77dc06c4bdc5e10f5d2705a51300ec028a7d785f tdreszer Fri Oct 1 10:51:48 2010 -0700 FindTracks now finds superTracks (Advanced only) and hgTrackUi now does superTrack reshaping when children have vis changed diff --git src/hg/hgTracks/hgTracks.c.old src/hg/hgTracks/hgTracks.c.old new file mode 100644 index 0000000..f68887d --- /dev/null +++ src/hg/hgTracks/hgTracks.c.old @@ -0,0 +1,5646 @@ +/* hgTracks - the original, and still the largest module for the UCSC Human Genome + * Browser main cgi script. Currently contains most of the track framework, though + * there's quite a bit of other framework type code in simpleTracks.c. The main + * routine got moved to create a new entry point to the bulk of the code for the + * hgRenderTracks web service. See mainMain.c for the main used by the hgTracks CGI. */ + +#include "common.h" +#include "hCommon.h" +#include "linefile.h" +#include "portable.h" +#include "memalloc.h" +#include "localmem.h" +#include "obscure.h" +#include "dystring.h" +#include "hash.h" +#include "jksql.h" +#include "gfxPoly.h" +#include "memgfx.h" +#include "hvGfx.h" +#include "psGfx.h" +#include "cheapcgi.h" +#include "hPrint.h" +#include "htmshell.h" +#include "cart.h" +#include "hdb.h" +#include "hui.h" +#include "hgFind.h" +#include "hgTracks.h" +#include "trashDir.h" +#include "grp.h" +#include "versionInfo.h" +#include "web.h" +#include "cds.h" +#include "cutterTrack.h" +#include "wikiTrack.h" +#include "ctgPos.h" +#include "bed.h" +#include "bigBed.h" +#include "bigWig.h" +#include "bedCart.h" +#include "customTrack.h" +#include "cytoBand.h" +#include "ensFace.h" +#include "liftOver.h" +#include "pcrResult.h" +#include "wikiLink.h" +#include "jsHelper.h" +#include "mafTrack.h" +#include "hgConfig.h" +#include "encode.h" +#include "agpFrag.h" +#include "imageV2.h" +#include "suggest.h" +#include "searchTracks.h" + +static char const rcsid[] = "$Id: doMiddle.c,v 1.1651 2010/06/11 17:53:06 larrym Exp $"; + +/* These variables persist from one incarnation of this program to the + * next - living mostly in the cart. */ +boolean baseShowPos; /* TRUE if should display full position at top of base track */ +boolean baseShowAsm; /* TRUE if should display assembly info at top of base track */ +boolean baseShowScaleBar; /* TRUE if should display scale bar at very top of base track */ +boolean baseShowRuler; /* TRUE if should display the basic ruler in the base track (default) */ +char *baseTitle = NULL; /* Title it should display top of base track (optional)*/ +static char *userSeqString = NULL; /* User sequence .fa/.psl file. */ + +/* These variables are set by getPositionFromCustomTracks() at the very + * beginning of tracksDisplay(), and then used by loadCustomTracks(). */ +char *ctFileName = NULL; /* Custom track file. */ +struct customTrack *ctList = NULL; /* Custom tracks. */ +boolean hasCustomTracks = FALSE; /* whether any custom tracks are for this db*/ +struct slName *browserLines = NULL; /* Custom track "browser" lines. */ + +boolean withNextItemArrows = FALSE; /* Display next feature (gene) navigation buttons near center labels? */ +boolean withPriorityOverride = FALSE; /* Display priority for each track to allow reordering */ + +int gfxBorder = hgDefaultGfxBorder; /* Width of graphics border. */ +int guidelineSpacing = 12; /* Pixels between guidelines. */ + +boolean withIdeogram = TRUE; /* Display chromosome ideogram? */ + +int rulerMode = tvHide; /* on, off, full */ + +char *rulerMenu[] = +/* dropdown for ruler visibility */ + { + "hide", + "dense", + "full" + }; + +char *protDbName; /* Name of proteome database for this genome. */ +#define MAX_CONTROL_COLUMNS 6 +#define LOW 1 +#define MEDIUM 2 +#define BRIGHT 3 +#define MAXCHAINS 50000000 +boolean hgDebug = FALSE; /* Activate debugging code. Set to true by hgDebug=on in command line*/ +int imagePixelHeight = 0; +boolean dragZooming = TRUE; +struct hash *oldVars = NULL; + +boolean hideControls = FALSE; /* Hide all controls? */ +boolean trackImgOnly = FALSE; /* caller wants just the track image and track table html */ +boolean ideogramToo = FALSE; /* caller wants the ideoGram (when requesting just one track) */ + +/* Structure returned from findGenomePos. + * We use this to to expand any tracks to full + * that were found to contain the searched-upon + * position string */ +struct hgPositions *hgp = NULL; + + +/* Other global variables. */ +struct group *groupList = NULL; /* List of all tracks. */ +char *browserName; /* Test or public browser */ +char *organization; /* UCSC */ + + +struct track *trackFindByName(struct track *tracks, char *trackName) +/* find a track in tracks by name, recursively searching subtracks */ +{ +struct track *track; +for (track = tracks; track != NULL; track = track->next) + { + if (sameString(track->track, trackName)) + return track; + else if (track->subtracks != NULL) + { + struct track *st = trackFindByName(track->subtracks, trackName); + if (st != NULL) + return st; + } + } +return NULL; +} + +int tgCmpPriority(const void *va, const void *vb) +/* Compare to sort based on priority; use shortLabel as secondary sort key. */ +{ +const struct track *a = *((struct track **)va); +const struct track *b = *((struct track **)vb); +float dif = a->group->priority - b->group->priority; + +if (dif == 0) + dif = a->priority - b->priority; +if (dif < 0) + return -1; +else if (dif == 0.0) + /* secondary sort on label */ + return strcasecmp(a->shortLabel, b->shortLabel); +else + return 1; +} + +int trackRefCmpPriority(const void *va, const void *vb) +/* Compare based on priority. */ +{ +const struct trackRef *a = *((struct trackRef **)va); +const struct trackRef *b = *((struct trackRef **)vb); +return tgCmpPriority(&a->track, &b->track); +} + +int gCmpPriority(const void *va, const void *vb) +/* Compare groups based on priority. */ +{ +const struct group *a = *((struct group **)va); +const struct group *b = *((struct group **)vb); +float dif = a->priority - b->priority; + +if (dif == 0) + return 0; +if (dif < 0) + return -1; +else if (dif == 0.0) + return 0; +else + return 1; +} + +void changeTrackVis(struct group *groupList, char *groupTarget, int changeVis) +/* Change track visibilities. If groupTarget is + * NULL then set visibility for tracks in all groups. Otherwise, + * just set it for the given group. If vis is -2, then visibility is + * unchanged. If -1 then set visibility to default, otherwise it should + * be tvHide, tvDense, etc. + * If we are going back to default visibility, then reset the track + * ordering also. */ +{ +struct group *group; +if (changeVis == -2) + return; +for (group = groupList; group != NULL; group = group->next) + { + struct trackRef *tr; + if (groupTarget == NULL || sameString(group->name,groupTarget)) + { + static char pname[512]; + /* if default vis then reset group priority */ + if (changeVis == -1) + group->priority = group->defaultPriority; + for (tr = group->trackList; tr != NULL; tr = tr->next) + { + struct track *track = tr->track; + struct trackDb *tdb = track->tdb; + if (changeVis == -1) // to default + { + if(tdbIsComposite(tdb)) + { + safef(pname, sizeof(pname),"%s.*",track->track); //to remove all settings associated with this composite! + cartRemoveLike(cart,pname); + struct track *subTrack; + for(subTrack = track->subtracks;subTrack != NULL; subTrack = subTrack->next) + { + subTrack->visibility = tdb->visibility; + cartRemove(cart, subTrack->track); + } + } + + /* restore defaults */ + if (tdbIsSuperTrackChild(tdb) || tdbIsCompositeChild(tdb)) + { + assert(tdb->parent != NULL && tdb->parent->track); + cartRemove(cart, tdb->parent->track); + if (withPriorityOverride) + { + safef(pname, sizeof(pname), "%s.priority",tdb->parent->track); + cartRemove(cart, pname); + } + } + + track->visibility = tdb->visibility; + cartRemove(cart, track->track); + + /* set the track priority back to the default value */ + if (withPriorityOverride) + { + safef(pname, sizeof(pname), "%s.priority",track->track); + cartRemove(cart, pname); + track->priority = track->defaultPriority; + } + } + else // to changeVis value (Usually tvHide) + { + /* change to specified visibility */ + if (tdbIsSuperTrackChild(tdb)) + { + assert(tdb->parent != NULL); + /* Leave supertrack members alone -- only change parent */ + struct trackDb *parentTdb = tdb->parent; + if ((changeVis == tvHide && !parentTdb->isShow) || + (changeVis != tvHide && parentTdb->isShow)) + { + /* remove if setting to default vis */ + cartRemove(cart, parentTdb->track); + } + else + cartSetString(cart, parentTdb->track, + changeVis == tvHide ? "hide" : "show"); + } + else // Not super child + { + if (changeVis == tdb->visibility) + /* remove if setting to default vis */ + cartRemove(cart, track->track); + else + cartSetString(cart, track->track, hStringFromTv(changeVis)); + track->visibility = changeVis; + } + + #ifdef SUBTRACKS_HAVE_VIS + // Whether super child or not, if its a composite, then handle the children + if (tdbIsComposite(tdb)) + { + struct track *subtrack; + for(subtrack=track->subtracks;subtrack!=NULL;subtrack=subtrack->next) + { + if (changeVis == tvHide) + cartRemove(cart, subtrack->track); // Since subtrack level vis is an override, simply remove it to hide it + else + cartSetString(cart, subtrack->track, hStringFromTv(changeVis)); + subtrack->visibility = changeVis; + } + } + #endif///def SUBTRACKS_HAVE_VIS + } + } + } + } +slSort(&groupList, gCmpPriority); +} + +int trackOffsetX() +/* Return x offset where track display proper begins. */ +{ +int x = gfxBorder; +if (withLeftLabels) + x += tl.leftLabelWidth + gfxBorder; +return x; +} + + +static void mapBoxTrackUi(struct hvGfx *hvg, int x, int y, int width, + int height, char *name, char *shortLabel, char *id) +/* Print out image map rectangle that invokes hgTrackUi. */ +{ +x = hvGfxAdjXW(hvg, x, width); +char *url = trackUrl(name, chromName); + +if(theImgBox && curImgTrack) + { + struct imgSlice *curSlice = imgTrackSliceGetByType(curImgTrack,stButton); + if(curSlice) + sliceAddLink(curSlice,url,shortLabel); + } +else + { + hPrintf("\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("string); + freeDyString(&ui); + if (message != NULL) + mapStatusMessage("%s", message); + hPrintf(">\n"); + } +} + +char *trackUrl(char *mapName, char *chromName) +/* Return hgTrackUi url; chromName is optional. */ +{ +char *encodedMapName = cgiEncode(mapName); +char buf[2048]; +if(chromName == NULL) + safef(buf, sizeof(buf), "%s?%s=%u&g=%s", hgTrackUiName(), cartSessionVarName(), cartSessionId(cart), encodedMapName); +else + safef(buf, sizeof(buf), "%s?%s=%u&c=%s&g=%s", hgTrackUiName(), cartSessionVarName(), cartSessionId(cart), chromName, encodedMapName); +freeMem(encodedMapName); +return(cloneString(buf)); +} + +void smallBreak() +/* Draw small horizontal break */ +{ +hPrintf("
\n"); +} + +static int trackPlusLabelHeight(struct track *track, int fontHeight) +/* Return the sum of heights of items in this track (or subtrack as it may be) + * and the center label(s) above the items (if any). */ +{ +int y = track->totalHeight(track, limitVisibility(track)); +if (isCenterLabelIncluded(track)) + y += fontHeight; +if (tdbIsComposite(track->tdb)) + { + struct track *subtrack; + for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next) + { + if (isSubtrackVisible(subtrack) && isCenterLabelIncluded(subtrack)) + y += fontHeight; + } + } +return y; +} + +void drawColoredButtonBox(struct hvGfx *hvg, int x, int y, int w, int h, + int enabled, Color shades[]) +/* draw button box, providing shades of the desired button color */ +{ +int light = shades[1], mid = shades[2], dark = shades[4]; +if (enabled) + { + hvGfxBox(hvg, x, y, w, 1, light); + hvGfxBox(hvg, x, y+1, 1, h-1, light); + hvGfxBox(hvg, x+1, y+1, w-2, h-2, mid); + hvGfxBox(hvg, x+1, y+h-1, w-1, 1, dark); + hvGfxBox(hvg, x+w-1, y+1, 1, h-1, dark); + } +else /* try to make the button look as if + * it is already depressed */ + { + hvGfxBox(hvg, x, y, w, 1, dark); + hvGfxBox(hvg, x, y+1, 1, h-1, dark); + hvGfxBox(hvg, x+1, y+1, w-2, h-2, light); + hvGfxBox(hvg, x+1, y+h-1, w-1, 1, light); + hvGfxBox(hvg, x+w-1, y+1, 1, h-1, light); + } +} + +void drawGrayButtonBox(struct hvGfx *hvg, int x, int y, int w, int h, int enabled) +/* Draw a gray min-raised looking button. */ +{ + drawColoredButtonBox(hvg, x, y, w, h, enabled, shadesOfGray); +} + +void drawBlueButtonBox(struct hvGfx *hvg, int x, int y, int w, int h, int enabled) +/* Draw a blue min-raised looking button. */ +{ + drawColoredButtonBox(hvg, x, y, w, h, enabled, shadesOfSea); +} + +void drawButtonBox(struct hvGfx *hvg, int x, int y, int w, int h, int enabled) +/* Draw a standard (gray) min-raised looking button. */ +{ + drawGrayButtonBox(hvg, x, y, w, h, enabled); +} + +void beforeFirstPeriod( char *str ) +{ +char *t = rindex( str, '.' ); + +if( t == NULL ) + return; +else + str[strlen(str) - strlen(t)] = '\0'; +} + +static void drawBases(struct hvGfx *hvg, int x, int y, int width, int height, + Color color, MgFont *font, boolean complementSeq, + struct dnaSeq *thisSeq) +/* Draw evenly spaced bases. */ +{ +struct dnaSeq *seq; + +if (thisSeq == NULL) + seq = hDnaFromSeq(database, chromName, winStart, winEnd, dnaUpper); +else + seq = thisSeq; + +if (complementSeq) + complement(seq->dna, seq->size); +spreadBasesString(hvg, x, y, width, height, color, font, + seq->dna, seq->size, FALSE); + +if (thisSeq == NULL) + freeDnaSeq(&seq); +} + +void drawComplementArrow( struct hvGfx *hvg, int x, int y, + int width, int height, MgFont *font) +/* Draw arrow and create clickbox for complementing ruler bases */ +{ +boolean baseCmpl = cartUsualBooleanDb(cart, database, COMPLEMENT_BASES_VAR, FALSE); +// reverse arrow when base complement doesn't match display +char *text = (baseCmpl == revCmplDisp) ? "--->" : "<---"; +hvGfxTextRight(hvg, x, y, width, height, MG_BLACK, font, text); +mapBoxToggleComplement(hvg, x, y, width, height, NULL, chromName, winStart, winEnd, + "complement bases"); +} + +struct track *chromIdeoTrack(struct track *trackList) +/* Find chromosome ideogram track */ +{ +struct track *track; +for(track = trackList; track != NULL; track = track->next) + { + if(sameString(track->track, "cytoBandIdeo")) + { + if (hTableExists(database, track->table)) + return track; + else + return NULL; + } + } +return NULL; +} + +void removeTrackFromGroup(struct track *track) +/* Remove track from group it is part of. */ +{ +struct trackRef *tr = NULL; +for(tr = track->group->trackList; tr != NULL; tr = tr->next) + { + if(tr->track == track) + { + slRemoveEl(&track->group->trackList, tr); + break; + } + } +} + + +void fillInStartEndBands(struct track *ideoTrack, char *startBand, char *endBand, int buffSize) +/* Loop through the bands and fill in the one that the current window starts + on and ends on. */ +{ +struct cytoBand *cb = NULL, *cbList = ideoTrack->items; +for(cb = cbList; cb != NULL; cb = cb->next) + { + /* If the start or end is encompassed by this band fill + it in. */ + if(winStart >= cb->chromStart && + winStart <= cb->chromEnd) + { + safef(startBand, buffSize, "%s", cb->name); + } + /* End is > rather than >= due to odditiy in the + cytoband track where the starts and ends of two + bands overlaps by one. */ + if(winEnd > cb->chromStart && + winEnd <= cb->chromEnd) + { + safef(endBand, buffSize, "%s", cb->name); + } + } +} + +void makeChromIdeoImage(struct track **pTrackList, char *psOutput, + struct tempName *ideoTn) +/* Make an ideogram image of the chromsome and our position in it. If the + * ideoTn parameter is not NULL, it is filled in if the ideogram is created. */ +{ +struct track *ideoTrack = NULL; +MgFont *font = tl.font; +char *mapName = "ideoMap"; +struct hvGfx *hvg; +boolean doIdeo = TRUE; +boolean ideogramAvail = FALSE; +int ideoWidth = round(.8 *tl.picWidth); +int ideoHeight = 0; +int textWidth = 0; +struct tempName gifTn; +if (ideoTn == NULL) + ideoTn = &gifTn; // not returning value + +ideoTrack = chromIdeoTrack(*pTrackList); + +/* If no ideogram don't draw. */ +if(ideoTrack == NULL) + doIdeo = FALSE; +else if(trackImgOnly && !ideogramToo) + { + doIdeo = FALSE; + } +else + { + ideogramAvail = TRUE; + /* Remove the track from the group and track list. */ + removeTrackFromGroup(ideoTrack); + slRemoveEl(pTrackList, ideoTrack); + + /* Fix for hide all button hiding the ideogram as well. */ + if(withIdeogram && ideoTrack->items == NULL) + { + ideoTrack->visibility = tvDense; + ideoTrack->loadItems(ideoTrack); + } + limitVisibility(ideoTrack); + + /* If hidden don't draw. */ + if(ideoTrack->limitedVis == tvHide || !withIdeogram) + doIdeo = FALSE; + } +if(doIdeo) + { + char startBand[16]; + char endBand[16]; + char title[32]; + startBand[0] = endBand[0] = '\0'; + fillInStartEndBands(ideoTrack, startBand, endBand, sizeof(startBand)); + /* Start up client side map. */ + if (!psOutput) + hPrintf("\n", mapName); + /* Draw the ideogram. */ + ideoHeight = gfxBorder + ideoTrack->height; + if (psOutput) + { + trashDirFile(ideoTn, "hgtIdeo", "hgtIdeo", ".ps"); + hvg = hvGfxOpenPostScript(ideoWidth, ideoHeight, ideoTn->forCgi); + } + else + { +#ifdef USE_PNG + trashDirFile(ideoTn, "hgtIdeo", "hgtIdeo", ".png"); + hvg = hvGfxOpenPng(ideoWidth, ideoHeight, ideoTn->forCgi, FALSE); +#else + trashDirFile(ideoTn, "hgtIdeo", "hgtIdeo", ".gif"); + hvg = hvGfxOpenGif(ideoWidth, ideoHeight, ideoTn->forCgi, FALSE); +#endif + } + hvg->rc = revCmplDisp; + initColors(hvg); + ideoTrack->ixColor = hvGfxFindRgb(hvg, &ideoTrack->color); + ideoTrack->ixAltColor = hvGfxFindRgb(hvg, &ideoTrack->altColor); + hvGfxSetClip(hvg, 0, gfxBorder, ideoWidth, ideoTrack->height); + if(sameString(startBand, endBand)) + safef(title, sizeof(title), "%s (%s)", chromName, startBand); + else + safef(title, sizeof(title), "%s (%s-%s)", chromName, startBand, endBand); + textWidth = mgFontStringWidth(font, title); + hvGfxTextCentered(hvg, 2, gfxBorder, textWidth, ideoTrack->height, MG_BLACK, font, title); + ideoTrack->drawItems(ideoTrack, winStart, winEnd, hvg, textWidth+4, gfxBorder, ideoWidth-textWidth-4, + font, ideoTrack->ixColor, ideoTrack->limitedVis); + hvGfxUnclip(hvg); + /* Save out picture and tell html file about it. */ + hvGfxClose(&hvg); + /* Finish map. */ + if (!psOutput) + hPrintf("\n"); + } +hPrintf(""); +if (doIdeo && !psOutput) + { + hPrintf(""); + hPrintf(""); + hPrintf("
", + ideoTn->forHtml, ideoWidth, ideoHeight, mapName); + hPrintf("
\n"); + } +else + hPrintf("\n"); +if(ideoTrack != NULL) + { + ideoTrack->limitedVisSet = TRUE; + ideoTrack->limitedVis = tvHide; /* Don't draw in main gif. */ + } +} + +char *pcrResultMapItemName(struct track *tg, void *item) +/* Stitch accession and display name back together (if necessary). */ +{ +struct linkedFeatures *lf = item; +return pcrResultItemAccName(lf->name, lf->extra); +} + +void pcrResultLoad(struct track *tg) +/* Load locations of primer matches into linkedFeatures items. */ +{ +char *pslFileName, *primerFileName; +struct targetDb *target; +if (! pcrResultParseCart(database, cart, &pslFileName, &primerFileName, &target)) + return; + +/* Don't free psl -- used in drawing phase by baseColor code. */ +struct psl *pslList = pslLoadAll(pslFileName), *psl; +struct linkedFeatures *itemList = NULL; +if (target != NULL) + { + int rowOffset = hOffsetPastBin(database, chromName, target->pslTable); + struct sqlConnection *conn = hAllocConn(database); + struct sqlResult *sr; + char **row; + char query[2048]; + struct psl *tpsl; + for (tpsl = pslList; tpsl != NULL; tpsl = tpsl->next) + { + char *itemAcc = pcrResultItemAccession(tpsl->tName); + char *itemName = pcrResultItemName(tpsl->tName); + /* Query target->pslTable to get target-to-genomic mapping: */ + safef(query, sizeof(query), "select * from %s where qName = '%s'", + target->pslTable, itemAcc); + sr = sqlGetResult(conn, query); + while ((row = sqlNextRow(sr)) != NULL) + { + struct psl *gpsl = pslLoad(row+rowOffset); + if (sameString(gpsl->tName, chromName) && gpsl->tStart < winEnd && gpsl->tEnd > winStart) + { + struct psl *trimmed = pslTrimToQueryRange(gpsl, tpsl->tStart, + tpsl->tEnd); + struct linkedFeatures *lf; + char *targetStyle = cartUsualString(cart, + PCR_RESULT_TARGET_STYLE, PCR_RESULT_TARGET_STYLE_DEFAULT); + if (sameString(targetStyle, PCR_RESULT_TARGET_STYLE_TALL)) + { + lf = lfFromPslx(gpsl, 1, FALSE, FALSE, tg); + lf->tallStart = trimmed->tStart; + lf->tallEnd = trimmed->tEnd; + } + else + { + lf = lfFromPslx(trimmed, 1, FALSE, FALSE, tg); + } + lf->name = cloneString(itemAcc); + char extraInfo[512]; + safef(extraInfo, sizeof(extraInfo), "%s|%d|%d", + (itemName ? itemName : ""), tpsl->tStart, tpsl->tEnd); + lf->extra = cloneString(extraInfo); + slAddHead(&itemList, lf); + } + } + } + hFreeConn(&conn); + } +else + for (psl = pslList; psl != NULL; psl = psl->next) + if (sameString(psl->tName, chromName) && psl->tStart < winEnd && psl->tEnd > winStart) + { + struct linkedFeatures *lf = + lfFromPslx(psl, 1, FALSE, FALSE, tg); + lf->name = cloneString(""); + lf->extra = cloneString(""); + slAddHead(&itemList, lf); + } +slSort(&itemList, linkedFeaturesCmp); +tg->items = itemList; +} + +char *pcrResultTrackItemName(struct track *tg, void *item) +/* If lf->extra is non-empty, return it (display name for item). + * Otherwise default to item name. */ +{ +struct linkedFeatures *lf = item; +char *extra = (char *)lf->extra; +if (isNotEmpty(extra)) + { + static char displayName[512]; + safecpy(displayName, sizeof(displayName), extra); + char *ptr = strchr(displayName, '|'); + if (ptr != NULL) + *ptr = '\0'; + if (isNotEmpty(displayName)) + return displayName; + } +return lf->name; +} + +struct track *pcrResultTg() +/* Make track of hgPcr results (alignments of user's submitted primers). */ +{ +struct trackDb *tdb = pcrResultFakeTdb(); +struct track *tg = trackFromTrackDb(tdb); +tg->loadItems = pcrResultLoad; +tg->itemName = pcrResultTrackItemName; +tg->mapItemName = pcrResultMapItemName; +tg->exonArrows = TRUE; +tg->hasUi = TRUE; +return tg; +} + +struct track *linkedFeaturesTg() +/* Return generic track for linked features. */ +{ +struct track *tg = trackNew(); +linkedFeaturesMethods(tg); +tg->colorShades = shadesOfGray; +return tg; +} + +void setTgDarkLightColors(struct track *tg, int r, int g, int b) +/* Set track color to r,g,b. Set altColor to a lighter version + * of the same. */ +{ +tg->colorShades = NULL; +tg->color.r = r; +tg->color.g = g; +tg->color.b = b; +tg->altColor.r = (r+255)/2; +tg->altColor.g = (g+255)/2; +tg->altColor.b = (b+255)/2; +} + +void parseSs(char *ss, char **retPsl, char **retFa) +/* Parse out ss variable into components. */ +{ +static char buf[1024]; +char *words[2]; +int wordCount; + +safecpy(buf, sizeof(buf), ss); +wordCount = chopLine(buf, words); +if (wordCount < 2) + errAbort("Badly formated ss variable"); +*retPsl = words[0]; +*retFa = words[1]; +} + +boolean ssFilesExist(char *ss) +/* Return TRUE if both files in ss exist. */ +{ +char *faFileName, *pslFileName; +parseSs(ss, &pslFileName, &faFileName); +return fileExists(pslFileName) && fileExists(faFileName); +} + +void loadUserPsl(struct track *tg) +/* Load up hgBlat results from table into track items. */ +{ +char *ss = userSeqString; +char buf2[3*512]; +char *faFileName, *pslFileName; +struct lineFile *f; +struct psl *psl; +struct linkedFeatures *lfList = NULL, *lf; +enum gfType qt, tt; +int sizeMul = 1; + +parseSs(ss, &pslFileName, &faFileName); +pslxFileOpen(pslFileName, &qt, &tt, &f); +if (qt == gftProt) + { + setTgDarkLightColors(tg, 0, 80, 150); + tg->colorShades = NULL; + sizeMul = 3; + } +tg->itemName = linkedFeaturesName; +while ((psl = pslNext(f)) != NULL) + { + if (sameString(psl->tName, chromName) && psl->tStart < winEnd && psl->tEnd > winStart) + { + lf = lfFromPslx(psl, sizeMul, TRUE, FALSE, tg); + sprintf(buf2, "%s %s", ss, psl->qName); + lf->extra = cloneString(buf2); + slAddHead(&lfList, lf); + /* Don't free psl -- used in drawing phase by baseColor code. */ + } + else + pslFree(&psl); + } +slSort(&lfList, linkedFeaturesCmpStart); +lineFileClose(&f); +tg->items = lfList; +} + +static void addUserSeqBaseAndIndelSettings(struct trackDb *tdb) +/* If user sequence is a dna or rna alignment, add settings to enable + * base-level differences and indel display. */ +{ +enum gfType qt, tt; +struct lineFile *lf; +char *faFileName, *pslFileName; +parseSs(userSeqString, &pslFileName, &faFileName); +pslxFileOpen(pslFileName, &qt, &tt, &lf); +lineFileClose(&lf); +if (qt != gftProt) + { + if (tdb->settingsHash == NULL) + tdb->settingsHash = hashNew(0); + hashAdd(tdb->settingsHash, BASE_COLOR_DEFAULT, cloneString("diffBases")); + hashAdd(tdb->settingsHash, BASE_COLOR_USE_SEQUENCE, cloneString("ss")); + hashAdd(tdb->settingsHash, SHOW_DIFF_BASES_ALL_SCALES, cloneString(".")); + hashAdd(tdb->settingsHash, INDEL_DOUBLE_INSERT, cloneString("on")); + hashAdd(tdb->settingsHash, INDEL_QUERY_INSERT, cloneString("on")); + hashAdd(tdb->settingsHash, INDEL_POLY_A, cloneString("on")); + } +} + +struct track *userPslTg() +/* Make track of user pasted sequence. */ +{ +struct track *tg = linkedFeaturesTg(); +struct trackDb *tdb; +tg->track = "hgUserPsl"; +tg->table = tg->track; +tg->canPack = TRUE; +tg->visibility = tvPack; +tg->longLabel = "Your Sequence from Blat Search"; +tg->shortLabel = "Blat Sequence"; +tg->loadItems = loadUserPsl; +tg->mapItemName = lfMapNameFromExtra; +tg->priority = 100; +tg->defaultPriority = tg->priority; +tg->groupName = "map"; +tg->defaultGroupName = cloneString(tg->groupName); +tg->exonArrows = TRUE; + +/* better to create the tdb first, then use trackFromTrackDb */ +AllocVar(tdb); +tdb->track = cloneString(tg->track); +tdb->table = cloneString(tg->table); +tdb->visibility = tg->visibility; +tdb->shortLabel = cloneString(tg->shortLabel); +tdb->longLabel = cloneString(tg->longLabel); +tdb->grp = cloneString(tg->groupName); +tdb->priority = tg->priority; +tdb->type = cloneString("psl"); +trackDbPolish(tdb); +addUserSeqBaseAndIndelSettings(tdb); +tg->tdb = tdb; +return tg; +} + +char *oligoMatchSeq() +/* Return sequence for oligo matching. */ +{ +char *s = cartOptionalString(cart, oligoMatchVar); +if (s != NULL) + { + int len; + tolowers(s); + dnaFilter(s, s); + len = strlen(s); + if (len < 2) + s = NULL; + } +if (s == NULL) + s = cloneString(oligoMatchDefault); +return s; +} + +char *oligoMatchName(struct track *tg, void *item) +/* Return name for oligo, which is just the base position. */ +{ +struct bed *bed = item; +static char buf[22]; +buf[0] = bed->strand[0]; +sprintLongWithCommas(buf+1, bed->chromStart+1); +return buf; +} + +char *dnaInWindow() +/* This returns the DNA in the window, all in lower case. */ +{ +static struct dnaSeq *seq = NULL; +if (seq == NULL) + seq = hDnaFromSeq(database, chromName, winStart, winEnd, dnaLower); +return seq->dna; +} + + +void oligoMatchLoad(struct track *tg) +/* Create track of perfect matches to oligo on either strand. */ +{ +char *dna = dnaInWindow(); +char *fOligo = oligoMatchSeq(); +int oligoSize = strlen(fOligo); +char *rOligo = cloneString(fOligo); +char *rMatch = NULL, *fMatch = NULL; +struct bed *bedList = NULL, *bed; +char strand; +int count = 0, maxCount = 1000000; + +if (oligoSize >= 2) + { + fMatch = stringIn(fOligo, dna); + reverseComplement(rOligo, oligoSize); + if (sameString(rOligo, fOligo)) + rOligo = NULL; + else + rMatch = stringIn(rOligo, dna); + for (;;) + { + char *oneMatch = NULL; + if (rMatch == NULL) + { + if (fMatch == NULL) + break; + else + { + oneMatch = fMatch; + fMatch = stringIn(fOligo, fMatch+1); + strand = '+'; + } + } + else if (fMatch == NULL) + { + oneMatch = rMatch; + rMatch = stringIn(rOligo, rMatch+1); + strand = '-'; + } + else if (rMatch < fMatch) + { + oneMatch = rMatch; + rMatch = stringIn(rOligo, rMatch+1); + strand = '-'; + } + else + { + oneMatch = fMatch; + fMatch = stringIn(fOligo, fMatch+1); + strand = '+'; + } + if (count < maxCount) + { + ++count; + AllocVar(bed); + bed->chromStart = winStart + (oneMatch - dna); + bed->chromEnd = bed->chromStart + oligoSize; + bed->strand[0] = strand; + slAddHead(&bedList, bed); + } + else + break; + } + slReverse(&bedList); + if (count < maxCount) + tg->items = bedList; + else + warn("More than %d items in %s, suppressing display", maxCount, tg->shortLabel); + } +} + +struct track *oligoMatchTg() +/* Make track of perfect matches to oligomer. */ +{ +struct track *tg = trackNew(); +char *oligo = oligoMatchSeq(); +int oligoSize = strlen(oligo); +char *medOligo = cloneString(oligo); +static char longLabel[80]; +struct trackDb *tdb; + +/* Generate abbreviated strings. */ +if (oligoSize >= 30) + { + memset(medOligo + 30-3, '.', 3); + medOligo[30] = 0; + } +touppers(medOligo); + +bedMethods(tg); +tg->track = "oligoMatch"; +tg->table = tg->track; +tg->canPack = TRUE; +tg->visibility = tvHide; +tg->hasUi = TRUE; +tg->shortLabel = cloneString(OLIGO_MATCH_TRACK_LABEL); +safef(longLabel, sizeof(longLabel), + "Perfect Matches to Short Sequence (%s)", medOligo); +tg->longLabel = longLabel; +tg->loadItems = oligoMatchLoad; +tg->itemName = oligoMatchName; +tg->mapItemName = oligoMatchName; +tg->priority = 99; +tg->defaultPriority = tg->priority; +tg->groupName = "map"; +tg->defaultGroupName = cloneString(tg->groupName); + +AllocVar(tdb); +tdb->track = cloneString(tg->track); +tdb->table = cloneString(tg->table); +tdb->visibility = tg->visibility; +tdb->shortLabel = cloneString(tg->shortLabel); +tdb->longLabel = cloneString(tg->longLabel); +tdb->grp = cloneString(tg->groupName); +tdb->priority = tg->priority; +trackDbPolish(tdb); +tg->tdb = tdb; +return tg; +} + +static int doLeftLabels(struct track *track, struct hvGfx *hvg, MgFont *font, + int y) +/* Draw left labels. Return y coord. */ +{ +struct slList *prev = NULL; + +/* for sample tracks */ +double minRangeCutoff, maxRangeCutoff; +double minRange, maxRange; +double min0, max0; +char minRangeStr[32]; +char maxRangeStr[32]; + +int ymin, ymax; +int start; +int newy; +char o4[256]; +char o5[256]; +struct slList *item; +enum trackVisibility vis = track->limitedVis; +enum trackVisibility savedVis = vis; +Color labelColor = (track->labelColor ? + track->labelColor : track->ixColor); +int fontHeight = mgFontLineHeight(font); +int tHeight = trackPlusLabelHeight(track, fontHeight); +if (vis == tvHide) + return y; + +/* if a track can do its own left labels, do them after drawItems */ +if (track->drawLeftLabels != NULL) + return y + tHeight; + +/* Wiggle tracks depend upon clipping. They are reporting + * totalHeight artifically high by 1 so this will leave a + * blank area one pixel high below the track. + */ +if (sameString("wig",track->tdb->type) || sameString("bedGraph",track->tdb->type)) + hvGfxSetClip(hvg, leftLabelX, y, leftLabelWidth, tHeight-1); +else + hvGfxSetClip(hvg, leftLabelX, y, leftLabelWidth, tHeight); + +minRange = 0.0; +safef( o4, sizeof(o4),"%s.min.cutoff", track->track); +safef( o5, sizeof(o5),"%s.max.cutoff", track->track); +minRangeCutoff = max( atof(cartUsualString(cart,o4,"0.0"))-0.1, + track->minRange ); +maxRangeCutoff = min( atof(cartUsualString(cart,o5,"1000.0"))+0.1, + track->maxRange); +if( sameString( track->table, "humMusL" ) || + sameString( track->table, "musHumL" ) || + sameString( track->table, "mm3Rn2L" ) || + sameString( track->table, "hg15Mm3L" ) || + sameString( track->table, "mm3Hg15L" ) || + sameString( track->table, "regpotent" ) || + sameString( track->table, "HMRConservation" ) ) + { + int binCount = round(1.0/track->scaleRange); + minRange = whichSampleBin( minRangeCutoff, track->minRange, track->maxRange, binCount ); + maxRange = whichSampleBin( maxRangeCutoff, track->minRange, track->maxRange ,binCount ); + min0 = whichSampleNum( minRange, track->minRange,track->maxRange, binCount ); + max0 = whichSampleNum( maxRange, track->minRange, track->maxRange, binCount ); + sprintf( minRangeStr, " " ); + sprintf( maxRangeStr, " " ); + if( vis == tvFull && track->heightPer >= 74 ) + { + samplePrintYAxisLabel( hvg, y+5, track, "1.0", min0, max0 ); + samplePrintYAxisLabel( hvg, y+5, track, "2.0", min0, max0 ); + samplePrintYAxisLabel( hvg, y+5, track, "3.0", min0, max0 ); + samplePrintYAxisLabel( hvg, y+5, track, "4.0", min0, max0 ); + samplePrintYAxisLabel( hvg, y+5, track, "5.0", min0, max0 ); + samplePrintYAxisLabel( hvg, y+5, track, "6.0", min0, max0 ); + } + } +else + { + sprintf( minRangeStr, "%d", (int)round(minRangeCutoff)); + sprintf( maxRangeStr, "%d", (int)round(maxRangeCutoff)); + } +/* special label handling for wigMaf type tracks -- they + display a left label in pack mode. To use the full mode + labeling, temporarily set visibility to full. + Restore savedVis later */ +if (startsWith("wigMaf", track->tdb->type) || startsWith("maf", track->tdb->type)) + vis = tvFull; + +switch (vis) + { + case tvHide: + break; /* Do nothing; */ + case tvPack: + case tvSquish: + y += tHeight; + break; + case tvFull: + if (isCenterLabelIncluded(track)) + y += fontHeight; + start = 1; + + if( track->subType == lfSubSample && track->items == NULL ) + y += track->height; + + for (item = track->items; item != NULL; item = item->next) + { + char *rootName; + char *name = track->itemName(track, item); + int itemHeight = track->itemHeight(track, item); + newy = y; + + if (track->itemLabelColor != NULL) + labelColor = track->itemLabelColor(track, item, hvg); + + /* Do some fancy stuff for sample tracks. + * Draw y-value limits for 'sample' tracks. */ + if (track->subType == lfSubSample ) + { + if( prev == NULL ) + newy += itemHeight; + else + newy += sampleUpdateY(name, + track->itemName(track, prev), itemHeight); + if( newy == y ) + continue; + + if( track->heightPer > (3 * fontHeight ) ) + { + ymax = y - (track->heightPer / 2) + (fontHeight / 2); + ymin = y + (track->heightPer / 2) - (fontHeight / 2); + hvGfxTextRight(hvg, leftLabelX, ymin, leftLabelWidth-1, + itemHeight, track->ixAltColor, + font, minRangeStr ); + hvGfxTextRight(hvg, leftLabelX, ymax, leftLabelWidth-1, + itemHeight, track->ixAltColor, + font, maxRangeStr ); + } + prev = item; + + rootName = cloneString( name ); + beforeFirstPeriod( rootName ); + if( sameString( track->table, "humMusL" ) || + sameString( track->table, "hg15Mm3L" )) + hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1, + itemHeight, track->ixColor, font, "Mouse Cons"); + else if( sameString( track->table, "musHumL" ) || + sameString( track->table, "mm3Hg15L")) + hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1, + itemHeight, track->ixColor, font, "Human Cons"); + else if( sameString( track->table, "mm3Rn2L" )) + hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1, + itemHeight, track->ixColor, font, "Rat Cons"); + else + hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1, + itemHeight, track->ixColor, font, rootName ); + freeMem( rootName ); + start = 0; + y = newy; + } + else + { + /* standard item labeling */ + if (highlightItem(track, item)) + { + int nameWidth = mgFontStringWidth(font, name); + int boxStart = leftLabelX + leftLabelWidth - 2 - nameWidth; + hvGfxBox(hvg, boxStart, y, nameWidth+1, itemHeight - 1, + labelColor); + hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth-1, + itemHeight, MG_WHITE, font, name); + } + else + hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth - 1, + itemHeight, labelColor, font, name); + y += itemHeight; + } + } + break; + case tvDense: + + if (isCenterLabelIncluded(track)) + y += fontHeight; + + /*draw y-value limits for 'sample' tracks. + * (always puts 0-100% range)*/ + if( track->subType == lfSubSample && + track->heightPer > (3 * fontHeight ) ) + { + ymax = y - (track->heightPer / 2) + (fontHeight / 2); + ymin = y + (track->heightPer / 2) - (fontHeight / 2); + hvGfxTextRight(hvg, leftLabelX, ymin, + leftLabelWidth-1, track->lineHeight, + track->ixAltColor, font, minRangeStr ); + hvGfxTextRight(hvg, leftLabelX, ymax, + leftLabelWidth-1, track->lineHeight, + track->ixAltColor, font, maxRangeStr ); + } + hvGfxTextRight(hvg, leftLabelX, y, leftLabelWidth-1, + track->lineHeight, labelColor, font, + track->shortLabel); + y += track->height; + break; + } +/* NOTE: might want to just restore savedVis here for all track types, + but I'm being cautious... */ +if (sameString(track->tdb->type, "wigMaf")) + vis = savedVis; +hvGfxUnclip(hvg); +return y; +} + +static void doLabelNextItemButtons(struct track *track, struct track *parentTrack, struct hvGfx *hvg, MgFont *font, int y, + int trackPastTabX, int trackPastTabWidth, int fontHeight, + int insideHeight, Color labelColor) +/* If the track allows label next-item buttons (next gene), draw them. */ +/* The button will cause hgTracks to run again with the additional CGI */ +/* vars nextItem=trackName or prevItem=trackName, which will then */ +/* signal the browser to find the next thing on the track before it */ +/* does anything else. */ +{ +int portWidth = insideWidth; +int portX = insideX; +#ifdef IMAGEv2_DRAG_SCROLL +// If a portal was established, then set the portal dimensions +int portalStart,chromStart; +double basesPerPixel; +if (imgBoxPortalDimensions(theImgBox,&chromStart,NULL,NULL,NULL,&portalStart,NULL,&portWidth,&basesPerPixel)) + { + portX = (int)((portalStart - chromStart) / basesPerPixel); + portX += gfxBorder; + if (withLeftLabels) + portX += tl.leftLabelWidth + gfxBorder; + portWidth = portWidth-gfxBorder-insideX; + } +#endif//def IMAGEv2_DRAG_SCROLL +int arrowWidth = insideHeight; +int arrowButtonWidth = arrowWidth + 2 * NEXT_ITEM_ARROW_BUFFER; +int rightButtonX = portX + portWidth - arrowButtonWidth - 1; +char buttonText[256]; +Color fillColor = lightGrayIndex(); +labelColor = blackIndex(); +hvGfxNextItemButton(hvg, rightButtonX + NEXT_ITEM_ARROW_BUFFER, y, arrowWidth, arrowWidth, labelColor, fillColor, TRUE); +hvGfxNextItemButton(hvg, portX + NEXT_ITEM_ARROW_BUFFER, y, arrowWidth, arrowWidth, labelColor, fillColor, FALSE); +safef(buttonText, ArraySize(buttonText), "hgt.prevItem=%s", track->track); +mapBoxReinvoke(hvg, portX, y + 1, arrowButtonWidth, insideHeight, NULL, + NULL, 0, 0, (revCmplDisp ? "Next item" : "Prev item"), buttonText); +mapBoxToggleVis(hvg, portX + arrowButtonWidth, y + 1, portWidth - (2 * arrowButtonWidth), + insideHeight, (theImgBox ? track : parentTrack)); +safef(buttonText, ArraySize(buttonText), "hgt.nextItem=%s", track->track); +mapBoxReinvoke(hvg, portX + portWidth - arrowButtonWidth, y + 1, arrowButtonWidth, insideHeight, NULL, + NULL, 0, 0, (revCmplDisp ? "Prev item" : "Next item"), buttonText); +} + +static int doCenterLabels(struct track *track, struct track *parentTrack, + struct hvGfx *hvg, MgFont *font, int y) +/* Draw center labels. Return y coord */ +{ +if (track->limitedVis != tvHide) + { + if (isCenterLabelIncluded(track)) + { + int trackPastTabX = (withLeftLabels ? trackTabWidth : 0); + int trackPastTabWidth = tl.picWidth - trackPastTabX; + int fontHeight = mgFontLineHeight(font); + int insideHeight = fontHeight-1; + boolean toggleDone = FALSE; + char *label = track->longLabel; + if (isCenterLabelConditional(track)) + label = track->tdb->parent->longLabel; + Color labelColor = (track->labelColor ? + track->labelColor : track->ixColor); + hvGfxTextCentered(hvg, insideX, y+1, insideWidth, insideHeight, + labelColor, font, label); + if (track->nextItemButtonable && track->nextPrevItem && !tdbIsComposite(track->tdb)) + { + if (withNextItemArrows || trackDbSettingOn(track->tdb, "nextItemButton")) + { + doLabelNextItemButtons(track, parentTrack, hvg, font, y, trackPastTabX, + trackPastTabWidth, fontHeight, insideHeight, labelColor); + toggleDone = TRUE; + } + } + if (!toggleDone) + mapBoxToggleVis(hvg, trackPastTabX, y+1,trackPastTabWidth, insideHeight, + (theImgBox ? track : parentTrack)); + y += fontHeight; + } + y += track->totalHeight(track, track->limitedVis); + } +return y; +} + +static int doDrawItems(struct track *track, struct hvGfx *hvg, MgFont *font, + int y, long *lastTime) +/* Draw track items. Return y coord */ +{ +int fontHeight = mgFontLineHeight(font); +int pixWidth = tl.picWidth; +if (isCenterLabelIncluded(track)) + y += fontHeight; +if (track->limitedVis == tvPack) + { + hvGfxSetClip(hvg, gfxBorder+trackTabWidth+1, y, + pixWidth-2*gfxBorder-trackTabWidth-1, track->height); + } +else + hvGfxSetClip(hvg, insideX, y, insideWidth, track->height); +track->drawItems(track, winStart, winEnd, hvg, insideX, y, insideWidth, + font, track->ixColor, track->limitedVis); +if (measureTiming && lastTime) + { + long thisTime = clock1000(); + track->drawTime = thisTime - *lastTime; + *lastTime = thisTime; + } +hvGfxUnclip(hvg); +y += track->totalHeight(track, track->limitedVis); +return y; +} + +static int doMapItems(struct track *track, struct hvGfx *hvg, int fontHeight, int y) +/* Draw map boxes around track items */ +{ +char *type = track->tdb->type; +int newy; +int trackPastTabX = (withLeftLabels ? trackTabWidth : 0); +int trackPastTabWidth = tl.picWidth - trackPastTabX; +int start = 1; +struct slList *item; +boolean isWig = (sameString("wig", type) || startsWith("wig ", type) || + startsWith("bedGraph", type)); + +if (isCenterLabelIncluded(track)) + y += fontHeight; +if (track->mapsSelf) + { + return y+track->height; + } +if (track->subType == lfSubSample && track->items == NULL) + y += track->lineHeight; + +/* override doMapItems for hapmapLd track */ +/* does not scale with subtracks right now, so this is commented out until it can be fixed +if (startsWith("hapmapLd",track->table)) + { + y += round((double)(scaleForPixels(insideWidth)*insideWidth/2)); + return y; + } +*/ +for (item = track->items; item != NULL; item = item->next) + { + int height = track->itemHeight(track, item); + + /*wiggle tracks don't always increment height (y-value) here*/ + if( track->subType == lfSubSample ) + { + newy = y; + if( !start && item->next != NULL ) + { + newy += sampleUpdateY( track->itemName(track, item), + track->itemName(track, item->next), + height ); + } + else if( item->next != NULL || start ) + newy += height; + start = 0; + y = newy; + } + else + { + if (track->mapItem == NULL) + track->mapItem = genericMapItem; + if (!track->mapsSelf) + { + track->mapItem(track, hvg, item, track->itemName(track, item), + track->mapItemName(track, item), + track->itemStart(track, item), + track->itemEnd(track, item), trackPastTabX, + y, trackPastTabWidth,height); + } + y += height; + } + } +/* Wiggle track's ->height is actually one less than what it returns from + * totalHeight()... I think the least disruptive way to account for this + * (and not touch Ryan Weber's Sample stuff) is to just correct here if + * we see wiggle or bedGraph: */ +if (isWig) + y++; +return y; +} + +static int doOwnLeftLabels(struct track *track, struct hvGfx *hvg, + MgFont *font, int y) +/* Track draws it own, custom left labels */ +{ +int fontHeight = mgFontLineHeight(font); +int tHeight = trackPlusLabelHeight(track, fontHeight); +Color labelColor = (track->labelColor ? track->labelColor : track->ixColor); +hvGfxSetClip(hvg, leftLabelX, y, leftLabelWidth, tHeight); +track->drawLeftLabels(track, winStart, winEnd, + hvg, leftLabelX, y, leftLabelWidth, tHeight, + isCenterLabelIncluded(track), font, labelColor, + track->limitedVis); +hvGfxUnclip(hvg); +y += tHeight; +return y; +} + +// defined below: +static int getMaxWindowToDraw(struct trackDb *tdb); + +int doTrackMap(struct track *track, struct hvGfx *hvg, int y, int fontHeight, + int trackPastTabX, int trackPastTabWidth) +/* Write out the map for this track. Return the new offset. */ +{ +int mapHeight = 0; +switch (track->limitedVis) + { + case tvPack: + case tvSquish: + y += trackPlusLabelHeight(track, fontHeight); + break; + case tvFull: + if (!nextItemCompatible(track)) + { + if (trackIsCompositeWithSubtracks(track)) //TODO: Change when tracks->subtracks are always set for composite + { + if (isCenterLabelIncluded(track)) + y += fontHeight; + struct track *subtrack; + for (subtrack = track->subtracks; subtrack != NULL;subtrack = subtrack->next) + { + if (isSubtrackVisible(subtrack)) + { + if(subtrack->limitedVis == tvFull) + y = doMapItems(subtrack, hvg, fontHeight, y); + else + { + if (isCenterLabelIncluded(subtrack)) + y += fontHeight; + if(theImgBox && subtrack->limitedVis == tvDense) + mapBoxToggleVis(hvg, trackPastTabX, y, trackPastTabWidth, track->lineHeight, subtrack); + y += subtrack->totalHeight(subtrack, subtrack->limitedVis); + } + } + } + } + else + y = doMapItems(track, hvg, fontHeight, y); + } + else + y += trackPlusLabelHeight(track, fontHeight); + break; + case tvDense: + if (isCenterLabelIncluded(track)) + y += fontHeight; + if (tdbIsComposite(track->tdb)) + mapHeight = track->height; + else + mapHeight = track->lineHeight; + int maxWinToDraw = getMaxWindowToDraw(track->tdb); + if (maxWinToDraw <= 1 || (winEnd - winStart) <= maxWinToDraw) + mapBoxToggleVis(hvg, trackPastTabX, y, trackPastTabWidth, mapHeight, track); + y += mapHeight; + break; + case tvHide: + default: + break; /* Do nothing; */ + } +return y; +} + +int computeScaleBar(int numBases, char scaleText[], int scaleTextSize) +/* Do some scalebar calculations and return the number of bases the scalebar will span. */ +{ +char *baseWord = "bases"; +int scaleBases = 0; +int scaleBasesTextNum = 0; +int numFigs = (int)log10(numBases); +int frontNum = (int)(numBases/pow(10,numFigs)); +if (frontNum == 1) + { + numFigs--; + scaleBases = 5 * pow(10, numFigs); + scaleBasesTextNum = 5 * pow(10, numFigs % 3); + } +else if ((frontNum > 1) && (frontNum <= 4)) + { + scaleBases = pow(10, numFigs); + scaleBasesTextNum = pow(10, numFigs % 3); + } +else if (frontNum > 4) + { + scaleBases = 2 * pow(10, numFigs); + scaleBasesTextNum = 2 * pow(10, numFigs % 3); + } +if ((numFigs >= 3) && (numFigs < 6)) + baseWord = "kb"; +else if ((numFigs >= 6) && (numFigs < 9)) + baseWord = "Mb"; +safef(scaleText, scaleTextSize, "%d %s", scaleBasesTextNum, baseWord); +return scaleBases; +} + +enum trackVisibility limitedVisFromComposite(struct track *subtrack) +/* returns the subtrack visibility which may be limited by composite with multi-view dropdowns. */ +{ +#ifdef SUBTRACKS_HAVE_VIS +if (tdbIsCompositeChild(subtrack->tdb)) + { + if (fourStateVisible(subtrackFourStateChecked(subtrack->tdb,cart))) // Don't need all 4 states here. Visible=checked&&enabled + { + char *var = cartOptionalString(cart, subtrack->track); + if (var) + { + subtrack->visibility = hTvFromString(var); + + if (subtrack->limitedVisSet) + subtrack->limitedVis = tvMin(subtrack->visibility,subtrack->limitedVis); + else + { + if (subtrack->visibility != tvHide && slCount(subtrack->items) == 0) + subtrack->loadItems(subtrack); + + limitVisibility(subtrack); + } + return hTvFromString(var); + } + } + else + return tvHide; + } +#endif///def SUBTRACKS_HAVE_VIS + +enum trackVisibility vis = subtrack->limitedVis == tvHide ? + subtrack->visibility : + tvMin(subtrack->visibility,subtrack->limitedVis); +struct trackDb *tdb = subtrack->tdb; +if(tdbIsCompositeChild(tdb)) + { + struct trackDb *parentTdb = tdbGetComposite(tdb); + assert(parentTdb != NULL); + + char *viewName = NULL; + if (subgroupFind(tdb,"view",&viewName)) + { + int len = strlen(parentTdb->track) + strlen(viewName) + 10; + + // Create the view dropdown var name. This needs to have the view name surrounded by dots + // in the middle for the javascript to work. + char ddName[len]; + safef(ddName,len,"%s.%s.vis", parentTdb->track,viewName); + char * fromParent = cartOptionalString(cart, ddName); + if(fromParent) + vis = tvMin(vis,hTvFromString(fromParent)); + else + vis = tvMin(vis,visCompositeViewDefault(parentTdb,viewName)); + subgroupFree(&viewName); + } + } +return vis; +} + +static int makeRulerZoomBoxes(struct hvGfx *hvg, struct cart *cart, int winStart,int winEnd, + int insideWidth,int seqBaseCount,int rulerClickY,int rulerClickHeight) +/* Make hit boxes that will zoom program around ruler. */ +{ +int boxes = 30; +int winWidth = winEnd - winStart; +int newWinWidth = winWidth; +int i, ws, we = 0, ps, pe = 0; +int mid, ns, ne; +double wScale = (double)winWidth/boxes; +double pScale = (double)insideWidth/boxes; +char message[32]; +char *zoomType = cartCgiUsualString(cart, RULER_BASE_ZOOM_VAR, ZOOM_3X); + +safef(message, sizeof(message), "%s zoom", zoomType); +if (sameString(zoomType, ZOOM_1PT5X)) + newWinWidth = winWidth/1.5; +else if (sameString(zoomType, ZOOM_3X)) + newWinWidth = winWidth/3; +else if (sameString(zoomType, ZOOM_10X)) + newWinWidth = winWidth/10; +else if (sameString(zoomType, ZOOM_BASE)) + newWinWidth = insideWidth/tl.mWidth; +else + errAbort("invalid zoom type %s", zoomType); + +if (newWinWidth < 1) + newWinWidth = 1; + +for (i=1; i<=boxes; ++i) + { + ps = pe; + ws = we; + pe = round(pScale*i); + we = round(wScale*i); + mid = (ws + we)/2 + winStart; + ns = mid-newWinWidth/2; + ne = ns + newWinWidth; + if (ns < 0) + { + ns = 0; + ne -= ns; + } + if (ne > seqBaseCount) + { + ns -= (ne - seqBaseCount); + ne = seqBaseCount; + } + if(!dragZooming) + { + mapBoxJumpTo(hvg, ps+insideX,rulerClickY,pe-ps,rulerClickHeight, + chromName, ns, ne, message); + } + } +return newWinWidth; +} + +static int doDrawRuler(struct hvGfx *hvg,int *newWinWidth,int *rulerClickHeight, + int rulerHeight, int yAfterRuler, int yAfterBases, MgFont *font, + int fontHeight,boolean rulerCds) +/* draws the ruler. */ +{ +int scaleBarPad = 2; +int scaleBarHeight = fontHeight; +int scaleBarTotalHeight = fontHeight + 2 * scaleBarPad; +int titleHeight = fontHeight; +int baseHeight = fontHeight; +//int yAfterBases = yAfterRuler; +int showPosHeight = fontHeight; +int codonHeight = fontHeight; +struct dnaSeq *seq = NULL; +int rulerClickY = 0; +*rulerClickHeight = rulerHeight; + +int y = rulerClickY; +hvGfxSetClip(hvg, insideX, y, insideWidth, yAfterRuler-y+1); +int relNumOff = winStart; + +if (baseTitle) + { + hvGfxTextCentered(hvg, insideX, y, insideWidth, titleHeight,MG_BLACK, font, baseTitle); + *rulerClickHeight += titleHeight; + y += titleHeight; + } +if (baseShowPos||baseShowAsm) + { + char txt[256]; + char numBuf[SMALLBUF]; + char *freezeName = NULL; + freezeName = hFreezeFromDb(database); + sprintLongWithCommas(numBuf, winEnd-winStart); + if(freezeName == NULL) + freezeName = "Unknown"; + if (baseShowPos&&baseShowAsm) + safef(txt,sizeof(txt),"%s %s %s (%s bp)",organism, + freezeName, addCommasToPos(database, position), numBuf); + else if (baseShowPos) + safef(txt,sizeof(txt),"%s (%s bp)",addCommasToPos(database, position),numBuf); + else + safef(txt,sizeof(txt),"%s %s",organism,freezeName); + hvGfxTextCentered(hvg, insideX, y, insideWidth, showPosHeight,MG_BLACK, font, txt); + *rulerClickHeight += showPosHeight; + freez(&freezeName); + y += showPosHeight; + } +if (baseShowScaleBar) + { + char scaleText[32]; + int numBases = winEnd-winStart; + int scaleBases = computeScaleBar(numBases, scaleText, sizeof(scaleText)); + int scalePixels = (int)((double)insideWidth*scaleBases/numBases); + int scaleBarX = insideX + (int)(((double)insideWidth-scalePixels)/2); + int scaleBarEndX = scaleBarX + scalePixels; + int scaleBarY = y + 0.5 * scaleBarTotalHeight; + *rulerClickHeight += scaleBarTotalHeight; + hvGfxTextRight(hvg, insideX, y + scaleBarPad, + (scaleBarX-2)-insideX, scaleBarHeight, MG_BLACK, font, scaleText); + hvGfxLine(hvg, scaleBarX, scaleBarY, scaleBarEndX, scaleBarY, MG_BLACK); + hvGfxLine(hvg, scaleBarX, y+scaleBarPad, scaleBarX, + y+scaleBarTotalHeight-scaleBarPad, MG_BLACK); + hvGfxLine(hvg, scaleBarEndX, y+scaleBarPad, scaleBarEndX, + y+scaleBarTotalHeight-scaleBarPad, MG_BLACK); + y += scaleBarTotalHeight; + } +if (baseShowRuler) + { + hvGfxDrawRulerBumpText(hvg, insideX, y, rulerHeight, insideWidth, MG_BLACK, + font, relNumOff, winBaseCount, 0, 1); + } +*newWinWidth = makeRulerZoomBoxes(hvg, cart,winStart,winEnd,insideWidth,seqBaseCount,rulerClickY,*rulerClickHeight); + +if (zoomedToBaseLevel || rulerCds) + { + Color baseColor = MG_BLACK; + int start, end, chromSize; + struct dnaSeq *extraSeq; + /* extraSeq has extra leading & trailing bases + * for translation in to amino acids */ + boolean complementRulerBases = + cartUsualBooleanDb(cart, database, COMPLEMENT_BASES_VAR, FALSE); + // gray bases if not matching the direction of display + if (complementRulerBases != revCmplDisp) + baseColor = MG_GRAY; + + /* get sequence, with leading & trailing 3 bases + * used for amino acid translation */ + start = max(winStart - 3, 0); + chromSize = hChromSize(database, chromName); + end = min(winEnd + 3, chromSize); + extraSeq = hDnaFromSeq(database, chromName, start, end, dnaUpper); + if (start != winStart - 3 || end != winEnd + 3) + { + /* at chromosome boundaries, pad with N's to assure + * leading & trailing 3 bases */ + char header[4] = "NNN", trailer[4] = "NNN"; + int size = winEnd - winStart + 6; + char *padded = (char *)needMem(size+1); + header[max(3 - winStart, 0)] = 0; + trailer[max(winEnd - chromSize + 3, 0)] = 0; + safef(padded, size+1, "%s%s%s", header, extraSeq->dna, trailer); + extraSeq = newDnaSeq(padded, strlen(padded), extraSeq->name); + } + + /* for drawing bases, must clip off leading and trailing 3 bases */ + seq = cloneDnaSeq(extraSeq); + seq = newDnaSeq(seq->dna+3, seq->size-6, seq->name); + + if (zoomedToBaseLevel) + drawBases(hvg, insideX, y+rulerHeight, insideWidth, baseHeight, + baseColor, font, complementRulerBases, seq); + + /* set up clickable area to toggle ruler visibility */ + { + char newRulerVis[100]; + safef(newRulerVis, 100, "%s=%s", RULER_TRACK_NAME, + rulerMode == tvFull ? + rulerMenu[tvDense] : + rulerMenu[tvFull]); + mapBoxReinvoke(hvg, insideX, y+rulerHeight, insideWidth,baseHeight, + NULL, NULL, 0, 0, "", newRulerVis); + } + if (rulerCds) + { + /* display codons */ + int frame; + int firstFrame = 0; + int mod; // for determining frame ordering on display + struct simpleFeature *sfList; + double scale = scaleForWindow(insideWidth, winStart, winEnd); + + /* WARNING: tricky code to assure that an amino acid + * stays in the same frame line on the browser during panning. + * There may be a simpler way... */ + if (complementRulerBases) + mod = (chromSize - winEnd) % 3; + else + mod = winStart % 3; + if (mod == 0) + firstFrame = 0; + else if (mod == 1) + firstFrame = 2; + else if (mod == 2) + firstFrame = 1; + + y = yAfterBases; + if (complementRulerBases) + reverseComplement(extraSeq->dna, extraSeq->size); + for (frame = 0; frame < 3; frame++, y += codonHeight) + { + /* reference frame to start of chromosome */ + int refFrame = (firstFrame + frame) % 3; + + /* create list of codons in the specified coding frame */ + sfList = baseColorCodonsFromDna(refFrame, winStart, winEnd, + extraSeq, complementRulerBases); + /* draw the codons in the list, with alternating colors */ + baseColorDrawRulerCodons(hvg, sfList, scale, insideX, y, + codonHeight, font, winStart, MAXPIXELS, + zoomedToCodonLevel); + } + } + } +hvGfxUnclip(hvg); +return y; +} + +static void rAddToTrackHash(struct hash *trackHash, struct track *trackList) +/* Add list and any children of list to hash. */ +{ +struct track *track; +for (track = trackList; track != NULL; track = track->next) + { + hashAddUnique(trackHash, track->track, track); + rAddToTrackHash(trackHash, track->subtracks); + } +} + +static void makeGlobalTrackHash(struct track *trackList) +/* Start a global track hash. */ +{ +trackHash = newHash(8); +rAddToTrackHash(trackHash, trackList); +} + + +void makeActiveImage(struct track *trackList, char *psOutput) +/* Make image and image map. */ +{ +struct track *track; +MgFont *font = tl.font; +struct hvGfx *hvg; +struct tempName gifTn; +char *mapName = "map"; +int fontHeight = mgFontLineHeight(font); +int trackPastTabX = (withLeftLabels ? trackTabWidth : 0); +int trackTabX = gfxBorder; +int trackPastTabWidth = tl.picWidth - trackPastTabX; +int pixWidth, pixHeight; +int y=0; +int titleHeight = fontHeight; +int scaleBarPad = 2; +int scaleBarHeight = fontHeight; +int scaleBarTotalHeight = fontHeight + 2 * scaleBarPad; +int showPosHeight = fontHeight; +int rulerHeight = fontHeight; +int baseHeight = fontHeight; +int basePositionHeight = rulerHeight; +int codonHeight = fontHeight; +int rulerTranslationHeight = codonHeight * 3; // 3 frames +int yAfterRuler = gfxBorder; +int yAfterBases = yAfterRuler; // differs if base-level translation shown +boolean rulerCds = zoomedToCdsColorLevel; +int rulerClickHeight = 0; +int newWinWidth = 0; + +/* Figure out dimensions and allocate drawing space. */ +pixWidth = tl.picWidth; + +leftLabelX = gfxBorder; +leftLabelWidth = insideX - gfxBorder*3; + +struct image *theOneImg = NULL; // No need to be global, only the map needs to be global +struct image *theSideImg = NULL; // Because dragScroll drags off end of image, the side label gets seen. Therefore we need 2 images!! +struct hvGfx *hvgSide = NULL; // Strategy an extra pointer to a side image that can be built if needed +//struct imgTrack *curImgTrack = NULL; // Make this global for now to avoid huge rewrite +struct imgSlice *curSlice = NULL; // No need to be global, only the map needs to be global +struct mapSet *curMap = NULL; // Make this global for now to avoid huge rewrite +// Set up imgBox dimensions +int sliceWidth[stMaxSliceTypes]; // Just being explicit +int sliceOffsetX[stMaxSliceTypes]; +int sliceHeight = 0; +int sliceOffsetY = 0; +char *rulerTtl = NULL; +if(theImgBox) +// theImgBox is a global for now to avoid huge rewrite of hgTracks. It is started +// prior to this in doTrackForm() + { + rulerTtl = (dragZooming?"drag select or click to zoom":"click to zoom 3x"); + hPrintf("\n", database); + hPrintf("\n", chromName); + hPrintf("\n", winStart); + hPrintf("\n", winEnd); + hPrintf("\n", tl.picWidth); + #ifdef IMAGEv2_DRAG_SCROLL + // If a portal was established, then set the global dimensions to the entire image size + if(imgBoxPortalDimensions(theImgBox,&winStart,&winEnd,&(tl.picWidth),NULL,NULL,NULL,NULL,NULL)) + { + pixWidth = tl.picWidth; + winBaseCount = winEnd - winStart; + insideWidth = tl.picWidth-gfxBorder-insideX; + } + #endif//def IMAGEv2_DRAG_SCROLL + memset((char *)sliceWidth, 0,sizeof(sliceWidth)); + memset((char *)sliceOffsetX,0,sizeof(sliceOffsetX)); + if (withLeftLabels) + { + sliceWidth[stButton] = trackTabWidth + 1; + sliceWidth[stSide] = leftLabelWidth - sliceWidth[stButton] + 2; + sliceOffsetX[stSide] = (revCmplDisp? (tl.picWidth - sliceWidth[stSide] - sliceWidth[stButton]) : sliceWidth[stButton]); + sliceOffsetX[stButton] = (revCmplDisp? (tl.picWidth - sliceWidth[stButton]) : 0); + } + sliceOffsetX[stData] = (revCmplDisp?0:sliceWidth[stSide] + sliceWidth[stButton]); + sliceWidth[stData] = tl.picWidth - (sliceWidth[stSide] + sliceWidth[stButton]); + } +struct flatTracks *flatTracks = NULL; +struct flatTracks *flatTrack = NULL; + +if (rulerMode != tvFull) + { + rulerCds = FALSE; + } + +/* Figure out height of each visible track. */ +pixHeight = gfxBorder; +if (rulerMode != tvHide) + { + if (!baseShowRuler && !baseTitle && !baseShowPos && !baseShowAsm && !baseShowScaleBar && !zoomedToBaseLevel && !rulerCds) + { + warn("Can't turn everything off in base position track. Turning ruler back on"); + baseShowRuler = TRUE; + cartSetBoolean(cart, BASE_SHOWRULER, TRUE); + } + + if (baseTitle) + basePositionHeight += titleHeight; + + if (baseShowPos||baseShowAsm) + basePositionHeight += showPosHeight; + + if (baseShowScaleBar) + basePositionHeight += scaleBarTotalHeight; + + if (!baseShowRuler) + { + basePositionHeight -= rulerHeight; + rulerHeight = 0; + } + + if (zoomedToBaseLevel) + basePositionHeight += baseHeight; + + yAfterRuler += basePositionHeight; + yAfterBases = yAfterRuler; + pixHeight += basePositionHeight; + if (rulerCds) + { + yAfterRuler += rulerTranslationHeight; + pixHeight += rulerTranslationHeight; + } + } + +boolean safeHeight = TRUE; +/* firefox on Linux worked almost up to 34,000 at the default 620 width */ +#define maxSafeHeight 32000 +/* Hash tracks/subtracks, limit visibility and calculate total image height: */ +for (track = trackList; track != NULL; track = track->next) + { + limitVisibility(track); + if (!safeHeight) + { + track->limitedVis = tvHide; + track->limitedVisSet = TRUE; + continue; + } +#ifndef SUBTRACKS_HAVE_VIS + if (track->limitedVis != tvHide) +#endif///ndef SUBTRACKS_HAVE_VIS + { + if (tdbIsComposite(track->tdb)) + { + struct track *subtrack; + for (subtrack = track->subtracks; subtrack != NULL; + subtrack = subtrack->next) + { + if (!isSubtrackVisible(subtrack)) + continue; + + // If the composite track has "view" based drop downs, set visibility based upon those + enum trackVisibility vis = limitedVisFromComposite(subtrack); + if(subtrack->visibility != vis) + { + subtrack->visibility = vis; + if (subtrack->limitedVisSet) + { + subtrack->limitedVis = tvMin(vis, subtrack->limitedVis); + } + else + { + subtrack->limitedVis = tvMin(vis,subtrack->visibility); + subtrack->limitedVisSet = (subtrack->limitedVis != tvHide && subtrack->visibility != subtrack->limitedVis); + } + } + if (!subtrack->limitedVisSet && track->limitedVisSet) + { + subtrack->visibility = track->visibility; + subtrack->limitedVis = track->limitedVis; + subtrack->limitedVisSet = track->limitedVisSet; + } + + #ifdef SUBTRACKS_HAVE_VIS + if (subtrack->limitedVis != tvHide) + #endif///def SUBTRACKS_HAVE_VIS + { + subtrack->hasUi = track->hasUi; + flatTracksAdd(&flatTracks,subtrack,cart); + } + } + } + else + #ifdef SUBTRACKS_HAVE_VIS + if (track->limitedVis != tvHide) + #endif///def SUBTRACKS_HAVE_VIS + flatTracksAdd(&flatTracks,track,cart); + if (maxSafeHeight < (pixHeight+trackPlusLabelHeight(track,fontHeight))) + { + char numBuf[SMALLBUF]; + sprintLongWithCommas(numBuf, maxSafeHeight); + printf("warning: image is over %s pixels high at " + "track '%s',
remaining tracks set to hide " + "for this view.
\n", numBuf, track->tdb->shortLabel); + safeHeight = FALSE; + track->limitedVis = tvHide; + track->limitedVisSet = TRUE; + } + } + } +flatTracksSort(&flatTracks); // Now we should have a perfectly good flat track list! +struct track *prevTrack = NULL; +for (flatTrack = flatTracks,prevTrack=NULL; flatTrack != NULL; flatTrack = flatTrack->next) + { + track = flatTrack->track; + if (maxSafeHeight < (pixHeight+trackPlusLabelHeight(track,fontHeight))) + { + char numBuf[SMALLBUF]; + sprintLongWithCommas(numBuf, maxSafeHeight); + printf("warning: image is over %s pixels high at " + "track '%s',
remaining tracks set to hide " + "for this view.
\n", numBuf, track->tdb->shortLabel); + safeHeight = FALSE; + track->limitedVis = tvHide; + track->limitedVisSet = TRUE; + } + if (track->limitedVis != tvHide) + { + track->prevTrack = prevTrack; // Important for keeping track of conditional center labels! + pixHeight += trackPlusLabelHeight(track, fontHeight); + prevTrack = track; + } + } + +imagePixelHeight = pixHeight; +if (psOutput) + { + hvg = hvGfxOpenPostScript(pixWidth, pixHeight, psOutput); + hvgSide = hvg; // Always only one image + } +else + { + boolean transparentImage = FALSE; + if (theImgBox!=NULL) + transparentImage = TRUE; // transparent because BG (blue ruler lines) is separate image + +#ifdef USE_PNG + trashDirFile(&gifTn, "hgt", "hgt", ".png"); + hvg = hvGfxOpenPng(pixWidth, pixHeight, gifTn.forCgi, transparentImage); +#else //ifndef + trashDirFile(&gifTn, "hgt", "hgt", ".gif"); + hvg = hvGfxOpenGif(pixWidth, pixHeight, gifTn.forCgi, transparentImage); +#endif //ndef USE_PNG + + if(theImgBox) + { + // Adds one single image for all tracks (COULD: build the track by track images) + theOneImg = imgBoxImageAdd(theImgBox,gifTn.forHtml,NULL,pixWidth, pixHeight,FALSE); + theSideImg = theOneImg; // Unlkess this is overwritten below, there is a single image + } + hvgSide = hvg; // Unlkess this is overwritten below, there is a single image + + if (theImgBox && theImgBox->showPortal && withLeftLabels) + { + // TODO: It would be great to make the images smaller, but keeping both the same full size for now + struct tempName gifTnSide; + #ifdef USE_PNG + trashDirFile(&gifTnSide, "hgt", "side", ".png"); + hvgSide = hvGfxOpenPng(pixWidth, pixHeight, gifTnSide.forCgi, transparentImage); + #else //ifndef + trashDirFile(&gifTnSide, "hgt", "side", ".gif"); + hvgSide = hvGfxOpenGif(pixWidth, pixHeight, gifTnSide.forCgi, transparentImage); + #endif //ndef USE_PNG + + // Also add the side image + theSideImg = imgBoxImageAdd(theImgBox,gifTnSide.forHtml,NULL,pixWidth, pixHeight,FALSE); + hvgSide->rc = revCmplDisp; + initColors(hvgSide); + } + } +hvg->rc = revCmplDisp; +initColors(hvg); + +/* Start up client side map. */ +hPrintf("\n", mapName); + +/* Find colors to draw in. */ +findTrackColors(hvg, trackList); + +// Good to go ahead and add all imgTracks regardless of buttons, left label, centerLabel, etc. +if(theImgBox) + { + if (rulerMode != tvHide) + { + curImgTrack = imgBoxTrackFindOrAdd(theImgBox,NULL,RULER_TRACK_NAME,rulerMode,FALSE,IMG_FIXEDPOS); // No tdb, no centerlabel, not reorderable + } + + for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) + { + track = flatTrack->track; + if (track->limitedVis != tvHide) + { + #ifdef SUBTRACKS_HAVE_VIS + if(track->labelColor == track->ixColor && track->ixColor == 0) + track->ixColor = hvGfxFindRgb(hvg, &track->color); + #endif//def SUBTRACKS_HAVE_VIS + int order = flatTrack->order; + curImgTrack = imgBoxTrackFindOrAdd(theImgBox,track->tdb,NULL,track->limitedVis,isCenterLabelIncluded(track),order); + } + } + } + + +/* Draw mini-buttons. */ +if (withLeftLabels && psOutput == NULL) + { + int butOff; + boolean grayButtonGroup = FALSE; + struct group *lastGroup = NULL; + y = gfxBorder; + if (rulerMode != tvHide) + { + /* draw button for Base Position pseudo-track */ + int height = basePositionHeight; + if (rulerCds) + height += rulerTranslationHeight; + if(theImgBox) + { + // Mini-buttons (side label slice) for ruler + sliceHeight = height + 1; + sliceOffsetY = 0; + curImgTrack = imgBoxTrackFind(theImgBox,NULL,RULER_TRACK_NAME); + curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stButton,NULL,NULL,sliceWidth[stButton],sliceHeight,sliceOffsetX[stButton],sliceOffsetY); // flatTracksButton is all html, no jpg + } + drawGrayButtonBox(hvgSide, trackTabX, y, trackTabWidth, height, TRUE); + mapBoxTrackUi(hvgSide, trackTabX, y, trackTabWidth, height, + RULER_TRACK_NAME, RULER_TRACK_LABEL, "ruler"); + y += height + 1; + } + + for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) + { + track = flatTrack->track; + int h, yStart = y, yEnd; + if (track->limitedVis != tvHide) + { + y += trackPlusLabelHeight(track, fontHeight); + yEnd = y; + h = yEnd - yStart - 1; + + /* alternate button colors for track groups*/ + if (track->group != lastGroup) + grayButtonGroup = !grayButtonGroup; + lastGroup = track->group; + if (grayButtonGroup) + drawGrayButtonBox(hvgSide, trackTabX, yStart, trackTabWidth, + h, track->hasUi); + else + drawBlueButtonBox(hvgSide, trackTabX, yStart, trackTabWidth, + h, track->hasUi); + if(theImgBox) + { + // Mini-buttons (side label slice) for tracks + sliceHeight = yEnd - yStart; + sliceOffsetY = yStart - 1; + curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); + curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stButton,NULL,NULL,sliceWidth[stButton],sliceHeight,sliceOffsetX[stButton],sliceOffsetY); // flatTracksButton is all html, no jpg + } + if (track->hasUi) + { + if(tdbIsCompositeChild(track->tdb)) + { + struct trackDb *parent = tdbGetComposite(track->tdb); + mapBoxTrackUi(hvgSide, trackTabX, yStart, trackTabWidth, (yEnd - yStart - 1), + parent->track, parent->shortLabel, track->track); + } + else + mapBoxTrackUi(hvgSide, trackTabX, yStart, trackTabWidth, h, track->track, track->shortLabel, track->track); + } + } + } + butOff = trackTabX + trackTabWidth; + leftLabelX += butOff; + leftLabelWidth -= butOff; + } + +if (withLeftLabels) + { + Color lightRed = hvGfxFindColorIx(hvgSide, 255, 180, 180); + + hvGfxBox(hvgSide, leftLabelX + leftLabelWidth, 0, + gfxBorder, pixHeight, lightRed); + y = gfxBorder; + if (rulerMode != tvHide) + { + if(theImgBox) + { + // side label slice for ruler + sliceHeight = basePositionHeight + (rulerCds ? rulerTranslationHeight : 0) + 1; + sliceOffsetY = 0; + curImgTrack = imgBoxTrackFind(theImgBox,NULL,RULER_TRACK_NAME); + curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL,sliceWidth[stSide],sliceHeight,sliceOffsetX[stSide],sliceOffsetY); + curMap = sliceMapFindOrStart(curSlice,RULER_TRACK_NAME,NULL); // No common linkRoot + } + if (baseTitle) + { + hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, titleHeight, + MG_BLACK, font, WIN_TITLE_LABEL); + y += titleHeight; + } + if (baseShowPos||baseShowAsm) + { + hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, showPosHeight, + MG_BLACK, font, WIN_POS_LABEL); + y += showPosHeight; + } + if (baseShowScaleBar) + { + y += scaleBarPad; + hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, scaleBarHeight, + MG_BLACK, font, SCALE_BAR_LABEL); + y += scaleBarHeight + scaleBarPad; + } + if (baseShowRuler) + { + char rulerLabel[SMALLBUF]; + char *shortChromName = cloneString(chromName); + safef(rulerLabel,ArraySize(rulerLabel),":%s",shortChromName); + int labelWidth = mgFontStringWidth(font,rulerLabel); + while ((labelWidth > 0) && (labelWidth > leftLabelWidth)) + { + int len = strlen(shortChromName); + shortChromName[len-1] = 0; + safef(rulerLabel,ArraySize(rulerLabel),":%s",shortChromName); + labelWidth = mgFontStringWidth(font,rulerLabel); + } + if (hvgSide->rc) + safef(rulerLabel,ArraySize(rulerLabel),":%s",shortChromName); + else + safef(rulerLabel,ArraySize(rulerLabel),"%s:",shortChromName); + hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, rulerHeight, + MG_BLACK, font, rulerLabel); + y += rulerHeight; + freeMem(shortChromName); + } + if (zoomedToBaseLevel || rulerCds) + { + /* disable complement toggle for HIV because HIV is single stranded RNA */ + if (!hIsGsidServer()) + drawComplementArrow(hvgSide,leftLabelX, y, + leftLabelWidth-1, baseHeight, font); + if (zoomedToBaseLevel) + y += baseHeight; + } + if (rulerCds) + y += rulerTranslationHeight; + } + for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) + { + track = flatTrack->track; + if (track->limitedVis == tvHide) + continue; + if(theImgBox) + { + // side label slice for tracks + sliceHeight = trackPlusLabelHeight(track, fontHeight); + sliceOffsetY = y; + curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); + curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL,sliceWidth[stSide],sliceHeight,sliceOffsetX[stSide],sliceOffsetY); + curMap = sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot + } + y = doLeftLabels(track, hvgSide, font, y); + } + } +else + { + leftLabelX = leftLabelWidth = 0; + } + +/* Draw guidelines. */ +if (withGuidelines) + { + //if(theImgBox) + // TODO: We should be making transparent data images and a separate background img for guidelines. + // This will allow the guidelines to dragscroll while the center labels are static. + // NOTE: The background image could easily be a reusable file, based upon zoom level and width. Height could propbaby easily be stretched. + // struct image *bgImg = imgBoxImageAdd(theImgBox,gifBg.forHtml, + // (char *)(dragZooming?"click or drag mouse in base position track to zoom in" : NULL), + // pixWidth, pixHeight,FALSE); + struct hvGfx *bgImg = hvg; // Default to the one image + if(theImgBox) + { + struct tempName gifBg; + #ifdef USE_PNG + trashDirFile(&gifBg, "hgt", "bg", ".png"); // TODO: We could have a few static files by (pixHeight*pixWidth) And I doubt pixHeight is needed! + bgImg = hvGfxOpenPng(pixWidth, pixHeight, gifBg.forCgi, TRUE); + #else //ifndef + trashDirFile(&gifBg, "hgt", "bg", ".gif"); + bgImg = hvGfxOpenGif(pixWidth, pixHeight, gifBg.forCgi, TRUE); + #endif //ndef USE_PNG + bgImg->rc = revCmplDisp; + imgBoxImageAdd(theImgBox,gifBg.forHtml,NULL,pixWidth, pixHeight,TRUE); // Adds BG image + } + int height = pixHeight - 2*gfxBorder; + int x; + Color lightBlue = hvGfxFindRgb(bgImg, &guidelineColor); + + hvGfxSetClip(bgImg, insideX, gfxBorder, insideWidth, height); + y = gfxBorder; + + for (x = insideX+guidelineSpacing-1; xnext) + { + track = flatTrack->track; + if (track->limitedVis == tvHide) + continue; + + if(theImgBox) + { + // center label slice of tracks Must always make, even if the centerLabel is empty + sliceHeight = fontHeight; + sliceOffsetY = y; + curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); + curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stCenter,theOneImg,NULL,sliceWidth[stData],sliceHeight,sliceOffsetX[stData],sliceOffsetY); + curMap = sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot + if (isCenterLabelConditional(track)) + imgTrackUpdateCenterLabelSeen(curImgTrack,isCenterLabelConditionallySeen(track)?clNowSeen:clNotSeen); + } + y = doCenterLabels(track, track, hvg, font, y); + } + hvGfxUnclip(hvg); + } + +/* Draw tracks. */ + { + long lastTime = 0; + y = yAfterRuler; + if (measureTiming) + lastTime = clock1000(); + for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) + { + track = flatTrack->track; + if (track->limitedVis == tvHide) + continue; + + int centerLabelHeight = (isCenterLabelIncluded(track) ? fontHeight : 0); + int yStart = y + centerLabelHeight; + int yEnd = y + trackPlusLabelHeight(track, fontHeight); + if(theImgBox) + { + // data slice of tracks + sliceOffsetY = yStart; + sliceHeight = yEnd - yStart - 1; + curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); + if(sliceHeight > 0) + { + curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stData,theOneImg,NULL,sliceWidth[stData],sliceHeight,sliceOffsetX[stData],sliceOffsetY); + curMap = sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot + } + } + y = doDrawItems(track, hvg, font, y, &lastTime); + + if (theImgBox && track->limitedVis == tvDense && tdbIsCompositeChild(track->tdb)) + mapBoxToggleVis(hvg, 0, yStart,tl.picWidth, sliceHeight,track); // Strange mabBoxToggleLogic handles reverse complement itself so x=0, width=tl.picWidth + + if(yEnd!=y) + warn("Slice height does not add up. Expecting %d != %d actual",yEnd - yStart - 1,y-yStart); + } + y++; + } +/* if a track can draw its left labels, now is the time since it + * knows what exactly happened during drawItems + */ +if (withLeftLabels) + { + y = yAfterRuler; + for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) + { + track = flatTrack->track; + if (track->limitedVis == tvHide) + continue; + if(theImgBox) + { + // side label slice of tracks + sliceHeight = trackPlusLabelHeight(track, fontHeight); + sliceOffsetY = y; + curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); + curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL,sliceWidth[stSide],sliceHeight,sliceOffsetX[stSide],sliceOffsetY); + curMap = sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot + } + + if (track->drawLeftLabels != NULL) + y = doOwnLeftLabels(track, hvgSide, font, y); + else + y += trackPlusLabelHeight(track, fontHeight); + } + } + + +/* Make map background. */ +y = yAfterRuler; +for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) + { + track = flatTrack->track; + if (track->limitedVis != tvHide) + { + if(theImgBox) + { + // Set imgTrack in case any map items will be set + sliceHeight = trackPlusLabelHeight(track, fontHeight); + sliceOffsetY = y; + curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); + } + y = doTrackMap(track, hvg, y, fontHeight, trackPastTabX, trackPastTabWidth); + } + } + +/* Finish map. */ +hPrintf("\n"); + +hPrintf("\n", dragZooming ? 1 : 0); +if(rulerClickHeight) + { + hPrintf("\n", rulerClickHeight); + } +if(newWinWidth) + { + hPrintf("\n", newWinWidth); + } + +/* Save out picture and tell html file about it. */ +if(hvgSide != hvg) + hvGfxClose(&hvgSide); +hvGfxClose(&hvg); +if(theImgBox) + { + imageBoxDraw(theImgBox); + #ifdef IMAGEv2_DRAG_SCROLL + // If a portal was established, then set the global dimensions back to the portal size + if(imgBoxPortalDimensions(theImgBox,NULL,NULL,NULL,NULL,&winStart,&winEnd,&(tl.picWidth),NULL)) + { + pixWidth = tl.picWidth; + winBaseCount = winEnd - winStart; + insideWidth = tl.picWidth-gfxBorder-insideX; + } + #endif//def IMAGEv2_DRAG_SCROLL + imgBoxFree(&theImgBox); + } +else + { + char *titleAttr = dragZooming ? "title='click or drag mouse in base position track to zoom in'" : ""; + hPrintf("
\n"); + } +flatTracksFree(&flatTracks); +} + +static void printEnsemblAnchor(char *database, char* archive, + char *chrName, int start, int end) +/* Print anchor to Ensembl display on same window. */ +{ +char *scientificName = hScientificName(database); +char *dir = ensOrgNameFromScientificName(scientificName); +struct dyString *ensUrl; +char *name; +int localStart, localEnd; + +name = chrName; + +if (sameWord(scientificName, "Takifugu rubripes")) + { + /* for Fugu, must give scaffold, not chr coordinates */ + /* Also, must give "chrom" as "scaffold_N", name below. */ + if (differentWord(chromName,"chrM") && + !hScaffoldPos(database, chromName, winStart, winEnd, + &name, &localStart, &localEnd)) + /* position doesn't appear on Ensembl browser. + * Ensembl doesn't show scaffolds < 2K */ + return; + } +else if (sameWord(scientificName, "Gasterosteus aculeatus")) + { + if (differentWord("chrM", chrName)) + { + char *fixupName = replaceChars(chrName, "chr", "group"); + name = fixupName; + } + } +else if (sameWord(scientificName, "Ciona intestinalis")) + { + if (stringIn("chr0", chrName)) + { + char *fixupName = replaceChars(chrName, "chr0", "chr"); + name = fixupName; + } + } +else if (sameWord(scientificName, "Saccharomyces cerevisiae")) + { + if (stringIn("2micron", chrName)) + { + char *fixupName = replaceChars(chrName, "2micron", "2-micron"); + name = fixupName; + } + } + +if (sameWord(chrName, "chrM")) + name = "chrMt"; +localStart = start; +localEnd = end + 1; // Ensembl base-1 display coordinates +ensUrl = ensContigViewUrl(database, dir, name, seqBaseCount, localStart, localEnd, archive); +hPrintf("", ensUrl->string); +/* NOTE: you can not freeMem(dir) because sometimes it is a literal + * constant */ +freeMem(scientificName); +dyStringFree(&ensUrl); +} + +void makeHgGenomeTrackVisible(struct track *track) +/* This turns on a track clicked from hgGenome, even if it was previously */ +/* hidden manually and there are cart vars to support that. */ +{ +struct hashEl *hels; +struct hashEl *hel; +char prefix[SMALLBUF]; +/* First check if the click was from hgGenome. If not, leave. */ +/* get the names of the tracks in the cart */ +safef(prefix, sizeof(prefix), "%s_", hggGraphPrefix); +hels = cartFindPrefix(cart, prefix); +/* loop through them and compare them to the track passed into this */ +/* function. */ +for (hel = hels; hel != NULL; hel = hel->next) + { + struct trackDb *subtrack; + char *subtrackName = hel->val; + /* check non-subtrack. */ + if (sameString(track->tdb->track, subtrackName)) + { + track->visibility = tvFull; + track->tdb->visibility = tvFull; + cartSetString(cart, track->tdb->track, "full"); + } + else if (track->tdb->subtracks != NULL) + { + struct slRef *tdbRef, *tdbRefList = trackDbListGetRefsToDescendants(track->tdb->subtracks); + for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next) + { + subtrack = tdbRef->val; + if (sameString(subtrack->track, subtrackName)) + { + char selName[SMALLBUF]; + track->visibility = tvFull; + cartSetString(cart, track->tdb->track, "full"); + track->tdb->visibility = tvFull; + subtrack->visibility = tvFull; + safef(selName, sizeof(selName), "%s_sel", subtrackName); + cartSetBoolean(cart, selName, TRUE); + } + } + slFreeList(&tdbRefList); + } + } +hashElFreeList(&hels); +} + +struct sqlConnection *remoteTrackConnection(struct track *tg) +/* Get a connection to remote database as specified in remoteSql settings... */ +{ +if (!tg->isRemoteSql) + { + internalErr(); + return NULL; + } +else + { + return sqlConnectRemote(tg->remoteSqlHost, tg->remoteSqlUser, tg->remoteSqlPassword, + tg->remoteSqlDatabase); + } +} + +void addTdbListToTrackList(struct trackDb *tdbList, char *trackNameFilter, + struct track **pTrackList) +/* Convert a list of trackDb's to tracks, and append these to trackList. */ +{ +struct trackDb *tdb, *next; +struct track *track; +TrackHandler handler; +tdbSortPrioritiesFromCart(cart, &tdbList); +for (tdb = tdbList; tdb != NULL; tdb = next) + { + next = tdb->next; + if(trackNameFilter != NULL && strcmp(trackNameFilter, tdb->track)) + // suppress loading & display of all tracks except for the one passed in via trackNameFilter + continue; + track = trackFromTrackDb(tdb); + track->hasUi = TRUE; + if (slCount(tdb->subtracks) != 0) + { + tdbSortPrioritiesFromCart(cart, &(tdb->subtracks)); + if (trackDbLocalSetting(tdb, "compositeTrack")) + makeCompositeTrack(track, tdb); + else if (trackDbLocalSetting(tdb, "container")) + makeContainerTrack(track, tdb); + } + else + { + handler = lookupTrackHandler(tdb->table); + if (handler != NULL) + handler(track); + } + if (cgiVarExists("hgGenomeClick")) + makeHgGenomeTrackVisible(track); + if (track->loadItems == NULL) + warn("No load handler for %s; possible missing trackDb `type' or `subTrack' attribute", tdb->track); + else if (track->drawItems == NULL) + warn("No draw handler for %s", tdb->track); + else + slAddHead(pTrackList, track); + } +} + +void loadFromTrackDb(struct track **pTrackList) +/* Load tracks from database, consulting handler list. */ +{ +char *trackNameFilter = cartOptionalString(cart, "hgt.trackNameFilter"); +struct trackDb *tdbList; +if(trackNameFilter == NULL) + tdbList = hTrackDb(database, chromName); +else + tdbList = hTrackDbForTrack(database, trackNameFilter); +addTdbListToTrackList(tdbList, trackNameFilter, pTrackList); +} + +static int getScoreFilter(char *trackName) +/* check for score filter configuration setting */ +{ +char optionScoreStr[256]; + +safef(optionScoreStr, sizeof(optionScoreStr), "%s.scoreFilter", trackName); +return cartUsualInt(cart, optionScoreStr, 0); +} + +void ctLoadSimpleBed(struct track *tg) +/* Load the items in one custom track - just move beds in + * window... */ +{ +struct customTrack *ct = tg->customPt; +struct bed *bed, *nextBed, *list = NULL; +int scoreFilter = getScoreFilter(ct->tdb->track); + +if (ct->dbTrack) + { + int fieldCount = ct->fieldCount; + int rowOffset; + char **row; + struct sqlConnection *conn = + hAllocConn(CUSTOM_TRASH); + struct sqlResult *sr = NULL; + + sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd, + NULL, &rowOffset); + while ((row = sqlNextRow(sr)) != NULL) + { + bed = bedLoadN(row+rowOffset, fieldCount); + if (scoreFilter && bed->score < scoreFilter) + continue; + slAddHead(&list, bed); + } + hFreeConn(&conn); + } +else + { + for (bed = ct->bedList; bed != NULL; bed = nextBed) + { + nextBed = bed->next; + if (bed->chromStart < winEnd && bed->chromEnd > winStart + && sameString(chromName, bed->chrom)) + { + if (scoreFilter && bed->score < scoreFilter) + continue; + slAddHead(&list, bed); + } + } + } +slSort(&list, bedCmp); +tg->items = list; +} + +void ctLoadBed9(struct track *tg) +/* Convert bed info in window to linked feature. */ +{ +struct customTrack *ct = tg->customPt; +struct bed *bed; +struct linkedFeatures *lfList = NULL, *lf; +boolean useItemRgb = FALSE; +int scoreFilter = getScoreFilter(ct->tdb->track); + +useItemRgb = bedItemRgb(ct->tdb); + +if (ct->dbTrack) + { + int rowOffset; + char **row; + struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); + struct sqlResult *sr = NULL; + + sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd, + NULL, &rowOffset); + while ((row = sqlNextRow(sr)) != NULL) + { + bed = bedLoadN(row+rowOffset, 9); + if (scoreFilter && bed->score < scoreFilter) + continue; + bed8To12(bed); + lf = lfFromBed(bed); + if (useItemRgb) + { + lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */ + lf->filterColor=bed->itemRgb; + } + slAddHead(&lfList, lf); + } + hFreeConn(&conn); + } +else + { + for (bed = ct->bedList; bed != NULL; bed = bed->next) + { + if (scoreFilter && bed->score < scoreFilter) + continue; + if (bed->chromStart < winEnd && bed->chromEnd > winStart + && sameString(chromName, bed->chrom)) + { + bed8To12(bed); + lf = lfFromBed(bed); + if (useItemRgb) + { + lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */ + lf->filterColor=bed->itemRgb; + } + slAddHead(&lfList, lf); + } + } + } +slReverse(&lfList); +slSort(&lfList, linkedFeaturesCmp); +tg->items = lfList; +} + + +void ctLoadBed8(struct track *tg) +/* Convert bed info in window to linked feature. */ +{ +struct customTrack *ct = tg->customPt; +struct bed *bed; +struct linkedFeatures *lfList = NULL, *lf; +int scoreFilter = getScoreFilter(ct->tdb->track); + +if (ct->dbTrack) + { + int fieldCount = ct->fieldCount; + int rowOffset; + char **row; + struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); + struct sqlResult *sr = NULL; + + sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd, + NULL, &rowOffset); + while ((row = sqlNextRow(sr)) != NULL) + { + bed = bedLoadN(row+rowOffset, fieldCount); + if (scoreFilter && bed->score < scoreFilter) + continue; + bed8To12(bed); + lf = lfFromBed(bed); + slAddHead(&lfList, lf); + } + hFreeConn(&conn); + } +else + { + for (bed = ct->bedList; bed != NULL; bed = bed->next) + { + if (scoreFilter && bed->score < scoreFilter) + continue; + if (bed->chromStart < winEnd && bed->chromEnd > winStart + && sameString(chromName, bed->chrom)) + { + bed8To12(bed); + lf = lfFromBed(bed); + slAddHead(&lfList, lf); + } + } + } +slReverse(&lfList); +slSort(&lfList, linkedFeaturesCmp); +tg->items = lfList; +} + +void ctLoadGappedBed(struct track *tg) +/* Convert bed info in window to linked feature. */ +{ +struct customTrack *ct = tg->customPt; +struct bed *bed; +struct linkedFeatures *lfList = NULL, *lf; +boolean useItemRgb = FALSE; +int scoreFilter = getScoreFilter(ct->tdb->track); + +useItemRgb = bedItemRgb(ct->tdb); + +if (ct->dbTrack) + { + int fieldCount = ct->fieldCount; + int rowOffset; + char **row; + struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); + struct sqlResult *sr = NULL; + + sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd, + NULL, &rowOffset); + while ((row = sqlNextRow(sr)) != NULL) + { + bed = bedLoadN(row+rowOffset, fieldCount); + lf = lfFromBed(bed); + if (scoreFilter && bed->score < scoreFilter) + continue; + if (useItemRgb) + { + lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */ + lf->filterColor=bed->itemRgb; + } + slAddHead(&lfList, lf); + } + hFreeConn(&conn); + } +else + { + for (bed = ct->bedList; bed != NULL; bed = bed->next) + { + if (scoreFilter && bed->score < scoreFilter) + continue; + if (bed->chromStart < winEnd && bed->chromEnd > winStart + && sameString(chromName, bed->chrom)) + { + lf = lfFromBed(bed); + if (useItemRgb) + { + lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */ + lf->filterColor=bed->itemRgb; + } + slAddHead(&lfList, lf); + } + } + } +slReverse(&lfList); +slSort(&lfList, linkedFeaturesCmp); +tg->items = lfList; +} + +void ctLoadColoredExon(struct track *tg) +/* Convert bed info in window to linked features series for custom track. */ +{ +struct customTrack *ct = tg->customPt; +struct bed *bed; +struct linkedFeaturesSeries *lfsList = NULL, *lfs; +if (ct->dbTrack) + { + int fieldCount = ct->fieldCount; + int rowOffset; + char **row; + struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); + struct sqlResult *sr = NULL; + sr = hRangeQuery(conn, ct->dbTableName, chromName, winStart, winEnd, + NULL, &rowOffset); + while ((row = sqlNextRow(sr)) != NULL) + { + bed = bedLoadN(row+rowOffset, fieldCount); + lfs = lfsFromColoredExonBed(bed); + slAddHead(&lfsList, lfs); + } + hFreeConn(&conn); + } +else + { + for (bed = ct->bedList; bed != NULL; bed = bed->next) + { + if (bed->chromStart < winEnd && bed->chromEnd > winStart + && sameString(chromName, bed->chrom)) + { + lfs = lfsFromColoredExonBed(bed); + slAddHead(&lfsList, lfs); + } + } + } +slReverse(&lfsList); +slSort(&lfsList, linkedFeaturesSeriesCmp); +tg->items = lfsList; +} + +char *ctMapItemName(struct track *tg, void *item) +/* Return composite item name for custom tracks. */ +{ +char *itemName = tg->itemName(tg, item); +static char buf[256]; +if (strlen(itemName) > 0) + sprintf(buf, "%s %s", ctFileName, itemName); +else + sprintf(buf, "%s NoItemName", ctFileName); +return buf; +} + + +void coloredExonMethodsFromCt(struct track *tg) +/* same as coloredExonMethods but different loader. */ +{ +linkedFeaturesSeriesMethods(tg); +tg->loadItems = ctLoadColoredExon; +tg->canPack = TRUE; +} + +struct track *newCustomTrack(struct customTrack *ct) +/* Make up a new custom track. */ +{ +struct track *tg = NULL; +struct trackDb *tdb = ct->tdb; +boolean useItemRgb = FALSE; +char *typeOrig = tdb->type; +char *typeDupe = cloneString(typeOrig); +char *typeParam = typeDupe; +char *type = nextWord(&typeParam); + +if (ct->dbTrack) + { + // make sure we can connect + struct sqlConnection *conn = hAllocConn(CUSTOM_TRASH); + hFreeConn(&conn); + } + +useItemRgb = bedItemRgb(tdb); + +if (sameString(type, "maf")) + { + tg = trackFromTrackDb(tdb); + tg->canPack = TRUE; + + wigMafMethods(tg, tdb, 0, NULL); + if (!ct->dbTrack) + errAbort("custom maf tracks must be in database"); + + struct mafPriv *mp; + AllocVar(mp); + mp->ct = ct; + + tg->customPt = mp; + tg->nextItemButtonable = FALSE; + } +else if (sameString(type, "wig")) + { + tg = trackFromTrackDb(tdb); + if (ct->dbTrack) + tg->loadItems = wigLoadItems; + else + tg->loadItems = ctWigLoadItems; + tg->customPt = ct; + tg->nextItemButtonable = FALSE; + } +else if (sameString(type, "bigWig")) + { + tg = trackFromTrackDb(tdb); + tg->bbiFile = ct->bbiFile; + tg->nextItemButtonable = FALSE; + } +else if (sameString(type, "bigBed")) + { + struct bbiFile *bbi = ct->bbiFile; + + /* Find field counts, and from that revise the tdb->type to be more complete. */ + char extra = (bbi->fieldCount > bbi->definedFieldCount ? '+' : '.'); + char typeBuf[64]; + safef(typeBuf, sizeof(typeBuf), "bigBed %d %c", bbi->definedFieldCount, extra); + tdb->type = cloneString(typeBuf); + + /* Finish wrapping track around tdb. */ + tg = trackFromTrackDb(tdb); + tg->bbiFile = bbi; + tg->nextItemButtonable = FALSE; + } +else if (sameString(type, "bedGraph")) + { + tg = trackFromTrackDb(tdb); + tg->canPack = FALSE; + tg->customPt = ct; + ct->wigFile = ctFileName; + tg->mapItemName = ctMapItemName; + tg->nextItemButtonable = FALSE; + } +else if (sameString(type, "bed")) + { + tg = trackFromTrackDb(tdb); + if (ct->fieldCount < 8) + { + tg->loadItems = ctLoadSimpleBed; + } + else if (useItemRgb && ct->fieldCount == 9) + { + tg->loadItems = ctLoadBed9; + } + else if (ct->fieldCount < 12) + { + tg->loadItems = ctLoadBed8; + } + else if (ct->fieldCount == 15) + { + char *theType = trackDbSetting(tdb, "type"); + if (theType && sameString(theType, "expRatio")) + { + tg = trackFromTrackDb(tdb); + expRatioMethodsFromCt(tg); + } + else + tg->loadItems = ctLoadGappedBed; + } + else + { + tg->loadItems = ctLoadGappedBed; + } + tg->mapItemName = ctMapItemName; + tg->canPack = TRUE; + tg->nextItemButtonable = TRUE; + tg->customPt = ct; + } +else if (sameString(type, "chromGraph")) + { + tdb->type = NULL; /* Swap out type for the moment. */ + tg = trackFromTrackDb(tdb); + chromGraphMethodsCt(tg); + tg->nextItemButtonable = FALSE; + tdb->type = typeOrig; + } +else if (sameString(type, "array")) + { + tg = trackFromTrackDb(tdb); + expRatioMethodsFromCt(tg); + tg->nextItemButtonable = TRUE; + tg->customPt = ct; + } +else if (sameString(type, "coloredExon")) + { + tg = trackFromTrackDb(tdb); + coloredExonMethodsFromCt(tg); + tg->nextItemButtonable = TRUE; + tg->customPt = ct; + } +else if (sameString(type, "encodePeak")) + { + tg = trackFromTrackDb(tdb); + encodePeakMethodsCt(tg); + tg->nextItemButtonable = TRUE; + tg->customPt = ct; + } +else if (sameString(type, "bam")) + { + tg = trackFromTrackDb(tdb); + tg->customPt = ct; + bamMethods(tg); + tg->mapItemName = ctMapItemName; + hashAdd(tdb->settingsHash, BASE_COLOR_USE_SEQUENCE, cloneString("lfExtra")); + hashAdd(tdb->settingsHash, BASE_COLOR_DEFAULT, cloneString("diffBases")); + hashAdd(tdb->settingsHash, SHOW_DIFF_BASES_ALL_SCALES, cloneString(".")); + hashAdd(tdb->settingsHash, INDEL_DOUBLE_INSERT, cloneString("on")); + hashAdd(tdb->settingsHash, INDEL_QUERY_INSERT, cloneString("on")); + hashAdd(tdb->settingsHash, INDEL_POLY_A, cloneString("on")); + hashAdd(tdb->settingsHash, "showDiffBasesMaxZoom", cloneString("100")); + } +else if (sameString(type, "makeItems")) + { + tg = trackFromTrackDb(tdb); + makeItemsMethods(tg); + tg->nextItemButtonable = TRUE; + tg->customPt = ct; + } +else if (sameString(type, "bedDetail")) + { + tg = trackFromTrackDb(tdb); + bedDetailCtMethods(tg, ct); + tg->mapItemName = ctMapItemName; /* must be here to see ctMapItemName */ + } +else if (sameString(type, "pgSnp")) + { + tg = trackFromTrackDb(tdb); + pgSnpCtMethods(tg); + //tg->mapItemName = ctMapItemName; + tg->customPt = ct; + } +else + { + errAbort("Unrecognized custom track type %s", type); + } +if (!ct->dbTrack) + tg->nextItemButtonable = FALSE; +tg->hasUi = TRUE; +freez(&typeDupe); +return tg; +} + +char *getPositionFromCustomTracks() +/* Parses custom track data to get the position variable + * return - The first chromosome position variable found in the + * custom track data. */ +{ +char *pos = NULL; +struct slName *bl = NULL; + +ctList = customTracksParseCart(database, cart, &browserLines, &ctFileName); + +for (bl = browserLines; bl != NULL; bl = bl->next) + { + char *words[96]; + int wordCount; + char *dupe = cloneString(bl->name); + + wordCount = chopLine(dupe, words); + if (wordCount >= 3) + { + char *command = words[1]; + if (sameString(command, "position")) + pos = cloneString(words[2]); + } + freez(&dupe); + if (pos != NULL) + break; + } +return pos; +} + +void loadCustomTracks(struct track **pTrackList) +/* Load up custom tracks and append to list. */ +{ +struct customTrack *ct; +struct track *tg; +struct slName *bl; + +/* build up browser lines from cart variables set by hgCustom */ +char *visAll = cartCgiUsualString(cart, "hgt.visAllFromCt", NULL); +if (visAll) + { + char buf[SMALLBUF]; + safef(buf, sizeof buf, "browser %s %s", visAll, "all"); + slAddTail(&browserLines, slNameNew(buf)); + } +struct hashEl *visEl; +struct hashEl *visList = cartFindPrefix(cart, "hgtct."); +for (visEl = visList; visEl != NULL; visEl = visEl->next) + { + char buf[256]; + safef(buf, sizeof buf, "browser %s %s", cartString(cart, visEl->name), + chopPrefix(cloneString(visEl->name))); + slAddTail(&browserLines, slNameNew(buf)); + cartRemove(cart, visEl->name); + } +hashElFreeList(&visList); + +/* The loading is now handled by getPositionFromCustomTracks(). */ +/* Process browser commands in custom track. */ +for (bl = browserLines; bl != NULL; bl = bl->next) + { + char *words[96]; + int wordCount; + + wordCount = chopLine(bl->name, words); + if (wordCount > 1) + { + char *command = words[1]; + if (sameString(command, "hide") + || sameString(command, "dense") + || sameString(command, "pack") + || sameString(command, "squish") + || sameString(command, "full")) + { + if (wordCount > 2) + { + int i; + for (i=2; inext) + { + if (toAll || sameString(s, tg->track)) + { + if (hTvFromString(command) == tg->tdb->visibility) + /* remove if setting to default vis */ + cartRemove(cart, tg->track); + else + cartSetString(cart, tg->track, command); + /* hide or show supertrack enclosing this track */ + if (tdbIsSuperTrackChild(tg->tdb)) + { + assert(tg->tdb->parentName != NULL); + cartSetString(cart, tg->tdb->parentName, + (sameString(command, "hide") ? + "hide" : "show")); + } + } + } + } + } + } + else if (sameString(command, "position")) + { + if (wordCount < 3) + errAbort("Expecting 3 words in browser position line"); + if (!hgIsChromRange(database, words[2])) + errAbort("browser position needs to be in chrN:123-456 format"); + hgParseChromRange(database, words[2], &chromName, &winStart, &winEnd); + + /*Fix a start window of -1 that is returned when a custom track position + begins at 0 + */ + if (winStart < 0) + { + winStart = 0; + } + } + else if (sameString(command, "pix")) + { + if (wordCount != 3) + errAbort("Expecting 3 words in pix line"); + trackLayoutSetPicWidth(&tl, words[2]); + } + } + } +for (ct = ctList; ct != NULL; ct = ct->next) + { + hasCustomTracks = TRUE; + tg = newCustomTrack(ct); + slAddHead(pTrackList, tg); + } +} + +void addTracksFromDataHub(char *hubUrl, struct track **pTrackList) +/* Load up stuff from data hub and append to list. The hubUrl points to + * a trackDb.ra format file. */ +{ +/* Squirrel away hub directory for later. */ +char hubDir[PATH_LEN]; +splitPath(hubUrl, hubDir, NULL, NULL); + +/* Load trackDb.ra file and make it into proper trackDb tree */ +struct trackDb *tdb, *tdbList = trackDbFromRa(hubUrl); +for (tdb = tdbList; tdb != NULL; tdb = tdb->next) + { + trackDbFieldsFromSettings(tdb); + trackDbPolish(tdb); + } +trackDbLinkUpGenerations(tdbList); +addTdbListToTrackList(tdbList, NULL, pTrackList); +} + +void loadDataHubs(struct track **pTrackList) +/* Load up stuff from data hubs and append to list. */ +{ +char *dataHubs = cloneString(cartUsualString(cart, "dataHubs", NULL)); +if (dataHubs == NULL) + return; +int hubCount = chopByWhite(dataHubs, NULL, 10); +char *hubArrays[hubCount]; +chopByWhite(dataHubs, hubArrays, hubCount); +int i; +for (i = 0; i%u", +chromName, winEnd, winStart); +sr = sqlGetResult(conn, query); + +int itemCount = 0; +struct agpFrag *agpItem = NULL; +while ((row = sqlNextRow(sr)) != NULL) + { + agpFragFree(&agpItem); // if there is a second one + agpItem = agpFragLoad(row+1); + ++itemCount; + if (itemCount > 1) + break; + } +sqlFreeResult(&sr); +hFreeConn(&conn); +if (1 == itemCount) + { // verify *entirely* within single contig + if ((winEnd <= agpItem->chromEnd) && + (winStart >= agpItem->chromStart)) + { + int agpStart = winStart - agpItem->chromStart; + int agpEnd = agpStart + winEnd - winStart; + hPuts(""); + printEnsemblAnchor(database, archive, agpItem->frag, + agpStart, agpEnd); + hPrintf("%s", "Ensembl"); + } + } +agpFragFree(&agpItem); // the one we maybe used +} + +void hotLinks() +/* Put up the hot links bar. */ +{ +boolean gotBlat = hIsBlatIndexedDatabase(database); +struct dyString *uiVars = uiStateUrlPart(NULL); +char *orgEnc = cgiEncode(organism); +boolean psOutput = cgiVarExists("hgt.psOutput"); + +hPrintf("
\n"); +hPrintf("\n"); +hPrintf(""); +hPuts("
\n"); +hPrintf("", + orgEnc, database, cartSessionVarName(), cartSessionId(cart)); + +if (hIsGisaidServer()) + { + /* disable hgGateway for gisaid for now */ + //hPrintf("", orgEnc, database); + hPrintf( + "", + '%', '%', + cartSessionVarName(), + cartSessionId(cart), + "Select Subjects"); + } +else +if (hIsGsidServer()) + { + hPrintf("", orgEnc, database); + hPrintf( + "", + '%', '%', "Select Subjects"); + } +else + { + hPrintf("", orgEnc, database, cartSessionVarName(), cartSessionId(cart)); + } +if (psOutput) + { + hPrintf("", orgEnc, database, cartSessionVarName(), cartSessionId(cart)); + } +if (gotBlat) + { + hPrintf("", uiVars->string); + } +if (hIsGisaidServer()) + { + hPrintf("", + database, + cartSessionVarName(), + cartSessionId(cart), + "Table View"); + } +else if (hIsGsidServer()) + { + hPrintf("", + database, "Table View"); + } +else + { + /* disable TB for CGB servers */ + if (!hIsCgbServer()) + { + hPrintf("", + database, chromName, winStart+1, winEnd, + cartSessionVarName(), + cartSessionId(cart), + "Tables"); + } + } + +if (hgNearOk(database)) + { + hPrintf("", + uiVars->string, "Gene Sorter"); + } +if (hgPcrOk(database)) + { + hPrintf("", uiVars->string); + } +if (!psOutput) + { + hPrintf("", hgcNameAndSettings(), + winStart, chromName, winStart, winEnd, database, uiVars->string, "DNA"); + } + +if (!psOutput) + { + /* disable Convert function for CGB servers for the time being */ + if (!hIsCgbServer()) + if (liftOverChainForDb(database) != NULL) + { + hPrintf(""); + } + } + +/* see if hgFixed.trackVersion exists */ +boolean trackVersionExists = hTableExists("hgFixed", "trackVersion"); +char ensVersionString[256]; +char ensDateReference[256]; +ensVersionString[0] = 0; +ensDateReference[0] = 0; +if (trackVersionExists) + { + struct sqlConnection *conn = hAllocConn("hgFixed"); + char query[256]; + safef(query, sizeof(query), "select version,dateReference from hgFixed.trackVersion where db = '%s' order by updateTime DESC limit 1", database); + struct sqlResult *sr = sqlGetResult(conn, query); + char **row; + + while ((row = sqlNextRow(sr)) != NULL) + { + safef(ensVersionString, sizeof(ensVersionString), "Ensembl %s", + row[0]); + safef(ensDateReference, sizeof(ensDateReference), "%s", + row[1]); + } + sqlFreeResult(&sr); + hFreeConn(&conn); + } + +if (!psOutput) + { + if (differentWord(database,"susScr2")) + { + /* Print Ensembl anchor for latest assembly of organisms we have + * supported by Ensembl == if versionString from trackVersion exists */ + if (sameWord(database,"hg19")) + { + hPrintf("", "Ensembl"); + } + else if (sameWord(database,"hg18")) + { + hPrintf("", "Ensembl"); + } + else if (ensVersionString[0]) + { + char *archive = NULL; + if (ensDateReference[0] && differentWord("current", ensDateReference)) + archive = cloneString(ensDateReference); + /* Can we perhaps map from a UCSC random chrom to an Ensembl contig ? */ + if (sameWord(database,"oryCun2") || isUnknownChrom(database, chromName)) + { + // which table to check + char *ctgPos = "ctgPos"; + if (sameWord(database,"oryCun2")) + ctgPos = "ctgPos2"; + + if (sameWord(database,"fr2")) + fr2ScaffoldEnsemblLink(archive); + else if (hTableExists(database, ctgPos)) + /* see if we are entirely within a single contig */ + { + struct sqlConnection *conn = hAllocConn(database); + struct sqlResult *sr = NULL; + char **row = NULL; + char query[256]; + safef(query, sizeof(query), + "select * from %s where chrom = '%s' and chromStart<%u and chromEnd>%u", + ctgPos, chromName, winEnd, winStart); + sr = sqlGetResult(conn, query); + + int itemCount = 0; + struct ctgPos *ctgItem = NULL; + while ((row = sqlNextRow(sr)) != NULL) + { + ctgPosFree(&ctgItem); // if there is a second one + ctgItem = ctgPosLoad(row); + ++itemCount; + if (itemCount > 1) + break; + } + sqlFreeResult(&sr); + hFreeConn(&conn); + if (1 == itemCount) + { // verify *entirely* within single contig + if ((winEnd <= ctgItem->chromEnd) && + (winStart >= ctgItem->chromStart)) + { + int ctgStart = winStart - ctgItem->chromStart; + int ctgEnd = ctgStart + winEnd - winStart; + hPrintf("", "Ensembl"); + } + } + ctgPosFree(&ctgItem); // the one we maybe used + } + } + else + { + hPrintf("", "Ensembl"); + } + } + } + } + +if (!psOutput) + { + /* Print NCBI MapView anchor */ + if (sameString(database, "hg18")) + { + hPrintf("", "NCBI"); + } + if (sameString(database, "hg19")) + { + hPrintf("", "NCBI"); + } + if (sameString(database, "mm8")) + { + hPrintf("", "NCBI"); + } + if (sameString(database, "danRer2")) + { + hPrintf("", "NCBI"); + } + if (sameString(database, "galGal3")) + { + hPrintf("", "NCBI"); + } + if (sameString(database, "canFam2")) + { + hPrintf("", "NCBI"); + } + if (sameString(database, "rheMac2")) + { + hPrintf("", "NCBI"); + } + if (sameString(database, "panTro2")) + { + hPrintf("", "NCBI"); + } + if (sameString(database, "anoGam1")) + { + hPrintf("", "NCBI"); + } + if (startsWith("oryLat", database)) + { + hPrintf("", + skipChr(chromName), winStart+1, winEnd, "UTGB"); + } + if (sameString(database, "cb3")) + { + hPrintf("", + skipChr(chromName), winStart+1, winEnd, "WormBase"); + } + if (sameString(database, "ce4")) + { + hPrintf("", + skipChr(chromName), winStart+1, winEnd, "WormBase"); + } + if (sameString(database, "ce2")) + { + hPrintf("", + skipChr(chromName), winStart+1, winEnd, "WormBase"); + } + } + +if (!psOutput) + { + hPrintf("",cartSessionVarName(), + cartSessionId(cart), "PDF/PS"); + } + +if (!psOutput) + { + if (wikiLinkEnabled()) + { + printf("", + cartSessionVarName(), cartSessionId(cart)); + } + } +if (hIsGisaidServer()) + { + //hPrintf("\n", "Help"); + hPrintf("\n", "Help"); + } +else +if (hIsGsidServer()) + { + hPrintf("\n", "Help"); + } +else + { + hPrintf("\n", "Help"); + } +hPuts("
Home    Sequence View Gateway    %s    Sequence View Gateway    %s    Genomes    Genome Browser    Blat    %s    %s    %s    %s    PCR    " + " %s     string, database, chromName, winStart+1, winEnd); + hPrintf("\" class=\"topbar\">Convert    "); + printEnsemblAnchor(database, NULL, chromName, winStart, winEnd); + hPrintf("%s    "); + printEnsemblAnchor(database, "ncbi36", chromName, winStart, winEnd); + hPrintf("%s    "); + printEnsemblAnchor(database, archive, ctgItem->contig, + ctgStart, ctgEnd); + hPrintf("%s    "); + printEnsemblAnchor(database, archive, chromName, winStart, winEnd); + hPrintf("%s    ", + skipChr(chromName), winStart+1, winEnd); + hPrintf("%s    ", + skipChr(chromName), winStart+1, winEnd); + hPrintf("%s  "); + hPrintf("", + skipChr(chromName), winStart+1, winEnd); + hPrintf("%s  "); + hPrintf("", + skipChr(chromName), winStart+1, winEnd); + hPrintf("%s  "); + hPrintf("", + skipChr(chromName), winStart+1, winEnd); + hPrintf("%s  "); + hPrintf("", + skipChr(chromName), winStart+1, winEnd); + hPrintf("%s  "); + hPrintf("", + skipChr(chromName), winStart+1, winEnd); + hPrintf("%s  "); + hPrintf("", + skipChr(chromName), winStart+1, winEnd); + hPrintf("%s  "); + hPrintf("", + skipChr(chromName), winStart+1, winEnd); + hPrintf("%s    %s    %s    %s    %s    %s    Session    %s    %s    %s    %s   
"); +hPuts("
\n"); +} + +static void setSuperTrackHasVisibleMembers(struct trackDb *tdb) +/* Determine if any member tracks are visible -- currently + * recording this in the parent's visibility setting */ +{ +tdb->visibility = tvDense; +} + +boolean superTrackHasVisibleMembers(struct trackDb *tdb) +/* Determine if any member tracks are visible -- currently + * recording this in the parent's visibility setting */ +{ +if (!tdbIsSuper(tdb)) + return FALSE; +return (tdb->visibility != tvHide); +} + +static void groupTracks(struct track **pTrackList, struct group **pGroupList, + int vis) +/* Make up groups and assign tracks to groups. + * If vis is -1, restore default groups to tracks. */ +{ +struct group *unknown = NULL; +struct group *group, *list = NULL; +struct hash *hash = newHash(8); +struct track *track; +struct trackRef *tr; +struct grp* grps = hLoadGrps(database); +struct grp *grp; + +/* build group objects from database. */ +for (grp = grps; grp != NULL; grp = grp->next) + { + /* deal with group reordering */ + float priority = grp->priority; + if (withPriorityOverride) + { + char cartVar[512]; + safef(cartVar, sizeof(cartVar), "%s.priority",grp->name); + if (vis != -1) + priority = (float)cartUsualDouble(cart, cartVar, grp->priority); + if (priority == grp->priority) + cartRemove(cart, cartVar); + } + /* create group object; add to list and hash */ + AllocVar(group); + group->name = cloneString(grp->name); + group->label = cloneString(grp->label); + group->defaultPriority = grp->priority; + group->priority = priority; + group->defaultIsClosed = grp->defaultIsClosed; + slAddHead(&list, group); + hashAdd(hash, grp->name, group); + } +grpFreeList(&grps); + +/* Loop through tracks and fill in their groups. + * If necessary make up an unknown group. */ +for (track = *pTrackList; track != NULL; track = track->next) + { + /* handle track reordering feature -- change group assigned to track */ + if (withPriorityOverride) + { + char *groupName = NULL; + char cartVar[256]; + + /* belt and suspenders -- accomodate inconsistent track/trackDb + * creation. Note -- with code cleanup, these default variables + * could be retired, and the tdb versions used as defaults */ + if (!track->defaultGroupName) + { + if (track->tdb && track->tdb->grp) + track->defaultGroupName = cloneString(track->tdb->grp); + else + track->defaultGroupName = cloneString("other"); + } + if (tdbIsSuperTrackChild(track->tdb)) + { + assert(track->tdb->parentName != NULL); + /* supertrack member must be in same group as its super */ + /* determine supertrack group */ + safef(cartVar, sizeof(cartVar), "%s.group",track->tdb->parentName); + groupName = cloneString( //1 + cartUsualString(cart, cartVar, track->tdb->parent->grp)); + track->tdb->parent->grp = cloneString(groupName); //2 + } + else + { + /* get group */ + safef(cartVar, sizeof(cartVar), "%s.group",track->track); + groupName = cloneString( //1 + cartUsualString(cart, cartVar, track->defaultGroupName)); + } + if (vis == -1) + groupName = track->defaultGroupName; //0 + track->groupName = cloneString(groupName); // wasting a few clones! //3 + if (sameString(groupName, track->defaultGroupName)) + cartRemove(cart, cartVar); + + /* get priority */ + safef(cartVar, sizeof(cartVar), "%s.priority",track->track); + float priority = (float)cartUsualDouble(cart, cartVar, + track->defaultPriority); + /* remove cart variables that are the same as the trackDb settings */ +/* UGLY - add me back when tdb->priority is no longer pre-clobbered by cart var value + if (priority == track->defaultPriority) + cartRemove(cart, cartVar); +*/ + track->priority = priority; + } + + /* assign group object to track */ + if (track->groupName == NULL) + group = NULL; + else + group = hashFindVal(hash, track->groupName); + if (group == NULL) + { + if (unknown == NULL) + { + AllocVar(unknown); + unknown->name = cloneString("other"); + unknown->label = cloneString("other"); + unknown->priority = 1000000; + slAddHead(&list, unknown); + } + group = unknown; + } + track->group = group; + } + +/* Sort tracks by combined group/track priority, and + * then add references to track to group. */ +slSort(pTrackList, tgCmpPriority); +for (track = *pTrackList; track != NULL; track = track->next) + { + AllocVar(tr); + tr->track = track; + slAddHead(&track->group->trackList, tr); + } + +/* Straighten things out, clean up, and go home. */ +for (group = list; group != NULL; group = group->next) + slReverse(&group->trackList); +slSort(&list, gCmpPriority); +hashFree(&hash); +*pGroupList = list; +} + +void groupTrackListAddSuper(struct cart *cart, struct group *group) +/* Construct a new track list that includes supertracks, sort by priority, + * and determine if supertracks have visible members. + * Replace the group track list with this new list. + * Shared by hgTracks and configure page to expand track list, + * in contexts where no track display functions (which don't understand + * supertracks) are invoked. */ +{ +struct trackRef *newList = NULL, *tr, *ref; +struct hash *superHash = hashNew(8); + +if (!group || !group->trackList) + return; +for (tr = group->trackList; tr != NULL; tr = tr->next) + { + struct track *track = tr->track; + AllocVar(ref); + ref->track = track; + slAddHead(&newList, ref); + if (tdbIsSuperTrackChild(track->tdb)) + { + assert(track->tdb->parentName != NULL); + if (hTvFromString(cartUsualString(cart, track->track, + hStringFromTv(track->tdb->visibility))) != tvHide) + setSuperTrackHasVisibleMembers(track->tdb->parent); + if (hashLookup(superHash, track->tdb->parentName)) + /* ignore supertrack if it's already been handled */ + continue; + /* create track and reference for the supertrack */ + struct track *superTrack = trackFromTrackDb(track->tdb->parent); + superTrack->hasUi = TRUE; + superTrack->group = group; + superTrack->groupName = cloneString(group->name); + superTrack->defaultGroupName = cloneString(group->name); + + /* handle track reordering */ + char cartVar[256]; + safef(cartVar, sizeof(cartVar), "%s.priority",track->tdb->parentName); + float priority = (float)cartUsualDouble(cart, cartVar, + track->tdb->parent->priority); + /* remove cart variables that are the same as the trackDb settings */ + if (priority == track->tdb->parent->priority) + cartRemove(cart, cartVar); + superTrack->priority = priority; + + AllocVar(ref); + ref->track = superTrack; + slAddHead(&newList, ref); + hashAdd(superHash, track->tdb->parentName, track->tdb->parent); + } + } +slSort(&newList, trackRefCmpPriority); +hashFree(&superHash); +/* we could free the old track list here, but it's a trivial amount of mem */ +group->trackList = newList; +} + +void topButton(char *var, char *label) +/* create a 3 or 4-char wide button for top line of display. + * 3 chars wide for odd-length labels, 4 for even length. + * Pad with spaces so label is centered */ +{ +char paddedLabel[5] = " "; +int len = strlen(label); +if (len > 4) + { + /* truncate */ + /* or maybe errabort ? */ + label[3] = 0; + len = 4; + } +if (len % 2 != 0) + paddedLabel[3] = 0; +if (len == strlen(paddedLabel)) + strcpy(paddedLabel, label); +else + { + int i; + for (i=0; itdb)) + { + assert(track->tdb->parent != NULL); + if (sameString("hide", cartUsualString(cart, track->tdb->parent->track, + track->tdb->parent->isShow ? "show" : "hide"))) + track->visibility = tvHide; + } +} + +struct track *rFindTrackWithTable(char *tableName, struct track *trackList) +/* Recursively search through track list looking for first one that matches table. */ +{ +struct track *track; +for (track = trackList; track != NULL; track = track->next) + { + if (sameString(tableName, track->table)) + return track; + struct track *subTrack = rFindTrackWithTable(tableName, track->subtracks); + if (subTrack != NULL) + return subTrack; + } +return NULL; +} + +static void setSearchedTrackToPackOrFull(struct track *trackList) +/* Open track associated with search position if any. Also open its parents + * if any. At the moment parents include composites but not supertracks. */ +{ +if (NULL != hgp && NULL != hgp->tableList && NULL != hgp->tableList->name) + { + char *tableName = hgp->tableList->name; + struct track *matchTrack = rFindTrackWithTable(tableName, trackList); + if (matchTrack != NULL) + { + struct track *track; + for (track = matchTrack; track != NULL; track = track->parent) + cartSetString(cart, track->track, hCarefulTrackOpenVis(database, track->track)); + } + } +} + + +struct track *getTrackList( struct group **pGroupList, int vis) +/* Return list of all tracks, organizing by groups. + * If vis is -1, restore default groups to tracks. + * Shared by hgTracks and configure page. */ +{ +struct track *track, *trackList = NULL; +registerTrackHandlers(); +/* Load regular tracks, blatted tracks, and custom tracks. + * Best to load custom last. */ +loadFromTrackDb(&trackList); +if (pcrResultParseCart(database, cart, NULL, NULL, NULL)) + slSafeAddHead(&trackList, pcrResultTg()); +if (userSeqString != NULL) slSafeAddHead(&trackList, userPslTg()); +slSafeAddHead(&trackList, oligoMatchTg()); +if (restrictionEnzymesOk()) + { + slSafeAddHead(&trackList, cuttersTg()); + } +if (wikiTrackEnabled(database, NULL)) + addWikiTrack(&trackList); +#ifdef SOON +loadDataHubs(&trackList); +#endif /* SOON */ +loadCustomTracks(&trackList); +groupTracks(&trackList, pGroupList, vis); +setSearchedTrackToPackOrFull(trackList); +if (cgiOptionalString( "hideTracks")) + changeTrackVis(groupList, NULL, tvHide); + +/* Get visibility values if any from ui. */ +for (track = trackList; track != NULL; track = track->next) + { + char *s = cartOptionalString(cart, track->track); + if (cgiOptionalString("hideTracks")) + { + s = cgiOptionalString(track->track); + if (s != NULL && (hTvFromString(s) != track->tdb->visibility)) + { + cartSetString(cart, track->track, s); + } + } + if (s != NULL && !track->limitedVisSet) + track->visibility = hTvFromString(s); + if (tdbIsComposite(track->tdb) && track->visibility != tvHide) + { + struct trackDb *parent = track->tdb->parent; + char *parentShow = NULL; + if (parent) + parentShow = cartUsualString(cart, parent->track, + parent->isShow ? "show" : "hide"); + if (!parent || sameString(parentShow, "show")) + compositeTrackVis(track); + } + } +if (measureTiming) + uglyTime("getTrackList"); +return trackList; +} + +void doNextPrevItem(boolean goNext, char *trackName) +/* In case a next item arrow was clicked on a track, change */ +/* position (i.e. winStart, winEnd, etc.) based on what track it was */ +{ +struct track *track = trackFindByName(trackList, trackName); +if ((track != NULL) && (track->nextPrevItem != NULL)) + track->nextPrevItem(track, goNext); +} + +char *collapseGroupVar(char *name) +/* Construct cart variable name for collapsing group */ +{ +static char varName[256]; +safef(varName, sizeof(varName), + "%s%s_%s_%s", "hgt", "group", name, "close"); +return (cloneString(varName)); +} + +boolean isCollapsedGroup(struct group *grp) +/* Determine if group is collapsed */ +{ +return cartUsualInt(cart, collapseGroupVar(grp->name), grp->defaultIsClosed); +} + +void collapseGroupGoodies(boolean isOpen, boolean wantSmallImage, + char **img, char **indicator, char **otherState) +/* Get image, char representation of image, and 'otherState' (1 or 0) + * for a group, based on whether it is collapsed, and whether we want + * larger or smaller image for collapse box */ +{ +if (otherState) + *otherState = (isOpen ? "1" : "0"); +if (indicator) + *indicator = (isOpen ? "-" : "+"); +if (img) + { + if (wantSmallImage) + *img = (isOpen ? "../images/remove_sm.gif" : "../images/add_sm.gif"); + else + *img = (isOpen ? "../images/remove.gif" : "../images/add.gif"); + } +} + +void collapseGroup(char *name, boolean doCollapse) +/* Set cart variable to cause group to collapse */ +{ +cartSetBoolean(cart, collapseGroupVar(name), doCollapse); +} + +void myControlGridStartCell(struct controlGrid *cg, boolean isOpen, char *id) +/* Start a new cell in control grid; support Javascript open/collapsing by including id's in tr's. + id is used as id prefix (a counter is added to make id's unique). */ +{ +static int counter = 1; +if (cg->columnIx == cg->columns) + controlGridEndRow(cg); +if (!cg->rowOpen) + { +#if 0 + /* This is unnecessary, b/c we can just use a blank display attribute to show the element rather + than figuring out what the browser specific string is to turn on display of the tr; + however, we may want to put in browser specific strings in the future, so I'm leaving this + code in as a reference. */ + char *ua = getenv("HTTP_USER_AGENT"); + char *display = ua && stringIn("MSIE", ua) ? "block" : "table-row"; +#endif + // use counter to ensure unique tr id's (prefix is used to find tr's in javascript). + printf("", isOpen ? "" : "style='display: none' ", id, counter++); + cg->rowOpen = TRUE; + } +if (cg->align) + printf("", cg->align); +else + printf(""); +} + +static void pruneRedundantCartVis(struct track *trackList) +/* When the config page or track form has been submitted, there usually + * are many track visibility cart variables that have not been changed + * from the default. To keep down cart bloat, prune those out before we + * save the cart. changeTrackVis does this too, but this is for the + * more common case where track visibilities are tweaked. */ +{ +struct track *track; +if (measureTiming) + uglyTime("Done with trackForm"); +for (track = trackList; track != NULL; track = track->next) + { + char *cartVis = cartOptionalString(cart, track->track); + if (cartVis != NULL && hTvFromString(cartVis) == track->tdb->visibility) + cartRemove(cart, track->track); + } +if (measureTiming) + { + uglyTime("Pruned redundant vis from cart"); + } +} + +static int getMaxWindowToDraw(struct trackDb *tdb) +/* If trackDb setting maxWindowToDraw exists and is a sensible size, return it, else 0. */ +{ +if (tdb == NULL) + return 0; +char *maxWinToDraw = trackDbSettingClosestToHome(tdb, "maxWindowToDraw"); +if (isNotEmpty(maxWinToDraw)) + { + unsigned maxWTD = sqlUnsigned(maxWinToDraw); + if (maxWTD > 1) + return maxWTD; + } +return 0; +} + +static void drawMaxWindowWarning(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, + int xOff, int yOff, int width, MgFont *font, Color color, + enum trackVisibility vis) +/* This is a stub drawItems handler to be swapped in for the usual drawItems when the window + * size is larger than the threshold specified by trackDb setting maxWindowToDraw. */ +{ +int maxWinToDraw = getMaxWindowToDraw(tg->tdb); +char commafied[256]; +sprintLongWithCommas(commafied, maxWinToDraw); +char message[512]; +safef(message, sizeof(message), "zoom in to <= %s bases to view items", commafied); +Color yellow = hvGfxFindRgb(hvg, &undefinedYellowColor); +hvGfxBox(hvg, xOff, yOff, width, tg->heightPer, yellow); +hvGfxTextCentered(hvg, xOff, yOff, width, tg->heightPer, MG_BLACK, font, message); +} + +static void dontLoadItems(struct track *tg) +/* No-op loadItems when we aren't going to try. */ +{ +} + +static void checkMaxWindowToDraw(struct track *tg) +/* If (winEnd - winStart) > trackDb setting maxWindowToDraw, force track to a dense line + * that will ask the user to zoom in closer to see track items and return TRUE so caller + * can skip loading items. */ +{ +int maxWinToDraw = getMaxWindowToDraw(tg->tdb); +if (tdbIsComposite(tg->tdb)) + { + struct track *subtrack; + for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next) + { + if (!isSubtrackVisible(subtrack)) + continue; + maxWinToDraw = getMaxWindowToDraw(subtrack->tdb); + if (maxWinToDraw > 1 && (winEnd - winStart) > maxWinToDraw) + { + subtrack->loadItems = dontLoadItems; + subtrack->drawItems = drawMaxWindowWarning; + subtrack->limitedVis = tvDense; + subtrack->limitedVisSet = TRUE; + } + } + } +else if (maxWinToDraw > 1 && (winEnd - winStart) > maxWinToDraw) + { + tg->loadItems = dontLoadItems; + tg->drawItems = drawMaxWindowWarning; + tg->limitedVis = tvDense; + tg->limitedVisSet = TRUE; + } +} + +void printTrackInitJavascript(struct track *trackList) +{ +hPrintf("\n", hgtJsCommand, hgtJsCommand); +hPrintf("\n"); +} + +void jsCommandDispatch(char *command, struct track *trackList) +/* Dispatch a command sent to us from some javaScript event. + * This gets executed after the track list is built, but before + * the track->loadItems methods are called. */ +{ +if (startsWithWord("makeItems", command)) + makeItemsJsCommand(command, trackList, trackHash); +else + warn("Unrecognized jsCommand %s", command); +} + +#ifdef SUBTRACKS_HAVE_VIS +static void parentChildCartCleanup(struct track *trackList,struct cart *newCart,struct hash *oldVars) +/* When composite/view settings changes, remove subtrack specific vis + When superTrackChild is found and selected, shape superTrack to match. */ +{ +struct track *track = trackList; +for (;track != NULL; track = track->next) + { + if (tdbIsMultiTrack(track->tdb)) + if(cartTdbTreeMatchSubtrackVis(cart,track->tdb)) // Note, this is done for found multi-track kids but composites are only straightened up in hgTrackUi + track->visibility = tdbVisLimitedByAncestry(cart,track->tdb,FALSE); + + if (cartTdbTreeCleanupOverrides(track->tdb,newCart,oldVars)) + { // Need to update track visibility + if (tdbIsSuperTrackChild(track->tdb)) + { + // Unfortunately, since supertracks are not in trackList, this occurs on superChildren, + // So now we need to find the supertrack and take changed cart values of its children + struct slRef *childRef; + for(childRef = track->tdb->parent->children;childRef != NULL;childRef = childRef->next) + { + struct trackDb * childTdb = childRef->val; + struct track *child = hashFindVal(trackHash, childTdb->track); + char *cartVis = cartOptionalString(cart,child->track); + if (cartVis) + child->visibility = hTvFromString(cartVis); + } + } + } + } +} +#endif///def SUBTRACKS_HAVE_VIS + +void doTrackForm(char *psOutput, struct tempName *ideoTn) +/* Make the tracks display form with the zoom/scroll buttons and the active + * image. If the ideoTn parameter is not NULL, it is filled in if the + * ideogram is created. */ +{ +struct group *group; +struct track *track; +char *freezeName = NULL; +boolean hideAll = cgiVarExists("hgt.hideAll"); +boolean defaultTracks = cgiVarExists("hgt.reset"); +boolean showedRuler = FALSE; +boolean showTrackControls = cartUsualBoolean(cart, "trackControlsOnMain", TRUE); +long thisTime = 0, lastTime = 0; +char *clearButtonJavascript; + +basesPerPixel = ((float)winBaseCount) / ((float)insideWidth); +zoomedToBaseLevel = (winBaseCount <= insideWidth / tl.mWidth); +zoomedToCodonLevel = (ceil(winBaseCount/3) * tl.mWidth) <= insideWidth; +zoomedToCdsColorLevel = (winBaseCount <= insideWidth*3); + +if (psOutput != NULL) + { + hPrintDisable(); + hideControls = TRUE; + withNextItemArrows = FALSE; + withNextExonArrows = FALSE; + hgFindMatches = NULL; + } + +/* Tell browser where to go when they click on image. */ +hPrintf("
\n\n", hgTracksName()); +hPrintf("\n", insideX); +hPrintf("\n", revCmplDisp); +if (!psOutput) cartSaveSession(cart); +clearButtonJavascript = "document.TrackHeaderForm.position.value=''; document.getElementById('suggest').value='';"; + +/* See if want to include sequence search results. */ +userSeqString = cartOptionalString(cart, "ss"); +if (userSeqString && !ssFilesExist(userSeqString)) + { + userSeqString = NULL; + cartRemove(cart, "ss"); + } +if (!hideControls) + hideControls = cartUsualBoolean(cart, "hideControls", FALSE); +if (measureTiming) + uglyTime("Time before getTrackList"); +trackList = getTrackList(&groupList, defaultTracks ? -1 : -2); +makeGlobalTrackHash(trackList); +#ifdef SOON +if (measureTiming) + uglyTime("getTrackList"); +#endif /* SOON */ + +// honor defaultImgOrder +if(cgiVarExists("hgt.defaultImgOrder")) + { + char wildCard[32]; + safef(wildCard,sizeof(wildCard),"*_%s",IMG_ORDER_VAR); + cartRemoveLike(cart, wildCard); + } +#ifdef SUBTRACKS_HAVE_VIS +parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated +#endif///def SUBTRACKS_HAVE_VIS + +/* Honor hideAll and visAll variables */ +if (hideAll || defaultTracks) + { + int vis = (hideAll ? tvHide : -1); + changeTrackVis(groupList, NULL, vis); + } + +/* Before loading items, deal with the next/prev item arrow buttons if pressed. */ +if (cgiVarExists("hgt.nextItem")) + doNextPrevItem(TRUE, cgiUsualString("hgt.nextItem", NULL)); +else if (cgiVarExists("hgt.prevItem")) + doNextPrevItem(FALSE, cgiUsualString("hgt.prevItem", NULL)); + +if(advancedJavascriptFeaturesEnabled(cart) && !psOutput && !cgiVarExists("hgt.imageV1")) + { + // Start an imagebox (global for now to avoid huge rewrite of hgTracks) + // Set up imgBox dimensions + int sideSliceWidth = 0; // Just being explicit + if (withLeftLabels) + sideSliceWidth = (insideX - gfxBorder*3) + 2; + theImgBox = imgBoxStart(database,chromName,winStart,winEnd,(!revCmplDisp),sideSliceWidth,tl.picWidth); + #ifdef IMAGEv2_DRAG_SCROLL + // Define a portal with a default expansion size, then set the global dimensions to the full image size + if(imgBoxPortalDefine(theImgBox,&winStart,&winEnd,&(tl.picWidth),0)) + { + winBaseCount = winEnd - winStart; + insideWidth = tl.picWidth-gfxBorder-insideX; + } + #endif//def IMAGEv2_DRAG_SCROLL + } + +char *jsCommand = cartCgiUsualString(cart, hgtJsCommand, ""); +if (!isEmpty(jsCommand)) + { + cartRemove(cart, hgtJsCommand); + jsCommandDispatch(jsCommand, trackList); + } + +/* Tell tracks to load their items. */ +for (track = trackList; track != NULL; track = track->next) + { + /* adjust track visibility based on supertrack just before load loop */ + if (tdbIsSuperTrackChild(track->tdb)) + limitSuperTrackVis(track); + + /* remove cart priority variables if they are set + to the default values in the trackDb */ + if(!hTrackOnChrom(track->tdb, chromName)) + { + track->limitedVis = tvHide; + track->limitedVisSet = TRUE; + } + else if (track->visibility != tvHide) + { + if (measureTiming) + lastTime = clock1000(); + checkMaxWindowToDraw(track); + track->loadItems(track); + + if (measureTiming) + { + thisTime = clock1000(); + track->loadTime = thisTime - lastTime; + } + } + } + +printTrackInitJavascript(trackList); + +/* Generate two lists of hidden variables for track group visibility. Kludgy, + but required b/c we have two different navigation forms on this page, but + we want open/close changes in the bottom form to be submitted even if the user + submits via the top form. */ +struct dyString *trackGroupsHidden1 = newDyString(1000); +struct dyString *trackGroupsHidden2 = newDyString(1000); +for (group = groupList; group != NULL; group = group->next) + { + if (group->trackList != NULL) + { + int looper; + for(looper=1;looper<=2;looper++) + { + boolean isOpen = !isCollapsedGroup(group); + char buf[1000]; + safef(buf, sizeof(buf), "\n", collapseGroupVar(group->name), collapseGroupVar(group->name), looper, isOpen ? "0" : "1"); + dyStringAppend(looper == 1 ? trackGroupsHidden1 : trackGroupsHidden2, buf); + } + } + } + +#ifdef IMAGEv2_DRAG_SCROLL +if(theImgBox) + { + // If a portal was established, then set the global dimensions back to the portal size + if(imgBoxPortalDimensions(theImgBox,NULL,NULL,NULL,NULL,&winStart,&winEnd,&(tl.picWidth),NULL)) + { + winBaseCount = winEnd - winStart; + insideWidth = tl.picWidth-gfxBorder-insideX; + } + } +#endif//def IMAGEv2_DRAG_SCROLL +/* Center everything from now on. */ +hPrintf("
\n"); + +if(trackImgOnly) + { + makeActiveImage(trackList, psOutput); + fflush(stdout); + return; // bail out b/c we are done + } + + +if (!hideControls) + { + /* set white-space to nowrap to prevent buttons from wrapping when screen is + * narrow */ + hPrintf("
\n"); + hotLinks(); + + /* Show title . */ + freezeName = hFreezeFromDb(database); + if(freezeName == NULL) + freezeName = "Unknown"; + hPrintf(""); + if (startsWith("zoo",database) ) + { + hPrintf("%s %s on %s June 2002 Assembly %s target1", + organization, browserName, organism, freezeName); + } + else + { + if (sameString(organism, "Archaea")) + { + hPrintf("%s %s on Archaeon %s Assembly", + organization, browserName, freezeName); + } + else + { + if (stringIn(database, freezeName)) + hPrintf("%s %s on %s %s Assembly", + organization, browserName, organism, freezeName); + else + hPrintf("%s %s on %s %s Assembly (%s)", + organization, browserName, organism, freezeName, database); + } + } + hPrintf("
\n"); + + /* This is a clear submit button that browsers will use by default when enter is pressed in position box. */ + hPrintf(""); + /* Put up scroll and zoom controls. */ +#ifndef USE_NAVIGATION_LINKS + hWrites("move "); + hButtonWithMsg("hgt.left3", "<<<", "move 95% to the left"); + hButtonWithMsg("hgt.left2", " <<", "move 47.5% to the left"); + hButtonWithMsg("hgt.left1", " < ", "move 10% to the left"); + hButtonWithMsg("hgt.right1", " > ", "move 10% to the right"); + hButtonWithMsg("hgt.right2", ">> ", "move 47.5% to the right"); + hButtonWithMsg("hgt.right3", ">>>", "move 95% to the right"); + hWrites(" zoom in "); + /* use button maker that determines padding, so we can share constants */ + topButton("hgt.in1", ZOOM_1PT5X); + topButton("hgt.in2", ZOOM_3X); + topButton("hgt.in3", ZOOM_10X); + topButton("hgt.inBase", ZOOM_BASE); + hWrites(" zoom out "); + topButton("hgt.out1", ZOOM_1PT5X); + topButton("hgt.out2", ZOOM_3X); + topButton("hgt.out3", ZOOM_10X); + hWrites("
\n"); +#endif//ndef USE_NAVIGATION_LINKS + + if (showTrackControls) + { + /* Break into a second form so that zooming and scrolling + * can be done with a 'GET' so that user can back up from details + * page without Internet Explorer popping up an annoying dialog. + * Do rest of page as a 'POST' so that the ultra-long URL from + * all the track controls doesn't break things. IE URL limit + * is 2000 bytes, but some firewalls impose a ~1000 byte limit. + * As a side effect of breaking up the page into two forms + * we need to repeat the position in a hidden variable here + * so that zoom/scrolling always has current position to work + * from. */ + hPrintf("", chromName, winStart+1, winEnd); + hPrintf("\n%s", trackGroupsHidden1->string); + hPrintf("
\n"); + hPrintf("
\n\n", hgTracksName()); + hPrintf("%s", trackGroupsHidden2->string); + freeDyString(&trackGroupsHidden1); + freeDyString(&trackGroupsHidden2); + if (!psOutput) cartSaveSession(cart); /* Put up hgsid= as hidden variable. */ + clearButtonJavascript = "document.TrackForm.position.value=''; document.getElementById('suggest').value='';"; + hPrintf("
"); + } + + + /* Make line that says position. */ + { + char buf[256]; + char *survey = cfgOptionEnv("HGDB_SURVEY", "survey"); + char *surveyLabel = cfgOptionEnv("HGDB_SURVEY_LABEL", "surveyLabel"); + char *javascript = "onchange=\"document.location = '/cgi-bin/hgTracks?db=' + document.TrackForm.db.options[document.TrackForm.db.selectedIndex].value;\""; + if (containsStringNoCase(database, "zoo")) + { + hPuts("Organism "); + printAssemblyListHtmlExtra(database, javascript); + } + + sprintf(buf, "%s:%d-%d", chromName, winStart+1, winEnd); + position = cloneString(buf); + hWrites("position/search "); + hTextVar("position", addCommasToPos(database, position), 30); + sprintLongWithCommas(buf, winEnd - winStart); + if(dragZooming && assemblySupportsGeneSuggest(database)) + hWrites(" gene \n"); + hWrites(" "); + hButtonWithOnClick("hgt.jump", "jump", NULL, "jumpButtonOnClick()"); + hOnClickButton(clearButtonJavascript,"clear"); + hPrintf(" size %s bp. ", buf); + hWrites(" "); + hButton("hgTracksConfigPage", "configure"); + //hPrintf("  Your feedback\n"); + if (survey && differentWord(survey, "off")) + hPrintf("  %s\n", survey, surveyLabel ? surveyLabel : "Take survey"); + // info for drag selection javascript + hPrintf("\n", winStart); + hPrintf("\n", winEnd); + hPrintf("\n", chromName); + + hPutc('\n'); + + } + } + +/* Make chromsome ideogram gif and map. */ +makeChromIdeoImage(&trackList, psOutput, ideoTn); + +#ifdef USE_NAVIGATION_LINKS + hPrintf("\n",tl.picWidth);//min(tl.picWidth, 800)); + hPrintf("\n"); // Without 'width=' this cell expand to table with, forcing other cells to the sides. + hPrintf("\n"); // Without 'width=' this cell expand to table with, forcing other cells to the sides. + hPrintf("\n"); // Without 'width=' this cell expand to table with, forcing other cells to the sides. + #ifdef IMAGEv2_DRAG_SCROLL + if(!advancedJavascriptFeaturesEnabled(cart)) + #endif//ndef IMAGEv2_DRAG_SCROLL + hPrintf("
<<<\n"); + hPrintf("<<\n"); + #ifdef IMAGEv2_DRAG_SCROLL + if(!advancedJavascriptFeaturesEnabled(cart)) + #endif//def IMAGEv2_DRAG_SCROLL + hPrintf("<\n"); + + hPrintf(" > <\n"); + hPrintf(">> <<\n"); + hPrintf(">>> <<<\n"); + hPrintf(">base<\n"); + + hPrintf(" < >\n"); + hPrintf("<< >>\n"); + hPrintf("<<< >>>\n"); + hPrintf(" >\n"); + + hPrintf(">>\n"); + hPrintf(">>>\n"); + hPrintf("
\n"); +#endif//def USE_NAVIGATION_LINKS + +/* Make clickable image and map. */ +makeActiveImage(trackList, psOutput); +fflush(stdout); + +if(trackImgOnly) + // bail out b/c we are done + return; + +if (!hideControls) + { + struct controlGrid *cg = NULL; + + /* note a trick of WIDTH=27 going on here. The 6,15,6 widths following + * go along with this trick */ + hPrintf("\n", + tl.picWidth, 27); +#ifndef USE_NAVIGATION_LINKS + hPrintf(""); + hPrintf("\n"); +#endif//ndef USE_NAVIGATION_LINKS + hPrintf(""); +#ifndef USE_NAVIGATION_LINKS + hPrintf("\n"); + hPrintf(""); +#endif//ndef USE_NAVIGATION_LINKS + hPrintf("
"); + hPrintf("move start
"); + hButton("hgt.dinkLL", " < "); + hTextVar("dinkL", cartUsualString(cart, "dinkL", "2.0"), 3); + hButton("hgt.dinkLR", " > "); + hPrintf("		 "); // allow this text to wrap + hWrites("Click on a feature for details. "); + hWrites(dragZooming ? "Click or drag in the base position track to zoom in. " : "Click on base position to zoom in around cursor. "); + hWrites("Click side bars for track options. "); + hWrites("Drag side bars or labels up or down to reorder tracks. "); +#ifdef IMAGEv2_DRAG_SCROLL + hWrites("Drag tracks left or right to new position. "); +#endif//def IMAGEv2_DRAG_SCROLL +//#if !defined(IMAGEv2_DRAG_SCROLL) && !defined(USE_NAVIGATION_LINKS) + hPrintf(" "); + hPrintf("move end
"); + hButton("hgt.dinkRL", " < "); + hTextVar("dinkR", cartUsualString(cart, "dinkR", "2.0"), 3); + hButton("hgt.dinkRR", " > "); + hPrintf("
\n"); + // smallBreak(); + + /* Display bottom control panel. */ + +#ifdef TRACK_SEARCH + if(isSearchTracksSupported(database)) + { + hPrintf("", searchTracks); + hPrintf(" "); + } +#endif + hButton("hgt.reset", "default tracks"); + hPrintf(" "); + hButton("hgt.defaultImgOrder", "default order"); + // if (showTrackControls) - always show "hide all", Hiram 2008-06-26 + { + hPrintf(" "); + hButton("hgt.hideAll", "hide all"); + } + + hPrintf(" "); + hOnClickButton("document.customTrackForm.submit();return false;", + hasCustomTracks ? + CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL); + + hPrintf(" "); + hButton("hgTracksConfigPage", "configure"); + hPrintf(" "); + + if (!hIsGsidServer()) + { + hButton("hgt.toggleRevCmplDisp", "reverse"); + hPrintf(" "); + } + + hButton("hgt.refresh", "refresh"); + + hPrintf("
\n"); + + if( chromosomeColorsMade ) + { + hPrintf("Chromosome Color Key:
"); + hPrintf("
\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("\n", CONTROL_TABLE_WIDTH); + hPrintf(""); + + hPrintf("\n", MAX_CONTROL_COLUMNS - 2); + + hPrintf(""); + + if (!hIsGsidServer()) + { + cg = startControlGrid(MAX_CONTROL_COLUMNS, "left"); + } + else + { + /* 4 cols fit GSID's display better */ + cg = startControlGrid(4, "left"); + } + boolean isFirstNotCtGroup = TRUE; + for (group = groupList; group != NULL; group = group->next) + { + if (group->trackList == NULL) + continue; + + struct trackRef *tr; + + /* check if group section should be displayed */ + char *otherState; + char *indicator; + char *indicatorImg; + boolean isOpen = !isCollapsedGroup(group); + collapseGroupGoodies(isOpen, TRUE, &indicatorImg, + &indicator, &otherState); + hPrintf(""); + cg->rowOpen = TRUE; + if (!hIsGsidServer()) + { + hPrintf("\n"); + controlGridEndRow(cg); + + /* First track group that is not custom track group gets ruler, + * unless it's collapsed. */ + if (!showedRuler && isFirstNotCtGroup && + differentString(group->name, "user")) + { + char *url = trackUrl(RULER_TRACK_NAME, chromName); + showedRuler = TRUE; + myControlGridStartCell(cg, isOpen, group->name); + hPrintf("", url); + hPrintf(" %s
", RULER_TRACK_LABEL); + hPrintf(""); + hDropListClassWithStyle("ruler", rulerMenu, + sizeof(rulerMenu)/sizeof(char *), rulerMenu[rulerMode], + rulerMode == tvHide ? "hiddenText" : "normalText", + TV_DROPDOWN_STYLE); + controlGridEndCell(cg); + freeMem(url); + } + if (differentString(group->name, "user")) + isFirstNotCtGroup = FALSE; + + /* Add supertracks to track list, sort by priority and + * determine if they have visible member tracks */ + groupTrackListAddSuper(cart, group); + + /* Display track controls */ + for (tr = group->trackList; tr != NULL; tr = tr->next) + { + struct track *track = tr->track; + if (tdbIsSuperTrackChild(track->tdb)) + /* don't display supertrack members */ + continue; + myControlGridStartCell(cg, isOpen, group->name); + if (track->hasUi) + { + char *url = trackUrl(track->track, chromName); + char *longLabel = replaceChars(track->longLabel, "\"", """); + if(trackDbSetting(track->tdb, "wgEncode") != NULL) + hPrintf("\n"); + hPrintf("", url, longLabel); + freeMem(url); + freeMem(longLabel); + } + hPrintf(" %s", track->shortLabel); + if (tdbIsSuper(track->tdb)) + hPrintf("..."); + hPrintf("
"); + if (track->hasUi) + hPrintf(""); + + if (hTrackOnChrom(track->tdb, chromName)) + { + if (tdbIsSuper(track->tdb)) + superTrackDropDown(cart, track->tdb, + superTrackHasVisibleMembers(track->tdb)); + else + { + /* check for option of limiting visibility to one mode */ + hTvDropDownClassVisOnly(track->track, track->visibility, + track->canPack, (track->visibility == tvHide) ? + "hiddenText" : "normalText", + trackDbSetting(track->tdb, "onlyVisibility")); + } + } + else + /* If track is not on this chrom print an informational + message for the user. */ + hPrintf("[No data-%s]", chromName); + controlGridEndCell(cg); + } + /* now finish out the table */ + if (group->next != NULL) + controlGridEndRow(cg); + } + endControlGrid(&cg); + } + + if (measureTiming) + { + hPrintf("track, load time, draw time, total
\n"); + for (track = trackList; track != NULL; track = track->next) + { + if (track->visibility == tvHide) + continue; + if (trackIsCompositeWithSubtracks(track)) //TODO: Change when tracks->subtracks are always set for composite + { + struct track *subtrack; + for (subtrack = track->subtracks; subtrack != NULL; + subtrack = subtrack->next) + if (isSubtrackVisible(subtrack)) + hPrintf("%s, %d, %d, %d
\n", subtrack->shortLabel, + subtrack->loadTime, subtrack->drawTime, + subtrack->loadTime + subtrack->drawTime); + } + else + { + hPrintf("%s, %d, %d, %d
\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
\n", + track->shortLabel, track->subtracks->loadTime); + } + } + } + hPrintf("\n"); + } +if (showTrackControls) + hButton("hgt.refresh", "refresh"); +hPrintf("\n"); + +#ifdef SLOW +/* We'll rely on the end of program to do the cleanup. + * It turns out that the 'free' routine on Linux is + * quite slow. For chromosome level views the browser + * spends about 1/3 of it's time doing the cleanup + * below if it's enabled. Since we really don't + * need to reclaim this memory at this point I'm + * taking this out. Please don't delete the code though. + * I'll like to keep it for testing now and then. -jk. */ + +/* Clean up. */ +for (track = trackList; track != NULL; track = track->next) + { + if (track->visibility != tvHide) + { + if (track->freeItems != NULL) + track->freeItems(track); + lmCleanup(&track->lm); + } + } +#endif /* SLOW */ +hPrintf("\n"); + +/* hidden form for custom tracks CGI */ +hPrintf("", hgCustomName()); +cartSaveSession(cart); +hPrintf("\n"); + +pruneRedundantCartVis(trackList); +} + +static void toggleRevCmplDisp() +/* toggle the reverse complement display mode */ +{ +// forces complement bases to match display +revCmplDisp = !revCmplDisp; +cartSetBooleanDb(cart, database, REV_CMPL_DISP, revCmplDisp); +cartSetBooleanDb(cart, database, COMPLEMENT_BASES_VAR, revCmplDisp); +} + +void zoomToSize(int newSize) +/* Zoom so that center stays in same place, + * but window is new size. If necessary move + * center a little bit to keep it from going past + * edges. */ +{ +int center = ((long long int)winStart + (long long int)winEnd)/2; +if (center < 0) + errAbort("zoomToSize: error computing center: %d = (%d + %d)/2\n", + center, winStart, winEnd); +if (newSize > seqBaseCount) + newSize = seqBaseCount; +winStart = center - newSize/2; +winEnd = winStart + newSize; +if (winStart <= 0) + { + winStart = 0; + winEnd = newSize; + } +else if (winEnd > seqBaseCount) + { + winEnd = seqBaseCount; + winStart = winEnd - newSize; + } +winBaseCount = winEnd - winStart; +} + +void zoomAroundCenter(double amount) +/* Set ends so as to zoom around center by scaling amount. */ +{ +double newSizeDbl = (winBaseCount*amount + 0.5); +int newSize; +if (newSizeDbl > seqBaseCount) + newSize = seqBaseCount; +else if (newSizeDbl < 1.0) + newSize = 1; +else + newSize = (int)newSizeDbl; +zoomToSize(newSize); +} + +void zoomToBaseLevel() +/* Set things so that it's zoomed to base level. */ +{ +zoomToSize(insideWidth/tl.mWidth); +if (rulerMode == tvHide) + cartSetString(cart, "ruler", "dense"); +} + +void relativeScroll(double amount) +/* Scroll percentage of visible window. */ +{ +int offset; +int newStart, newEnd; +if (revCmplDisp) + amount = -amount; +offset = (int)(amount * winBaseCount); +/* Make sure don't scroll of ends. */ +newStart = winStart + offset; +newEnd = winEnd + offset; +if (newStart < 0) + offset = -winStart; +else if (newEnd > seqBaseCount) + offset = seqBaseCount - winEnd; + +/* Move window. */ +winStart += offset; +winEnd += offset; +} + +void dinkWindow(boolean start, int dinkAmount) +/* Move one end or other of window a little. */ +{ +if (revCmplDisp) + { + start = !start; + dinkAmount = -dinkAmount; + } +if (start) + { + winStart += dinkAmount; + if (winStart < 0) winStart = 0; + } +else + { + winEnd += dinkAmount; + if (winEnd > seqBaseCount) + winEnd = seqBaseCount; + } +} + +int dinkSize(char *var) +/* Return size to dink. */ +{ +char *stringVal = cartOptionalString(cart, var); +double x; +int insideX = trackOffsetX(); /* The global versions of these are not yet set */ +int insideWidth = tl.picWidth-gfxBorder-insideX; +double guideBases = (double)guidelineSpacing * (double)(winEnd - winStart) + / ((double)insideWidth); + +if (stringVal == NULL || !isdigit(stringVal[0])) + { + stringVal = "1"; + cartSetString(cart, var, stringVal); + } +x = atof(stringVal); +int ret = round(x*guideBases); + +return (ret == 0) ? 1 : ret; +} + +void handlePostscript() +/* Deal with Postscript output. */ +{ +struct tempName psTn, ideoPsTn; +char *pdfFile = NULL, *ideoPdfFile = NULL; +ZeroVar(&ideoPsTn); +trashDirFile(&psTn, "hgt", "hgt", ".eps"); + +hotLinks(); +printf("

PostScript/PDF Output

\n"); +printf("PostScript images can be printed at high resolution " + "and edited by many drawing programs such as Adobe " + "Illustrator."); +doTrackForm(psTn.forCgi, &ideoPsTn); + +// postscript +printf("
    \n"); +printf("
  • Click here " + "to download the current browser graphic in PostScript. ", psTn.forCgi); +if (strlen(ideoPsTn.forCgi)) + printf("
  • Click here " + "to download the current chromosome ideogram in PostScript. ", ideoPsTn.forCgi); +printf("
\n"); + +pdfFile = convertEpsToPdf(psTn.forCgi); +if (strlen(ideoPsTn.forCgi)) + ideoPdfFile = convertEpsToPdf(ideoPsTn.forCgi); +if(pdfFile != NULL) + { + printf("
PDF can be viewed with Adobe Acrobat Reader.\n"); + printf("
    \n"); + printf("
  • Click here " + "to download the current browser graphic in PDF.", pdfFile); + if (ideoPdfFile != NULL) + printf("
  • Click here " + "to download the current chromosome ideogram in PDF.", ideoPdfFile); + printf("
\n"); + freez(&pdfFile); + freez(&ideoPdfFile); + } +else + printf("

PDF format not available"); + + #define RETURN_BUTTON "" + printf(RETURN_BUTTON); +} + +boolean isGenome(char *pos) +/* Return TRUE if pos is genome. */ +{ +pos = trimSpaces(pos); +return(sameWord(pos, "genome") || sameWord(pos, "hgBatch")); +} + +void setRulerMode() +/* Set the rulerMode variable from cart. */ +{ +char *s = cartUsualString(cart, RULER_TRACK_NAME, "dense"); +if (sameWord(s, "full") || sameWord(s, "on")) + rulerMode = tvFull; +else if (sameWord(s, "dense")) + rulerMode = tvDense; +else + rulerMode = tvHide; +} + +void setLayoutGlobals() +/* Figure out basic dimensions of display. */ +{ +withIdeogram = cartUsualBoolean(cart, "ideogram", TRUE); +withLeftLabels = cartUsualBoolean(cart, "leftLabels", TRUE); +withCenterLabels = cartUsualBoolean(cart, "centerLabels", TRUE); +withGuidelines = cartUsualBoolean(cart, "guidelines", TRUE); +withNextItemArrows = cartUsualBoolean(cart, "nextItemArrows", FALSE); +withNextExonArrows = cartUsualBoolean(cart, "nextExonArrows", TRUE); +if (!hIsGsidServer()) + { + revCmplDisp = cartUsualBooleanDb(cart, database, REV_CMPL_DISP, FALSE); + } +withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE); +insideX = trackOffsetX(); +insideWidth = tl.picWidth-gfxBorder-insideX; + +} + +void tracksDisplay() +/* Put up main tracks display. This routine handles zooming and + * scrolling. */ +{ +char newPos[256]; +char *defaultPosition = hDefaultPos(database); +char titleVar[256]; +position = getPositionFromCustomTracks(); +if (NULL == position) + { + position = cloneString(cartUsualString(cart, "position", NULL)); + } + +/* default if not set at all, as would happen if it came from a URL with no + * position. Otherwise tell them to go back to the gateway. Also recognize + * "default" as specifying the default position. */ +if (((position == NULL) || sameString(position, "default")) + && (defaultPosition != NULL)) + position = cloneString(defaultPosition); +if (sameString(position, "")) + { + hUserAbort("Please go back and enter a coordinate rangeor a search term in the \"position\" field.
For example: chr22:20100000-20200000.\n"); + } + +chromName = NULL; +winStart = 0; +if (isGenome(position) || NULL == + (hgp = findGenomePos(database, position, &chromName, &winStart, &winEnd, cart))) + { + if (winStart == 0) /* number of positions found */ + { + freeMem(position); + position = cloneString(cartUsualString(cart, "lastPosition", defaultPosition)); + hgp = findGenomePos(database, position, &chromName, &winStart, &winEnd,cart); + if(hgp != NULL && position != defaultPosition) + cartSetString(cart, "position", position); + } + } + +/* After position is found set up hash of matches that should + be drawn with names highlighted for easy identification. */ +createHgFindMatchHash(); + +/* This means that no single result was found +I.e., multiple results may have been found and are printed out prior to this code*/ +if (NULL == chromName) + { + return; + } + +seqBaseCount = hChromSize(database, chromName); +winBaseCount = winEnd - winStart; + +/* Figure out basic dimensions of display. This + * needs to be done early for the sake of the + * zooming and dinking routines. */ +setLayoutGlobals(); + +baseShowPos = cartUsualBoolean(cart, BASE_SHOWPOS, FALSE); +baseShowAsm = cartUsualBoolean(cart, BASE_SHOWASM, FALSE); +baseShowScaleBar = cartUsualBoolean(cart, BASE_SCALE_BAR, TRUE); +baseShowRuler = cartUsualBoolean(cart, BASE_SHOWRULER, TRUE); +safef(titleVar,sizeof(titleVar),"%s_%s", BASE_TITLE, database); +baseTitle = cartUsualString(cart, titleVar, ""); +if (sameString(baseTitle, "")) + baseTitle = NULL; + +if (cgiVarExists("hgt.toggleRevCmplDisp")) + toggleRevCmplDisp(); +setRulerMode(); + +/* Do zoom/scroll if they hit it. */ +if (cgiVarExists("hgt.left3")) + relativeScroll(-0.95); +else if (cgiVarExists("hgt.left2")) + relativeScroll(-0.475); +else if (cgiVarExists("hgt.left1")) + relativeScroll(-0.1); +else if (cgiVarExists("hgt.right1")) + relativeScroll(0.1); +else if (cgiVarExists("hgt.right2")) + relativeScroll(0.475); +else if (cgiVarExists("hgt.right3")) + relativeScroll(0.95); +else if (cgiVarExists("hgt.inBase")) + zoomToBaseLevel(); +else if (cgiVarExists("hgt.in3")) + zoomAroundCenter(1.0/10.0); +else if (cgiVarExists("hgt.in2")) + zoomAroundCenter(1.0/3.0); +else if (cgiVarExists("hgt.in1")) + zoomAroundCenter(1.0/1.5); +else if (cgiVarExists("hgt.out1")) + zoomAroundCenter(1.5); +else if (cgiVarExists("hgt.out2")) + zoomAroundCenter(3.0); +else if (cgiVarExists("hgt.out3")) + zoomAroundCenter(10.0); +else if (cgiVarExists("hgt.dinkLL")) + dinkWindow(TRUE, -dinkSize("dinkL")); +else if (cgiVarExists("hgt.dinkLR")) + dinkWindow(TRUE, dinkSize("dinkL")); +else if (cgiVarExists("hgt.dinkRL")) + dinkWindow(FALSE, -dinkSize("dinkR")); +else if (cgiVarExists("hgt.dinkRR")) + dinkWindow(FALSE, dinkSize("dinkR")); + +/* Clip chromosomal position to fit. */ +if (winEnd < winStart) + { + int temp = winEnd; + winEnd = winStart; + winStart = temp; + } +else if (winStart == winEnd) + { + winStart -= 1; + winEnd += 1; + } + +if (winStart < 0) + { + winStart = 0; + } + +if (winEnd > seqBaseCount) + { + winEnd = seqBaseCount; + } + +if (winStart > seqBaseCount) + { + winStart = seqBaseCount - 1000; + } + +winBaseCount = winEnd - winStart; +if (winBaseCount <= 0) + hUserAbort("Window out of range on %s", chromName); +/* Save computed position in cart. */ +sprintf(newPos, "%s:%d-%d", chromName, winStart+1, winEnd); +cartSetString(cart, "org", organism); +cartSetString(cart, "db", database); +cartSetString(cart, "position", newPos); +if (cgiVarExists("hgt.psOutput")) + handlePostscript(); +else + doTrackForm(NULL, NULL); +} + +void chromInfoTotalRow(int count, long long total) +/* Make table row with total number of sequences and size from chromInfo. */ +{ +cgiSimpleTableRowStart(); +cgiSimpleTableFieldStart(); +printf("Total: %d", count); +cgiTableFieldEnd(); +cgiSimpleTableFieldStart(); +printLongWithCommas(stdout, total); +cgiTableFieldEnd(); +cgiTableRowEnd(); +} + +void chromInfoRowsChrom() +/* Make table rows of chromosomal chromInfo name & size, sorted by name. */ +{ +struct slName *chromList = hAllChromNames(database); +struct slName *chromPtr = NULL; +long long total = 0; + +slSort(&chromList, chrSlNameCmp); +for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) + { + unsigned size = hChromSize(database, chromPtr->name); + cgiSimpleTableRowStart(); + cgiSimpleTableFieldStart(); + printf("%s", + hgTracksName(), cartSessionVarName(), cartSessionId(cart), + chromPtr->name, chromPtr->name); + cgiTableFieldEnd(); + cgiTableFieldStartAlignRight(); + printLongWithCommas(stdout, size); + puts("  "); + cgiTableFieldEnd(); + cgiTableRowEnd(); + total += size; + } +chromInfoTotalRow(slCount(chromList), total); +slFreeList(&chromList); +} + +void chromInfoRowsNonChrom(int limit) +/* Make table rows of non-chromosomal chromInfo name & size, sorted by size. */ +{ +struct sqlConnection *conn = hAllocConn(database); +struct sqlResult *sr = NULL; +char **row = NULL; +long long total = 0; +char query[512]; +char msg1[512], msg2[512]; +int seqCount = 0; +boolean truncating; + +seqCount = sqlQuickNum(conn, "select count(*) from chromInfo"); +truncating = (limit > 0) && (seqCount > limit); + +if (!truncating) + { + sr = sqlGetResult(conn, "select chrom,size from chromInfo order by size desc"); + } +else + { + + safef(query, sizeof(query), "select chrom,size from chromInfo order by size desc limit %d", limit); + sr = sqlGetResult(conn, query); + } + +while ((row = sqlNextRow(sr)) != NULL) + { + unsigned size = sqlUnsigned(row[1]); + cgiSimpleTableRowStart(); + cgiSimpleTableFieldStart(); + printf("%s", + hgTracksName(), cartSessionVarName(), cartSessionId(cart), + row[0], row[0]); + cgiTableFieldEnd(); + cgiTableFieldStartAlignRight(); + printLongWithCommas(stdout, size); + puts("  "); + cgiTableFieldEnd(); + cgiTableRowEnd(); + total += size; + } +if (!truncating) + { + chromInfoTotalRow(seqCount, total); + } +else + { + safef(msg1, sizeof(msg1), "Limit reached"); + safef(msg2, sizeof(msg2), "%d rows displayed", limit); + cgiSimpleTableRowStart(); + cgiSimpleTableFieldStart(); + puts(msg1); + cgiTableFieldEnd(); + cgiSimpleTableFieldStart(); + puts(msg2); + cgiTableFieldEnd(); + sqlFreeResult(&sr); + safef(query, sizeof(query), "select count(*),sum(size) from chromInfo"); + sr = sqlGetResult(conn, query); + if ((row = sqlNextRow(sr)) != NULL) + { + unsigned scafCount = sqlUnsigned(row[0]); + unsigned totalSize = sqlUnsigned(row[1]); + cgiTableRowEnd(); + safef(msg1, sizeof(msg1), "contig/scaffold
count:"); + safef(msg2, sizeof(msg2), "total size:"); + cgiSimpleTableRowStart(); + cgiSimpleTableFieldStart(); + puts(msg1); + cgiTableFieldEnd(); + cgiSimpleTableFieldStart(); + puts(msg2); + cgiTableFieldEnd(); + cgiTableRowEnd(); + cgiSimpleTableRowStart(); + cgiSimpleTableFieldStart(); + printLongWithCommas(stdout, scafCount); + cgiTableFieldEnd(); + cgiSimpleTableFieldStart(); + printLongWithCommas(stdout, totalSize); + cgiTableFieldEnd(); + } + cgiTableRowEnd(); + } +sqlFreeResult(&sr); +hFreeConn(&conn); +} + +void chromInfoPage() +/* Show list of chromosomes (or scaffolds, etc) on which this db is based. */ +{ +char *position = cartUsualString(cart, "position", hDefaultPos(database)); +char *defaultChrom = hDefaultChrom(database); +char *freeze = hFreezeFromDb(database); +struct dyString *title = dyStringNew(512); +if (stringIn(database, freeze)) + dyStringPrintf(title, "%s %s Browser Sequences", + hOrganism(database), freeze); +else + dyStringPrintf(title, "%s %s (%s) Browser Sequences", + hOrganism(database), freeze, database); +webStartWrapperDetailedNoArgs(cart, database, "", title->string, FALSE, FALSE, FALSE, FALSE); +printf("\n", hgTracksName()); +cartSaveSession(cart); + +puts("Enter a position, or click on a sequence name to view the entire " + "sequence in the genome browser.

"); +puts("position "); +hTextVar("position", addCommasToPos(database, position), 30); +cgiMakeButton("Submit", "submit"); +puts("

"); + +hTableStart(); +cgiSimpleTableRowStart(); +cgiSimpleTableFieldStart(); +puts("Sequence name  "); +cgiTableFieldEnd(); +cgiSimpleTableFieldStart(); +puts("Length (bp) including gaps  "); +cgiTableFieldEnd(); +cgiTableRowEnd(); + +if ((startsWith("chr", defaultChrom) || startsWith("Group", defaultChrom)) && + hChromCount(database) < 100) + chromInfoRowsChrom(); +else + chromInfoRowsNonChrom(1000); + +hTableEnd(); + +hgPositionsHelpHtml(organism, database); +puts(""); +dyStringFree(&title); +webEndSectionTables(); +} + + +void resetVars() +/* Reset vars except for position and database. */ +{ +static char *except[] = {"db", "position", NULL}; +char *cookieName = hUserCookie(); +int sessionId = cgiUsualInt(cartSessionVarName(), 0); +char *hguidString = findCookieData(cookieName); +int userId = (hguidString == NULL ? 0 : atoi(hguidString)); +struct cart *oldCart = cartNew(userId, sessionId, NULL, NULL); +cartRemoveExcept(oldCart, except); +cartCheckout(&oldCart); +cgiVarExcludeExcept(except); +} + +void doMiddle(struct cart *theCart) +/* Print the body of an html file. */ +{ +char *debugTmp = NULL; +/* Uncomment this to see parameters for debugging. */ +/* struct dyString *state = NULL; */ +/* Initialize layout and database. */ +cart = theCart; + +/* #if 1 this to see parameters for debugging. */ +/* Be careful though, it breaks if custom track + * is more than 4k */ +#if 0 +state = cgiUrlString(); +printf("State: %s\n", state->string); +#endif +getDbAndGenome(cart, &database, &organism, oldVars); + +protDbName = hPdbFromGdb(database); +debugTmp = cartUsualString(cart, "hgDebug", "off"); +if(sameString(debugTmp, "on")) + hgDebug = TRUE; +else + hgDebug = FALSE; + +if (hIsGisaidServer()) + { + validateGisaidUser(cart); + } + +setUdcCacheDir(); + +initTl(); +measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming")); + +char *configPageCall = cartCgiUsualString(cart, "hgTracksConfigPage", "notSet"); + +dragZooming = advancedJavascriptFeaturesEnabled(cart); + +/* Do main display. */ + +if (cartUsualBoolean(cart, "hgt.trackImgOnly", FALSE)) + { + trackImgOnly = TRUE; + ideogramToo = cartUsualBoolean(cart, "hgt.ideogramToo", FALSE); + hideControls = TRUE; + withNextItemArrows = FALSE; + withNextExonArrows = FALSE; + hgFindMatches = NULL; // XXXX necessary ??? + } + +hWrites(commonCssStyles()); +jsIncludeFile("jquery.js", NULL); +jsIncludeFile("utils.js", NULL); +if(dragZooming) + { + jsIncludeFile("jquery.imgareaselect.js", NULL); + jsIncludeFile("ajax.js", NULL); + hPrintf("\n"); + jsIncludeFile("jquery.autocomplete.js", NULL); + jsIncludeFile("autocomplete.js", NULL); + } +jsIncludeFile("hgTracks.js", NULL); + +#ifdef LOWELAB +jsIncludeFile("lowetooltip.js", NULL); +#endif + +#if defined(CONTEXT_MENU) || defined(TRACK_SEARCH) +hPrintf("\n"); +hPrintf("\n"); +#ifdef CONTEXT_MENU +jsIncludeFile("jquery.contextmenu.js", NULL); +#endif/// def CONTEXT_MENU +jsIncludeFile("jquery-ui.js", NULL); + +//if (!trackImgOnly) + { +hPrintf("

\n"); +// XXXX stole this and '.hidden' from bioInt.css - needs work +hPrintf("\n"); + } +#endif/// defined(CONTEXT_MENU) || defined(TRACK_SEARCH) +if (cartVarExists(cart, "chromInfoPage")) + { + cartRemove(cart, "chromInfoPage"); + chromInfoPage(); + } +else if (sameWord(configPageCall, "configure") || + sameWord(configPageCall, "configure tracks and display")) + { + cartRemove(cart, "hgTracksConfigPage"); + configPage(); + } +else if (cartVarExists(cart, configHideAll)) + { + cartRemove(cart, configHideAll); + configPageSetTrackVis(tvHide); + } +else if (cartVarExists(cart, configShowAll)) + { + cartRemove(cart, configShowAll); + configPageSetTrackVis(tvDense); + } +else if (cartVarExists(cart, configDefaultAll)) + { + cartRemove(cart, configDefaultAll); + configPageSetTrackVis(-1); + } +else if (cartVarExists(cart, configHideAllGroups)) + { + cartRemove(cart, configHideAllGroups); + struct grp *grp = NULL, *grps = hLoadGrps(database); + for (grp = grps; grp != NULL; grp = grp->next) + collapseGroup(grp->name, TRUE); + configPageSetTrackVis(-2); + } +else if (cartVarExists(cart, configShowAllGroups)) + { + cartRemove(cart, configShowAllGroups); + struct grp *grp = NULL, *grps = hLoadGrps(database); + for (grp = grps; grp != NULL; grp = grp->next) + collapseGroup(grp->name, FALSE); + configPageSetTrackVis(-2); + } +else if (cartVarExists(cart, configHideEncodeGroups)) + { + /* currently not used */ + cartRemove(cart, configHideEncodeGroups); + struct grp *grp = NULL, *grps = hLoadGrps(database); + for (grp = grps; grp != NULL; grp = grp->next) + if (startsWith("encode", grp->name)) + collapseGroup(grp->name, TRUE); + configPageSetTrackVis(-2); + } +else if (cartVarExists(cart, configShowEncodeGroups)) + { + /* currently not used */ + cartRemove(cart, configShowEncodeGroups); + struct grp *grp = NULL, *grps = hLoadGrps(database); + for (grp = grps; grp != NULL; grp = grp->next) + if (startsWith("encode", grp->name)) + collapseGroup(grp->name, FALSE); + configPageSetTrackVis(-2); + } +#ifdef TRACK_SEARCH +else if (cartVarExists(cart, searchTracks)) + { + doSearchTracks(groupList); + } +#endif +else + { + tracksDisplay(); + } +} + +void doDown(struct cart *cart) +{ +printf("

The Browser is Being Updated

\n"); +printf("The browser is currently unavailable. We are in the process of\n"); +printf("updating the database and the display software with a number of\n"); +printf("new tracks, including some gene predictions. Please try again tomorrow.\n"); +} +
\n"); + + hButtonWithOnClick("hgt.collapseGroups", "collapse all", "collapse all track groups", "return setAllTrackGroupVisibility(false)"); + hPrintf("" + "Use drop-down controls below and press refresh to alter tracks " + "displayed.
" + "Tracks with lots of items will automatically be displayed in " + "more compact modes.		"); + hButtonWithOnClick("hgt.expandGroups", "expand all", "expand all track groups", "return setAllTrackGroupVisibility(true)"); + hPrintf("
", + MAX_CONTROL_COLUMNS); + } + else + { + hPrintf("", + MAX_CONTROL_COLUMNS-1); + } + hPrintf("
"); + hPrintf("\n",group->name); + hPrintf("\"%s\"  ", + hgTracksName(), cartSidUrlString(cart), + collapseGroupVar(group->name), + otherState, group->name, + group->name, group->name, indicatorImg, indicator); + hPrintf("\n"); + hPrintf("%s", wrapWhiteFont(group->label)); + hPrintf("\n"); + hPrintf("\n"); + hPrintf("