ba31086d08e0c051ad23953fc9bb462e9135cb58 galt Wed Feb 24 13:06:05 2016 -0800 Removing DEBUG warnings from hgTracks multi-region code. diff --git src/hg/hgTracks/hgTracks.c src/hg/hgTracks/hgTracks.c index 743d1c0..ca571e3 100644 --- src/hg/hgTracks/hgTracks.c +++ src/hg/hgTracks/hgTracks.c @@ -620,69 +620,65 @@ struct track *ideoTrack = NULL; MgFont *font = tl.font; char *mapName = "ideoMap"; struct hvGfx *hvg; boolean doIdeo = TRUE; int ideoWidth = round(.8 *tl.picWidth); int ideoHeight = 0; int textWidth = 0; struct tempName pngTn; boolean nukeIdeoFromList = FALSE; if (ideoTn == NULL) ideoTn = &pngTn; // not returning value ideoTrack = chromIdeoTrack(*pTrackList); -//warn("makeChromIdeoImage ideoTrack=%lu ideoTrack->track=%s", (unsigned long) ideoTrack, ideoTrack ? ideoTrack->track : ""); // DEBUG REMOVE - /* If no ideogram don't draw. */ if(ideoTrack == NULL) { doIdeo = FALSE; } else if(trackImgOnly && !ideogramToo) { doIdeo = FALSE; } else { - //warn("makeChromIdeoImage about to remove track from group and tracklist"); // DEBUG REMOVE /* Remove the track from the group and track list. */ removeTrackFromGroup(ideoTrack); slRemoveEl(pTrackList, ideoTrack); nukeIdeoFromList = TRUE; /* Fix for hide all button hiding the ideogram as well. */ if(withIdeogram && ideoTrack->items == NULL) { ideoTrack->visibility = tvDense; ideoTrack->loadItems(ideoTrack); } limitVisibility(ideoTrack); /* If hidden don't draw. */ if(ideoTrack->limitedVis == tvHide || !withIdeogram) doIdeo = FALSE; } // TODO use DIV in future (can update entire div at once in hgTracks.js) //hPrintf("<DIV id='chromIdeoDiv'>\n"); // FYI from testing, I see that there is code that inserts warning error messages // right before ideoMap, so any changes to that name or adding the DIV would require // updating the warning-insertion target name. if(doIdeo) { - //warn("makeChromIdeoImage doIdeo = TRUE"); // DEBUG REMOVE char startBand[16]; char endBand[16]; char title[64]; // was 32 startBand[0] = endBand[0] = '\0'; fillInStartEndBands(ideoTrack, startBand, endBand, sizeof(startBand)); /* Start up client side map. */ if (!psOutput) hPrintf("<MAP Name=%s>\n", mapName); /* Draw the ideogram. */ ideoHeight = gfxBorder + ideoTrack->height; if (psOutput) { trashDirFile(ideoTn, "hgtIdeo", "hgtIdeo", ".ps"); hvg = hvGfxOpenPostScript(ideoWidth, ideoHeight, ideoTn->forCgi); } @@ -1421,50 +1417,46 @@ portWidth = portWidth-gfxBorder-insideX; } int arrowWidth = insideHeight; int arrowButtonWidth = arrowWidth + 2 * NEXT_ITEM_ARROW_BUFFER; int rightButtonX = portX + portWidth - arrowButtonWidth - 1; char buttonText[256]; Color fillColor = lightGrayIndex(); labelColor = blackIndex(); hvGfxNextItemButton(hvg, rightButtonX + NEXT_ITEM_ARROW_BUFFER, y, arrowWidth, arrowWidth, labelColor, fillColor, TRUE); hvGfxNextItemButton(hvg, portX + NEXT_ITEM_ARROW_BUFFER, y, arrowWidth, arrowWidth, labelColor, fillColor, FALSE); safef(buttonText, ArraySize(buttonText), "hgt.prevItem=%s", track->track); -// warn("portX=%d y+1=%d portWidth=%d arrowButtonWidth=%d track=%s", portX, y+1, portWidth, arrowButtonWidth, track->track); // DEBUG REMOVE - mapBoxReinvoke(hvg, portX, y + 1, arrowButtonWidth, insideHeight, track, FALSE, NULL, 0, 0, (revCmplDisp ? "Next item" : "Prev item"), buttonText); #ifdef IMAGEv2_SHORT_TOGGLE char *label = (theImgBox ? track->longLabel : parentTrack->longLabel); int width = portWidth - (2 * arrowButtonWidth); int x = portX + arrowButtonWidth; // make toggle cover only actual label int size = mgFontStringWidth(font,label) + 12; // get close enough to the label if (width > size) { x += width/2 - size/2; width = size; } mapBoxToggleVis(hvg, x, y + 1, width, insideHeight, (theImgBox ? track : parentTrack)); #else///ifndef IMAGEv2_SHORT_TOGGLE -//warn("portX+arrowButtonWidth=%d y+1=%d portWidth-(2*arrowButtonWidth)=%d arrowButtonWidth=%d track=%s", - //portX + arrowButtonWidth, y+1, portWidth - (2 * arrowButtonWidth), arrowButtonWidth, track->track); // DEBUG REMOVE mapBoxToggleVis(hvg, portX + arrowButtonWidth, y + 1, portWidth - (2 * arrowButtonWidth), insideHeight, (theImgBox ? track : parentTrack)); #endif///ndef IMAGEv2_SHORT_TOGGLE // use the last window globals instead of the first struct window *w=windows; while(w->next) w = w->next; setGlobalsFromWindow(w); // use last window safef(buttonText, ArraySize(buttonText), "hgt.nextItem=%s", track->track); mapBoxReinvoke(hvg, portX + portWidth - arrowButtonWidth, y + 1, arrowButtonWidth, insideHeight, track, FALSE, NULL, 0, 0, (revCmplDisp ? "Prev item" : "Next item"), buttonText); setGlobalsFromWindow(windows); // restore first window @@ -2085,44 +2077,41 @@ // store highlight information { char *db; char *chrom; long chromStart; long chromEnd; char *hexColor; }; struct highlightVar *parseHighlightInfo() // Parse highlight info from cart var // db.chrom:start-end#hexColor { struct highlightVar *h = NULL; char *highlightDef = cartOptionalString(cart, "highlight"); -//warn("parseHighlightInfo highlight=%s", highlightDef); // DEBUG REMOVE if(highlightDef) { AllocVar(h); h->db = cloneNextWordByDelimiter(&highlightDef,'.'); h->chrom = cloneNextWordByDelimiter(&highlightDef,':'); // long to handle virt chrom coordinates h->chromStart = atol(cloneNextWordByDelimiter(&highlightDef,'-')); h->chromEnd = atol(cloneNextWordByDelimiter(&highlightDef,'#')); h->chromStart--; // Not zero based if (highlightDef && *highlightDef != '\0') h->hexColor = cloneString(highlightDef); - //verbose(1, "DEBUG GALT highlightRegion() db=%s chrom=%s chromStart=%ld chromEnd=%ld virtChromName=%s winStart=%ld winEnd=%ld\n", - //h->db, h->chrom, h->chromStart, h->chromEnd, virtChromName, virtWinStart, virtWinEnd); // DEBUG REMOVE } return h; } void highlightRegion(struct cart *cart, struct hvGfx *hvg, int imagePixelHeight) // Highlights a region in the image. Only done if theImgBox is not defined. // Thus it is done for ps/pdf and view image but the hgTracks image is highlighted via js { struct highlightVar *h = parseHighlightInfo(); if(h && theImgBox == NULL) // Only highlight region when imgBox is not used. (pdf and show-image) { if (virtualSingleChrom()) // DISGUISE VMODE { if ((h->db && sameString(h->db, database)) @@ -2192,32 +2181,30 @@ //void menuBarAppendExtTools() ///* printf a little javascript that adds entries to a menu */ //{ // char url[SMALLBUF]; // safef(url,ArraySize(url),"hgTracks?%s=%s&hgt.redirectTool=crispor",cartSessionVarName(), cartSessionId(cart)); // printf("<script>\n"); // printf("jQuery(document).ready( function() {\n"); // domAddMenu("view", "sendto", "Send to"); // domAppendToMenu("sendto", url, "Tefor CRISPR sites"); // printf("});\n"); // printf("</script>\n"); //} -//--- GALT - char *rgbColorToString(struct rgbColor color) /* make rgbColor into printable string */ { char buf[256]; safef(buf, sizeof buf, "rgbColor r:%d g:%d b:%d", color.r, color.g, color.b); return cloneString(buf); } char *trackDumpString(struct track *track) /* Write out info on track to string */ { struct dyString *dy = dyStringNew(256); dyStringPrintf(dy, "next: %lu\n", (unsigned long)track->next); // struct track *next; /* Next on list. */ @@ -2569,114 +2556,107 @@ char *dash = strchr(vPos, '-'); if (!dash) errAbort("position has no dash"); *colon = 0; *dash = 0; *pChrom = cloneString(vPos); *pStart = atoi(colon+1) - 1; *pEnd = atoi(dash+1); } char *disguisePositionVirtSingleChrom(char *position) // DISGUISE VMODE /* Hide the virt position, convert to real single chrom span. * position should be virt chrom span. * Can handle anything in the virt single chrom. */ { -//warn("disguisePosition position="+position); // DEBUG REMOVE /* parse Virt position */ char *chrom = NULL; long start = 0; long end = 0; parseVPosition(position, &chrom, &start, &end); if (!sameString(chrom, "virt")) return position; // return original -//warn("start="+start+" end="+end); // DEBUG REMOVE struct window *windows = makeWindowListFromVirtChrom(start, end); char *nonVirtChromName = windows->chromName; if (!sameString(nonVirtChromName, chromName)) return position; // return original int nonVirtWinStart = windows->winStart; int nonVirtWinEnd = windows->winEnd; struct window *w; for (w=windows->next; w; w=w->next) { - //warn("w->chromName=%s w->winStart=%d w->winEnd=%d",w->chromName, w->winStart, w->winEnd); // DEBUG REMOVE if (!sameString(w->chromName, nonVirtChromName)) return position; // return original if (w->winEnd < nonVirtWinEnd) return position; // return original nonVirtWinEnd = w->winEnd; } char nvPos[256]; safef(nvPos, sizeof nvPos, "%s:%d-%d", nonVirtChromName, nonVirtWinStart+1, nonVirtWinEnd); slFreeList(&windows); return cloneString(nvPos); } char *undisguisePosition(char *position) // UN-DISGUISE VMODE /* Find the virt position * position should be real chrom span. * Limitation: can only convert things in the current windows set. */ { -//warn("undisguisePosition position="+position); // DEBUG REMOVE /* parse NonVirt position */ char *chrom = NULL; int start = 0; int end = 0; parseNVPosition(position, &chrom, &start, &end); if (!sameString(chrom, chromName)) return position; // return original long newStart = -1; long newEnd = -1; struct window *lastW = NULL; struct window *w = NULL; -//warn("start="+start+" end="+end); // DEBUG REMOVE for (w = windows; w; w=w->next) { // double check chrom is same thoughout all windows, otherwise warning, return original value if (!sameString(w->chromName, chromName)) { return position; // return original } // check that the regions are ascending and non-overlapping if (lastW && w->winStart < lastW->winEnd) { return position; // return original } // overlap with position? // if intersection, if (w->winEnd > start && end > w->winStart) { int s = max(start, w->winStart); int e = min(end, w->winEnd); long cs = s - w->winStart + w->virtStart; long ce = e - w->winStart + w->virtStart; - //warn("cs="+cs+" ce="+ce); // DEBUG REMOVE 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); -//warn("undisguisePosition newPos="+newPos); // DEBUG REMOVE 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; @@ -2747,72 +2727,69 @@ } } v->start = virtRegion->start - leftWindowPadding; v->end = virtRegion->end + rightWindowPadding; if (v->start < 0) v->start = 0; if (v->end >= chromSize) v->end = chromSize; regionBases += (v->end - v->start); slAddHead(&newList, v); lastVirtRegion = virtRegion; lastChrom = virtRegion->chrom; ++regionCount; } -//warn("After padding, %d regions", regionCount); // DEBUG REMOVE slReverse(&newList); -virtRegionList = newList; // update new list -- TODO should the old one be freed? if so, the chrom name should use cloneString +virtRegionList = newList; // update new list -- +// TODO should the old one be freed? if so, the chrom name should use cloneString } void makeVirtChrom() /* build virtual chrom array from virt region list */ { virtRegionCount = slCount(virtRegionList); AllocArray(virtChrom, virtRegionCount); struct virtRegion *v; int i = 0; long totalBases = 0; for(v=virtRegionList;v;v=v->next,++i) { virtChrom[i].virtPos = totalBases; virtChrom[i].virtRegion = v; totalBases += (v->end - v->start); - //warn("virtChrom[%d] .virtPos=%ld", i, virtChrom[i].virtPos); // DEBUG REMOVE } virtSeqBaseCount = totalBases; } void virtChromBinarySearch(long target, long *resultIndex, int *resultOffset) /* Do a binary search for the target position in the virtual chrom. * Return virtChrom Index and Offset if found. * Return -1 if target out of range. TODO maybe change to errAbort*/ { //The binary search will either return match or out-of-range. long index = -1; int offset = -1; long a = 0; // start of the array long b = virtRegionCount - 1; // end of array where N = count of regions if (target >=0 && target < virtSeqBaseCount) { while(1) { long c = (a + b) / 2; - //warn("target=%ld a=%ld b=%ld c=%ld virtRegionCount=%d", target, a, b, c, virtRegionCount); // DEBUG REMOVE - if (a > b) { index = b; break; } else if (target == virtChrom[c].virtPos) { // (exact match) index = c; break; } else if (target > virtChrom[c].virtPos) { a = c + 1; } @@ -2880,32 +2857,30 @@ errAbort("unexpected error. virtWinEnd=%ld out of range. virtSeqBaseCount=%ld", virtWinEnd, virtSeqBaseCount); if (virtWinEnd - virtWinStart < 1) errAbort("unexpected error. virtual window size < 1 base. virtWinStart=%ld virtWinEnd=%ld virtSeqBaseCount=%ld", virtWinStart, virtWinEnd, virtSeqBaseCount); long virtIndexStart; int virtOffsetStart; virtChromBinarySearch(virtWinStart, &virtIndexStart, &virtOffsetStart); if (virtIndexStart == -1) errAbort("unexpected failure to find target virtWinStart %ld in virtChrom Array", virtWinStart); long virtIndexEnd; int virtOffsetEnd; virtChromBinarySearch(virtWinEnd, &virtIndexEnd, &virtOffsetEnd); if (virtIndexEnd == -1) errAbort("unexpected failure to find target virtWinEnd %ld in virtChrom Array", virtWinEnd); -//warn("after binary searches, virtIndexStart=%ld virtOffsetStart=%d , virtIndexEnd=%ld virtOffsetEnd=%d", virtIndexStart, virtOffsetStart, virtIndexEnd, virtOffsetEnd); // DEBUG REMOVE - // create new windows list from virt chrom struct window *windows = NULL; long i = virtIndexStart; int winCount = 0; long basesInWindows = 0; // TODO not actually using this variable for(i=virtIndexStart; i <= virtIndexEnd; ++i) { struct window *w; AllocVar(w); w->organism = organism; // obsolete w->database = database; // obsolete struct virtRegion *v = virtChrom[i].virtRegion; long virtPos = virtChrom[i].virtPos; w->chromName = v->chrom; if (i == virtIndexStart) @@ -2960,47 +2935,43 @@ nonVirtWinEnd = w->winEnd; } // TODO Also consider preserving the original bases in windows width (with clipping). char nvPos[256]; safef(nvPos, sizeof nvPos, "%s:%d-%d", nonVirtChromName, nonVirtWinStart+1, nonVirtWinEnd); return cloneString(nvPos); } char *nonVirtPositionFromHighlightPos() /* Must have created the virtual chrom first. * Currently just a hack to use windows, * use the (first) window(s) from that to get real chrom name start end */ { struct highlightVar *h = parseHighlightInfo(); -//if (h) -// warn("remapHighlightPos h-> chrom=%s chromStart=%ld chromEnd=%ld", h->chrom, h->chromStart, h->chromEnd); // DEBUG REMOVE - if (!(h && h->db && sameString(h->db, database) && sameString(h->chrom,"virt"))) return NULL; struct window *windows = makeWindowListFromVirtChrom(h->chromStart, h->chromEnd); char *nonVirtChromName = windows->chromName; int nonVirtWinStart = windows->winStart; int nonVirtWinEnd = windows->winEnd; // Extending this through more of the windows, // if it is on the same chrom and maybe not too far separated. struct window *w; for (w=windows->next; w; w=w->next) { - //warn("w->chromName=%s w->winStart=%d w->winEnd=%d",w->chromName, w->winStart, w->winEnd); // DEBUG REMOVE if (sameString(w->chromName, nonVirtChromName) && w->winEnd > nonVirtWinEnd) nonVirtWinEnd = w->winEnd; } // TODO Also consider preserving the original bases in windows width (with clipping). char nvPos[256]; safef(nvPos, sizeof nvPos, "%s.%s:%d-%d#%s", h->db, nonVirtChromName, nonVirtWinStart+1, nonVirtWinEnd, h->hexColor); return cloneString(nvPos); } void allocPixelsToWindows() /* Allocate pixels to windows, sets insideWidth and insideX * * TODO currently uses a strategy that places a window at a pixel location * directly, because of round-off and missing small windows this can occasionally * lead to gaps not covered by any pixel. Consider replacing it with something @@ -3009,56 +2980,41 @@ { double pixelsPerBase = (double)fullInsideWidth / virtWinBaseCount; long basesUsed = 0; int windowsTooSmall = 0; struct window **pWindows = &windows; struct window *window; int winCount = slCount(windows); for(window=windows;window;window=window->next) { int basesInWindow = window->winEnd - window->winStart; int pixelsInWindow = 0.5 + (double)basesInWindow * pixelsPerBase; // should this round up ? + 0.5? window->insideWidth = pixelsInWindow; window->insideX = fullInsideX + basesUsed * pixelsPerBase; basesUsed += basesInWindow; - //warn("window x = %d width = %d x + width=%d basesInWindow=%d", - //window->insideX, window->insideWidth, window->insideX + window->insideWidth, basesInWindow); // DEBUG REMOVE - if (pixelsInWindow < 1) // remove windows less than one pixel from the list { - //if (windowsTooSmall < 5) - // warn("window x = %d width = %d x + width=%d", window->insideX, window->insideWidth, window->insideX + window->insideWidth); *pWindows = window->next; --winCount; ++windowsTooSmall; } else { pWindows = &window->next; } } -//if (windowsTooSmall > 0) -// warn("Summary: %d windowsTooSmall: (pixelsInWindow < 1)", windowsTooSmall); - -//warn("winCount=%d slCount(windows)=%d #LessThan1Pixel=%d fullInsideWidth=%d virtWinBaseCount=%ld basesUsed=%ld", - //winCount, slCount(windows), windowsTooSmall, fullInsideWidth, virtWinBaseCount, basesUsed); - -// DEBUG REMOVE: -// nextExonArrows are working now -//if (winCount >= 2) -// withNextExonArrows = FALSE; /* Display next exon navigation buttons near center labels? */ } struct positionMatch *virtChromSearchForPosition(char *chrom, int start, int end, boolean findNearest) /* Search the virtual chrom for the query chrom, start, end position * * TODO GALT: Intially this can be a simple brute-force search of the entire virtChrom array. * * However, this will need to be upgraded to using a rangeTree or similar structure * to rapidly return multiple regions that overlap the query position. * */ { struct positionMatch *list=NULL, *p; int nearestRegion = -1; boolean nearestAfter = TRUE; int nearestDistance = INT_MAX; @@ -3104,32 +3060,30 @@ v = virtChrom[i].virtRegion; virtPos = virtChrom[i].virtPos; AllocVar(p); if (nearestAfter) { p->virtStart = virtPos; p->virtEnd = p->virtStart + (end - start); } else { p->virtEnd = virtPos + (v->end - v->start); p->virtStart = p->virtEnd - (end - start); } if (p->virtEnd > virtSeqBaseCount) p->virtEnd = virtSeqBaseCount; - //warn("findNearest: nearestRegion=%d nearestDistance=%d p->virtStart=%ld p->virtEnd=%ld ", - //nearestRegion, nearestDistance, p->virtStart, p->virtEnd); // DEBUG REMOVE slAddHead(&list, p); } slReverse(&list); return list; } int matchVPosCompare(const void *elem1, const void *elem2) /* compare elements based on vPos */ { const struct positionMatch *a = *((struct positionMatch **)elem1); const struct positionMatch *b = *((struct positionMatch **)elem2); if (a->virtStart == b->virtStart) errAbort("matchVPosCompare error should not happen: 2 elements being sorted have the same virtStart=%ld", a->virtStart); else if (a->virtStart > b->virtStart) return 1; @@ -3195,33 +3149,30 @@ } if (!m) break; lastStart = m->virtStart; lastEnd = m->virtEnd; lastM = m; } slReverse(&newList); return newList; } // ---------------------------------- -static void checkMaxWindowToDraw(struct track *tg); // forward declaration // DEBUG REMOVE? - - void initVirtRegionsFromSOD1Hardwired() /* create a testing regionlist from SOD1 (uc002ypa.3) hardwired */ { virtRegionList = NULL; char *chrom="chr21"; //int exonStarts[] = {33031934,33036102,33038761,33039570,33040783}; //int exonEnds[] = {33032154,33036199,33038831,33039688,33041243}; // BASE-level zoom in two 20 bp exons and their on-screen junction int exonStarts[] = {33032134,33036102}; int exonEnds[] = {33032154,33036122}; int i; for(i=0; i<ArraySize(exonStarts); ++i) { struct virtRegion *v; AllocVar(v); @@ -3299,31 +3250,30 @@ char query[256]; sqlSafef(query, sizeof(query), "select chrom, chromStart, chromEnd from %s where name='%s'", table, haplotypeId); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (!row) { warn("no haplotype found for [%s]", haplotypeId); return FALSE; } char *haploChrom = cloneString(row[0]); int haploStart = sqlUnsigned(row[1]); int haploEnd = sqlUnsigned(row[2]); sqlFreeResult(&sr); // what is the size of the alt haplo? int haploSize = hChromSize(database, haplotypeId); // hopefully this will work -//warn("database=%s, haplotypeId=%s, haploSize=%d", database, haplotypeId, haploSize); // DEBUG REMOVE // insert into list replacing original haploChrom record struct virtRegion *before = NULL; boolean found = FALSE; long offset = 0; struct virtRegion *v; while ((v=slPopHead(&after))) { if (sameString(haploChrom, v->chrom)) { found = TRUE; break; } offset += (v->end - v->start); slAddHead(&before, v); @@ -3365,39 +3315,30 @@ v->end = chromSize; defaultVirtWinEnd += haploSize; if (defaultVirtWinEnd > chromSize) defaultVirtWinEnd = chromSize; slAddHead(&virtRegionList, v); slReverse(&virtRegionList); hFreeConn(&conn); defaultVirtWinStart += offset; defaultVirtWinEnd += offset; // concatenate the 3 lists. virtRegionList = slCat(before,slCat(virtRegionList,after)); -// DEBUG REMOVE testing -//warn("initSingleAltHaplotype: offset=%ld", offset); -//long testOffset = 0; -//for (v=virtRegionList; v; v=v->next) -// { -// testOffset += (v->end - v->start); -// warn("%s:%d-%d cumuulative offset %ld", v->chrom, v->start, v->end, testOffset); -// } - return TRUE; } void initVirtRegionsFromKnownCanonicalGenes(char *table) // OBSOLETED by initVirtRegionsFromEMGeneTableExons() /* Create a regionlist from knownCanonical genes (not exons) */ // I was not expecting it, but 20% of the KC genes overlap with others. // Some are cDNAs, some are non-coding RNAs, some just look like junk. // But I have to add special logic to accomodate them. // Currently I just merge until there is no more overlap, // and then I start a new region. So 30K regions should reduce to about 24K regions or less. { struct sqlConnection *conn = hAllocConn(database); virtRegionList = NULL; @@ -3566,31 +3507,30 @@ int rowOffset = 0; char query[256]; int padding = emPadding; if (sameString(virtModeType, "geneMostly")) padding = gmPadding; // knownCanonical Hash struct hash *kcHash = NULL; if (knownCanonical) // filter out alt splicing variants { // load up hash of canonical transcriptIds sqlSafef(query, sizeof(query), "select transcript from %s" //" where chrom not like '%%_hap_%%' and chrom not like '%%_random'" , knownCanonical); if (virtualSingleChrom()) sqlSafefAppend(query, sizeof(query), " where chrom='%s'", chromName); - //warn("query = [%s]", query); // DEBUG REMOVE kcHash = newHash(10); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { hashAdd(kcHash, row[0], NULL); } sqlFreeResult(&sr); } // knownToTag basic hash struct hash *ktHash = NULL; if (knownToTag) // filter out all but Basic { // load up hash of canonical transcriptIds sqlSafef(query, sizeof(query), "select name from %s where value='basic'", knownToTag); ktHash = newHash(10); @@ -3601,31 +3541,30 @@ } sqlFreeResult(&sr); } setEMGeneTrack(); if (!emGeneTable) errAbort("Unexpected error, emGeneTable=NULL in initVirtRegionsFromEMGeneTableExons"); if (hIsBinned(database, emGeneTable)) // skip first bin column if any ++rowOffset; sqlSafef(query, sizeof(query), "select * from %s", emGeneTable); if (virtualSingleChrom()) sqlSafefAppend(query, sizeof(query), " where chrom='%s'", chromName); // TODO GALT may have to change this to in-memory sorting? // refGene is out of order because of genbank continuous loading // also, using where chrom= causes it to use indexes which disturb order returned. sqlSafefAppend(query, sizeof(query), " order by chrom, txStart"); -//warn("query = [%s]", query); // DEBUG REMOVE sr = sqlGetResult(conn, query); char chrom[256] = ""; int start = -1; int end = -1; char lastChrom[256] = ""; int lastStart = -1; int lastEnd = -1; int chromSize = -1; char lastChromSizeChrom[256] = ""; boolean firstTime = TRUE; boolean isEOF = FALSE; struct kce *kceList = NULL, *bestKce, *prevKce; struct genePred *gene = NULL; while (1) @@ -3633,250 +3572,231 @@ while(1) // get input if possible { boolean readIt = FALSE; if (!gene) readIt = TRUE; if (isEOF) readIt = FALSE; if (readIt) { row = sqlNextRow(sr); if (row) { gene = genePredLoad(row+rowOffset); - //warn("GALT loaded gene %s\n", gene->name); // DEBUG REMOVE if (geneMostly) convertGenePredGeneToExon(gene); if (!sameString(lastChromSizeChrom, gene->chrom)) { chromSize = hChromSize(database, gene->chrom); safecpy(lastChromSizeChrom, sizeof lastChromSizeChrom, gene->chrom); } if (padding > 0) padExons(gene, chromSize, padding); // handle padding } else { isEOF = TRUE; } } if (gene && !showNoncoding && (gene->cdsStart == gene->cdsEnd)) { - //warn("GALT skip non-coding gene %s cdsStart==cdsEnd", gene->name); // DEBUG REMOVE + //skip non-coding gene genePredFree(&gene); } if (gene && knownCanonical && !hashLookup(kcHash, gene->name)) { - //warn("GALT skip not in knownCanonical hash gene %s", gene->name); // DEBUG REMOVE + //skip gene not in knownCanonical hash genePredFree(&gene); } if (gene && knownToTag && !hashLookup(ktHash, gene->name)) { - //warn("GALT skip not in knownToTag Basic hash gene %s", gene->name); // DEBUG REMOVE + // skip gene not in knownToTag Basic hash genePredFree(&gene); } boolean transferIt = FALSE; if (gene && !kceList) { transferIt = TRUE; } else if (gene && kceList) { // TODO need to check the chrom equality first int best = findBestKce(kceList, &bestKce, &prevKce); - //warn("GALT check chrom gene->chrom=%s, lastChrom=%s, chrom=%s", gene->chrom, lastChrom, chrom); // DEBUG REMOVE if (sameString(gene->chrom, chrom)) { - //warn("GALT best=%d gene %s exonStart[0]=%d", best, gene->name, gene->exonStarts[0]); // DEBUG REMOVE if (gene->exonStarts[0] < best) transferIt = TRUE; } } if (transferIt) { - //warn("GALT transferred gene %s to kcelist", gene->name); // DEBUG REMOVE // add gene to kce list struct kce *kce; AllocVar(kce); kce->gene = gene; kce->exonNumber = 0; slAddHead(&kceList, kce); safecpy(chrom, sizeof chrom, gene->chrom); gene = NULL; // do not free since it is still in use } - //warn("GALT readIt=%d transferIt=%d", readIt, transferIt); // DEBUG REMOVE if (gene && kceList && !transferIt) break; if (isEOF && !gene) { if (kceList) // flush out the last of the items in kcelist findBestKce(kceList, &bestKce, &prevKce); break; } } boolean printIt = FALSE; if (kceList) { safecpy(chrom, sizeof chrom, bestKce->gene->chrom); start = bestKce->gene->exonStarts[bestKce->exonNumber]; end = bestKce->gene->exonEnds[bestKce->exonNumber]; - //warn("GALT GOT DATA chrom=%s start=%d end=%d lastChrom=%s lastStart=%d lastEnd=%d", - //chrom, start, end, lastChrom, lastStart, lastEnd); // DEBUG REMOVE - if (sameString(chrom, lastChrom)) { if (start <= lastEnd) { - //warn("GALT overlap extend start=%d <= lastEnd=%d, end=%d", start, lastEnd, end); // DEBUG REMOVE - // overlap detected in knownCanonical - // extend current region + // overlap detected, extend current region if (end > lastEnd) { lastEnd = end; } } else { printIt = TRUE; } } else { printIt = TRUE; } } else { printIt = TRUE; isEOF = TRUE; } - //warn("GALT printIt=%d", printIt); // DEBUG REMOVE - if (printIt) { if (firstTime) { firstTime = FALSE; } else { - //warn("GALT adding region %s:%d-%d", lastChrom, lastStart, lastEnd); // DEBUG REMOVE struct virtRegion *v; AllocVar(v); v->chrom = cloneString(lastChrom); v->start = lastStart; v->end = lastEnd; v->strand[0] = '.'; // TODO we should probably just remove the strand field v->strand[1] = 0; slAddHead(&virtRegionList, v); } } if (isEOF && !kceList && !gene) break; if (printIt) { safecpy(lastChrom, sizeof lastChrom, chrom); lastStart = start; lastEnd = end; } - //warn("used up %s exon# %d", bestKce->gene->name, bestKce->exonNumber); // DEBUG REMOVE - // TODO update or remove current thing from kceList ++bestKce->exonNumber; if (bestKce->exonNumber >= bestKce->gene->exonCount) { // remove from kceList genePredFree(&bestKce->gene); if (prevKce) prevKce->next = bestKce->next; else kceList = bestKce->next; freeMem(bestKce); } } sqlFreeResult(&sr); slReverse(&virtRegionList); hashFree(&kcHash); hashFree(&ktHash); hFreeConn(&conn); } void testRegionList() /* check if it is ascending non-overlapping regions. (this is not always a requirement in the most general case, i.e. user-regions) */ { char lastChrom[256]; int lastEnd = -1; struct virtRegion *v; -warn("testRegionList() started DEBUG."); // DEBUG REMOVE for (v=virtRegionList; v; v=v->next) { if (sameString(v->chrom,lastChrom)) { if (v->end < v->start) errAbort("check of region list reveals invalid region %s:%d-%d", v->chrom, v->start, v->end); if (lastEnd > v->start) errAbort("check of region list reveals overlapping regions region %s:%d-%d lastEnd=%d", v->chrom, v->start, v->end, lastEnd); } else { safecpy(lastChrom, sizeof lastChrom, v->chrom); } lastEnd = v->end; } -warn("testRegionList() completed OK."); } // multi-window variables global to hgTracks void setGlobalsFromWindow(struct window *window) /* set global window values */ { currentWindow = window; organism = window->organism; database = window->database; chromName = window->chromName; winStart = window->winStart; winEnd = window->winEnd; insideX = window->insideX; insideWidth = window->insideWidth; winBaseCount = winEnd - winStart; } void initExonStep() /* create exon-like pattern with exonSize and stepSize */ { int winCount = cartUsualInt(cart, "demo2NumWindows", demo2NumWindows); int i; -//int avgWidth = fullInsideWidth/winCount ; // can shrink down to 1 ok! // DEBUG REMOVE -//int x = fullInsideX; int exonSize = cartUsualInt(cart, "demo2WindowSize", demo2WindowSize); //200; //9974; //200; int intronSize = cartUsualInt(cart, "demo2StepSize", demo2StepSize); //200; //15000; // really using it like stepSize as that allows overlapping windows. struct virtRegion *v; for(i=0;i<winCount;++i) { AllocVar(v); //chr21:33,031,597-33,041,570 v->chrom = "chr21"; v->start = 33031597 - 1 + i*(intronSize); v->end = v->start + exonSize; //33041570; slAddHead(&virtRegionList, v); } slReverse(&virtRegionList); //if (winCount >= 2) // withNextExonArrows = FALSE; /* Display next exon navigation buttons near center labels? */ @@ -3892,39 +3812,36 @@ int winCount = 0; char *query = "NOSQLINJ select chrom, size from chromInfo" " where chrom like 'chr%'" " and chrom not like '%_random'" " and chrom not like 'chrUn%'"; // allow alternate haplotypes for now //" and chrom not like '%_hap%'" //" and chrom not like '%_alt'" //warn("%s",query); struct virtRegion *v; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { unsigned chromSize = sqlUnsigned(row[1]); - //warn("chrom=%s size=%d", row[0], chromSize); AllocVar(v); v->chrom = cloneString(row[0]); v->start = 1 - 1; v->end = chromSize; slAddHead(&virtRegionList, v); ++winCount; - //if (winCount >= 2) // DEBUG HACK REMOVE - //break; } sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&virtRegionList); } void initWindowsAltLoci() /* initialize window list showing alt (alternate haplotype)*/ { struct virtRegion *v; //chr1:153520530-153700530 AllocVar(v); @@ -3945,150 +3862,135 @@ AllocVar(v); v->chrom = "chr1"; v->start = 153865739 - 1; v->end = 154045739; slAddHead(&virtRegionList, v); slReverse(&virtRegionList); } boolean initVirtRegionsFromBedUrl(time_t *bedDateTime) /* Read custom regions from BED URL */ { multiRegionsBedUrl = cartUsualString(cart, "multiRegionsBedUrl", multiRegionsBedUrl); int bedPadding = 0; // default no padding -//warn("initVirtRegionsFromBedUrl got here multiRegionsBedUrl=%s", multiRegionsBedUrl); // DEBUG REMOVE // TODO add some checks for db change? save in cart var? if (sameString(multiRegionsBedUrl,"")) { warn("No BED URL specified."); return FALSE; } if (!strstr(multiRegionsBedUrl,"://")) { warn("No protocol specified in BED URL %s", multiRegionsBedUrl); return FALSE; } struct lineFile *lf = lineFileUdcMayOpen(multiRegionsBedUrl, FALSE); if (!lf) { warn("Unable to open [%s] with udc", multiRegionsBedUrl); return FALSE; } *bedDateTime = udcTimeFromCache(multiRegionsBedUrl, NULL); -//warn("unix time = %ld on BED file %s", (long)*bedDateTime, multiRegionsBedUrl); // DEBUG REMOVE char *line; int lineSize; int expectedFieldCount = -1; struct bed *bed, *bedList = NULL; while (lineFileNext(lf, &line, &lineSize)) { // Process comments for keywords like database, shortDesc, and maybe others if (startsWith("#",line)) { if (startsWith("#database ",line)) { char *dbFromBed = line+strlen("#database "); - //warn("got #database setting: %s, current database %s", dbFromBed, database); // DEBUG REMOVE if (!sameString(database,dbFromBed)) { warn("Multi-Region BED URL error: The database (%s) specified in input does not match current database %s", dbFromBed, database); return FALSE; } } if (startsWith("#shortDesc ",line)) { virtModeShortDescr = cloneString(line+strlen("#shortDesc ")); - //warn("got #shortDesc setting: %s", virtModeShortDescr); // DEBUG REMOVE } if (startsWith("#padding ",line)) { bedPadding = sqlSigned(line+strlen("#padding ")); - //warn("got #padding setting: %d", bedPadding); // DEBUG REMOVE } continue; } char *row[15]; int numFields = chopByWhite(line, row, ArraySize(row)); if (numFields < 3) { warn("%s doesn't appear to be in BED format. 3 or more fields required, got %d", multiRegionsBedUrl, numFields); return FALSE; } if (expectedFieldCount == -1) { expectedFieldCount = numFields; - //warn("got expectedFieldCount=%d", expectedFieldCount); // DEBUG REMOVE } else { - //warn("got numFields=%d, expectedFieldCount=%d", numFields, expectedFieldCount); // DEBUG REMOVE if (numFields != expectedFieldCount) errAbort("Multi-Region BED was detected to have %d columns. But this row has %d columns. " "All rows except comment lines should have the same number of columns", numFields, expectedFieldCount); } - //warn("got about to call load and validate bed"); // DEBUG REMOVE - AllocVar(bed); // All fields are standard BED fields, no bedplus fields supported at this time. // note: this function does not validate chrom name or end beyond chrom size loadAndValidateBed(row, numFields, numFields+0, lf, bed, NULL, TRUE); bed->chrom=cloneString(bed->chrom); // loadAndValidateBed does not do it for speed. but bedFree needs it. struct chromInfo *ci = hGetChromInfo(database, bed->chrom); if (ci == NULL) { warn("Couldn't find chromosome/scaffold %s in database", bed->chrom); return FALSE; } if (bed->chromEnd > ci->size) { warn("BED chromEnd %u > size %u for chromosome/scaffold %s", bed->chromEnd, ci->size, bed->chrom); return FALSE; } slAddHead(&bedList, bed); - //warn("got after load and validate bed"); // DEBUG REMOVE - struct virtRegion *v; if (numFields < 12) { AllocVar(v); v->chrom = cloneString(bed->chrom); v->start = bed->chromStart; v->end = bed->chromEnd; slAddHead(&virtRegionList, v); - //warn("got BED region %s %d %d", v->chrom, v->start, v->end); // DEBUG REMOVE } else { int e; - //warn("got BED12 blockCount=%d bed->chrom=%s", bed->blockCount, bed->chrom); // DEBUG REMOVE for (e = 0; e < bed->blockCount; ++e) { - //warn("got BED12 exon blockSizes[e]=%d chromStarts[e]=%d", bed->blockSizes[e], bed->chromStarts[e]); // DEBUG REMOVE AllocVar(v); v->chrom = cloneString(bed->chrom); v->start = bed->chromStart + bed->chromStarts[e]; v->end = v->start + bed->blockSizes[e]; - //warn("got BED12 exon region %s %d %d", v->chrom, v->start, v->end); // DEBUG REMOVE slAddHead(&virtRegionList, v); } } } lineFileClose(&lf); bedFreeList(&bedList); slReverse(&virtRegionList); if (bedPadding > 0) padVirtRegions(bedPadding); return TRUE; } // TODO OBSOLETED by lastDbPosCart boolean restoreCartSetting(char *cartSetting) @@ -4142,71 +4044,61 @@ void dySaveCartSetting(struct dyString *dy, char *cartVar, boolean saveBoth) /* Grab var and value from cart, save as var=val to dy string. */ { if (dy->stringSize > 0) dyStringAppend(dy, " "); dyStringPrintf(dy, "%s=%s", cartVar, cartUsualString(cart, cartVar, NULL)); if (saveBoth) lastDbPosSaveCartSetting(cartVar); } boolean initRegionList() /* initialize window list */ { -//warn("initRegionList got here 0"); // TODO GALT -// if we are going to support windows from any org and db, -// then we are going to have to loosen up assumptions -// about trackList consistencey across windows. -// But it seems like much of the rest of the code would work. -// Not sure about speed either -- but might be ok. -// // update, well by 2015-04-28 it seems like we are not going to support windows from other assemblies // due to difficulties with tracklist. - struct virtRegion *v; virtRegionList = NULL; virtModeExtraState = ""; // This is state that determines if the virtChrom has changed lastDbPosCart = cartOfNothing(); // USED to store and restore cart settings related to position and virtMode struct dyString *dy = dyStringNew(256); // used to build virtModeExtraState if (sameString(virtModeType, "default")) { - //warn("demo type single original window"); // DEBUG REMOVE // Single window same as normal window // mostly good to test nothing was broken with single window AllocVar(v); v->chrom = chromName; v->start = 0; v->end = hChromSize(database, chromName); virtWinStart = winStart; virtWinEnd = winEnd; slAddHead(&virtRegionList, v); slReverse(&virtRegionList); } else if (sameString(virtModeType, "exonMostly") || sameString(virtModeType, "geneMostly")) { - //warn("emGeneTable %s", emGeneTable); // DEBUG REMOVE // Gencode settings: comprehensive, alt-splice, non-coding char *knownCanonical = NULL; // show splice-variants, not filtered out via knownCanonical boolean showNoncoding = TRUE; // show non-coding where cdsStart==cdsEnd char *knownToTag = NULL; // show comprehensive set not filtered by knownToTag char varName[SMALLBUF]; boolean geneMostly = FALSE; lastDbPosSaveCartSetting("emGeneTable"); //DISGUISE makes obsolete dySaveCartSetting(dy, "emGeneTable"); //DISGUISE makes obsolete dySaveCartSetting(dy, "emPadding"); if (sameString(virtModeType, "geneMostly")) geneMostly = TRUE; if (sameString(emGeneTable, "knownGene")) @@ -4238,273 +4130,244 @@ { knownToTag = "knownToTag"; } } } if (sameString(emGeneTable, "refGene")) { char varName[SMALLBUF]; safef(varName, sizeof(varName), "%s.hideNoncoding", emGeneTable); showNoncoding = !cartUsualBoolean(cart, varName, FALSE); //DISGUISE makes obsolete dySaveCartSetting(dy, varName); } initVirtRegionsFromEMGeneTableExons(showNoncoding, knownCanonical, knownToTag, geneMostly); - //warn("slCount(virtRegionList)=%d", slCount(virtRegionList)); // DEBUG REMOVE if (!virtRegionList) { warn("No genes found on chrom %s for track %s, returning to default view", chromName, emGeneTrack->shortLabel); return FALSE; // regionList is empty, nothing found. } if (geneMostly) virtModeShortDescr = "genes"; else virtModeShortDescr = "exons"; // DISGUISE makes obsolete dyStringPrintf(dy," %s %s", dy->string, knownCanonical, knownToTag); } else if (sameString(virtModeType, "kcGenes")) // TODO obsolete { - //warn("demo KnownCanonical gene regions genome-wide."); // DEBUG REMOVE initVirtRegionsFromKnownCanonicalGenes("knownCanonical"); virtModeShortDescr = "genes"; } else if (sameString(virtModeType, "customUrl")) { - //warn("custom regions from BED URL."); // DEBUG REMOVE + // custom regions from BED URL virtModeShortDescr = "customUrl"; // can be overridden by comment in input bed file time_t bedDateTime = 0; if (!initVirtRegionsFromBedUrl(&bedDateTime)) { return FALSE; // return to default mode } dySaveCartSetting(dy, "multiRegionsBedUrl", TRUE); dyStringPrintf(dy, " %ld", (long)bedDateTime); } else if (sameString(virtModeType, "singleTrans")) { - //warn("Single Transcript Id"); // DEBUG REMOVE singleTransId = cartUsualString(cart, "singleTransId", singleTransId); if (sameString(singleTransId, "")) { warn("Single transcript Id should not be blank"); return FALSE; // return to default mode } setEMGeneTrack(); dySaveCartSetting(dy, "singleTransId", TRUE); } else if (sameString(virtModeType, "singleAltHaplo")) { - //warn("Single Haplotype Id"); // DEBUG REMOVE - singleAltHaploId = cartUsualString(cart, "singleAltHaploId", singleAltHaploId); // currently default is chr6_cox_hap2 + singleAltHaploId = cartUsualString(cart, "singleAltHaploId", singleAltHaploId); // default is chr6_cox_hap2 initAllChroms(); // we want to default to full genome view. if (!initSingleAltHaplotype(singleAltHaploId)) { virtRegionList = NULL; return FALSE; // return to default mode } virtModeShortDescr = "alt haplo"; // was "single haplo" but that might confuse some users. dySaveCartSetting(dy, "singleAltHaploId", TRUE); } else if (sameString(virtModeType, "allChroms")) - { + { // TODO more work on this mode //warn("show all regular chromosomes (not alts)\n" - //"Warning must turn off all tracks except big*"); // DEBUG REMOVE + //"Warning must turn off all tracks except big*"); initAllChroms(); } else if (sameString(virtModeType, "demo1")) { - //warn("demo two windows on two chroms (default posn chr21, and same loc on chr22"); // DEBUG REMOVE - - // NOTE we are losing the ability to specify org and db + // demo two windows on two chroms (default posn chr21, and same loc on chr22 //chr21:33,031,597-33,041,570 AllocVar(v); //chr21:33,031,597-33,041,570 v->chrom = "chr21"; v->start = 33031597 - 1; v->end = 33041570; slAddHead(&virtRegionList, v); struct virtRegion *v2; AllocVar(v2); //chr22:33,031,597-33,041,570 //window2->organism = "Mouse"; //window2->database = "mm10"; //window2->database = "hg38"; v2->chrom = "chr22"; v2->start = 33031597 - 1; v2->end = 33041570; slAddHead(&virtRegionList, v2); slReverse(&virtRegionList); } else if (sameString(virtModeType, "demo2")) { - //warn("demo multiple (70) windows on one chrom chr21 def posn, window size and step exon-like"); // DEBUG REMOVE + // demo multiple (70) windows on one chrom chr21 def posn, window size and step exon-like initExonStep(); } else if (sameString(virtModeType, "demo4")) { - //warn("demo multiple (20) windows showing exons from TITIN gene uc031rqd.1."); // DEBUG REMOVE + // demo multiple (20) windows showing exons from TITIN gene uc031rqd.1. initVirtRegionsFromEmGeneTable("uc031rqd.1"); // TITIN // "uc002ypa.3"); // SOD1 } else if (sameString(virtModeType, "demo5")) { - //warn("demo alt locus on hg38\n" - //"Shows alt chrom surrounded by preceding and following regions of same size from reference genome "); // DEBUG REMOVE + // demo alt locus on hg38 + // Shows alt chrom surrounded by preceding and following regions of same size from reference genome. initWindowsAltLoci(); } else if (sameString(virtModeType, "demo6")) { - //warn("demo SOD1\n" - //"Shows zoomed in exon-exon junction from SOD1 gene, between exon1 and exon2."); // DEBUG REMOVE + // demo SOD1 + // Shows zoomed in exon-exon junction from SOD1 gene, between exon1 and exon2. initVirtRegionsFromSOD1Hardwired(); } else { - //warn("unrecognized virtModeType = %s", virtModeType); + // Unrecognized virtModeType return FALSE; // return to default mode } virtModeExtraState = dyStringCannibalize(&dy); if (!virtRegionList) return FALSE; // regionList is empty, nothing found. return TRUE; } boolean isLimitedVisHiddenForAllWindows(struct track *track) /* Check if track limitedVis == hidden for all windows. * Return true if all are hidden */ { boolean result = TRUE; for(;track;track=track->nextWindow) if (track->limitedVis != tvHide) result = FALSE; return result; } boolean isTypeBedLike(struct track *track) /* Check if track type is BED-like packable thing (but not rmsk or joinedRmsk) */ { // TODO GALT do we have all the types needed? // TODO could it be as simple as whether track->items exists? char *typeLine = track->tdb->type, *words[8], *type; int wordCount; -//warn("track %s has type %s", track->track, typeLine); if (typeLine == NULL) return FALSE; wordCount = chopLine(cloneString(typeLine), words); if (wordCount <= 0) return FALSE; type = words[0]; -//warn("track %s has type word[0] = %s, canPack=%d", track->track, type, track->canPack); if ( ( sameWord(type, "bed") || sameWord(type, "bed5FloatScore") || sameWord(type, "bed6FloatScore") || sameWord(type, "bedDetail") || sameWord(type, "bigBed") || sameWord(type, "bigGenePred") || sameWord(type, "broadPeak") || sameWord(type, "chain") || sameWord(type, "factorSource") || sameWord(type, "genePred") || sameWord(type, "gvf") || sameWord(type, "narrowPeak") || sameWord(type, "psl") //|| track->loadItems == loadSimpleBed //|| track->bedSize >= 3 // should pick up several ENCODE BED-Plus types. ) && track->canPack ) { - //warn("track %s is BEDLIKE", track->track); return TRUE; } -//warn("track %s is NOT BEDLIKE", track->track); return FALSE; } boolean isTypeUseItemNameAsKey(struct track *track) /* Check if track type is like expRatio and key is just item name. */ { - char *typeLine = track->tdb->type, *words[8], *type; int wordCount; -//warn("track %s has type %s", track->track, typeLine); if (typeLine == NULL) return FALSE; wordCount = chopLine(cloneString(typeLine), words); if (wordCount <= 0) return FALSE; type = words[0]; -//warn("track %s has type word[0] = %s", track->track, type); if (sameWord(type, "expRatio")) { - //warn("track %s is like expRatio, needs one row per item", track->track); + // track is like expRatio, needs one row per item return TRUE; } - -//warn("track %s is NOT like expRatio, which needs only one row per item", track->track); return FALSE; } void setFlatTrackMaxHeight(struct flatTracks *flatTrack, int fontHeight) /* for each flatTrack, figure out maximum height needed from all windows */ { struct track *track = flatTrack->track; int maxHeight = 0; struct track *winTrack; struct window *window; for (window=windows, winTrack=track; window; window=window->next, winTrack=winTrack->nextWindow) { setGlobalsFromWindow(window); int trackHeight = trackPlusLabelHeight(winTrack, fontHeight); - //warn("track %s height=%d isCenterLabelIncluded(winTrack)=%d\n", winTrack->track, trackHeight, isCenterLabelIncluded(winTrack)); // DEBUG REMOVE - //fflush(stdout); // DEBUG REMOVE - if (trackHeight > maxHeight) maxHeight = trackHeight; } setGlobalsFromWindow(windows); // first window flatTrack->maxHeight = maxHeight; - -//warn("track %s maxHeight=%d\n", track->track, maxHeight); // DEBUG REMOVE -//fflush(stdout); // DEBUG REMOVE } void makeActiveImage(struct track *trackList, char *psOutput) /* Make image and image map. */ { - -boolean galtDebug = FALSE; - -if (galtDebug) -warn("makeActiveImage begins"); - -struct window *window = NULL; - struct track *track; MgFont *font = tl.font; struct hvGfx *hvg; struct tempName pngTn; char *mapName = "map"; int fontHeight = mgFontLineHeight(font); int trackPastTabX = (withLeftLabels ? trackTabWidth : 0); int trackTabX = gfxBorder; int trackPastTabWidth = tl.picWidth - trackPastTabX; int pixWidth, pixHeight; int y=0; int titleHeight = fontHeight; int scaleBarPad = 2; int scaleBarHeight = fontHeight; int scaleBarTotalHeight = fontHeight + 2 * scaleBarPad; @@ -4528,32 +4391,30 @@ leftLabelWidth = insideX - gfxBorder*3; struct image *theOneImg = NULL; // No need to be global, only the map needs to be global struct image *theSideImg = NULL; // Because dragScroll drags off end of image, // the side label gets seen. Therefore we need 2 images!! //struct imgTrack *curImgTrack = NULL; // Make this global for now to avoid huge rewrite struct imgSlice *curSlice = NULL; // No need to be global, only the map needs to be global //struct mapSet *curMap = NULL; // Make this global for now to avoid huge rewrite // Set up imgBox dimensions int sliceWidth[stMaxSliceTypes]; // Just being explicit int sliceOffsetX[stMaxSliceTypes]; int sliceHeight = 0; int sliceOffsetY = 0; char *rulerTtl = NULL; -//warn("theImgBox=%lu", (unsigned long)theImgBox); // DEBUG REMOVE - if (theImgBox) // if theImgBox == NULL then we are rendering a simple single image such as right-click View image. // theImgBox is a global for now to avoid huge rewrite of hgTracks. It is started // prior to this in doTrackForm() { rulerTtl = "drag select or click to zoom"; hPrintf("<input type='hidden' name='db' value='%s'>\n", database); hPrintf("<input type='hidden' name='c' value='%s'>\n", chromName); hPrintf("<input type='hidden' name='l' value='%d'>\n", winStart); hPrintf("<input type='hidden' name='r' value='%d'>\n", winEnd); hPrintf("<input type='hidden' name='pix' value='%d'>\n", tl.picWidth); // If a portal was established, then set the global dimensions to the entire expanded image size if (imgBoxPortalDimensions(theImgBox,&virtWinStart,&virtWinEnd,&(tl.picWidth),NULL,NULL,NULL,NULL,NULL)) { pixWidth = tl.picWidth; @@ -4617,192 +4478,164 @@ yAfterBases = yAfterRuler; pixHeight += basePositionHeight; if (rulerCds) { yAfterRuler += rulerTranslationHeight; pixHeight += rulerTranslationHeight; } } /* Hash tracks/subtracks, limit visibility and calculate total image height: */ // For multiple windows, sets height and visibility // as well as making the flatTrack list. -if (galtDebug) -warn("organism=%s database=%s", organism, database); // DEBUG REMOVE - // TODO there is a chance that for pack and squish // I might need to trigger a track-height check here // since it is after all items are loaded for all windows // but before things are checked for overflow or limitedVis? // The fixed non-overflow tracks like knownGene used to initialize // ss and track height during loadItems(). That was delayed // because we now need all windows to be fully loaded before // calculating their joint ss layout and height. // set heights and visibilities. -if (galtDebug) -warn("set heights and visibilities"); // DEBUG REMOVE +struct window *window = NULL; for(window=windows;window;window=window->next) { - //warn("**** window=%lu insideX=%d insideWidth=%d", (unsigned long) window, window->insideX, window->insideWidth); // DEBUG REMOVE setGlobalsFromWindow(window); trackList = window->trackList; for (track = trackList; track != NULL; track = track->next) { if (tdbIsCompositeChild(track->tdb)) // When single track is requested via AJAX, limitedVisFromComposite(track); // it could be a subtrack else { - //warn("DEBUG REMOVE regular track %s", track->track); // DEBUG REMOVE limitVisibility(track); } if (tdbIsComposite(track->tdb)) { struct track *subtrack; for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next) { if (!isSubtrackVisible(subtrack)) continue; // subtrack vis can be explicit or inherited from composite/view. // Then it could be limited because of pixel height limitedVisFromComposite(subtrack); if (subtrack->limitedVis != tvHide) { subtrack->hasUi = track->hasUi; } } } - - //warn("heights and vis: track %s vis=%d limitedVis==%d limitedVisSet=%d", track->track, track->visibility, track->limitedVis, track->limitedVisSet); // DEBUG REMOVE } } trackList = windows->trackList; setGlobalsFromWindow(windows); // first window // Construct flatTracks -if (galtDebug) -warn("Construct flatTracks"); for (track = trackList; track != NULL; track = track->next) { - //warn("construct flat track %s vis=%d limitedVis==%d", track->track, track->visibility, track->limitedVis); // DEBUG REMOVE if (tdbIsComposite(track->tdb)) { struct track *subtrack; for (subtrack = track->subtracks; subtrack != NULL; subtrack = subtrack->next) { if (!isSubtrackVisible(subtrack)) continue; - //warn("about to call isLimitedVisHiddenForAllWindows(%s) on subtrack", subtrack->track); if (!isLimitedVisHiddenForAllWindows(subtrack)) { - //warn("adding flatTrack subtrack (%s)", subtrack->track); // DEBUG REMOVE flatTracksAdd(&flatTracks,subtrack,cart); } } } else { - //warn("about to call isLimitedVisHiddenForAllWindows(%s) on track", track->track);// DEBUG REMOVE if (!isLimitedVisHiddenForAllWindows(track)) { - //warn("adding flatTrack track (%s)", track->track); // DEBUG REMOVE flatTracksAdd(&flatTracks,track,cart); } } } -//warn("slCount(flatTracks)=%d", slCount(flatTracks)); // DEBUG REMOVE flatTracksSort(&flatTracks); // Now we should have a perfectly good flat track list! // for each track, figure out maximum height needed from all windows -if (galtDebug) -warn("for each track, figure out maximum height needed from all windows"); for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) { track = flatTrack->track; if (track->limitedVis == tvHide) { - //warn("flat track %s limitedVis==tvHide. why?", track->track); // DEBUG REMOVE continue; } setFlatTrackMaxHeight(flatTrack, fontHeight); } -//warn("got done with flatTrack->maxHeight"); - // fill out track->prevTrack, and check for maxSafeHeight -if (galtDebug) -warn("fill out track->prevTrack, and check for maxSafeHeight"); boolean safeHeight = TRUE; /* firefox on Linux worked almost up to 34,000 at the default 620 width */ #define maxSafeHeight 32000 struct track *prevTrack = NULL; for (flatTrack = flatTracks,prevTrack=NULL; flatTrack != NULL; flatTrack = flatTrack->next) { track = flatTrack->track; assert(track->limitedVis != tvHide); // ORIG int totalHeight = pixHeight+trackPlusLabelHeight(track,fontHeight); - //warn("track %s flat maxHeight=%d", track->track, flatTrack->maxHeight); // DEBUG REMOVE int totalHeight = pixHeight+flatTrack->maxHeight; if (totalHeight > maxSafeHeight) { char numBuf[SMALLBUF]; sprintLongWithCommas(numBuf, maxSafeHeight); if (safeHeight) // Only one message warn("Image is over %s pixels high (%d pix) at the following track which is now " "hidden:<BR>\"%s\".%s", numBuf, totalHeight, track->tdb->longLabel, (flatTrack->next != NULL ? "<BR>Additional tracks may have also been hidden at this zoom level." : "")); safeHeight = FALSE; struct track *winTrack; for(winTrack=track;winTrack;winTrack=winTrack->nextWindow) { track->limitedVis = tvHide; track->limitedVisSet = TRUE; } } if (!isLimitedVisHiddenForAllWindows(track)) { - //warn("setting winTracks ->prevTrack to %lu for all windows", (unsigned long) prevTrack); // DEBUG REMOVE struct track *winTrack; for(winTrack=track;winTrack;winTrack=winTrack->nextWindow) { // TODO this is currently still only using one prev track value. winTrack->prevTrack = prevTrack; // Important for keeping track of conditional center labels! } // ORIG pixHeight += trackPlusLabelHeight(track, fontHeight); if (!theImgBox) // prevTrack may have altered the height, so recalc height setFlatTrackMaxHeight(flatTrack, fontHeight); pixHeight += flatTrack->maxHeight; prevTrack = track; } } -if (galtDebug) -warn("About to allocate hvg png pixWidth=%d, pixHeight=%d", pixWidth, pixHeight); -fflush(stdout); // DEBUG REMOVE - +// allocate hvg png of pixWidth, pixHeight imagePixelHeight = pixHeight; if (psOutput) { hvg = hvGfxOpenPostScript(pixWidth, pixHeight, psOutput); hvgSide = hvg; // Always only one image } else { boolean transparentImage = FALSE; if (theImgBox!=NULL) transparentImage = TRUE; // transparent because BG (blue ruler lines) is separate image if (measureTiming) measureTime("Time at start of obtaining trash hgt png image file"); trashDirFile(&pngTn, "hgt", "hgt", ".png"); @@ -4849,57 +4682,50 @@ // Good to go ahead and add all imgTracks regardless of buttons, left label, centerLabel, etc. if (theImgBox) { if (rulerMode != tvHide) { curImgTrack = imgBoxTrackFindOrAdd(theImgBox,NULL,RULER_TRACK_NAME,rulerMode,FALSE, IMG_FIXEDPOS); // No tdb, no centerLbl, not reorderable } for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) { track = flatTrack->track; if (!isLimitedVisHiddenForAllWindows(track)) { - //warn("hvGfxFindRgb !isLimitedVisHiddenForAllWindows(%s)", track->track); // DEBUG REMOVE struct track *winTrack; for (winTrack=track; winTrack; winTrack=winTrack->nextWindow) { - //warn("hvGfxFindRgb (%s) winTrack labelColor=%d ixColor=%d color=%s", track->track, winTrack->labelColor, winTrack->ixColor, rgbColorToString(winTrack->color)); // DEBUG REMOVE if (winTrack->labelColor == winTrack->ixColor && winTrack->ixColor == 0) { - //warn("hvGfxFindRgb got here window : %s %s %s:%d-%d offset %d width %d", // DEBUG REMOVE - //window->organism, window->database, window->chromName, window->winStart+1, window->winEnd, window->insideX, window->insideWidth); - winTrack->ixColor = hvGfxFindRgb(hvg, &winTrack->color); - } } int order = flatTrack->order; curImgTrack = imgBoxTrackFindOrAdd(theImgBox,track->tdb,NULL,track->limitedVis, isCenterLabelIncluded(track),order); if (trackShouldUseAjaxRetrieval(track)) imgTrackMarkForAjaxRetrieval(curImgTrack,TRUE); } } } /* Draw mini-buttons. */ -if (galtDebug) -warn("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 @@ -4914,45 +4740,44 @@ { // advanced features off // TODO: Should remove wasted pixels too drawGrayButtonBox(hvgSide, trackTabX, y, trackTabWidth, height, TRUE); } mapBoxTrackUi(hvgSide, trackTabX, y, trackTabWidth, height, RULER_TRACK_NAME, RULER_TRACK_LABEL, "ruler"); y += height + 1; } for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) { track = flatTrack->track; int h, yStart = y, yEnd; if (track->limitedVis != tvHide) { // ORIG y += trackPlusLabelHeight(track, fontHeight); - y += flatTrack->maxHeight; // DEBUG REMOVE + y += flatTrack->maxHeight; yEnd = y; h = yEnd - yStart - 1; /* alternate button colors for track groups*/ if (track->group != lastGroup) grayButtonGroup = !grayButtonGroup; lastGroup = track->group; if (theImgBox) { // Mini-buttons (side label slice) for tracks sliceHeight = yEnd - yStart; sliceOffsetY = yStart - 1; curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); - //warn("GTEX 2: track %s, sliceHeight=%d\n", track->shortLabel, sliceHeight); curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stButton,NULL,NULL, sliceWidth[stButton],sliceHeight, sliceOffsetX[stButton],sliceOffsetY); } else if (!trackImgOnly) // Side buttons only need to be drawn when drawing page { // with js advanced features off if (grayButtonGroup) drawGrayButtonBox(hvgSide, trackTabX, yStart, trackTabWidth, h, track->hasUi); else drawBlueButtonBox(hvgSide, trackTabX, yStart, trackTabWidth, h, track->hasUi); } if (track->hasUi) { if (tdbIsCompositeChild(track->tdb)) @@ -4962,51 +4787,49 @@ parent->track, parent->shortLabel, track->track); } else mapBoxTrackUi(hvgSide, trackTabX, yStart, trackTabWidth, h, track->track, track->shortLabel, track->track); } } } butOff = trackTabX + trackTabWidth; leftLabelX += butOff; leftLabelWidth -= butOff; } /* Draw left labels. */ -if (galtDebug) -warn("Draw left labels"); + if (withLeftLabels) { if (theImgBox == NULL) { Color lightRed = hvGfxFindColorIx(hvgSide, 255, 180, 180); hvGfxBox(hvgSide, leftLabelX + leftLabelWidth, 0, gfxBorder, pixHeight, lightRed); } y = gfxBorder; if (rulerMode != tvHide) { if (theImgBox) { // side label slice for ruler sliceHeight = basePositionHeight + (rulerCds ? rulerTranslationHeight : 0) + 1; sliceOffsetY = 0; curImgTrack = imgBoxTrackFind(theImgBox,NULL,RULER_TRACK_NAME); - //warn("GTEX 3: track %s, sliceHeight=%d\n", track->shortLabel, sliceHeight); curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL, sliceWidth[stSide],sliceHeight, sliceOffsetX[stSide],sliceOffsetY); (void) sliceMapFindOrStart(curSlice,RULER_TRACK_NAME,NULL); // No common linkRoot } if (baseTitle) { hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, titleHeight, MG_BLACK, font, WIN_TITLE_LABEL); y += titleHeight; } if (baseShowPos||baseShowAsm) { hvGfxTextRight(hvgSide, leftLabelX, y, leftLabelWidth-1, showPosHeight, MG_BLACK, font, WIN_POS_LABEL); @@ -5049,72 +4872,67 @@ if (zoomedToBaseLevel) y += baseHeight; } if (rulerCds) y += rulerTranslationHeight; } for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) { track = flatTrack->track; if (track->limitedVis == tvHide) continue; if (theImgBox) { // side label slice for tracks //ORIG sliceHeight = trackPlusLabelHeight(track, fontHeight); - sliceHeight = flatTrack->maxHeight; // DEBUG REMOVE + sliceHeight = flatTrack->maxHeight; sliceOffsetY = y; curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); - //warn("GTEX 4: track %s, sliceHeight=%d\n", track->shortLabel, sliceHeight); curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL, sliceWidth[stSide],sliceHeight, sliceOffsetX[stSide],sliceOffsetY); (void) sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot } if (trackShouldUseAjaxRetrieval(track)) y += REMOTE_TRACK_HEIGHT; else { #ifdef IMAGEv2_NO_LEFTLABEL_ON_FULL if (theImgBox && track->limitedVis != tvDense) y += sliceHeight; else #endif ///def IMAGEv2_NO_LEFTLABEL_ON_FULL { setGlobalsFromWindow(windows); // use GLOBALS from first window int ynew = doLeftLabels(track, hvgSide, font, y); - //setGlobalsFromWindow(windows); // first window // REMOVE? this is the same as above - - y += flatTrack->maxHeight; // DEBUG REMOVE + y += flatTrack->maxHeight; if ((ynew - y) > flatTrack->maxHeight) { // TODO should be errAbort? warn("doLeftLabels(y=%d) returned new y value %d that is too high - should be %d at most.", y, ynew, flatTrack->maxHeight); } } } } } else { leftLabelX = leftLabelWidth = 0; } /* Draw guidelines. */ -if (galtDebug) -warn("Draw guidelines"); // OR window separators in virtMode multi-window mode if (virtMode && emAltHighlight) withGuidelines = TRUE; // we cannot draw the alternating backgrounds without guidelines layer if (withGuidelines) { struct hvGfx *bgImg = hvg; // Default to the one image boolean exists = FALSE; if (theImgBox) { struct tempName gifBg; char base[64]; if (virtMode) // window separators { safecpy(base,sizeof(base),"winSeparators"); // non-reusable temp file @@ -5169,187 +4987,160 @@ { int x; Color lightBlue = hvGfxFindRgb(bgImg, &guidelineColor); for (x = fullInsideX+guidelineSpacing-1; x<pixWidth; x += guidelineSpacing) hvGfxBox(bgImg, x, 0, 1, pixHeight, lightBlue); } hvGfxUnclip(bgImg); if (bgImg != hvg) hvGfxClose(&bgImg); } } /* Draw ruler */ -if (galtDebug) -warn("Draw rulers"); -/* Show ruler at top. */ if (rulerMode != tvHide) { newWinWidth = calcNewWinWidth(cart,virtWinStart,virtWinEnd,fullInsideWidth); if (theImgBox) { // data slice for ruler sliceHeight = basePositionHeight + (rulerCds ? rulerTranslationHeight : 0) + 1; sliceOffsetY = 0; curImgTrack = imgBoxTrackFind(theImgBox,NULL,RULER_TRACK_NAME); - //warn("GTEX 5: track %s, sliceHeight=%d\n", track->shortLabel, sliceHeight); curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stData,theOneImg,rulerTtl, sliceWidth[stData],sliceHeight, sliceOffsetX[stData],sliceOffsetY); (void) sliceMapFindOrStart(curSlice,RULER_TRACK_NAME,NULL); // No common linkRoot } // need to have real winBaseCount to draw ruler scale for (window=windows; window; window=window->next) { - - // DETAILS - // warn("window : %s %s %s:%d-%d offset %d width %d window=%lu", // DEBUG REMOVE - // window->organism, window->database, window->chromName, window->winStart+1, window->winEnd, - // window->insideX, window->insideWidth, (unsigned long) window); - setGlobalsFromWindow(window); if (theImgBox) { // Show window positions as mouseover if (virtMode) { char position[256]; safef(position, sizeof position, "%s:%d-%d", window->chromName, window->winStart+1, window->winEnd); int x = window->insideX; if (revCmplDisp) x = tl.picWidth - (x + window->insideWidth); imgTrackAddMapItem(curImgTrack, "#", position, x, sliceOffsetY, x+window->insideWidth, sliceOffsetY+sliceHeight, RULER_TRACK_NAME); } } y = doDrawRuler(hvg,&rulerClickHeight,rulerHeight,yAfterRuler,yAfterBases,font, fontHeight,rulerCds, scaleBarTotalHeight, window); } setGlobalsFromWindow(windows); // first window } /* Draw center labels. */ -if (galtDebug) -warn("Draw center labels."); + if (withCenterLabels) { - setGlobalsFromWindow(windows); // use GLOBALS from first window + setGlobalsFromWindow(windows); // first window hvGfxSetClip(hvg, fullInsideX, gfxBorder, fullInsideWidth, pixHeight - 2*gfxBorder); y = yAfterRuler; for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) { track = flatTrack->track; if (track->limitedVis == tvHide) continue; if (theImgBox) { // center label slice of tracks Must always make, even if the centerLabel is empty sliceHeight = fontHeight; sliceOffsetY = y; curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stCenter,theOneImg,NULL, sliceWidth[stData],sliceHeight, sliceOffsetX[stData],sliceOffsetY); (void) sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot if (isCenterLabelConditional(track)) // sometimes calls track height, especially when no data there { - //warn("isCenterLabelConditional(track)=TRUE %s", track->track); imgTrackUpdateCenterLabelSeen(curImgTrack,isCenterLabelConditionallySeen(track) ? clNowSeen : clNotSeen); } } if (trackShouldUseAjaxRetrieval(track)) { - //warn("trackShouldUseAjaxRetrieval(%s)", track->track); // DEBUG REMOVE y += REMOTE_TRACK_HEIGHT; } else { int savey = y; // GALT - //warn("calling doCenterLabels fullInsideWidth=%d", fullInsideWidth); // DEBUG REMOVE y = doCenterLabels(track, track, hvg, font, y, fullInsideWidth); // calls track height // TODO GALT why do I just pass track here instead of parentTrack? Did I lose something? // have to look at old code to see. - - y = savey + flatTrack->maxHeight; // GALT + y = savey + flatTrack->maxHeight; } } hvGfxUnclip(hvg); setGlobalsFromWindow(windows); // first window } -//warn("Start window draw: %s:%d-%d offset %d width %d", - // chromName, winStart+1, winEnd, insideX, insideWidth); - /* Draw tracks. */ -if (galtDebug) -warn("Draw tracks"); - - { + { // brace allows local vars long lastTime = 0; y = yAfterRuler; if (measureTiming) lastTime = clock1000(); for (flatTrack = flatTracks; flatTrack != NULL; flatTrack = flatTrack->next) { track = flatTrack->track; // parallelize more this?: //ORIG if (track->limitedVis == tvHide) if (isLimitedVisHiddenForAllWindows(track)) continue; - //warn("flatTrack->track->track: %s", flatTrack->track->track); // DEBUG REMOVE - //fflush(stdout); // DEBUG REMOVE int centerLabelHeight = (isCenterLabelIncluded(track) ? fontHeight : 0); - //warn("flatTrack->track->track: %s isCenterLabelIncluded(track): %d " - // "trackPlusLabelHeight(track, fontHeight): %d", - //flatTrack->track->track, isCenterLabelIncluded(track), trackPlusLabelHeight(track, fontHeight)); // DEBUG REMOVE int yStart = y + centerLabelHeight; // ORIG int yEnd = y + trackPlusLabelHeight(track, fontHeight); - int yEnd = y + flatTrack->maxHeight; // DEBUG REMOVE + int yEnd = y + flatTrack->maxHeight; if (theImgBox) { // data slice of tracks sliceOffsetY = yStart; sliceHeight = yEnd - yStart - 1; curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); if (sliceHeight > 0) { - //warn("GTEX 7: track %s, sliceHeight=%d\n", track->shortLabel, sliceHeight); curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stData,theOneImg,NULL, sliceWidth[stData],sliceHeight, sliceOffsetX[stData],sliceOffsetY); (void) sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot } } if (trackShouldUseAjaxRetrieval(track)) y += REMOTE_TRACK_HEIGHT; else { int savey = y; struct track *winTrack; // do preDraw if (track->preDrawItems) @@ -5368,133 +5159,128 @@ } } } setGlobalsFromWindow(windows); // first window // do preDrawMultiRegion across all windows, e.g. wig autoScale if (track->preDrawMultiRegion) { track->preDrawMultiRegion(track); } // doDrawItems for (window=windows, winTrack=track; window; window=window->next, winTrack=winTrack->nextWindow) { setGlobalsFromWindow(window); - //warn("Draw tracks track dump %s\n", makeTrackDumpLink(track)); // DEBUG REMOVE if (winTrack->limitedVis == tvHide) { warn("Draw tracks skipping %s because winTrack->limitedVis=hide", winTrack->track); continue; } if (insideWidth >= 1) // do not try to draw if width < 1. { int ynew = doDrawItems(winTrack, hvg, font, y, &lastTime); - //warn("y=%d ynew=%d (ynew-y)=%d flatTrack->maxHeight=%d", y, ynew, ynew - y, flatTrack->maxHeight); if ((ynew-y) > flatTrack->maxHeight) // so compiler does not complain ynew is not used. errAbort("oops track too high!"); } } setGlobalsFromWindow(windows); // first window y = savey + flatTrack->maxHeight; } if (theImgBox && track->limitedVis == tvDense && tdbIsCompositeChild(track->tdb)) mapBoxToggleVis(hvg, 0, yStart,tl.picWidth, sliceHeight,track); // Strange mapBoxToggleLogic handles reverse complement itself so x=0,width=tl.picWidth if (yEnd != y) warn("Slice height for track %s does not add up. Expecting %d != %d actual", track->shortLabel, yEnd - yStart - 1, y - yStart); } y++; } -if (galtDebug) -warn("post draw tracks leftLabels"); +/* post draw tracks leftLabels */ /* if a track can draw its left labels, now is the time since it * knows what exactly happened during drawItems */ // TODO GALT Parellelize or not? 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 // ORIG sliceHeight = trackPlusLabelHeight(track, fontHeight); - sliceHeight = flatTrack->maxHeight; // DEBUG REMOVE + sliceHeight = flatTrack->maxHeight; sliceOffsetY = y; curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); - //warn("WARN 8: track %s, sliceHeight=%d\n", track->shortLabel, sliceHeight); curSlice = imgTrackSliceUpdateOrAdd(curImgTrack,stSide,theSideImg,NULL, sliceWidth[stSide],sliceHeight, sliceOffsetX[stSide],sliceOffsetY); (void) sliceMapFindOrStart(curSlice,track->tdb->track,NULL); // No common linkRoot } if (trackShouldUseAjaxRetrieval(track)) y += REMOTE_TRACK_HEIGHT; #ifdef IMAGEv2_NO_LEFTLABEL_ON_FULL else if (track->drawLeftLabels != NULL && (theImgBox == NULL || track->limitedVis == tvDense)) #else ///ndef IMAGEv2_NO_LEFTLABEL_ON_FULL else if (track->drawLeftLabels != NULL) #endif ///ndef IMAGEv2_NO_LEFTLABEL_ON_FULL { // TODO parallelize? setGlobalsFromWindow(windows); y = doOwnLeftLabels(track, hvgSide, font, y); setGlobalsFromWindow(windows); // first window } else // ORIG y += trackPlusLabelHeight(track, fontHeight); - y += flatTrack->maxHeight; // DEBUG REMOVE + y += flatTrack->maxHeight; } } /* Make map background. */ -if (galtDebug) -warn("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 // ORIG sliceHeight = trackPlusLabelHeight(track, fontHeight); - sliceHeight = flatTrack->maxHeight; // DEBUG REMOVE + sliceHeight = flatTrack->maxHeight; sliceOffsetY = y; curImgTrack = imgBoxTrackFind(theImgBox,track->tdb,NULL); } // TODO Parallelize? setGlobalsFromWindow(windows); // first window doTrackMap(track, hvg, y, fontHeight, trackPastTabX, trackPastTabWidth); // ORIG y += trackPlusLabelHeight(track, fontHeight); - y += flatTrack->maxHeight; // DEBUG REMOVE + y += flatTrack->maxHeight; } } /* Finish map. */ hPrintf("</MAP>\n"); // turn off inPlaceUpdate when rows in imgTbl can arbitrarily reappear and disappear (see redmine #7306 and #6944) jsonObjectAdd(jsonForClient, "inPlaceUpdate", newJsonBoolean(withLeftLabels && withCenterLabels)); jsonObjectAdd(jsonForClient, "rulerClickHeight", newJsonNumber(rulerClickHeight)); if(newWinWidth) { jsonObjectAdd(jsonForClient, "newWinWidth", newJsonNumber(newWinWidth)); } /* Save out picture and tell html file about it. */ @@ -5682,31 +5468,30 @@ 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"); -//warn("DEBUG loadFromTrackDb:: hgt.trackNameFilter=%s\n", trackNameFilter); // DEBUG REMOVE GALT struct trackDb *tdbList; if(trackNameFilter == NULL) tdbList = hTrackDb(database); else tdbList = hTrackDbForTrack(database, trackNameFilter); addTdbListToTrackList(tdbList, trackNameFilter, pTrackList); } static int getScoreFilter(char *trackName) /* check for score filter configuration setting */ { char optionScoreStr[256]; safef(optionScoreStr, sizeof(optionScoreStr), "%s.scoreFilter", trackName); return cartUsualInt(cart, optionScoreStr, 0); @@ -7470,31 +7255,30 @@ ///////////////// // NEED TO LOAD ALL WINDOWS NOW // // Need to load one window at a time! // // The use of the global values for a window // means that differerent threads cannot use different global window values. // Threads must run on just one window value at a time. // // Begin by making a copy of the track structure for visible tracks // for all windows. -//warn("copy track structures for multiple windows"); // DEBUG REMOVE // COPY TRACK STRUCTURES for other windows. // TODO: due to an issue where some loading code is modifying the visibility // of subtracks from hide to visible, I am forced to remove the optimization // of cloning ONLY non-hidden tracks and subtracks. If the offending code // can be identified and moved into a step proceding the track cloning, // then we can return to that optimization. // if (track->visibility != tvHide) // if (subtrack->visibility != tvHide) windows->trackList = trackList; // save current track list in window struct window *window; for (window=windows; window->next; window=window->next) { struct track *newTrackList = NULL; @@ -7520,52 +7304,44 @@ { //if (subtrack->visibility != tvHide) // Unable to use this optimization at present { struct track *subcopy; AllocVar(subcopy); memmove(subcopy,subtrack,sizeof(struct track)); subcopy->next = NULL; subcopy->bbiFile = NULL; // bigDataUrl custom tracks have already been opened, will re-open for other windows. subcopy->nextWindow = NULL; subcopy->prevWindow = subtrack; slAddHead(©->subtracks, subcopy); subtrack->nextWindow = subcopy; } } slReverse(©->subtracks); - //warn("%s track subs: %d copy subs: %d", track->track, slCount(track->subtracks), slCount(copy->subtracks)); } } slReverse(&newTrackList); trackList = newTrackList; window->next->trackList = trackList; // save new track list in window } trackList = windows->trackList; // restore original track list -// DEBUG REMOVE verify results. -//for (window=windows; window; window=window->next) -// { -// warn("%s %d", window->chromName, slCount(window->trackList)); -// } - // Loop over each window loading all tracks -//warn("Loop over each window loading all tracks"); // DEBUG REMOVE trackLoadingInProgress = TRUE; // TEMP HACK GALT REMOVE bool loadHack = FALSE; //TRUE; // probably should only be tried on non-wiggle tracks -//warn ("loadHack = %d", loadHack); // DEBUG REMOVE +//warn ("loadHack = %d", loadHack); // TODO int lastWinEnd = 0; for (window=windows; window; window=window->next) lastWinEnd = window->winEnd; for (window=windows; window; window=window->next) { trackList = window->trackList; // set track list setGlobalsFromWindow(window); // TEMP HACK GALT REMOVE if (loadHack) { if (currentWindow == windows) // first window winEnd = lastWinEnd; // so now we load the entire span inside the first window. } @@ -7585,96 +7361,77 @@ AllocArray(threads, ptMax); /* Create threads */ int pt; for (pt = 0; pt < ptMax; ++pt) { int rc = pthread_create(&threads[pt], NULL, remoteParallelLoad, &threads[pt]); if (rc) { errAbort("Unexpected error %d from pthread_create(): %s",rc,strerror(rc)); } } } } // TODO GALT - //warn("slCount(trackList) just before load regular tracks: %d", slCount(trackList)); // DEBUG REMOVE - int visCount = 0; // DEBUG REMOVE /* load regular tracks */ for (track = trackList; track != NULL; track = track->next) { if (track->visibility != tvHide) { - ++visCount; // DEBUG REMOVE if (!track->parallelLoading) { if (measureTiming) lastTime = clock1000(); - //warn("load regular tracks BEFORE load and check max window to draw %s\n", makeTrackDumpLink(track)); // DEBUG REMOVE checkMaxWindowToDraw(track); - //warn("load regular tracks BEFORE check if wiggling %s\n", makeTrackDumpLink(track)); // DEBUG REMOVE checkIfWiggling(cart, track); - //warn("load regular tracks ABOUT to call loadItems() %s\n", makeTrackDumpLink(track)); // DEBUG REMOVE - if (!loadHack) { - track->loadItems(track); // DEBUG RESTORE !!! + track->loadItems(track); } else { // TEMP HACK GALT REMOVE if (currentWindow == windows) // first window { track->loadItems(track); } else { track->items = track->prevWindow->items; // just point to the previous windows items (faster than loading) // apparently loadItems is setting some other fields that we want, but which ones? track->visibility = track->prevWindow->visibility; track->limitedVis = track->prevWindow->limitedVis; track->limitedVisSet = track->prevWindow->limitedVisSet; track->height = track->prevWindow->height; track->lineHeight = track->prevWindow->lineHeight; track->heightPer = track->prevWindow->heightPer; // TODO does this work for subtracks or parents/children? } } - // DEBUG REMOVE how many visible subtracks? - int visSubCount = 0; - struct track *sub; - for (sub=track->subtracks; sub; sub=sub->next) - if (sub->visibility != tvHide) - ++visSubCount; - - //warn("load regular tracks AFTER loadItems #%d %s type %s subtracks %d vis %d %s\n", - //visCount, track->track, trackDbSetting(track->tdb, "type"), - //slCount(track->subtracks), visSubCount, makeTrackDumpLink(track)); // DEBUG REMOVE - if (measureTiming) { thisTime = clock1000(); track->loadTime = thisTime - lastTime; } } } } - //warn("after load regular tracks: %d", visCount); // DEBUG REMOVE if (ptMax > 0) { // TODO GALT parallel actually not sure if anything to worry about here /* wait for remote parallel load to finish */ remoteParallelLoadWait(atoi(cfgOptionDefault("parallelFetch.timeout", "90"))); // wait up to default 90 seconds. if (measureTiming) measureTime("Waiting for parallel (%d threads for %d tracks) remote data fetch", ptMax, pfdListCount); } } trackLoadingInProgress = FALSE; setGlobalsFromWindow(windows); // first window // restore globals trackList = windows->trackList; // restore track list @@ -7721,45 +7478,36 @@ } } if (theImgBox) { // If a portal was established, then set the global dimensions back to the portal size if (imgBoxPortalDimensions(theImgBox,NULL,NULL,NULL,NULL,&virtWinStart,&virtWinEnd,&(tl.picWidth),NULL)) { virtWinBaseCount = virtWinEnd - virtWinStart; fullInsideWidth = tl.picWidth-gfxBorder-fullInsideX; } } /* Center everything from now on. */ hPrintf("<CENTER>\n"); -// OLD WAY -//jsonObjectAdd(jsonForClient, "winStart", newJsonNumber(winStart)); -//jsonObjectAdd(jsonForClient, "winEnd", newJsonNumber(winEnd)); -//jsonObjectAdd(jsonForClient, "chromName", newJsonString(chromName)); -// DONE instead of trying to add new variables here, -// see if we can pass the virt versions in as if they were the original variables. -// That way less of hgTracks.js would need to be changed. jsonObjectAdd(jsonForClient, "winStart", newJsonNumber(virtWinStart)); jsonObjectAdd(jsonForClient, "winEnd", newJsonNumber(virtWinEnd)); jsonObjectAdd(jsonForClient, "chromName", newJsonString(virtChromName)); // Tell javascript about multiple windows info -// GALT TODO if end up not using this information, turn this off -// as it sends several K of extra data on a view with many windows. if (virtMode) { // pre windows long preVWinStart = virtWinStart - virtWinBaseCount; if (preVWinStart < 0) preVWinStart = 0; long preVWinEnd = virtWinStart; struct window *preWindows = makeWindowListFromVirtChrom(preVWinStart, preVWinEnd); struct jsonElement *jsonForList = newJsonList(NULL); for(window=preWindows;window;window=window->next) { struct jsonElement *jsonForWindow = NULL; jsonForWindow = newJsonObject(newHash(8)); jsonObjectAdd(jsonForWindow, "chromName", newJsonString(window->chromName)); jsonObjectAdd(jsonForWindow, "winStart", newJsonNumber(window->winStart)); @@ -7918,31 +7666,30 @@ if (showTrackControls) { /* Break into a second form so that zooming and scrolling * can be done with a 'GET' so that user can back up from details * page without Internet Explorer popping up an annoying dialog. * Do rest of page as a 'POST' so that the ultra-long URL from * all the track controls doesn't break things. IE URL limit * is 2000 bytes, but some firewalls impose a ~1000 byte limit. * As a side effect of breaking up the page into two forms * we need to repeat the position in a hidden variable here * so that zoom/scrolling always has current position to work * from. */ // This 'dirty' field is used to check if js/ajax changes to the page have occurred. // If so and it is reached by the back button, a page reload will occur instead. char buf[256]; - // DEBUG RESTORE if (virtualSingleChrom()) // DISGUISE VMODE safef(buf, sizeof buf, "%s", windowsSpanPosition()); else safef(buf, sizeof buf, "%s:%ld-%ld", virtChromName, virtWinStart+1, virtWinEnd); hPrintf("<INPUT TYPE='text' style='display:none;' name='dirty' id='dirty' VALUE='false'>\n"); hPrintf("<INPUT TYPE=HIDDEN id='positionHidden' name='position' " "VALUE=\"%s\">", buf); hPrintf("\n%s", trackGroupsHidden1->string); hPrintf("</CENTER></FORM>\n"); hPrintf("<FORM ACTION=\"%s\" NAME=\"TrackForm\" id=\"TrackForm\" METHOD=\"POST\">\n\n", hgTracksName()); hPrintf("%s", trackGroupsHidden2->string); freeDyString(&trackGroupsHidden1); freeDyString(&trackGroupsHidden2); if (!psOutput) cartSaveSession(cart); /* Put up hgsid= as hidden variable. */ @@ -7950,31 +7697,30 @@ } /* 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); } - // DEBUG RESTORE if (virtualSingleChrom()) // DISGUISE VMODE safef(buf, sizeof buf, "%s", windowsSpanPosition()); else safef(buf, sizeof buf, "%s:%ld-%ld", virtChromName, virtWinStart+1, virtWinEnd); position = cloneString(buf); hPrintf("<span class='positionDisplay' id='positionDisplay' title='click to copy position to input box'>%s</span>", addCommasToPos(database, position)); hPrintf("<input type='hidden' name='position' id='position' value='%s'>\n", buf); sprintLongWithCommas(buf, virtWinEnd - virtWinStart); hPrintf(" <span id='size'>%s</span> bp. ", buf); hPrintf("<input class='positionInput' type='text' name='hgt.positionInput' id='positionInput' size='60'>\n"); hWrites(" "); hButton("hgt.jump", "go"); if (!trackHubDatabase(database)) { @@ -8429,32 +8175,30 @@ /* Scroll percentage of visible window. */ { long offset; long newStart, newEnd; if (revCmplDisp) amount = -amount; offset = (long)(amount * virtWinBaseCount); /* Make sure don't scroll of ends. */ newStart = virtWinStart + offset; newEnd = virtWinEnd + offset; if (newStart < 0) offset = -virtWinStart; else if (newEnd > virtSeqBaseCount) offset = virtSeqBaseCount - virtWinEnd; -//warn("\nGALT relativeScroll %f results in offset %ld to apply to virtWinStart,End\n", amount, offset); // DEBUG REMOVE - /* Move window. */ virtWinStart += offset; virtWinEnd += offset; } void dinkWindow(boolean start, long dinkAmount) /* Move one end or other of window a little. */ { if (revCmplDisp) { start = !start; dinkAmount = -dinkAmount; } if (start) { @@ -8643,39 +8387,30 @@ } boolean findNearestVirtMatch(char *chrom, int start, int end, boolean findNearest, long *retVirtStart, long *retVirtEnd) /* find nearest match on virt chrom. * findNearest flag means of no direct hits found, take the closest miss. */ { // search for one or more overlapping windows struct positionMatch *mList = virtChromSearchForPosition(chrom, start, end, findNearest); // sort positions by virtPos (will be sorted by chrom, start, end) matchSortOnVPos(&mList); // merge contiguous matches spanning multiple touching windows mList = matchMergeContiguousVPos(mList); -// DEBUG SHOW matching regions found. -//warn("DEBUG mList post-sort-merge search positions: %d", slCount(mList)); -//struct positionMatch *m; -//for (m=mList; m; m=m->next) - //{ - //long span = m->virtEnd - m->virtStart; - //warn("virtStar=%ld virtEnd=%ld span=%ld", m->virtStart, m->virtEnd, span); - //} - // TODO search for the best match in pList // TODO this is crude, needs to fix, just finds the largest match: struct positionMatch *p, *best = NULL; long bigSpan = 0; for (p=mList; p; p=p->next) { long span = p->virtEnd - p->virtStart; if (span > bigSpan) { bigSpan = span; best = p; } } if (best) // TODO do something better { @@ -8684,185 +8419,165 @@ *retVirtEnd = best->virtEnd; } else { return FALSE; } return TRUE; } void remapHighlightPos() // Remap non-virt highlight position if any to new virtMode chrom. { if (virtualSingleChrom()) return; struct highlightVar *h = parseHighlightInfo(); -//warn("remapHighlightPos h-> chrom=%s chromStart=%ld chromEnd=%ld", h->chrom, h->chromStart, h->chromEnd); // DEBUG REMOVE if (h && h->db && sameString(h->db, database)) { long virtStart = 0, virtEnd = 0; if (findNearestVirtMatch(h->chrom, h->chromStart, h->chromEnd, FALSE, &virtStart, &virtEnd)) // try to find the nearest match { // save new highlight position to cart var char cartVar[1024]; safef(cartVar, sizeof cartVar, "%s.%s:%ld-%ld#%s", h->db, "virt", virtStart, virtEnd, h->hexColor); cartSetString(cart, "highlight", cartVar); } else { // erase the highlight cartvar if it has no overlap with the new virt chrom cartRemove(cart, "highlight"); } } } void tracksDisplay() /* Put up main tracks display. This routine handles zooming and * scrolling. */ { -//warn("top of tracksDisplay()\n"); // DEBUG REMOVE -//warn("<a href=cartDump?hgsid=%s target=_blank>cartdump</a>", cartSessionId(cart)); // DEBUG REMOVE char *defaultPosition = hDefaultPos(database); char titleVar[256]; char *oldPosition = cartUsualString(cart, "oldPosition", ""); boolean findNearest = cartUsualBoolean(cart, "findNearest", FALSE); cartRemove(cart, "findNearest"); -//warn("findNearest = %d\n", findNearest); // DEBUG REMOVE boolean positionIsVirt = FALSE; position = getPositionFromCustomTracks(); if (NULL == position) { - //warn("cartGetPosition: database=%s position=%s", database, position); // DEBUG REMOVE position = cartGetPosition(cart, database, &lastDbPosCart); if (sameOk(cgiOptionalString("position"), "lastDbPos")) { - // DEBUG REMOVE - //struct dyString *encoded = newDyString(4096); - //cartEncodeState(lastDbPosCart, encoded); - //warn("restored lastDbPosCart encoded state = [%s]", encoded->string); // DEBUG REMOVE restoreSavedVirtPosition(); } - //warn("position = %s\n", position); // DEBUG REMOVE if (startsWith("virt:", position)) { position = stripCommas(position); // sometimes the position string arrives with commas in it. - //warn("positionIsVirt=TRUE position = %s\n", position); // DEBUG REMOVE 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) { chromName = NULL; winStart = 0; if (isGenome(position) || NULL == (hgp = findGenomePos(database, position, &chromName, &winStart, &winEnd, cart))) { - //warn("doing weird stuff with isGenome() and findGenomePos(), add more debugging"); if (winStart == 0) /* number of positions found */ { freeMem(position); position = cloneString(cartUsualString(cart, "lastPosition", defaultPosition)); hgp = findGenomePos(database, position, &chromName, &winStart, &winEnd,cart); if (hgp != NULL && differentString(position, defaultPosition)) cartSetString(cart, "position", position); } } /* After position is found set up hash of matches that should be drawn with names highlighted for easy identification. */ createHgFindMatchHash(); /* This means that no single result was found I.e., multiple results may have been found and are printed out prior to this code*/ if (NULL == chromName) { // In case user manually edits the browser location as described in #13009, // revert the position. If they instead choose from the list as we expect, // that will set the position to their choice. // lastPosition gets set in cart.c char *lastPosition = cartUsualString(cart, "lastPosition", hDefaultPos(database)); cartSetString(cart, "position", lastPosition); return; } } virtMode = cartUsualBoolean(cart, "virtMode", FALSE); -//warn("virtMode=%d\n", virtMode); // DEBUG REMOVE /* Figure out basic dimensions of display. This * needs to be done early for the sake of the * zooming and dinking routines. */ setLayoutGlobals(); -//warn("after setLayoutGlobals() fullInsideX=%d fullInsideWidth=%d tl.picWidth=%d gfxBorder=%d\n", - //fullInsideX, fullInsideWidth, tl.picWidth, gfxBorder); // DEBUG REMOVE virtModeType = cartUsualString(cart, "virtModeType", virtModeType); -//warn("virtModeType=%s\n", virtModeType); // DEBUG REMOVE if (positionIsVirt && virtualSingleChrom()) { // we need chromName to be set before initRegionList() gets called. position = cartUsualString(cart, "nonVirtPosition", ""); - //warn("positionIsVirt && virtualSingleChrom(), going to nonVirtPosition %s", position); // DEBUG REMOVE if (!sameString(position,"")) parseNonVirtPosition(position); } -//warn("chromName=%s", chromName); // DEBUG REMOVE // TODO GALT do we need to add in other types that now depend on emGeneTable too? maybe singleTrans? +// OR maybe this code should just be part of initRegionList() if (sameString(virtModeType, "exonMostly") || sameString(virtModeType, "geneMostly")) { setEMGeneTrack(); if (!emGeneTable) // there is no available gene table, undo exonMostly or geneMostly { //warn("setEMGeneTrack unable to find default gene track"); virtModeType = "default"; cartSetString(cart, "virtModeType", virtModeType); } } lastVirtModeType = cartUsualString(cart, "lastVirtModeType", lastVirtModeType); while(TRUE) { - //warn("virtModeType=%s lastVirtModeType=%s\n", virtModeType, lastVirtModeType); // DEBUG REMOVE if (sameString(virtModeType, "default") && !(sameString(lastVirtModeType, "default"))) { // RETURNING TO DEFAULT virtModeType virtModeType = "default"; cartSetString(cart, "virtModeType", virtModeType); findNearest = TRUE; if (positionIsVirt) position = cartUsualString(cart, "nonVirtPosition", ""); char *nvh = cartUsualString(cart, "nonVirtHighlight", NULL); if (nvh) cartSetString(cart, "highlight", nvh); - //warn("leaving virtMode, going to position %s", position); // DEBUG REMOVE if (!sameString(position,"")) parseNonVirtPosition(position); } - //warn("\nGALT before initRegionList chromName=%s winStart=%d winEnd=%d\n", chromName, winStart,winEnd); // DEBUG REMOVE if (initRegionList()) // initialize the region list, sets virtModeExtraState { break; } else { // virt mode failed, forced to return to default virtModeType = "default"; cartSetString(cart, "virtModeType", virtModeType); position = cloneString(hDefaultPos(database)); hgp = findGenomePos(database, position, &chromName, &winStart, &winEnd, cart); cartSetString(cart, "position", position); positionIsVirt=FALSE; virtMode=FALSE; } } @@ -8875,113 +8590,105 @@ makeVirtChrom(); //testVirtChromBinarySearch(); // ajax callback to convert chrom position to virt chrom position if (cartVarExists(cart, "hgt.convertChromToVirtChrom")) { position = cartString(cart, "hgt.convertChromToVirtChrom"); char nvh[256]; safef(nvh, sizeof nvh, "%s.%s", database, position); cartSetString(cart, "nonVirtHighlight", nvh); parseNonVirtPosition(position); if (findNearestVirtMatch(chromName, winStart, winEnd, FALSE, &virtWinStart, &virtWinEnd)) { - //hPrintf("<p id=virtWinStart>%ld</p><br>\n", virtWinStart); - //hPrintf("<p id=virtWinEnd>%ld</p><br>\n", virtWinEnd); struct jsonElement *jsonForConvert = NULL; jsonForConvert = newJsonObject(newHash(8)); jsonObjectAdd(jsonForConvert, "virtWinStart", newJsonNumber(virtWinStart)); jsonObjectAdd(jsonForConvert, "virtWinEnd", newJsonNumber(virtWinEnd)); hPrintf("<script type='text/javascript'>\n"); jsonPrint((struct jsonElement *) jsonForConvert, "convertChromToVirtChrom", 0); hPrintf("</script>\n"); } return; } lastVirtModeExtraState = cartUsualString(cart, "lastVirtModeExtraState", lastVirtModeExtraState); -//warn("\nGALT virtModeExtraState=%s lastVirtModeExtraState=%s\n", virtModeExtraState, lastVirtModeExtraState); // DEBUG REMOVE // DISGUISED POSITION if (!startsWith("virt:", position) && (virtualSingleChrom())) { - //warn("virtualSingleChrom trying to find best vchrom location corresponding to chrom=%s, winStart=%d, winEnd=%d\n", chromName, winStart, winEnd); // DEBUG REMOVE + // "virtualSingleChrom trying to find best vchrom location corresponding to chromName, winStart, winEnd findNearest = TRUE; - if (!(chromName && findNearestVirtMatch(chromName, winStart, winEnd, findNearest, &virtWinStart, &virtWinEnd))) // try to find the nearest match + // try to find the nearest match + if (!(chromName && findNearestVirtMatch(chromName, winStart, winEnd, findNearest, &virtWinStart, &virtWinEnd))) { // create 1k window near middle of vchrom - warn("Unable to find any region near the position on the chromosome in the multi-regions. Now using middle of view."); // KEEP? + warn("Unable to find any region near the position on the chromosome in the multi-regions. Now using middle of view."); virtWinStart = virtSeqBaseCount / 2; virtWinEnd = virtWinStart + 1000; if (virtWinEnd > virtSeqBaseCount) virtWinEnd = virtSeqBaseCount; } virtMode = TRUE; } // when changing modes (or state like padding), first try to revert to plain non-virt position if (!sameString(virtModeType, "default") && !sameString(lastVirtModeType, "default") && !(sameString(virtModeType, lastVirtModeType) && sameString(virtModeExtraState, lastVirtModeExtraState))) { // CHANGE FROM ONE NON-DEFAULT virtMode to another. virtChromChanged = TRUE; // virtChrom changed lastVirtModeType = "default"; cartSetString(cart, "lastVirtModeType", lastVirtModeType); // I think I do not need this lastVirtModeExtraState = ""; findNearest = TRUE; position = cartUsualString(cart, "nonVirtPosition", ""); - //warn("leaving virtMode, going to position %s", position); // DEBUG REMOVE if (!sameString(position,"")) parseNonVirtPosition(position); char *nvh = cartUsualString(cart, "nonVirtHighlight", ""); - //warn("CHANGE FROM ONE NON-DEFAULT virtMode to another nvh=%s",nvh); // DEBUG REMOVE - if (!sameString(nvh, "")) // DEBUG REMOVE? not needed probably + if (!sameString(nvh, "")) // REMOVE? not needed probably { cartSetString(cart, "highlight", nvh); } } // virt mode has not changed if (sameString(virtModeType, lastVirtModeType) && sameString(virtModeExtraState, lastVirtModeExtraState)) { if (virtMode) { if (positionIsVirt) { parseVirtPosition(position); - //warn("\nGALT after parseVirtPosition(%s), virtWinStart=%ld virtWinEnd=%ld\n", position, virtWinStart, virtWinEnd); // DEBUG REMOVE } else { // Is this a new position to navigate to // or just an old inherited position. position = stripCommas(position); // sometimes the position string arrives with commas in it. if (!sameString(position, oldPosition)) { - //warn("\nGALT before virtChromSearchForPosition(), position=%s oldPosition=%s\n", position, oldPosition); // DEBUG REMOVE - - //warn("\nGALT chrom=%s, winStart=%d, winEnd=%d\n", chromName, winStart, winEnd); // DEBUG REMOVE - if (!findNearestVirtMatch(chromName, winStart, winEnd, findNearest, &virtWinStart, &virtWinEnd)) { // errAbort has kind of harsh behavior, and does not work well with ajax anyways warn("Location not found in Multi-Region View. " - "To return to default view at that location, click <a href=%s?%s=%s&position=%s:%d-%d&virtModeType=default>here</a>.\n" - , hgTracksName(), cartSessionVarName(), cartSessionId(cart), chromName, winStart+1, winEnd); // DEBUG REMOVE + "To return to default view at that location, " + "click <a href=%s?%s=%s&position=%s:%d-%d&virtModeType=default>here</a>.\n" + , hgTracksName(), cartSessionVarName(), cartSessionId(cart), chromName, winStart+1, winEnd); // try to resume using oldPosition parseVirtPosition(oldPosition); } } } } else { if (positionIsVirt) errAbort("positionIsVirt=%d but virtMode=%d", positionIsVirt, virtMode); } } else @@ -8994,72 +8701,69 @@ } else { // ENTERING VIRTMODE // First time initialization findNearest = TRUE; // For now, do this manually here: // sets window to full genome size, which for these demos should be small except for allChroms if (sameString(virtModeType, "exonMostly") || sameString(virtModeType, "geneMostly") || sameString(virtModeType, "kcGenes")) // create 1k window near middle of vchrom { - //warn("trying to find best vchrom location corresponding to chrom=%s, winStart=%d, winEnd=%d\n", chromName, winStart, winEnd); // DEBUG REMOVE - - if (!(chromName && findNearestVirtMatch(chromName, winStart, winEnd, findNearest, &virtWinStart, &virtWinEnd))) // try to find the nearest match + // trying to find best vchrom location corresponding to chromName, winStart, winEnd); + // try to find the nearest match + if (!(chromName && findNearestVirtMatch(chromName, winStart, winEnd, findNearest, &virtWinStart, &virtWinEnd))) { - warn("Unable to find any region near the position on the chromosome in the multi-regions. Now using middle of view."); // KEEP? + warn("Unable to find any region near the position on the chromosome in the multi-regions. Now using middle of view."); virtWinStart = virtSeqBaseCount / 2; virtWinEnd = virtWinStart + 1000; if (virtWinEnd > virtSeqBaseCount) virtWinEnd = virtSeqBaseCount; } virtMode = TRUE; } else if (sameString(virtModeType, "singleAltHaplo")) { virtWinStart = defaultVirtWinStart; virtWinEnd = defaultVirtWinEnd; virtMode = TRUE; } else if (!sameString(virtModeType, "default")) { virtWinStart = 0; virtWinEnd = virtSeqBaseCount; virtMode = TRUE; } remapHighlightPos(); } - //warn("\nGALT default virtWinStart=%ld virtWinEnd=%ld\n", virtWinStart, virtWinEnd); // DEBUG REMOVE } if (virtMode) virtChromName = "virt"; else virtChromName = chromName; virtWinBaseCount = virtWinEnd - virtWinStart; -//warn("\nGALT BEFORE navigation section, virtChromName=%s virtWinStart=%ld virtWinEnd=%ld\n", virtChromName, virtWinStart, virtWinEnd); // DEBUG REMOVE - 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")) @@ -9093,156 +8797,135 @@ else if (cgiVarExists("hgt.dinkLL")) dinkWindow(TRUE, -dinkSize("dinkL")); else if (cgiVarExists("hgt.dinkLR")) dinkWindow(TRUE, dinkSize("dinkL")); else if (cgiVarExists("hgt.dinkRL")) dinkWindow(FALSE, -dinkSize("dinkR")); else if (cgiVarExists("hgt.dinkRR")) dinkWindow(FALSE, dinkSize("dinkR")); /* Before loading items, deal with the next/prev item arrow buttons if pressed. */ if (cgiVarExists("hgt.nextItem")) doNextPrevItem(TRUE, cgiUsualString("hgt.nextItem", NULL)); else if (cgiVarExists("hgt.prevItem")) doNextPrevItem(FALSE, cgiUsualString("hgt.prevItem", NULL)); -//warn("\nGALT BEFORE clipping section, virtChromName=%s virtWinStart=%ld virtWinEnd=%ld\n", virtChromName, virtWinStart, virtWinEnd); // DEBUG REMOVE - /* Clip chromosomal position to fit. */ if (virtWinEnd < virtWinStart) { - // swap start and end + // swap start and end (user entered coordinates backwards) long temp = virtWinEnd; virtWinEnd = virtWinStart; virtWinStart = temp; } else if (virtWinStart == virtWinEnd) { - //warn("\nGALT weird virtWinStart == virtWinEnd = %ld\n", virtWinStart); // DEBUG REMOVE // Size 0 window virtWinStart -= 1; virtWinEnd += 1; } if (virtWinStart < 0) { virtWinStart = 0; } if (virtWinEnd > virtSeqBaseCount) { virtWinEnd = virtSeqBaseCount; } if (virtWinStart > virtSeqBaseCount) { virtWinStart = virtSeqBaseCount - 1000; } virtWinBaseCount = virtWinEnd - virtWinStart; if (virtWinBaseCount <= 0) hUserAbort("Window out of range on %s", virtChromName); -//warn("\nGALT BEFORE portal start section, virtChromName=%s virtWinStart=%ld virtWinEnd=%ld\n", virtChromName, virtWinStart, virtWinEnd); // DEBUG REMOVE - if (!cartUsualBoolean(cart, "hgt.psOutput", FALSE) && !cartUsualBoolean(cart, "hgt.imageV1" , FALSE)) { // TODO GALT Guidelines broken on virtChrom for 3X. // works in demo0 or real chrom. Only the guidelines seem to be messed up. // Other stuff works. 1X works too. // Since we are not using 3X for now, I will leave this for a future fix. // To test 3X, do make clean; make CFLAGS=-DIMAGEv2_DRAG_SCROLL_SZ=3 // Start an imagebox (global for now to avoid huge rewrite of hgTracks) // Set up imgBox dimensions int sideSliceWidth = 0; // Just being explicit if (withLeftLabels) sideSliceWidth = (fullInsideX - gfxBorder*3) + 2; // for the 3X expansion effect to work, this needs to happen BEFORE we create the windows list // in makeWindowListFromVirtChrom() theImgBox = imgBoxStart(database,virtChromName,virtWinStart,virtWinEnd, (!revCmplDisp),sideSliceWidth,tl.picWidth); // Define a portal with a default expansion size, // then set the global dimensions to the full image size if (imgBoxPortalDefine(theImgBox,&virtWinStart,&virtWinEnd,&(tl.picWidth),0)) { virtWinBaseCount = virtWinEnd - virtWinStart; fullInsideWidth = tl.picWidth - gfxBorder - fullInsideX; } } -//warn("AFTER portal start section, virtChromName=%s virtWinStart=%ld virtWinEnd=%ld\n", virtChromName, virtWinStart, virtWinEnd); // DEBUG REMOVE - // For portal 3x expansion to work right, it would have to take effect, at least temporarily, // right here before we call makeWindowListFromVirtChrom(). windows = makeWindowListFromVirtChrom(virtWinStart, virtWinEnd); // creates windows, sets chrom, winStart, winEnd from virtual chrom if (slCount(windows) > 4000) // TODO a more graceful response errAbort("Too many windows in view. Unable to display image at requested zoom level."); -//warn("winCount=%d\n", slCount(windows)); - -//warn("AFTER makeWindowListFromVirtChrom, virtChromName=%s virtWinStart=%ld virtWinEnd=%ld\n", virtChromName, virtWinStart, virtWinEnd); // DEBUG REMOVE - - allocPixelsToWindows(); // sets windows insideWidth and insideX -//warn("AFTER allocPixelsToWindows, virtChromName=%s virtWinStart=%ld virtWinEnd=%ld\n", virtChromName, virtWinStart, virtWinEnd); // DEBUG REMOVE - - - if (theImgBox) { // If a portal was established, then set the global dimensions back to the portal size if (imgBoxPortalDimensions(theImgBox,NULL,NULL,NULL,NULL,&virtWinStart,&virtWinEnd,&(tl.picWidth),NULL)) { virtWinBaseCount = virtWinEnd - virtWinStart; fullInsideWidth = tl.picWidth-gfxBorder-fullInsideX; } } -//warn("AFTER portal demensions section, virtChromName=%s virtWinStart=%ld virtWinEnd=%ld\n", virtChromName, virtWinStart, virtWinEnd); // DEBUG REMOVE - - setGlobalsFromWindow(windows); // first window seqBaseCount = hChromSize(database, chromName); -//warn("virtWinStart=%ld virtWinEnd=%ld\n", virtWinStart, virtWinEnd); // DEBUG REMOVE -//warn("virtWinBaseCount=%ld virtSeqBaseCount=%ld\n", virtWinBaseCount, virtSeqBaseCount); // DEBUG REMOVE - /* Save computed position in cart. */ cartSetString(cart, "org", organism); cartSetString(cart, "db", database); char newPos[256]; // disguise the cart pos var if (virtualSingleChrom()) // DISGUISE VMODE safef(newPos, sizeof newPos, "%s", windowsSpanPosition()); else // usual safef(newPos, sizeof newPos, "%s:%ld-%ld", virtChromName, virtWinStart+1, virtWinEnd); position = cloneString(newPos); cartSetString(cart, "position", position); -cartSetString(cart, "oldPosition", position); // DEBUG REMOVE MAYBE -//cartSetString(cart, "lastPosition", position); // DEBUG REMOVE TESTING. +cartSetString(cart, "oldPosition", position); +//cartSetString(cart, "lastPosition", position); // this is set in cart.c +// TODO GALT is it possible and worthwhile to just use lastPosition instead of oldPosition? cartSetBoolean(cart, "virtMode", virtMode); cartSetString(cart, "virtModeType", virtModeType); virtModeType = cartString(cart, "virtModeType"); // refresh the pointer after changing hash lastVirtModeType=virtModeType; cartSetString(cart, "lastVirtModeType", lastVirtModeType); lastVirtModeType = cartString(cart, "lastVirtModeType"); // refresh lastVirtModeExtraState=virtModeExtraState; cartSetString(cart, "lastVirtModeExtraState", lastVirtModeExtraState); lastVirtModeExtraState = cartString(cart, "lastVirtModeExtraState"); // refresh @@ -9258,36 +8941,30 @@ nvh = nonVirtPositionFromHighlightPos(); if (virtMode && nvh) cartSetString(cart, "nonVirtHighlight", nvh); else cartRemove(cart, "nonVirtHighlight"); // save lastDbPos. save the current position and other important cart vars related to virtual view. lastDbPosSaveCartSetting("position"); lastDbPosSaveCartSetting("nonVirtPosition"); lastDbPosSaveCartSetting("virtMode"); lastDbPosSaveCartSetting("virtModeType"); lastDbPosSaveCartSetting("lastVirtModeType"); lastDbPosSaveCartSetting("lastVirtModeExtraState"); -// DEBUG REMOVE -//struct dyString *encoded = newDyString(4096); -//cartEncodeState(lastDbPosCart, encoded); -//warn("lastDbPosCart encoded state = [%s]", encoded->string); // DEBUG REMOVE - -//warn("database=%s, position=%s, virtModeType=%s, virtModeExtraState=%s", database, position, virtModeType, virtModeExtraState); // DEBUG REMOVE cartSetDbPosition(cart, database, lastDbPosCart); if (cartUsualBoolean(cart, "hgt.psOutput", FALSE)) handlePostscript(); else doTrackForm(NULL, NULL); } void chromInfoTotalRow(int count, long long total) /* Make table row with total number of sequences and size from chromInfo. */ { cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); printf("Total: %d", count); cgiTableFieldEnd();