c2e376e7b6d980f41ff903e6374378d668f11770 kate Thu Oct 22 14:41:52 2020 -0700 Multi-region features for sparse tracks. With virt->multi, needs debug. refs #26385 diff --git src/hg/hgTracks/hgTracks.c src/hg/hgTracks/hgTracks.c index d541c7d..d214c99 100644 --- src/hg/hgTracks/hgTracks.c +++ src/hg/hgTracks/hgTracks.c @@ -2238,31 +2238,33 @@ struct highlightVar *hlList = parseHighlightInfo(); if(hlList && theImgBox == NULL) // Only highlight region when imgBox is not used. (pdf and show-image) { struct highlightVar *h; for (h=hlList; h; h=h->next) { if (virtualSingleChrom()) // DISGUISE VMODE { if ((h->db && sameString(h->db, database)) && (h->chrom && sameString(h->chrom,chromName))) { char position[1024]; safef(position, sizeof position, "%s:%ld-%ld", h->chrom, h->chromStart, h->chromEnd); char *newPosition = undisguisePosition(position); // UN-DISGUISE VMODE - if (startsWith("virt:", newPosition)) + if (startsWith(MULTI_REGION_CHROM, newPosition)) + newPosition = replaceChars(position, OLD_MULTI_REGION_CHROM, MULTI_REGION_CHROM); + if (startsWith(MULTI_REGION_CHROM, newPosition)) { parseVPosition(newPosition, &h->chrom, &h->chromStart, &h->chromEnd); } } } if ((h->db && sameString(h->db, database)) && (h->chrom && sameString(h->chrom,virtChromName)) && (h->chromEnd != 0) && (h->chromStart <= virtWinEnd && h->chromEnd >= virtWinStart)) { h->chromStart = max(h->chromStart, virtWinStart); h->chromEnd = min(h->chromEnd, virtWinEnd); double pixelsPerBase = (double)fullInsideWidth/(virtWinEnd - virtWinStart); @@ -2765,31 +2767,31 @@ { int s = max(start, w->winStart); int e = min(end, w->winEnd); long cs = s - w->winStart + w->virtStart; long ce = e - w->winStart + w->virtStart; if (newStart == -1) newStart = cs; newEnd = ce; } lastW = w; } if (newStart == -1) // none of the windows intersected with the position return position; // return original // return new virt undisguised position as a string char newPos[1024]; -safef (newPos, sizeof newPos, "virt:%ld-%ld", (newStart+1), newEnd); +safef (newPos, sizeof newPos, "%s:%ld-%ld", MULTI_REGION_CHROM, (newStart+1), newEnd); return cloneString(newPos); } char *windowsSpanPosition() /* Return a position string that spans all the windows. * Windows should be on same chrom and ascending and non-overlapping.*/ { char buf[256]; char *chromName = windows->chromName; int start = windows->winStart; struct window *w = windows, *last = NULL; while(w->next) // find last window { last = w; @@ -5364,35 +5366,37 @@ } if (!exists) { hvGfxSetClip(bgImg, fullInsideX, 0, fullInsideWidth, pixHeight); y = gfxBorder; if (virtMode) { // vertical windows separators if (emAltHighlight) { // light blue alternating backgrounds - Color lightBlue = hvGfxFindRgb(bgImg, &guidelineColor); + Color lightBlue = hvGfxFindRgb(bgImg, &lightGuidelineColor); + //int highlightY = (baseTitle ? titleHeight+1000 : 0); + int highlightY = 0; for (window=windows; window; window=window->next) // background under every other window { if (window->regionOdd) - hvGfxBox(bgImg, window->insideX, 0, window->insideWidth, pixHeight, lightBlue); + hvGfxBox(bgImg, window->insideX, highlightY, window->insideWidth, pixHeight, lightBlue); } } else { // red vertical lines Color lightRed = hvGfxFindRgb(bgImg, &vertWindowSeparatorColor); for (window=windows->next; window; window=window->next) // skip first window, not needed hvGfxBox(bgImg, window->insideX, 0, 1, pixHeight, lightRed); } } else { int x; Color lightBlue = hvGfxFindRgb(bgImg, &guidelineColor); for (x = fullInsideX+guidelineSpacing-1; x<pixWidth; x += guidelineSpacing) @@ -8597,30 +8601,41 @@ hPrintf("<CENTER>"); } /* Make line that says position. */ { char buf[256]; char *survey = cfgOptionEnv("HGDB_SURVEY", "survey"); char *surveyLabel = cfgOptionEnv("HGDB_SURVEY_LABEL", "surveyLabel"); char *javascript = "document.location = '/cgi-bin/hgTracks?db=' + document.TrackForm.db.options[document.TrackForm.db.selectedIndex].value;"; if (containsStringNoCase(database, "zoo")) { hPuts("Organism "); printAssemblyListHtmlExtra(database, "change", javascript); } + if (sameString(virtModeType, "default")) + { + hButtonMaybePressed("hgTracksConfigMultiRegionPage", "multi-region", + "Configure view in multi-region display mode", + "popUpHgt.hgTracks('multi-region config'); return false;", FALSE); + } + else + { + hButtonWithMsg("hgt.exitMultiRegion", "exit multi-region", "Exit multi-region display mode"); + } + hPrintf(" "); if (virtualSingleChrom()) // DISGUISE VMODE safef(buf, sizeof buf, "%s", windowsSpanPosition()); else safef(buf, sizeof buf, "%s:%ld-%ld", virtChromName, virtWinStart+1, virtWinEnd); position = cloneString(buf); char *pressedClass = "", *showVirtRegions = ""; if (differentString(virtModeType, "default")) { pressedClass = "pressed"; showVirtRegions = "show multi-region position ranges and "; } hPrintf("<span class='positionDisplay %s' id='positionDisplay' " "title='click to %s copy position to input box'>%s</span>", @@ -9442,49 +9457,57 @@ { char titleVar[256]; char *oldPosition = cartUsualString(cart, "oldPosition", ""); boolean findNearest = cartUsualBoolean(cart, "findNearest", FALSE); cartRemove(cart, "findNearest"); boolean positionIsVirt = FALSE; position = getPositionFromCustomTracks(); if (NULL == position) { position = cartGetPosition(cart, database, &lastDbPosCart); if (sameOk(cgiOptionalString("position"), "lastDbPos")) { restoreSavedVirtPosition(); } - if (startsWith("virt:", position)) + if (startsWith(OLD_MULTI_REGION_CHROM, position)) + position = replaceChars(position, OLD_MULTI_REGION_CHROM, MULTI_REGION_CHROM); + if (startsWith(MULTI_REGION_CHROM, position)) { position = stripCommas(position); // sometimes the position string arrives with commas in it. positionIsVirt = TRUE; } } - if (sameString(position, "")) { hUserAbort("Please go back and enter a coordinate range or a search term in the \"search term\" field.<br>For example: chr22:20100000-20200000.\n"); } if (!positionIsVirt) { if (! resolvePosition(&position)) return; } +if (cgiVarExists("hgt.exitMultiRegion")) + { + cartRemove(cart, "hgt.exitMultiRegion"); + cartSetString(cart, "virtModeType", "default"); + cartSetBoolean(cart, "virtMode", FALSE); + } + virtMode = cartUsualBoolean(cart, "virtMode", FALSE); /* Figure out basic dimensions of display. This * needs to be done early for the sake of the * zooming and dinking routines. */ setLayoutGlobals(); virtModeType = cartUsualString(cart, "virtModeType", virtModeType); if (positionIsVirt && virtualSingleChrom()) { // we need chromName to be set before initRegionList() gets called. position = cartUsualString(cart, "nonVirtPosition", ""); if (!sameString(position,"")) parseNonVirtPosition(position); @@ -9560,31 +9583,33 @@ jsonForConvert = newJsonObject(newHash(8)); jsonObjectAdd(jsonForConvert, "virtWinStart", newJsonNumber(virtWinStart)); jsonObjectAdd(jsonForConvert, "virtWinEnd", newJsonNumber(virtWinEnd)); struct dyString *dy = dyStringNew(1024); jsonDyStringPrint(dy, (struct jsonElement *) jsonForConvert, "convertChromToVirtChrom", 0); jsInline(dy->string); dyStringFree(&dy); } return; } lastVirtModeExtraState = cartUsualString(cart, "lastVirtModeExtraState", lastVirtModeExtraState); // DISGUISED POSITION -if (!startsWith("virt:", position) && (virtualSingleChrom())) +if (startsWith(OLD_MULTI_REGION_CHROM, position)) + position = replaceChars(position, OLD_MULTI_REGION_CHROM, MULTI_REGION_CHROM); +if (!startsWith(MULTI_REGION_CHROM, position) && (virtualSingleChrom())) { // "virtualSingleChrom trying to find best vchrom location corresponding to chromName, winStart, winEnd findNearest = TRUE; // try to find the nearest match if (!(chromName && findNearestVirtMatch(chromName, winStart, winEnd, findNearest, &virtWinStart, &virtWinEnd))) { // create 10k window near middle of vchrom warn("Your new regions are not near previous location. Using middle of new coordinates."); virtWinStart = virtSeqBaseCount / 2; virtWinEnd = virtWinStart + 10000; if (virtWinEnd > virtSeqBaseCount) virtWinEnd = virtSeqBaseCount; } virtMode = TRUE; } @@ -9695,31 +9720,31 @@ { // try to set view to entire vchrom virtWinStart = 0; virtWinEnd = virtSeqBaseCount; virtMode = TRUE; // TODO what if the full-vchrom view has "too many windows" // check if virtRegionCount > 4000? } remapHighlightPos(); } } if (virtMode) - virtChromName = "virt"; + virtChromName = MULTI_REGION_CHROM; else virtChromName = chromName; virtWinBaseCount = virtWinEnd - virtWinStart; baseShowPos = cartUsualBoolean(cart, BASE_SHOWPOS, FALSE); baseShowAsm = cartUsualBoolean(cart, BASE_SHOWASM, FALSE); baseShowScaleBar = cartUsualBoolean(cart, BASE_SCALE_BAR, TRUE); baseShowRuler = cartUsualBoolean(cart, BASE_SHOWRULER, TRUE); safef(titleVar,sizeof(titleVar),"%s_%s", BASE_TITLE, database); baseTitle = cartUsualString(cart, titleVar, ""); if (sameString(baseTitle, "")) baseTitle = NULL;