f5ba7e5371b8bcf6c260d065b971e57c09eca1ad Merge parents 189bd07 d24ed48 kate Wed Sep 25 10:56:06 2019 -0700 Merging diff --cc src/hg/hgTracks/hgTracks.c index 6d319cf,f5125d5..e883494 --- src/hg/hgTracks/hgTracks.c +++ src/hg/hgTracks/hgTracks.c @@@ -1,10426 -1,10270 +1,10402 @@@ /* hgTracks - the /riginal, 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 <limits.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 "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 "basicBed.h" #include "customFactory.h" #include "genbank.h" #include "bigWarn.h" #include "wigCommon.h" #include "knetUdc.h" #include "hex.h" #include <openssl/sha.h> #include "customComposite.h" +#include "bed3Sources.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", "sortExp", "sortSim", "hideTracks", "ignoreCookie", 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 resolvePosition. * 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); } 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]; char *hgTrackUi = hTrackUiForTrack(mapName); if(chromName == NULL) safef(buf, sizeof(buf), "%s?%s=%s&g=%s", hgTrackUi, cartSessionVarName(), cartSessionId(cart), encodedMapName); else safef(buf, sizeof(buf), "%s?%s=%s&c=%s&g=%s", hgTrackUi, 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("pslSnake",track->tdb->type) || - startsWithWord("bigPsl",track->tdb->type) || - startsWithWord("bigGenePred",track->tdb->type) || - startsWithWord("bigChain",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 boolean isCompositeInAggregate(struct track *track) // Check to see if this is a custom composite in aggregate mode. { if (!isCustomComposite(track->tdb)) return FALSE; char *aggregateVal = cartOrTdbString(cart, track->tdb, "aggregate", NULL); if ((aggregateVal == NULL) || sameString(aggregateVal, "none")) return FALSE; struct track *subtrack = NULL; for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next) { if (isSubtrackVisible(subtrack)) break; } if (subtrack == NULL) return FALSE; for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next) { subtrack->mapsSelf = FALSE; /* Round about way to tell wig not to do own mapping. */ } multiWigContainerMethods(track); //struct wigCartOptions *wigCart = wigCartOptionsNew(cart, track->tdb, 0, NULL); //track->wigCartData = (void *) wigCart; //track->lineHeight = wigCart->defaultHeight; //wigCart->isMultiWig = TRUE; //wigCart->autoScale = wiggleScaleAuto; //wigCart->defaultHeight = track->lineHeight; //struct wigGraphOutput *wgo = setUpWgo(xOff, yOff, width, tg->height, numTracks, wigCart, hvg); //tg->wigGraphOutput = wgo; return TRUE; } 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; - enum trackVisibility vis = limitVisibility(track); int y = track->totalHeight(track, vis); if (isCenterLabelIncluded(track)) y += fontHeight; if (tdbIsComposite(track->tdb) && !isCompositeInAggregate(track)) { 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(trackHubSkipHubName(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); } } } boolean makeChromIdeoImage(struct track **pTrackList, char *psOutput, struct tempName *ideoTn) /* Make an ideogram image of the chromosome 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; int ideoWidth = round(.8 *tl.picWidth); int ideoHeight = 0; int textWidth = 0; struct tempName pngTn; boolean nukeIdeoFromList = FALSE; 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 { /* Remove the track from the group and track list. */ removeTrackFromGroup(ideoTrack); slRemoveEl(pTrackList, ideoTrack); nukeIdeoFromList = TRUE; /* 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; } // TODO use DIV in future (can update entire div at once in hgTracks.js) //hPrintf("<DIV id='chromIdeoDiv'>\n"); // FYI from testing, I see that there is code that inserts warning error messages // right before ideoMap, so any changes to that name or adding the DIV would require // updating the warning-insertion target name. if(doIdeo) { char startBand[1024]; char endBand[1024]; char title[1024]; 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 (virtMode) { if (!sameString(virtModeShortDescr,"")) safef(title, sizeof(title), "%s (%s)", chromName, virtModeShortDescr); else safef(title, sizeof(title), "%s (%s)", chromName, virtModeType); } else 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); // cytoBandDrawAt() clips x based on insideX+insideWidth, // but in virtMode we may be in a window that is smaller than the ideo width // so temporarily set them to the actual ideo graphic offset and width int saveInsideX = insideX; int saveInsideWidth = insideWidth; insideX = textWidth+4; insideWidth = ideoWidth-insideX; ideoTrack->drawItems(ideoTrack, winStart, winEnd, hvg, insideX, gfxBorder, insideWidth, font, ideoTrack->ixColor, ideoTrack->limitedVis); insideX = saveInsideX; insideWidth = saveInsideWidth; hvGfxUnclip(hvg); /* Save out picture and tell html file about it. */ hvGfxClose(&hvg); /* Finish map. */ if (!psOutput) { hPrintf("</MAP>\n"); jsInline("$('area.cytoBand').click(function(){return false;});\n"); } } // create an empty hidden-map place holder which can change dynamically with ajax callbacks. if (!doIdeo && !psOutput) { hPrintf("<MAP Name=%s>\n", mapName); hPrintf("</MAP>\n"); } hPrintf("<TABLE BORDER=0 CELLPADDING=0>"); if (!psOutput) { // by default, create an empty hidden ideo place holder for future dynamic ajax update char *srcPath = ""; char *style = "display: none;"; if (doIdeo) { srcPath = ideoTn->forHtml; style = "display: inline;"; } hPrintf("<TR><TD HEIGHT=5></TD></TR>"); hPrintf("<TR><TD><IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d USEMAP=#%s id='chrom' style='%s'>", srcPath, ideoWidth, ideoHeight, mapName, style); hPrintf("</TD></TR>"); hPrintf("<TR><TD HEIGHT=5></TD></TR></TABLE>\n"); } else hPrintf("<TR><TD HEIGHT=10></TD></TR></TABLE>\n"); //hPrintf("</DIV>\n"); // TODO use DIV in future if(ideoTrack != NULL) { ideoTrack->limitedVisSet = TRUE; ideoTrack->limitedVis = tvHide; /* Don't draw in main gif. */ } return nukeIdeoFromList; } 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; } Color maybeDarkerLabels(struct track *track, struct hvGfx *hvg, Color color) /* For tracks having light track display but needing a darker label */ { if (trackDbSetting(track->tdb, "darkerLabels")) { struct hsvColor hsv = mgRgbToHsv(mgColorIxToRgb(NULL, color)); // check if really pale if (hsv.s < 500 ||(hsv.h > 40.0 && hsv.h < 150.0)) return somewhatDarkerColor(hvg, color); return slightlyDarkerColor(hvg, color); } return color; } boolean isCenterLabelsPackOff(struct track *track) /* Check for trackDb setting to suppress center labels of composite in pack mode */ { if (!track || !track->tdb) return FALSE; char *centerLabelsPack = trackDbSetting(track->tdb, "centerLabelsPack"); return (centerLabelsPack && sameWord(centerLabelsPack, "off")); } 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 newy; char o4[256]; char o5[256]; struct slList *item; enum trackVisibility vis = track->limitedVis; Color labelColor = (track->labelColor ? track->labelColor : track->ixColor); labelColor = maybeDarkerLabels(track, hvg, labelColor); 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("bigMaf", track->tdb->type) || startsWith("wigMaf", track->tdb->type) || startsWith("maf", track->tdb->type)) vis = tvFull; /* behave temporarily like pack for these */ if (track->limitedVis == tvFull && isTypeBedLike(track)) vis = tvPack; switch (vis) { case tvHide: break; /* Do nothing; */ case tvPack: if (isCenterLabelsPackOff(track)) // draw left labels for pack mode track with center labels off { if (isCenterLabelIncluded(track)) y += fontHeight; hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth-1, track->lineHeight, labelColor, font, track->shortLabel); y += track->height; } else y += tHeight; break; case tvSquish: y += tHeight; break; case tvFull: if (isCenterLabelIncluded(track)) y += fontHeight; 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); else labelColor = maybeDarkerLabels(track, hvg, labelColor); /* 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 ); 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)) { int ymax = y - (track->heightPer / 2) + (fontHeight / 2); int 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; } hvGfxUnclip(hvg); return y; } void setGlobalsFromWindow(struct window *window); // FORWARD DECLARATION 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 = fullInsideWidth; int portX = fullInsideX; // If a portal was established, then set the portal dimensions long 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 // use the last window globals instead of the first struct window *w=windows; while(w->next) w = w->next; setGlobalsFromWindow(w); // use last window 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); setGlobalsFromWindow(windows); // restore first window } static int doCenterLabels(struct track *track, struct track *parentTrack, struct hvGfx *hvg, MgFont *font, int y, int fullInsideWidth ) /* 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); } } labelColor = maybeDarkerLabels(track, hvg, labelColor); hvGfxTextCentered(hvg, insideX, y+1, fullInsideWidth, 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 void doPreDrawItems(struct track *track, struct hvGfx *hvg, MgFont *font, int y, long *lastTime) /* Do Pre-Draw track items. */ { int fontHeight = mgFontLineHeight(font); if (isCenterLabelIncluded(track)) y += fontHeight; if (track->preDrawItems) track->preDrawItems(track, winStart, winEnd, hvg, insideX, y, insideWidth, font, track->ixColor, track->limitedVis); if (measureTiming && lastTime) { long thisTime = clock1000(); track->drawTime = thisTime - *lastTime; *lastTime = thisTime; } } 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); labelColor = maybeDarkerLabels(track, hvg, labelColor); 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; } long computeScaleBar(long numBases, char scaleText[], int scaleTextSize) /* Do some scalebar calculations and return the number of bases the scalebar will span. */ { char *baseWord = "bases"; long 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"; else if ((numFigs >= 9) && (numFigs < 12)) baseWord = "Gb"; 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 calcNewWinWidth(struct cart *cart, int winStart, int winEnd, int insideWidth) /* Calc width of hit boxes that will zoom program around ruler. */ // TODO GALT // probably should change this to use full and virt vars and make it // go across the entire full image width. Especially since this is about // zooming on the virt chrom when user clicks on scalebar or chrom-ruler // Default is to just zoom current window in by 3x to 1/3 of current width. { int winWidth = winEnd - winStart; int newWinWidth = winWidth; 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; return newWinWidth; } static void drawScaleBar( struct hvGfx *hvg, MgFont *font, int fontHeight, int yAfterRuler, int y, int scaleBarTotalHeight ) /* draws the scale bar */ { int scaleBarPad = 2; int scaleBarHeight = fontHeight; // can have one for entire multi-window image char scaleText[32]; long numBases = 0; struct window *w; for (w=windows; w; w=w->next) numBases += (w->winEnd - w->winStart); long scaleBases = computeScaleBar(numBases, scaleText, sizeof(scaleText)); int scalePixels = (int)((double)fullInsideWidth*scaleBases/numBases); int scaleBarX = fullInsideX + (int)(((double)fullInsideWidth-scalePixels)/2); int scaleBarEndX = scaleBarX + scalePixels; int scaleBarY = y + 0.5 * scaleBarTotalHeight; hvGfxTextRight(hvg, fullInsideX, y + scaleBarPad, (scaleBarX-2)-fullInsideX, 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)); } } static int doDrawRuler(struct hvGfx *hvg, int *rulerClickHeight, int rulerHeight, int yAfterRuler, int yAfterBases, MgFont *font, int fontHeight, boolean rulerCds, int scaleBarTotalHeight, struct window *window) /* draws the ruler. */ { 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) { if (window == windows) // first window, only need to do once { hvGfxUnclip(hvg); hvGfxSetClip(hvg, fullInsideX, y, fullInsideWidth, yAfterRuler-y+1); hvGfxTextCentered(hvg, fullInsideX, y, fullInsideWidth, titleHeight,MG_BLACK, font, baseTitle); hvGfxUnclip(hvg); hvGfxSetClip(hvg, insideX, y, insideWidth, yAfterRuler-y+1); } *rulerClickHeight += titleHeight; y += titleHeight; } if (baseShowPos||baseShowAsm) { if (window == windows) // first window, only need to do once { hvGfxUnclip(hvg); hvGfxSetClip(hvg, fullInsideX, y, fullInsideWidth, yAfterRuler-y+1); char txt[256]; char numBuf[SMALLBUF]; char *freezeName = NULL; freezeName = hFreezeFromDb(database); sprintLongWithCommas(numBuf, virtWinEnd-virtWinStart); 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); freez(&freezeName); hvGfxTextCentered(hvg, fullInsideX, y, fullInsideWidth, showPosHeight,MG_BLACK, font, txt); hvGfxUnclip(hvg); hvGfxSetClip(hvg, insideX, y, insideWidth, yAfterRuler-y+1); } *rulerClickHeight += showPosHeight; y += showPosHeight; } if (baseShowScaleBar) { if (window == windows) // first window { hvGfxUnclip(hvg); hvGfxSetClip(hvg, fullInsideX, y, fullInsideWidth, yAfterRuler-y+1); drawScaleBar(hvg, font, fontHeight, yAfterRuler, y, scaleBarTotalHeight); hvGfxUnclip(hvg); hvGfxSetClip(hvg, insideX, y, insideWidth, yAfterRuler-y+1); } y += scaleBarTotalHeight; *rulerClickHeight += scaleBarTotalHeight; } if (baseShowRuler && (insideWidth >=36)) { hvGfxDrawRulerBumpText(hvg, insideX, y, rulerHeight, insideWidth, MG_BLACK, font, relNumOff, winBaseCount, 0, 1); } 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]); // GALT TODO should this be fullInsideX and fullInsideWidth? 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); } } struct highlightVar // store highlight information { struct highlightVar *next; char *db; char *chrom; long chromStart; long chromEnd; char *hexColor; }; struct highlightVar *parseHighlightInfo() // Parse highlight info from cart var to a linked list of highlightVar structs // db.chrom:start-end#hexColor|db.chrom:start-end#hexColor|... { struct highlightVar *hlList = NULL; char *highlightDef = cartOptionalString(cart, "highlight"); if(highlightDef) { char *hlArr[256]; int hlCount = chopByChar(cloneString(highlightDef), '|', hlArr, ArraySize(hlArr)); int i; for (i=0; i<hlCount; i++) { char *oneHl = hlArr[i]; struct highlightVar *h; AllocVar(h); h->db = cloneNextWordByDelimiter(&oneHl,'.'); h->chrom = cloneNextWordByDelimiter(&oneHl,':'); // long to handle virt chrom coordinates h->chromStart = atol(cloneNextWordByDelimiter(&oneHl,'-')); h->chromEnd = atol(cloneNextWordByDelimiter(&oneHl,'#')); h->chromStart--; // Not zero based if (highlightDef && *highlightDef != '\0') h->hexColor = cloneString(oneHl); slAddHead(&hlList, h); } slReverse(&hlList); } return hlList; } static void highlightRegions(struct cart *cart, struct hvGfx *hvg, int imagePixelHeight) // Highlights regions 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 { struct highlightVar *hlList = parseHighlightInfo(); if(hlList && theImgBox == NULL) // Only highlight region when imgBox is not used. (pdf and show-image) { struct highlightVar *h; for (h=hlList; h; h=h->next) { if (virtualSingleChrom()) // DISGUISE VMODE { if ((h->db && sameString(h->db, database)) && (h->chrom && sameString(h->chrom,chromName))) { char position[1024]; safef(position, sizeof position, "%s:%ld-%ld", h->chrom, h->chromStart, h->chromEnd); char *newPosition = undisguisePosition(position); // UN-DISGUISE VMODE if (startsWith("virt:", newPosition)) { parseVPosition(newPosition, &h->chrom, &h->chromStart, &h->chromEnd); } } } if ((h->db && sameString(h->db, database)) && (h->chrom && sameString(h->chrom,virtChromName)) && (h->chromEnd != 0) && (h->chromStart <= virtWinEnd && h->chromEnd >= virtWinStart)) { h->chromStart = max(h->chromStart, virtWinStart); h->chromEnd = min(h->chromEnd, virtWinEnd); double pixelsPerBase = (double)fullInsideWidth/(virtWinEnd - virtWinStart); int startPixels = pixelsPerBase * (h->chromStart - virtWinStart); // floor if (startPixels < 0) startPixels *= -1; // reverse complement int width = pixelsPerBase * (double)(h->chromEnd - h->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 (h->hexColor) { long rgb = strtol(h->hexColor,NULL,16); // Big and little Endians hexColor = MAKECOLOR_32( ((rgb>>16)&0xff), ((rgb>>8)&0xff), (rgb&0xff) ); } hvGfxBox(hvg, fullInsideX + 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"); //} char *rgbColorToString(struct rgbColor color) /* make rgbColor into printable string */ { char buf[256]; safef(buf, sizeof buf, "rgbColor r:%d g:%d b:%d", color.r, color.g, color.b); return cloneString(buf); } char *trackDumpString(struct track *track) /* Write out info on track to string */ { struct dyString *dy = dyStringNew(256); dyStringPrintf(dy, "next: %lu\n", (unsigned long)track->next); // struct track *next; /* Next on list. */ // dyStringPrintf(dy, "track: %s\n", track->track); //char *track; /* Track symbolic name. Name on image map etc. Same as tdb->track. */ dyStringPrintf(dy, "table: %s\n", track->table); //char *table; /* Table symbolic name. Name of database table. Same as tdb->table.*/ dyStringPrintf(dy, "visibility: %s\n", hStringFromTv(track->visibility)); //enum trackVisibility visibility; /* How much of this want to see. */ dyStringPrintf(dy, "limitedVis: %s\n", hStringFromTv(track->limitedVis)); //enum trackVisibility limitedVis; /* How much of this actually see. */ dyStringPrintf(dy, "limitedVisSet: %d\n", track->limitedVisSet); //boolean limitedVisSet; /* Is limited visibility set? */ dyStringPrintf(dy, "longLabel: %s\n", track->longLabel); //char *longLabel; /* Long label to put in center. */ dyStringPrintf(dy, "shortLabel: %s\n", track->shortLabel); //char *shortLabel; /* Short label to put on side. */ dyStringPrintf(dy, "mapsSelf: %d\n", track->mapsSelf); //bool mapsSelf; /* True if system doesn't need to do map box. */ dyStringPrintf(dy, "drawName: %d\n", track->drawName); //bool drawName; /* True if BED wants name drawn in box. */ dyStringPrintf(dy, "colorShades: %lu\n", (unsigned long)track->colorShades); //Color *colorShades; /* Color scale (if any) to use. */ dyStringPrintf(dy, "color: %s\n", rgbColorToString(track->color)); //struct rgbColor color; /* Main color. */ dyStringPrintf(dy, "ixColor: %u\n", track->ixColor); //Color ixColor; /* Index of main color. */ dyStringPrintf(dy, "altColorShades: %lu\n", (unsigned long)track->altColorShades); //Color *altColorShades; /* optional alternate color scale */ dyStringPrintf(dy, "altColor: %s\n", rgbColorToString(track->altColor)); //struct rgbColor altColor; /* Secondary color. */ dyStringPrintf(dy, "ixAltColor: %u\n", track->ixAltColor); //Color ixAltColor; //void (*loadItems)(struct track *tg); /* loadItems loads up items for the chromosome range indicated. */ dyStringPrintf(dy, "items: %lu\n", (unsigned long) track->items); //void *items; /* Some type of slList of items. */ //char *(*itemName)(struct track *tg, void *item); /* Return name of one of an item to display on left side. */ //char *(*mapItemName)(struct track *tg, void *item); /* Return name to associate on map. */ //int (*totalHeight)(struct track *tg, enum trackVisibility vis); /* Return total height. Called before and after drawItems. * Must set the following variables. */ dyStringPrintf(dy, "height: %d\n", track->height); //int height; /* Total height - must be set by above call. */ dyStringPrintf(dy, "lineHeight: %d\n", track->lineHeight); //int lineHeight; /* Height per item line including border. */ dyStringPrintf(dy, "heightPer: %d\n", track->heightPer); //int heightPer; /* Height per item line minus border. */ //int (*itemHeight)(struct track *tg, void *item); /* Return height of one item. */ //int (*itemRightPixels)(struct track *tg, void *item); /* Return number of pixels needed to right of item for additional labeling. (Optional) */ //void (*drawItems)(struct track *tg, int seqStart, int seqEnd, //struct hvGfx *hvg, int xOff, int yOff, int width, //MgFont *font, Color color, enum trackVisibility vis); /* Draw item list, one per track. */ //void (*drawItemAt)(struct track *tg, void *item, struct hvGfx *hvg, //int xOff, int yOff, double scale, //MgFont *font, Color color, enum trackVisibility vis); /* Draw a single option. This is optional, but if it's here * then you can plug in genericDrawItems into the drawItems, * which takes care of all sorts of things including packing. */ //int (*itemStart)(struct track *tg, void *item); /* Return start of item in base pairs. */ //int (*itemEnd)(struct track *tg, void *item); /* Return end of item in base pairs. */ //void (*freeItems)(struct track *tg); /* Free item list. */ //Color (*itemColor)(struct track *tg, void *item, struct hvGfx *hvg); /* Get color of item (optional). */ //Color (*itemNameColor)(struct track *tg, void *item, struct hvGfx *hvg); /* Get color for the item's name (optional). */ //Color (*itemLabelColor)(struct track *tg, void *item, struct hvGfx *hvg); /* Get color for the item's label (optional). */ //void (*mapItem)(struct track *tg, struct hvGfx *hvg, void *item, //char *itemName, char *mapItemName, int start, int end, //int x, int y, int width, int height); /* Write out image mapping for a given item */ dyStringPrintf(dy, "hasUi: %d\n", track->hasUi); //boolean hasUi; /* True if has an extended UI page. */ dyStringPrintf(dy, "wigCartData: %lu\n", (unsigned long)track->wigCartData); //void *wigCartData; /* pointer to wigCart */ dyStringPrintf(dy, "extraUiData: %lu\n", (unsigned long)track->extraUiData); //void *extraUiData; /* Pointer for track specific filter etc. data. */ //void (*trackFilter)(struct track *tg); /* Stuff to handle user interface parts. */ dyStringPrintf(dy, "customPt: %lu\n", (unsigned long)track->customPt); //void *customPt; /* Misc pointer variable unique to track. */ dyStringPrintf(dy, "customInt: %d\n", track->customInt); //int customInt; /* Misc int variable unique to track. */ dyStringPrintf(dy, "subType: %d\n", track->subType); //int subType; /* Variable to say what subtype this is for similar tracks to share code. */ /* Stuff for the various wig incarnations - sample, wig, bigWig */ dyStringPrintf(dy, "minRange: %.2f, maxRange: %.2f\n", track->minRange, track->maxRange); //float minRange, maxRange; /*min and max range for sample tracks 0.0 to 1000.0*/ dyStringPrintf(dy, "scaleRange: %.2f\n", track->scaleRange); //float scaleRange; /* What to scale samples by to get logical 0-1 */ dyStringPrintf(dy, "graphUpperLimit: %e, grapLowerLimit: %e\n", track->graphUpperLimit, track->graphLowerLimit); //double graphUpperLimit, graphLowerLimit; /* Limits of actual data in window for wigs. */ dyStringPrintf(dy, "preDrawContainer: %lu\n", (unsigned long)track->preDrawContainer); //struct preDrawContainer *preDrawContainer; /* Numbers to graph in wig, one per pixel */ //struct preDrawContainer *(*loadPreDraw)(struct track *tg, int seqStart, int seqEnd, int width); dyStringPrintf(dy, "wigGraphOutput: %lu\n", (unsigned long)track->wigGraphOutput); //struct wigGraphOutput *wigGraphOutput; /* Where to draw wig - different for transparency */ /* Do bits that load the predraw buffer. Called to set preDrawContainer */ dyStringPrintf(dy, "bbiFile: %lu\n", (unsigned long)track->bbiFile); //struct bbiFile *bbiFile; /* Associated bbiFile for bigWig or bigBed. */ dyStringPrintf(dy, "bedSize: %d\n", track->bedSize); //int bedSize; /* Number of fields if a bed file. */ dyStringPrintf(dy, "isBigBed: %d\n", track->isBigBed); //boolean isBigBed; /* If a bed, is it a bigBed? */ dyStringPrintf(dy, "isRemoteSql: %d\n", track->isRemoteSql); //boolean isRemoteSql; /* Is using a remote mySQL connection. */ dyStringPrintf(dy, "remoteSqlHost: %s\n", track->remoteSqlHost); //char *remoteSqlHost; /* Host machine name for remote DB. */ dyStringPrintf(dy, "remoteSqlUser: %s\n", track->remoteSqlUser); //char *remoteSqlUser; /* User name for remote DB. */ dyStringPrintf(dy, "remoteSqlPassword: %s\n", track->remoteSqlPassword); //char *remoteSqlPassword; /* Password for remote DB. */ dyStringPrintf(dy, "remoteSqlDatabase: %s\n", track->remoteSqlDatabase); //char *remoteSqlDatabase; /* Database in remote DB. */ dyStringPrintf(dy, "remoteSqlTable: %s\n", track->remoteSqlTable); //char *remoteSqlTable; /* Table name in remote DB. */ dyStringPrintf(dy, "otherDb: %s\n", track->otherDb); //char *otherDb; /* Other database for an axt track. */ dyStringPrintf(dy, "private: %d\n", track->private); //unsigned short private; /* True(1) if private, false(0) otherwise. */ dyStringPrintf(dy, "priority: %.2f\n", track->priority); //float priority; /* Tracks are drawn in priority order. */ dyStringPrintf(dy, "defaultPriority: %.2f\n", track->defaultPriority); //float defaultPriority; /* Tracks are drawn in priority order. */ dyStringPrintf(dy, "groupName: %s\n", track->groupName); //char *groupName; /* Name of group if any. */ dyStringPrintf(dy, "group: %lu\n", (unsigned long)track->group); //struct group *group; /* Group this track is associated with. */ dyStringPrintf(dy, "defaultGroupName: %s\n", track->defaultGroupName); //char *defaultGroupName; /* default Group this track is associated with. */ dyStringPrintf(dy, "canPack: %d\n", track->canPack); //boolean canPack; /* Can we pack the display for this track? */ dyStringPrintf(dy, "spaceSaver: %lu\n", (unsigned long)track->ss); //struct spaceSaver *ss; /* Layout when packed. */ dyStringPrintf(dy, "tdb: %lu\n", (unsigned long)track->tdb); //struct trackDb *tdb; /*todo:change visibility, etc. to use this */ // ADDED by GALT if (track->tdb) dyStringPrintf(dy, "tdb settings:\n%s\n", track->tdb->settings); dyStringPrintf(dy, "expScale: %.2f\n", track->expScale); //float expScale; /* What to scale expression tracks by. */ dyStringPrintf(dy, "expTable: %s\n", track->expTable); //char *expTable; /* Expression table in hgFixed. */ // factorSource dyStringPrintf(dy, "sourceCount: %d\n", track->sourceCount); //int sourceCount; /* Number of sources for factorSource tracks. */ dyStringPrintf(dy, "sources: %lu\n", (unsigned long)track->sources); //struct expRecord **sources; /* Array of sources */ dyStringPrintf(dy, "sourceRightPixels: %d\n", track->sourceRightPixels); //int sourceRightPixels; /* Number of pixels to right we'll need. */ // exon/Next dyStringPrintf(dy, "exonArrows: %d\n", track->exonArrows); //boolean exonArrows; /* Draw arrows on exons? */ dyStringPrintf(dy, "exonArrowsAlways: %d\n", track->exonArrowsAlways); //boolean exonArrowsAlways; /* Draw arrows on exons even with introns showing? */ dyStringPrintf(dy, "nextExonButtonable: %d\n", track->nextExonButtonable); //boolean nextExonButtonable; /* Use the next-exon buttons? */ dyStringPrintf(dy, "nextItemButtonable: %d\n", track->nextItemButtonable); //boolean nextItemButtonable; /* Use the next-gene buttons? */ dyStringPrintf(dy, "itemAttrTbl: %lu\n", (unsigned long)track->itemAttrTbl); //struct itemAttrTbl *itemAttrTbl; /* relational attributes for specific items (color) */ /* fill in left label drawing area */ dyStringPrintf(dy, "labelColor: %u\n", track->labelColor); //Color labelColor; /* Fixed color for the track label (optional) */ //void (*drawLeftLabels)(struct track *tg, int seqStart, int seqEnd, // struct hvGfx *hvg, int xOff, int yOff, int width, int height, // boolean withCenterLabels, MgFont *font, // Color color, enum trackVisibility vis); dyStringPrintf(dy, "subtracks: %lu\n", (unsigned long)track->subtracks); //struct track *subtracks; /* list of subsidiary tracks that are //loaded and drawn by this track. This //is used for "composite" tracks, such //as "mafWiggle */ dyStringPrintf(dy, "parent: %lu\n", (unsigned long)track->parent); //struct track *parent; /* Parent track if any */ dyStringPrintf(dy, "prevTrack: %lu\n", (unsigned long)track->prevTrack); //struct track *prevTrack; // if not NULL, points to track immediately above in the image. // Needed by ConditionalCenterLabel logic //void (*nextPrevExon)(struct track *tg, struct hvGfx *hvg, void *item, int x, int y, int w, int h, boolean next); /* Function will draw the button on a track item and assign a map */ /* box to it as well, so that a click will move the browser window */ /* to the next (or previous if next==FALSE) item. This is meant to */ /* jump to parts of an item already partially in the window but is */ /* hanging off the edge... e.g. the next exon in a gene. */ //void (*nextPrevItem)(struct track *tg, boolean next); /* If this function is given, it can dictate where the browser loads */ /* up based on whether a next-item button on the longLabel line of */ /* the track was pressed (as opposed to the next-item buttons on the */ /* track items themselves... see nextPrevExon() ). This is meant for */ /* going to the next/previous item currently unseen in the browser, */ /* e.g. the next gene. SO FAR THIS IS UNIMPLEMENTED. */ //char *(*itemDataName)(struct track *tg, char *itemName); /* If not NULL, function to translated an itemName into a data name. * This is can be used for looking up sequence, CDS, etc. It is used * to support item names that have uniqueness identifiers added to deal * with multiple alignments. The resulting value should *not* be freed, * and it should be assumed that it might only remain valid for a short * period of time.*/ dyStringPrintf(dy, "loadTime: %d\n", track->loadTime); //int loadTime; /* Time it takes to load (for performance tuning) */ dyStringPrintf(dy, "drawTime: %d\n", track->drawTime); //int drawTime; /* Time it takes to draw (for performance tuning) */ dyStringPrintf(dy, "remoteDataSource: %d\n", track->remoteDataSource); //enum enumBool remoteDataSource; /* The data for this track is from a remote source */ /* Slow retrieval means image can be rendered via an AJAX callback. */ dyStringPrintf(dy, "customTrack: %d\n", track->customTrack); //boolean customTrack; /* Need to explicitly declare this is a custom track */ dyStringPrintf(dy, "syncChildVisToSelf: %d\n", track->syncChildVisToSelf); //boolean syncChildVisToSelf; /* If TRUE sync visibility to of children to self. */ dyStringPrintf(dy, "networkErrMsg: %s\n", track->networkErrMsg); //char *networkErrMsg; /* Network layer error message */ dyStringPrintf(dy, "parallelLoading: %d\n", track->parallelLoading); //boolean parallelLoading; /* If loading in parallel, usually network resources. */ dyStringPrintf(dy, "summary: %lu\n", (unsigned long) track->summary); //struct bbiSummaryElement *summary; /* for bigBed */ dyStringPrintf(dy, "summAll: %lu\n", (unsigned long) track->sumAll); //struct bbiSummaryElement *sumAll; /* for bigBed */ dyStringPrintf(dy, "drawLabelInBox: %d\n", track->drawLabelInBox); //boolean drawLabelInBox; /* draw labels into the features instead of next to them */ //}; return dyStringCannibalize(&dy); } char *makeDumpURL(char *text) /* Make a temp file to hold big dump. Return URL to it. */ { // trackDump output is quite large struct tempName trkDmp; trashDirFile(&trkDmp, "hgt", "hgt", ".txt"); FILE *f = mustOpen(trkDmp.forCgi, "w"); fprintf(f, "%s", text); carefulClose(&f); return cloneString(trkDmp.forHtml); } char *makeTrackDumpLink(struct track *track) /* Make a track dump to trash, and return html link to it */ { char *tds = trackDumpString(track); char *url = makeDumpURL(tds); char buf[1024]; safef(buf, sizeof buf, "<A HREF=%s>URL</A>", url); freeMem(tds); freeMem(url); return cloneString(buf); } boolean regionsAreInOrder(struct virtRegion *virtRegion1, struct virtRegion *virtRegion2) /* Return TRUE if the regions are on the same chrom and non-overlapping * and are in-order, i.e. region 1 appears before region2. */ { if (sameString(virtRegion1->chrom, virtRegion2->chrom) && virtRegion1->end <= virtRegion2->start) return TRUE; return FALSE; } /* --- Virtual Chromosome Functions --- */ boolean virtualSingleChrom() /* Return TRUE if using virtual single chromosome mode */ { return (sameString(virtModeType,"exonMostly") || sameString(virtModeType,"geneMostly")); } void parseVPosition(char *position, char **pChrom, long *pStart, long *pEnd) /* parse Virt position */ { if (!position) { errAbort("position NULL"); } char *vPos = cloneString(position); stripChar(vPos, ','); char *colon = strchr(vPos, ':'); if (!colon) errAbort("position has no colon"); char *dash = strchr(vPos, '-'); if (!dash) errAbort("position has no dash"); *colon = 0; *dash = 0; *pChrom = cloneString(vPos); *pStart = atol(colon+1) - 1; *pEnd = atol(dash+1); } void parseNVPosition(char *position, char **pChrom, int *pStart, int *pEnd) /* parse NonVirt position */ { if (!position) { errAbort("position NULL"); } char *vPos = cloneString(position); stripChar(vPos, ','); char *colon = strchr(vPos, ':'); if (!colon) errAbort("position has no colon"); char *dash = strchr(vPos, '-'); if (!dash) errAbort("position has no dash"); *colon = 0; *dash = 0; *pChrom = cloneString(vPos); *pStart = atoi(colon+1) - 1; *pEnd = atoi(dash+1); } char *disguisePositionVirtSingleChrom(char *position) // DISGUISE VMODE /* Hide the virt position, convert to real single chrom span. * position should be virt chrom span. * Can handle anything in the virt single chrom. */ { /* parse Virt position */ char *chrom = NULL; long start = 0; long end = 0; parseVPosition(position, &chrom, &start, &end); if (!sameString(chrom, "virt")) return position; // return original struct window *windows = makeWindowListFromVirtChrom(start, end); char *nonVirtChromName = windows->chromName; if (!sameString(nonVirtChromName, chromName)) return position; // return original int nonVirtWinStart = windows->winStart; int nonVirtWinEnd = windows->winEnd; struct window *w; for (w=windows->next; w; w=w->next) { if (!sameString(w->chromName, nonVirtChromName)) return position; // return original if (w->winEnd < nonVirtWinEnd) return position; // return original nonVirtWinEnd = w->winEnd; } char nvPos[256]; safef(nvPos, sizeof nvPos, "%s:%d-%d", nonVirtChromName, nonVirtWinStart+1, nonVirtWinEnd); slFreeList(&windows); return cloneString(nvPos); } char *undisguisePosition(char *position) // UN-DISGUISE VMODE /* Find the virt position * position should be real chrom span. * Limitation: can only convert things in the current windows set. */ { /* parse NonVirt position */ char *chrom = NULL; int start = 0; int end = 0; parseNVPosition(position, &chrom, &start, &end); if (!sameString(chrom, chromName)) return position; // return original long newStart = -1; long newEnd = -1; struct window *lastW = NULL; struct window *w = NULL; for (w = windows; w; w=w->next) { // double check chrom is same thoughout all windows, otherwise warning, return original value if (!sameString(w->chromName, chromName)) { return position; // return original } // check that the regions are ascending and non-overlapping if (lastW && w->winStart < lastW->winEnd) { return position; // return original } // overlap with position? // if intersection, if (w->winEnd > start && end > w->winStart) { int s = max(start, w->winStart); int e = min(end, w->winEnd); long cs = s - w->winStart + w->virtStart; long ce = e - w->winStart + w->virtStart; if (newStart == -1) newStart = cs; newEnd = ce; } lastW = w; } if (newStart == -1) // none of the windows intersected with the position return position; // return original // return new virt undisguised position as a string char newPos[1024]; safef (newPos, sizeof newPos, "virt:%ld-%ld", (newStart+1), newEnd); return cloneString(newPos); } char *windowsSpanPosition() /* Return a position string that spans all the windows. * Windows should be on same chrom and ascending and non-overlapping.*/ { char buf[256]; char *chromName = windows->chromName; int start = windows->winStart; struct window *w = windows, *last = NULL; while(w->next) // find last window { last = w; w = w->next; if (!sameString(chromName, w->chromName)) errAbort("windowsSpanPosition: expected all windows to be on the same chrom but found %s and %s", chromName, w->chromName); if (w->winStart < last->winEnd) errAbort("windowsSpanPosition: expected all windows to be ascending non-overlapping, found %d < %d", w->winStart, last->winEnd); } int end = w->winEnd; safef(buf, sizeof buf, "%s:%d-%d", chromName, start+1, end); return cloneString(buf); } void padVirtRegions(int windowPadding) /* Pad virt regions with windowPadding bases * * NOTE a simple padding would not worry about merging or order. Just expand the beginning and end of each region. * NOTE this assumes that the regions are in order, but tolerates hiccups in order. * DONE make it handle multiple chromosomes * * TODO what about just modifying the original list directly? * I do not know if this is handling merging correctly. * DONE Maybe I should just add the padding directly into the exon-fetch-merge code. * I have looked at that earlier, and it should work easily. * It might also have the advantage of not having to create a duplicate list? * * TODO how do I test that the output is correct. * if the input has ordered non-duplicate regions, then the output should be likewise. * */ { int regionCount = 0; long regionBases=0; struct virtRegion *virtRegion, *lastVirtRegion = NULL; int leftWindowPadding = 0; int rightWindowPadding = 0; struct virtRegion *v, *newList = NULL; char *lastChrom = NULL; int chromSize = -1; for(virtRegion=virtRegionList; virtRegion; virtRegion = virtRegion->next) { AllocVar(v); if (!sameOk(virtRegion->chrom, lastChrom)) { chromSize = hChromSize(database, virtRegion->chrom); } v->chrom = virtRegion->chrom; // TODO is cloning the string needed? leftWindowPadding = windowPadding; rightWindowPadding = windowPadding; if (lastVirtRegion && regionsAreInOrder(lastVirtRegion, virtRegion)) { int distToPrevRegion = virtRegion->start - lastVirtRegion->end; if (distToPrevRegion < (2*windowPadding)) { leftWindowPadding = distToPrevRegion/2; } } if (virtRegion->next && regionsAreInOrder(virtRegion, virtRegion->next)) { int distToNextRegion = virtRegion->next->start - virtRegion->end; if (distToNextRegion < (2*windowPadding)) { rightWindowPadding = (distToNextRegion+1)/2; // +1 to balance for odd number of bases between, arbitrarily adding it to right side } } v->start = virtRegion->start - leftWindowPadding; v->end = virtRegion->end + rightWindowPadding; if (v->start < 0) v->start = 0; if (v->end >= chromSize) v->end = chromSize; regionBases += (v->end - v->start); slAddHead(&newList, v); lastVirtRegion = virtRegion; lastChrom = virtRegion->chrom; ++regionCount; } slReverse(&newList); virtRegionList = newList; // update new list -- // TODO should the old one be freed? if so, the chrom name should use cloneString } void makeVirtChrom() /* build virtual chrom array from virt region list */ { virtRegionCount = slCount(virtRegionList); AllocArray(virtChrom, virtRegionCount); struct virtRegion *v; int i = 0; long totalBases = 0; for(v=virtRegionList;v;v=v->next,++i) { virtChrom[i].virtPos = totalBases; virtChrom[i].virtRegion = v; totalBases += (v->end - v->start); } virtSeqBaseCount = totalBases; } void virtChromBinarySearch(long target, long *resultIndex, int *resultOffset) /* Do a binary search for the target position in the virtual chrom. * Return virtChrom Index and Offset if found. * Return -1 if target out of range. TODO maybe change to errAbort*/ { //The binary search will either return match or out-of-range. long index = -1; int offset = -1; long a = 0; // start of the array long b = virtRegionCount - 1; // end of array where N = count of regions if (target >=0 && target < virtSeqBaseCount) { while(1) { long c = (a + b) / 2; if (a > b) { index = b; break; } else if (target == virtChrom[c].virtPos) { // (exact match) index = c; break; } else if (target > virtChrom[c].virtPos) { a = c + 1; } else if (target < virtChrom[c].virtPos) { b = c - 1; } else { // probably should not happen errAbort("Unexpected outcome in virtChromBinarySearch."); } } } else if (target == virtSeqBaseCount) { // tolerate this special case index = virtRegionCount - 1; } if (index >= 0) offset = target - virtChrom[index].virtPos; *resultIndex = index; *resultOffset = offset; } void testVirtChromBinarySearch() /* test virt chrom binary search */ { warn("about to test virt chrom binary search: virtSeqBaseCount=%ld virtRegionCount=%d", virtSeqBaseCount, virtRegionCount); long i; int o; long target = -1; virtChromBinarySearch(target, &i, &o); if (i != -1) errAbort("target %ld result %ld %d ", target, i, o); for(target=0; target < virtSeqBaseCount; ++target) { virtChromBinarySearch(target, &i, &o); if (virtChrom[i].virtPos + o != target) errAbort("target = %ld result %ld %d ", target, i, o); struct virtRegion *v = virtChrom[i].virtRegion; int size = v->end - v->start; if (o > size) errAbort("target = %ld result %ld %d > size=%d", target, i, o, size); } target = virtSeqBaseCount; virtChromBinarySearch(target, &i, &o); if (i != virtRegionCount - 1) errAbort("target = virtSeqBaseCount = %ld result %ld %d ", target, i, o); target = virtSeqBaseCount+1; virtChromBinarySearch(target, &i, &o); if (i != -1) errAbort("target = virtSeqBaseCount = %ld result %ld %d ", target, i, o); warn("Got past test virt chrom binary search"); } struct window *makeWindowListFromVirtChrom(long virtWinStart, long virtWinEnd) /* make list of windows from virtual position on virtualChrom */ { // quick check of virt win start and end if (virtWinEnd == virtWinStart) return NULL; if (virtWinStart < 0 || virtWinStart >= virtSeqBaseCount) errAbort("unexpected error. virtWinStart=%ld out of range. virtSeqBaseCount=%ld", virtWinStart, virtSeqBaseCount); if (virtWinEnd < 0 || virtWinEnd > virtSeqBaseCount) errAbort("unexpected error. virtWinEnd=%ld out of range. virtSeqBaseCount=%ld", virtWinEnd, virtSeqBaseCount); if (virtWinEnd - virtWinStart < 1) errAbort("unexpected error. virtual window size < 1 base. virtWinStart=%ld virtWinEnd=%ld virtSeqBaseCount=%ld", virtWinStart, virtWinEnd, virtSeqBaseCount); long virtIndexStart; int virtOffsetStart; virtChromBinarySearch(virtWinStart, &virtIndexStart, &virtOffsetStart); if (virtIndexStart == -1) errAbort("unexpected failure to find target virtWinStart %ld in virtChrom Array", virtWinStart); long virtIndexEnd; int virtOffsetEnd; virtChromBinarySearch(virtWinEnd, &virtIndexEnd, &virtOffsetEnd); if (virtIndexEnd == -1) errAbort("unexpected failure to find target virtWinEnd %ld in virtChrom Array", virtWinEnd); // create new windows list from virt chrom struct window *windows = NULL; long i = virtIndexStart; int winCount = 0; long basesInWindows = 0; // TODO not actually using this variable for(i=virtIndexStart; i <= virtIndexEnd; ++i) { struct window *w; AllocVar(w); w->organism = organism; // obsolete w->database = database; // obsolete struct virtRegion *v = virtChrom[i].virtRegion; long virtPos = virtChrom[i].virtPos; w->chromName = v->chrom; if (i == virtIndexStart) { w->winStart = v->start + virtOffsetStart; w->virtStart = virtPos + virtOffsetStart; } else { w->winStart = v->start; w->virtStart = virtPos; } if (i == virtIndexEnd) { if (virtOffsetEnd == 0) continue; w->winEnd = v->start + virtOffsetEnd; } else { w->winEnd = v->end; } w->virtEnd = w->virtStart + (w->winEnd - w->winStart); w->regionOdd = i % 2; basesInWindows += (w->winEnd - w->winStart); slAddHead(&windows, w); ++winCount; } slReverse(&windows); if (basesInWindows != (virtWinEnd-virtWinStart)) // was virtWinBaseCount but now I call this routine for highlight pos as well as virt pos. errAbort("makeWindowListFromVirtChrom: unexpected error basesInWindows(%ld) != virtWinBaseCount(%ld)", basesInWindows, virtWinEnd-virtWinStart); return windows; } char *nonVirtPositionFromWindows() /* Must have created the virtual chrom first. * Currently just a hack to use windows, * use the (first) window(s) from that to get real chrom name start end */ { // assumes makeWindowListFromVirtChrom() has already been called. if (!windows) errAbort("nonVirtPositionFromWindows() unexpected error, windows list not initialized yet"); char *nonVirtChromName = windows->chromName; int nonVirtWinStart = windows->winStart; int nonVirtWinEnd = windows->winEnd; // Extending this through more of the windows, // if it is on the same chrom and maybe not too far separated. struct window *w; for (w=windows->next; w; w=w->next) { if (sameString(w->chromName, nonVirtChromName) && w->winEnd > nonVirtWinEnd) nonVirtWinEnd = w->winEnd; } // TODO Also consider preserving the original bases in windows width (with clipping). char nvPos[256]; safef(nvPos, sizeof nvPos, "%s:%d-%d", nonVirtChromName, nonVirtWinStart+1, nonVirtWinEnd); return cloneString(nvPos); } char *nonVirtPositionFromHighlightPos() /* Must have created the virtual chrom first. * Currently just a hack to use windows, * use the (first) window(s) from that to get real chrom name start end */ { struct highlightVar *h = parseHighlightInfo(); if (!(h && h->db && sameString(h->db, database) && sameString(h->chrom,"virt"))) return NULL; struct window *windows = makeWindowListFromVirtChrom(h->chromStart, h->chromEnd); char *nonVirtChromName = windows->chromName; int nonVirtWinStart = windows->winStart; int nonVirtWinEnd = windows->winEnd; // Extending this through more of the windows, // if it is on the same chrom and maybe not too far separated. struct window *w; for (w=windows->next; w; w=w->next) { if (sameString(w->chromName, nonVirtChromName) && w->winEnd > nonVirtWinEnd) nonVirtWinEnd = w->winEnd; } // TODO Also consider preserving the original bases in windows width (with clipping). char nvPos[256]; safef(nvPos, sizeof nvPos, "%s.%s:%d-%d#%s", h->db, nonVirtChromName, nonVirtWinStart+1, nonVirtWinEnd, h->hexColor); return cloneString(nvPos); } void allocPixelsToWindows() /* Allocate pixels to windows, sets insideWidth and insideX * * TODO currently uses a strategy that places a window at a pixel location * directly, because of round-off and missing small windows this can occasionally * lead to gaps not covered by any pixel. Consider replacing it with something * that tries not to leave many gaps -- but how to do it without distortion of some window sizes? * */ { double pixelsPerBase = (double)fullInsideWidth / virtWinBaseCount; long basesUsed = 0; int windowsTooSmall = 0; struct window **pWindows = &windows; struct window *window; int winCount = slCount(windows); for(window=windows;window;window=window->next) { int basesInWindow = window->winEnd - window->winStart; int pixelsInWindow = 0.5 + (double)basesInWindow * pixelsPerBase; // should this round up ? + 0.5? window->insideWidth = pixelsInWindow; window->insideX = fullInsideX + basesUsed * pixelsPerBase; basesUsed += basesInWindow; if (pixelsInWindow < 1) // remove windows less than one pixel from the list { *pWindows = window->next; --winCount; ++windowsTooSmall; } else { pWindows = &window->next; } } } struct positionMatch *virtChromSearchForPosition(char *chrom, int start, int end, boolean findNearest) /* Search the virtual chrom for the query chrom, start, end position * * TODO GALT: Intially this can be a simple brute-force search of the entire virtChrom array. * * However, this will need to be upgraded to using a rangeTree or similar structure * to rapidly return multiple regions that overlap the query position. * */ { struct positionMatch *list=NULL, *p; int nearestRegion = -1; boolean nearestAfter = TRUE; int nearestDistance = INT_MAX; int i; struct virtRegion *v = NULL; long virtPos = 0; for(i=0; i < virtRegionCount; ++i) { v = virtChrom[i].virtRegion; virtPos = virtChrom[i].virtPos; if (sameString(v->chrom,chrom)) { // TODO will we need to support finding closest misses too? if (v->end > start && end > v->start) // overlap { int s = max(start, v->start); int e = min(end , v->end ); AllocVar(p); p->virtStart = virtPos + (s - v->start); p->virtEnd = virtPos + (e - v->start); slAddHead(&list, p); } else if (findNearest && (!list)) { int thisDist = v->start - start; boolean thisAfter = TRUE; if (thisDist < 0) // absolute value { thisDist = -thisDist; thisAfter = FALSE; } if (thisDist < nearestDistance) { nearestRegion = i; nearestDistance = thisDist; nearestAfter = thisAfter; } } } } if (findNearest && (!list) && nearestRegion != -1) { i = nearestRegion; v = virtChrom[i].virtRegion; virtPos = virtChrom[i].virtPos; AllocVar(p); if (nearestAfter) { p->virtStart = virtPos; p->virtEnd = p->virtStart + (end - start); } else { p->virtEnd = virtPos + (v->end - v->start); p->virtStart = p->virtEnd - (end - start); } if (p->virtEnd > virtSeqBaseCount) p->virtEnd = virtSeqBaseCount; slAddHead(&list, p); } slReverse(&list); return list; } int matchVPosCompare(const void *elem1, const void *elem2) /* compare elements based on vPos */ { const struct positionMatch *a = *((struct positionMatch **)elem1); const struct positionMatch *b = *((struct positionMatch **)elem2); if (a->virtStart == b->virtStart) errAbort("matchVPosCompare error should not happen: 2 elements being sorted have the same virtStart=%ld", a->virtStart); else if (a->virtStart > b->virtStart) return 1; return -1; } void matchSortOnVPos(struct positionMatch **pList) /* Sort positions by virtPos * pList will be sorted by chrom, start, end but we want it ordered by vPos */ { slSort(pList, matchVPosCompare); } struct positionMatch *matchMergeContiguousVPos(struct positionMatch *list) /* Merge contiguous matches spanning multiple touching windows */ { struct positionMatch *newList = NULL; struct positionMatch *m; long lastStart = -1; long lastEnd = -1; struct positionMatch *lastM = NULL; boolean inMerge = FALSE; long mergeStart = -1; long mergeEnd = -1; if (!list) return NULL; for(m=list; 1; m=m->next) // special loop condition allows it to stop AFTER it goes thru the loop once as m=NULL. // this flushes out the last value. { if (inMerge) { if (m && m->virtStart == lastEnd) { // continue merging, do nothing. // maybe could be freeing a skipped node here. } else { inMerge = FALSE; mergeEnd = lastEnd; // create new merged node and add it to new list struct positionMatch *n; AllocVar(n); n->virtStart = mergeStart; n->virtEnd = mergeEnd; slAddHead(&newList, n); } } else { if (m && m->virtStart == lastEnd) { inMerge = TRUE; mergeStart = lastStart; } else if (lastM) // just transfer the last node unmodified to the new list. { slAddHead(&newList, lastM); } } if (!m) break; lastStart = m->virtStart; lastEnd = m->virtEnd; lastM = m; } slReverse(&newList); return newList; } // ---------------------------------- void initVirtRegionsFromSOD1Hardwired() /* create a testing regionlist from SOD1 (uc002ypa.3) hardwired */ { virtRegionList = NULL; char *chrom="chr21"; //int exonStarts[] = {33031934,33036102,33038761,33039570,33040783}; //int exonEnds[] = {33032154,33036199,33038831,33039688,33041243}; // BASE-level zoom in two 20 bp exons and their on-screen junction int exonStarts[] = {33032134,33036102}; int exonEnds[] = {33032154,33036122}; int i; for(i=0; i<ArraySize(exonStarts); ++i) { struct virtRegion *v; AllocVar(v); v->chrom = cloneString(chrom); v->start = exonStarts[i]; v->end = exonEnds[i]; v->strand[0] = '+'; v->strand[1] = 0; slAddHead(&virtRegionList, v); } slReverse(&virtRegionList); } void initVirtRegionsFromEmGeneTable(char *ucscTranscriptId) /* create a testing regionlist from knownGene transcript with given id */ { struct sqlConnection *conn = hAllocConn(database); virtRegionList = NULL; struct sqlResult *sr; char **row; int rowOffset = 0; if (hIsBinned(database, emGeneTable)) // skip first bin column if any ++rowOffset; char query[256]; sqlSafef(query, sizeof(query), "select * from %s where name='%s'", emGeneTable, ucscTranscriptId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { struct genePred *gene = genePredLoad(row+rowOffset); int i; for(i=0; i< gene->exonCount; ++i) { struct virtRegion *v; AllocVar(v); v->chrom = cloneString(gene->chrom); v->start = gene->exonStarts[i]; v->end = gene->exonEnds[i]; v->strand[0] = gene->strand[0]; v->strand[1] = 0; slAddHead(&virtRegionList, v); } genePredFree(&gene); } sqlFreeResult(&sr); slReverse(&virtRegionList); hFreeConn(&conn); } boolean initSingleAltHaplotype(char *haplotypeId) /* create a testing regionlist from haplotype with given id */ { struct sqlConnection *conn = hAllocConn(database); if (!virtRegionList) // this should already contain allchroms. errAbort("unexpected error in initSingleAltHaplotype: virtRegionList is NULL, should contain all chroms"); struct virtRegion *after = virtRegionList; virtRegionList = NULL; struct sqlResult *sr; char **row; char *table = endsWith(haplotypeId, "_fix") ? "fixLocations" : "altLocations"; if (! hTableExists(database, table)) { warn("initSingleAltHaplotype: table '%s' not found in database %s, " "can't find %s", table, database, haplotypeId); return FALSE; } // where is the alt haplo placed? char query[256]; sqlSafef(query, sizeof(query), "select chrom, chromStart, chromEnd from %s " "where name rlike '^%s(:[0-9-]+)?'", table, haplotypeId); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (!row) { warn("no haplotype found for [%s] in %s", haplotypeId, table); return FALSE; } char *haploChrom = cloneString(row[0]); int haploStart = sqlUnsigned(row[1]); int haploEnd = sqlUnsigned(row[2]); sqlFreeResult(&sr); // what is the size of the alt haplo? int haploSize = hChromSize(database, haplotypeId); // hopefully this will work // insert into list replacing original haploChrom record struct virtRegion *before = NULL; boolean found = FALSE; long offset = 0; struct virtRegion *v; while ((v=slPopHead(&after))) { if (sameString(haploChrom, v->chrom)) { found = TRUE; break; } offset += (v->end - v->start); slAddHead(&before, v); } if (!found) { warn("initSingleAltHaplotype: chrom %s on which alt %s is placed is not found in all chroms list!", haploChrom, haplotypeId); return FALSE; } slReverse(&before); // for now, make virtchrom with just one chrom plus its haplo in the middle defaultVirtWinStart = 0; defaultVirtWinEnd = 0;; AllocVar(v); v->chrom = haploChrom; v->start = 0; v->end = haploStart; defaultVirtWinStart = v->end - haploSize; if (defaultVirtWinStart < 0) defaultVirtWinStart = 0; defaultVirtWinEnd = v->end; slAddHead(&virtRegionList, v); AllocVar(v); v->chrom = haplotypeId; v->start = 0; v->end = haploSize; defaultVirtWinEnd += haploSize; slAddHead(&virtRegionList, v); AllocVar(v); v->chrom = haploChrom; v->start = haploEnd; int chromSize = hChromSize(database, haploChrom); // size of the regular chrom v->end = chromSize; defaultVirtWinEnd += haploSize; if (defaultVirtWinEnd > chromSize) defaultVirtWinEnd = chromSize; slAddHead(&virtRegionList, v); slReverse(&virtRegionList); hFreeConn(&conn); defaultVirtWinStart += offset; defaultVirtWinEnd += offset; // concatenate the 3 lists. virtRegionList = slCat(before,slCat(virtRegionList,after)); return TRUE; } void initVirtRegionsFromKnownCanonicalGenes(char *table) // OBSOLETED by initVirtRegionsFromEMGeneTableExons() /* Create a regionlist from knownCanonical genes (not exons) */ // I was not expecting it, but 20% of the KC genes overlap with others. // Some are cDNAs, some are non-coding RNAs, some just look like junk. // But I have to add special logic to accomodate them. // Currently I just merge until there is no more overlap, // and then I start a new region. So 30K regions should reduce to about 24K regions or less. { struct sqlConnection *conn = hAllocConn(database); virtRegionList = NULL; struct sqlResult *sr; char **row; char query[256]; sqlSafef(query, sizeof(query), "select chrom, chromStart, chromEnd from %s where chrom not like '%%_hap_%%' and chrom not like '%%_random'", table); sr = sqlGetResult(conn, query); char chrom[256] = ""; int start = -1; int end = -1; char lastChrom[256] = ""; int lastStart = -1; int lastEnd = -1; boolean firstTime = TRUE; boolean isEOF = FALSE; while (1) { boolean printIt = FALSE; row = sqlNextRow(sr); if (row) { safecpy(chrom, sizeof chrom, row[0]); start = sqlUnsigned(row[1]); end = sqlUnsigned(row[2]); if (sameString(chrom, lastChrom)) { if (start <= lastEnd) { // overlap detected in knownCanonical // extend current region if (end > lastEnd) lastEnd = end; } else { printIt = TRUE; } } else { printIt = TRUE; } } else { printIt = TRUE; isEOF = TRUE; } if (printIt) { if (firstTime) { firstTime = FALSE; } else { struct virtRegion *v; AllocVar(v); v->chrom = cloneString(lastChrom); v->start = lastStart; v->end = lastEnd; v->strand[0] = '.'; // TODO we should probably just remove the strand field v->strand[1] = 0; slAddHead(&virtRegionList, v); } } if (isEOF) break; if (printIt) { safecpy(lastChrom, sizeof lastChrom, chrom); lastStart = start; lastEnd = end; } } sqlFreeResult(&sr); slReverse(&virtRegionList); hFreeConn(&conn); } struct kce // keep list of overlapping genes and their exons { struct kce *next; struct genePred *gene; int exonNumber; }; int findBestKce(struct kce *list, struct kce **pBestKce, struct kce **pPrevKce) // find best kce by having minimum exon start // TODO could replace this with a heap or a doubly-linked list { int best = -1; struct kce *e, *prev = NULL; for(e=list; e; prev=e, e=e->next) { int start = e->gene->exonStarts[e->exonNumber]; if ((start < best) || (best == -1)) { best = start; *pBestKce = e; *pPrevKce = prev; } } return best; } static void padExons(struct genePred *gene, int chromSize, int padding) /* pad all of the exons */ { int i; for(i=0; i < gene->exonCount; ++i) { gene->exonStarts[i] -= padding; if (gene->exonStarts[i] < 0) gene->exonStarts[i] = 0; gene->exonEnds[i] += padding; if (gene->exonEnds[i] > chromSize) gene->exonEnds[i] = chromSize; } } static void convertGenePredGeneToExon(struct genePred *gene) /* convert gene into a gene with just one exon that spans the entire gene */ { if (gene->exonCount < 1) errAbort("unexpected input in convertGenePredGeneToExon(), gene->exonCount=%d < 1", gene->exonCount); gene->exonEnds[0] = gene->exonEnds[gene->exonCount - 1]; gene->exonCount = 1; } void initVirtRegionsFromEMGeneTableExons(boolean showNoncoding, char *knownCanonical, char *knownToTag, boolean geneMostly) /* Create a regionlist from knownGene exons. */ // Merge exon regions that overlap. // DONE Jim indicated that he would prefer it to include all transcripts, not just knownCanonical. // DONE Jim also suggested that we might want to handle padding right here in this step. // After thinking about it, I do not think it would be very hard because we are merging already. // Basically, just take the record from the db table row, add padding to start and end, // and clip for chromosome size. // TODO If we keep it at full genome level (instead of single chrom), then there is an apparent // sorting issue because although they are sorted on disk, they are usually sorted by chrom alphabetically // so that chr11 (not chr2) comes after chr1. Instead of trying to specify the sort order in the query, // which is slow, or trying to read one chrom at a time in the sorted order which is also slow, we can instead // just fetch them in their native order, and then create a duplicate array and copy the contents // to it in memory, one chunk per chrom, which would be very fast, but temporarily require duplicate vchrom array mem. // Not sure what to do about assemblies with many scaffolds. // // Adding support for extra options from Gencode hg38 so we can filter for // comprehensive, splice-variants, non-coding subsets. { struct sqlConnection *conn = hAllocConn(database); virtRegionList = NULL; struct sqlResult *sr; char **row; int rowOffset = 0; char query[256]; int padding = emPadding; if (sameString(virtModeType, "geneMostly")) padding = gmPadding; // knownCanonical Hash struct hash *kcHash = NULL; if (knownCanonical) // filter out alt splicing variants { // load up hash of canonical transcriptIds sqlSafef(query, sizeof(query), "select transcript from %s" //" where chrom not like '%%_hap_%%' and chrom not like '%%_random'" , knownCanonical); if (virtualSingleChrom()) sqlSafefAppend(query, sizeof(query), " where chrom='%s'", chromName); kcHash = newHash(10); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { hashAdd(kcHash, row[0], NULL); } sqlFreeResult(&sr); } // knownToTag basic hash struct hash *ktHash = NULL; if (knownToTag) // filter out all but Basic { // load up hash of canonical transcriptIds sqlSafef(query, sizeof(query), "select name from %s where value='basic'", knownToTag); ktHash = newHash(10); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { hashAdd(ktHash, row[0], NULL); } sqlFreeResult(&sr); } setEMGeneTrack(); if (!emGeneTable) errAbort("Unexpected error, emGeneTable=NULL in initVirtRegionsFromEMGeneTableExons"); if (hIsBinned(database, emGeneTable)) // skip first bin column if any ++rowOffset; sqlSafef(query, sizeof(query), "select * from %s", emGeneTable); if (virtualSingleChrom()) sqlSafefAppend(query, sizeof(query), " where chrom='%s'", chromName); // TODO GALT may have to change this to in-memory sorting? // refGene is out of order because of genbank continuous loading // also, using where chrom= causes it to use indexes which disturb order returned. sqlSafefAppend(query, sizeof(query), " order by chrom, txStart"); sr = sqlGetResult(conn, query); char chrom[256] = ""; int start = -1; int end = -1; char lastChrom[256] = ""; int lastStart = -1; int lastEnd = -1; int chromSize = -1; char lastChromSizeChrom[256] = ""; boolean firstTime = TRUE; boolean isEOF = FALSE; struct kce *kceList = NULL, *bestKce, *prevKce; struct genePred *gene = NULL; while (1) { while(1) // get input if possible { boolean readIt = FALSE; if (!gene) readIt = TRUE; if (isEOF) readIt = FALSE; if (readIt) { row = sqlNextRow(sr); if (row) { gene = genePredLoad(row+rowOffset); if (geneMostly) convertGenePredGeneToExon(gene); if (!sameString(lastChromSizeChrom, gene->chrom)) { chromSize = hChromSize(database, gene->chrom); safecpy(lastChromSizeChrom, sizeof lastChromSizeChrom, gene->chrom); } if (padding > 0) padExons(gene, chromSize, padding); // handle padding } else { isEOF = TRUE; } } if (gene && !showNoncoding && (gene->cdsStart == gene->cdsEnd)) { //skip non-coding gene genePredFree(&gene); } if (gene && knownCanonical && !hashLookup(kcHash, gene->name)) { //skip gene not in knownCanonical hash genePredFree(&gene); } if (gene && knownToTag && !hashLookup(ktHash, gene->name)) { // skip gene not in knownToTag Basic hash genePredFree(&gene); } boolean transferIt = FALSE; if (gene && !kceList) { transferIt = TRUE; } else if (gene && kceList) { // TODO need to check the chrom equality first int best = findBestKce(kceList, &bestKce, &prevKce); if (sameString(gene->chrom, chrom)) { if (gene->exonStarts[0] < best) transferIt = TRUE; } } if (transferIt) { // add gene to kce list struct kce *kce; AllocVar(kce); kce->gene = gene; kce->exonNumber = 0; slAddHead(&kceList, kce); safecpy(chrom, sizeof chrom, gene->chrom); gene = NULL; // do not free since it is still in use } if (gene && kceList && !transferIt) break; if (isEOF && !gene) { if (kceList) // flush out the last of the items in kcelist findBestKce(kceList, &bestKce, &prevKce); break; } } boolean printIt = FALSE; if (kceList) { safecpy(chrom, sizeof chrom, bestKce->gene->chrom); start = bestKce->gene->exonStarts[bestKce->exonNumber]; end = bestKce->gene->exonEnds[bestKce->exonNumber]; if (sameString(chrom, lastChrom)) { if (start <= lastEnd) { // overlap detected, extend current region if (end > lastEnd) { lastEnd = end; } } else { printIt = TRUE; } } else { printIt = TRUE; } } else { printIt = TRUE; isEOF = TRUE; } if (printIt) { if (firstTime) { firstTime = FALSE; } else { struct virtRegion *v; AllocVar(v); v->chrom = cloneString(lastChrom); v->start = lastStart; v->end = lastEnd; v->strand[0] = '.'; // TODO we should probably just remove the strand field v->strand[1] = 0; slAddHead(&virtRegionList, v); } } if (isEOF && !kceList && !gene) break; if (printIt) { safecpy(lastChrom, sizeof lastChrom, chrom); lastStart = start; lastEnd = end; } ++bestKce->exonNumber; if (bestKce->exonNumber >= bestKce->gene->exonCount) { // remove from kceList genePredFree(&bestKce->gene); if (prevKce) prevKce->next = bestKce->next; else kceList = bestKce->next; freeMem(bestKce); } } sqlFreeResult(&sr); slReverse(&virtRegionList); hashFree(&kcHash); hashFree(&ktHash); hFreeConn(&conn); } void testRegionList() /* check if it is ascending non-overlapping regions. (this is not always a requirement in the most general case, i.e. user-regions) */ { char lastChrom[256]; int lastEnd = -1; struct virtRegion *v; for (v=virtRegionList; v; v=v->next) { if (sameString(v->chrom,lastChrom)) { if (v->end < v->start) errAbort("check of region list reveals invalid region %s:%d-%d", v->chrom, v->start, v->end); if (lastEnd > v->start) errAbort("check of region list reveals overlapping regions region %s:%d-%d lastEnd=%d", v->chrom, v->start, v->end, lastEnd); } else { safecpy(lastChrom, sizeof lastChrom, v->chrom); } lastEnd = v->end; } } // multi-window variables global to hgTracks void setGlobalsFromWindow(struct window *window) /* set global window values */ { currentWindow = window; organism = window->organism; database = window->database; chromName = window->chromName; winStart = window->winStart; winEnd = window->winEnd; insideX = window->insideX; insideWidth = window->insideWidth; winBaseCount = winEnd - winStart; } void initExonStep() /* create exon-like pattern with exonSize and stepSize */ { int winCount = cartUsualInt(cart, "demo2NumWindows", demo2NumWindows); int i; int exonSize = cartUsualInt(cart, "demo2WindowSize", demo2WindowSize); //200; //9974; //200; int intronSize = cartUsualInt(cart, "demo2StepSize", demo2StepSize); //200; //15000; // really using it like stepSize as that allows overlapping windows. struct virtRegion *v; for(i=0;i<winCount;++i) { AllocVar(v); //chr21:33,031,597-33,041,570 v->chrom = "chr21"; v->start = 33031597 - 1 + i*(intronSize); v->end = v->start + exonSize; //33041570; slAddHead(&virtRegionList, v); } slReverse(&virtRegionList); //if (winCount >= 2) // withNextExonArrows = FALSE; /* Display next exon navigation buttons near center labels? */ //warn("winCount=%d, exonSize=%d, intronSize=%d", winCount, exonSize, intronSize); } void initAllChroms() /* initialize virt region list for main chromosomes */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int winCount = 0; char *query = NOSQLINJ "select chrom, size from chromInfo" " where chrom like 'chr%'" " and chrom not like '%_random'" " and chrom not like 'chrUn%'"; // allow alternate haplotypes for now //" and chrom not like '%_hap%'" //" and chrom not like '%_alt'" //warn("%s",query); struct virtRegion *v; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { unsigned chromSize = sqlUnsigned(row[1]); AllocVar(v); v->chrom = cloneString(row[0]); v->start = 1 - 1; v->end = chromSize; slAddHead(&virtRegionList, v); ++winCount; } sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&virtRegionList); } void initWindowsAltLoci() /* initialize window list showing alt (alternate haplotype)*/ { struct virtRegion *v; //chr1:153520530-153700530 AllocVar(v); v->chrom = "chr1"; v->start = 153520530 - 1; v->end = 153700530; //chr1:153,520,529-154,045,739 as a single window slAddHead(&virtRegionList, v); //chr1_GL383518v1_alt:1-182439 AllocVar(v); v->chrom = "chr1_GL383518v1_alt"; v->start = 1 - 1; v->end = 182439; slAddHead(&virtRegionList, v); //chr1:153865739-154045739 AllocVar(v); v->chrom = "chr1"; v->start = 153865739 - 1; v->end = 154045739; slAddHead(&virtRegionList, v); slReverse(&virtRegionList); } void checkmultiRegionsBedInput() /* Check if multiRegionsBedInput needs processing. * If BED submitted, see if it has changed, and if so, save it to trash * and update cart and global vars. Uses sha1 hash for faster change check. */ { enum custRgnType { empty, url, trashFile }; enum custRgnType oldType = empty; enum custRgnType newType = empty; // OLD input char *newMultiRegionsBedUrl = NULL; multiRegionsBedUrl = cartUsualString(cart, "multiRegionsBedUrl", multiRegionsBedUrl); char multiRegionsBedUrlSha1Name[1024]; safef(multiRegionsBedUrlSha1Name, sizeof multiRegionsBedUrlSha1Name, "%s.sha1", multiRegionsBedUrl); if (!multiRegionsBedUrl) { multiRegionsBedUrl = ""; cartSetString(cart, "multiRegionsBedUrl", multiRegionsBedUrl); } if (sameString(multiRegionsBedUrl,"")) oldType = empty; else if (strstr(multiRegionsBedUrl,"://")) oldType = url; else oldType = trashFile; // NEW input char *multiRegionsBedInput = cartOptionalString(cart, "multiRegionsBedInput"); if (!multiRegionsBedInput) return; // create cleaned up dyString from input. // remove blank lines, trim leading and trailing spaces, change CRLF from TEXTAREA input to LF. struct dyString *dyInput = dyStringNew(1024); char *input = cloneString(multiRegionsBedInput); // make a copy, linefile modifies struct lineFile *lf = lineFileOnString("multiRegionsBedInput", TRUE, input); char *line; int lineSize; while (lineFileNext(lf, &line, &lineSize)) { line = trimSpaces(line); if (sameString(line, "")) // skip blank lines continue; dyStringAppend(dyInput,line); dyStringAppend(dyInput,"\n"); } lineFileClose(&lf); // test multiRegionsBedInput. empty? url? trashFile? input = cloneString(dyInput->string); // make a copy, linefile modifies lf = lineFileOnString("multiRegionsBedInput", TRUE, input); int lineCount = 0; while (lineFileNext(lf, &line, &lineSize)) { ++lineCount; if (lineCount==1 && (startsWithNoCase("http://" ,line) || startsWithNoCase("https://",line) || startsWithNoCase("ftp://" ,line))) { // new value is a URL. set vars and cart. newMultiRegionsBedUrl = cloneString(line); newType = url; } break; } lineFileClose(&lf); if (newType != url) { if (lineCount == 0) // there are no non-blank lines { newMultiRegionsBedUrl = ""; newType = empty; } else newType = trashFile; } char newSha1[(SHA_DIGEST_LENGTH + 1) * 2]; if (newType==trashFile) { // calculate sha1 checksum on new input. unsigned char hash[SHA_DIGEST_LENGTH]; SHA1((const unsigned char *)dyInput->string, dyInput->stringSize, hash); hexBinaryString(hash, SHA_DIGEST_LENGTH, newSha1, (SHA_DIGEST_LENGTH + 1) * 2); } // compare input sha1 to trashFile sha1 to see if same boolean filesAreSame = FALSE; if (oldType==trashFile && newType==trashFile) { lf = lineFileMayOpen(multiRegionsBedUrlSha1Name, TRUE); while (lineFileNext(lf, &line, &lineSize)) { if (sameString(line, newSha1)) filesAreSame = TRUE; } lineFileClose(&lf); } // save new trashFile unless no changes. if (newType==trashFile && (!(oldType==trashFile && filesAreSame) )) { struct tempName bedTn; trashDirFile(&bedTn, "hgt", "custRgn", ".bed"); FILE *f = mustOpen(bedTn.forCgi, "w"); mustWrite(f, dyInput->string, dyInput->stringSize); carefulClose(&f); // new value is a trash file. newMultiRegionsBedUrl = cloneString(bedTn.forCgi); // save new input sha1 to trash file. safef(multiRegionsBedUrlSha1Name, sizeof multiRegionsBedUrlSha1Name, "%s.sha1", bedTn.forCgi); f = mustOpen(multiRegionsBedUrlSha1Name, "w"); mustWrite(f, newSha1, strlen(newSha1)); carefulClose(&f); } dyStringFree(&dyInput); // if new value, set vars and cart if (newMultiRegionsBedUrl) { multiRegionsBedUrl = newMultiRegionsBedUrl; cartSetString(cart, "multiRegionsBedUrl", multiRegionsBedUrl); } cartRemove(cart, "multiRegionsBedInput"); } boolean initVirtRegionsFromBedUrl(time_t *bedDateTime) /* Read custom regions from BED URL */ { multiRegionsBedUrl = cartUsualString(cart, "multiRegionsBedUrl", multiRegionsBedUrl); int bedPadding = 0; // default no padding if (sameString(multiRegionsBedUrl,"")) { warn("No BED or BED URL specified."); return FALSE; } struct lineFile *lf = NULL; if (strstr(multiRegionsBedUrl,"://")) { lf = lineFileUdcMayOpen(multiRegionsBedUrl, FALSE); if (!lf) { warn("Unable to open [%s] with udc", multiRegionsBedUrl); return FALSE; } *bedDateTime = udcTimeFromCache(multiRegionsBedUrl, NULL); } else { lf = lineFileMayOpen(multiRegionsBedUrl, TRUE); if (!lf) { warn("BED custom regions file [%s] not found.", multiRegionsBedUrl); return FALSE; } *bedDateTime = 0; // touch corresponding .sha1 file to save it from trash cleaner. char multiRegionsBedUrlSha1Name[1024]; safef(multiRegionsBedUrlSha1Name, sizeof multiRegionsBedUrlSha1Name, "%s.sha1", multiRegionsBedUrl); if (fileExists(multiRegionsBedUrlSha1Name)) readAndIgnore(multiRegionsBedUrlSha1Name); } char *line; int lineSize; int expectedFieldCount = -1; struct bed *bed, *bedList = NULL; while (lineFileNext(lf, &line, &lineSize)) { // Process comments for keywords like database, shortDesc, and maybe others if (startsWith("#",line)) { if (startsWith("#database ",line)) { char *dbFromBed = line+strlen("#database "); if (!sameString(database,dbFromBed)) { warn("Multi-Region BED URL error: The database (%s) specified in input does not match current database %s", dbFromBed, database); return FALSE; } } if (startsWith("#shortDesc ",line)) { virtModeShortDescr = cloneString(line+strlen("#shortDesc ")); } if (startsWith("#padding ",line)) { bedPadding = sqlSigned(line+strlen("#padding ")); } continue; } char *row[15]; int numFields = chopByWhite(line, row, ArraySize(row)); if (numFields < 3) { warn("%s doesn't appear to be in BED format. 3 or more fields required, got %d", multiRegionsBedUrl, numFields); return FALSE; } if (expectedFieldCount == -1) { expectedFieldCount = numFields; } else { if (numFields != expectedFieldCount) errAbort("Multi-Region BED was detected to have %d columns. But this row has %d columns. " "All rows except comment lines should have the same number of columns", numFields, expectedFieldCount); } AllocVar(bed); // All fields are standard BED fields, no bedplus fields supported at this time. // note: this function does not validate chrom name or end beyond chrom size struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { loadAndValidateBed(row, numFields, numFields+0, lf, bed, NULL, TRUE); // can errAbort } errCatchEnd(errCatch); if (errCatch->gotError) { warn("%s", errCatch->message->string); return FALSE; } errCatchFree(&errCatch); bed->chrom=cloneString(bed->chrom); // loadAndValidateBed does not do it for speed. but bedFree needs it. struct chromInfo *ci = hGetChromInfo(database, bed->chrom); if (ci == NULL) { warn("Couldn't find chromosome/scaffold %s in database", bed->chrom); return FALSE; } if (bed->chromEnd > ci->size) { warn("BED chromEnd %u > size %u for chromosome/scaffold %s", bed->chromEnd, ci->size, bed->chrom); return FALSE; } slAddHead(&bedList, bed); struct virtRegion *v; if (numFields < 12) { AllocVar(v); v->chrom = cloneString(bed->chrom); v->start = bed->chromStart; v->end = bed->chromEnd; slAddHead(&virtRegionList, v); } else { int e; for (e = 0; e < bed->blockCount; ++e) { AllocVar(v); v->chrom = cloneString(bed->chrom); v->start = bed->chromStart + bed->chromStarts[e]; v->end = v->start + bed->blockSizes[e]; slAddHead(&virtRegionList, v); } } } lineFileClose(&lf); bedFreeList(&bedList); slReverse(&virtRegionList); if (bedPadding > 0) padVirtRegions(bedPadding); return TRUE; } void restoreSavedVirtPosition() /* Set state from lastDbPosCart. * This involves parsing the extra state that was saved.*/ { struct hashEl *el, *elList = hashElListHash(lastDbPosCart->hash); for (el = elList; el != NULL; el = el->next) { char *cartVar = el->name; char *cartVal = cartOptionalString(lastDbPosCart, cartVar); if (cartVal) { /* do we need this feature? if (sameString(cartVal,"(null)")) cartRemove(cart, cartVar); else */ cartSetString(cart, cartVar, cartVal); } } hashElFreeList(&elList); } void lastDbPosSaveCartSetting(char *cartVar) /* Save var and value from cart into lastDbPosCart. */ { cartSetString(lastDbPosCart, cartVar, cartUsualString(cart, cartVar, NULL)); } void dySaveCartSetting(struct dyString *dy, char *cartVar, boolean saveBoth) /* Grab var and value from cart, save as var=val to dy string. */ { if (dy->stringSize > 0) dyStringAppend(dy, " "); dyStringPrintf(dy, "%s=%s", cartVar, cartUsualString(cart, cartVar, NULL)); if (saveBoth) lastDbPosSaveCartSetting(cartVar); } boolean initRegionList() /* initialize window list */ { checkmultiRegionsBedInput(); struct virtRegion *v; virtRegionList = NULL; virtModeExtraState = ""; // This is state that determines if the virtChrom has changed lastDbPosCart = cartOfNothing(); // USED to store and restore cart settings related to position and virtMode struct dyString *dy = dyStringNew(256); // used to build virtModeExtraState if (sameString(virtModeType, "default")) { // Single window same as normal window // mostly good to test nothing was broken with single window AllocVar(v); v->chrom = chromName; v->start = 0; v->end = hChromSize(database, chromName); virtWinStart = winStart; virtWinEnd = winEnd; slAddHead(&virtRegionList, v); slReverse(&virtRegionList); } else if (sameString(virtModeType, "exonMostly") || sameString(virtModeType, "geneMostly")) { // Gencode settings: comprehensive, alt-splice, non-coding char *knownCanonical = NULL; // show splice-variants, not filtered out via knownCanonical boolean showNoncoding = TRUE; // show non-coding where cdsStart==cdsEnd char *knownToTag = NULL; // show comprehensive set not filtered by knownToTag char varName[SMALLBUF]; boolean geneMostly = FALSE; lastDbPosSaveCartSetting("emGeneTable"); //DISGUISE makes obsolete dySaveCartSetting(dy, "emGeneTable"); //DISGUISE makes obsolete dySaveCartSetting(dy, "emPadding"); if (sameString(virtModeType, "geneMostly")) geneMostly = TRUE; if (sameString(emGeneTable, "knownGene")) { // test cart var knownGene.show.noncoding // check for alternate table name. // if found, set and pass to gene-table reading routine // Some code borrowed from simpleTracks.c::loadKnownGene() safef(varName, sizeof(varName), "%s.show.noncoding", emGeneTable); showNoncoding = cartUsualBoolean(cart, varName, TRUE); //DISGUISE makes obsolete dySaveCartSetting(dy, varName); safef(varName, sizeof(varName), "%s.show.spliceVariants", emGeneTable); boolean showSpliceVariants = cartUsualBoolean(cart, varName, TRUE); //DISGUISE makes obsolete dySaveCartSetting(dy, varName); if (!showSpliceVariants) { char *canonicalTable = trackDbSettingOrDefault(emGeneTrack->tdb, "canonicalTable", "knownCanonical"); if (hTableExists(database, canonicalTable)) knownCanonical = canonicalTable; } safef(varName, sizeof(varName), "%s.show.comprehensive", emGeneTable); boolean showComprehensive = cartUsualBoolean(cart, varName, FALSE); //DISGUISE makes obsolete dySaveCartSetting(dy, varName); if (!showComprehensive) { if (hTableExists(database, "knownToTag")) { knownToTag = "knownToTag"; } } } if (sameString(emGeneTable, "refGene")) { char varName[SMALLBUF]; safef(varName, sizeof(varName), "%s.hideNoncoding", emGeneTable); showNoncoding = !cartUsualBoolean(cart, varName, FALSE); //DISGUISE makes obsolete dySaveCartSetting(dy, varName); } initVirtRegionsFromEMGeneTableExons(showNoncoding, knownCanonical, knownToTag, geneMostly); if (!virtRegionList) { warn("No genes found on chrom %s for track %s, returning to default view", chromName, emGeneTrack->shortLabel); return FALSE; // regionList is empty, nothing found. } if (geneMostly) virtModeShortDescr = "genes"; else virtModeShortDescr = "exons"; // DISGUISE makes obsolete dyStringPrintf(dy," %s %s", dy->string, knownCanonical, knownToTag); } else if (sameString(virtModeType, "kcGenes")) // TODO obsolete { initVirtRegionsFromKnownCanonicalGenes("knownCanonical"); virtModeShortDescr = "genes"; } else if (sameString(virtModeType, "customUrl")) { // custom regions from BED URL virtModeShortDescr = "customUrl"; // can be overridden by comment in input bed file time_t bedDateTime = 0; if (!initVirtRegionsFromBedUrl(&bedDateTime)) { return FALSE; // return to default mode } dySaveCartSetting(dy, "multiRegionsBedUrl", TRUE); dyStringPrintf(dy, " %ld", (long)bedDateTime); } else if (sameString(virtModeType, "singleTrans")) { singleTransId = cartUsualString(cart, "singleTransId", singleTransId); if (sameString(singleTransId, "")) { warn("Single transcript Id should not be blank"); return FALSE; // return to default mode } setEMGeneTrack(); dySaveCartSetting(dy, "singleTransId", TRUE); } else if (sameString(virtModeType, "singleAltHaplo")) { singleAltHaploId = cartUsualString(cart, "singleAltHaploId", singleAltHaploId); // default is chr6_cox_hap2 initAllChroms(); // we want to default to full genome view. if (!initSingleAltHaplotype(singleAltHaploId)) { virtRegionList = NULL; return FALSE; // return to default mode } // was "single haplo" but that might confuse some users. virtModeShortDescr = endsWith(singleAltHaploId, "_fix") ? "fix patch" : "alt haplo"; dySaveCartSetting(dy, "singleAltHaploId", TRUE); } else if (sameString(virtModeType, "allChroms")) { // TODO more work on this mode //warn("show all regular chromosomes (not alts)\n" //"Warning must turn off all tracks except big*"); initAllChroms(); } else if (sameString(virtModeType, "demo1")) { // demo two windows on two chroms (default posn chr21, and same loc on chr22 //chr21:33,031,597-33,041,570 AllocVar(v); //chr21:33,031,597-33,041,570 v->chrom = "chr21"; v->start = 33031597 - 1; v->end = 33041570; slAddHead(&virtRegionList, v); struct virtRegion *v2; AllocVar(v2); //chr22:33,031,597-33,041,570 v2->chrom = "chr22"; v2->start = 33031597 - 1; v2->end = 33041570; slAddHead(&virtRegionList, v2); slReverse(&virtRegionList); } else if (sameString(virtModeType, "demo2")) { // demo multiple (70) windows on one chrom chr21 def posn, window size and step exon-like initExonStep(); } else if (sameString(virtModeType, "demo4")) { // demo multiple (20) windows showing exons from TITIN gene uc031rqd.1. initVirtRegionsFromEmGeneTable("uc031rqd.1"); // TITIN // "uc002ypa.3"); // SOD1 } else if (sameString(virtModeType, "demo5")) { // demo alt locus on hg38 // Shows alt chrom surrounded by preceding and following regions of same size from reference genome. initWindowsAltLoci(); } else if (sameString(virtModeType, "demo6")) { // demo SOD1 // Shows zoomed in exon-exon junction from SOD1 gene, between exon1 and exon2. initVirtRegionsFromSOD1Hardwired(); } else { // Unrecognized virtModeType return FALSE; // return to default mode } virtModeExtraState = dyStringCannibalize(&dy); if (!virtRegionList) return FALSE; // regionList is empty, nothing found. return TRUE; } boolean isLimitedVisHiddenForAllWindows(struct track *track) /* Check if track limitedVis == hidden for all windows. * Return true if all are hidden */ { boolean result = TRUE; for(;track;track=track->nextWindow) if (track->limitedVis != tvHide) result = FALSE; return result; } boolean isTypeBedLike(struct track *track) /* Check if track type is BED-like packable thing (but not rmsk or joinedRmsk) */ { // TODO GALT do we have all the types needed? // TODO could it be as simple as whether track->items exists? char *typeLine = track->tdb->type, *words[8], *type; int wordCount; if (typeLine == NULL) return FALSE; wordCount = chopLine(cloneString(typeLine), words); if (wordCount <= 0) return FALSE; type = words[0]; // NOTE: if type is missing here, full mode fails to return an hgTracks object if ( ( sameWord(type, "bed") || sameWord(type, "bed5FloatScore") || sameWord(type, "bed6FloatScore") || sameWord(type, "bedDetail") || sameWord(type, "bigBed") || sameWord(type, "bigGenePred") || sameWord(type, "broadPeak") || sameWord(type, "chain") || sameWord(type, "factorSource") || sameWord(type, "genePred") || sameWord(type, "gvf") || sameWord(type, "narrowPeak") || sameWord(type, "psl") || sameWord(type, "barChart") || sameWord(type, "bigBarChart") || sameWord(type, "interact") || sameWord(type, "bigInteract") || sameWord(type, "bigLolly") //|| track->loadItems == loadSimpleBed //|| track->bedSize >= 3 // should pick up several ENCODE BED-Plus types. ) && track->canPack ) { return TRUE; } return FALSE; } boolean isTypeUseItemNameAsKey(struct track *track) - /* Check if track type is like expRatio and key is just item name. */ + /* Check if track type is like expRatio and key is just item name, to link across multi regions */ { char *typeLine = track->tdb->type, *words[8], *type; int wordCount; if (typeLine == NULL) return FALSE; wordCount = chopLine(cloneString(typeLine), words); if (wordCount <= 0) return FALSE; type = words[0]; if (sameWord(type, "expRatio")) { // track is like expRatio, needs one row per item return TRUE; } return FALSE; } + boolean isTypeUseMapItemNameAsKey(struct track *track) + /* Check if track type is like interact and uses map item name to link across multi regions */ + { + char *typeLine = track->tdb->type, *words[8], *type; + int wordCount; + if (typeLine == NULL) + return FALSE; + wordCount = chopLine(cloneString(typeLine), words); + if (wordCount <= 0) + return FALSE; + type = words[0]; + if (sameWord(type, "interact") || sameWord(type, "bigInteract")) + return TRUE; + return FALSE; + } + void setFlatTrackMaxHeight(struct flatTracks *flatTrack, int fontHeight) /* for each flatTrack, figure out maximum height needed from all windows */ { struct track *track = flatTrack->track; int maxHeight = 0; struct track *winTrack; struct window *window; for (window=windows, winTrack=track; window; window=window->next, winTrack=winTrack->nextWindow) { setGlobalsFromWindow(window); int trackHeight = trackPlusLabelHeight(winTrack, fontHeight); if (trackHeight > maxHeight) maxHeight = trackHeight; } setGlobalsFromWindow(windows); // first window flatTrack->maxHeight = maxHeight; } - char *collapseEmptySubtracksSetting(struct track *track) -boolean doCollapseEmptySubtracks(struct track *track) -/* Suppress display of empty subtracks. Initial support only for bed's. */ ++char *hideEmptySubtracksSetting(struct track *track) +/* Setting to suppress display of empty subtracks */ { +if (!tdbIsComposite(track->tdb)) + return FALSE; - return trackDbSetting(track->tdb, "collapseEmptySubtracks"); + char *collapse = trackDbSetting(track->tdb, "hideEmptySubtracks"); + if (!collapse) + // previous syntax (not documented, but used by Regeneron) + collapse = trackDbSetting(track->tdb, "collapseEmptySubtracks"); -return (collapse && (sameWord(collapse, "on") || - sameWord(collapse, "true"))); ++return (collapse); +} + - boolean doCollapseEmptySubtracksNoMultiBed(struct track *track) - /* TRUE if collapseEmptySubtracks setting is 'on' (no file specs for multiBed */ ++boolean doHideEmptySubtracksNoMultiBed(struct track *track) ++/* TRUE if hideEmptySubtracks setting is 'on' or 'true' (no file specs for multiBed */ +{ - char *setting = collapseEmptySubtracksSetting(track); - if (setting && sameString(setting, "on")) ++char *setting = hideEmptySubtracksSetting(track); ++if (setting && (sameString(setting, "on") || sameString(setting, "true"))) + return TRUE; +return FALSE; +} + - boolean doCollapseEmptySubtracks(struct track *track, char **multiBedFile, char **subtrackIdFile) ++boolean doHideEmptySubtracks(struct track *track, char **multiBedFile, char **subtrackIdFile) +{ +/* Support setting to suppress display of empty subtracks. + * (Initial support only for bed's). + * - * Format: collapseEmptySubtracks on ++ * Format: hideEmptySubtracks on + * or - * collapseEmptySubtracks multiBed.bed subtrackIds.tab ++ * hideEmptySubtracks multiBed.bed subtrackIds.tab + * where multiBed.bed is a bed3Sources bigBed, generated with bedtools multiinter + * post-processed by UCSC multiBed.pl tool + * subtrackIds.tab is a tab-sep file: id subtrackName + */ - char *collapse = collapseEmptySubtracksSetting(track); ++char *collapse = hideEmptySubtracksSetting(track); +if (!collapse) + return FALSE; - if (doCollapseEmptySubtracksNoMultiBed(track)) ++if (doHideEmptySubtracksNoMultiBed(track)) + return TRUE; +char *orig = cloneString(collapse); +char *words[2]; +int wordCount = chopByWhite(collapse, words, ArraySize(words)); +if (wordCount == 2) + { + if (multiBedFile) + *multiBedFile = cloneString(hReplaceGbdb(words[0])); + if (subtrackIdFile) + *subtrackIdFile = cloneString(words[1]); + return TRUE; + } - warn("Track %s collapseEmptySubtracks setting invalid: %s", ++warn("Track %s hideEmptySubtracks setting invalid: %s", + track->track, orig); +return FALSE; +} + +struct hash *getNonEmptySubtracks(struct track *track) +{ +/* Support setting to suppress display of empty subtracks. + * (Initial support only for bed's). + * - * Format: collapseEmptySubtracks on ++ * Format: hideEmptySubtracks on + * or - * collapseEmptySubtracks multiBed.bed subtrackIds.tab ++ * hideEmptySubtracks multiBed.bed subtrackIds.tab + * where multiBed.bed is a bed3Sources bigBed, generated with bedtools multiinter + * post-processed by UCSC multiBed.pl tool + * subtrackIds.tab is a tab-sep file: id subtrackName + * + * Return hash with subtrack names as keys + */ + +char *multiBedFile = NULL; +char *subtracksIdFile = NULL; - if (!doCollapseEmptySubtracks(track, &multiBedFile, &subtracksIdFile)) ++if (!doHideEmptySubtracks(track, &multiBedFile, &subtracksIdFile)) + return NULL; +if (!multiBedFile) + return NULL; + +// load multiBed items in window +// TODO: filters here ? +// TODO: protect against temporary network error ? */ +struct lm *lm = lmInit(0); +struct bbiFile *bbi = bigBedFileOpen(multiBedFile); +struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chromName, winStart, winEnd, 0, lm); +char *row[bbi->fieldCount]; +char startBuf[16], endBuf[16]; +struct hash *nonEmptySubtracksHash = hashNew(0); +for (bb = bbList; bb != NULL; bb = bb->next) + { + bigBedIntervalToRow(bb, chromName, startBuf, endBuf, row, ArraySize(row)); + // TODO: do this in bed3Sources.c + char *idList = row[4]; + struct slName *ids = slNameListFromComma(idList); + struct slName *id = NULL; + for (id = ids; id != NULL; id = id->next) + hashStore(nonEmptySubtracksHash, id->name); + // TODO: free some stuff ? + } + +// read file containing ids of subtracks +struct lineFile *lf = udcWrapShortLineFile(subtracksIdFile, NULL, 0); +char *words[2]; +while (lineFileChopNext(lf, words, sizeof words)) + { + char *id = words[0]; + char *name = words[1]; + if (hashLookup(nonEmptySubtracksHash, id)) + { + hashStore(nonEmptySubtracksHash, cloneString(name)); + } + } +lineFileClose(&lf); +return nonEmptySubtracksHash; ++ } 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) // if theImgBox == NULL then we are rendering a simple single image such as right-click View image. // 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 expanded image size if (imgBoxPortalDimensions(theImgBox,&virtWinStart,&virtWinEnd,&(tl.picWidth),NULL,NULL,NULL,NULL,NULL)) { pixWidth = tl.picWidth; virtWinBaseCount = virtWinEnd - virtWinStart; fullInsideWidth = tl.picWidth - gfxBorder - fullInsideX; } 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; // figure out height of ruler 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; } } /* Hash tracks/subtracks, limit visibility and calculate total image height: */ // For multiple windows, sets height and visibility // as well as making the flatTrack list. // TODO there is a chance that for pack and squish // I might need to trigger a track-height check here // since it is after all items are loaded for all windows // but before things are checked for overflow or limitedVis? // The fixed non-overflow tracks like knownGene used to initialize // ss and track height during loadItems(). That was delayed // because we now need all windows to be fully loaded before // calculating their joint ss layout and height. // set heights and visibilities. struct window *window = NULL; for(window=windows;window;window=window->next) { setGlobalsFromWindow(window); trackList = window->trackList; 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 (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; } } } } } trackList = windows->trackList; setGlobalsFromWindow(windows); // first window struct slName *orderedWiggles = NULL; char *sortTrack; char *wigOrder = NULL; if ((sortTrack = cgiOptionalString( "sortSim")) != NULL) { char buffer[1024]; safef(buffer, sizeof buffer, "simOrder_%s", sortTrack); wigOrder = cartString(cart, buffer); } if ((sortTrack = cgiOptionalString( "sortExp")) != NULL) { char buffer[1024]; safef(buffer, sizeof buffer, "expOrder_%s", sortTrack); wigOrder = cartString(cart, buffer); } if (wigOrder != NULL) { orderedWiggles = slNameListFromString(wigOrder, ' '); struct slName *name = orderedWiggles; // if we're sorting, remove existing sort order for this composite for(; name; name = name->next) { char buffer[1024]; safef(buffer, sizeof buffer, "%s_imgOrd", name->name); cartRemove(cart, buffer); } } // Construct flatTracks for (track = trackList; track != NULL; track = track->next) { if (tdbIsComposite(track->tdb)) { struct track *subtrack; if (isCompositeInAggregate(track)) flatTracksAdd(&flatTracks,track,cart, orderedWiggles); else { - boolean doCollapse = doCollapseEmptySubtracksNoMultiBed(track); - boolean doCollapse = doCollapseEmptySubtracks(track); ++ boolean doHideEmpties = doHideEmptySubtracksNoMultiBed(track); + // If multibed was found, it has been used to suppress loading, + // and subtracks lacking items in window are already set hidden for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next) { if (!isSubtrackVisible(subtrack)) continue; if (!isLimitedVisHiddenForAllWindows(subtrack) && -- !(doCollapse && slCount(subtrack->items) == 0)) ++ !(doHideEmpties && slCount(subtrack->items) == 0)) + // Ignore subtracks with no items in window { flatTracksAdd(&flatTracks,subtrack,cart, orderedWiggles); } } } } else { if (!isLimitedVisHiddenForAllWindows(track)) { flatTracksAdd(&flatTracks,track,cart, orderedWiggles); } } } flatTracksSort(&flatTracks); // Now we should have a perfectly good flat track list! if (orderedWiggles) { // save order to cart struct flatTracks *ft; char buffer[4096]; int count = 1; for(ft = flatTracks; ft; ft = ft->next) { safef(buffer, sizeof buffer, "%s_imgOrd", ft->track->track); cartSetInt(cart, buffer, count++); } } // for each track, figure out maximum height needed from all windows for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) { track = flatTrack->track; if (track->limitedVis == tvHide) { continue; } setFlatTrackMaxHeight(flatTrack, fontHeight); } // fill out track->prevTrack, and check for maxSafeHeight boolean safeHeight = TRUE; /* firefox on Linux worked almost up to 34,000 at the default 620 width */ #define maxSafeHeight 32000 struct track *prevTrack = NULL; for (flatTrack = flatTracks,prevTrack=NULL; flatTrack != NULL; flatTrack = flatTrack->next) { track = flatTrack->track; assert(track->limitedVis != tvHide); // ORIG int totalHeight = pixHeight+trackPlusLabelHeight(track,fontHeight); int totalHeight = pixHeight+flatTrack->maxHeight; if (totalHeight > maxSafeHeight) { 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 ? "\nAdditional tracks may have also been hidden at this zoom level." : "")); safeHeight = FALSE; struct track *winTrack; for(winTrack=track;winTrack;winTrack=winTrack->nextWindow) { track->limitedVis = tvHide; track->limitedVisSet = TRUE; } } if (!isLimitedVisHiddenForAllWindows(track)) { struct track *winTrack; for(winTrack=track;winTrack;winTrack=winTrack->nextWindow) { // TODO this is currently still only using one prev track value. winTrack->prevTrack = prevTrack; // Important for keeping track of conditional center labels! } // ORIG pixHeight += trackPlusLabelHeight(track, fontHeight); if (!theImgBox) // prevTrack may have altered the height, so recalc height setFlatTrackMaxHeight(flatTrack, fontHeight); pixHeight += flatTrack->maxHeight; prevTrack = track; } } // allocate hvg png of pixWidth, pixHeight 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; // Unless 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. This does pdf and view-image highlight highlightRegions(cart, hvg, imagePixelHeight); for (window=windows; window; window=window->next) { /* Find colors to draw in. */ findTrackColors(hvg, window->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 (!isLimitedVisHiddenForAllWindows(track)) { struct track *winTrack; for (winTrack=track; winTrack; winTrack=winTrack->nextWindow) { if (winTrack->labelColor == winTrack->ixColor && winTrack->ixColor == 0) { winTrack->ixColor = hvGfxFindRgb(hvg, &winTrack->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) { // ORIG y += trackPlusLabelHeight(track, fontHeight); y += flatTrack->maxHeight; 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); 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; } /* Draw left labels. */ 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); curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL, sliceWidth[stSide],sliceHeight, sliceOffsetX[stSide],sliceOffsetY); (void) 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 //ORIG sliceHeight = trackPlusLabelHeight(track, fontHeight); sliceHeight = flatTrack->maxHeight; sliceOffsetY = y; curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL, sliceWidth[stSide],sliceHeight, sliceOffsetX[stSide],sliceOffsetY); (void) sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot } - if (trackShouldUseAjaxRetrieval(track)) - y += REMOTE_TRACK_HEIGHT; - else - { + boolean doWiggle = cartOrTdbBoolean(cart, track->tdb, "doWiggle" , FALSE); if (doWiggle) track->drawLeftLabels = wigLeftLabels; #ifdef IMAGEv2_NO_LEFTLABEL_ON_FULL if (theImgBox && track->limitedVis != tvDense) y += sliceHeight; else #endif ///def IMAGEv2_NO_LEFTLABEL_ON_FULL { setGlobalsFromWindow(windows); // use GLOBALS from first window int ynew = 0; /* rmskJoined tracks are non-standard in FULL mode they are just their track height, not per-item height */ if (startsWith("rmskJoined", track->track)) ynew = flatTrack->maxHeight + y; else ynew = doLeftLabels(track, hvgSide, font, y); y += flatTrack->maxHeight; if ((ynew - y) > flatTrack->maxHeight) { // TODO should be errAbort? warn("doLeftLabels(y=%d) returned new y value %d that is too high - should be %d at most.", y, ynew, flatTrack->maxHeight); } } } } - } else { leftLabelX = leftLabelWidth = 0; } /* Draw guidelines. */ if (virtMode && emAltHighlight) withGuidelines = TRUE; // we cannot draw the alternating backgrounds without guidelines layer if (withGuidelines) { struct hvGfx *bgImg = hvg; // Default to the one image boolean exists = FALSE; if (theImgBox) { struct tempName gifBg; char base[64]; if (virtMode) // window separators { safecpy(base,sizeof(base),"winSeparators"); // non-reusable temp file trashDirFile(&gifBg, "hgt", base, ".png"); exists = FALSE; } else // re-usable guidelines { safef(base,sizeof(base),"blueLines%d-%s%d-%d",pixWidth,(revCmplDisp?"r":""),fullInsideX, 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) { hvGfxSetClip(bgImg, fullInsideX, 0, fullInsideWidth, pixHeight); y = gfxBorder; if (virtMode) { // vertical windows separators if (emAltHighlight) { // light blue alternating backgrounds Color lightBlue = hvGfxFindRgb(bgImg, &guidelineColor); for (window=windows; window; window=window->next) // background under every other window { if (window->regionOdd) hvGfxBox(bgImg, window->insideX, 0, window->insideWidth, pixHeight, lightBlue); } } else { // red vertical lines Color lightRed = hvGfxFindRgb(bgImg, &vertWindowSeparatorColor); for (window=windows->next; window; window=window->next) // skip first window, not needed hvGfxBox(bgImg, window->insideX, 0, 1, pixHeight, lightRed); } } else { int x; Color lightBlue = hvGfxFindRgb(bgImg, &guidelineColor); for (x = fullInsideX+guidelineSpacing-1; x<pixWidth; x += guidelineSpacing) hvGfxBox(bgImg, x, 0, 1, pixHeight, lightBlue); } hvGfxUnclip(bgImg); if (bgImg != hvg) hvGfxClose(&bgImg); } } /* Draw ruler */ if (rulerMode != tvHide) { newWinWidth = calcNewWinWidth(cart,virtWinStart,virtWinEnd,fullInsideWidth); if (theImgBox) { // data slice for ruler sliceHeight = basePositionHeight + (rulerCds ? rulerTranslationHeight : 0) + 1; sliceOffsetY = 0; curImgTrack = imgBoxTrackFind(theImgBox,NULL,RULER_TRACK_NAME); curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stData,theOneImg,rulerTtl, sliceWidth[stData],sliceHeight, sliceOffsetX[stData],sliceOffsetY); (void) sliceMapFindOrStart(curSlice,RULER_TRACK_NAME,NULL); // No common linkRoot } // need to have real winBaseCount to draw ruler scale for (window=windows; window; window=window->next) { setGlobalsFromWindow(window); if (theImgBox) { // Show window positions as mouseover if (virtMode) { char position[256]; safef(position, sizeof position, "%s:%d-%d", window->chromName, window->winStart+1, window->winEnd); int x = window->insideX; if (revCmplDisp) x = tl.picWidth - (x + window->insideWidth); imgTrackAddMapItem(curImgTrack, "#", position, x, sliceOffsetY, x+window->insideWidth, sliceOffsetY+sliceHeight, RULER_TRACK_NAME); } } y = doDrawRuler(hvg,&rulerClickHeight,rulerHeight,yAfterRuler,yAfterBases,font, fontHeight,rulerCds, scaleBarTotalHeight, window); } setGlobalsFromWindow(windows); // first window } /* Draw center labels. */ if (withCenterLabels) { setGlobalsFromWindow(windows); // first window hvGfxSetClip(hvg, fullInsideX, gfxBorder, fullInsideWidth, pixHeight - 2*gfxBorder); y = yAfterRuler; for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) { track = flatTrack->track; if (track->limitedVis == tvHide) continue; if (theImgBox) { // center label slice of tracks Must always make, even if the centerLabel is empty sliceHeight = fontHeight; sliceOffsetY = y; curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stCenter,theOneImg,NULL, sliceWidth[stData],sliceHeight, sliceOffsetX[stData],sliceOffsetY); (void) sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot if (isCenterLabelConditional(track)) // sometimes calls track height, especially when no data there { imgTrackUpdateCenterLabelSeen(curImgTrack,isCenterLabelConditionallySeen(track) ? clNowSeen : clNotSeen); } } - if (trackShouldUseAjaxRetrieval(track)) - { - y += REMOTE_TRACK_HEIGHT; - } - else - { + int savey = y; // GALT y = doCenterLabels(track, track, hvg, font, y, fullInsideWidth); // calls track height y = savey + flatTrack->maxHeight; } - } hvGfxUnclip(hvg); setGlobalsFromWindow(windows); // first window } /* Draw tracks. */ { // brace allows local vars long lastTime = 0; y = yAfterRuler; if (measureTiming) lastTime = clock1000(); + + // first do predraw for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) { track = flatTrack->track; - // parallelize more this?: - - //ORIG if (track->limitedVis == tvHide) if (isLimitedVisHiddenForAllWindows(track)) continue; - int centerLabelHeight = (isCenterLabelIncluded(track) ? fontHeight : 0); - int yStart = y + centerLabelHeight; - // ORIG int yEnd = y + trackPlusLabelHeight(track, fontHeight); - int yEnd = y + flatTrack->maxHeight; - if (theImgBox) - { - // data slice of tracks - sliceOffsetY = yStart; - sliceHeight = yEnd - yStart - 1; - curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); - if (sliceHeight > 0) - { - curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stData,theOneImg,NULL, - sliceWidth[stData],sliceHeight, - sliceOffsetX[stData],sliceOffsetY); - (void) sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot - } - } - if (trackShouldUseAjaxRetrieval(track)) - y += REMOTE_TRACK_HEIGHT; - else - { - int savey = y; struct track *winTrack; // do preDraw if (track->preDrawItems) { for (window=windows, winTrack=track; window; window=window->next, winTrack=winTrack->nextWindow) { setGlobalsFromWindow(window); if (winTrack->limitedVis == tvHide) { warn("Draw tracks skipping %s because winTrack->limitedVis=hide", winTrack->track); continue; } if (insideWidth >= 1) // do not try to draw if width < 1. { doPreDrawItems(winTrack, hvg, font, y, &lastTime); } } } setGlobalsFromWindow(windows); // first window // do preDrawMultiRegion across all windows, e.g. wig autoScale if (track->preDrawMultiRegion) { track->preDrawMultiRegion(track); } + } + // now do the actual draw + for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) + { + int savey = y; + struct track *winTrack; + track = flatTrack->track; + if (isLimitedVisHiddenForAllWindows(track)) + continue; + + int centerLabelHeight = (isCenterLabelIncluded(track) ? fontHeight : 0); + int yStart = y + centerLabelHeight; + int yEnd = y + flatTrack->maxHeight; + + if (theImgBox) + { + // data slice of tracks + sliceOffsetY = yStart; + sliceHeight = yEnd - yStart - 1; + curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); + if (sliceHeight > 0) + { + curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stData,theOneImg,NULL, + sliceWidth[stData],sliceHeight, + sliceOffsetX[stData],sliceOffsetY); + (void) sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot + } + } // doDrawItems for (window=windows, winTrack=track; window; window=window->next, winTrack=winTrack->nextWindow) { setGlobalsFromWindow(window); if (winTrack->limitedVis == tvHide) { warn("Draw tracks skipping %s because winTrack->limitedVis=hide", winTrack->track); continue; } if (insideWidth >= 1) // do not try to draw if width < 1. { int ynew = doDrawItems(winTrack, hvg, font, y, &lastTime); if ((ynew-y) > flatTrack->maxHeight) // so compiler does not complain ynew is not used. errAbort("oops track too high!"); } } setGlobalsFromWindow(windows); // first window y = savey + flatTrack->maxHeight; - } if (theImgBox && tdbIsCompositeChild(track->tdb) && (track->limitedVis == tvDense || (track->limitedVis == tvPack && centerLabelHeight == 0))) 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 for track %s does not add up. Expecting %d != %d actual", track->shortLabel, yEnd - yStart - 1, y - yStart); } calcWiggleOrdering(cart, flatTracks); y++; } /* post draw tracks leftLabels */ /* 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 = flatTrack->maxHeight; sliceOffsetY = y; curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL, sliceWidth[stSide],sliceHeight, sliceOffsetX[stSide],sliceOffsetY); (void) sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot } - if (trackShouldUseAjaxRetrieval(track)) - y += REMOTE_TRACK_HEIGHT; - else if (track->drawLeftLabels != NULL) + if (track->drawLeftLabels != NULL) { setGlobalsFromWindow(windows); y = doOwnLeftLabels(track, hvgSide, font, y); setGlobalsFromWindow(windows); // first window } else y += flatTrack->maxHeight; } } /* 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 = flatTrack->maxHeight; sliceOffsetY = y; curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); } setGlobalsFromWindow(windows); // first window doTrackMap(track, hvg, y, fontHeight, trackPastTabX, trackPastTabWidth); y += flatTrack->maxHeight; } } /* 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,&virtWinStart,&virtWinEnd,&(tl.picWidth),NULL)) { pixWidth = tl.picWidth; virtWinBaseCount = virtWinEnd - virtWinStart; fullInsideWidth = tl.picWidth - gfxBorder - fullInsideX; } 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); if (tdbList && tdbList->parent) // we want to give the composite parent a chance to load and set options { while(tdbList->parent) { if (tdbList->parent->subtracks == NULL) // we don't want to go up to a supertrack break; tdbList = tdbList->parent; } trackNameFilter = tdbList->track; } } 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, "bigNarrowPeak") || sameString(type, "bigPsl") || sameString(type, "bigMaf")|| sameString(type, "bigChain") || sameString(type, "bigLolly") || sameString(type, "bigBarChart") || sameString(type, "bigInteract")) { 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, "bigNarrowPeak")) safef(typeBuf, sizeof(typeBuf), "bigNarrowPeak"); else if (sameString(type, "bigChain")) safef(typeBuf, sizeof(typeBuf), "bigChain"); else if (sameString(type, "bigMaf")) safef(typeBuf, sizeof(typeBuf), "bigMaf"); else if (sameString(type, "bigPsl")) safef(typeBuf, sizeof(typeBuf), "bigPsl"); else if (sameString(type, "bigBarChart")) safef(typeBuf, sizeof(typeBuf), "bigBarChart"); else if (sameString(type, "bigLolly")) safef(typeBuf, sizeof(typeBuf), "bigLolly"); else if (sameString(type, "bigInteract")) safef(typeBuf, sizeof(typeBuf), "bigInteract"); 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, "bedTabix") || sameString(type, "longTabix")) { knetUdcInstall(); tg = trackFromTrackDb(tdb); tg->customPt = ct; tg->mapItemName = ctMapItemName; /* must be here to see ctMapItemName */ } 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 if (sameString(type, "barChart")) { tg = trackFromTrackDb(tdb); barChartCtMethods(tg); tg->customPt = ct; } else if (sameString(type, "interact")) { tg = trackFromTrackDb(tdb); interactCtMethods(tg); tg->customPt = ct; } else if (sameString(type, "hic")) { tg = trackFromTrackDb(tdb); hicCtMethods(tg); 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 boolean foundMap = FALSE; /* build group objects from database. */ for (grp = grps; grp != NULL; grp = grp->next) { if (sameString(grp->name, "map")) foundMap = TRUE; /* 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 = 1.00001; 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); } // // If there isn't a map group, make one and set the priority so it will be right after custom tracks // and hub groups. if (!foundMap) { AllocVar(group); group->name = cloneString("map"); group->label = cloneString("Mapping and Sequencing"); group->defaultPriority = priority; group->priority = priority; group->defaultIsClosed = FALSE; slAddHead(&list, group); hashAdd(hash, "map", 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 (measureTiming) measureTime("Time after trackDbLoad "); 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); boolean hideTracks = cgiOptionalString( "hideTracks") != NULL; if (hideTracks) changeTrackVis(groupList, NULL, tvHide); // set all top-level tracks to hide /* Get visibility values if any from ui. */ struct hash *superTrackHash = newHash(5); // cache whether supertrack is hiding tracks or not char buffer[4096]; for (track = trackList; track != NULL; track = track->next) { // deal with any supertracks we're seeing for the first time if (tdbIsSuperTrackChild(track->tdb)) { struct hashEl *hel = NULL; if ((hel = hashLookup(superTrackHash, track->tdb->parent->track)) == NULL) // we haven't seen this guy { // first deal with visibility of super track char *s = hideTracks ? cgiOptionalString(track->tdb->parent->track) : cartOptionalString(cart, track->tdb->parent->track); if (s) { track->tdb->parent->visibility = hTvFromString(s) ; cartSetString(cart, track->tdb->parent->track, s); } else if (startsWith("hub_", track->tdb->parent->track)) { s = hideTracks ? cgiOptionalString( trackHubSkipHubName(track->tdb->parent->track)) : cartOptionalString( cart, trackHubSkipHubName(track->tdb->parent->track)); if (s) { cartSetString(cart, track->tdb->parent->track, s); cartRemove(cart, trackHubSkipHubName(track->tdb->parent->track)); // remove the undecorated version track->tdb->parent->visibility = hTvFromString(s) ; } } // now look to see if we have a _hideKids statement to turn off all subtracks (including the current one) unsigned hideKids = 0; char *usedThis = buffer; safef(buffer, sizeof buffer, "%s_hideKids", track->tdb->parent->track); s = cartOptionalString(cart, buffer); if (s == NULL && startsWith("hub_", track->tdb->parent->track)) s = cartOptionalString(cart, usedThis = trackHubSkipHubName(buffer)); if (s != NULL) { hideKids = 1; cartRemove(cart, usedThis); // we don't want this hanging out in the cart } // mark this as having been addressed hel = hashAddInt(superTrackHash, track->tdb->parent->track, hideKids ); } if ( ptToInt(hel->val) == 1) // we want to hide this track { if (tvHide == track->tdb->visibility) /* remove if setting to default vis */ cartRemove(cart, track->track); else cartSetString(cart, track->track, "hide"); track->visibility = tvHide; } } // we use cgiOptionString because the above code may have turned off the track in the cart if // the user requested that all the default tracks be turned off char *s = hideTracks ? cgiOptionalString(track->track) : cartOptionalString(cart, track->track); if (s != NULL) { if (!track->limitedVisSet) { track->visibility = hTvFromString(s); cartSetString(cart, track->track, s); } } else { // maybe this track is on the URL without the hub_ prefix if (startsWith("hub_", track->track)) s = cgiOptionalString(trackHubSkipHubName(track->track)); if (s != NULL && !track->limitedVisSet) { track->visibility = hTvFromString(s); cartSetString(cart, track->track, s); // add the decorated visibility to the cart cartRemove(cart, trackHubSkipHubName(track->track)); // remove the undecorated version } } // now deal with composite track children if (tdbIsComposite(track->tdb)) { char *usedThis = buffer; // first check to see if we've been asked to hide all the subtracks boolean hideKids = FALSE; safef(buffer, sizeof buffer, "%s_hideKids", track->track); s = cartOptionalString(cart, buffer); if (s == NULL && startsWith("hub_", track->track)) s = cartOptionalString(cart, usedThis = trackHubSkipHubName(buffer)); if (s != NULL) hideKids = TRUE; cartRemove(cart, usedThis); // we don't want these _hideKids variables in the cart // now see if we have any specified visibilities struct track *subtrack; for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next) { boolean undecoratedVis = FALSE; char *s = hideTracks ? cgiOptionalString( subtrack->track) : cartOptionalString(cart, subtrack->track); if (s == NULL && startsWith("hub_", subtrack->track)) { undecoratedVis = TRUE; s = hideTracks ? cgiOptionalString(trackHubSkipHubName(subtrack->track)) : cartOptionalString(cart, trackHubSkipHubName(subtrack->track)); } safef(buffer, sizeof buffer, "%s_sel", subtrack->track); if (s != NULL) { subtrack->visibility = hTvFromString(s); cartSetString(cart, subtrack->track, s); if (sameString("hide", s)) cartSetString(cart, buffer, "0"); else cartSetString(cart, buffer, "1"); if (undecoratedVis) cartRemove(cart, trackHubSkipHubName(subtrack->track)); // remove the undecorated version } else if (hideKids && isSubtrackVisible(subtrack)) cartSetString(cart, buffer, "0"); } } } return trackList; } 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; } } - static void checkCollapseEmptySubtracks(struct track *tg) ++static void checkHideEmptySubtracks(struct track *tg) +/* Suppress queries on subtracks w/o data in window (identified from multiIntersect file) */ +{ +if (!tdbIsComposite(tg->tdb)) + return; +struct hash *nonEmptySubtracksHash = getNonEmptySubtracks(tg); +if (!nonEmptySubtracksHash) + return; +struct track *subtrack; +for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next) + { + if (!isSubtrackVisible(subtrack)) + continue; + if (!hashLookup(nonEmptySubtracksHash, subtrack->track)) + { + subtrack->loadItems = dontLoadItems; + subtrack->limitedVis = tvHide; + subtrack->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("mathWig" , track->tdb->type) || startsWithWord("bigBed" , track->tdb->type) || startsWithWord("bigPsl" , track->tdb->type) || startsWithWord("bigNarrowPeak" , track->tdb->type) || startsWithWord("bigGenePred" , track->tdb->type) || startsWithWord("bigChain" , track->tdb->type) || startsWithWord("bam" , track->tdb->type) || startsWithWord("halSnake", track->tdb->type) || startsWithWord("bigLolly", track->tdb->type) || startsWithWord("vcfTabix", track->tdb->type)) // 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); - checkCollapseEmptySubtracks(pfd->track); ++ checkHideEmptySubtracks(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 int avgLoadTime(struct track *track) /* calculate average loadtime across all windows */ { int totalLoadTime = 0; int winCount = 0; while(track) { ++winCount; totalLoadTime += track->loadTime; track = track->nextWindow; } return (((float)totalLoadTime / winCount) + 0.5); } static int avgDrawTime(struct track *track) /* calculate average drawtime across all windows */ { int totalDrawTime = 0; int winCount = 0; while(track) { ++winCount; totalDrawTime += track->drawTime; track = track->nextWindow; } return (((float)totalDrawTime / winCount) + 0.5); } static int avgWigMafLoadTime(struct track *track) /* calculate average wigMaf loadtime across all windows */ { int totalLoadTime = 0; int winCount = 0; while(track) { ++winCount; if (startsWith("wigMaf", track->tdb->type)) if (track->subtracks) if (track->subtracks->loadTime) totalLoadTime += track->subtracks->loadTime; track = track->nextWindow; } return (((float)totalLoadTime / winCount) + 0.5); } static void printTrackTiming() { hPrintf("<span class='trackTiming'>track, load time, draw time, total (first window)<br />\n"); if (virtMode) hPrintf("<span class='trackTiming'><idiv style='color:red' >average for all windows in red</idiv><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); if (virtMode) { int avgLoad = avgLoadTime(subtrack); int avgDraw = avgDrawTime(subtrack); hPrintf("<idiv style='color:red' >%s, %d, %d, %d</idiv><br />\n", subtrack->shortLabel, avgLoad, avgDraw, avgLoad + avgDraw); } } } 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); } if (virtMode) { int avgLoad = avgLoadTime(track); int avgDraw = avgDrawTime(track); hPrintf("<idiv style='color:red' >%s, %d, %d, %d</idiv><br />\n", track->shortLabel, avgLoad, avgDraw, avgLoad + avgDraw); int avgWigMafLoad = avgWigMafLoadTime(track); if (avgWigMafLoad > 0) { hPrintf("<idiv style='color:red' > %s wiggle, load %d</idiv><br />\n", track->shortLabel, avgWigMafLoad); } } } hPrintf("</span>\n"); } void initTrackList() /* need to init tracklist, sometimes early */ { if (!trackList) { if (measureTiming) measureTime("Time before getTrackList"); boolean defaultTracks = cgiVarExists("hgt.reset"); trackList = getTrackList(&groupList, defaultTracks ? -1 : -2); if (measureTiming) measureTime("Time after visibilities"); makeGlobalTrackHash(trackList); } } struct track *getTrackListForOneTrack(char *trackName) /* Fetch trackList for a single trackName using hgt.trackNameFilter. */ { struct track *saveTrackList = trackList; struct group *saveGroupList = groupList; char *saveTrackNameFilter = cloneString(cartOptionalString(cart, "hgt.trackNameFilter")); // This is an attempt to both get around the limitation imposed by ajax callback hgt.trackNameFilter, // and also to try to optimize it a little so that callbacks only have to load a trackList containing // only the emGeneTable. cartSetString(cart, "hgt.trackNameFilter", trackName); initTrackList(); // initialize trackList early if needed struct track *returnTrackList = trackList; cartRemove(cart, "hgt.trackNameFilter"); // restore if (saveTrackNameFilter) { cartSetString(cart, "hgt.trackNameFilter", saveTrackNameFilter); } trackList = saveTrackList; groupList = saveGroupList; return returnTrackList; } 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 */ { // create new trackList with just trackName struct track *myTrackList = getTrackListForOneTrack(trackName); struct track *track = trackFindByName(myTrackList, trackName); if ((track != NULL) && (track->nextPrevItem != NULL)) { // custom track big* tracks have pre-opened handle which we should not use // because that same bbiFile will get used later in the full track list track->bbiFile = NULL; track->nextPrevItem(track, goNext); } } void findBestEMGeneTable(struct track *myTrackList) /* Find the best gene table to use for exonMostly and geneMostly. */ { // TODO add support for choosing any gene table of type genePred, genePreExt, bigGenePred // TODO add support for assembly hubs if (trackHubDatabase(database)) // assembly hub? not supported yet return; // any table-name matches might just be coincidence in an assembly hub // although the hub_ prefix on the track name would help prevent name collisions. char *orderedTables[] = {"knownGene", "refGene", "ensGene", "flybaseGene", "sangerGene", "augustusGene", "genscan"}; int i, len; for(i=0, len=ArraySize(orderedTables); i <len; ++i) { char *table = orderedTables[i]; emGeneTrack = rFindTrackWithTable(table, myTrackList); if (emGeneTrack) { emGeneTable = table; cartSetString(cart, "emGeneTable", emGeneTable); break; } } } void setEMGeneTrack() /* Find the track for the gene table to use for exonMostly and geneMostly. */ { if (emGeneTable) // we already have it! return; if (trackHubDatabase(database)) // assembly hub? not supported yet return; emGeneTable = cloneString(cartOptionalString(cart, "emGeneTable")); if (emGeneTable) { struct track *myTrackList = getTrackListForOneTrack(emGeneTable); emGeneTrack = rFindTrackWithTable(emGeneTable, myTrackList); } if (!emGeneTable || !emGeneTrack) { cartRemove(cart, "emGeneTable"); // It is preferable not to create a complete track list early on, // but now we need one to find the best default emGeneTable and track. initTrackList(); findBestEMGeneTable(trackList); } } boolean windowsHaveMultipleChroms() /* Are there multiple different chromosomes in the windows list? */ { struct window *window; for (window=windows->next; window; window=window->next) { if (!sameString(window->chromName,windows->chromName)) return TRUE; } return FALSE; } static void setSharedLimitedVisAcrossWindows(struct track *track) /* Look for lowest limitedVis across all windows * if found, set all windows to same lowest limited vis. */ { enum trackVisibility sharedVis = 99; struct track *tg; for (tg=track; tg; tg=tg->nextWindow) { if (tg->limitedVisSet) { if (tg->limitedVis < sharedVis) sharedVis = tg->limitedVis; } } if (sharedVis != 99) { for (tg=track; tg; tg=tg->nextWindow) { tg->limitedVis = sharedVis; tg->limitedVisSet = TRUE; } } } static void setSharedErrorsAcrossWindows(struct track *track) /* Look for network errors across all windows * if found, set all windows to same errMsg and set bigWarn track handlers. */ { char *sharedErrMsg = NULL; struct track *tg; for (tg=track; tg; tg=tg->nextWindow) { if (!sharedErrMsg && tg->networkErrMsg) { sharedErrMsg = tg->networkErrMsg; break; } } if (sharedErrMsg) { for (tg=track; tg; tg=tg->nextWindow) { tg->networkErrMsg = sharedErrMsg; tg->drawItems = bigDrawWarning; tg->totalHeight = bigWarnTotalHeight; } } } void outCollectionsToJson() /* Output the current collections to the hgTracks JSON block. */ { struct grp *groupList = NULL; char buffer[4096]; safef(buffer, sizeof buffer, "%s-%s", customCompositeCartName, database); char *hubFile = cartOptionalString(cart, buffer); if (hubFile != NULL) { char *hubName = hubNameFromUrl(hubFile); struct trackDb *hubTdbs = hubCollectTracks( database, &groupList); struct trackDb *tdb; struct jsonElement *jsonList = NULL; for(tdb = hubTdbs; tdb; tdb = tdb->next) { if (sameString(tdb->grp, hubName)) { if (jsonList == NULL) jsonList = newJsonList(NULL); struct jsonElement *collection = newJsonObject(newHash(4)); jsonObjectAdd(collection, "track", newJsonString(tdb->track)); jsonObjectAdd(collection, "shortLabel", newJsonString(tdb->shortLabel)); jsonListAdd(jsonList, collection); } } if (jsonList != NULL) jsonObjectAdd(jsonForClient, "collections", jsonList); } } 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; basesPerPixel = ((float)virtWinBaseCount) / ((float)fullInsideWidth); zoomedToBaseLevel = (virtWinBaseCount <= fullInsideWidth / tl.mWidth); zoomedToCodonLevel = (ceil(virtWinBaseCount/3) * tl.mWidth) <= fullInsideWidth; zoomedToCdsColorLevel = (virtWinBaseCount <= fullInsideWidth*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)); // TODO GALT fullInsideX? or does not matter? jsonObjectAdd(jsonForClient, "revCmplDisp", newJsonBoolean(revCmplDisp)); if (hPrintStatus()) cartSaveSession(cart); /* 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); initTrackList(); //warn("slCount(trackList) after getTrackList: %d", slCount(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); } if(!psOutput && !cartUsualBoolean(cart, "hgt.imageV1", FALSE)) { // re-establish the enlarged portal if (imgBoxPortalDimensions(theImgBox,&virtWinStart,&virtWinEnd,&(tl.picWidth),NULL,NULL,NULL,NULL,NULL)) { virtWinBaseCount = virtWinEnd - virtWinStart; fullInsideWidth = tl.picWidth - gfxBorder - fullInsideX; } } 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); /* hide tracks not on any windows chromNames */ boolean hideIt = TRUE; struct window *w; for (w = windows; w; w=w->next) { if (hTrackOnChrom(track->tdb, w->chromName)) hideIt = FALSE; } if (hideIt) { track->limitedVis = tvHide; track->limitedVisSet = TRUE; } } if (sameString(cfgOptionDefault("trackLog", "off"), "on")) logTrackVisibilities(cartSessionId(cart), trackList); ///////////////// // NEED TO LOAD ALL WINDOWS NOW // // Need to load one window at a time! // // The use of the global values for a window // means that differerent threads cannot use different global window values. // Threads must run on just one window value at a time. // // Begin by making a copy of the track structure for visible tracks // for all windows. // COPY TRACK STRUCTURES for other windows. // TODO: due to an issue where some loading code is modifying the visibility // of subtracks from hide to visible, I am forced to remove the optimization // of cloning ONLY non-hidden tracks and subtracks. If the offending code // can be identified and moved into a step proceding the track cloning, // then we can return to that optimization. // if (track->visibility != tvHide) // if (subtrack->visibility != tvHide) windows->trackList = trackList; // save current track list in window struct window *window; for (window=windows; window->next; window=window->next) { struct track *newTrackList = NULL; for (track = trackList; track != NULL; track = track->next) { isCompositeInAggregate(track); // allow track to recognize its true self track->nextWindow = NULL; //if (track->visibility != tvHide) // Unable to use this optimization at present { struct track *copy; AllocVar(copy); memmove(copy,track,sizeof(struct track)); copy->next = NULL; copy->bbiFile = NULL; // bigDataUrl custom tracks have already been opened, will re-open for other windows. copy->nextWindow = NULL; copy->prevWindow = track; slAddHead(&newTrackList, copy); track->nextWindow = copy; // copy subtracks. copy->subtracks = NULL; struct track *subtrack; for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next) { //if (subtrack->visibility != tvHide) // Unable to use this optimization at present { struct track *subcopy; AllocVar(subcopy); memmove(subcopy,subtrack,sizeof(struct track)); subcopy->next = NULL; subcopy->bbiFile = NULL; // bigDataUrl custom tracks have already been opened, will re-open for other windows. subcopy->nextWindow = NULL; subcopy->prevWindow = subtrack; slAddHead(©->subtracks, subcopy); subtrack->nextWindow = subcopy; } } slReverse(©->subtracks); } } slReverse(&newTrackList); trackList = newTrackList; window->next->trackList = trackList; // save new track list in window } trackList = windows->trackList; // restore original track list // Loop over each window loading all tracks trackLoadingInProgress = TRUE; // LOAD OPTIMIZATION HACK GALT // This is an attempt to try to optimize loading by having multiple regions // treated as a single span. The hack just grabs the dimensions of the first and last windows // and uses the loader in the first window to load them, then copies the results to all tracks. // This basically has only been tried on BED-like tracks, and only for exon/gene-mostly vmodes. // I am not re-partitioning the results after the load, so this means all windows see all items. // The reason that tends to work is that by luck most BED handlers have code to check if the item // overlaps the current window and to skip it if it does not. // I do not expect something so simple would work with wigs and other track types. // Even if we do want to optimize the BED-like tracks (which are already the fastest loading type), // to handle all of the virtmodes properly, this would have be be done differently. // Instead of just lumping them all into a single range, you would have to cluster together // ranges that are close together and on the same chromosome. // Clearly this was just to test an idea for optimizing. // NOT FINISHED. bool loadHack = FALSE; //TRUE; // probably should only be tried on non-wiggle tracks //warn ("loadHack = %d", loadHack); // TODO int lastWinEnd = 0; for (window=windows; window; window=window->next) lastWinEnd = window->winEnd; for (window=windows; window; window=window->next) { trackList = window->trackList; // set track list setGlobalsFromWindow(window); // TEMP HACK GALT REMOVE if (loadHack) { if (currentWindow == windows) // first window winEnd = lastWinEnd; // so now we load the entire span inside the first window. } /* 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)); } } } } // TODO GALT /* load regular tracks */ for (track = trackList; track != NULL; track = track->next) { if (track->visibility != tvHide) { if (!track->parallelLoading) { if (measureTiming) lastTime = clock1000(); checkMaxWindowToDraw(track); - checkCollapseEmptySubtracks(track); // TODO: Test with multi-window feature ++ checkHideEmptySubtracks(track); // TODO: Test with multi-window feature + checkIfWiggling(cart, track); if (!loadHack) { track->loadItems(track); } else { // TEMP HACK GALT REMOVE if (currentWindow == windows) // first window { track->loadItems(track); } else { track->items = track->prevWindow->items; // just point to the previous windows items (faster than loading) // apparently loadItems is setting some other fields that we want, but which ones? track->visibility = track->prevWindow->visibility; track->limitedVis = track->prevWindow->limitedVis; track->limitedVisSet = track->prevWindow->limitedVisSet; track->height = track->prevWindow->height; track->lineHeight = track->prevWindow->lineHeight; track->heightPer = track->prevWindow->heightPer; // TODO does this work for subtracks or parents/children? } } 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); } } trackLoadingInProgress = FALSE; setGlobalsFromWindow(windows); // first window // restore globals trackList = windows->trackList; // restore track list // Some loadItems() calls will have already set limitedVis. // Look for lowest limitedVis across all windows // if found, set all windows to same lowest limitedVis for (track = trackList; track != NULL; track = track->next) { setSharedLimitedVisAcrossWindows(track); struct track *sub; for (sub=track->subtracks; sub; sub=sub->next) { setSharedLimitedVisAcrossWindows(sub); } } // Look for network errors across all windows // if found, set all windows to same errMsg and set bigWarn track handlers. for (track = trackList; track != NULL; track = track->next) { setSharedErrorsAcrossWindows(track); struct track *sub; for (sub=track->subtracks; sub; sub=sub->next) { setSharedErrorsAcrossWindows(sub); } } ////////////// END OF MULTI-WINDOW LOOP 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,&virtWinStart,&virtWinEnd,&(tl.picWidth),NULL)) { virtWinBaseCount = virtWinEnd - virtWinStart; fullInsideWidth = tl.picWidth-gfxBorder-fullInsideX; } } /* Center everything from now on. */ hPrintf("<CENTER>\n"); outCollectionsToJson(); jsonObjectAdd(jsonForClient, "winStart", newJsonNumber(virtWinStart)); jsonObjectAdd(jsonForClient, "winEnd", newJsonNumber(virtWinEnd)); jsonObjectAdd(jsonForClient, "chromName", newJsonString(virtChromName)); // Tell javascript about multiple windows info if (virtMode) { // pre windows long preVWinStart = virtWinStart - virtWinBaseCount; if (preVWinStart < 0) preVWinStart = 0; long preVWinEnd = virtWinStart; struct window *preWindows = makeWindowListFromVirtChrom(preVWinStart, preVWinEnd); struct jsonElement *jsonForList = newJsonList(NULL); for(window=preWindows;window;window=window->next) { struct jsonElement *jsonForWindow = NULL; jsonForWindow = newJsonObject(newHash(8)); jsonObjectAdd(jsonForWindow, "chromName", newJsonString(window->chromName)); jsonObjectAdd(jsonForWindow, "winStart", newJsonNumber(window->winStart)); jsonObjectAdd(jsonForWindow, "winEnd", newJsonNumber(window->winEnd)); jsonObjectAdd(jsonForWindow, "insideX", newJsonNumber(window->insideX)); jsonObjectAdd(jsonForWindow, "insideWidth", newJsonNumber(window->insideWidth)); jsonObjectAdd(jsonForWindow, "virtStart", newJsonNumber(window->virtStart)); jsonObjectAdd(jsonForWindow, "virtEnd", newJsonNumber(window->virtEnd)); jsonListAdd(jsonForList, jsonForWindow); } slReverse(&jsonForList->val.jeList); jsonObjectAdd(jsonForClient, "windowsBefore", jsonForList); jsonForList = newJsonList(NULL); for(window=windows;window;window=window->next) { struct jsonElement *jsonForWindow = NULL; jsonForWindow = newJsonObject(newHash(8)); jsonObjectAdd(jsonForWindow, "chromName", newJsonString(window->chromName)); jsonObjectAdd(jsonForWindow, "winStart", newJsonNumber(window->winStart)); jsonObjectAdd(jsonForWindow, "winEnd", newJsonNumber(window->winEnd)); jsonObjectAdd(jsonForWindow, "insideX", newJsonNumber(window->insideX)); jsonObjectAdd(jsonForWindow, "insideWidth", newJsonNumber(window->insideWidth)); jsonObjectAdd(jsonForWindow, "virtStart", newJsonNumber(window->virtStart)); jsonObjectAdd(jsonForWindow, "virtEnd", newJsonNumber(window->virtEnd)); jsonListAdd(jsonForList, jsonForWindow); } slReverse(&jsonForList->val.jeList); jsonObjectAdd(jsonForClient, "windows", jsonForList); // post windows long postVWinStart = virtWinEnd; long postVWinEnd = virtWinEnd + virtWinBaseCount; if (postVWinEnd > virtSeqBaseCount) postVWinEnd = virtSeqBaseCount; struct window *postWindows = makeWindowListFromVirtChrom(postVWinStart, postVWinEnd); jsonForList = newJsonList(NULL); for(window=postWindows;window;window=window->next) { struct jsonElement *jsonForWindow = NULL; jsonForWindow = newJsonObject(newHash(8)); jsonObjectAdd(jsonForWindow, "chromName", newJsonString(window->chromName)); jsonObjectAdd(jsonForWindow, "winStart", newJsonNumber(window->winStart)); jsonObjectAdd(jsonForWindow, "winEnd", newJsonNumber(window->winEnd)); jsonObjectAdd(jsonForWindow, "insideX", newJsonNumber(window->insideX)); jsonObjectAdd(jsonForWindow, "insideWidth", newJsonNumber(window->insideWidth)); jsonObjectAdd(jsonForWindow, "virtStart", newJsonNumber(window->virtStart)); jsonObjectAdd(jsonForWindow, "virtEnd", newJsonNumber(window->virtEnd)); jsonListAdd(jsonForList, jsonForWindow); } slReverse(&jsonForList->val.jeList); jsonObjectAdd(jsonForClient, "windowsAfter", jsonForList); jsonForList = newJsonList(NULL); // also store js nonVirtPosition jsonObjectAdd(jsonForClient, "nonVirtPosition", newJsonString(cartString(cart, "nonVirtPosition"))); jsonObjectAdd(jsonForClient, "virtChromChanged", newJsonBoolean(virtChromChanged)); jsonObjectAdd(jsonForClient, "virtualSingleChrom", newJsonBoolean(virtualSingleChrom())); // DISGUISE POS } char dbPosKey[256]; safef(dbPosKey, sizeof(dbPosKey), "position.%s", database); jsonObjectAdd(jsonForClient, "lastDbPos", newJsonString(cartString(cart, dbPosKey))); // hide chromIdeo if ((trackImgOnly && !ideogramToo) || (sameString(virtModeType, "customUrl") && windowsHaveMultipleChroms()) // Special case hide by request ) { for(window=windows;window;window=window->next) { struct track *ideoTrack = chromIdeoTrack(window->trackList); if (ideoTrack) { ideoTrack->limitedVisSet = TRUE; ideoTrack->limitedVis = tvHide; /* Don't draw in main gif. */ } } } if (trackImgOnly && !ideogramToo) { 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. char buf[256]; if (virtualSingleChrom()) // DISGUISE VMODE safef(buf, sizeof buf, "%s", windowsSpanPosition()); else safef(buf, sizeof buf, "%s:%ld-%ld", virtChromName, virtWinStart+1, virtWinEnd); hPrintf("<INPUT TYPE='text' style='display:none;' name='dirty' id='dirty' VALUE='false'>\n"); hPrintf("<INPUT TYPE=HIDDEN id='positionHidden' name='position' " "VALUE=\"%s\">", buf); 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. */ 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 = "document.location = '/cgi-bin/hgTracks?db=' + document.TrackForm.db.options[document.TrackForm.db.selectedIndex].value;"; if (containsStringNoCase(database, "zoo")) { hPuts("Organism "); printAssemblyListHtmlExtra(database, "change", javascript); } if (virtualSingleChrom()) // DISGUISE VMODE safef(buf, sizeof buf, "%s", windowsSpanPosition()); else safef(buf, sizeof buf, "%s:%ld-%ld", virtChromName, virtWinStart+1, virtWinEnd); position = cloneString(buf); - hPrintf("<span class='positionDisplay' id='positionDisplay' title='click to copy position to input box'>%s</span>", addCommasToPos(database, position)); + char *pressedClass = "", *showVirtRegions = ""; + if (differentString(virtModeType, "default")) + { + pressedClass = "pressed"; + showVirtRegions = "show multi-region position ranges and "; + } + hPrintf("<span class='positionDisplay %s' id='positionDisplay' " + "title='click to %s copy position to input box'>%s</span>", + pressedClass, showVirtRegions, addCommasToPos(database, position)); hPrintf("<input type='hidden' name='position' id='position' value='%s'>\n", buf); sprintLongWithCommas(buf, virtWinEnd - virtWinStart); 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'); } } // TODO GALT how to handle ideos? boolean nukeIdeoFromList = FALSE; for(window=windows;window;window=window->next) { setGlobalsFromWindow(window); if (window == windows) // first window { /* Make chromosome ideogram gif and map. */ nukeIdeoFromList = makeChromIdeoImage(&trackList, psOutput, ideoTn); window->trackList = trackList; // the variable may have been updated. // TODO make this not just be centered over the entire image, // but rather centered over the individual chromosome. // notice that it modifies trackList, and visibility settings potentially need parallelization for windows } else { // TODO should be more than this. But at least this makes the same trackList mods to the other windows. if (nukeIdeoFromList) { struct track *ideoTrack = chromIdeoTrack(window->trackList); if (ideoTrack) { slRemoveEl(&window->trackList, ideoTrack); } } } } setGlobalsFromWindow(windows); // first window // restore globals #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 class='infoText' 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. "); hWrites("Press \"?\" for keyboard shortcuts. "); 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' id='ct_add' VALUE='%s' title='%s'>", hasCustomTracks ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL, hasCustomTracks ? "Manage your custom tracks" : "Add your own custom tracks"); jsOnEventById("click", "ct_add", "document.customTrackForm.submit();return false;"); hPrintf(" "); if (hubConnectTableExists()) { hPrintf("<INPUT TYPE='button' id='th_form' VALUE='track hubs'" "return false;' title='Import tracks from hubs'>"); jsOnEventById("click", "th_form", "document.trackHubForm.submit();"); hPrintf(" "); } hButtonWithMsg("hgTracksConfigPage", "configure","Configure image and track selection"); hPrintf(" "); - hButtonWithOnClick("hgTracksConfigMultiRegionPage", - "multi-region", "Configure multi-region display options", "popUpHgt.hgTracks('multi-region config'); return false;"); + hButtonMaybePressed("hgTracksConfigMultiRegionPage", "multi-region", + "Configure multi-region display options", + "popUpHgt.hgTracks('multi-region config'); return false;", virtMode); hPrintf(" "); if (!hIsGsidServer()) { - hButtonWithMsg("hgt.toggleRevCmplDisp", "reverse", + hButtonMaybePressed("hgt.toggleRevCmplDisp", "reverse", revCmplDisp ? "Show forward strand at this location" - : "Show reverse strand at this location"); + : "Show reverse strand at this location", + NULL, revCmplDisp); 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' class='infoText' 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); char idText[256]; safef(idText, sizeof idText, "%s_button", group->name); hPrintf("<IMG class='toggleButton'" " id='%s' src=\"%s\" alt=\"%s\" title='%s this group'> ", idText, indicatorImg, indicator,isOpen?"Collapse":"Expand"); jsOnEventByIdF("click", idText, "return vis.toggleForGroup(this, '%s');", group->name); if (isHubTrack(group->name)) { if (strstr(group->label, "Collections")) { safef(idText, sizeof idText, "%s_edit", group->name); hPrintf("<input name=\"hubEditButton\" id='%s'" " type=\"button\" value=\"edit\">\n", idText); jsOnEventByIdF("click", idText, "document.editHubForm.submit();return true;"); } } hPrintf("</td><td style='text-align:center; width:90%%;'>\n<B>%s</B>", group->label); hPrintf("</td><td style='text-align:right;'>\n"); if (isHubTrack(group->name)) { safef(idText, sizeof idText, "%s_disconn", group->name); hPrintf("<input name=\"hubDisconnectButton\" id='%s'" " type=\"button\" value=\"disconnect\">\n", idText); jsOnEventByIdF("click", idText, "document.disconnectHubForm.elements['hubId'].value='%s';" "document.disconnectHubForm.submit();return true;", group->name + strlen(hubTrackPrefix)); } hPrintf("<input type='submit' name='hgt.refresh' value='refresh' " "title='Update image with your changes'>\n"); hPrintf("</td></tr></table></th>\n"); controlGridEndRow(cg); /* Base Position track goes into map group, which will always exist. */ if (!showedRuler && sameString(group->name, "map") ) { 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. */ // TODO GALT cleanup sibs too? probably can do for window copies but low priority. /* 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 composite builder CGI */ hPrintf("<FORM ACTION='%s' NAME='editHubForm'>", hgCollectionName()); cartSaveSession(cart); hPrintf("</FORM>\n"); /* hidden form for track hub CGI */ hPrintf("<FORM ACTION='%s' NAME='trackHubForm'>", hgHubConnectName()); cartSaveSession(cart); hPrintf("</FORM>\n"); // this is the form for the disconnect hub button hPrintf("<FORM ACTION=\"%s\" NAME=\"disconnectHubForm\">\n", "../cgi-bin/hgTracks"); cgiMakeHiddenVar("hubId", ""); cgiMakeHiddenVar(hgHubDoDisconnect, "on"); cgiMakeHiddenVar(hgHubConnectRemakeTrackHub, "on"); cartSaveSession(cart); puts("</FORM>"); // TODO GALT nothing to do here. 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(long 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. */ { long center = ((long long)virtWinStart + (long long)virtWinEnd)/2; if (center < 0) errAbort("zoomToSize: error computing center: %ld = (%ld + %ld)/2\n", center, virtWinStart, virtWinEnd); if (newSize > virtSeqBaseCount) newSize = virtSeqBaseCount; virtWinStart = center - newSize/2; virtWinEnd = virtWinStart + newSize; if (virtWinStart <= 0) { virtWinStart = 0; virtWinEnd = newSize; } else if (virtWinEnd > virtSeqBaseCount) { virtWinEnd = virtSeqBaseCount; virtWinStart = virtWinEnd - newSize; } virtWinBaseCount = virtWinEnd - virtWinStart; } void zoomAroundCenter(double amount) /* Set ends so as to zoom around center by scaling amount. */ { double newSizeDbl = (virtWinBaseCount*amount + 0.5); long newSize; if (newSizeDbl > virtSeqBaseCount) newSize = virtSeqBaseCount; else if (newSizeDbl < 1.0) newSize = 1; else newSize = (long)newSizeDbl; zoomToSize(newSize); } void zoomToBaseLevel() /* Set things so that it's zoomed to base level. */ { zoomToSize(fullInsideWidth/tl.mWidth); if (rulerMode == tvHide) cartSetString(cart, "ruler", "dense"); } void relativeScroll(double amount) /* Scroll percentage of visible window. */ { long offset; long newStart, newEnd; if (revCmplDisp) amount = -amount; offset = (long)(amount * virtWinBaseCount); /* Make sure don't scroll of ends. */ newStart = virtWinStart + offset; newEnd = virtWinEnd + offset; if (newStart < 0) offset = -virtWinStart; else if (newEnd > virtSeqBaseCount) offset = virtSeqBaseCount - virtWinEnd; /* Move window. */ virtWinStart += offset; virtWinEnd += offset; } void dinkWindow(boolean start, long dinkAmount) /* Move one end or other of window a little. */ { if (revCmplDisp) { start = !start; dinkAmount = -dinkAmount; } if (start) { virtWinStart += dinkAmount; if (virtWinStart < 0) virtWinStart = 0; } else { virtWinEnd += dinkAmount; if (virtWinEnd > virtSeqBaseCount) virtWinEnd = virtSeqBaseCount; } } long dinkSize(char *var) /* Return size to dink. */ { char *stringVal = cartOptionalString(cart, var); double x; int fullInsideX = trackOffsetX(); /* The global versions of these are not yet set */ int fullInsideWidth = tl.picWidth-gfxBorder-fullInsideX; double guideBases = (double)guidelineSpacing * (double)(virtWinEnd - virtWinStart) / ((double)fullInsideWidth); if (stringVal == NULL || !isdigit(stringVal[0])) { stringVal = "1"; cartSetString(cart, var, stringVal); } x = atof(stringVal); long 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='%s?%s=%s'><input type='button' VALUE='Return to Browser'></a>\n", hgTracksName(), cartSessionVarName(), cartSessionId(cart)); } 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); emAltHighlight = cartUsualBoolean(cart, "emAltHighlight", FALSE); if (!hIsGsidServer()) { revCmplDisp = cartUsualBooleanDb(cart, database, REV_CMPL_DISP, FALSE); } emPadding = cartUsualInt(cart, "emPadding", emPadding); gmPadding = cartUsualInt(cart, "gmPadding", gmPadding); withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE); fullInsideX = trackOffsetX(); fullInsideWidth = tl.picWidth-gfxBorder-fullInsideX; } static boolean resolvePosition(char **pPosition) /* Position may be an already-resolved chr:start-end, or a search term. * If it is a search term: * 1 match ==> set globals chromName, winStart, winEnd, return TRUE. * 0 matches ==> switch back to lastPosition, hopefully get 1 match from that; * set globals chromName, winStart, winEnd, return TRUE. If no lastPosition, try w/hDefaultPos(). * multiple matches ==> Display a page with links to match positions, return FALSE. */ { boolean resolved = TRUE; struct dyString *dyWarn = dyStringNew(0); hgp = hgFindSearch(cart, pPosition, &chromName, &winStart, &winEnd, hgTracksName(), dyWarn); if (isNotEmpty(dyWarn->string)) warn("%s", dyWarn->string); if (hgp->singlePos) { createHgFindMatchHash(); } else { char *menuStr = menuBar(cart, database); if (menuStr) puts(menuStr); hgPositionsHtml(database, hgp, hgTracksName(), cart); resolved = FALSE; } cartSetString(cart, "position", *pPosition); return resolved; } void parseVirtPosition(char *position) /* parse virtual position * TODO this is just temporary */ { if (!position) { errAbort("position NULL"); } char *vPos = cloneString(position); stripChar(vPos, ','); char *colon = strchr(vPos, ':'); if (!colon) errAbort("position has no colon"); char *dash = strchr(vPos, '-'); if (!dash) errAbort("position has no dash"); *colon = 0; *dash = 0; virtWinStart = atol(colon+1) - 1; virtWinEnd = atol(dash+1); } void parseNonVirtPosition(char *position) /* parse non-virtual position */ { if (!position) { errAbort("position NULL"); } char *vPos = cloneString(position); stripChar(vPos, ','); char *colon = strchr(vPos, ':'); if (!colon) errAbort("position has no colon"); char *dash = strchr(vPos, '-'); if (!dash) errAbort("position has no dash"); *colon = 0; *dash = 0; chromName = cloneString(vPos); winStart = atol(colon+1) - 1; winEnd = atol(dash+1); } boolean findNearestVirtMatch(char *chrom, int start, int end, boolean findNearest, long *retVirtStart, long *retVirtEnd) /* find nearest match on virt chrom. * findNearest flag means of no direct hits found, take the closest miss. */ { // search for one or more overlapping windows struct positionMatch *mList = virtChromSearchForPosition(chrom, start, end, findNearest); // sort positions by virtPos (will be sorted by chrom, start, end) matchSortOnVPos(&mList); // merge contiguous matches spanning multiple touching windows mList = matchMergeContiguousVPos(mList); // TODO search for the best match in pList // TODO this is crude, needs to fix, just finds the largest match: struct positionMatch *p, *best = NULL; long bigSpan = 0; for (p=mList; p; p=p->next) { long span = p->virtEnd - p->virtStart; if (span > bigSpan) { bigSpan = span; best = p; } } if (best) // TODO do something better { // return the new location *retVirtStart = best->virtStart; *retVirtEnd = best->virtEnd; } else { return FALSE; } return TRUE; } void remapHighlightPos() // Remap non-virt highlight position if any to new virtMode chrom. { if (virtualSingleChrom()) return; struct highlightVar *h = parseHighlightInfo(); if (h && h->db && sameString(h->db, database)) { long virtStart = 0, virtEnd = 0; if (findNearestVirtMatch(h->chrom, h->chromStart, h->chromEnd, FALSE, &virtStart, &virtEnd)) // try to find the nearest match { // save new highlight position to cart var char cartVar[1024]; safef(cartVar, sizeof cartVar, "%s.%s:%ld-%ld#%s", h->db, "virt", virtStart, virtEnd, h->hexColor); cartSetString(cart, "highlight", cartVar); } else { // erase the highlight cartvar if it has no overlap with the new virt chrom cartRemove(cart, "highlight"); } } } void tracksDisplay() /* Put up main tracks display. This routine handles zooming and * scrolling. */ { char titleVar[256]; char *oldPosition = cartUsualString(cart, "oldPosition", ""); boolean findNearest = cartUsualBoolean(cart, "findNearest", FALSE); cartRemove(cart, "findNearest"); boolean positionIsVirt = FALSE; position = getPositionFromCustomTracks(); if (NULL == position) { position = cartGetPosition(cart, database, &lastDbPosCart); if (sameOk(cgiOptionalString("position"), "lastDbPos")) { restoreSavedVirtPosition(); } if (startsWith("virt:", position)) { position = stripCommas(position); // sometimes the position string arrives with commas in it. positionIsVirt = TRUE; } } 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"); } if (!positionIsVirt) { if (! resolvePosition(&position)) return; } virtMode = cartUsualBoolean(cart, "virtMode", FALSE); /* Figure out basic dimensions of display. This * needs to be done early for the sake of the * zooming and dinking routines. */ setLayoutGlobals(); virtModeType = cartUsualString(cart, "virtModeType", virtModeType); if (positionIsVirt && virtualSingleChrom()) { // we need chromName to be set before initRegionList() gets called. position = cartUsualString(cart, "nonVirtPosition", ""); if (!sameString(position,"")) parseNonVirtPosition(position); } // TODO GALT do we need to add in other types that now depend on emGeneTable too? maybe singleTrans? // OR maybe this code should just be part of initRegionList() if (sameString(virtModeType, "exonMostly") || sameString(virtModeType, "geneMostly")) { setEMGeneTrack(); if (!emGeneTable) // there is no available gene table, undo exonMostly or geneMostly { //warn("setEMGeneTrack unable to find default gene track"); virtModeType = "default"; cartSetString(cart, "virtModeType", virtModeType); } } lastVirtModeType = cartUsualString(cart, "lastVirtModeType", lastVirtModeType); while(TRUE) { if (sameString(virtModeType, "default") && !(sameString(lastVirtModeType, "default"))) { // RETURNING TO DEFAULT virtModeType virtModeType = "default"; cartSetString(cart, "virtModeType", virtModeType); findNearest = TRUE; if (positionIsVirt) position = cartUsualString(cart, "nonVirtPosition", ""); char *nvh = cartUsualString(cart, "nonVirtHighlight", NULL); if (nvh) cartSetString(cart, "highlight", nvh); if (!sameString(position,"")) parseNonVirtPosition(position); } if (initRegionList()) // initialize the region list, sets virtModeExtraState { break; } else { // virt mode failed, forced to return to default virtModeType = "default"; cartSetString(cart, "virtModeType", virtModeType); position = cloneString(hDefaultPos(database)); resolvePosition(&position); positionIsVirt=FALSE; virtMode=FALSE; } } // PAD padding of exon regions is now being done inside the fetch/merge. //if (emPadding > 0) //padVirtRegions(emPadding); // this old routine does not handle multiple chroms yet //testRegionList(); // check if it is ascending non-overlapping regions. (this is not the case with custom user-defined-regions) makeVirtChrom(); //testVirtChromBinarySearch(); // ajax callback to convert chrom position to virt chrom position if (cartVarExists(cart, "hgt.convertChromToVirtChrom")) { position = cartString(cart, "hgt.convertChromToVirtChrom"); char nvh[256]; safef(nvh, sizeof nvh, "%s.%s", database, position); cartSetString(cart, "nonVirtHighlight", nvh); parseNonVirtPosition(position); if (findNearestVirtMatch(chromName, winStart, winEnd, FALSE, &virtWinStart, &virtWinEnd)) { struct jsonElement *jsonForConvert = NULL; jsonForConvert = newJsonObject(newHash(8)); jsonObjectAdd(jsonForConvert, "virtWinStart", newJsonNumber(virtWinStart)); jsonObjectAdd(jsonForConvert, "virtWinEnd", newJsonNumber(virtWinEnd)); struct dyString *dy = dyStringNew(1024); jsonDyStringPrint(dy, (struct jsonElement *) jsonForConvert, "convertChromToVirtChrom", 0); jsInline(dy->string); dyStringFree(&dy); } return; } lastVirtModeExtraState = cartUsualString(cart, "lastVirtModeExtraState", lastVirtModeExtraState); // DISGUISED POSITION if (!startsWith("virt:", position) && (virtualSingleChrom())) { // "virtualSingleChrom trying to find best vchrom location corresponding to chromName, winStart, winEnd findNearest = TRUE; // try to find the nearest match if (!(chromName && findNearestVirtMatch(chromName, winStart, winEnd, findNearest, &virtWinStart, &virtWinEnd))) { // create 10k window near middle of vchrom warn("Your new regions are not near previous location. Using middle of new coordinates."); virtWinStart = virtSeqBaseCount / 2; virtWinEnd = virtWinStart + 10000; if (virtWinEnd > virtSeqBaseCount) virtWinEnd = virtSeqBaseCount; } virtMode = TRUE; } // when changing modes (or state like padding), first try to revert to plain non-virt position if (!sameString(virtModeType, "default") && !sameString(lastVirtModeType, "default") && !(sameString(virtModeType, lastVirtModeType) && sameString(virtModeExtraState, lastVirtModeExtraState))) { // CHANGE FROM ONE NON-DEFAULT virtMode to another. virtChromChanged = TRUE; // virtChrom changed lastVirtModeType = "default"; cartSetString(cart, "lastVirtModeType", lastVirtModeType); // I think I do not need this lastVirtModeExtraState = ""; findNearest = TRUE; position = cartUsualString(cart, "nonVirtPosition", ""); if (!sameString(position,"")) parseNonVirtPosition(position); char *nvh = cartUsualString(cart, "nonVirtHighlight", ""); if (!sameString(nvh, "")) // REMOVE? not needed probably { cartSetString(cart, "highlight", nvh); } } // virt mode has not changed if (sameString(virtModeType, lastVirtModeType) && sameString(virtModeExtraState, lastVirtModeExtraState)) { if (virtMode) { if (positionIsVirt) { parseVirtPosition(position); } else { // Is this a new position to navigate to // or just an old inherited position. position = stripCommas(position); // sometimes the position string arrives with commas in it. if (!sameString(position, oldPosition)) { if (!findNearestVirtMatch(chromName, winStart, winEnd, findNearest, &virtWinStart, &virtWinEnd)) { // errAbort has kind of harsh behavior, and does not work well with ajax anyways warn("Location not found in Multi-Region View. " "To return to default view at that location, " "click <a href=%s?%s=%s&position=%s:%d-%d&virtModeType=default>here</a>.\n" , hgTracksName(), cartSessionVarName(), cartSessionId(cart), chromName, winStart+1, winEnd); // try to resume using oldPosition parseVirtPosition(oldPosition); } } } } else { if (positionIsVirt) errAbort("positionIsVirt=%d but virtMode=%d", positionIsVirt, virtMode); } } else { if (sameString(virtModeType,"default")) // we are leaving virtMode { virtMode = FALSE; cartRemove(cart, "virtWinFull"); cartRemove(cart, "virtShortDesc"); } else { // ENTERING VIRTMODE // First time initialization findNearest = TRUE; // For now, do this manually here: // sets window to full genome size, which for these demos should be small except for allChroms if (sameString(virtModeType, "exonMostly") || sameString(virtModeType, "geneMostly") || sameString(virtModeType, "kcGenes") || (sameString(virtModeType, "customUrl") && !cartUsualBoolean(cart, "virtWinFull", FALSE))) { // trying to find best vchrom location corresponding to chromName, winStart, winEnd); // try to find the nearest match if (!(chromName && findNearestVirtMatch(chromName, winStart, winEnd, findNearest, &virtWinStart, &virtWinEnd))) { // create 10k window near middle of vchrom warn("Your new regions are not near previous location. Using middle of new coordinates."); virtWinStart = virtSeqBaseCount / 2; virtWinEnd = virtWinStart + 10000; if (virtWinEnd > virtSeqBaseCount) virtWinEnd = virtSeqBaseCount; } virtMode = TRUE; } else if (sameString(virtModeType, "singleAltHaplo")) { virtWinStart = defaultVirtWinStart; virtWinEnd = defaultVirtWinEnd; virtMode = TRUE; } else if (!sameString(virtModeType, "default")) { // try to set view to entire vchrom virtWinStart = 0; virtWinEnd = virtSeqBaseCount; virtMode = TRUE; // TODO what if the full-vchrom view has "too many windows" // check if virtRegionCount > 4000? } remapHighlightPos(); } } if (virtMode) virtChromName = "virt"; else virtChromName = chromName; virtWinBaseCount = virtWinEnd - virtWinStart; 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")); /* 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)); /* Clip chromosomal position to fit. */ if (virtWinEnd < virtWinStart) { // swap start and end (user entered coordinates backwards) long temp = virtWinEnd; virtWinEnd = virtWinStart; virtWinStart = temp; } else if (virtWinStart == virtWinEnd) { // Size 0 window virtWinStart -= 1; virtWinEnd += 1; } if (virtWinStart < 0) { virtWinStart = 0; } if (virtWinEnd > virtSeqBaseCount) { virtWinEnd = virtSeqBaseCount; } if (virtWinStart > virtSeqBaseCount) { virtWinStart = virtSeqBaseCount - 1000; } virtWinBaseCount = virtWinEnd - virtWinStart; if (virtWinBaseCount <= 0) hUserAbort("Window out of range on %s", virtChromName); if (!cartUsualBoolean(cart, "hgt.psOutput", FALSE) && !cartUsualBoolean(cart, "hgt.imageV1" , FALSE)) { // TODO GALT Guidelines broken on virtChrom for 3X. // works in demo0 or real chrom. Only the guidelines seem to be messed up. // Other stuff works. 1X works too. // Since we are not using 3X for now, I will leave this for a future fix. // To test 3X, do make clean; make CFLAGS=-DIMAGEv2_DRAG_SCROLL_SZ=3 // 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 = (fullInsideX - gfxBorder*3) + 2; // for the 3X expansion effect to work, this needs to happen BEFORE we create the windows list // in makeWindowListFromVirtChrom() theImgBox = imgBoxStart(database,virtChromName,virtWinStart,virtWinEnd, (!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,&virtWinStart,&virtWinEnd,&(tl.picWidth),0)) { virtWinBaseCount = virtWinEnd - virtWinStart; fullInsideWidth = tl.picWidth - gfxBorder - fullInsideX; } } // For portal 3x expansion to work right, it would have to take effect, at least temporarily, // right here before we call makeWindowListFromVirtChrom(). windows = makeWindowListFromVirtChrom(virtWinStart, virtWinEnd); // creates windows, sets chrom, winStart, winEnd from virtual chrom if (slCount(windows) > 4000) // TODO a more graceful response errAbort("Too many windows in view. Unable to display image at requested zoom level."); allocPixelsToWindows(); // sets windows insideWidth and insideX if (theImgBox) { // If a portal was established, then set the global dimensions back to the portal size if (imgBoxPortalDimensions(theImgBox,NULL,NULL,NULL,NULL,&virtWinStart,&virtWinEnd,&(tl.picWidth),NULL)) { virtWinBaseCount = virtWinEnd - virtWinStart; fullInsideWidth = tl.picWidth-gfxBorder-fullInsideX; } } setGlobalsFromWindow(windows); // first window seqBaseCount = hChromSize(database, chromName); /* Save computed position in cart. */ cartSetString(cart, "org", organism); cartSetString(cart, "db", database); char newPos[256]; // disguise the cart pos var if (virtualSingleChrom()) // DISGUISE VMODE safef(newPos, sizeof newPos, "%s", windowsSpanPosition()); else // usual safef(newPos, sizeof newPos, "%s:%ld-%ld", virtChromName, virtWinStart+1, virtWinEnd); position = cloneString(newPos); cartSetString(cart, "position", position); cartSetString(cart, "oldPosition", position); //cartSetString(cart, "lastPosition", position); // this is set in cart.c cartSetBoolean(cart, "virtMode", virtMode); cartSetString(cart, "virtModeType", virtModeType); virtModeType = cartString(cart, "virtModeType"); // refresh the pointer after changing hash lastVirtModeType=virtModeType; cartSetString(cart, "lastVirtModeType", lastVirtModeType); lastVirtModeType = cartString(cart, "lastVirtModeType"); // refresh lastVirtModeExtraState=virtModeExtraState; cartSetString(cart, "lastVirtModeExtraState", lastVirtModeExtraState); lastVirtModeExtraState = cartString(cart, "lastVirtModeExtraState"); // refresh // save a quick position to use if user leaves virtMode. if (virtMode) cartSetString(cart, "nonVirtPosition", nonVirtPositionFromWindows()); else cartRemove(cart, "nonVirtPosition"); // save a highlight position to use if user leaves virtMode. char *nvh = NULL; if (virtMode) nvh = nonVirtPositionFromHighlightPos(); if (virtMode && nvh) cartSetString(cart, "nonVirtHighlight", nvh); else cartRemove(cart, "nonVirtHighlight"); // save lastDbPos. save the current position and other important cart vars related to virtual view. lastDbPosSaveCartSetting("position"); lastDbPosSaveCartSetting("nonVirtPosition"); lastDbPosSaveCartSetting("virtMode"); lastDbPosSaveCartSetting("virtModeType"); lastDbPosSaveCartSetting("lastVirtModeType"); lastDbPosSaveCartSetting("lastVirtModeExtraState"); cartSetDbPosition(cart, database, lastDbPosCart); if (cartUsualBoolean(cart, "hgt.psOutput", FALSE)) handlePostscript(); else doTrackForm(NULL, NULL); boolean gotExtTools = extToolsEnabled(); setupHotkeys(gotExtTools); if (gotExtTools) printExtMenuData(chromName); } 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(); htmlPrintf("<A HREF=\"%s|none|?%s|url|=%s|url|&position=%s|url|\">%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(); htmlPrintf("<A HREF=\"%s|none|?%s|url|=%s|url|&position=%s|url|\">%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; 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, total); 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(); htmlPrintf("<A HREF=\"%s|none|?%s|url|=%s|url|&position=%s|url|\">%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]); long long totalSize = sqlLongLong(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 */ { struct dyString *dy = dyStringNew(1024); // wire the keyboard hotkeys // left dyStringPrintf(dy,"Mousetrap.bind('ctrl+j', function() { $('input[name=\"hgt.left1\"]').click(); return false; }); \n"); dyStringPrintf(dy,"Mousetrap.bind('j', function() { $('input[name=\"hgt.left2\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('J', function() { $('input[name=\"hgt.left3\"]').click() }); \n"); // right dyStringPrintf(dy,"Mousetrap.bind('ctrl+l', function() { $('input[name=\"hgt.right1\"]').click(); return false; }); \n"); dyStringPrintf(dy,"Mousetrap.bind('l', function() { $('input[name=\"hgt.right2\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('L', function() { $('input[name=\"hgt.right3\"]').click() }); \n"); // zoom in dyStringPrintf(dy,"Mousetrap.bind('ctrl+i', function() { $('input[name=\"hgt.in1\"]').click(); return false; }); \n"); dyStringPrintf(dy,"Mousetrap.bind('i', function() { $('input[name=\"hgt.in2\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('I', function() { $('input[name=\"hgt.in3\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('b', function() { $('input[name=\"hgt.inBase\"]').click() }); \n"); // zoom out dyStringPrintf(dy,"Mousetrap.bind('ctrl+k', function() { $('input[name=\"hgt.out1\"]').click(); return false; }); \n"); dyStringPrintf(dy,"Mousetrap.bind('k', function() { $('input[name=\"hgt.out2\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('K', function() { $('input[name=\"hgt.out3\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('0', function() { $('input[name=\"hgt.out4\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('ctrl+k', function() { $('input[name=\"hgt.out1\"]').click(); return false; }); \n"); dyStringPrintf(dy,"Mousetrap.bind('k', function() { $('input[name=\"hgt.out2\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('K', function() { $('input[name=\"hgt.out3\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('0', function() { $('input[name=\"hgt.out4\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('1', function() { zoomTo(50);} ); \n"); dyStringPrintf(dy,"Mousetrap.bind('2', function() { zoomTo(500);} ); \n"); dyStringPrintf(dy,"Mousetrap.bind('3', function() { zoomTo(5000);} ); \n"); dyStringPrintf(dy,"Mousetrap.bind('4', function() { zoomTo(50000);} ); \n"); dyStringPrintf(dy,"Mousetrap.bind('5', function() { zoomTo(500000);} ); \n"); dyStringPrintf(dy,"Mousetrap.bind('6', function() { zoomTo(5000000);} ); \n"); // buttons dyStringPrintf(dy,"Mousetrap.bind('c f', function() { $('input[name=\"hgTracksConfigPage\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('t s', function() { $('input[name=\"hgt_tSearch\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('h a', function() { $('input[name=\"hgt.hideAll\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('d t', function() { $('input[name=\"hgt.reset\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('d o', function() { $('input[name=\"hgt.defaultImgOrder\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('c t', function() { document.customTrackForm.submit();return false; }); \n"); dyStringPrintf(dy,"Mousetrap.bind('t h', function() { document.trackHubForm.submit();return false; }); \n"); dyStringPrintf(dy,"Mousetrap.bind('t c', function() { document.editHubForm.submit();return false; }); \n"); dyStringPrintf(dy,"Mousetrap.bind('r s', function() { $('input[name=\"hgt.setWidth\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('r f', function() { $('input[name=\"hgt.refresh\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('r v', function() { $('input[name=\"hgt.toggleRevCmplDisp\"]').click() }); \n"); dyStringPrintf(dy,"Mousetrap.bind('v d', gotoGetDnaPage); \n"); // highlight dyStringPrintf(dy,"Mousetrap.bind('h c', function() { highlightCurrentPosition('clear'); }); \n"); dyStringPrintf(dy,"Mousetrap.bind('h m', function() { highlightCurrentPosition('add'); }); \n"); //dyStringPrintf(dy,"Mousetrap.bind('h n', function() { highlightCurrentPosition('new'); }); \n"); superfluos as it is just hc + hm? // focus dyStringPrintf(dy,"Mousetrap.bind('/', function() { $('input[name=\"hgt.positionInput\"]').focus(); return false; }, 'keydown'); \n"); dyStringPrintf(dy,"Mousetrap.bind('?', showHotkeyHelp);\n"); // menu if (gotExtTools) dyStringPrintf(dy,"Mousetrap.bind('s t', showExtToolDialog); \n"); // multi-region views dyStringPrintf(dy,"Mousetrap.bind('e v', function() { window.location.href='%s?%s=%s&virtModeType=exonMostly'; }); \n", hgTracksName(), cartSessionVarName(), cartSessionId(cart)); dyStringPrintf(dy,"Mousetrap.bind('d v', function() { window.location.href='%s?%s=%s&virtModeType=default'; }); \n", hgTracksName(), cartSessionVarName(), cartSessionId(cart)); dyStringPrintf(dy,"Mousetrap.bind('v s', function() { window.location.href='%s?chromInfoPage=&%s=%s'; }); \n", hgTracksName(), cartSessionVarName(), cartSessionId(cart)); // links to a few tools dyStringPrintf(dy,"Mousetrap.bind('t b', function() { $('#blatMenuLink')[0].click()});\n"); dyStringPrintf(dy,"Mousetrap.bind('t i', function() { $('#ispMenuLink')[0].click()});\n"); dyStringPrintf(dy,"Mousetrap.bind('t t', function() { $('#tableBrowserMenuLink')[0].click()});\n"); dyStringPrintf(dy,"Mousetrap.bind('c r', function() { $('#cartResetMenuLink')[0].click()});\n"); dyStringPrintf(dy,"Mousetrap.bind('s s', function() { $('#sessionsMenuLink')[0].click()});\n"); dyStringPrintf(dy,"Mousetrap.bind('p s', function() { $('#publicSessionsMenuLink')[0].click()});\n"); // also add an entry to the help menu that shows the keyboard shortcut help dialog dyStringPrintf(dy,"$(document).ready(addKeyboardHelpEntries);\n"); jsInline(dy->string); dyStringFree(&dy); // help dialog hPrintf("<div style=\"display:none\" id=\"hotkeyHelp\" title=\"Keyboard shortcuts\">\n"); hPrintf("<table style=\"width:600px; 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 collections</td><td class=\"hotkey\">t then c</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> jump to position box</td><td class=\"hotkey\">/</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 1.5x</td><td class=\"hotkey\">ctrl+k</td><td> view chrom names</td><td class=\"hotkey\">v then s</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> <td> exon view</td><td class=\"hotkey\">e then v</td> </tr>\n"); hPrintf("<tr><td> zoom out 100x</td><td class=\"hotkey\">0</td> <td> default view</td><td class=\"hotkey\">d then v</td> </tr>\n"); hPrintf("<tr><td> zoom to ...</td><td class=\"hotkey\"></td><td> view DNA</td><td class='hotkey'>v then d</td></tr>\n"); hPrintf("<tr><td> 50bp (1 zero)</td><td class=\"hotkey\">1</td><td>Reset all User Settings</td><td class='hotkey'>c then r</td></tr>\n"); hPrintf("<tr><td> 500bp (2 zeros)</td><td class=\"hotkey\">2</td><td>Tools - BLAT</td><td class='hotkey'>t then b</td></tr>\n"); hPrintf("<tr><td> 5000bp (3 zeros)</td><td class=\"hotkey\">3</td><td>Tools - Table Browser</td><td class='hotkey'>t then t</td></tr>\n"); hPrintf("<tr><td> 50kbp (4 zeros)</td><td class=\"hotkey\">4</td><td>Tools - PCR</td><td class='hotkey'>t then i</td></tr>\n"); hPrintf("<tr><td> 500kbp (5 zeros)</td><td class=\"hotkey\">5</td><td>My Sessions</td><td class='hotkey'>s then s</td></tr>\n"); hPrintf("<tr><td> 5Mbp (6 zeros)</td><td class=\"hotkey\">6</td><td>Public Sessions</td><td class='hotkey'>p then s</td></tr>\n"); hPrintf("<tr><td>Highlight all (mark)</td><td class=\"hotkey\">h then m</td><td>Clear all Highlights</td><td class='hotkey'>h then c</td></tr>\n"); - hPrintf("<tr><td>View chrom names</td><td class=\"hotkey\">v then s</td><td></td><td class='hotkey'></td></tr>\n"); hPrintf("</table>\n"); hPrintf("<img style=\"margin:8px\" src=\"../images/shortcutHelp.png\">"); hPrintf("</div>\n"); } static void checkAddHighlight() /* If the cart variable addHighlight is set, merge it into the highlight variable. */ { char *newHighlight = cartOptionalString(cart, "addHighlight"); if (newHighlight) { char *existing = cartOptionalString(cart, "highlight"); if (isNotEmpty(existing)) { // Add region only if it is not already in the existing highlight setting. char *alreadyIn = strstr(existing, newHighlight); int len = strlen(newHighlight); if (! (alreadyIn && (alreadyIn[len] == '|' || alreadyIn[len] == '\0'))) { struct dyString *dy = dyStringCreate("%s|%s", newHighlight, existing); cartSetString(cart, "highlight", dy->string); } } else cartSetString(cart, "highlight", newHighlight); cartRemove(cart, "addHighlight"); } } + extern boolean issueBotWarning; + void doMiddle(struct cart *theCart) /* Print the body of an html file. */ { cart = theCart; measureTiming = hPrintStatus() && isNotEmpty(cartOptionalString(cart, "measureTiming")); if (measureTiming) - measureTime("Startup"); + measureTime("Startup (bottleneck %d ms) ", botDelayMillis); - hgBotDelayFrac(0.25); /* Impose a quarter of the standard CGI penalty */ - if (measureTiming) - measureTime("Bottleneck delay"); + if (issueBotWarning) + { + char *ip = getenv("REMOTE_ADDR"); + botDelayMessage(ip, botDelayMillis); + } 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); initGenbankTableNames(database); 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); // tell UDC where to put its statistics file char *udcLogFile; if ((udcLogFile = cfgOption("udcLog")) != NULL) { FILE *fp = mustOpen(udcLogFile, "a"); udcSetLog(fp); } initTl(); char *configPageCall = cartCgiUsualString(cart, "hgTracksConfigPage", "notSet"); char *configMultiRegionPageCall = cartCgiUsualString(cart, "hgTracksConfigMultiRegionPage", "notSet"); checkAddHighlight(); /* 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("es5-shim.4.0.3.min.js", NULL); jsIncludeFile("es5-sham.4.0.3.min.js", NULL); jsIncludeFile("lodash.3.10.0.compat.min.js", NULL); jsIncludeFile("autocompleteCat.js", NULL); jsIncludeFile("hgTracks.js", NULL); jsIncludeFile("spectrum.min.js", NULL); #ifdef LOWELAB jsIncludeFile("lowetooltip.js", NULL); #endif///def LOWELAB webIncludeResourceFile("spectrum.min.css"); 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"); hPrintf("<div id='hgTracksDialog' 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 (sameWord(configMultiRegionPageCall, "multi-region")) { cartRemove(cart, "hgTracksConfigMultiRegionPage"); configMultiRegionPage(); } 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(); } if (cartVarExists(cart, "hgt.convertChromToVirtChrom")) { cartRemove(cart, "hgt.convertChromToVirtChrom"); return; } jsonObjectAdd(jsonForClient, "measureTiming", newJsonBoolean(measureTiming)); // js code needs to know if a highlightRegion is defined for this db checkAddHighlight(); // call again in case tracksDisplay's call to resolvePosition changed vars 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))); struct dyString *dy = dyStringNew(1024); jsonDyStringPrint(dy, (struct jsonElement *) jsonForClient, "hgTracks", 0); jsInline(dy->string); dyStringFree(&dy); 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|url|&udcTimeout=[]'>here</A>.",cartSessionId(cart)); } } void labelTrackAsFiltered(struct track *tg) /* add text to track long label to indicate filter is active */ { char *oldLabel = tg->longLabel; tg->longLabel = catTwoStrings(oldLabel, " (filter activated)"); - freeMem(oldLabel); }