapName); //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->mapName);
}
}
/* restore defaults */
if (tdbIsSuperTrackChild(tdb) || tdbIsCompositeChild(tdb))
{
assert(tdb->parent != NULL && tdb->parent->tableName);
cartRemove(cart, tdb->parent->tableName);
if (withPriorityOverride)
{
safef(pname, sizeof(pname), "%s.priority",tdb->parent->tableName);
cartRemove(cart, pname);
}
}
track->visibility = tdb->visibility;
cartRemove(cart, track->mapName);
/* set the track priority back to the default value */
if (withPriorityOverride)
{
safef(pname, sizeof(pname), "%s.priority",track->mapName);
cartRemove(cart, pname);
track->priority = track->defaultPriority;
}
}
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->tableName);
}
else
cartSetString(cart, parentTdb->tableName,
changeVis == tvHide ? "hide" : "show");
}
else
{
/* regular track */
if (changeVis == tdb->visibility)
/* remove if setting to default vis */
cartRemove(cart, track->mapName);
else
cartSetString(cart, track->mapName,
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)
/* Print out image map rectangle that invokes hgTrackUi. */
{
x = hvGfxAdjXW(hvg, x, width);
char *encodedName = cgiEncode(name);
hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", x, y, x+width, y+height);
hPrintf("HREF=\"%s?%s=%u&c=%s&g=%s\"", hgTrackUiName(), cartSessionVarName(),
cartSessionId(cart), chromName, encodedName);
mapStatusMessage("%s controls", shortLabel);
hPrintf(">\n");
freeMem(encodedName);
}
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);
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");
}
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->mapName, "cytoBandIdeo"))
{
if (hTableExists(database, track->mapName))
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
{
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);
}
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);
}
safecpy(lf->name, sizeof(lf->name), 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);
safecpy(lf->name, sizeof(lf->name), "");
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->mapName = "hgUserPsl";
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->tableName = cloneString(tg->mapName);
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->mapName = "oligoMatch";
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->tableName = cloneString(tg->mapName);
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[128];
char o5[128];
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->mapName);
safef( o5, sizeof(o5),"%s.max.cutoff", track->mapName);
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->mapName, "humMusL" ) ||
sameString( track->mapName, "musHumL" ) ||
sameString( track->mapName, "mm3Rn2L" ) ||
sameString( track->mapName, "hg15Mm3L" ) ||
sameString( track->mapName, "mm3Hg15L" ) ||
sameString( track->mapName, "regpotent" ) ||
sameString( track->mapName, "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->mapName, "humMusL" ) ||
sameString( track->mapName, "hg15Mm3L" ))
hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1,
itemHeight, track->ixColor, font, "Mouse Cons");
else if( sameString( track->mapName, "musHumL" ) ||
sameString( track->mapName, "mm3Hg15L"))
hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1,
itemHeight, track->ixColor, font, "Human Cons");
else if( sameString( track->mapName, "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[100];
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->mapName);
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, parentTrack);
safef(buttonText, ArraySize(buttonText), "hgt.nextItem=%s", track->mapName);
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 */
{
int trackPastTabX = (withLeftLabels ? trackTabWidth : 0);
int trackPastTabWidth = tl.picWidth - trackPastTabX;
int fontHeight = mgFontLineHeight(font);
int insideHeight = fontHeight-1;
if (track->limitedVis != tvHide)
{
Color labelColor = (track->labelColor ?
track->labelColor : track->ixColor);
hvGfxTextCentered(hvg, insideX, y+1, insideWidth, insideHeight,
labelColor, font, track->longLabel);
if (withNextItemArrows && track->labelNextItemButtonable && track->labelNextPrevItem && !tdbIsComposite(track->tdb))
doLabelNextItemButtons(track, parentTrack, hvg, font, y, trackPastTabX,
trackPastTabWidth, fontHeight, insideHeight, labelColor);
else
mapBoxToggleVis(hvg, trackPastTabX, y+1,
trackPastTabWidth, insideHeight, 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->mapName))
{
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;
}
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;
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;
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);
if(tdbIsCompositeChild(subtrack->tdb))
{
char *stView;
// If the composite track has "view" based drop downs, set visibility based upon those
if(subgroupFind(subtrack->tdb,"view",&stView))
{
int len = strlen(subtrack->tdb->parent->tableName) + strlen(stView) + 10;
char *ddName = needMem(len);
safef(ddName,len,"%s.%s.vis",subtrack->tdb->parent->tableName,stView);
char * fromParent = cartOptionalString(cart, ddName);
if(fromParent)
vis = hTvFromString(fromParent);
else
vis = visCompositeViewDefault(subtrack->tdb->parent,stView);
freeMem(ddName);
subgroupFree(&stView);
}
}
return vis;
}
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;
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
int relNumOff;
boolean rulerCds = zoomedToCdsColorLevel;
int rulerClickHeight = 0;
int newWinWidth = 0;
/* Start a global track hash. */
trackHash = newHash(8);
/* Figure out dimensions and allocate drawing space. */
pixWidth = tl.picWidth;
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)
{
hashAddUnique(trackHash, track->mapName, track);
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)
{
hashAddUnique(trackHash, subtrack->mapName, subtrack);
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;
subtrack->limitedVis = tvMin(track->visibility,subtrack->visibility);
subtrack->limitedVisSet = (subtrack->limitedVis != tvHide && subtrack->visibility != subtrack->limitedVis);
}
}
}
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
pixHeight += trackPlusLabelHeight(track, fontHeight);
}
}
imagePixelHeight = pixHeight;
if (psOutput)
hvg = hvGfxOpenPostScript(pixWidth, pixHeight, psOutput);
else
{
trashDirFile(&gifTn, "hgt", "hgt", ".gif");
hvg = hvGfxOpenGif(pixWidth, pixHeight, gifTn.forCgi);
}
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);
leftLabelX = gfxBorder;
leftLabelWidth = insideX - gfxBorder*3;
/* 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;
drawGrayButtonBox(hvg, trackTabX, y, trackTabWidth, height, TRUE);
mapBoxTrackUi(hvg, trackTabX, y, trackTabWidth, height,
RULER_TRACK_NAME, RULER_TRACK_LABEL);
y += height + 1;
}
for (track = trackList; track != NULL; track = track->next)
{
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(hvg, trackTabX, yStart, trackTabWidth,
h, track->hasUi);
else
drawBlueButtonBox(hvg, trackTabX, yStart, trackTabWidth,
h, track->hasUi);
if (track->hasUi)
mapBoxTrackUi(hvg, trackTabX, yStart, trackTabWidth, h,
track->mapName, track->shortLabel);
}
}
butOff = trackTabX + trackTabWidth;
leftLabelX += butOff;
leftLabelWidth -= butOff;
}
if (withLeftLabels)
{
Color lightRed = hvGfxFindColorIx(hvg, 255, 180, 180);
hvGfxBox(hvg, leftLabelX + leftLabelWidth, 0,
gfxBorder, pixHeight, lightRed);
y = gfxBorder;
if (rulerMode != tvHide)
{
if (baseTitle)
{
hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth-1, titleHeight,
MG_BLACK, font, WIN_TITLE_LABEL);
y += titleHeight;
}
if (baseShowPos||baseShowAsm)
{
hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth-1, showPosHeight,
MG_BLACK, font, WIN_POS_LABEL);
y += showPosHeight;
}
if (baseShowScaleBar)
{
y += scaleBarPad;
hvGfxTextRight(hvg, 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 (hvg->rc)
safef(rulerLabel,ArraySize(rulerLabel),":%s",shortChromName);
else
safef(rulerLabel,ArraySize(rulerLabel),"%s:",shortChromName);
hvGfxTextRight(hvg, 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(hvg,leftLabelX, y,
leftLabelWidth-1, baseHeight, font);
if (zoomedToBaseLevel)
y += baseHeight;
}
if (rulerCds)
y += rulerTranslationHeight;
}
for (track = trackList; track != NULL; track = track->next)
{
if (track->limitedVis == tvHide)
continue;
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 = doLeftLabels(subtrack, hvg, font, y);
//if (track->limitedVis == tvDense)
//track->labelNextItemButtonable = FALSE;
}
track->labelNextItemButtonable = FALSE; // Composites are not NextItemButtonable (but subtracks may be)
}
else
y = doLeftLabels(track, hvg, font, y);
}
}
else
{
leftLabelX = leftLabelWidth = 0;
}
/* Draw guidelines. */
if (withGuidelines)
{
int height = pixHeight - 2*gfxBorder;
int x;
Color lightBlue = hvGfxFindRgb(hvg, &guidelineColor);
hvGfxSetClip(hvg, insideX, gfxBorder, insideWidth, height);
y = gfxBorder;
for (x = insideX+guidelineSpacing-1; x<pixWidth; x += guidelineSpacing)
hvGfxBox(hvg, x, y, 1, height, lightBlue);
hvGfxUnclip(hvg);
}
/* Show ruler at top. */
if (rulerMode != tvHide)
{
struct dnaSeq *seq = NULL;
int rulerClickY = 0;
rulerClickHeight = rulerHeight;
y = rulerClickY;
hvGfxSetClip(hvg, insideX, y, insideWidth, yAfterRuler-y+1);
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);
}
{
/* Make hit boxes that will zoom program around ruler. */
int boxes = 30;
int winWidth = winEnd - winStart;
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);
}
}
}
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);
}
/* Draw center labels. */
if (withCenterLabels)
{
hvGfxSetClip(hvg, insideX, gfxBorder, insideWidth, pixHeight - 2*gfxBorder);
y = yAfterRuler;
for (track = trackList; track != NULL; track = track->next)
{
struct track *subtrack;
if (track->limitedVis == tvHide)
continue;
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: */
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
y = doCenterLabels(track, track, hvg, font, y);
}
hvGfxUnclip(hvg);
}
/* Draw tracks. */
{
long lastTime = 0;
y = yAfterRuler;
if (measureTiming)
lastTime = clock1000();
for (track = trackList; track != NULL; track = track->next)
{
if (track->limitedVis == tvHide)
continue;
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
y = doDrawItems(track, hvg, font, y, &lastTime);
}
}
/* if a track can draw its left labels, now is the time since it
* knows what exactly happened during drawItems
*/
if (withLeftLabels)
{
y = yAfterRuler;
for (track = trackList; track != NULL; track = track->next)
{
if (track->limitedVis == tvHide)
continue;
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, hvg, font, y);
else
y += trackPlusLabelHeight(subtrack, fontHeight);
}
}
else if (track->drawLeftLabels != NULL)
{
y = doOwnLeftLabels(track, hvg, font, y);
}
else
{
y += trackPlusLabelHeight(track, fontHeight);
}
}
}
/* Make map background. */
y = yAfterRuler;
for (track = trackList; track != NULL; track = track->next)
{
if (track->limitedVis != tvHide)
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. */
hvGfxClose(&hvg);
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");
}
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 *table = hel->val;
/* check non-subtrack. */
if (sameString(track->tdb->tableName, table))
{
track->visibility = tvFull;
track->tdb->visibility = tvFull;
cartSetString(cart, track->tdb->tableName, "full");
}
else if (track->tdb->subtracks != NULL)
{
for (subtrack = track->tdb->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (sameString(subtrack->tableName, table))
{
char selName[SMALLBUF];
track->visibility = tvFull;
cartSetString(cart, track->tdb->tableName, "full");
track->tdb->visibility = tvFull;
subtrack->visibility = tvFull;
safef(selName, sizeof(selName), "%s_sel", table);
cartSetBoolean(cart, selName, TRUE);
}
}
}
}
hashElFreeList(&hels);
}
void loadFromTrackDb(struct track **pTrackList)
/* Load tracks from database, consulting handler list. */
{
struct trackDb *tdb, *tdbList = NULL;
struct track *track;
TrackHandler handler;
tdbList = hTrackDb(database, chromName);
tdbSortPrioritiesFromCart(cart, &tdbList);
for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
{
track = trackFromTrackDb(tdb);
track->hasUi = TRUE;
if (slCount(tdb->subtracks) != 0) {
tdbSortPrioritiesFromCart(cart, &(tdb->subtracks));
makeCompositeTrack(track, tdb);
}
else
{
handler = lookupTrackHandler(tdb->tableName);
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->tableName);
else if (track->drawItems == NULL)
warn("No draw handler for %s", tdb->tableName);
else
slAddHead(pTrackList, track);
}
}
static int getScoreFilter(char *tableName)
/* check for score filter configuration setting */
{
char optionScoreStr[128];
safef(optionScoreStr, sizeof(optionScoreStr), "%s.scoreFilter", tableName);
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->tableName);
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->tableName);
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->tableName);
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->tableName);
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->labelNextItemButtonable = FALSE;
}
else if (sameString(type, "wig"))
{
tg = trackFromTrackDb(tdb);
if (ct->dbTrack)
tg->loadItems = wigLoadItems;
else
tg->loadItems = ctWigLoadItems;
tg->customPt = ct;
tg->labelNextItemButtonable = FALSE;
}
else if (sameString(type, "bigWig"))
{
tg = trackFromTrackDb(tdb);
tg->bbiFileName = trackDbSetting(tdb, "dataUrl");
tg->labelNextItemButtonable = FALSE;
}
else if (sameString(type, "bigBed"))
{
/* Figure out file name from settings. */
char *fileName = trackDbSetting(tdb, "dataUrl");
/* Briefly open file to find field counts, and from that revise the
* tdb->type to be more complete. */
struct bbiFile *bbi = bigBedFileOpen(fileName);
char extra = (bbi->fieldCount > bbi->definedFieldCount ? '+' : '.');
char typeBuf[64];
safef(typeBuf, sizeof(typeBuf), "bigBed %d %c", bbi->definedFieldCount, extra);
tdb->type = cloneString(typeBuf);
bbiFileClose(&bbi);
/* Finish wrapping track around tdb. */
tg = trackFromTrackDb(tdb);
tg->bbiFileName = fileName;
}
else if (sameString(type, "bedGraph"))
{
tg = trackFromTrackDb(tdb);
tg->canPack = FALSE;
tg->customPt = ct;
ct->wigFile = ctFileName;
tg->mapItemName = ctMapItemName;
tg->labelNextItemButtonable = 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->labelNextItemButtonable = TRUE;
tg->customPt = ct;
}
else if (sameString(type, "chromGraph"))
{
tdb->type = NULL; /* Swap out type for the moment. */
tg = trackFromTrackDb(tdb);
chromGraphMethodsCt(tg);
tg->labelNextItemButtonable = FALSE;
tdb->type = typeOrig;
}
else if (sameString(type, "array"))
{
tg = trackFromTrackDb(tdb);
expRatioMethodsFromCt(tg);
tg->labelNextItemButtonable = TRUE;
tg->customPt = ct;
}
else if (sameString(type, "coloredExon"))
{
tg = trackFromTrackDb(tdb);
coloredExonMethodsFromCt(tg);
tg->labelNextItemButtonable = TRUE;
tg->customPt = ct;
}
else if (sameString(type, "encodePeak"))
{
tg = trackFromTrackDb(tdb);
encodePeakMethodsCt(tg);
tg->labelNextItemButtonable = TRUE;
tg->customPt = ct;
}
else
{
errAbort("Unrecognized custom track type %s", type);
}
if (!ct->dbTrack)
tg->labelNextItemButtonable = 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[128];
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->mapName))
{
if (hTvFromString(command) == tg->tdb->visibility)
/* remove if setting to default vis */
cartRemove(cart, tg->mapName);
else
cartSetString(cart, tg->mapName, 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())
{
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\" class=\"topbar\">%s</A></TD>",
'%', '%', "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\" class=\"topbar\">%s</A></TD>",
database, "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);
}
/* 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 (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 (isUnknownChrom(database, chromName))
{
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 ctgPos where chrom = '%s' and chromStart<%u and chromEnd>%u",
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\" 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\" 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");
}
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;
}
static 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;
char cartVar[512];
/* build group objects from database. */
for (grp = grps; grp != NULL; grp = grp->next)
{
/* deal with group reordering */
float priority = grp->priority;
if (withPriorityOverride)
{
safef(cartVar, sizeof(cartVar), "%s.priority",grp->name);
if (vis != -1)
priority = (float)cartUsualDouble(cart, cartVar, grp->priority);
if (priority == grp->priority)
cartRemove(cart, cartVar);
}
/* create group object; add to list and hash */
AllocVar(group);
group->name = cloneString(grp->name);
group->label = cloneString(grp->label);
group->defaultPriority = grp->priority;
group->priority = priority;
group->defaultIsClosed = grp->defaultIsClosed;
slAddHead(&list, group);
hashAdd(hash, grp->name, group);
}
grpFreeList(&grps);
/* Loop through tracks and fill in their groups.
* If necessary make up an unknown group. */
for (track = *pTrackList; track != NULL; track = track->next)
{
/* handle track reordering feature -- change group assigned to track */
if (withPriorityOverride)
{
char *groupName = NULL;
char cartVar[128];
/* 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->mapName);
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->mapName);
float priority = (float)cartUsualDouble(cart, cartVar,
track->defaultPriority);
/* remove cart variables that are the same as the trackDb settings */
/* UGLY - add me back when tdb->priority is no longer pre-clobbered by cart var value
if (priority == track->defaultPriority)
cartRemove(cart, cartVar);
*/
track->priority = priority;
}
/* assign group object to track */
if (track->groupName == NULL)
group = NULL;
else
group = hashFindVal(hash, track->groupName);
if (group == NULL)
{
if (unknown == NULL)
{
AllocVar(unknown);
unknown->name = cloneString("other");
unknown->label = cloneString("other");
unknown->priority = 1000000;
slAddHead(&list, unknown);
}
group = unknown;
}
track->group = group;
}
/* Sort tracks by combined group/track priority, and
* then add references to track to group. */
slSort(pTrackList, tgCmpPriority);
for (track = *pTrackList; track != NULL; track = track->next)
{
AllocVar(tr);
tr->track = track;
slAddHead(&track->group->trackList, tr);
}
/* Straighten things out, clean up, and go home. */
for (group = list; group != NULL; group = group->next)
slReverse(&group->trackList);
slSort(&list, gCmpPriority);
hashFree(&hash);
*pGroupList = list;
}
void groupTrackListAddSuper(struct cart *cart, struct group *group)
/* Construct a new track list that includes supertracks, sort by priority,
* and determine if supertracks have visible members.
* Replace the group track list with this new list.
* Shared by hgTracks and configure page to expand track list,
* in contexts where no track display functions (which don't understand
* supertracks) are invoked. */
{
struct trackRef *newList = NULL, *tr, *ref;
struct hash *superHash = hashNew(8);
if (!group || !group->trackList)
return;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
AllocVar(ref);
ref->track = track;
slAddHead(&newList, ref);
if (tdbIsSuperTrackChild(track->tdb))
{
assert(track->tdb->parentName != NULL);
if (hTvFromString(cartUsualString(cart, track->mapName,
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[128];
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->tableName,
track->tdb->parent->isShow ? "show" : "hide")))
track->visibility = tvHide;
}
}
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);
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->mapName);
if (cgiOptionalString("hideTracks"))
{
s = cgiOptionalString(track->mapName);
if (s != NULL && (hTvFromString(s) != track->tdb->visibility))
{
cartSetString(cart, track->mapName, 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->tableName,
parent->isShow ? "show" : "hide");
if (!parent || sameString(parentShow, "show"))
compositeTrackVis(track);
}
}
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->labelNextPrevItem != NULL)
track->labelNextPrevItem(track, goNext);
}
char *collapseGroupVar(char *name)
/* Construct cart variable name for collapsing group */
{
static char varName[128];
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->mapName);
if (cartVis != NULL && hTvFromString(cartVis) == track->tdb->visibility)
cartRemove(cart, track->mapName);
}
if (measureTiming)
{
uglyTime("Pruned redundant vis from cart");
}
}
void doTrackForm(char *psOutput, struct tempName *ideoTn)
/* Make the tracks display form with the zoom/scroll buttons and the active
* image. If the ideoTn parameter is not NULL, it is filled in if the
* ideogram is created. */
{
struct group *group;
struct track *track;
char *freezeName = NULL;
boolean hideAll = cgiVarExists("hgt.hideAll");
boolean defaultTracks = cgiVarExists("hgt.reset");
boolean showedRuler = FALSE;
boolean showTrackControls = cartUsualBoolean(cart, "trackControlsOnMain", TRUE);
long thisTime = 0, lastTime = 0;
char *clearButtonJavascript;
basesPerPixel = ((float)winBaseCount) / ((float)insideWidth);
zoomedToBaseLevel = (winBaseCount <= insideWidth / tl.mWidth);
zoomedToCodonLevel = (ceil(winBaseCount/3) * tl.mWidth) <= insideWidth;
zoomedToCdsColorLevel = (winBaseCount <= insideWidth*3);
if (psOutput != NULL)
{
hPrintDisable();
hideControls = TRUE;
withNextItemArrows = FALSE;
withNextExonArrows = FALSE;
hgFindMatches = NULL;
}
/* Tell browser where to go when they click on image. */
hPrintf("<FORM ACTION=\"%s\" NAME=\"TrackHeaderForm\" id=\"TrackHeaderForm\" METHOD=\"GET\">\n\n", hgTracksName());
hPrintf("<input type='hidden' id='hgt.insideX' name='insideX' value='%d'>\n", insideX);
hPrintf("<input type='hidden' id='hgt.revCmplDisp' name='revCmplDisp' value='%d'>\n", revCmplDisp);
if (!psOutput) cartSaveSession(cart);
clearButtonJavascript = "document.TrackHeaderForm.position.value=''";
/* 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);
if (measureTiming)
uglyTime("getTrackList");
/* 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));
/* 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();
track->loadItems(track);
if (measureTiming)
{
thisTime = clock1000();
track->loadTime = thisTime - lastTime;
}
}
}
/* 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);
}
}
}
/* 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
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. */
hWrites("move ");
hButtonWithMsg("hgt.left3", "<<<", "move 95% to the left");
hButtonWithMsg("hgt.left2", " <<", "move 45% to the left");
hButtonWithMsg("hgt.left1", " < ", "move 10% to the left");
hButtonWithMsg("hgt.right1", " > ", "move 10% to the right");
hButtonWithMsg("hgt.right2", ">> ", "move 45% 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");
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(trackGroupsHidden2->string);
freeDyString(&trackGroupsHidden1);
freeDyString(&trackGroupsHidden2);
if (!psOutput) cartSaveSession(cart); /* Put up hgsid= as hidden variable. */
clearButtonJavascript = "document.TrackForm.position.value=''";
hPrintf("<CENTER>");
}
/* Make line that says position. */
{
char buf[256];
char *survey = cfgOptionEnv("HGDB_SURVEY", "survey");
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);
hWrites(" ");
hButton("hgt.jump", "jump");
hOnClickButton(clearButtonJavascript,"clear");
hPrintf(" size <span id='size'>%s</span> bp. ", buf);
hButton("hgTracksConfigPage", "configure");
#define SURVEY 1
#ifdef SURVEY
//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 && sameWord(survey, "on"))
hPrintf(" <FONT SIZE=3><A STYLE=\"background-color:yellow;\" HREF=\"http://www.surveymonkey.com/s.asp?u=881163743177\" TARGET=_BLANK><EM><B>Take survey</EM></B></A></FONT>\n");
#endif
// 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);
/* Make clickable image and map. */
makeActiveImage(trackList, psOutput);
fflush(stdout);
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=CENTER NOWRAP>");
hPrintf("move start<BR>");
hButton("hgt.dinkLL", " < ");
hTextVar("dinkL", cartUsualString(cart, "dinkL", "2.0"), 3);
hButton("hgt.dinkLR", " > ");
hPrintf("</TD><TD COLSPAN=15 style=\"white-space:normal\">"); // allow this text to wrap
hWrites("Click on a feature for details. ");
hWrites(dragZooming ? "Click or drag in the base position track to zoom in. " : "Click on base position to zoom in around cursor. ");
hWrites("Click gray/blue bars on left for track options and descriptions.");
hPrintf("</TD><TD COLSPAN=6 ALIGN=CENTER NOWRAP>");
hPrintf("move end<BR>");
hButton("hgt.dinkRL", " < ");
hTextVar("dinkR", cartUsualString(cart, "dinkR", "2.0"), 3);
hButton("hgt.dinkRR", " > ");
hPrintf("</TD></TR></TABLE>\n");
// smallBreak();
/* Display bottom control panel. */
hButton("hgt.reset", "default tracks");
// 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(" ");
}
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"))
{
showedRuler = TRUE;
myControlGridStartCell(cg, isOpen, group->name);
hPrintf("<A HREF=\"%s?%s=%u&c=%s&g=%s\">", hgTrackUiName(),
cartSessionVarName(), cartSessionId(cart),
chromName, RULER_TRACK_NAME);
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);
}
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 *encodedMapName = cgiEncode(track->mapName);
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?%s=%u&c=%s&g=%s\">", hgTrackUiName(),
cartSessionVarName(), cartSessionId(cart),
chromName, encodedMapName);
freeMem(encodedMapName);
}
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->mapName, 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, ""))
{
errAbort("Please go back and enter a coordinate range 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);
}
withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE);
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, 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)
errAbort("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(long long total)
/* Make table row with total size from chromInfo. */
{
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
printf("Total");
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(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(total);
}
else
{
safef(msg1, sizeof(msg1), "Limit reached");
safef(msg2, sizeof(msg2), "%d rows displayed", limit);
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
printf(msg1);
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
printf(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();
printf(msg1);
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
printf(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);
struct dyString *title = dyStringNew(512);
dyStringPrintf(title, "%s %s (%s) Browser Sequences",
hOrganism(database), hFreezeFromDb(database), 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;
setUdcCacheDir();
initTl();
char *configPageCall = cartCgiUsualString(cart, "hgTracksConfigPage", "notSet");
dragZooming = cartUsualBoolean(cart, "dragZooming", TRUE);
/* Do main display. */
jsIncludeFile("jquery.js", NULL);
if(dragZooming)
{
jsIncludeFile("jquery.imgareaselect.js", NULL);
jsIncludeFile("utils.js", NULL);
}
jsIncludeFile("hgTracks.js", NULL);
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);
}
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.jump", "hgt.refresh",
NULL };
int main(int argc, char *argv[])
{
enteredMainTime = clock1000();
uglyTime(NULL);
browserName = (hIsPrivateHost() ? "Test Browser" : "Genome Browser");
organization = (hIsMgcServer() ? "MGC/ORFeome" : "UCSC");
/* change title if this is for GSID */
browserName = (hIsGsidServer() ? "Sequence View" : browserName);
organization = (hIsGsidServer() ? "GSID" : 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;
}