2e3514ccacc941c9b8ffcaecb83438b4c3053e5e
Merge parents 4cbae69 a13fa51
kate
Thu Oct 22 20:35:34 2015 -0700
Resolving merge
diff --cc src/hg/hgTracks/hgTracks.c
index 08486bd,5735c0c..7ed2472
--- src/hg/hgTracks/hgTracks.c
+++ src/hg/hgTracks/hgTracks.c
@@@ -1,6076 -1,6088 +1,6084 @@@
/* hgTracks - the original, and still the largest module for the UCSC Human Genome
* Browser main cgi script. Currently contains most of the track framework, though
* there's quite a bit of other framework type code in simpleTracks.c. The main
* routine got moved to create a new entry point to the bulk of the code for the
* hgRenderTracks web service. See mainMain.c for the main used by the hgTracks CGI. */
/* Copyright (C) 2014 The Regents of the University of California
* See README in this or parent directory for licensing information. */
#include <pthread.h>
#include "common.h"
#include "hCommon.h"
#include "linefile.h"
#include "portable.h"
#include "memalloc.h"
#include "localmem.h"
#include "obscure.h"
#include "dystring.h"
#include "hash.h"
#include "jksql.h"
#include "gfxPoly.h"
#include "memgfx.h"
#include "hvGfx.h"
#include "psGfx.h"
#include "cheapcgi.h"
#include "hPrint.h"
#include "htmshell.h"
#include "cart.h"
#include "hdb.h"
#include "hui.h"
#include "hgFind.h"
#include "hgTracks.h"
#include "trashDir.h"
#include "grp.h"
#include "versionInfo.h"
#include "web.h"
#include "cds.h"
#include "cutterTrack.h"
#include "wikiTrack.h"
#include "ctgPos.h"
#include "bed.h"
#include "bigBed.h"
#include "bigWig.h"
#include "bedCart.h"
#include "udc.h"
#include "customTrack.h"
#include "trackHub.h"
#include "hubConnect.h"
#include "cytoBand.h"
#include "ensFace.h"
#include "liftOver.h"
#include "pcrResult.h"
#include "jsHelper.h"
#include "mafTrack.h"
#include "hgConfig.h"
#include "encode.h"
#include "agpFrag.h"
#include "imageV2.h"
#include "suggest.h"
#include "search.h"
#include "errCatch.h"
#include "iupac.h"
#include "botDelay.h"
#include "chromInfo.h"
#include "extTools.h"
+#include "customFactory.h"
/* 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 its 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", "dirty", "hgt.reset",
"hgt.in1", "hgt.in2", "hgt.in3", "hgt.inBase",
"hgt.out1", "hgt.out2", "hgt.out3", "hgt.out4",
"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.collapseGroups", "hgt.expandGroups", "hgt.suggest",
"hgt.jump", "hgt.refresh", "hgt.setWidth",
"hgt.trackImgOnly", "hgt.ideogramToo", "hgt.trackNameFilter", "hgt.imageV1", "hgt.suggestTrack", "hgt.setWidth",
TRACK_SEARCH, TRACK_SEARCH_ADD_ROW, TRACK_SEARCH_DEL_ROW, TRACK_SEARCH_PAGER,
"hgt.contentType", "hgt.positionInput", "hgt.internal",
NULL };
/* 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 */
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 */
struct hvGfx *hvgSide = NULL; // Extra pointer to a sideLabel image that can be built if needed
char *rulerMenu[] =
/* dropdown for ruler visibility */
{
"hide",
"dense",
"full"
};
char *protDbName; /* Name of proteome database for this genome. */
#define MAX_CONTROL_COLUMNS 6
#define LOW 1
#define MEDIUM 2
#define BRIGHT 3
#define MAXCHAINS 50000000
boolean hgDebug = FALSE; /* Activate debugging code. Set to true by hgDebug=on in command line*/
int imagePixelHeight = 0;
struct hash *oldVars = NULL;
struct jsonElement *jsonForClient = NULL;
boolean hideControls = FALSE; /* Hide all controls? */
boolean trackImgOnly = FALSE; /* caller wants just the track image and track table html */
boolean ideogramToo = FALSE; /* caller wants the ideoGram (when requesting just one track) */
/* Structure returned from findGenomePos.
* We use this to to expand any tracks to full
* that were found to contain the searched-upon
* position string */
struct hgPositions *hgp = NULL;
/* Other global variables. */
struct group *groupList = NULL; /* List of all tracks. */
char *browserName; /* Test, preview, or public browser */
char *organization; /* UCSC */
struct hash *trackHash = NULL; /* Hash of the tracks by their name. */
#ifdef DEBUG
void uglySnoopTrackList(int depth, struct track *trackList)
/* Print out some info on track list. */
{
struct track *track;
for (track = trackList; track != NULL; track = track->next)
{
if (stringIn("FaireH1h", track->track))
{
repeatCharOut(uglyOut, '+', depth);
uglyf("%s pri=%g defPri=%g<BR>\n", track->track, track->priority, track->defaultPriority);
}
uglySnoopTrackList(depth+1, track->subtracks);
}
}
#endif /* DEBUG */
struct track *trackFindByName(struct track *tracks, char *trackName)
/* find a track in tracks by name, recursively searching subtracks */
{
struct track *track;
for (track = tracks; track != NULL; track = track->next)
{
if (sameString(track->track, trackName))
return track;
else if (track->subtracks != NULL)
{
struct track *st = trackFindByName(track->subtracks, trackName);
if (st != NULL)
return st;
}
}
return NULL;
}
int tgCmpPriority(const void *va, const void *vb)
/* Compare to sort based on priority; use shortLabel as secondary sort key. */
{
const struct track *a = *((struct track **)va);
const struct track *b = *((struct track **)vb);
float dif = 0;
if (a->group && b->group)
dif = a->group->priority - b->group->priority;
if (dif == 0)
dif = a->priority - b->priority;
if (dif < 0)
return -1;
else if (dif == 0.0)
/* secondary sort on label */
return strcasecmp(a->shortLabel, b->shortLabel);
else
return 1;
}
int trackRefCmpPriority(const void *va, const void *vb)
/* Compare based on priority. */
{
const struct trackRef *a = *((struct trackRef **)va);
const struct trackRef *b = *((struct trackRef **)vb);
return tgCmpPriority(&a->track, &b->track);
}
int gCmpPriority(const void *va, const void *vb)
/* Compare groups based on priority. */
{
const struct group *a = *((struct group **)va);
const struct group *b = *((struct group **)vb);
float dif = a->priority - b->priority;
if (dif == 0)
return 0;
if (dif < 0)
return -1;
else if (dif == 0.0)
return 0;
else
return 1;
}
void changeTrackVis(struct group *groupList, char *groupTarget, int changeVis)
/* Change track visibilities. If groupTarget is
* NULL then set visibility for tracks in all groups. Otherwise,
* just set it for the given group. If vis is -2, then visibility is
* unchanged. If -1 then set visibility to default, otherwise it should
* be tvHide, tvDense, etc.
* If we are going back to default visibility, then reset the track
* ordering also. */
{
struct group *group;
if (changeVis == -2)
return;
for (group = groupList; group != NULL; group = group->next)
{
struct trackRef *tr;
if (groupTarget == NULL || sameString(group->name,groupTarget))
{
static char pname[512];
/* if default vis then reset group priority */
if (changeVis == -1)
group->priority = group->defaultPriority;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
struct trackDb *tdb = track->tdb;
if (changeVis == -1) // to default
{
if (tdbIsComposite(tdb))
{
safef(pname, sizeof(pname),"%s.*",track->track); //to remove all settings associated with this composite!
cartRemoveLike(cart,pname);
struct track *subTrack;
for (subTrack = track->subtracks;subTrack != NULL; subTrack = subTrack->next)
{
subTrack->visibility = tdb->visibility;
cartRemove(cart, subTrack->track);
}
}
/* restore defaults */
if (tdbIsSuperTrackChild(tdb) || tdbIsCompositeChild(tdb))
{
assert(tdb->parent != NULL && tdb->parent->track);
cartRemove(cart, tdb->parent->track);
if (withPriorityOverride)
{
safef(pname, sizeof(pname), "%s.priority",tdb->parent->track);
cartRemove(cart, pname);
}
}
track->visibility = tdb->visibility;
cartRemove(cart, track->track);
/* set the track priority back to the default value */
if (withPriorityOverride)
{
safef(pname, sizeof(pname), "%s.priority",track->track);
cartRemove(cart, pname);
track->priority = track->defaultPriority;
}
}
else // to changeVis value (Usually tvHide)
{
/* change to specified visibility */
if (tdbIsSuperTrackChild(tdb))
{
assert(tdb->parent != NULL);
/* Leave supertrack members alone -- only change parent */
struct trackDb *parentTdb = tdb->parent;
if ((changeVis == tvHide && !parentTdb->isShow) ||
(changeVis != tvHide && parentTdb->isShow))
{
/* remove if setting to default vis */
cartRemove(cart, parentTdb->track);
}
else
cartSetString(cart, parentTdb->track,
changeVis == tvHide ? "hide" : "show");
}
else // Not super child
{
if (changeVis == tdb->visibility)
/* remove if setting to default vis */
cartRemove(cart, track->track);
else
cartSetString(cart, track->track, hStringFromTv(changeVis));
track->visibility = changeVis;
}
// Whether super child or not, if its a composite, then handle the children
if (tdbIsComposite(tdb))
{
struct track *subtrack;
for (subtrack=track->subtracks;subtrack!=NULL;subtrack=subtrack->next)
{
if (changeVis == tvHide) // Since subtrack level vis is an
cartRemove(cart, subtrack->track); // override, simply remove to hide
else
cartSetString(cart, subtrack->track, hStringFromTv(changeVis));
subtrack->visibility = changeVis;
}
}
}
}
}
}
slSort(&groupList, gCmpPriority);
}
int trackOffsetX()
/* Return x offset where track display proper begins. */
{
int x = gfxBorder;
if (withLeftLabels)
x += tl.leftLabelWidth + gfxBorder;
return x;
}
static void mapBoxTrackUi(struct hvGfx *hvg, int x, int y, int width,
int height, char *name, char *shortLabel, char *id)
/* Print out image map rectangle that invokes hgTrackUi. */
{
x = hvGfxAdjXW(hvg, x, width);
char *url = trackUrl(name, chromName);
if (theImgBox && curImgTrack)
{
struct imgSlice *curSlice = imgTrackSliceGetByType(curImgTrack,stButton);
if (curSlice)
sliceAddLink(curSlice,url,shortLabel);
}
else
{
hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", x, y, x+width, y+height);
hPrintf("HREF=\"%s\"", url);
mapStatusMessage("%s controls", shortLabel);
hPrintf(">\n");
}
freeMem(url);
}
static void mapBoxToggleComplement(struct hvGfx *hvg, int x, int y, int width, int height,
struct track *toggleGroup, char *chrom,
int start, int end, char *message)
/*print out a box along the DNA bases that toggles a cart variable
* "complement" to complement the DNA bases at the top by the ruler*/
{
struct dyString *ui = uiStateUrlPart(toggleGroup);
x = hvGfxAdjXW(hvg, x, width);
if (theImgBox && curImgTrack)
{
char link[512];
safef(link,sizeof(link),"%s?complement_%s=%d&%s", hgTracksName(), database,
!cartUsualBooleanDb(cart, database, COMPLEMENT_BASES_VAR, FALSE),ui->string);
imgTrackAddMapItem(curImgTrack,link,(char *)(message != NULL?message:NULL),x, y, x+width, y+height, NULL);
}
else
{
hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", x, y, x+width, y+height);
hPrintf("HREF=\"%s?complement_%s=%d", hgTracksName(), database,
!cartUsualBooleanDb(cart, database, COMPLEMENT_BASES_VAR, FALSE));
hPrintf("&%s\"", ui->string);
freeDyString(&ui);
if (message != NULL)
mapStatusMessage("%s", message);
hPrintf(">\n");
}
}
char *trackUrl(char *mapName, char *chromName)
/* Return hgTrackUi url; chromName is optional. */
{
char *encodedMapName = cgiEncode(mapName);
char buf[2048];
if(chromName == NULL)
safef(buf, sizeof(buf), "%s?%s=%s&g=%s", hgTrackUiName(), cartSessionVarName(), cartSessionId(cart), encodedMapName);
else
safef(buf, sizeof(buf), "%s?%s=%s&c=%s&g=%s", hgTrackUiName(), cartSessionVarName(), cartSessionId(cart), chromName, encodedMapName);
freeMem(encodedMapName);
return(cloneString(buf));
}
#ifdef REMOTE_TRACK_AJAX_CALLBACK
static boolean trackUsesRemoteData(struct track *track)
/* returns TRUE is this track has a remote datasource */
{
if (!IS_KNOWN(track->remoteDataSource))
{
SET_TO_NO(track->remoteDataSource);
//if (track->bbiFile != NULL) // FIXME: Chicken or the egg. bigWig/bigBed "bbiFile" filled
// // in by loadItems, but we don't want to load items.
// {
// if (!startsWith("/gbdb/",track->bbiFile->fileName))
// SET_TO_YES(track->remoteDataSource);
// }
if (startsWithWord("bigWig",track->tdb->type) || startsWithWord("bigBed",track->tdb->type) ||
startsWithWord("halSnake",track->tdb->type) ||
startsWithWord("bigPsl",track->tdb->type) ||
startsWithWord("bigGenePred",track->tdb->type) ||
+ startsWithWord("bigMaf",track->tdb->type) ||
startsWithWord("bam",track->tdb->type) || startsWithWord("vcfTabix", track->tdb->type))
{
SET_TO_YES(track->remoteDataSource);
}
}
return IS_YES(track->remoteDataSource);
}
boolean trackShouldUseAjaxRetrieval(struct track *track)
/* Tracks with remote data sources should berendered via an ajax callback */
{
return (theImgBox && !trackImgOnly && trackUsesRemoteData(track));
}
#endif///def REMOTE_TRACK_AJAX_CALLBACK
static int trackPlusLabelHeight(struct track *track, int fontHeight)
/* Return the sum of heights of items in this track (or subtrack as it may be)
* and the center label(s) above the items (if any). */
{
if (trackShouldUseAjaxRetrieval(track))
return REMOTE_TRACK_HEIGHT;
int y = track->totalHeight(track, limitVisibility(track));
if (isCenterLabelIncluded(track))
y += fontHeight;
if (tdbIsComposite(track->tdb))
{
struct track *subtrack;
for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack) && isCenterLabelIncluded(subtrack))
y += fontHeight;
}
}
return y;
}
void drawColoredButtonBox(struct hvGfx *hvg, int x, int y, int w, int h,
int enabled, Color shades[])
/* draw button box, providing shades of the desired button color */
{
int light = shades[1], mid = shades[2], dark = shades[4];
if (enabled)
{
hvGfxBox(hvg, x, y, w, 1, light);
hvGfxBox(hvg, x, y+1, 1, h-1, light);
hvGfxBox(hvg, x+1, y+1, w-2, h-2, mid);
hvGfxBox(hvg, x+1, y+h-1, w-1, 1, dark);
hvGfxBox(hvg, x+w-1, y+1, 1, h-1, dark);
}
else /* try to make the button look as if
* it is already depressed */
{
hvGfxBox(hvg, x, y, w, 1, dark);
hvGfxBox(hvg, x, y+1, 1, h-1, dark);
hvGfxBox(hvg, x+1, y+1, w-2, h-2, light);
hvGfxBox(hvg, x+1, y+h-1, w-1, 1, light);
hvGfxBox(hvg, x+w-1, y+1, 1, h-1, light);
}
}
void drawGrayButtonBox(struct hvGfx *hvg, int x, int y, int w, int h, int enabled)
/* Draw a gray min-raised looking button. */
{
drawColoredButtonBox(hvg, x, y, w, h, enabled, shadesOfGray);
}
void drawBlueButtonBox(struct hvGfx *hvg, int x, int y, int w, int h, int enabled)
/* Draw a blue min-raised looking button. */
{
drawColoredButtonBox(hvg, x, y, w, h, enabled, shadesOfSea);
}
void drawButtonBox(struct hvGfx *hvg, int x, int y, int w, int h, int enabled)
/* Draw a standard (gray) min-raised looking button. */
{
drawGrayButtonBox(hvg, x, y, w, h, enabled);
}
void beforeFirstPeriod( char *str )
{
char *t = rindex( str, '.' );
if( t == NULL )
return;
else
str[strlen(str) - strlen(t)] = '\0';
}
static void drawBases(struct hvGfx *hvg, int x, int y, int width, int height,
Color color, MgFont *font, boolean complementSeq,
struct dnaSeq *thisSeq)
/* Draw evenly spaced bases. */
{
struct dnaSeq *seq;
if (thisSeq == NULL)
seq = hDnaFromSeq(database, chromName, winStart, winEnd, dnaUpper);
else
seq = thisSeq;
if (complementSeq)
complement(seq->dna, seq->size);
spreadBasesString(hvg, x, y, width, height, color, font,
seq->dna, seq->size, FALSE);
if (thisSeq == NULL)
freeDnaSeq(&seq);
}
void drawComplementArrow( struct hvGfx *hvg, int x, int y,
int width, int height, MgFont *font)
/* Draw arrow and create clickbox for complementing ruler bases */
{
boolean baseCmpl = cartUsualBooleanDb(cart, database, COMPLEMENT_BASES_VAR, FALSE);
// reverse arrow when base complement doesn't match display
char *text = (baseCmpl == revCmplDisp) ? "--->" : "<---";
hvGfxTextRight(hvg, x, y, width, height, MG_BLACK, font, text);
mapBoxToggleComplement(hvg, x, y, width, height, NULL, chromName, winStart, winEnd,
"complement bases");
}
struct track *chromIdeoTrack(struct track *trackList)
/* Find chromosome ideogram track */
{
struct track *track;
for(track = trackList; track != NULL; track = track->next)
{
if(sameString(track->track, "cytoBandIdeo"))
{
if (hTableExists(database, track->table))
return track;
else
return NULL;
}
}
return NULL;
}
void removeTrackFromGroup(struct track *track)
/* Remove track from group it is part of. */
{
struct trackRef *tr = NULL;
for(tr = track->group->trackList; tr != NULL; tr = tr->next)
{
if(tr->track == track)
{
slRemoveEl(&track->group->trackList, tr);
break;
}
}
}
void fillInStartEndBands(struct track *ideoTrack, char *startBand, char *endBand, int buffSize)
/* Loop through the bands and fill in the one that the current window starts
on and ends on. */
{
struct cytoBand *cb = NULL, *cbList = ideoTrack->items;
for(cb = cbList; cb != NULL; cb = cb->next)
{
/* If the start or end is encompassed by this band fill
it in. */
if (winStart >= cb->chromStart
&& winStart <= cb->chromEnd)
{
safef(startBand, buffSize, "%s", cb->name);
}
/* End is > rather than >= due to odditiy in the
cytoband track where the starts and ends of two
bands overlaps by one. */
if (winEnd > cb->chromStart
&& winEnd <= cb->chromEnd)
{
safef(endBand, buffSize, "%s", cb->name);
}
}
}
void makeChromIdeoImage(struct track **pTrackList, char *psOutput,
struct tempName *ideoTn)
/* Make an ideogram image of the chromsome and our position in it. If the
* ideoTn parameter is not NULL, it is filled in if the ideogram is created. */
{
struct track *ideoTrack = NULL;
MgFont *font = tl.font;
char *mapName = "ideoMap";
struct hvGfx *hvg;
boolean doIdeo = TRUE;
-boolean ideogramAvail = FALSE;
int ideoWidth = round(.8 *tl.picWidth);
int ideoHeight = 0;
int textWidth = 0;
struct tempName pngTn;
if (ideoTn == NULL)
ideoTn = &pngTn; // not returning value
ideoTrack = chromIdeoTrack(*pTrackList);
/* If no ideogram don't draw. */
if(ideoTrack == NULL)
doIdeo = FALSE;
else if(trackImgOnly && !ideogramToo)
{
doIdeo = FALSE;
}
else
{
- ideogramAvail = TRUE;
/* Remove the track from the group and track list. */
removeTrackFromGroup(ideoTrack);
slRemoveEl(pTrackList, ideoTrack);
/* Fix for hide all button hiding the ideogram as well. */
if(withIdeogram && ideoTrack->items == NULL)
{
ideoTrack->visibility = tvDense;
ideoTrack->loadItems(ideoTrack);
}
limitVisibility(ideoTrack);
/* If hidden don't draw. */
if(ideoTrack->limitedVis == tvHide || !withIdeogram)
doIdeo = FALSE;
}
if(doIdeo)
{
char startBand[16];
char endBand[16];
char title[32];
startBand[0] = endBand[0] = '\0';
fillInStartEndBands(ideoTrack, startBand, endBand, sizeof(startBand));
/* Start up client side map. */
if (!psOutput)
hPrintf("<MAP Name=%s>\n", mapName);
/* Draw the ideogram. */
ideoHeight = gfxBorder + ideoTrack->height;
if (psOutput)
{
trashDirFile(ideoTn, "hgtIdeo", "hgtIdeo", ".ps");
hvg = hvGfxOpenPostScript(ideoWidth, ideoHeight, ideoTn->forCgi);
}
else
{
trashDirFile(ideoTn, "hgtIdeo", "hgtIdeo", ".png");
hvg = hvGfxOpenPng(ideoWidth, ideoHeight, ideoTn->forCgi, FALSE);
}
hvg->rc = revCmplDisp;
initColors(hvg);
ideoTrack->ixColor = hvGfxFindRgb(hvg, &ideoTrack->color);
ideoTrack->ixAltColor = hvGfxFindRgb(hvg, &ideoTrack->altColor);
hvGfxSetClip(hvg, 0, gfxBorder, ideoWidth, ideoTrack->height);
if (isEmpty(startBand))
safef(title, sizeof(title), "%s", chromName);
else 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: */
sqlSafef(query, sizeof(query), "select * from %s where qName = '%s'",
target->pslTable, itemAcc);
sr = sqlGetResult(conn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
struct psl *gpsl = pslLoad(row+rowOffset);
if (sameString(gpsl->tName, chromName) && gpsl->tStart < winEnd && gpsl->tEnd > winStart)
{
struct psl *trimmed = pslTrimToQueryRange(gpsl, tpsl->tStart,
tpsl->tEnd);
struct linkedFeatures *lf;
char *targetStyle = cartUsualString(cart,
PCR_RESULT_TARGET_STYLE, PCR_RESULT_TARGET_STYLE_DEFAULT);
if (sameString(targetStyle, PCR_RESULT_TARGET_STYLE_TALL))
{
lf = lfFromPslx(gpsl, 1, FALSE, FALSE, tg);
lf->tallStart = trimmed->tStart;
lf->tallEnd = trimmed->tEnd;
}
else
{
lf = lfFromPslx(trimmed, 1, FALSE, FALSE, tg);
}
lf->name = cloneString(itemAcc);
char extraInfo[512];
safef(extraInfo, sizeof(extraInfo), "%s|%d|%d",
(itemName ? itemName : ""), tpsl->tStart, tpsl->tEnd);
lf->extra = cloneString(extraInfo);
slAddHead(&itemList, lf);
}
}
}
hFreeConn(&conn);
}
else
for (psl = pslList; psl != NULL; psl = psl->next)
if (sameString(psl->tName, chromName) && psl->tStart < winEnd && psl->tEnd > winStart)
{
struct linkedFeatures *lf = lfFromPslx(psl, 1, FALSE, FALSE, tg);
lf->name = cloneString("");
lf->extra = cloneString("");
slAddHead(&itemList, lf);
}
slSort(&itemList, linkedFeaturesCmp);
tg->items = itemList;
}
char *pcrResultTrackItemName(struct track *tg, void *item)
/* If lf->extra is non-empty, return it (display name for item).
* Otherwise default to item name. */
{
struct linkedFeatures *lf = item;
char *extra = (char *)lf->extra;
if (isNotEmpty(extra))
{
static char displayName[512];
safecpy(displayName, sizeof(displayName), extra);
char *ptr = strchr(displayName, '|');
if (ptr != NULL)
*ptr = '\0';
if (isNotEmpty(displayName))
return displayName;
}
return lf->name;
}
struct track *pcrResultTg()
/* Make track of hgPcr results (alignments of user's submitted primers). */
{
struct trackDb *tdb = pcrResultFakeTdb();
struct track *tg = trackFromTrackDb(tdb);
tg->loadItems = pcrResultLoad;
tg->itemName = pcrResultTrackItemName;
tg->mapItemName = pcrResultMapItemName;
tg->exonArrows = TRUE;
tg->hasUi = TRUE;
return tg;
}
struct track *linkedFeaturesTg()
/* Return generic track for linked features. */
{
struct track *tg = trackNew();
linkedFeaturesMethods(tg);
tg->colorShades = shadesOfGray;
return tg;
}
void setTgDarkLightColors(struct track *tg, int r, int g, int b)
/* Set track color to r,g,b. Set altColor to a lighter version
* of the same. */
{
tg->colorShades = NULL;
tg->color.r = r;
tg->color.g = g;
tg->color.b = b;
tg->altColor.r = (r+255)/2;
tg->altColor.g = (g+255)/2;
tg->altColor.b = (b+255)/2;
}
void parseSs(char *ss, char **retPsl, char **retFa)
/* Parse out ss variable into components. */
{
static char buf[1024];
char *words[2];
int wordCount;
safecpy(buf, sizeof(buf), ss);
wordCount = chopLine(buf, words);
if (wordCount < 2)
errAbort("Badly formated ss variable");
*retPsl = words[0];
*retFa = words[1];
}
boolean ssFilesExist(char *ss)
/* Return TRUE if both files in ss exist. */
{
char *faFileName, *pslFileName;
parseSs(ss, &pslFileName, &faFileName);
return fileExists(pslFileName) && fileExists(faFileName);
}
void loadUserPsl(struct track *tg)
/* Load up hgBlat results from table into track items. */
{
char *ss = userSeqString;
char buf2[3*512];
char *faFileName, *pslFileName;
struct lineFile *f;
struct psl *psl;
struct linkedFeatures *lfList = NULL, *lf;
enum gfType qt, tt;
int sizeMul = 1;
parseSs(ss, &pslFileName, &faFileName);
pslxFileOpen(pslFileName, &qt, &tt, &f);
if (qt == gftProt)
{
setTgDarkLightColors(tg, 0, 80, 150);
tg->colorShades = NULL;
sizeMul = 3;
}
tg->itemName = linkedFeaturesName;
while ((psl = pslNext(f)) != NULL)
{
if (sameString(psl->tName, chromName) && psl->tStart < winEnd && psl->tEnd > winStart)
{
lf = lfFromPslx(psl, sizeMul, TRUE, FALSE, tg);
sprintf(buf2, "%s %s", ss, psl->qName);
lf->extra = cloneString(buf2);
slAddHead(&lfList, lf);
/* Don't free psl -- used in drawing phase by baseColor code. */
}
else
pslFree(&psl);
}
slSort(&lfList, linkedFeaturesCmpStart);
lineFileClose(&f);
tg->items = lfList;
}
static void addUserSeqBaseAndIndelSettings(struct trackDb *tdb)
/* If user sequence is a dna or rna alignment, add settings to enable
* base-level differences and indel display. */
{
enum gfType qt, tt;
struct lineFile *lf;
char *faFileName, *pslFileName;
parseSs(userSeqString, &pslFileName, &faFileName);
pslxFileOpen(pslFileName, &qt, &tt, &lf);
lineFileClose(&lf);
if (qt != gftProt)
{
if (tdb->settingsHash == NULL)
tdb->settingsHash = hashNew(0);
hashAdd(tdb->settingsHash, BASE_COLOR_DEFAULT, cloneString("diffBases"));
hashAdd(tdb->settingsHash, BASE_COLOR_USE_SEQUENCE, cloneString("ss"));
hashAdd(tdb->settingsHash, SHOW_DIFF_BASES_ALL_SCALES, cloneString("."));
hashAdd(tdb->settingsHash, INDEL_DOUBLE_INSERT, cloneString("on"));
hashAdd(tdb->settingsHash, INDEL_QUERY_INSERT, cloneString("on"));
hashAdd(tdb->settingsHash, INDEL_POLY_A, cloneString("on"));
}
}
struct track *userPslTg()
/* Make track of user pasted sequence. */
{
struct track *tg = linkedFeaturesTg();
struct trackDb *tdb;
tg->track = "hgUserPsl";
tg->table = tg->track;
tg->canPack = TRUE;
tg->visibility = tvPack;
tg->longLabel = "Your Sequence from Blat Search";
tg->shortLabel = "Blat Sequence";
tg->loadItems = loadUserPsl;
tg->mapItemName = lfMapNameFromExtra;
tg->priority = 103;
tg->defaultPriority = tg->priority;
tg->groupName = "map";
tg->defaultGroupName = cloneString(tg->groupName);
tg->exonArrows = TRUE;
/* better to create the tdb first, then use trackFromTrackDb */
AllocVar(tdb);
tdb->track = cloneString(tg->track);
tdb->table = cloneString(tg->table);
tdb->visibility = tg->visibility;
tdb->shortLabel = cloneString(tg->shortLabel);
tdb->longLabel = cloneString(tg->longLabel);
tdb->grp = cloneString(tg->groupName);
tdb->priority = tg->priority;
tdb->type = cloneString("psl");
tdb->canPack = tg->canPack;
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);
iupacFilter(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;
}
char *stringInWrapper(char *needle, char *haystack)
/* Wrapper around string in to make it so it's a function rather than a macro. */
{
return stringIn(needle, haystack);
}
void oligoMatchLoad(struct track *tg)
/* Create track of perfect matches to oligo on either strand.
*
* Note that if you are extending this code, there is also a parallel copy
* in src/hg/utils/oligoMatch/ that should be kept up to date!
*
*/
{
char *dna = dnaInWindow();
char *fOligo = oligoMatchSeq();
char *(*finder)(char *needle, char *haystack) = (anyIupac(fOligo) ? iupacIn : stringInWrapper);
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 = finder(fOligo, dna);
iupacReverseComplement(rOligo, oligoSize);
if (sameString(rOligo, fOligo))
rOligo = NULL;
else
rMatch = finder(rOligo, dna);
for (;;)
{
char *oneMatch = NULL;
if (rMatch == NULL)
{
if (fMatch == NULL)
break;
else
{
oneMatch = fMatch;
fMatch = finder(fOligo, fMatch+1);
strand = '+';
}
}
else if (fMatch == NULL)
{
oneMatch = rMatch;
rMatch = finder(rOligo, rMatch+1);
strand = '-';
}
else if (rMatch < fMatch)
{
oneMatch = rMatch;
rMatch = finder(rOligo, rMatch+1);
strand = '-';
}
else
{
oneMatch = fMatch;
fMatch = finder(fOligo, fMatch+1);
strand = '+';
}
if (count < maxCount)
{
++count;
AllocVar(bed);
bed->chromStart = winStart + (oneMatch - dna);
bed->chromEnd = bed->chromStart + oligoSize;
bed->strand[0] = strand;
slAddHead(&bedList, bed);
}
else
break;
}
slReverse(&bedList);
if (count < maxCount)
tg->items = bedList;
else
warn("More than %d items in %s, suppressing display", maxCount, tg->shortLabel);
}
}
struct track *oligoMatchTg()
/* Make track of perfect matches to oligomer. */
{
struct track *tg = trackNew();
char *oligo = oligoMatchSeq();
int oligoSize = strlen(oligo);
char *medOligo = cloneString(oligo);
static char longLabel[80];
struct trackDb *tdb;
/* Generate abbreviated strings. */
if (oligoSize >= 30)
{
memset(medOligo + 30-3, '.', 3);
medOligo[30] = 0;
}
touppers(medOligo);
bedMethods(tg);
tg->track = "oligoMatch";
tg->table = tg->track;
tg->canPack = TRUE;
tg->visibility = tvHide;
tg->hasUi = TRUE;
tg->shortLabel = cloneString(OLIGO_MATCH_TRACK_LABEL);
safef(longLabel, sizeof(longLabel),
"Perfect Matches to Short Sequence (%s)", medOligo);
tg->longLabel = longLabel;
tg->loadItems = oligoMatchLoad;
tg->itemName = oligoMatchName;
tg->mapItemName = oligoMatchName;
tg->priority = OLIGO_MATCH_TRACK_PRIORITY;
tg->defaultPriority = tg->priority;
tg->groupName = "map";
tg->defaultGroupName = cloneString(tg->groupName);
AllocVar(tdb);
tdb->track = cloneString(tg->track);
tdb->table = cloneString(tg->table);
tdb->visibility = tg->visibility;
tdb->shortLabel = cloneString(tg->shortLabel);
tdb->longLabel = cloneString(tg->longLabel);
tdb->grp = cloneString(tg->groupName);
tdb->priority = tg->priority;
tdb->canPack = tg->canPack;
trackDbPolish(tdb);
tg->tdb = tdb;
return tg;
}
static int doLeftLabels(struct track *track, struct hvGfx *hvg, MgFont *font,
int y)
/* Draw left labels. Return y coord. */
{
struct slList *prev = NULL;
/* for sample tracks */
double minRangeCutoff, maxRangeCutoff;
double minRange, maxRange;
double min0, max0;
char minRangeStr[32];
char maxRangeStr[32];
int ymin, ymax;
-int start;
int newy;
char o4[256];
char o5[256];
struct slList *item;
enum trackVisibility vis = track->limitedVis;
enum trackVisibility savedVis = vis;
Color labelColor = (track->labelColor ?
track->labelColor : track->ixColor);
int fontHeight = mgFontLineHeight(font);
int tHeight = trackPlusLabelHeight(track, fontHeight);
if (vis == tvHide)
return y;
/* if a track can do its own left labels, do them after drawItems */
if (track->drawLeftLabels != NULL)
return y + tHeight;
/* Wiggle tracks depend upon clipping. They are reporting
* totalHeight artifically high by 1 so this will leave a
* blank area one pixel high below the track.
*/
if (sameString("wig",track->tdb->type) || sameString("bedGraph",track->tdb->type))
hvGfxSetClip(hvg, leftLabelX, y, leftLabelWidth, tHeight-1);
else
hvGfxSetClip(hvg, leftLabelX, y, leftLabelWidth, tHeight);
minRange = 0.0;
safef( o4, sizeof(o4),"%s.min.cutoff", track->track);
safef( o5, sizeof(o5),"%s.max.cutoff", track->track);
minRangeCutoff = max( atof(cartUsualString(cart,o4,"0.0"))-0.1,
track->minRange );
maxRangeCutoff = min( atof(cartUsualString(cart,o5,"1000.0"))+0.1,
track->maxRange);
if( sameString( track->table, "humMusL" ) ||
sameString( track->table, "musHumL" ) ||
sameString( track->table, "mm3Rn2L" ) ||
sameString( track->table, "hg15Mm3L" ) ||
sameString( track->table, "mm3Hg15L" ) ||
sameString( track->table, "regpotent" ) ||
sameString( track->table, "HMRConservation" ) )
{
int binCount = round(1.0/track->scaleRange);
minRange = whichSampleBin( minRangeCutoff, track->minRange, track->maxRange, binCount );
maxRange = whichSampleBin( maxRangeCutoff, track->minRange, track->maxRange, binCount );
min0 = whichSampleNum( minRange, track->minRange,track->maxRange, binCount );
max0 = whichSampleNum( maxRange, track->minRange, track->maxRange, binCount );
sprintf( minRangeStr, " " );
sprintf( maxRangeStr, " " );
if( vis == tvFull && track->heightPer >= 74 )
{
samplePrintYAxisLabel( hvg, y+5, track, "1.0", min0, max0 );
samplePrintYAxisLabel( hvg, y+5, track, "2.0", min0, max0 );
samplePrintYAxisLabel( hvg, y+5, track, "3.0", min0, max0 );
samplePrintYAxisLabel( hvg, y+5, track, "4.0", min0, max0 );
samplePrintYAxisLabel( hvg, y+5, track, "5.0", min0, max0 );
samplePrintYAxisLabel( hvg, y+5, track, "6.0", min0, max0 );
}
}
else
{
sprintf( minRangeStr, "%d", (int)round(minRangeCutoff));
sprintf( maxRangeStr, "%d", (int)round(maxRangeCutoff));
}
/* special label handling for wigMaf type tracks -- they
display a left label in pack mode. To use the full mode
labeling, temporarily set visibility to full.
Restore savedVis later */
-if (startsWith("wigMaf", track->tdb->type) || startsWith("maf", track->tdb->type))
+if (startsWith("bigMaf", track->tdb->type) || startsWith("wigMaf", track->tdb->type) || startsWith("maf", track->tdb->type))
vis = tvFull;
switch (vis)
{
case tvHide:
break; /* Do nothing; */
case tvPack:
case tvSquish:
y += tHeight;
break;
case tvFull:
if (isCenterLabelIncluded(track))
y += fontHeight;
- start = 1;
if( track->subType == lfSubSample && track->items == NULL )
y += track->height;
for (item = track->items; item != NULL; item = item->next)
{
char *rootName;
char *name = track->itemName(track, item);
int itemHeight = track->itemHeight(track, item);
+ //warn(" track %s, itemHeight %d\n", track->shortLabel, itemHeight);
newy = y;
if (track->itemLabelColor != NULL)
labelColor = track->itemLabelColor(track, item, hvg);
/* Do some fancy stuff for sample tracks.
* Draw y-value limits for 'sample' tracks. */
if (track->subType == lfSubSample )
{
if( prev == NULL )
newy += itemHeight;
else
newy += sampleUpdateY(name,
track->itemName(track, prev), itemHeight);
if( newy == y )
continue;
if( track->heightPer > (3 * fontHeight ) )
{
ymax = y - (track->heightPer / 2) + (fontHeight / 2);
ymin = y + (track->heightPer / 2) - (fontHeight / 2);
hvGfxTextRight(hvg, leftLabelX, ymin, leftLabelWidth-1,
itemHeight, track->ixAltColor,
font, minRangeStr );
hvGfxTextRight(hvg, leftLabelX, ymax, leftLabelWidth-1,
itemHeight, track->ixAltColor,
font, maxRangeStr );
}
prev = item;
rootName = cloneString( name );
beforeFirstPeriod( rootName );
if( sameString( track->table, "humMusL" ) ||
sameString( track->table, "hg15Mm3L" ))
hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1,
itemHeight, track->ixColor, font, "Mouse Cons");
else if( sameString( track->table, "musHumL" ) ||
sameString( track->table, "mm3Hg15L"))
hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1,
itemHeight, track->ixColor, font, "Human Cons");
else if( sameString( track->table, "mm3Rn2L" ))
hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1,
itemHeight, track->ixColor, font, "Rat Cons");
else
hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1,
itemHeight, track->ixColor, font, rootName );
freeMem( rootName );
- start = 0;
y = newy;
}
else
{
/* standard item labeling */
if (highlightItem(track, item))
{
int nameWidth = mgFontStringWidth(font, name);
int boxStart = leftLabelX + leftLabelWidth - 2 - nameWidth;
hvGfxBox(hvg, boxStart, y, nameWidth+1, itemHeight - 1,
labelColor);
hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth-1,
itemHeight, MG_WHITE, font, name);
}
else
hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1,
itemHeight, labelColor, font, name);
y += itemHeight;
}
}
break;
case tvDense:
if (isCenterLabelIncluded(track))
y += fontHeight;
/*draw y-value limits for 'sample' tracks.
* (always puts 0-100% range)*/
if (track->subType == lfSubSample && track->heightPer > (3 * fontHeight))
{
ymax = y - (track->heightPer / 2) + (fontHeight / 2);
ymin = y + (track->heightPer / 2) - (fontHeight / 2);
hvGfxTextRight(hvg, leftLabelX, ymin,
leftLabelWidth-1, track->lineHeight,
track->ixAltColor, font, minRangeStr );
hvGfxTextRight(hvg, leftLabelX, ymax,
leftLabelWidth-1, track->lineHeight,
track->ixAltColor, font, maxRangeStr );
}
hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth-1,
track->lineHeight, labelColor, font,
track->shortLabel);
y += track->height;
break;
}
/* NOTE: might want to just restore savedVis here for all track types,
but I'm being cautious... */
if (sameString(track->tdb->type, "wigMaf"))
vis = savedVis;
hvGfxUnclip(hvg);
return y;
}
static void doLabelNextItemButtons(struct track *track, struct track *parentTrack,
struct hvGfx *hvg, MgFont *font, int y,
int trackPastTabX, int trackPastTabWidth, int fontHeight,
int insideHeight, Color labelColor)
/* If the track allows label next-item buttons (next gene), draw them. */
/* The button will cause hgTracks to run again with the additional CGI */
/* vars nextItem=trackName or prevItem=trackName, which will then */
/* signal the browser to find the next thing on the track before it */
/* does anything else. */
{
int portWidth = insideWidth;
int portX = insideX;
// If a portal was established, then set the portal dimensions
int portalStart,chromStart;
double basesPerPixel;
if (theImgBox
&& imgBoxPortalDimensions(theImgBox,&chromStart,NULL,NULL,NULL,&portalStart,NULL,
&portWidth,&basesPerPixel))
{
portX = (int)((portalStart - chromStart) / basesPerPixel);
portX += gfxBorder;
if (withLeftLabels)
portX += tl.leftLabelWidth + gfxBorder;
portWidth = portWidth-gfxBorder-insideX;
}
int arrowWidth = insideHeight;
int arrowButtonWidth = arrowWidth + 2 * NEXT_ITEM_ARROW_BUFFER;
int rightButtonX = portX + portWidth - arrowButtonWidth - 1;
char buttonText[256];
Color fillColor = lightGrayIndex();
labelColor = blackIndex();
hvGfxNextItemButton(hvg, rightButtonX + NEXT_ITEM_ARROW_BUFFER, y, arrowWidth, arrowWidth,
labelColor, fillColor, TRUE);
hvGfxNextItemButton(hvg, portX + NEXT_ITEM_ARROW_BUFFER, y, arrowWidth, arrowWidth,
labelColor, fillColor, FALSE);
safef(buttonText, ArraySize(buttonText), "hgt.prevItem=%s", track->track);
mapBoxReinvoke(hvg, portX, y + 1, arrowButtonWidth, insideHeight, track, FALSE,
NULL, 0, 0, (revCmplDisp ? "Next item" : "Prev item"), buttonText);
#ifdef IMAGEv2_SHORT_TOGGLE
char *label = (theImgBox ? track->longLabel : parentTrack->longLabel);
int width = portWidth - (2 * arrowButtonWidth);
int x = portX + arrowButtonWidth;
// make toggle cover only actual label
int size = mgFontStringWidth(font,label) + 12; // get close enough to the label
if (width > size)
{
x += width/2 - size/2;
width = size;
}
mapBoxToggleVis(hvg, x, y + 1, width, insideHeight, (theImgBox ? track : parentTrack));
#else///ifndef IMAGEv2_SHORT_TOGGLE
mapBoxToggleVis(hvg, portX + arrowButtonWidth, y + 1, portWidth - (2 * arrowButtonWidth),
insideHeight, (theImgBox ? track : parentTrack));
#endif///ndef IMAGEv2_SHORT_TOGGLE
safef(buttonText, ArraySize(buttonText), "hgt.nextItem=%s", track->track);
mapBoxReinvoke(hvg, portX + portWidth - arrowButtonWidth, y + 1, arrowButtonWidth, insideHeight,
track, FALSE, NULL, 0, 0, (revCmplDisp ? "Prev item" : "Next item"), buttonText);
}
static int doCenterLabels(struct track *track, struct track *parentTrack,
struct hvGfx *hvg, MgFont *font, int y)
/* Draw center labels. Return y coord */
{
if (track->limitedVis != tvHide)
{
if (isCenterLabelIncluded(track))
{
int trackPastTabX = (withLeftLabels ? trackTabWidth : 0);
int trackPastTabWidth = tl.picWidth - trackPastTabX;
int fontHeight = mgFontLineHeight(font);
int insideHeight = fontHeight-1;
boolean toggleDone = FALSE;
char *label = track->longLabel;
Color labelColor = (track->labelColor ?
track->labelColor : track->ixColor);
if (isCenterLabelConditional(track))
{
struct trackDb* tdbComposite = tdbGetComposite(track->tdb);
if (tdbComposite != NULL)
{
label = tdbComposite->longLabel;
labelColor = hvGfxFindColorIx(hvg, tdbComposite->colorR,
tdbComposite->colorG, tdbComposite->colorB);
}
}
hvGfxTextCentered(hvg, insideX, y+1, insideWidth, insideHeight,
labelColor, font, label);
if (track->nextItemButtonable && track->nextPrevItem && !tdbIsComposite(track->tdb))
{
if (withNextItemArrows || trackDbSettingOn(track->tdb, "nextItemButton"))
{
doLabelNextItemButtons(track, parentTrack, hvg, font, y, trackPastTabX,
trackPastTabWidth, fontHeight, insideHeight, labelColor);
toggleDone = TRUE;
}
}
if (!toggleDone)
{
#ifdef IMAGEv2_SHORT_TOGGLE
// make toggle cover only actual label
int size = mgFontStringWidth(font,label) + 12; // get close enough to the label
if (trackPastTabWidth > size)
{
trackPastTabX = insideX + insideWidth/2 - size/2;
trackPastTabWidth = size;
}
#endif///def IMAGEv2_SHORT_TOGGLE
mapBoxToggleVis(hvg, trackPastTabX, y+1,trackPastTabWidth, insideHeight,
(theImgBox ? track : parentTrack));
}
y += fontHeight;
}
y += track->totalHeight(track, track->limitedVis);
}
return y;
}
static int doDrawItems(struct track *track, struct hvGfx *hvg, MgFont *font,
int y, long *lastTime)
/* Draw track items. Return y coord */
{
int fontHeight = mgFontLineHeight(font);
int pixWidth = tl.picWidth;
if (isCenterLabelIncluded(track))
y += fontHeight;
if (track->limitedVis == tvPack)
{
hvGfxSetClip(hvg, gfxBorder+trackTabWidth+1, y,
pixWidth-2*gfxBorder-trackTabWidth-1, track->height);
}
else
hvGfxSetClip(hvg, insideX, y, insideWidth, track->height);
track->drawItems(track, winStart, winEnd, hvg, insideX, y, insideWidth,
font, track->ixColor, track->limitedVis);
if (measureTiming && lastTime)
{
long thisTime = clock1000();
track->drawTime = thisTime - *lastTime;
*lastTime = thisTime;
}
hvGfxUnclip(hvg);
y += track->totalHeight(track, track->limitedVis);
return y;
}
static int doMapItems(struct track *track, struct hvGfx *hvg, int fontHeight, int y)
/* Draw map boxes around track items */
{
char *type = track->tdb->type;
int newy;
int trackPastTabX = (withLeftLabels ? trackTabWidth : 0);
int trackPastTabWidth = tl.picWidth - trackPastTabX;
int start = 1;
struct slList *item;
boolean isWig = (sameString("wig", type) || startsWith("wig ", type) ||
startsWith("bedGraph", type));
if (isCenterLabelIncluded(track))
y += fontHeight;
if (track->mapsSelf)
{
return y+track->height;
}
if (track->subType == lfSubSample && track->items == NULL)
y += track->lineHeight;
/* override doMapItems for hapmapLd track */
/* does not scale with subtracks right now, so this is commented out until it can be fixed
if (startsWith("hapmapLd",track->table))
{
y += round((double)(scaleForPixels(insideWidth)*insideWidth/2));
return y;
}
*/
for (item = track->items; item != NULL; item = item->next)
{
int height = track->itemHeight(track, item);
/*wiggle tracks don't always increment height (y-value) here*/
if( track->subType == lfSubSample )
{
newy = y;
if( !start && item->next != NULL )
{
newy += sampleUpdateY( track->itemName(track, item),
track->itemName(track, item->next),
height );
}
else if( item->next != NULL || start )
newy += height;
start = 0;
y = newy;
}
else
{
if (track->mapItem == NULL)
track->mapItem = genericMapItem;
if (!track->mapsSelf)
{
track->mapItem(track, hvg, item, track->itemName(track, item),
track->mapItemName(track, item),
track->itemStart(track, item),
track->itemEnd(track, item), trackPastTabX,
y, trackPastTabWidth,height);
}
y += height;
}
}
/* Wiggle track's ->height is actually one less than what it returns from
* totalHeight()... I think the least disruptive way to account for this
* (and not touch Ryan Weber's Sample stuff) is to just correct here if
* we see wiggle or bedGraph: */
if (isWig)
y++;
return y;
}
static int doOwnLeftLabels(struct track *track, struct hvGfx *hvg,
MgFont *font, int y)
/* Track draws it own, custom left labels */
{
int fontHeight = mgFontLineHeight(font);
int tHeight = trackPlusLabelHeight(track, fontHeight);
Color labelColor = (track->labelColor ? track->labelColor : track->ixColor);
hvGfxSetClip(hvg, leftLabelX, y, leftLabelWidth, tHeight);
track->drawLeftLabels(track, winStart, winEnd,
hvg, leftLabelX, y, leftLabelWidth, tHeight,
isCenterLabelIncluded(track), font, labelColor,
track->limitedVis);
hvGfxUnclip(hvg);
y += tHeight;
return y;
}
// defined below:
static int getMaxWindowToDraw(struct trackDb *tdb);
int doTrackMap(struct track *track, struct hvGfx *hvg, int y, int fontHeight,
int trackPastTabX, int trackPastTabWidth)
/* Write out the map for this track. Return the new offset. */
{
int mapHeight = 0;
switch (track->limitedVis)
{
case tvPack:
case tvSquish:
y += trackPlusLabelHeight(track, fontHeight);
break;
case tvFull:
if (!nextItemCompatible(track))
{
if (trackIsCompositeWithSubtracks(track)) // TODO: Change when tracks->subtracks
{ // are always set for composite
if (isCenterLabelIncluded(track))
y += fontHeight;
struct track *subtrack;
for (subtrack = track->subtracks; subtrack != NULL;subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack))
{
if (subtrack->limitedVis == tvFull)
y = doMapItems(subtrack, hvg, fontHeight, y);
else
{
if (isCenterLabelIncluded(subtrack))
y += fontHeight;
if (theImgBox && subtrack->limitedVis == tvDense)
mapBoxToggleVis(hvg, trackPastTabX, y, trackPastTabWidth,
track->lineHeight, subtrack);
y += subtrack->totalHeight(subtrack, subtrack->limitedVis);
}
}
}
}
else
y = doMapItems(track, hvg, fontHeight, y);
}
else
y += trackPlusLabelHeight(track, fontHeight);
break;
case tvDense:
if (isCenterLabelIncluded(track))
y += fontHeight;
if (tdbIsComposite(track->tdb))
mapHeight = track->height;
else
mapHeight = track->lineHeight;
int maxWinToDraw = getMaxWindowToDraw(track->tdb);
if (maxWinToDraw <= 1 || (winEnd - winStart) <= maxWinToDraw)
mapBoxToggleVis(hvg, trackPastTabX, y, trackPastTabWidth, mapHeight, track);
y += mapHeight;
break;
case tvHide:
default:
break; /* Do nothing; */
}
return y;
}
int computeScaleBar(int numBases, char scaleText[], int scaleTextSize)
/* Do some scalebar calculations and return the number of bases the scalebar will span. */
{
char *baseWord = "bases";
int scaleBases = 0;
int scaleBasesTextNum = 0;
int numFigs = (int)log10(numBases);
int frontNum = (int)(numBases/pow(10,numFigs));
if (frontNum == 1)
{
numFigs--;
scaleBases = 5 * pow(10, numFigs);
scaleBasesTextNum = 5 * pow(10, numFigs % 3);
}
else if ((frontNum > 1) && (frontNum <= 4))
{
scaleBases = pow(10, numFigs);
scaleBasesTextNum = pow(10, numFigs % 3);
}
else if (frontNum > 4)
{
scaleBases = 2 * pow(10, numFigs);
scaleBasesTextNum = 2 * pow(10, numFigs % 3);
}
if ((numFigs >= 3) && (numFigs < 6))
baseWord = "kb";
else if ((numFigs >= 6) && (numFigs < 9))
baseWord = "Mb";
safef(scaleText, scaleTextSize, "%d %s", scaleBasesTextNum, baseWord);
return scaleBases;
}
enum trackVisibility limitedVisFromComposite(struct track *subtrack)
/* returns the subtrack visibility which may be limited by composite with multi-view dropdowns. */
{
if (tdbIsCompositeChild(subtrack->tdb))
{
if (!subtrack->limitedVisSet)
{
subtrack->visibility = tdbVisLimitedByAncestors(cart, subtrack->tdb, TRUE, TRUE);
limitVisibility(subtrack);
}
}
else
limitVisibility(subtrack);
return subtrack->limitedVis;
}
static int makeRulerZoomBoxes(struct hvGfx *hvg, struct cart *cart, int winStart,int winEnd,
int insideWidth,int seqBaseCount,int rulerClickY,
int rulerClickHeight)
/* Make hit boxes that will zoom program around ruler. */
{
int boxes = 30;
int winWidth = winEnd - winStart;
int newWinWidth = winWidth;
-int i, ws, we = 0, ps, pe = 0;
+int i, ws, we = 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_100X))
newWinWidth = winWidth/100;
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;
}
}
return newWinWidth;
}
static int doDrawRuler(struct hvGfx *hvg,int *newWinWidth,int *rulerClickHeight,
int rulerHeight, int yAfterRuler, int yAfterBases, MgFont *font,
int fontHeight,boolean rulerCds)
/* draws the ruler. */
{
int scaleBarPad = 2;
int scaleBarHeight = fontHeight;
int scaleBarTotalHeight = fontHeight + 2 * scaleBarPad;
int titleHeight = fontHeight;
int baseHeight = fontHeight;
//int yAfterBases = yAfterRuler;
int showPosHeight = fontHeight;
int codonHeight = fontHeight;
struct dnaSeq *seq = NULL;
int rulerClickY = 0;
*rulerClickHeight = rulerHeight;
int y = rulerClickY;
hvGfxSetClip(hvg, insideX, y, insideWidth, yAfterRuler-y+1);
int relNumOff = winStart;
if (baseTitle)
{
hvGfxTextCentered(hvg, insideX, y, insideWidth, titleHeight,MG_BLACK, font, baseTitle);
*rulerClickHeight += titleHeight;
y += titleHeight;
}
if (baseShowPos||baseShowAsm)
{
char txt[256];
char numBuf[SMALLBUF];
char *freezeName = NULL;
freezeName = hFreezeFromDb(database);
sprintLongWithCommas(numBuf, winEnd-winStart);
if (freezeName == NULL)
freezeName = cloneString("Unknown");
if (baseShowPos&&baseShowAsm)
safef(txt,sizeof(txt),"%s %s %s (%s bp)",trackHubSkipHubName(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",trackHubSkipHubName(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);
if(cartUsualBoolean(cart, BASE_SHOWASM_SCALEBAR, TRUE))
{
int fHeight = vgGetFontPixelHeight(hvg->vg, font);
hvGfxText(hvg, scaleBarEndX + 10,
y + (scaleBarTotalHeight - fHeight)/2 + ((font == mgSmallFont()) ? 1 : 0),
MG_BLACK, font, trackHubSkipHubName(database));
}
y += scaleBarTotalHeight;
}
if (baseShowRuler)
{
hvGfxDrawRulerBumpText(hvg, insideX, y, rulerHeight, insideWidth, MG_BLACK,
font, relNumOff, winBaseCount, 0, 1);
}
*newWinWidth = makeRulerZoomBoxes(hvg, cart,winStart,winEnd,insideWidth,seqBaseCount,
rulerClickY,*rulerClickHeight);
if (zoomedToBaseLevel || rulerCds)
{
Color baseColor = MG_BLACK;
int start, end, chromSize;
struct dnaSeq *extraSeq;
/* extraSeq has extra leading & trailing bases
* for translation in to amino acids */
boolean complementRulerBases = cartUsualBooleanDb(cart, database, COMPLEMENT_BASES_VAR, FALSE);
// gray bases if not matching the direction of display
if (complementRulerBases != revCmplDisp)
baseColor = MG_GRAY;
/* get sequence, with leading & trailing 3 bases
* used for amino acid translation */
start = max(winStart - 3, 0);
chromSize = hChromSize(database, chromName);
end = min(winEnd + 3, chromSize);
extraSeq = hDnaFromSeq(database, chromName, start, end, dnaUpper);
if (start != winStart - 3 || end != winEnd + 3)
{
/* at chromosome boundaries, pad with N's to assure
* leading & trailing 3 bases */
char header[4] = "NNN", trailer[4] = "NNN";
int size = winEnd - winStart + 6;
char *padded = (char *)needMem(size+1);
header[max(3 - winStart, 0)] = 0;
trailer[max(winEnd - chromSize + 3, 0)] = 0;
safef(padded, size+1, "%s%s%s", header, extraSeq->dna, trailer);
extraSeq = newDnaSeq(padded, strlen(padded), extraSeq->name);
}
/* for drawing bases, must clip off leading and trailing 3 bases */
seq = cloneDnaSeq(extraSeq);
seq = newDnaSeq(seq->dna+3, seq->size-6, seq->name);
if (zoomedToBaseLevel)
drawBases(hvg, insideX, y+rulerHeight, insideWidth, baseHeight,
baseColor, font, complementRulerBases, seq);
/* set up clickable area to toggle ruler visibility */
{
char newRulerVis[100];
safef(newRulerVis, 100, "%s=%s", RULER_TRACK_NAME,
rulerMode == tvFull ? rulerMenu[tvDense] : rulerMenu[tvFull]);
mapBoxReinvoke(hvg, insideX, y+rulerHeight, insideWidth,baseHeight, NULL,
FALSE, NULL, 0, 0, "", newRulerVis);
}
if (rulerCds)
{
/* display codons */
int frame;
int firstFrame = 0;
int mod; // for determining frame ordering on display
struct simpleFeature *sfList;
double scale = scaleForWindow(insideWidth, winStart, winEnd);
/* WARNING: tricky code to assure that an amino acid
* stays in the same frame line on the browser during panning.
* There may be a simpler way... */
if (complementRulerBases)
mod = (chromSize - winEnd) % 3;
else
mod = winStart % 3;
if (mod == 0)
firstFrame = 0;
else if (mod == 1)
firstFrame = 2;
else if (mod == 2)
firstFrame = 1;
y = yAfterBases;
if (complementRulerBases)
reverseComplement(extraSeq->dna, extraSeq->size);
for (frame = 0; frame < 3; frame++, y += codonHeight)
{
/* reference frame to start of chromosome */
int refFrame = (firstFrame + frame) % 3;
/* create list of codons in the specified coding frame */
sfList = baseColorCodonsFromDna(refFrame, winStart, winEnd,
extraSeq, complementRulerBases);
/* draw the codons in the list, with alternating colors */
baseColorDrawRulerCodons(hvg, sfList, scale, insideX, y,
codonHeight, font, winStart, MAXPIXELS,
zoomedToCodonLevel);
}
}
}
hvGfxUnclip(hvg);
return y;
}
static void logTrackList(struct dyString *dy, struct track *trackList)
/* add visibile tracks to dyString, recursively called */
{
if (trackList == NULL)
return;
struct track *track;
for (track = trackList; track != NULL; track = track->next)
{
int vis = track->limitedVisSet ? track->limitedVis : track->visibility;
if (vis)
{
logTrackList(dy, track->subtracks);
if (dy->stringSize)
dyStringAppendC(dy, ',');
dyStringPrintf(dy,"%s:%d", track->track, vis);
}
}
}
static void logTrackVisibilities (char *hgsid, struct track *trackList)
/* log visibile tracks and hgsid */
{
struct dyString *dy = newDyString(1024);
// build up dyString
logTrackList(dy, trackList);
// put out ~1024 bye blocks to error_log because otherwise
// Apache will chop up the lines
char *begin = dy->string;
char *ptr = begin;
int count = 0;
for(ptr=begin; ((ptr = strchr(ptr, ',')) != NULL); ptr++)
{
if (ptr - begin > 800)
{
*ptr = 0;
fprintf(stderr, "trackLog %d %s %s %s\n", count++, database, hgsid, begin);
begin = ptr+1;
}
}
fprintf(stderr, "trackLog %d %s %s %s\n", count++, database, hgsid, begin);
dyStringFree(&dy);
}
static void rAddToTrackHash(struct hash *trackHash, struct track *trackList)
/* Add list and any children of list to hash. */
{
struct track *track;
for (track = trackList; track != NULL; track = track->next)
{
hashAddUnique(trackHash, track->track, track);
rAddToTrackHash(trackHash, track->subtracks);
}
}
void highlightRegion(struct cart *cart, struct hvGfx *hvg, int insideX, int imagePixelHeight,
int winStart, int winEnd)
// Highlights a region in the image. Only done if theImgBox is not defined.
// Thus it is done for ps/pdf and view image but the hgTracks image is highlighted via js
{
char *highlightDef = cartOptionalString(cart, "highlight");
if(highlightDef && theImgBox == NULL) // Only highlight region when imgBox is not used.
{
// expect db.chrom:start-end#hexColor
char *db = cloneNextWordByDelimiter(&highlightDef,'.');
char *chrom = cloneNextWordByDelimiter(&highlightDef,':');
int chromStart = atoi(cloneNextWordByDelimiter(&highlightDef,'-'));
int chromEnd = atoi(cloneNextWordByDelimiter(&highlightDef,'#'));
if ((db != NULL && sameString(db, database ))
&& (chrom != NULL && sameString(chrom,chromName))
&& (chromEnd != 0)
&& (chromStart <= winEnd && chromEnd >= winStart))
{
chromStart--; // Not zero based
chromStart = max(chromStart, winStart);
chromEnd = min(chromEnd, winEnd);
double pixelsPerBase = scaleForPixels(insideWidth + 1);
int startPixels = pixelsPerBase * (chromStart - winStart); // floor
if (startPixels < 0)
startPixels *= -1; // reverse complement
int width = pixelsPerBase * (double)(chromEnd - chromStart) + 0.5; // round up
if (width < 2)
width = 2;
// Default color to light blue, but if setting has color, use it.
unsigned int hexColor = MAKECOLOR_32(170, 255, 255);
if (highlightDef != NULL && *highlightDef != '\0')
{
long rgb = strtol(highlightDef,NULL,16); // Big and little Endians
hexColor = MAKECOLOR_32( ((rgb>>16)&0xff), ((rgb>>8)&0xff), (rgb&0xff) );
}
hvGfxBox(hvg, insideX + startPixels, 0, width, imagePixelHeight,hexColor);
}
}
}
struct hash *makeGlobalTrackHash(struct track *trackList)
/* Create a global track hash and returns a pointer to it. */
{
trackHash = newHash(8);
rAddToTrackHash(trackHash, trackList);
return trackHash;
}
//void domAddMenu(char *afterMenuId, char *newMenuId, char *label)
///* Append a new drop down menu after a given menu, by changing the DOM with jquery */
//{
//printf("$('#%s').last().after('<li class=\"menuparent\" id=\"%s\"><span>%s</span>"
// "<ul style=\"display: none; visibility: hidden;\"></ul></li>');\n",
// afterMenuId, newMenuId, label);
//}
//
//void domAppendToMenu(char *menuId, char *url, char *label)
///* Add an entry to a drop down menu, by changing the DOM with jquery */
//{
////printf("$('#%s ul').last().after('<li><a target=\"_BLANK\" href=\"%s\">%s</a></li>');\n", menuId, url, label);
//printf("$('#%s ul').append('<li><a target=\"_BLANK\" href=\"%s\">%s</a></li>');\n", menuId, url, label);
//}
//void menuBarAppendExtTools()
///* printf a little javascript that adds entries to a menu */
//{
// char url[SMALLBUF];
// safef(url,ArraySize(url),"hgTracks?%s=%s&hgt.redirectTool=crispor",cartSessionVarName(), cartSessionId(cart));
// printf("<script>\n");
// printf("jQuery(document).ready( function() {\n");
// domAddMenu("view", "sendto", "Send to");
// domAppendToMenu("sendto", url, "Tefor CRISPR sites");
// printf("});\n");
// printf("</script>\n");
//}
void makeActiveImage(struct track *trackList, char *psOutput)
/* Make image and image map. */
{
struct track *track;
MgFont *font = tl.font;
struct hvGfx *hvg;
struct tempName pngTn;
char *mapName = "map";
int fontHeight = mgFontLineHeight(font);
int trackPastTabX = (withLeftLabels ? trackTabWidth : 0);
int trackTabX = gfxBorder;
int trackPastTabWidth = tl.picWidth - trackPastTabX;
int pixWidth, pixHeight;
int y=0;
int titleHeight = fontHeight;
int scaleBarPad = 2;
int scaleBarHeight = fontHeight;
int scaleBarTotalHeight = fontHeight + 2 * scaleBarPad;
int showPosHeight = fontHeight;
int rulerHeight = fontHeight;
int baseHeight = fontHeight;
int basePositionHeight = rulerHeight;
int codonHeight = fontHeight;
int rulerTranslationHeight = codonHeight * 3; // 3 frames
int yAfterRuler = gfxBorder;
int yAfterBases = yAfterRuler; // differs if base-level translation shown
boolean rulerCds = zoomedToCdsColorLevel;
int rulerClickHeight = 0;
int newWinWidth = 0;
/* Figure out dimensions and allocate drawing space. */
pixWidth = tl.picWidth;
leftLabelX = gfxBorder;
leftLabelWidth = insideX - gfxBorder*3;
struct image *theOneImg = NULL; // No need to be global, only the map needs to be global
struct image *theSideImg = NULL; // Because dragScroll drags off end of image,
// the side label gets seen. Therefore we need 2 images!!
//struct imgTrack *curImgTrack = NULL; // Make this global for now to avoid huge rewrite
struct imgSlice *curSlice = NULL; // No need to be global, only the map needs to be global
struct mapSet *curMap = NULL; // Make this global for now to avoid huge rewrite
+
// Set up imgBox dimensions
int sliceWidth[stMaxSliceTypes]; // Just being explicit
int sliceOffsetX[stMaxSliceTypes];
int sliceHeight = 0;
int sliceOffsetY = 0;
char *rulerTtl = NULL;
if (theImgBox)
// theImgBox is a global for now to avoid huge rewrite of hgTracks. It is started
// prior to this in doTrackForm()
{
- rulerTtl = "drag select or click to zoom";
hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
hPrintf("<input type='hidden' name='c' value='%s'>\n", chromName);
hPrintf("<input type='hidden' name='l' value='%d'>\n", winStart);
hPrintf("<input type='hidden' name='r' value='%d'>\n", winEnd);
hPrintf("<input type='hidden' name='pix' value='%d'>\n", tl.picWidth);
// If a portal was established, then set the global dimensions to the entire image size
if (imgBoxPortalDimensions(theImgBox,&winStart,&winEnd,&(tl.picWidth),NULL,NULL,NULL,NULL,NULL))
{
pixWidth = tl.picWidth;
winBaseCount = winEnd - winStart;
insideWidth = tl.picWidth-gfxBorder-insideX;
}
memset((char *)sliceWidth, 0,sizeof(sliceWidth));
memset((char *)sliceOffsetX,0,sizeof(sliceOffsetX));
if (withLeftLabels)
{
sliceWidth[stButton] = trackTabWidth + 1;
sliceWidth[stSide] = leftLabelWidth - sliceWidth[stButton] + 1;
sliceOffsetX[stSide] =
(revCmplDisp ? (tl.picWidth - sliceWidth[stSide] - sliceWidth[stButton])
: sliceWidth[stButton]);
sliceOffsetX[stButton] = (revCmplDisp ? (tl.picWidth - sliceWidth[stButton]) : 0);
}
sliceOffsetX[stData] = (revCmplDisp ? 0 : sliceWidth[stSide] + sliceWidth[stButton]);
sliceWidth[stData] = tl.picWidth - (sliceWidth[stSide] + sliceWidth[stButton]);
}
struct flatTracks *flatTracks = NULL;
struct flatTracks *flatTrack = NULL;
if (rulerMode != tvFull)
{
rulerCds = FALSE;
}
/* Figure out height of each visible track. */
pixHeight = gfxBorder;
if (rulerMode != tvHide)
{
if (!baseShowRuler && !baseTitle && !baseShowPos && !baseShowAsm && !baseShowScaleBar && !zoomedToBaseLevel && !rulerCds)
{
warn("Can't turn everything off in base position track. Turning ruler back on");
baseShowRuler = TRUE;
cartSetBoolean(cart, BASE_SHOWRULER, TRUE);
}
if (baseTitle)
basePositionHeight += titleHeight;
if (baseShowPos||baseShowAsm)
basePositionHeight += showPosHeight;
if (baseShowScaleBar)
basePositionHeight += scaleBarTotalHeight;
if (!baseShowRuler)
{
basePositionHeight -= rulerHeight;
rulerHeight = 0;
}
if (zoomedToBaseLevel)
basePositionHeight += baseHeight;
yAfterRuler += basePositionHeight;
yAfterBases = yAfterRuler;
pixHeight += basePositionHeight;
if (rulerCds)
{
yAfterRuler += rulerTranslationHeight;
pixHeight += rulerTranslationHeight;
}
}
boolean safeHeight = TRUE;
/* firefox on Linux worked almost up to 34,000 at the default 620 width */
#define maxSafeHeight 32000
/* Hash tracks/subtracks, limit visibility and calculate total image height: */
for (track = trackList; track != NULL; track = track->next)
{
if (tdbIsCompositeChild(track->tdb)) // When single track is requested via AJAX,
limitedVisFromComposite(track); // it could be a subtrack
else
limitVisibility(track);
if (!safeHeight)
{
track->limitedVis = tvHide;
track->limitedVisSet = TRUE;
continue;
}
if (tdbIsComposite(track->tdb))
{
struct track *subtrack;
for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (!isSubtrackVisible(subtrack))
continue;
// subtrack vis can be explicit or inherited from composite/view.
// Then it could be limited because of pixel height
limitedVisFromComposite(subtrack);
if (subtrack->limitedVis != tvHide)
{
subtrack->hasUi = track->hasUi;
flatTracksAdd(&flatTracks,subtrack,cart);
}
}
}
else if (track->limitedVis != tvHide)
flatTracksAdd(&flatTracks,track,cart);
}
flatTracksSort(&flatTracks); // Now we should have a perfectly good flat track list!
struct track *prevTrack = NULL;
for (flatTrack = flatTracks,prevTrack=NULL; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
assert(track->limitedVis != tvHide);
int totalHeight = pixHeight+trackPlusLabelHeight(track,fontHeight);
if (maxSafeHeight < totalHeight)
{
char numBuf[SMALLBUF];
sprintLongWithCommas(numBuf, maxSafeHeight);
if (safeHeight) // Only one message
warn("Image is over %s pixels high (%d pix) at the following track which is now "
"hidden:<BR>\"%s\".%s", numBuf, totalHeight, track->tdb->longLabel,
(flatTrack->next != NULL ?
"<BR>Additional tracks may have also been hidden at this zoom level." : ""));
safeHeight = FALSE;
track->limitedVis = tvHide;
track->limitedVisSet = TRUE;
}
if (track->limitedVis != tvHide)
{
track->prevTrack = prevTrack; // Important for keeping track of conditional center labels!
pixHeight += trackPlusLabelHeight(track, fontHeight);
prevTrack = track;
}
}
imagePixelHeight = pixHeight;
if (psOutput)
{
hvg = hvGfxOpenPostScript(pixWidth, pixHeight, psOutput);
hvgSide = hvg; // Always only one image
}
else
{
boolean transparentImage = FALSE;
if (theImgBox!=NULL)
transparentImage = TRUE; // transparent because BG (blue ruler lines) is separate image
if (measureTiming)
measureTime("Time at start of obtaining trash hgt png image file");
trashDirFile(&pngTn, "hgt", "hgt", ".png");
hvg = hvGfxOpenPng(pixWidth, pixHeight, pngTn.forCgi, transparentImage);
if (theImgBox)
{
// Adds one single image for all tracks (COULD: build the track by track images)
theOneImg = imgBoxImageAdd(theImgBox,pngTn.forHtml,NULL,pixWidth, pixHeight,FALSE);
theSideImg = theOneImg; // Unlkess this is overwritten below, there is a single image
}
+
hvgSide = hvg; // Unlkess this is overwritten below, there is a single image
if (theImgBox && theImgBox->showPortal && withLeftLabels)
{
// TODO: It would be great to make the two images smaller,
// but keeping both the same full size for now
struct tempName pngTnSide;
trashDirFile(&pngTnSide, "hgtSide", "side", ".png");
hvgSide = hvGfxOpenPng(pixWidth, pixHeight, pngTnSide.forCgi, transparentImage);
// Also add the side image
theSideImg = imgBoxImageAdd(theImgBox,pngTnSide.forHtml,NULL,pixWidth, pixHeight,FALSE);
hvgSide->rc = revCmplDisp;
initColors(hvgSide);
}
}
hvg->rc = revCmplDisp;
initColors(hvg);
/* Start up client side map. */
hPrintf("<MAP id='map' Name=%s>\n", mapName);
if (theImgBox == NULL) // imageV2 highlighting is done by javascript.
highlightRegion(cart, hvg, insideX, imagePixelHeight, winStart, winEnd);
/* Find colors to draw in. */
findTrackColors(hvg, trackList);
// Good to go ahead and add all imgTracks regardless of buttons, left label, centerLabel, etc.
if (theImgBox)
{
if (rulerMode != tvHide)
{
curImgTrack = imgBoxTrackFindOrAdd(theImgBox,NULL,RULER_TRACK_NAME,rulerMode,FALSE,
IMG_FIXEDPOS); // No tdb, no centerLbl, not reorderable
}
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
if (track->limitedVis != tvHide)
{
if (track->labelColor == track->ixColor && track->ixColor == 0)
track->ixColor = hvGfxFindRgb(hvg, &track->color);
int order = flatTrack->order;
curImgTrack = imgBoxTrackFindOrAdd(theImgBox,track->tdb,NULL,track->limitedVis,
isCenterLabelIncluded(track),order);
if (trackShouldUseAjaxRetrieval(track))
imgTrackMarkForAjaxRetrieval(curImgTrack,TRUE);
}
}
}
/* Draw mini-buttons. */
if (withLeftLabels && psOutput == NULL)
{
int butOff;
boolean grayButtonGroup = FALSE;
struct group *lastGroup = NULL;
y = gfxBorder;
if (rulerMode != tvHide)
{
/* draw button for Base Position pseudo-track */
int height = basePositionHeight;
if (rulerCds)
height += rulerTranslationHeight;
if (theImgBox)
{
// Mini-buttons (side label slice) for ruler
sliceHeight = height + 1;
sliceOffsetY = 0;
curImgTrack = imgBoxTrackFind(theImgBox,NULL,RULER_TRACK_NAME);
curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stButton,NULL,NULL,
sliceWidth[stButton],sliceHeight,
sliceOffsetX[stButton],sliceOffsetY);
}
else if (!trackImgOnly) // Side buttons only need to be drawn when drawing page with js
{ // advanced features off // TODO: Should remove wasted pixels too
drawGrayButtonBox(hvgSide, trackTabX, y, trackTabWidth, height, TRUE);
}
mapBoxTrackUi(hvgSide, trackTabX, y, trackTabWidth, height,
RULER_TRACK_NAME, RULER_TRACK_LABEL, "ruler");
y += height + 1;
}
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
int h, yStart = y, yEnd;
if (track->limitedVis != tvHide)
{
y += trackPlusLabelHeight(track, fontHeight);
yEnd = y;
h = yEnd - yStart - 1;
/* alternate button colors for track groups*/
if (track->group != lastGroup)
grayButtonGroup = !grayButtonGroup;
lastGroup = track->group;
if (theImgBox)
{
// Mini-buttons (side label slice) for tracks
sliceHeight = yEnd - yStart;
sliceOffsetY = yStart - 1;
curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL);
+ //warn("GTEX 2: track %s, sliceHeight=%d\n", track->shortLabel, sliceHeight);
curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stButton,NULL,NULL,
sliceWidth[stButton],sliceHeight,
sliceOffsetX[stButton],sliceOffsetY);
}
else if (!trackImgOnly) // Side buttons only need to be drawn when drawing page
{ // with js advanced features off
if (grayButtonGroup)
drawGrayButtonBox(hvgSide, trackTabX, yStart, trackTabWidth, h, track->hasUi);
else
drawBlueButtonBox(hvgSide, trackTabX, yStart, trackTabWidth, h, track->hasUi);
}
if (track->hasUi)
{
if (tdbIsCompositeChild(track->tdb))
{
struct trackDb *parent = tdbGetComposite(track->tdb);
mapBoxTrackUi(hvgSide, trackTabX, yStart, trackTabWidth, (yEnd - yStart - 1),
parent->track, parent->shortLabel, track->track);
}
else
mapBoxTrackUi(hvgSide, trackTabX, yStart, trackTabWidth, h, track->track,
track->shortLabel, track->track);
}
}
}
butOff = trackTabX + trackTabWidth;
leftLabelX += butOff;
leftLabelWidth -= butOff;
}
if (withLeftLabels)
{
if (theImgBox == NULL)
{
Color lightRed = hvGfxFindColorIx(hvgSide, 255, 180, 180);
hvGfxBox(hvgSide, leftLabelX + leftLabelWidth, 0,
gfxBorder, pixHeight, lightRed);
}
y = gfxBorder;
if (rulerMode != tvHide)
{
if (theImgBox)
{
// side label slice for ruler
sliceHeight = basePositionHeight + (rulerCds ? rulerTranslationHeight : 0) + 1;
sliceOffsetY = 0;
curImgTrack = imgBoxTrackFind(theImgBox,NULL,RULER_TRACK_NAME);
+ //warn("GTEX 3: track %s, sliceHeight=%d\n", track->shortLabel, sliceHeight);
curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL,
sliceWidth[stSide],sliceHeight,
sliceOffsetX[stSide],sliceOffsetY);
curMap = sliceMapFindOrStart(curSlice,RULER_TRACK_NAME,NULL); // No common linkRoot
}
if (baseTitle)
{
hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, titleHeight,
MG_BLACK, font, WIN_TITLE_LABEL);
y += titleHeight;
}
if (baseShowPos||baseShowAsm)
{
hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, showPosHeight,
MG_BLACK, font, WIN_POS_LABEL);
y += showPosHeight;
}
if (baseShowScaleBar)
{
y += scaleBarPad;
hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, scaleBarHeight,
MG_BLACK, font, SCALE_BAR_LABEL);
y += scaleBarHeight + scaleBarPad;
}
if (baseShowRuler)
{
char rulerLabel[SMALLBUF];
char *shortChromName = cloneString(chromName);
safef(rulerLabel,ArraySize(rulerLabel),":%s",shortChromName);
int labelWidth = mgFontStringWidth(font,rulerLabel);
while ((labelWidth > 0) && (labelWidth > leftLabelWidth))
{
int len = strlen(shortChromName);
shortChromName[len-1] = 0;
safef(rulerLabel,ArraySize(rulerLabel),":%s",shortChromName);
labelWidth = mgFontStringWidth(font,rulerLabel);
}
if (hvgSide->rc)
safef(rulerLabel,ArraySize(rulerLabel),":%s",shortChromName);
else
safef(rulerLabel,ArraySize(rulerLabel),"%s:",shortChromName);
hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, rulerHeight,
MG_BLACK, font, rulerLabel);
y += rulerHeight;
freeMem(shortChromName);
}
if (zoomedToBaseLevel || rulerCds)
{
/* disable complement toggle for HIV because HIV is single stranded RNA */
if (!hIsGsidServer())
drawComplementArrow(hvgSide,leftLabelX, y, leftLabelWidth-1, baseHeight, font);
if (zoomedToBaseLevel)
y += baseHeight;
}
if (rulerCds)
y += rulerTranslationHeight;
}
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
if (track->limitedVis == tvHide)
continue;
if (theImgBox)
{
// side label slice for tracks
sliceHeight = trackPlusLabelHeight(track, fontHeight);
sliceOffsetY = y;
curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL);
+ //warn("GTEX 4: track %s, sliceHeight=%d\n", track->shortLabel, sliceHeight);
curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL,
sliceWidth[stSide],sliceHeight,
sliceOffsetX[stSide],sliceOffsetY);
curMap = sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot
}
if (trackShouldUseAjaxRetrieval(track))
y += REMOTE_TRACK_HEIGHT;
else
{
#ifdef IMAGEv2_NO_LEFTLABEL_ON_FULL
if (theImgBox && track->limitedVis != tvDense)
y += sliceHeight;
else
#endif ///def IMAGEv2_NO_LEFTLABEL_ON_FULL
y = doLeftLabels(track, hvgSide, font, y);
}
}
}
else
{
leftLabelX = leftLabelWidth = 0;
}
/* Draw guidelines. */
if (withGuidelines)
{
struct hvGfx *bgImg = hvg; // Default to the one image
boolean exists = FALSE;
if (theImgBox)
{
struct tempName gifBg;
char base[64];
safef(base,sizeof(base),"blueLines%d-%s%d-%d",pixWidth,(revCmplDisp?"r":""),insideX,
guidelineSpacing); // reusable file needs width, leftLabel start and guidelines
exists = trashDirReusableFile(&gifBg, "hgt", base, ".png");
if (exists && cgiVarExists("hgt.reset")) // exists means don't remake bg image. However,
exists = FALSE; // for now, rebuild on "default tracks" request
if (!exists)
{
bgImg = hvGfxOpenPng(pixWidth, pixHeight, gifBg.forCgi, TRUE);
bgImg->rc = revCmplDisp;
}
imgBoxImageAdd(theImgBox,gifBg.forHtml,NULL,pixWidth, pixHeight,TRUE); // Adds BG image
}
if (!exists)
{
int x;
Color lightBlue = hvGfxFindRgb(bgImg, &guidelineColor);
hvGfxSetClip(bgImg, insideX, 0, insideWidth, pixHeight);
y = gfxBorder;
for (x = insideX+guidelineSpacing-1; x<pixWidth; x += guidelineSpacing)
hvGfxBox(bgImg, x, 0, 1, pixHeight, lightBlue);
hvGfxUnclip(bgImg);
if (bgImg != hvg)
hvGfxClose(&bgImg);
}
}
/* Show ruler at top. */
if (rulerMode != tvHide)
{
if (theImgBox)
{
// data slice for ruler
sliceHeight = basePositionHeight + (rulerCds ? rulerTranslationHeight : 0) + 1;
sliceOffsetY = 0;
curImgTrack = imgBoxTrackFind(theImgBox,NULL,RULER_TRACK_NAME);
+ //warn("GTEX 5: track %s, sliceHeight=%d\n", track->shortLabel, sliceHeight);
curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stData,theOneImg,rulerTtl,
sliceWidth[stData],sliceHeight,
sliceOffsetX[stData],sliceOffsetY);
curMap = sliceMapFindOrStart(curSlice,RULER_TRACK_NAME,NULL); // No common linkRoot
}
y = doDrawRuler(hvg,&newWinWidth,&rulerClickHeight,rulerHeight,yAfterRuler,yAfterBases,font,
fontHeight,rulerCds);
}
/* Draw center labels. */
if (withCenterLabels)
{
hvGfxSetClip(hvg, insideX, gfxBorder, insideWidth, pixHeight - 2*gfxBorder);
y = yAfterRuler;
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
if (track->limitedVis == tvHide)
continue;
if (theImgBox)
{
// center label slice of tracks Must always make, even if the centerLabel is empty
sliceHeight = fontHeight;
sliceOffsetY = y;
curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL);
+ //warn("GTEX 6: track %s, sliceHeight=%d\n", track->shortLabel, sliceHeight);
curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stCenter,theOneImg,NULL,
sliceWidth[stData],sliceHeight,
sliceOffsetX[stData],sliceOffsetY);
curMap = sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot
if (isCenterLabelConditional(track))
imgTrackUpdateCenterLabelSeen(curImgTrack,isCenterLabelConditionallySeen(track) ?
clNowSeen : clNotSeen);
}
if (trackShouldUseAjaxRetrieval(track))
y += REMOTE_TRACK_HEIGHT;
else
y = doCenterLabels(track, track, hvg, font, y);
}
hvGfxUnclip(hvg);
}
/* Draw tracks. */
{
long lastTime = 0;
y = yAfterRuler;
if (measureTiming)
lastTime = clock1000();
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
if (track->limitedVis == tvHide)
continue;
int centerLabelHeight = (isCenterLabelIncluded(track) ? fontHeight : 0);
int yStart = y + centerLabelHeight;
int yEnd = y + trackPlusLabelHeight(track, fontHeight);
if (theImgBox)
{
// data slice of tracks
sliceOffsetY = yStart;
sliceHeight = yEnd - yStart - 1;
curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL);
if (sliceHeight > 0)
{
+ //warn("GTEX 7: track %s, sliceHeight=%d\n", track->shortLabel, sliceHeight);
curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stData,theOneImg,NULL,
sliceWidth[stData],sliceHeight,
sliceOffsetX[stData],sliceOffsetY);
curMap = sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot
}
}
if (trackShouldUseAjaxRetrieval(track))
y += REMOTE_TRACK_HEIGHT;
else
y = doDrawItems(track, hvg, font, y, &lastTime);
if (theImgBox && track->limitedVis == tvDense && tdbIsCompositeChild(track->tdb))
mapBoxToggleVis(hvg, 0, yStart,tl.picWidth, sliceHeight,track);
// Strange mapBoxToggleLogic handles reverse complement itself so x=0,width=tl.picWidth
- if (yEnd!=y)
- warn("Slice height does not add up. Expecting %d != %d actual",
- yEnd - yStart - 1,y-yStart);
+ if (yEnd != y)
+ warn("Slice height for track %s does not add up. Expecting %d != %d actual",
+ track->shortLabel, yEnd - yStart - 1, y - yStart);
}
y++;
}
/* if a track can draw its left labels, now is the time since it
* knows what exactly happened during drawItems
*/
if (withLeftLabels)
{
y = yAfterRuler;
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
if (track->limitedVis == tvHide)
continue;
if (theImgBox)
{
// side label slice of tracks
sliceHeight = trackPlusLabelHeight(track, fontHeight);
sliceOffsetY = y;
curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL);
+ //warn("WARN 8: track %s, sliceHeight=%d\n", track->shortLabel, sliceHeight);
curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL,
sliceWidth[stSide],sliceHeight,
sliceOffsetX[stSide],sliceOffsetY);
curMap = sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot
}
if (trackShouldUseAjaxRetrieval(track))
y += REMOTE_TRACK_HEIGHT;
#ifdef IMAGEv2_NO_LEFTLABEL_ON_FULL
else if (track->drawLeftLabels != NULL
&& (theImgBox == NULL || track->limitedVis == tvDense))
#else ///ndef IMAGEv2_NO_LEFTLABEL_ON_FULL
else if (track->drawLeftLabels != NULL)
#endif ///ndef IMAGEv2_NO_LEFTLABEL_ON_FULL
y = doOwnLeftLabels(track, hvgSide, font, y);
else
y += trackPlusLabelHeight(track, fontHeight);
}
}
/* Make map background. */
y = yAfterRuler;
for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next)
{
track = flatTrack->track;
if (track->limitedVis != tvHide)
{
if (theImgBox)
{
// Set imgTrack in case any map items will be set
sliceHeight = trackPlusLabelHeight(track, fontHeight);
sliceOffsetY = y;
curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL);
}
doTrackMap(track, hvg, y, fontHeight, trackPastTabX, trackPastTabWidth);
y += trackPlusLabelHeight(track, fontHeight);
}
}
/* Finish map. */
hPrintf("</MAP>\n");
// turn off inPlaceUpdate when rows in imgTbl can arbitrarily reappear and disappear (see redmine #7306 and #6944)
jsonObjectAdd(jsonForClient, "inPlaceUpdate", newJsonBoolean(withLeftLabels && withCenterLabels));
jsonObjectAdd(jsonForClient, "rulerClickHeight", newJsonNumber(rulerClickHeight));
if(newWinWidth)
{
jsonObjectAdd(jsonForClient, "newWinWidth", newJsonNumber(newWinWidth));
}
/* Save out picture and tell html file about it. */
if (hvgSide != hvg)
hvGfxClose(&hvgSide);
hvGfxClose(&hvg);
if (measureTiming)
measureTime("Time completed writing trash hgt png image file");
#ifdef SUPPORT_CONTENT_TYPE
char *type = cartUsualString(cart, "hgt.contentType", "html");
if(sameString(type, "jsonp"))
{
struct jsonElement *json = newJsonObject(newHash(8));
printf("Content-Type: application/json\n\n");
errAbortSetDoContentType(FALSE);
jsonObjectAdd(json, "track", newJsonString(cartString(cart, "hgt.trackNameFilter")));
jsonObjectAdd(json, "height", newJsonNumber(pixHeight));
jsonObjectAdd(json, "width", newJsonNumber(pixWidth));
jsonObjectAdd(json, "img", newJsonString(pngTn.forHtml));
printf("%s(", cartString(cart, "jsonp"));
hPrintEnable();
jsonPrint((struct jsonElement *) json, NULL, 0);
hPrintDisable();
printf(")\n");
return;
}
else if(sameString(type, "png") || sameString(type, "pdf") || sameString(type, "eps"))
{
// following code bypasses html and return png's directly - see redmine 4888
char *file;
if(sameString(type, "pdf"))
{
printf("Content-Disposition: filename=hgTracks.pdf\nContent-Type: application/pdf\n\n");
file = convertEpsToPdf(psOutput);
unlink(psOutput);
}
else if(sameString(type, "eps"))
{
printf("Content-Disposition: filename=hgTracks.eps\nContent-Type: application/eps\n\n");
file = psOutput;
}
else
{
printf("Content-Disposition: filename=hgTracks.png\nContent-Type: image/png\n\n");
file = pngTn.forCgi;
}
char buf[4096];
FILE *fd = fopen(file, "r");
if(fd == NULL)
// fail some other way (e.g. HTTP 500)?
errAbort("Couldn't open png for reading");
while (TRUE)
{
size_t n = fread(buf, 1, sizeof(buf), fd);
if(n)
fwrite(buf, 1, n, stdout);
else
break;
}
fclose(fd);
unlink(file);
return;
}
#endif///def SUPPORT_CONTENT_TYPE
if (theImgBox)
{
imageBoxDraw(theImgBox);
// If a portal was established, then set the global dimensions back to the portal size
if (imgBoxPortalDimensions(theImgBox,NULL,NULL,NULL,NULL,&winStart,&winEnd,&(tl.picWidth),NULL))
{
pixWidth = tl.picWidth;
winBaseCount = winEnd - winStart;
insideWidth = tl.picWidth-gfxBorder-insideX;
}
imgBoxFree(&theImgBox);
}
else
{
char *titleAttr = "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'",
pngTn.forHtml, pixWidth, pixHeight, mapName, titleAttr);
hPrintf("><BR>\n");
}
flatTracksFree(&flatTracks);
}
void makeHgGenomeTrackVisible(struct track *track)
/* This turns on a track clicked from hgGenome, even if it was previously */
/* hidden manually and there are cart vars to support that. */
{
struct hashEl *hels;
struct hashEl *hel;
char prefix[SMALLBUF];
/* First check if the click was from hgGenome. If not, leave. */
/* get the names of the tracks in the cart */
safef(prefix, sizeof(prefix), "%s_", hggGraphPrefix);
hels = cartFindPrefix(cart, prefix);
/* loop through them and compare them to the track passed into this */
/* function. */
for (hel = hels; hel != NULL; hel = hel->next)
{
struct trackDb *subtrack;
char *subtrackName = hel->val;
/* check non-subtrack. */
if (sameString(track->tdb->track, subtrackName))
{
track->visibility = tvFull;
track->tdb->visibility = tvFull;
cartSetString(cart, track->tdb->track, "full");
}
else if (track->tdb->subtracks != NULL)
{
struct slRef *tdbRef, *tdbRefList = trackDbListGetRefsToDescendants(track->tdb->subtracks);
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
subtrack = tdbRef->val;
if (sameString(subtrack->track, subtrackName))
{
char selName[SMALLBUF];
track->visibility = tvFull;
cartSetString(cart, track->tdb->track, "full");
track->tdb->visibility = tvFull;
subtrack->visibility = tvFull;
safef(selName, sizeof(selName), "%s_sel", subtrackName);
cartSetBoolean(cart, selName, TRUE);
}
}
slFreeList(&tdbRefList);
}
}
hashElFreeList(&hels);
}
struct sqlConnection *remoteTrackConnection(struct track *tg)
/* Get a connection to remote database as specified in remoteSql settings... */
{
if (!tg->isRemoteSql)
{
internalErr();
return NULL;
}
else
{
return sqlConnectRemote(tg->remoteSqlHost, tg->remoteSqlUser, tg->remoteSqlPassword,
tg->remoteSqlDatabase);
}
}
void addTdbListToTrackList(struct trackDb *tdbList, char *trackNameFilter,
struct track **pTrackList)
/* Convert a list of trackDb's to tracks, and append these to trackList. */
{
struct trackDb *tdb, *next;
struct track *track;
TrackHandler handler;
tdbSortPrioritiesFromCart(cart, &tdbList);
for (tdb = tdbList; tdb != NULL; tdb = next)
{
next = tdb->next;
if(trackNameFilter != NULL && strcmp(trackNameFilter, tdb->track))
// suppress loading & display of all tracks except for the one passed in via trackNameFilter
continue;
if (sameString(tdb->type, "downloadsOnly")) // These tracks should not even be seen by hgTracks.
continue;
track = trackFromTrackDb(tdb);
track->hasUi = TRUE;
if (slCount(tdb->subtracks) != 0)
{
tdbSortPrioritiesFromCart(cart, &(tdb->subtracks));
if (trackDbLocalSetting(tdb, "compositeTrack"))
makeCompositeTrack(track, tdb);
else if (trackDbLocalSetting(tdb, "container"))
makeContainerTrack(track, tdb);
}
else
{
handler = lookupTrackHandlerClosestToHome(tdb);
if (handler != NULL)
handler(track);
}
if (cgiVarExists("hgGenomeClick"))
makeHgGenomeTrackVisible(track);
if (track->loadItems == NULL)
warn("No load handler for %s; possible missing trackDb `type' or `subTrack' attribute", tdb->track);
else if (track->drawItems == NULL)
warn("No draw handler for %s", tdb->track);
else
slAddHead(pTrackList, track);
}
}
void loadFromTrackDb(struct track **pTrackList)
/* Load tracks from database, consulting handler list. */
{
char *trackNameFilter = cartOptionalString(cart, "hgt.trackNameFilter");
struct trackDb *tdbList;
if(trackNameFilter == NULL)
tdbList = hTrackDb(database);
else
tdbList = hTrackDbForTrack(database, trackNameFilter);
addTdbListToTrackList(tdbList, trackNameFilter, pTrackList);
}
static int getScoreFilter(char *trackName)
/* check for score filter configuration setting */
{
char optionScoreStr[256];
safef(optionScoreStr, sizeof(optionScoreStr), "%s.scoreFilter", trackName);
return cartUsualInt(cart, optionScoreStr, 0);
}
void ctLoadSimpleBed(struct track *tg)
/* Load the items in one custom track - just move beds in
* window... */
{
struct customTrack *ct = tg->customPt;
struct bed *bed, *nextBed, *list = NULL;
int scoreFilter = getScoreFilter(ct->tdb->track);
if (ct->dbTrack)
{
int fieldCount = ct->fieldCount;
int rowOffset;
char **row;
struct sqlConnection *conn =
hAllocConn(CUSTOM_TRASH);
struct sqlResult *sr = NULL;
sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd,
NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoadN(row+rowOffset, fieldCount);
if (scoreFilter && bed->score < scoreFilter)
continue;
slAddHead(&list, bed);
}
hFreeConn(&conn);
}
else
{
for (bed = ct->bedList; bed != NULL; bed = nextBed)
{
nextBed = bed->next;
if (bed->chromStart < winEnd && bed->chromEnd > winStart
&& sameString(chromName, bed->chrom))
{
if (scoreFilter && bed->score < scoreFilter)
continue;
slAddHead(&list, bed);
}
}
}
slSort(&list, bedCmp);
tg->items = list;
}
void ctLoadBed9(struct track *tg)
/* Convert bed info in window to linked feature. */
{
struct customTrack *ct = tg->customPt;
struct bed *bed;
struct linkedFeatures *lfList = NULL, *lf;
boolean useItemRgb = FALSE;
int scoreFilter = getScoreFilter(ct->tdb->track);
useItemRgb = bedItemRgb(ct->tdb);
if (ct->dbTrack)
{
int rowOffset;
char **row;
struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
struct sqlResult *sr = NULL;
sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd,
NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoadN(row+rowOffset, 9);
if (scoreFilter && bed->score < scoreFilter)
continue;
bed8To12(bed);
lf = lfFromBed(bed);
if (useItemRgb)
{
lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */
lf->filterColor=bed->itemRgb;
}
slAddHead(&lfList, lf);
}
hFreeConn(&conn);
}
else
{
for (bed = ct->bedList; bed != NULL; bed = bed->next)
{
if (scoreFilter && bed->score < scoreFilter)
continue;
if (bed->chromStart < winEnd && bed->chromEnd > winStart
&& sameString(chromName, bed->chrom))
{
bed8To12(bed);
lf = lfFromBed(bed);
if (useItemRgb)
{
lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */
lf->filterColor=bed->itemRgb;
}
slAddHead(&lfList, lf);
}
}
}
slReverse(&lfList);
slSort(&lfList, linkedFeaturesCmp);
tg->items = lfList;
}
void ctLoadBed8(struct track *tg)
/* Convert bed info in window to linked feature. */
{
struct customTrack *ct = tg->customPt;
struct bed *bed;
struct linkedFeatures *lfList = NULL, *lf;
int scoreFilter = getScoreFilter(ct->tdb->track);
if (ct->dbTrack)
{
int fieldCount = ct->fieldCount;
int rowOffset;
char **row;
struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
struct sqlResult *sr = NULL;
sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd,
NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoadN(row+rowOffset, fieldCount);
if (scoreFilter && bed->score < scoreFilter)
continue;
bed8To12(bed);
lf = lfFromBed(bed);
slAddHead(&lfList, lf);
}
hFreeConn(&conn);
}
else
{
for (bed = ct->bedList; bed != NULL; bed = bed->next)
{
if (scoreFilter && bed->score < scoreFilter)
continue;
if (bed->chromStart < winEnd && bed->chromEnd > winStart
&& sameString(chromName, bed->chrom))
{
bed8To12(bed);
lf = lfFromBed(bed);
slAddHead(&lfList, lf);
}
}
}
slReverse(&lfList);
slSort(&lfList, linkedFeaturesCmp);
tg->items = lfList;
}
void ctLoadGappedBed(struct track *tg)
/* Convert bed info in window to linked feature. */
{
struct customTrack *ct = tg->customPt;
struct bed *bed;
struct linkedFeatures *lfList = NULL, *lf;
boolean useItemRgb = FALSE;
int scoreFilter = getScoreFilter(ct->tdb->track);
useItemRgb = bedItemRgb(ct->tdb);
if (ct->dbTrack)
{
int fieldCount = ct->fieldCount;
int rowOffset;
char **row;
struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
struct sqlResult *sr = NULL;
sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd,
NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoadN(row+rowOffset, fieldCount);
lf = lfFromBed(bed);
if (scoreFilter && bed->score < scoreFilter)
continue;
if (useItemRgb)
{
lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */
lf->filterColor=bed->itemRgb;
}
slAddHead(&lfList, lf);
}
hFreeConn(&conn);
}
else
{
for (bed = ct->bedList; bed != NULL; bed = bed->next)
{
if (scoreFilter && bed->score < scoreFilter)
continue;
if (bed->chromStart < winEnd && bed->chromEnd > winStart
&& sameString(chromName, bed->chrom))
{
lf = lfFromBed(bed);
if (useItemRgb)
{
lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */
lf->filterColor=bed->itemRgb;
}
slAddHead(&lfList, lf);
}
}
}
slReverse(&lfList);
slSort(&lfList, linkedFeaturesCmp);
tg->items = lfList;
}
void ctLoadColoredExon(struct track *tg)
/* Convert bed info in window to linked features series for custom track. */
{
struct customTrack *ct = tg->customPt;
struct bed *bed;
struct linkedFeaturesSeries *lfsList = NULL, *lfs;
if (ct->dbTrack)
{
int fieldCount = ct->fieldCount;
int rowOffset;
char **row;
struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
struct sqlResult *sr = NULL;
sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd,
NULL, &rowOffset);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = bedLoadN(row+rowOffset, fieldCount);
lfs = lfsFromColoredExonBed(bed);
slAddHead(&lfsList, lfs);
}
hFreeConn(&conn);
}
else
{
for (bed = ct->bedList; bed != NULL; bed = bed->next)
{
if (bed->chromStart < winEnd && bed->chromEnd > winStart
&& sameString(chromName, bed->chrom))
{
lfs = lfsFromColoredExonBed(bed);
slAddHead(&lfsList, lfs);
}
}
}
slReverse(&lfsList);
slSort(&lfsList, linkedFeaturesSeriesCmp);
tg->items = lfsList;
}
char *ctMapItemName(struct track *tg, void *item)
/* Return composite item name for custom tracks. */
{
char *itemName = tg->itemName(tg, item);
static char buf[512];
if (strlen(itemName) > 0)
safef(buf, sizeof(buf), "%s %s", ctFileName, itemName);
else
safef(buf, sizeof(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;
}
void dontLoadItems(struct track *tg)
/* No-op loadItems when we aren't going to try. */
{
}
struct track *newCustomTrack(struct customTrack *ct)
/* Make up a new custom track. */
{
struct track *tg = NULL;
struct trackDb *tdb = ct->tdb;
boolean useItemRgb = FALSE;
char *typeOrig = tdb->type;
char *typeDupe = cloneString(typeOrig);
char *typeParam = typeDupe;
char *type = nextWord(&typeParam);
if (ct->dbTrack)
{
// make sure we can connect
struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH);
hFreeConn(&conn);
}
useItemRgb = bedItemRgb(tdb);
if (sameString(type, "maf"))
{
tg = trackFromTrackDb(tdb);
tg->canPack = TRUE;
wigMafMethods(tg, tdb, 0, NULL);
if (!ct->dbTrack)
errAbort("custom maf tracks must be in database");
struct mafPriv *mp;
AllocVar(mp);
mp->ct = ct;
tg->customPt = mp;
tg->nextItemButtonable = FALSE;
}
else if (sameString(type, "wig"))
{
tg = trackFromTrackDb(tdb);
if (ct->dbTrack)
tg->loadItems = wigLoadItems;
else
tg->loadItems = ctWigLoadItems;
tg->customPt = ct;
tg->nextItemButtonable = FALSE;
}
else if (sameString(type, "bigWig"))
{
tg = trackFromTrackDb(tdb);
tg->bbiFile = ct->bbiFile;
tg->nextItemButtonable = FALSE;
if (trackShouldUseAjaxRetrieval(tg))
tg->loadItems = dontLoadItems;
}
-else if (sameString(type, "bigBed")|| sameString(type, "bigGenePred") || sameString(type, "bigPsl"))
+else if (sameString(type, "bigBed")|| sameString(type, "bigGenePred") || sameString(type, "bigPsl") || sameString(type, "bigMaf"))
{
struct bbiFile *bbi = ct->bbiFile;
/* Find field counts, and from that revise the tdb->type to be more complete. */
char extra = (bbi->fieldCount > bbi->definedFieldCount ? '+' : '.');
char typeBuf[64];
if (sameString(type, "bigGenePred"))
safef(typeBuf, sizeof(typeBuf), "bigGenePred");
+ else if (sameString(type, "bigMaf"))
+ safef(typeBuf, sizeof(typeBuf), "bigMaf");
else if (sameString(type, "bigPsl"))
safef(typeBuf, sizeof(typeBuf), "bigPsl");
else
safef(typeBuf, sizeof(typeBuf), "bigBed %d %c", bbi->definedFieldCount, extra);
tdb->type = cloneString(typeBuf);
/* Finish wrapping track around tdb. */
tg = trackFromTrackDb(tdb);
tg->bbiFile = bbi;
tg->nextItemButtonable = TRUE;
if (trackShouldUseAjaxRetrieval(tg))
tg->loadItems = dontLoadItems;
}
else if (sameString(type, "bedGraph"))
{
tg = trackFromTrackDb(tdb);
tg->canPack = FALSE;
tg->customPt = ct;
ct->wigFile = ctFileName;
tg->mapItemName = ctMapItemName;
tg->nextItemButtonable = FALSE;
}
else if (sameString(type, "bed"))
{
tg = trackFromTrackDb(tdb);
if (ct->fieldCount < 8)
{
tg->loadItems = ctLoadSimpleBed;
}
else if (useItemRgb && ct->fieldCount == 9)
{
tg->loadItems = ctLoadBed9;
}
else if (ct->fieldCount < 12)
{
tg->loadItems = ctLoadBed8;
}
else if (ct->fieldCount == 15)
{
char *theType = trackDbSetting(tdb, "type");
if (theType && sameString(theType, "expRatio"))
{
tg = trackFromTrackDb(tdb);
expRatioMethodsFromCt(tg);
}
else
tg->loadItems = ctLoadGappedBed;
}
else
{
tg->loadItems = ctLoadGappedBed;
}
tg->mapItemName = ctMapItemName;
tg->canPack = TRUE;
tg->nextItemButtonable = TRUE;
tg->customPt = ct;
}
else if (sameString(type, "chromGraph"))
{
tdb->type = NULL; /* Swap out type for the moment. */
tg = trackFromTrackDb(tdb);
chromGraphMethodsCt(tg);
tg->nextItemButtonable = FALSE;
tdb->type = typeOrig;
}
else if (sameString(type, "array"))
{
tg = trackFromTrackDb(tdb);
expRatioMethodsFromCt(tg);
tg->nextItemButtonable = TRUE;
tg->customPt = ct;
}
else if (sameString(type, "coloredExon"))
{
tg = trackFromTrackDb(tdb);
coloredExonMethodsFromCt(tg);
tg->nextItemButtonable = TRUE;
tg->customPt = ct;
}
else if (sameString(type, "encodePeak"))
{
tg = trackFromTrackDb(tdb);
encodePeakMethodsCt(tg);
tg->nextItemButtonable = TRUE;
tg->customPt = ct;
}
else if (sameString(type, "bam"))
{
tg = trackFromTrackDb(tdb);
tg->customPt = ct;
bamMethods(tg);
if (trackShouldUseAjaxRetrieval(tg))
tg->loadItems = dontLoadItems;
tg->mapItemName = ctMapItemName;
}
else if (sameString(type, "vcfTabix"))
{
tg = trackFromTrackDb(tdb);
tg->customPt = ct;
vcfTabixMethods(tg);
if (trackShouldUseAjaxRetrieval(tg))
tg->loadItems = dontLoadItems;
tg->mapItemName = ctMapItemName;
}
else if (sameString(type, "vcf"))
{
tg = trackFromTrackDb(tdb);
tg->customPt = ct;
vcfMethods(tg);
tg->mapItemName = ctMapItemName;
}
else if (sameString(type, "makeItems"))
{
tg = trackFromTrackDb(tdb);
makeItemsMethods(tg);
tg->nextItemButtonable = TRUE;
tg->customPt = ct;
}
else if (sameString(type, "bedDetail"))
{
tg = trackFromTrackDb(tdb);
bedDetailCtMethods(tg, ct);
tg->mapItemName = ctMapItemName; /* must be here to see ctMapItemName */
}
else if (sameString(type, "adjacency"))
{
extern void adjacencyMethods(struct track *track);
tg = trackFromTrackDb(tdb);
adjacencyMethods(tg);
//tg->mapItemName = ctMapItemName;
tg->customPt = ct;
}
else if (sameString(type, "pgSnp"))
{
tg = trackFromTrackDb(tdb);
pgSnpCtMethods(tg);
//tg->mapItemName = ctMapItemName;
tg->customPt = ct;
}
else
{
errAbort("Unrecognized custom track type %s", type);
}
tg->hasUi = TRUE;
tg->customTrack = TRUE;// Explicitly declare this a custom track for flatTrack ordering
freez(&typeDupe);
return tg;
}
char *getPositionFromCustomTracks()
/* Parses custom track data to get the position variable
* return - The first chromosome position variable found in the
* custom track data. */
{
char *pos = NULL;
struct slName *bl = NULL;
ctList = customTracksParseCart(database, cart, &browserLines, &ctFileName);
for (bl = browserLines; bl != NULL; bl = bl->next)
{
char *words[96];
int wordCount;
char *dupe = cloneString(bl->name);
wordCount = chopLine(dupe, words);
if (wordCount >= 3)
{
char *command = words[1];
if (sameString(command, "position"))
pos = cloneString(words[2]);
}
freez(&dupe);
if (pos != NULL)
break;
}
return pos;
}
void loadCustomTracks(struct track **pTrackList)
/* Load up custom tracks and append to list. */
{
struct customTrack *ct;
struct track *tg;
struct slName *bl;
/* build up browser lines from cart variables set by hgCustom */
char *visAll = cartCgiUsualString(cart, "hgt.visAllFromCt", NULL);
if (visAll)
{
char buf[SMALLBUF];
safef(buf, sizeof buf, "browser %s %s", visAll, "all");
slAddTail(&browserLines, slNameNew(buf));
}
struct hashEl *visEl;
struct hashEl *visList = cartFindPrefix(cart, "hgtct.");
for (visEl = visList; visEl != NULL; visEl = visEl->next)
{
char buf[256];
safef(buf, sizeof buf, "browser %s %s", cartString(cart, visEl->name),
chopPrefix(cloneString(visEl->name)));
slAddTail(&browserLines, slNameNew(buf));
cartRemove(cart, visEl->name);
}
hashElFreeList(&visList);
/* The loading is now handled by getPositionFromCustomTracks(). */
/* Process browser commands in custom track. */
for (bl = browserLines; bl != NULL; bl = bl->next)
{
char *words[96];
int wordCount;
wordCount = chopLine(bl->name, words);
if (wordCount > 1)
{
char *command = words[1];
if (sameString(command, "hide")
|| sameString(command, "dense")
|| sameString(command, "pack")
|| sameString(command, "squish")
|| sameString(command, "full"))
{
if (wordCount > 2)
{
int i;
for (i=2; i<wordCount; ++i)
{
char *s = words[i];
struct track *tg;
boolean toAll = sameWord(s, "all");
for (tg = *pTrackList; tg != NULL; tg = tg->next)
{
if (toAll || sameString(s, tg->track))
{
if (hTvFromString(command) == tg->tdb->visibility)
/* remove if setting to default vis */
cartRemove(cart, tg->track);
else
cartSetString(cart, tg->track, command);
/* hide or show supertrack enclosing this track */
if (tdbIsSuperTrackChild(tg->tdb))
{
assert(tg->tdb->parentName != NULL);
cartSetString(cart, tg->tdb->parentName,
(sameString(command, "hide") ?
"hide" : "show"));
}
}
}
}
}
}
else if (sameString(command, "position"))
{
if (wordCount < 3)
errAbort("Expecting 3 words in browser position line");
if (!hgIsChromRange(database, words[2]))
errAbort("browser position needs to be in chrN:123-456 format");
hgParseChromRange(database, words[2], &chromName, &winStart, &winEnd);
/*Fix a start window of -1 that is returned when a custom track position
begins at 0
*/
if (winStart < 0)
{
winStart = 0;
}
}
else if (sameString(command, "pix"))
{
if (wordCount != 3)
errAbort("Expecting 3 words in pix line");
trackLayoutSetPicWidth(&tl, words[2]);
}
}
}
for (ct = ctList; ct != NULL; ct = ct->next)
{
hasCustomTracks = TRUE;
tg = newCustomTrack(ct);
slAddHead(pTrackList, tg);
}
}
void loadTrackHubs(struct track **pTrackList, struct grp **pGrpList)
/* Load up stuff from data hubs and append to lists. */
{
struct trackDb *tdbList = hubCollectTracks(database, pGrpList);
addTdbListToTrackList(tdbList, NULL, pTrackList);
}
boolean restrictionEnzymesOk()
/* Check to see if it's OK to do restriction enzymes. */
{
return (sqlDatabaseExists("hgFixed") && hTableExists("hgFixed", "cutters") &&
hTableExists("hgFixed", "rebaseRefs") &&
hTableExists("hgFixed", "rebaseCompanies"));
}
static void setSuperTrackHasVisibleMembers(struct trackDb *tdb)
/* Determine if any member tracks are visible -- currently
* recording this in the parent's visibility setting */
{
tdb->visibility = tvDense;
}
boolean superTrackHasVisibleMembers(struct trackDb *tdb)
/* Determine if any member tracks are visible -- currently
* recording this in the parent's visibility setting */
{
if (!tdbIsSuper(tdb))
return FALSE;
return (tdb->visibility != tvHide);
}
int hubCmpAlpha(const void *va, const void *vb)
/* Compare to sort hubs based on name */
{
const struct trackHub *a = *((struct trackHub **)va);
const struct trackHub *b = *((struct trackHub **)vb);
return strcmp(a->shortLabel, b->shortLabel);
}
static void rPropagateGroup(struct track *track, struct group *group)
// group should spread to multiple levels of children.
{
struct track *subtrack = track->subtracks;
for ( ;subtrack != NULL;subtrack = subtrack->next)
{
subtrack->group = group;
rPropagateGroup(subtrack, group);
}
}
static void groupTracks(struct track **pTrackList,
struct group **pGroupList, struct grp *grpList, 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;
float minPriority = 100000; // something really large
/* build group objects from database. */
for (grp = grps; grp != NULL; grp = grp->next)
{
/* deal with group reordering */
float priority = grp->priority;
// we want to get the minimum priority over 1 (which is custom tracks)
if ((priority > 1.0) && (priority < minPriority)) minPriority = priority;
if (withPriorityOverride)
{
char cartVar[512];
safef(cartVar, sizeof(cartVar), "%s.priority",grp->name);
if (vis != -1)
priority = (float)cartUsualDouble(cart, cartVar, grp->priority);
if (priority == grp->priority)
cartRemove(cart, cartVar);
}
/* create group object; add to list and hash */
AllocVar(group);
group->name = cloneString(grp->name);
group->label = cloneString(grp->label);
group->defaultPriority = grp->priority;
group->priority = priority;
group->defaultIsClosed = grp->defaultIsClosed;
slAddHead(&list, group);
hashAdd(hash, grp->name, group);
}
grpFreeList(&grps);
double priorityInc;
double priority;
if (grpList)
{
minPriority -= 1.0; // priority is 1-based
// the idea here is to get enough room between priority 1
// (which is custom tracks) and the group with the next
// priority number, so that the hub nestle inbetween the
// custom tracks and everything else at the top of the list
// of track groups
priorityInc = (0.9 * minPriority) / slCount(grpList);
priority = 1.0 + priorityInc;
}
for(; grpList; grpList = grpList->next)
{
AllocVar(group);
group->name = cloneString(grpList->name);
group->label = cloneString(grpList->label);
group->defaultPriority = group->priority = priority;
priority += priorityInc;
slAddHead(&list, group);
hashAdd(hash, group->name, group);
}
/* Loop through tracks and fill in their groups.
* If necessary make up an unknown group. */
for (track = *pTrackList; track != NULL; track = track->next)
{
/* handle track reordering feature -- change group assigned to track */
if (withPriorityOverride)
{
char *groupName = NULL;
char cartVar[256];
/* belt and suspenders -- accomodate inconsistent track/trackDb
* creation. Note -- with code cleanup, these default variables
* could be retired, and the tdb versions used as defaults */
if (!track->defaultGroupName)
{
if (track->tdb && track->tdb->grp)
track->defaultGroupName = cloneString(track->tdb->grp);
else
track->defaultGroupName = cloneString("other");
}
if (tdbIsSuperTrackChild(track->tdb))
{
assert(track->tdb->parentName != NULL);
/* supertrack member must be in same group as its super */
/* determine supertrack group */
safef(cartVar, sizeof(cartVar), "%s.group",track->tdb->parentName);
groupName = cloneString( //1
cartUsualString(cart, cartVar, track->tdb->parent->grp));
track->tdb->parent->grp = cloneString(groupName); //2
}
else
{
/* get group */
safef(cartVar, sizeof(cartVar), "%s.group",track->track);
groupName = cloneString( //1
cartUsualString(cart, cartVar, track->defaultGroupName));
}
if (vis == -1)
groupName = track->defaultGroupName; //0
track->groupName = cloneString(groupName); // wasting a few clones! //3
if (sameString(groupName, track->defaultGroupName))
cartRemove(cart, cartVar);
/* get priority */
safef(cartVar, sizeof(cartVar), "%s.priority",track->track);
float priority = (float)cartUsualDouble(cart, cartVar,
track->defaultPriority);
/* remove cart variables that are the same as the trackDb settings */
/* UGLY - add me back when tdb->priority is no longer pre-clobbered by cart var value
if (priority == track->defaultPriority)
cartRemove(cart, cartVar);
*/
track->priority = priority;
}
/* assign group object to track */
if (track->groupName == NULL)
group = NULL;
else
group = hashFindVal(hash, track->groupName);
if (group == NULL)
{
if (unknown == NULL)
{
AllocVar(unknown);
unknown->name = cloneString("other");
unknown->label = cloneString("other");
unknown->priority = 1000000;
slAddHead(&list, unknown);
}
group = unknown;
}
track->group = group;
rPropagateGroup(track, group);
}
/* Sort tracks by combined group/track priority, and
* then add references to track to group. */
slSort(pTrackList, tgCmpPriority);
for (track = *pTrackList; track != NULL; track = track->next)
{
AllocVar(tr);
tr->track = track;
slAddHead(&track->group->trackList, tr);
}
/* Straighten things out, clean up, and go home. */
for (group = list; group != NULL; group = group->next)
slReverse(&group->trackList);
slSort(&list, gCmpPriority);
hashFree(&hash);
*pGroupList = list;
}
void groupTrackListAddSuper(struct cart *cart, struct group *group)
/* Construct a new track list that includes supertracks, sort by priority,
* and determine if supertracks have visible members.
* Replace the group track list with this new list.
* Shared by hgTracks and configure page to expand track list,
* in contexts where no track display functions (which don't understand
* supertracks) are invoked. */
{
struct trackRef *newList = NULL, *tr, *ref;
struct hash *superHash = hashNew(8);
if (!group || !group->trackList)
return;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
AllocVar(ref);
ref->track = track;
slAddHead(&newList, ref);
if (tdbIsSuperTrackChild(track->tdb))
{
assert(track->tdb->parentName != NULL);
if (hTvFromString(cartUsualString(cart, track->track,
hStringFromTv(track->tdb->visibility))) != tvHide)
setSuperTrackHasVisibleMembers(track->tdb->parent);
assert(track->parent == NULL);
track->parent = hashFindVal(superHash, track->tdb->parentName);
if (track->parent)
continue;
/* create track and reference for the supertrack */
struct track *superTrack = track->parent = trackFromTrackDb(track->tdb->parent);
track->parent = superTrack;
if (trackHash != NULL)
hashAddUnique(trackHash,superTrack->track,superTrack);
superTrack->hasUi = TRUE;
superTrack->group = group;
superTrack->groupName = cloneString(group->name);
superTrack->defaultGroupName = cloneString(group->name);
/* handle track reordering */
char cartVar[256];
safef(cartVar, sizeof(cartVar), "%s.priority",track->tdb->parentName);
float priority = (float)cartUsualDouble(cart, cartVar,
track->tdb->parent->priority);
/* remove cart variables that are the same as the trackDb settings */
if (priority == track->tdb->parent->priority)
cartRemove(cart, cartVar);
superTrack->priority = priority;
AllocVar(ref);
ref->track = superTrack;
slAddHead(&newList, ref);
hashAdd(superHash, track->tdb->parentName, superTrack);
}
}
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];
}
hButtonWithOnClick(var, paddedLabel, NULL, "return imageV2.navigateButtonClick(this);");
}
void limitSuperTrackVis(struct track *track)
/* Limit track visibility by supertrack parent */
{
if (tdbIsSuperTrackChild(track->tdb))
{
assert(track->tdb->parent != NULL);
if (sameString("hide", cartUsualString(cart, track->tdb->parent->track,
track->tdb->parent->isShow ? "show" : "hide")))
track->visibility = tvHide;
}
}
struct track *rFindTrackWithTable(char *tableName, struct track *trackList)
/* Recursively search through track list looking for first one that matches table. */
{
struct track *track;
for (track = trackList; track != NULL; track = track->next)
{
if (sameString(tableName, track->table))
return track;
struct track *subTrack = rFindTrackWithTable(tableName, track->subtracks);
if (subTrack != NULL)
return subTrack;
}
return NULL;
}
static void setSearchedTrackToPackOrFull(struct track *trackList)
// Open track associated with search position if any. Also open its parents if any.
{
if (NULL != hgp && NULL != hgp->tableList && NULL != hgp->tableList->name)
{
char *tableName = hgp->tableList->name;
struct track *matchTrack = rFindTrackWithTable(tableName, trackList);
if (matchTrack != NULL)
tdbSetCartVisibility(matchTrack->tdb, cart, hCarefulTrackOpenVis(database, matchTrack->track));
}
}
struct track *getTrackList( struct group **pGroupList, int vis)
/* Return list of all tracks, organizing by groups.
* If vis is -1, restore default groups to tracks.
* Shared by hgTracks and configure page. */
{
struct track *track, *trackList = NULL;
registerTrackHandlers();
/* Load regular tracks, blatted tracks, and custom tracks.
* Best to load custom last. */
loadFromTrackDb(&trackList);
if (pcrResultParseCart(database, cart, NULL, NULL, NULL))
slSafeAddHead(&trackList, pcrResultTg());
if (userSeqString != NULL)
slSafeAddHead(&trackList, userPslTg());
slSafeAddHead(&trackList, oligoMatchTg());
if (restrictionEnzymesOk())
{
slSafeAddHead(&trackList, cuttersTg());
}
if (wikiTrackEnabled(database, NULL))
{
addWikiTrack(&trackList);
struct sqlConnection *conn = wikiConnect();
if (sqlTableExists(conn, "variome"))
addVariomeWikiTrack(&trackList);
wikiDisconnect(&conn);
}
struct grp *grpList = NULL;
if (cartOptionalString(cart, "hgt.trackNameFilter") == NULL)
{ // If a single track was asked for and it is from a hub, then it is already in trackList
loadTrackHubs(&trackList, &grpList);
}
loadCustomTracks(&trackList);
groupTracks( &trackList, pGroupList, grpList, vis);
setSearchedTrackToPackOrFull(trackList);
if (cgiOptionalString( "hideTracks"))
changeTrackVis(groupList, NULL, tvHide);
/* Get visibility values if any from ui. */
for (track = trackList; track != NULL; track = track->next)
{
char *s = cartOptionalString(cart, track->track);
if (cgiOptionalString("hideTracks"))
{
s = cgiOptionalString(track->track);
if (s != NULL)
{
if (hTvFromString(s) == track->tdb->visibility)
cartRemove(cart, track->track);
else
cartSetString(cart, track->track, s);
}
}
if (s != NULL && !track->limitedVisSet)
track->visibility = hTvFromString(s);
if (tdbIsCompositeChild(track->tdb))
track->visibility = tdbVisLimitedByAncestry(cart, track->tdb, FALSE);
else if (tdbIsComposite(track->tdb) && track->visibility != tvHide)
{
struct trackDb *parent = track->tdb->parent;
char *parentShow = NULL;
if (parent)
parentShow = cartUsualString(cart, parent->track,
parent->isShow ? "show" : "hide");
if (!parent || sameString(parentShow, "show"))
compositeTrackVis(track);
}
}
return trackList;
}
void doNextPrevItem(boolean goNext, char *trackName)
/* In case a next item arrow was clicked on a track, change */
/* position (i.e. winStart, winEnd, etc.) based on what track it was */
{
struct track *track = trackFindByName(trackList, trackName);
if ((track != NULL) && (track->nextPrevItem != NULL))
track->nextPrevItem(track, goNext);
}
char *collapseGroupVar(char *name)
/* Construct cart variable name for collapsing group */
{
static char varName[256];
safef(varName, sizeof(varName),
"%s%s_%s_%s", "hgt", "group", name, "close");
return (cloneString(varName));
}
boolean isCollapsedGroup(struct group *grp)
/* Determine if group is collapsed */
{
return cartUsualInt(cart, collapseGroupVar(grp->name), grp->defaultIsClosed);
}
void collapseGroupGoodies(boolean isOpen, boolean wantSmallImage,
char **img, char **indicator, char **otherState)
/* Get image, char representation of image, and 'otherState' (1 or 0)
* for a group, based on whether it is collapsed, and whether we want
* larger or smaller image for collapse box */
{
if (otherState)
*otherState = (isOpen ? "1" : "0");
if (indicator)
*indicator = (isOpen ? "-" : "+");
if (img)
{
if (wantSmallImage)
*img = (isOpen ? "../images/remove_sm.gif" : "../images/add_sm.gif");
else
*img = (isOpen ? "../images/remove.gif" : "../images/add.gif");
}
}
void collapseGroup(char *name, boolean doCollapse)
/* Set cart variable to cause group to collapse */
{
cartSetBoolean(cart, collapseGroupVar(name), doCollapse);
}
void myControlGridStartCell(struct controlGrid *cg, boolean isOpen, char *id)
/* Start a new cell in control grid; support Javascript open/collapsing by including id's in tr's.
id is used as id prefix (a counter is added to make id's unique). */
{
static int counter = 1;
if (cg->columnIx == cg->columns)
controlGridEndRow(cg);
if (!cg->rowOpen)
{
#if 0
/* This is unnecessary, b/c we can just use a blank display attribute to show the element rather
than figuring out what the browser specific string is to turn on display of the tr;
however, we may want to put in browser specific strings in the future, so I'm leaving this
code in as a reference. */
char *ua = getenv("HTTP_USER_AGENT");
char *display = ua && stringIn("MSIE", ua) ? "block" : "table-row";
#endif
// use counter to ensure unique tr id's (prefix is used to find tr's in javascript).
printf("<tr %sid='%s-%d'>", isOpen ? "" : "style='display: none' ", id, counter++);
cg->rowOpen = TRUE;
}
if (cg->align)
printf("<td align=%s>", cg->align);
else
printf("<td>");
}
static void pruneRedundantCartVis(struct track *trackList)
/* When the config page or track form has been submitted, there usually
* are many track visibility cart variables that have not been changed
* from the default. To keep down cart bloat, prune those out before we
* save the cart. changeTrackVis does this too, but this is for the
* more common case where track visibilities are tweaked. */
{
struct track *track;
for (track = trackList; track != NULL; track = track->next)
{
char *cartVis = cartOptionalString(cart, track->track);
if (cartVis != NULL && hTvFromString(cartVis) == track->tdb->visibility)
cartRemove(cart, track->track);
}
}
static int getMaxWindowToDraw(struct trackDb *tdb)
/* If trackDb setting maxWindowToDraw exists and is a sensible size, return it, else 0. */
{
if (tdb == NULL)
return 0;
char *maxWinToDraw = trackDbSettingClosestToHome(tdb, "maxWindowToDraw");
if (isNotEmpty(maxWinToDraw))
{
unsigned maxWTD = sqlUnsigned(maxWinToDraw);
if (maxWTD > 1)
return maxWTD;
}
return 0;
}
static void drawMaxWindowWarning(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg,
int xOff, int yOff, int width, MgFont *font, Color color,
enum trackVisibility vis)
/* This is a stub drawItems handler to be swapped in for the usual drawItems when the window
* size is larger than the threshold specified by trackDb setting maxWindowToDraw. */
{
int maxWinToDraw = getMaxWindowToDraw(tg->tdb);
char commafied[256];
sprintLongWithCommas(commafied, maxWinToDraw);
char message[512];
safef(message, sizeof(message), "zoom in to <= %s bases to view items", commafied);
Color yellow = hvGfxFindRgb(hvg, &undefinedYellowColor);
hvGfxBox(hvg, xOff, yOff, width, tg->heightPer, yellow);
hvGfxTextCentered(hvg, xOff, yOff, width, tg->heightPer, MG_BLACK, font, message);
}
static void checkMaxWindowToDraw(struct track *tg)
/* If (winEnd - winStart) > trackDb setting maxWindowToDraw, force track to a dense line
* that will ask the user to zoom in closer to see track items and return TRUE so caller
* can skip loading items. */
{
int maxWinToDraw = getMaxWindowToDraw(tg->tdb);
if (tdbIsComposite(tg->tdb))
{
struct track *subtrack;
for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (!isSubtrackVisible(subtrack))
continue;
maxWinToDraw = getMaxWindowToDraw(subtrack->tdb);
if (maxWinToDraw > 1 && (winEnd - winStart) > maxWinToDraw)
{
subtrack->loadItems = dontLoadItems;
subtrack->drawItems = drawMaxWindowWarning;
subtrack->limitedVis = tvDense;
subtrack->limitedVisSet = TRUE;
}
}
}
else if (maxWinToDraw > 1 && (winEnd - winStart) > maxWinToDraw)
{
tg->loadItems = dontLoadItems;
tg->drawItems = drawMaxWindowWarning;
tg->limitedVis = tvDense;
tg->limitedVisSet = TRUE;
}
}
void printTrackInitJavascript(struct track *trackList)
{
hPrintf("<input type='hidden' id='%s' name='%s' value=''>\n", hgtJsCommand, hgtJsCommand);
}
void jsCommandDispatch(char *command, struct track *trackList)
/* Dispatch a command sent to us from some javaScript event.
* This gets executed after the track list is built, but before
* the track->loadItems methods are called. */
{
if (startsWithWord("makeItems", command))
makeItemsJsCommand(command, trackList, trackHash);
else
warn("Unrecognized jsCommand %s", command);
}
void parentChildCartCleanup(struct track *trackList,struct cart *newCart,struct hash *oldVars)
/* When composite/view settings changes, remove subtrack specific vis
When superTrackChild is found and selected, shape superTrack to match. */
{
struct lm *lm = lmInit(0); /* Speed tweak cleanup with scatch memory pool. */
struct track *track = trackList;
for (;track != NULL; track = track->next)
{
boolean shapedByubtrackOverride = FALSE;
boolean cleanedByContainerSettings = FALSE;
// Top-down 'cleanup' MUST GO BEFORE bottom up reshaping.
cleanedByContainerSettings = cartTdbTreeCleanupOverrides(track->tdb,newCart,oldVars, lm);
if (tdbIsContainer(track->tdb))
{
shapedByubtrackOverride = cartTdbTreeReshapeIfNeeded(cart,track->tdb);
if (shapedByubtrackOverride)
track->visibility = tdbVisLimitedByAncestors(cart,track->tdb,TRUE,TRUE);
}
if ((shapedByubtrackOverride || cleanedByContainerSettings)
&& tdbIsSuperTrackChild(track->tdb)) // Either cleanup may require supertrack intervention
{ // Need to update track visibility
// Unfortunately, since supertracks are not in trackList, this occurs on superChildren,
// So now we need to find the supertrack and take changed cart values of its children
struct slRef *childRef;
for (childRef = track->tdb->parent->children;childRef != NULL;childRef = childRef->next)
{
struct trackDb * childTdb = childRef->val;
struct track *child = hashFindVal(trackHash, childTdb->track);
if (child != NULL && child->track!=NULL)
{
char *cartVis = cartOptionalString(cart,child->track);
if (cartVis)
child->visibility = hTvFromString(cartVis);
}
}
}
}
lmCleanup(&lm);
}
struct paraFetchData
{
struct paraFetchData *next;
struct track *track;
boolean done;
};
static boolean isTrackForParallelLoad(struct track *track)
/* Is this a track that should be loaded in parallel ? */
{
char *bdu = trackDbSetting(track->tdb, "bigDataUrl");
return (startsWithWord("bigWig" , track->tdb->type)
|| startsWithWord("bigBed" , track->tdb->type)
|| startsWithWord("bigPsl" , track->tdb->type)
|| startsWithWord("bigGenePred" , track->tdb->type)
+ || startsWithWord("bigMaf" , track->tdb->type)
|| startsWithWord("bam" , track->tdb->type)
|| startsWithWord("halSnake", track->tdb->type)
|| startsWithWord("vcfTabix", track->tdb->type))
- && (bdu && strstr(bdu,"://"))
+ // XX code-review: shouldn't we error abort if the URL is not valid?
+ && (bdu && isValidBigDataUrl(bdu, FALSE))
&& !(containsStringNoCase(bdu, "dl.dropboxusercontent.com"))
&& (track->subtracks == NULL);
}
static void findLeavesForParallelLoad(struct track *trackList, struct paraFetchData **ppfdList)
/* Find leaves of track tree that are remote network resources for parallel-fetch loading */
{
struct track *track;
if (!trackList)
return;
for (track = trackList; track != NULL; track = track->next)
{
if (track->visibility != tvHide)
{
if (isTrackForParallelLoad(track))
{
struct paraFetchData *pfd;
AllocVar(pfd);
pfd->track = track; // need pointer to be stable
slAddHead(ppfdList, pfd);
track->parallelLoading = TRUE;
}
struct track *subtrack;
for (subtrack=track->subtracks; subtrack; subtrack=subtrack->next)
{
if (isTrackForParallelLoad(subtrack))
{
if (tdbVisLimitedByAncestors(cart,subtrack->tdb,TRUE,TRUE) != tvHide)
{
struct paraFetchData *pfd;
AllocVar(pfd);
pfd->track = subtrack; // need pointer to be stable
slAddHead(ppfdList, pfd);
subtrack->parallelLoading = TRUE;
}
}
}
}
}
}
static pthread_mutex_t pfdMutex = PTHREAD_MUTEX_INITIALIZER;
static struct paraFetchData *pfdList = NULL, *pfdRunning = NULL, *pfdDone = NULL, *pfdNeverStarted = NULL;
static void *remoteParallelLoad(void *threadParam)
/* Each thread loads tracks in parallel until all work is done. */
{
pthread_t *pthread = threadParam;
struct paraFetchData *pfd = NULL;
pthread_detach(*pthread); // this thread will never join back with it's progenitor
// Canceled threads that might leave locks behind,
// so the theads are detached and will be neither joined nor canceled.
boolean allDone = FALSE;
while(1)
{
pthread_mutex_lock( &pfdMutex );
if (!pfdList)
{
allDone = TRUE;
}
else
{ // move it from the waiting queue to the running queue
pfd = slPopHead(&pfdList);
slAddHead(&pfdRunning, pfd);
}
pthread_mutex_unlock( &pfdMutex );
if (allDone)
return NULL;
long thisTime = 0, lastTime = 0;
if (measureTiming)
lastTime = clock1000();
/* protect against errAbort */
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
pfd->done = FALSE;
checkMaxWindowToDraw(pfd->track);
pfd->track->loadItems(pfd->track);
pfd->done = TRUE;
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
pfd->track->networkErrMsg = cloneString(errCatch->message->string);
pfd->done = TRUE;
}
errCatchFree(&errCatch);
if (measureTiming)
{
thisTime = clock1000();
pfd->track->loadTime = thisTime - lastTime;
}
pthread_mutex_lock( &pfdMutex );
slRemoveEl(&pfdRunning, pfd); // this list will not be huge
slAddHead(&pfdDone, pfd);
pthread_mutex_unlock( &pfdMutex );
}
}
static int remoteParallelLoadWait(int maxTimeInSeconds)
/* Wait, checking to see if finished (completed or errAborted).
* If timed-out or never-ran, record error status.
* Return error count. */
{
int maxTimeInMilliseconds = 1000 * maxTimeInSeconds;
struct paraFetchData *pfd;
int errCount = 0;
int waitTime = 0;
while(1)
{
sleep1000(50); // milliseconds
waitTime += 50;
boolean done = TRUE;
pthread_mutex_lock( &pfdMutex );
if (pfdList || pfdRunning)
done = FALSE;
pthread_mutex_unlock( &pfdMutex );
if (done)
break;
if (waitTime >= maxTimeInMilliseconds)
break;
}
pthread_mutex_lock( &pfdMutex );
pfdNeverStarted = pfdList;
pfdList = NULL; // stop the workers from starting any more waiting track loads
for (pfd = pfdNeverStarted; pfd; pfd = pfd->next)
{
// track was never even started
char temp[256];
safef(temp, sizeof temp, "Ran out of time (%d milliseconds) unable to process %s", maxTimeInMilliseconds, pfd->track->track);
pfd->track->networkErrMsg = cloneString(temp);
++errCount;
}
for (pfd = pfdRunning; pfd; pfd = pfd->next)
{
// unfinished track
char temp[256];
safef(temp, sizeof temp, "Timeout %d milliseconds exceeded processing %s", maxTimeInMilliseconds, pfd->track->track);
pfd->track->networkErrMsg = cloneString(temp);
++errCount;
}
for (pfd = pfdDone; pfd; pfd = pfd->next)
{
// some done tracks may have errors
if (pfd->track->networkErrMsg)
++errCount;
}
pthread_mutex_unlock( &pfdMutex );
return errCount;
}
static void printTrackTiming()
{
hPrintf("<span class='trackTiming'>track, load time, draw time, total<br />\n");
struct track *track;
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("</span>\n");
}
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());
jsonObjectAdd(jsonForClient, "insideX", newJsonNumber(insideX));
jsonObjectAdd(jsonForClient, "revCmplDisp", newJsonBoolean(revCmplDisp));
if (hPrintStatus()) cartSaveSession(cart);
-clearButtonJavascript = "document.TrackHeaderForm.position.value=''; document.getElementById('suggest').value='';";
/* See if want to include sequence search results. */
userSeqString = cartOptionalString(cart, "ss");
if (userSeqString && !ssFilesExist(userSeqString))
{
userSeqString = NULL;
cartRemove(cart, "ss");
}
if (!hideControls)
hideControls = cartUsualBoolean(cart, "hideControls", FALSE);
if (measureTiming)
measureTime("Time before getTrackList");
trackList = getTrackList(&groupList, defaultTracks ? -1 : -2);
if (measureTiming)
measureTime("getTrackList");
makeGlobalTrackHash(trackList);
/* Tell tracks to load their items. */
// honor defaultImgOrder
if (cgiVarExists("hgt.defaultImgOrder"))
{
char wildCard[32];
safef(wildCard,sizeof(wildCard),"*_%s",IMG_ORDER_VAR);
cartRemoveLike(cart, wildCard);
}
// Subtrack settings must be removed when composite/view settings are updated
parentChildCartCleanup(trackList,cart,oldVars);
if (measureTiming)
measureTime("parentChildCartCleanup");
/* Honor hideAll and visAll variables */
if (hideAll || defaultTracks)
{
int vis = (hideAll ? tvHide : -1);
changeTrackVis(groupList, NULL, vis);
}
/* Before loading items, deal with the next/prev item arrow buttons if pressed. */
if (cgiVarExists("hgt.nextItem"))
doNextPrevItem(TRUE, cgiUsualString("hgt.nextItem", NULL));
else if (cgiVarExists("hgt.prevItem"))
doNextPrevItem(FALSE, cgiUsualString("hgt.prevItem", NULL));
if(!psOutput && !cartUsualBoolean(cart, "hgt.imageV1", FALSE))
{
// Start an imagebox (global for now to avoid huge rewrite of hgTracks)
// Set up imgBox dimensions
int sideSliceWidth = 0; // Just being explicit
if (withLeftLabels)
sideSliceWidth = (insideX - gfxBorder*3) + 2;
theImgBox = imgBoxStart(database,chromName,winStart,winEnd,
(!revCmplDisp),sideSliceWidth,tl.picWidth);
// Define a portal with a default expansion size,
// then set the global dimensions to the full image size
if (imgBoxPortalDefine(theImgBox,&winStart,&winEnd,&(tl.picWidth),0))
{
winBaseCount = winEnd - winStart;
insideWidth = tl.picWidth-gfxBorder-insideX;
}
}
char *jsCommand = cartCgiUsualString(cart, hgtJsCommand, "");
if (!isEmpty(jsCommand))
{
cartRemove(cart, hgtJsCommand);
jsCommandDispatch(jsCommand, trackList);
}
/* adjust visibility */
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;
}
}
if (sameString(cfgOptionDefault("trackLog", "off"), "on"))
logTrackVisibilities(cartSessionId(cart), trackList);
/* pre-load remote tracks in parallel */
int ptMax = atoi(cfgOptionDefault("parallelFetch.threads", "20")); // default number of threads for parallel fetch.
int pfdListCount = 0;
pthread_t *threads = NULL;
if (ptMax > 0) // parallelFetch.threads=0 to disable parallel fetch
{
findLeavesForParallelLoad(trackList, &pfdList);
pfdListCount = slCount(pfdList);
/* launch parallel threads */
ptMax = min(ptMax, pfdListCount);
if (ptMax > 0)
{
AllocArray(threads, ptMax);
/* Create threads */
int pt;
for (pt = 0; pt < ptMax; ++pt)
{
int rc = pthread_create(&threads[pt], NULL, remoteParallelLoad, &threads[pt]);
if (rc)
{
errAbort("Unexpected error %d from pthread_create(): %s",rc,strerror(rc));
}
}
}
}
/* load regular tracks */
for (track = trackList; track != NULL; track = track->next)
{
if (track->visibility != tvHide)
{
if (!track->parallelLoading)
{
if (measureTiming)
lastTime = clock1000();
checkMaxWindowToDraw(track);
checkIfWiggling(cart, track);
track->loadItems(track);
if (measureTiming)
{
thisTime = clock1000();
track->loadTime = thisTime - lastTime;
}
}
}
}
if (ptMax > 0)
{
/* wait for remote parallel load to finish */
remoteParallelLoadWait(atoi(cfgOptionDefault("parallelFetch.timeout", "90"))); // wait up to default 90 seconds.
if (measureTiming)
measureTime("Waiting for parallel (%d threads for %d tracks) remote data fetch", ptMax, pfdListCount);
}
printTrackInitJavascript(trackList);
/* Generate two lists of hidden variables for track group visibility. Kludgy,
but required b/c we have two different navigation forms on this page, but
we want open/close changes in the bottom form to be submitted even if the user
submits via the top form. */
struct dyString *trackGroupsHidden1 = newDyString(1000);
struct dyString *trackGroupsHidden2 = newDyString(1000);
for (group = groupList; group != NULL; group = group->next)
{
if (group->trackList != NULL)
{
int looper;
for (looper=1;looper<=2;looper++)
{
boolean isOpen = !isCollapsedGroup(group);
char buf[1000];
safef(buf, sizeof(buf), "<input type='hidden' name=\"%s\" id=\"%s_%d\" value=\"%s\">\n", collapseGroupVar(group->name), collapseGroupVar(group->name), looper, isOpen ? "0" : "1");
dyStringAppend(looper == 1 ? trackGroupsHidden1 : trackGroupsHidden2, buf);
}
}
}
if (theImgBox)
{
// If a portal was established, then set the global dimensions back to the portal size
if (imgBoxPortalDimensions(theImgBox,NULL,NULL,NULL,NULL,&winStart,&winEnd,&(tl.picWidth),NULL))
{
winBaseCount = winEnd - winStart;
insideWidth = tl.picWidth-gfxBorder-insideX;
}
}
/* Center everything from now on. */
hPrintf("<CENTER>\n");
// info for drag selection javascript
jsonObjectAdd(jsonForClient, "winStart", newJsonNumber(winStart));
jsonObjectAdd(jsonForClient, "winEnd", newJsonNumber(winEnd));
jsonObjectAdd(jsonForClient, "chromName", newJsonString(chromName));
if(trackImgOnly && !ideogramToo)
{
struct track *ideoTrack = chromIdeoTrack(trackList);
if (ideoTrack)
{
ideoTrack->limitedVisSet = TRUE;
ideoTrack->limitedVis = tvHide; /* Don't draw in main gif. */
}
makeActiveImage(trackList, psOutput);
fflush(stdout);
return; // bail out b/c we are done
}
if (!hideControls)
{
/* set white-space to nowrap to prevent buttons from wrapping when screen is
* narrow */
hPrintf("<DIV STYLE=\"white-space:nowrap;\">\n");
printMenuBar();
//menuBarAppendExtTools();
/* Show title . */
freezeName = hFreezeFromDb(database);
if(freezeName == NULL)
freezeName = "Unknown";
hPrintf("<span style='font-size:x-large;'><B>");
if (startsWith("zoo",database) )
{
hPrintf("%s %s on %s June 2002 Assembly %s target1",
organization, browserName, organism, freezeName);
}
else
{
if (sameString(organism, "Archaea"))
{
hPrintf("%s %s on Archaeon %s Assembly",
organization, browserName, freezeName);
}
else
{
if (stringIn(database, freezeName))
hPrintf("%s %s on %s %s Assembly",
organization, browserName, organism, freezeName);
else
hPrintf("%s %s on %s %s Assembly (%s)",
organization, browserName, trackHubSkipHubName(organism), freezeName, trackHubSkipHubName(database));
}
}
hPrintf("</B></span><BR>\n");
/* This is a clear submit button that browsers will use by default when enter is pressed in position box. */
hPrintf("<INPUT TYPE=IMAGE BORDER=0 NAME=\"hgt.dummyEnterButton\" src=\"../images/DOT.gif\">");
/* Put up scroll and zoom controls. */
#ifndef USE_NAVIGATION_LINKS
hWrites("move ");
hButtonWithOnClick("hgt.left3", "<<<", "move 95% to the left",
"return imageV2.navigateButtonClick(this);");
hButtonWithOnClick("hgt.left2", " <<", "move 47.5% to the left",
"return imageV2.navigateButtonClick(this);");
hButtonWithOnClick("hgt.left1", " < ", "move 10% to the left",
"return imageV2.navigateButtonClick(this);");
hButtonWithOnClick("hgt.right1", " > ", "move 10% to the right",
"return imageV2.navigateButtonClick(this);");
hButtonWithOnClick("hgt.right2", ">> ", "move 47.5% to the right",
"return imageV2.navigateButtonClick(this);");
hButtonWithOnClick("hgt.right3", ">>>", "move 95% to the right",
"return imageV2.navigateButtonClick(this);");
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);
topButton("hgt.out4", ZOOM_100X);
hWrites("<div style='height:0.3em;'></div>\n");
#endif//ndef USE_NAVIGATION_LINKS
if (showTrackControls)
{
/* Break into a second form so that zooming and scrolling
* can be done with a 'GET' so that user can back up from details
* page without Internet Explorer popping up an annoying dialog.
* Do rest of page as a 'POST' so that the ultra-long URL from
* all the track controls doesn't break things. IE URL limit
* is 2000 bytes, but some firewalls impose a ~1000 byte limit.
* As a side effect of breaking up the page into two forms
* we need to repeat the position in a hidden variable here
* so that zoom/scrolling always has current position to work
* from. */
// This 'dirty' field is used to check if js/ajax changes to the page have occurred.
// If so and it is reached by the back button, a page reload will occur instead.
hPrintf("<INPUT TYPE='text' style='display:none;' name='dirty' id='dirty' VALUE='false'>\n");
hPrintf("<INPUT TYPE=HIDDEN id='positionHidden' NAME=\"position\" "
"VALUE=\"%s:%d-%d\">", chromName, winStart+1, winEnd);
hPrintf("\n%s", trackGroupsHidden1->string);
hPrintf("</CENTER></FORM>\n");
hPrintf("<FORM ACTION=\"%s\" NAME=\"TrackForm\" id=\"TrackForm\" METHOD=\"POST\">\n\n",
hgTracksName());
hPrintf("%s", trackGroupsHidden2->string);
freeDyString(&trackGroupsHidden1);
freeDyString(&trackGroupsHidden2);
if (!psOutput) cartSaveSession(cart); /* Put up hgsid= as hidden variable. */
- clearButtonJavascript = "document.TrackForm.position.value=''; document.getElementById('suggest').value='';";
hPrintf("<CENTER>");
}
/* Make line that says position. */
{
char buf[256];
char *survey = cfgOptionEnv("HGDB_SURVEY", "survey");
char *surveyLabel = cfgOptionEnv("HGDB_SURVEY_LABEL", "surveyLabel");
char *javascript = "onchange=\"document.location = '/cgi-bin/hgTracks?db=' + document.TrackForm.db.options[document.TrackForm.db.selectedIndex].value;\"";
if (containsStringNoCase(database, "zoo"))
{
hPuts("Organism ");
printAssemblyListHtmlExtra(database, javascript);
}
sprintf(buf, "%s:%d-%d", chromName, winStart+1, winEnd);
position = cloneString(buf);
hPrintf("<span class='positionDisplay' id='positionDisplay' title='click to copy position to input box'>%s</span>", addCommasToPos(database, position));
hPrintf("<input type='hidden' name='position' id='position' value='%s'>\n", buf);
sprintLongWithCommas(buf, winEnd - winStart);
hPrintf(" <span id='size'>%s</span> bp. ", buf);
hPrintf("<input class='positionInput' type='text' name='hgt.positionInput' id='positionInput' size='60'>\n");
hWrites(" ");
hButton("hgt.jump", "go");
if (!trackHubDatabase(database))
{
jsonObjectAdd(jsonForClient, "assemblySupportsGeneSuggest", newJsonBoolean(assemblySupportsGeneSuggest(database)));
if (assemblySupportsGeneSuggest(database))
hPrintf("<input type='hidden' name='hgt.suggestTrack' id='suggestTrack' value='%s'>\n", assemblyGeneSuggestTrack(database));
}
if (survey && differentWord(survey, "off"))
hPrintf(" <span style='background-color:yellow;'>"
"<A HREF='%s' TARGET=_BLANK><EM><B>%s</EM></B></A></span>\n",
survey, surveyLabel ? surveyLabel : "Take survey");
hPutc('\n');
}
}
/* Make chromsome ideogram gif and map. */
makeChromIdeoImage(&trackList, psOutput, ideoTn);
#ifdef USE_NAVIGATION_LINKS
hPrintf("<TABLE BORDER=0 CELLPADDING=0 width='%d'><tr style='font-size:small;'>\n",
tl.picWidth);//min(tl.picWidth, 800));
hPrintf("<td width='40' align='left'><a href='?hgt.left3=1' "
"title='move 95% to the left'><<<</a>\n");
hPrintf("<td width='30' align='left'><a href='?hgt.left2=1' "
"title='move 47.5% to the left'><<</a>\n");
hPrintf("<td width='20' align='left'><a href='?hgt.left1=1' "
"title='move 10% to the left'><</a>\n");
hPrintf("<td> </td>\n"); // Without width cell expands table with, forcing others to sides
hPrintf("<td width='40' align='left'><a href='?hgt.in1=1' "
"title='zoom in 1.5x'>> <</a>\n");
hPrintf("<td width='60' align='left'><a href='?hgt.in2=1' "
"title='zoom in 3x'>>> <<</a>\n");
hPrintf("<td width='80' align='left'><a href='?hgt.in3=1' "
"title='zoom in 10x'>>>> <<<</a>\n");
hPrintf("<td width='40' align='left'><a href='?hgt.inBase=1' "
"title='zoom in to base range'>><i>base</i><</a>\n");
hPrintf("<td> </td>\n"); // Without width cell expands table with, forcing others to sides
hPrintf("<td width='40' align='right'><a href='?hgt.out1=1' "
"title='zoom out 1.5x'>< ></a>\n");
hPrintf("<td width='60' align='right'><a href='?hgt.out2=1' "
"title='zoom out 3x'><< >></a>\n");
hPrintf("<td width='80' align='right'><a href='?hgt.out3=1' "
"title='zoom out 10x'><<< >>></a>\n");
hPrintf("<td width='80' align='right'><a href='?hgt.out4=1' "
"title='zoom out 100x'><<< >>></a>\n");
hPrintf("<td> </td>\n"); // Without width cell expands table width, forcing others to sides
hPrintf("<td width='20' align='right'><a href='?hgt.right1=1' "
"title='move 10% to the right'>></a>\n");
hPrintf("<td width='30' align='right'><a href='?hgt.right2=1' "
"title='move 47.5% to the right'>>></a>\n");
hPrintf("<td width='40' align='right'><a href='?hgt.right3=1' """
"title='move 95% to the right'>>>></a>\n");
hPrintf("</tr></table>\n");
#endif///def USE_NAVIGATION_LINKS
/* Make clickable image and map. */
makeActiveImage(trackList, psOutput);
fflush(stdout);
if(trackImgOnly)
{
// bail out b/c we are done
if (measureTiming)
{
printTrackTiming();
}
return;
}
if (!hideControls)
{
struct controlGrid *cg = NULL;
/* note a trick of WIDTH=27 going on here. The 6,15,6 widths following
* go along with this trick */
hPrintf("<TABLE BORDER=0 CELLSPACING=1 CELLPADDING=1 WIDTH=%d COLS=%d><TR>\n",
tl.picWidth, 27);
#ifndef USE_NAVIGATION_LINKS
hPrintf("<TD COLSPAN=6 ALIGN=left NOWRAP>");
hPrintf("move start<BR>");
hButtonWithOnClick("hgt.dinkLL", " < ", "move start position to the left",
"return imageV2.navigateButtonClick(this);");
hTextVar("dinkL", cartUsualString(cart, "dinkL", "2.0"), 3);
hButtonWithOnClick("hgt.dinkLR", " > ", "move start position to the right",
"return imageV2.navigateButtonClick(this);");
hPrintf("</TD>");
hPrintf("<td width='30'> </td>\n");
#endif//ndef USE_NAVIGATION_LINKS
hPrintf("<TD COLSPAN=15 style=\"white-space:normal\">"); // allow this text to wrap
hWrites("Click on a feature for details. ");
hWrites("Click or drag in the base position track to zoom in. ");
hWrites("Click side bars for track options. ");
hWrites("Drag side bars or labels up or down to reorder tracks. ");
hWrites("Drag tracks left or right to new position. ");
hPrintf("</TD>");
#ifndef USE_NAVIGATION_LINKS
hPrintf("<td width='30'> </td>\n");
hPrintf("<TD COLSPAN=6 ALIGN=right NOWRAP>");
hPrintf("move end<BR>");
hButtonWithOnClick("hgt.dinkRL", " < ", "move end position to the left",
"return imageV2.navigateButtonClick(this);");
hTextVar("dinkR", cartUsualString(cart, "dinkR", "2.0"), 3);
hButtonWithOnClick("hgt.dinkRR", " > ", "move end position to the right",
"return imageV2.navigateButtonClick(this);");
hPrintf("</TD>");
#endif//ndef USE_NAVIGATION_LINKS
hPrintf("</TR></TABLE>\n");
/* Display bottom control panel. */
if (isSearchTracksSupported(database,cart))
{
cgiMakeButtonWithMsg(TRACK_SEARCH, TRACK_SEARCH_BUTTON,TRACK_SEARCH_HINT);
hPrintf(" ");
}
hButtonWithMsg("hgt.reset", "default tracks","Display only default tracks");
hPrintf(" ");
hButtonWithMsg("hgt.defaultImgOrder", "default order",
"Display current tracks in their default order");
// if (showTrackControls) - always show "hide all", Hiram 2008-06-26
{
hPrintf(" ");
hButtonWithMsg("hgt.hideAll", "hide all","Hide all currently visibile tracks");
}
hPrintf(" ");
hPrintf("<INPUT TYPE='button' VALUE='%s' onClick='document.customTrackForm.submit();"
"return false;' title='%s'>",
hasCustomTracks ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL,
hasCustomTracks ? "Manage your custom tracks" : "Add your own custom tracks");
hPrintf(" ");
if (hubConnectTableExists())
{
hPrintf("<INPUT TYPE='button' VALUE='track hubs' onClick='document.trackHubForm.submit();"
"return false;' title='Import tracks from hubs'>");
hPrintf(" ");
}
hButtonWithMsg("hgTracksConfigPage", "configure","Configure image and track selection");
hPrintf(" ");
if (!hIsGsidServer())
{
hButtonWithMsg("hgt.toggleRevCmplDisp", "reverse",
revCmplDisp ? "Show forward strand at this location"
: "Show reverse strand at this location");
hPrintf(" ");
}
hButtonWithOnClick("hgt.setWidth", "resize", "Resize image width to browser window size", "hgTracksSetWidth()");
hPrintf(" ");
hButtonWithMsg("hgt.refresh", "refresh","Refresh image");
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 vis.expandAllGroups(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 vis.expandAllGroups(true)");
hPrintf("</td></tr>");
if (!hIsGsidServer())
{
cg = startControlGrid(MAX_CONTROL_COLUMNS, "left");
}
else
{
/* 4 cols fit GSID's display better */
cg = startControlGrid(4, "left");
}
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 class='blueToggleBar'>",MAX_CONTROL_COLUMNS);
else
hPrintf("<th align=\"left\" colspan=%d class='blueToggleBar'>",
MAX_CONTROL_COLUMNS-1);
hPrintf("<table style='width:100%%;'><tr><td style='text-align:left;'>");
hPrintf("\n<A NAME=\"%sGroup\"></A>",group->name);
hPrintf("<IMG class='toggleButton' onclick=\"return vis.toggleForGroup(this, '%s');\" "
"id=\"%s_button\" src=\"%s\" alt=\"%s\" title='%s this group'> ",
group->name, group->name, indicatorImg, indicator,isOpen?"Collapse":"Expand");
hPrintf("</td><td style='text-align:center; width:90%%;'>\n<B>%s</B>", group->label);
hPrintf("</td><td style='text-align:right;'>\n");
hPrintf("<input type='submit' name='hgt.refresh' value='refresh' "
"title='Update image with your changes'>\n");
hPrintf("</td></tr></table></th>\n");
controlGridEndRow(cg);
/* First track group that is not the custom track group (#1)
* or a track hub, gets the Base Position track
* unless it's collapsed. */
if (!showedRuler && !isHubTrack(group->name) &&
differentString(group->name, "user") )
{
char *url = trackUrl(RULER_TRACK_NAME, chromName);
showedRuler = TRUE;
myControlGridStartCell(cg, isOpen, group->name);
hPrintf("<A HREF=\"%s\">", url);
hPrintf(" %s<BR> ", RULER_TRACK_LABEL);
hPrintf("</A>");
hDropListClassWithStyle("ruler", rulerMenu,
sizeof(rulerMenu)/sizeof(char *), rulerMenu[rulerMode],
rulerMode == tvHide ? "hiddenText" : "normalText",
TV_DROPDOWN_STYLE);
controlGridEndCell(cg);
freeMem(url);
}
/* Add supertracks to track list, sort by priority and
* determine if they have visible member tracks */
groupTrackListAddSuper(cart, group);
/* Display track controls */
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
if (tdbIsSuperTrackChild(track->tdb))
/* don't display supertrack members */
continue;
myControlGridStartCell(cg, isOpen, group->name);
if (track->hasUi)
{
char *url = trackUrl(track->track, chromName);
char *longLabel = replaceChars(track->longLabel, "\"", """);
hPrintPennantIcon(track->tdb);
// Print an icon before the title when one is defined
hPrintf("<A HREF=\"%s\" title=\"%s\">", url, longLabel);
freeMem(url);
freeMem(longLabel);
}
hPrintf(" %s", track->shortLabel);
if (tdbIsSuper(track->tdb))
hPrintf("...");
hPrintf("<BR> ");
if (track->hasUi)
hPrintf("</A>");
if (hTrackOnChrom(track->tdb, chromName))
{
if (tdbIsSuper(track->tdb))
superTrackDropDown(cart, track->tdb,
superTrackHasVisibleMembers(track->tdb));
else
{
/* check for option of limiting visibility to one mode */
hTvDropDownClassVisOnly(track->track, track->visibility,
rTdbTreeCanPack(track->tdb),
(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)
printTrackTiming();
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");
/* hidden form for track hub CGI */
hPrintf("<FORM ACTION='%s' NAME='trackHubForm'>", hgHubConnectName());
cartSaveSession(cart);
hPrintf("</FORM>\n");
pruneRedundantCartVis(trackList);
if (measureTiming)
measureTime("Done with trackForm");
}
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");
if(!trackImgOnly)
{
printMenuBar();
printf("<div style=\"margin: 10px\">\n");
printf("<H1>PDF Output</H1>\n");
printf("PDF images can be printed with Acrobat Reader "
"and edited by many drawing programs such as Adobe "
"Illustrator or Inkscape.<BR>");
}
doTrackForm(psTn.forCgi, &ideoPsTn);
pdfFile = convertEpsToPdf(psTn.forCgi);
if (strlen(ideoPsTn.forCgi))
ideoPdfFile = convertEpsToPdf(ideoPsTn.forCgi);
if (pdfFile != NULL)
{
printf("<UL style=\"margin-top:5px;\">\n");
printf("<LI>Download <A TARGET=_blank HREF=\"%s\">"
"the current browser graphic in PDF</A>\n", pdfFile);
if (ideoPdfFile != NULL)
printf("<LI>Download <A TARGET=_blank HREF=\"%s\">"
"the current chromosome ideogram in PDF</A>\n", ideoPdfFile);
printf("</UL>\n");
freez(&pdfFile);
freez(&ideoPdfFile);
// postscript
printf("EPS (Postscript) images are a variant of PDF and easier to import into some "
"drawing programs.\n");
printf("<UL style=\"margin-top: 5px;\">\n");
printf("<LI>Download <A HREF=\"%s\">the current browser graphic in EPS</A>", psTn.forCgi);
if (strlen(ideoPsTn.forCgi))
printf("<LI>Download <A HREF=\"%s\">the current chromosome ideogram in EPS</A>", ideoPsTn.forCgi);
printf("</UL>\n");
// see redmine #1077
printf("<div style=\"margin-top:15px\">Tips for producing quality images for publication:</div>\n");
printf("<UL style=\"margin-top:0px\">\n");
printf("<LI>Add assembly name and chromosome range to the image on the\n"
"<A HREF=\"hgTrackUi?g=ruler\">configuration page of the base position track</A>.\n");
printf("<LI>If using the UCSC Genes track, consider showing only one transcript per gene by turning off splice variants on the track configuration page.\n");
printf("<LI>Increase the font size and remove the light blue vertical guidelines in the \n"
"<A HREF=\"hgTracks?hgTracksConfigPage=configure\">image configuration menu</A>.");
printf("<LI>In the image configuration menu, change the size of the image,\n"
"to make it look more square.\n");
printf("</UL>\n");
printf("</div>\n");
}
else
printf("<BR><BR>PDF format not available");
printf("<a href='../cgi-bin/hgTracks'><input type='button' VALUE='Return to Browser'></a>\n");
}
boolean isGenome(char *pos)
/* Return TRUE if pos is genome. */
{
pos = trimSpaces(pos);
return(sameWord(pos, "genome") || sameWord(pos, "hgBatch"));
}
void setRulerMode()
/* Set the rulerMode variable from cart. */
{
char *s = cartUsualString(cart, RULER_TRACK_NAME, "dense");
if (sameWord(s, "full") || sameWord(s, "on"))
rulerMode = tvFull;
else if (sameWord(s, "dense"))
rulerMode = tvDense;
else
rulerMode = tvHide;
}
void setLayoutGlobals()
/* Figure out basic dimensions of display. */
{
withIdeogram = cartUsualBoolean(cart, "ideogram", TRUE);
withLeftLabels = cartUsualBoolean(cart, "leftLabels", TRUE);
withCenterLabels = cartUsualBoolean(cart, "centerLabels", TRUE);
withGuidelines = cartUsualBoolean(cart, "guidelines", TRUE);
if (!cartUsualBoolean(cart, "hgt.imageV1", FALSE))
withNextItemArrows = cartUsualBoolean(cart, "nextItemArrows", FALSE);
withNextExonArrows = cartUsualBoolean(cart, "nextExonArrows", TRUE);
withExonNumbers = cartUsualBoolean(cart, "exonNumbers", TRUE);
if (!hIsGsidServer())
{
revCmplDisp = cartUsualBooleanDb(cart, database, REV_CMPL_DISP, FALSE);
}
withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE);
insideX = trackOffsetX();
insideWidth = tl.picWidth-gfxBorder-insideX;
}
void tracksDisplay()
/* Put up main tracks display. This routine handles zooming and
* scrolling. */
{
char newPos[256];
char *defaultPosition = hDefaultPos(database);
char titleVar[256];
position = getPositionFromCustomTracks();
if (position == NULL)
position = cartGetPosition(cart, database);
if (sameString(position, ""))
{
hUserAbort("Please go back and enter a coordinate range or a search term in the \"search term\" 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 && differentString(position, defaultPosition))
cartSetString(cart, "position", position);
}
}
/* After position is found set up hash of matches that should
be drawn with names highlighted for easy identification. */
createHgFindMatchHash();
/* This means that no single result was found
I.e., multiple results may have been found and are printed out prior to this code*/
if (NULL == chromName)
{
// In case user manually edits the browser location as described in #13009,
// revert the position. If they instead choose from the list as we expect,
// that will set the position to their choice.
char *lastPosition = cartUsualString(cart, "lastPosition", hDefaultPos(database));
cartSetString(cart, "position", lastPosition);
return;
}
// save the current position to the cart var position.<db>
cartSetDbPosition(cart, database, position);
seqBaseCount = hChromSize(database, chromName);
winBaseCount = winEnd - winStart;
/* Figure out basic dimensions of display. This
* needs to be done early for the sake of the
* zooming and dinking routines. */
setLayoutGlobals();
baseShowPos = cartUsualBoolean(cart, BASE_SHOWPOS, FALSE);
baseShowAsm = cartUsualBoolean(cart, BASE_SHOWASM, FALSE);
baseShowScaleBar = cartUsualBoolean(cart, BASE_SCALE_BAR, TRUE);
baseShowRuler = cartUsualBoolean(cart, BASE_SHOWRULER, TRUE);
safef(titleVar,sizeof(titleVar),"%s_%s", BASE_TITLE, database);
baseTitle = cartUsualString(cart, titleVar, "");
if (sameString(baseTitle, ""))
baseTitle = NULL;
if (cgiVarExists("hgt.toggleRevCmplDisp"))
toggleRevCmplDisp();
setRulerMode();
/* Do zoom/scroll if they hit it. */
if (cgiVarExists("hgt.left3"))
relativeScroll(-0.95);
else if (cgiVarExists("hgt.left2"))
relativeScroll(-0.475);
else if (cgiVarExists("hgt.left1"))
relativeScroll(-0.1);
else if (cgiVarExists("hgt.right1"))
relativeScroll(0.1);
else if (cgiVarExists("hgt.right2"))
relativeScroll(0.475);
else if (cgiVarExists("hgt.right3"))
relativeScroll(0.95);
else if (cgiVarExists("hgt.inBase"))
zoomToBaseLevel();
else if (cgiVarExists("hgt.in3"))
zoomAroundCenter(1.0/10.0);
else if (cgiVarExists("hgt.in2"))
zoomAroundCenter(1.0/3.0);
else if (cgiVarExists("hgt.in1"))
zoomAroundCenter(1.0/1.5);
else if (cgiVarExists("hgt.out1"))
zoomAroundCenter(1.5);
else if (cgiVarExists("hgt.out2"))
zoomAroundCenter(3.0);
else if (cgiVarExists("hgt.out3"))
zoomAroundCenter(10.0);
else if (cgiVarExists("hgt.out4"))
zoomAroundCenter(100.0);
else if (cgiVarExists("hgt.dinkLL"))
dinkWindow(TRUE, -dinkSize("dinkL"));
else if (cgiVarExists("hgt.dinkLR"))
dinkWindow(TRUE, dinkSize("dinkL"));
else if (cgiVarExists("hgt.dinkRL"))
dinkWindow(FALSE, -dinkSize("dinkR"));
else if (cgiVarExists("hgt.dinkRR"))
dinkWindow(FALSE, dinkSize("dinkR"));
/* Clip chromosomal position to fit. */
if (winEnd < winStart)
{
int temp = winEnd;
winEnd = winStart;
winStart = temp;
}
else if (winStart == winEnd)
{
winStart -= 1;
winEnd += 1;
}
if (winStart < 0)
{
winStart = 0;
}
if (winEnd > seqBaseCount)
{
winEnd = seqBaseCount;
}
if (winStart > seqBaseCount)
{
winStart = seqBaseCount - 1000;
}
winBaseCount = winEnd - winStart;
if (winBaseCount <= 0)
hUserAbort("Window out of range on %s", chromName);
/* Save computed position in cart. */
sprintf(newPos, "%s:%d-%d", chromName, winStart+1, winEnd);
cartSetString(cart, "org", organism);
cartSetString(cart, "db", database);
cartSetString(cart, "position", newPos);
if (cartUsualBoolean(cart, "hgt.psOutput", FALSE))
handlePostscript();
else
doTrackForm(NULL, NULL);
}
void chromInfoTotalRow(int count, long long total)
/* Make table row with total number of sequences and size from chromInfo. */
{
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
printf("Total: %d", count);
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
printLongWithCommas(stdout, total);
cgiTableFieldEnd();
cgiTableRowEnd();
}
void chromInfoRowsChromExt(char *sortType)
/* Make table rows of chromosomal chromInfo name & size, sorted by name. */
{
struct slName *chromList = hAllChromNames(database);
struct slName *chromPtr = NULL;
long long total = 0;
if (sameString(sortType,"default"))
slSort(&chromList, chrSlNameCmp);
else if (sameString(sortType,"withAltRandom"))
slSort(&chromList, chrSlNameCmpWithAltRandom);
else
errAbort("unknown sort type in chromInfoRowsChromExt: %s", sortType);
for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
{
unsigned size = hChromSize(database, chromPtr->name);
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
printf("<A HREF=\"%s?%s=%s&position=%s\">%s</A>",
hgTracksName(), cartSessionVarName(), cartSessionId(cart),
chromPtr->name, chromPtr->name);
cgiTableFieldEnd();
cgiTableFieldStartAlignRight();
printLongWithCommas(stdout, size);
puts(" ");
cgiTableFieldEnd();
cgiTableRowEnd();
total += size;
}
chromInfoTotalRow(slCount(chromList), total);
slFreeList(&chromList);
}
void chromInfoRowsChrom()
/* Make table rows of chromosomal chromInfo name & size, sorted by name. */
{
chromInfoRowsChromExt("default");
}
static int chromInfoCmpSize(const void *va, const void *vb)
/* Compare to sort based on chrom size */
{
const struct chromInfo *a = *((struct chromInfo **)va);
const struct chromInfo *b = *((struct chromInfo **)vb);
return b->size - a->size;
}
void chromInfoRowsNonChromTrackHub(int limit)
/* Make table rows of non-chromosomal chromInfo name & size */
/* leaks chromInfo list */
{
struct chromInfo *chromInfo = trackHubAllChromInfo(database);
slSort(&chromInfo, chromInfoCmpSize);
int seqCount = slCount(chromInfo);
long long total = 0;
char msg1[512], msg2[512];
boolean truncating;
int count = limit;
truncating = (limit > 0) && (seqCount > limit);
for(;count-- && (chromInfo != NULL); chromInfo = chromInfo->next)
{
unsigned size = chromInfo->size;
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
printf("<A HREF=\"%s?%s=%s&position=%s\">%s</A>",
hgTracksName(), cartSessionVarName(), cartSessionId(cart),
chromInfo->chrom,chromInfo->chrom);
cgiTableFieldEnd();
cgiTableFieldStartAlignRight();
printLongWithCommas(stdout, size);
puts(" ");
cgiTableFieldEnd();
cgiTableRowEnd();
total += size;
}
if (!truncating)
{
chromInfoTotalRow(seqCount, total);
}
else
{
safef(msg1, sizeof(msg1), "Limit reached");
safef(msg2, sizeof(msg2), "%d rows displayed", limit);
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
puts(msg1);
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
puts(msg2);
cgiTableFieldEnd();
for(;limit-- && (chromInfo != NULL); chromInfo = chromInfo->next)
total += chromInfo->size;
unsigned scafCount = seqCount;
unsigned totalSize = total;
cgiTableRowEnd();
safef(msg1, sizeof(msg1), "contig/scaffold<BR>count:");
safef(msg2, sizeof(msg2), "total size:");
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
puts(msg1);
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
puts(msg2);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
printLongWithCommas(stdout, scafCount);
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
printLongWithCommas(stdout, totalSize);
cgiTableFieldEnd();
cgiTableRowEnd();
}
}
void chromInfoRowsNonChrom(int limit)
/* Make table rows of non-chromosomal chromInfo name & size, sorted by size. */
{
if (trackHubDatabase(database))
{
chromInfoRowsNonChromTrackHub(limit);
return;
}
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, "NOSQLINJ select count(*) from chromInfo");
truncating = (limit > 0) && (seqCount > limit);
if (!truncating)
{
sr = sqlGetResult(conn, "NOSQLINJ select chrom,size from chromInfo order by size desc");
}
else
{
sqlSafef(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=%s&position=%s\">%s</A>",
hgTracksName(), cartSessionVarName(), cartSessionId(cart),
row[0], row[0]);
cgiTableFieldEnd();
cgiTableFieldStartAlignRight();
printLongWithCommas(stdout, size);
puts(" ");
cgiTableFieldEnd();
cgiTableRowEnd();
total += size;
}
if (!truncating)
{
chromInfoTotalRow(seqCount, total);
}
else
{
safef(msg1, sizeof(msg1), "Limit reached");
safef(msg2, sizeof(msg2), "%d rows displayed", limit);
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
puts(msg1);
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
puts(msg2);
cgiTableFieldEnd();
sqlFreeResult(&sr);
sqlSafef(query, sizeof(query), "select count(*),sum(size) from chromInfo");
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
unsigned scafCount = sqlUnsigned(row[0]);
unsigned totalSize = sqlUnsigned(row[1]);
cgiTableRowEnd();
safef(msg1, sizeof(msg1), "contig/scaffold<BR>count:");
safef(msg2, sizeof(msg2), "total size:");
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
puts(msg1);
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
puts(msg2);
cgiTableFieldEnd();
cgiTableRowEnd();
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
printLongWithCommas(stdout, scafCount);
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
printLongWithCommas(stdout, totalSize);
cgiTableFieldEnd();
}
cgiTableRowEnd();
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
static void chromSizesDownloadRow()
/* Show link to chrom.sizes file at end of chromInfo table (unless this is a hub) */
{
if (! trackHubDatabase(database))
{
cgiSimpleTableRowStart();
cgiSimpleTableFieldStart();
puts("Download as file");
cgiTableFieldEnd();
cgiSimpleTableFieldStart();
printf("<A HREF='http://%s/goldenPath/%s/bigZips/%s.chrom.sizes'>%s.chrom.sizes</A>",
hDownloadsServer(), database, database, database);
cgiTableFieldEnd();
cgiTableRowEnd();
}
}
void chromInfoPage()
/* Show list of chromosomes (or scaffolds, etc) on which this db is based. */
{
char *position = cartUsualString(cart, "position", hDefaultPos(database));
char *defaultChrom = hDefaultChrom(database);
char *freeze = hFreezeFromDb(database);
struct dyString *title = dyStringNew(512);
if (freeze == NULL)
dyStringPrintf(title, "%s Browser Sequences",
hOrganism(database));
else if (stringIn(database, freeze))
dyStringPrintf(title, "%s %s Browser Sequences",
hOrganism(database), freeze);
else
dyStringPrintf(title, "%s %s (%s) Browser Sequences",
trackHubSkipHubName(hOrganism(database)), freeze, trackHubSkipHubName(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 (sameString(database,"hg38"))
chromInfoRowsChromExt("withAltRandom");
else if ((startsWith("chr", defaultChrom) || startsWith("Group", defaultChrom)) &&
hChromCount(database) < 100)
chromInfoRowsChrom();
else
chromInfoRowsNonChrom(1000);
chromSizesDownloadRow();
hTableEnd();
cgiDown(0.9);
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();
char *sessionId = cgiOptionalString(cartSessionVarName());
char *userId = findCookieData(cookieName);
struct cart *oldCart = cartNew(userId, sessionId, NULL, NULL);
cartRemoveExcept(oldCart, except);
cartCheckout(&oldCart);
cgiVarExcludeExcept(except);
}
void setupHotkeys(boolean gotExtTools)
/* setup keyboard shortcuts and a help dialog for it */
{
// wire the keyboard hotkeys
hPrintf("<script type='text/javascript'>\n");
// left
hPrintf("Mousetrap.bind('ctrl+j', function() { $('input[name=\"hgt.left1\"]').click(); return false; }); \n");
hPrintf("Mousetrap.bind('j', function() { $('input[name=\"hgt.left2\"]').click() }); \n");
hPrintf("Mousetrap.bind('J', function() { $('input[name=\"hgt.left3\"]').click() }); \n");
// right
hPrintf("Mousetrap.bind('ctrl+l', function() { $('input[name=\"hgt.right1\"]').click(); return false; }); \n");
hPrintf("Mousetrap.bind('l', function() { $('input[name=\"hgt.right2\"]').click() }); \n");
hPrintf("Mousetrap.bind('L', function() { $('input[name=\"hgt.right3\"]').click() }); \n");
// zoom in
hPrintf("Mousetrap.bind('ctrl+i', function() { $('input[name=\"hgt.in1\"]').click(); return false; }); \n");
hPrintf("Mousetrap.bind('i', function() { $('input[name=\"hgt.in2\"]').click() }); \n");
hPrintf("Mousetrap.bind('I', function() { $('input[name=\"hgt.in3\"]').click() }); \n");
hPrintf("Mousetrap.bind('b', function() { $('input[name=\"hgt.inBase\"]').click() }); \n");
// zoom out
hPrintf("Mousetrap.bind('ctrl+k', function() { $('input[name=\"hgt.out1\"]').click(); return false; }); \n");
hPrintf("Mousetrap.bind('k', function() { $('input[name=\"hgt.out2\"]').click() }); \n");
hPrintf("Mousetrap.bind('K', function() { $('input[name=\"hgt.out3\"]').click() }); \n");
hPrintf("Mousetrap.bind('0', function() { $('input[name=\"hgt.out4\"]').click() }); \n");
// buttons
hPrintf("Mousetrap.bind('c f', function() { $('input[name=\"hgTracksConfigPage\"]').click() }); \n");
hPrintf("Mousetrap.bind('t s', function() { $('input[name=\"hgt_tSearch\"]').click() }); \n");
hPrintf("Mousetrap.bind('h a', function() { $('input[name=\"hgt.hideAll\"]').click() }); \n");
hPrintf("Mousetrap.bind('d t', function() { $('input[name=\"hgt.reset\"]').click() }); \n");
hPrintf("Mousetrap.bind('d o', function() { $('input[name=\"hgt.defaultImgOrder\"]').click() }); \n");
hPrintf("Mousetrap.bind('c t', function() { document.customTrackForm.submit();return false; }); \n");
hPrintf("Mousetrap.bind('t h', function() { document.trackHubForm.submit();return false; }); \n");
hPrintf("Mousetrap.bind('r s', function() { $('input[name=\"hgt.setWidth\"]').click() }); \n");
hPrintf("Mousetrap.bind('r f', function() { $('input[name=\"hgt.refresh\"]').click() }); \n");
hPrintf("Mousetrap.bind('r v', function() { $('input[name=\"hgt.toggleRevCmplDisp\"]').click() }); \n");
// focus
hPrintf("Mousetrap.bind('/', function() { $('input[name=\"hgt.positionInput\"]').focus(); return false; }, 'keydown'); \n");
hPrintf("Mousetrap.bind('?', function() { $( \"#hotkeyHelp\" ).dialog({width:'600'});}); \n");
// menu
if (gotExtTools)
hPrintf("Mousetrap.bind('s t', showExtToolDialog); \n");
hPrintf("</script>\n");
// help dialog
hPrintf("<div style=\"display:none\" id=\"hotkeyHelp\" title=\"Keyboard shortcuts\">\n");
hPrintf("<table style=\"width:580px; border-color:#666666; border-collapse:collapse\">\n");
hPrintf("<tr><td style=\"width:18ch\">left 10%</td><td width=\"auto\" class=\"hotkey\">ctrl+j</td> <td style=\"width:24ch\"> track search</td><td class=\"hotkey\">t then s</td> </tr>\n"); // percent sign
hPrintf("<tr><td> left 1/2 screen</td><td class=\"hotkey\">j</td> <td> default tracks</td><td class=\"hotkey\">d then t</td> </tr>\n");
hPrintf("<tr><td> left one screen</td><td class=\"hotkey\">J</td> <td> default order</td><td class=\"hotkey\">d then o</td> </tr>\n");
hPrintf("<tr><td> right 10%</td><td class=\"hotkey\">ctrl+l</td><td> hide all</td><td class=\"hotkey\">h then a</td> </tr>\n"); // percent sign
hPrintf("<tr><td> right 1/2 screen</td><td class=\"hotkey\">l</td> <td> custom tracks</td><td class=\"hotkey\">c then t</td> </tr>\n");
hPrintf("<tr><td> right one screen</td><td class=\"hotkey\">L</td> <td> track hubs</td><td class=\"hotkey\">t then h</td> </tr>\n");
hPrintf("<tr><td> zoom in 1.5x</td><td class=\"hotkey\">ctrl+i</td> <td> configure</td><td class=\"hotkey\">c then f</td> </tr>\n");
hPrintf("<tr><td> zoom in 3x</td><td class=\"hotkey\">i</td> <td> reverse</td><td class=\"hotkey\">r then v</td> </tr>\n");
hPrintf("<tr><td> zoom in 10x</td><td class=\"hotkey\">I</td> <td> resize</td><td class=\"hotkey\">r then s</td> </tr>\n");
hPrintf("<tr><td> zoom in base level</td><td class=\"hotkey\">b</td><td> refresh</td><td class=\"hotkey\">r then f</td> </tr>\n");
hPrintf("<tr><td> zoom out 1.5x</td><td class=\"hotkey\">ctrl+k</td><td> jump to position box</td><td class=\"hotkey\">/</td> </tr>\n");
hPrintf("<tr><td> zoom out 3x</td><td class=\"hotkey\">k</td>");
if (gotExtTools)
hPrintf("<td>Send to external tool</td><td class=\"hotkey\">s then t</td>");
hPrintf(" </tr>\n");
hPrintf("<tr><td> zoom out 10x</td><td class=\"hotkey\">K</td> </tr>\n");
hPrintf("<tr><td> zoom out 100x</td><td class=\"hotkey\">0</td> </tr>\n");
hPrintf("</table>\n");
hPrintf("<img style=\"margin:8px\" src=\"../images/shortcutHelp.png\">");
hPrintf("</div>\n");
}
void doMiddle(struct cart *theCart)
/* Print the body of an html file. */
{
cart = theCart;
measureTiming = hPrintStatus() && isNotEmpty(cartOptionalString(cart, "measureTiming"));
if (measureTiming)
measureTime("Startup");
hgBotDelay();
if (measureTiming)
measureTime("Bottleneck delay");
char *debugTmp = NULL;
/* Uncomment this to see parameters for debugging. */
/* struct dyString *state = NULL; */
/* Initialize layout and database. */
if (measureTiming)
measureTime("Get cart of %d for user:%s session:%s", theCart->hash->elCount,
theCart->userId, theCart->sessionId);
/* #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;
int timeout = cartUsualInt(cart, "udcTimeout", 300);
if (udcCacheTimeout() < timeout)
udcSetCacheTimeout(timeout);
initTl();
char *configPageCall = cartCgiUsualString(cart, "hgTracksConfigPage", "notSet");
/* Do main display. */
if (cartUsualBoolean(cart, "hgt.trackImgOnly", FALSE))
{
trackImgOnly = TRUE;
ideogramToo = cartUsualBoolean(cart, "hgt.ideogramToo", FALSE);
hideControls = TRUE;
withNextItemArrows = FALSE;
withNextExonArrows = FALSE;
hgFindMatches = NULL; // XXXX necessary ???
}
jsonForClient = newJsonObject(newHash(8));
jsonObjectAdd(jsonForClient, "cgiVersion", newJsonString(CGI_VERSION));
boolean searching = differentString(cartUsualString(cart, TRACK_SEARCH,"0"), "0");
if(!trackImgOnly)
{
// Write out includes for css and js files
hWrites(commonCssStyles());
jsIncludeFile("mousetrap.min.js", NULL);
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("jquery-ui.js", NULL);
jsIncludeFile("utils.js", NULL);
jsIncludeFile("ajax.js", NULL);
jsIncludeFile("jquery.watermarkinput.js", NULL);
if(!searching)
{
jsIncludeFile("jquery.history.js", NULL);
jsIncludeFile("jquery.imgareaselect.js", NULL);
}
jsIncludeFile("autocomplete.js", NULL);
jsIncludeFile("hgTracks.js", NULL);
#ifdef LOWELAB
jsIncludeFile("lowetooltip.js", NULL);
#endif///def LOWELAB
webIncludeResourceFile("jquery-ui.css");
if (!searching) // NOT doing search
{
webIncludeResourceFile("jquery.contextmenu.css");
jsIncludeFile("jquery.contextmenu.js", NULL);
webIncludeResourceFile("ui.dropdownchecklist.css");
jsIncludeFile("ui.dropdownchecklist.js", NULL);
jsIncludeFile("ddcl.js", NULL);
}
hPrintf("<div id='hgTrackUiDialog' style='display: none'></div>\n");
cartFlushHubWarnings();
}
if (cartVarExists(cart, "chromInfoPage"))
{
cartRemove(cart, "chromInfoPage");
chromInfoPage();
}
else if (differentString(cartUsualString(cart, TRACK_SEARCH,"0"),"0"))
{
doSearchTracks(groupList);
}
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();
}
jsonObjectAdd(jsonForClient, "measureTiming", newJsonBoolean(measureTiming));
// js code needs to know if a highlightRegion is defined for this db
char *highlightDef = cartOptionalString(cart, "highlight");
if (highlightDef && startsWith(database,highlightDef) && highlightDef[strlen(database)] == '.')
jsonObjectAdd(jsonForClient, "highlight", newJsonString(highlightDef));
jsonObjectAdd(jsonForClient, "enableHighlightingDialog",
newJsonBoolean(cartUsualBoolean(cart, "enableHighlightingDialog", TRUE)));
hPrintf("<script type='text/javascript'>\n");
jsonPrint((struct jsonElement *) jsonForClient, "hgTracks", 0);
hPrintf("</script>\n");
if (measureTiming)
measureTime("Time at end of doMiddle, next up cart write");
if (cartOptionalString(cart, "udcTimeout"))
{
warn("The Genome Browser cart currently includes the \"udcTimeout\" string. "
"While this is useful for debugging hubs, it may negatively impact "
"performance. To clear this variable, click "
"<A HREF=hgTracks?hgsid=%s&udcTimeout=[]>here</A>.",cartSessionId(cart));
}
boolean gotExtTools = extToolsEnabled();
setupHotkeys(gotExtTools);
if (gotExtTools)
printExtMenuData();
}