5b97c90762187cf1993742fe8c422308e08d082c tdreszer Wed Jul 11 17:08:55 2012 -0700 Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way. diff --git src/hg/hgTracks/wigTrack.c src/hg/hgTracks/wigTrack.c index d423ba4..63784a6 100644 --- src/hg/hgTracks/wigTrack.c +++ src/hg/hgTracks/wigTrack.c @@ -1,1666 +1,1665 @@ /* wigTrack - stuff to handle loading and display of * wig type tracks in browser. Wigs are arbitrary data graphs */ #include "common.h" #include "obscure.h" #include "hash.h" #include "linefile.h" #include "jksql.h" #include "hdb.h" #include "hgTracks.h" #include "wiggle.h" #include "hmmstats.h" #include "scoredRef.h" #ifndef GBROWSE #include "customTrack.h" #endif /* GBROWSE */ #include "wigCommon.h" #include "imageV2.h" struct wigItem /* A wig track item. */ { struct wigItem *next; int start, end; /* Start/end in chrom (aka browser) coordinates. */ char *db; /* Database */ int ix; /* Position in list. */ int height; /* Pixel height of item. */ unsigned span; /* each value spans this many bases */ unsigned count; /* number of values to use */ unsigned offset; /* offset in File to fetch data */ char *file; /* path name to data file, one byte per value */ double lowerLimit; /* lowest data value in this block */ double dataRange; /* lowerLimit + dataRange = upperLimit */ unsigned validCount; /* number of valid data values in this block */ double sumData; /* sum of the data points, for average and stddev calc */ double sumSquares; /* sum of data points squared, for stddev calc */ double graphUpperLimit; /* filled in by DrawItems */ double graphLowerLimit; /* filled in by DrawItems */ }; static void wigFillInColorLfArray(struct track *wigTrack, Color *colArray, int colSize, struct track *colorTrack) /* Fill in a color array with the linkedFeatures based colorTrack's color where it would normally have an exon. */ { struct linkedFeatures *lf = NULL, *lfList = colorTrack->items; struct simpleFeature *sf = NULL; double scale = scaleForPixels(colSize); int x1 = 0, x2 = 0; int i = 0; for(lf = lfList; lf != NULL; lf = lf->next) { for (sf = lf->components; sf != NULL; sf = sf->next) { x1 = round((double)((int)sf->start-winStart)*scale); x2 = round((double)((int)sf->end-winStart)*scale); if(x1 < 0) x1 = 0; if(x2 > colSize) x2 = colSize; if(x1 == x2) x2++; for(i = x1; i < x2; i++) colArray[i] = colorTrack->ixAltColor; } } } static void wigFillInColorBedArray(struct track *wigTrack, Color *colArray, int colSize, struct track *colorTrack, struct hvGfx *hvg) /* Fill in a color array with the simple bed based colorTrack's color where it would normally have an block. */ { struct bed *bed = NULL, *bedList = colorTrack->items; double scale = scaleForPixels(colSize); int x1 = 0, x2 = 0; int i = 0; for (bed = bedList; bed != NULL; bed = bed->next) { x1 = round((double)((int)bed->chromStart-winStart)*scale); x2 = round((double)((int)bed->chromEnd-winStart)*scale); if(x1 < 0) x1 = 0; if(x2 > colSize) x2 = colSize; if(x1 == x2) x2++; for(i = x1; i < x2 && i < colSize; i++) { if(colorTrack->itemColor != NULL) colArray[i] = colorTrack->itemColor(colorTrack, bed, hvg); else colArray[i] = colorTrack->ixColor; } } } void wigFillInColorArray(struct track *wigTrack, struct hvGfx *hvg, Color *colorArray, int colSize, struct track *colorTrack) /* Fill in a color array with the colorTrack's color where it would normally have an exon. */ { boolean trackLoaded = FALSE; /* If the track is hidden currently, load the items. */ if(colorTrack->limitedVis == tvHide) { trackLoaded = TRUE; colorTrack->loadItems(colorTrack); colorTrack->ixColor = hvGfxFindRgb(hvg, &colorTrack->color); colorTrack->ixAltColor = hvGfxFindRgb(hvg, &colorTrack->altColor); } if(colorTrack->drawItemAt == linkedFeaturesDrawAt) wigFillInColorLfArray(wigTrack, colorArray, colSize, colorTrack); else if(colorTrack->drawItemAt == bedDrawSimpleAt) wigFillInColorBedArray(wigTrack, colorArray, colSize, colorTrack, hvg); if(trackLoaded && colorTrack->freeItems != NULL) colorTrack->freeItems(colorTrack); } void wigSetCart(struct track *track, char *dataID, void *dataValue) /* set one of the variables in the wigCart. Actually just MIN_Y or MAX_Y */ { struct wigCartOptions *wigCart; wigCart = (struct wigCartOptions *) track->extraUiData; if (sameWord(dataID, MIN_Y)) wigCart->minY = *((double *)dataValue); else if (sameWord(dataID, MAX_Y)) wigCart->maxY = *((double *)dataValue); else internalErr(); } /* these two routines unused at this time */ #if defined(NOT) static void wigItemFree(struct wigItem **pEl) /* Free up a wigItem. */ { struct wigItem *el = *pEl; if (el != NULL) { /* freeMem(el->name); DO NOT - this belongs to tg->mapName */ freeMem(el->db); freeMem(el->file); freez(pEl); } } static void wigItemFreeList(struct wigItem **pList) /* Free a list of dynamically allocated wigItem's */ { struct wigItem *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; wigItemFree(&el); } *pList = NULL; } #endif /* trackSpans - hash of hashes, first hash is keyed via trackName * the value for key trackName is a hash itself where each element * is a Span found in the data (==zoom level indication) * The key for the second hash is the ascii string for the span * value, and the value at that key is the binary equivalent for * that number. */ static struct hash *trackSpans = NULL; /* hash of hashes */ /* The item names have been massaged during the Load. An * individual item may have been read in on multiple table rows and * had an extension on it to make it unique from the others. Also, * each different zoom level had a different extension name. * All these names were condensed into the root of the name with * the extensions removed. */ char *wigNameCallback(struct track *tg, void *item) /* Return name of wig level track. */ { return tg->track; } /* NOT used at this time, maybe later */ #if defined(NOT) /* This is practically identical to sampleUpdateY in sampleTracks.c * In fact is is functionally identical except jkLib functions are * used instead of the actual string functions. I will consult * with Ryan to see if one of these copies can be removed. */ static boolean sameWigGroup(char *name, char *nextName, int lineHeight) /* Only increment height when name root (extension removed) * is different from previous one. Assumes entries are sorted by name. */ { int different = 0; char *s0; char *s1; s0 = cloneString(name); s1 = cloneString(nextName); chopSuffix(s0); chopSuffix(s1); different = differentString(s0,s1); freeMem(s0); freeMem(s1); if (different) return lineHeight; else return 0; } #endif #define FONT_HEIGHT (tl.fontHeight) #define WIG_DENSE_HEIGHT FONT_HEIGHT #define WIG_PACK_HEIGHT FONT_HEIGHT #define WIG_SQUISH_HEIGHT (((FONT_HEIGHT/2) & 1) ? (FONT_HEIGHT/2) : (FONT_HEIGHT/2) - 1) int wigTotalHeight(struct track *tg, enum trackVisibility vis) /* Wiggle track will use this to figure out the height they use as defined in the cart */ { struct wigCartOptions *wigCart; int saveHeight = tg->height; wigCart = (struct wigCartOptions *) tg->extraUiData; /* * A track is just one * item, so there is nothing to do here, either it is the tvFull * height as chosen by the user from TrackUi, or it is the dense * mode. * ADDENDUM: wiggle options for squish and pack are being added. */ /* Wiggle tracks depend upon clipping. They are reporting * totalHeight artifically high by 1 so this will leave a * blank area one pixel high below the track. hgTracks will set * our clipping rectangle one less than what we report here to get * this accomplished. In the meantime our actual drawing height is * recorded properly in lineHeight, heightPer and height */ if (vis == tvDense) tg->lineHeight = WIG_DENSE_HEIGHT; else if (vis == tvPack) tg->lineHeight = WIG_PACK_HEIGHT; else if (vis == tvSquish) tg->lineHeight = WIG_SQUISH_HEIGHT; else if (vis == tvFull) tg->lineHeight = max(wigCart->minHeight, wigCart->defaultHeight); tg->heightPer = tg->lineHeight; tg->height = tg->lineHeight; if (saveHeight == tg->height + 1) { tg->height = saveHeight; return tg->height; } else return tg->height + 1; } static void wigSetItemData(struct track *tg, struct wigItem *wi, struct wiggle *wiggle, struct hash *spans) /* copy values from *wiggle to *wi, maintain trackSpans hash */ { static char *previousFileName = (char *)NULL; char spanName[SMALLBUF]; struct hashEl *el; char *trackName = tg->track; /* Allocate trackSpans one time only, for all tracks */ if (! trackSpans) trackSpans = newHash(4); wi->start = wiggle->chromStart; wi->end = wiggle->chromEnd; if ((previousFileName == (char *)NULL) || differentString(previousFileName,wiggle->file)) { if (! fileExists(wiggle->file)) errAbort("wigSetItemData: can't open file '%s' (%s)", wiggle->file, strerror(errno)); freez(&previousFileName); previousFileName = cloneString(wiggle->file); } wi->file = cloneString(wiggle->file); wi->span = wiggle->span; wi->count = wiggle->count; wi->offset = wiggle->offset; wi->lowerLimit = wiggle->lowerLimit; wi->dataRange = wiggle->dataRange; wi->validCount = wiggle->validCount; wi->sumData = wiggle->sumData; wi->sumSquares = wiggle->sumSquares; /* see if we have a spans hash for this track already */ el = hashLookup(trackSpans, trackName); /* no, then let's start one */ if ( el == NULL) hashAdd(trackSpans, trackName, spans); /* see if this span is already in our hash for this track */ safef(spanName, sizeof(spanName), "%d", wi->span); el = hashLookup(spans, spanName); /* no, then add this span to the spans list for this track */ if ( el == NULL) hashAddInt(spans, spanName, wi->span); } #ifndef GBROWSE void ctWigLoadItems(struct track *tg) /* load custom wiggle track data */ { struct customTrack *ct; char *row[13]; struct lineFile *lf = NULL; struct wiggle wiggle; struct wigItem *wiList = NULL; int itemsLoaded = 0; struct hash *spans = NULL; /* Spans encountered during load */ ct = tg->customPt; /* Verify this is a custom track */ if (ct == (void *)NULL) errAbort("ctWigLoadItems: did not find a custom wiggle track: %s", tg->track); /* and should *not* be here for a database custom track */ if (ct->dbTrack) errAbort("ctWigLoadItems: this custom wiggle track is in database: %s", tg->track); /* Each instance of this LoadItems will create a new spans hash * It will be the value included in the trackSpans hash */ spans = newHash(3); /* Each row read will be turned into an instance of a wigItem * A growing list of wigItems will be the items list to return */ itemsLoaded = 0; tg->items = wiList; lf = lineFileOpen(ct->wigFile, TRUE); while (lineFileChopNextTab(lf, row, ArraySize(row))) { - wiggleStaticLoad(row, &wiggle); /* we have to do hRangeQuery's job here since we are reading a * file. We need to be on the correct chromosome, and the data * needs to be in the current view. */ if (sameWord(chromName,wiggle.chrom)) { if ((winStart < wiggle.chromEnd) && (winEnd > wiggle.chromStart)) { struct wigItem *wi; ++itemsLoaded; AllocVar(wi); wigSetItemData(tg, wi, &wiggle, spans); slAddHead(&wiList, wi); } /* if in viewing window */ } /* if in same chromosome */ } /* while reading lines */ slReverse(&wiList); tg->items = wiList; tg->mapsSelf = TRUE; lineFileClose(&lf); } #endif /* GBROWSE */ void wigLoadItems(struct track *tg) /* wigLoadItems - read the table rows that hRangeQuery returns * With appropriate adjustment to help hRangeQuery limit its * result to specific "Span" based on the basesPerPixel. * From the rows returned, turn each one into a wigItem, add it to * the growing wiList, and return that wiList as the tg->items. * * To help DrawItems, we are going to make up a list of Spans that * were read in for this track. DrawItems can use that list to * limit itself to the appropriate span. (Even though we tried to * use Span to limit the hRangeQuery, there may be other Spans in * the result that are not needed during the drawing.) * This list of spans is actually a hash of hashes. * The first level is a hash of track names from each call to * wigLoadItems. The second level chosen from the track name is * the actual hash of Spans for this particular track. * * With 1K zoom Spans available, no more than approximately 1024 * rows will need to be loaded at any one time. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; int rowOffset; struct wiggle wiggle; struct wigItem *wiList = NULL; char *whereNULL = NULL; int itemsLoaded = 0; char *previousFileName; struct hash *spans = NULL; /* Spans encountered during load */ /* Check our scale from the global variables that exist in * hgTracks.c - This can give us a guide about which rows to load. * If the scale is more than 1000 bases per pixel, we can try loading * only those rows with Span >= 1000 to see if an appropriate zoom * level exists. */ int basesPerPixel = (int)((double)(winEnd - winStart)/(double)insideWidth); char *span1K = "Span >= 1000 limit 1"; char *spanOver1K = "Span >= 1000"; char whereSpan[SMALLBUF]; int spanMinimum = 1; char *dbTableName = NULL; struct trackDb *tdb = NULL; int loadStart = winStart, loadEnd = winEnd; #ifndef GBROWSE struct customTrack *ct = NULL; /* custom tracks have different database */ if (isCustomTrack(tg->table) && tg->customPt) { hFreeConn(&conn); conn = hAllocConn(CUSTOM_TRASH); ct = tg->customPt; dbTableName = ct->dbTableName; tdb = ct->tdb; } else #endif /* GBROWSE */ { dbTableName = tg->table; tdb = tg->tdb; } /* Allocate trackSpans one time only */ if (! trackSpans) trackSpans = newHash(0); /* find the minimum span to see if there are actually any data * points in this area at that span. If there are not, then there * is no data here even if a zoomed view covers this section. * protect against less than 1 with the max(1,minSpan()); * This business will fix the problem mentioned in RT #1186 */ spanMinimum = max(1, minSpan(conn, dbTableName, chromName, winStart, winEnd, cart, tdb)); itemsLoaded = 0; safef(whereSpan, sizeof(whereSpan), "span=%d limit 1", spanMinimum); sr = hRangeQuery(conn, dbTableName, chromName, loadStart, loadEnd, whereSpan, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) ++itemsLoaded; sqlFreeResult(&sr); /* if nothing here, bail out */ if (itemsLoaded < 1) { tg->items = (struct wigItem *)NULL; hFreeConn(&conn); return; } itemsLoaded = 0; if (basesPerPixel >= 1000) { sr = hRangeQuery(conn, dbTableName, chromName, loadStart, loadEnd, span1K, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) ++itemsLoaded; sqlFreeResult(&sr); } /* If that worked, excellent, then we have at least another zoom level * So, for our actual load, use spanOver1K to fetch not only the 1K * zooms, but potentially others that may be useful. This will * save us a huge amount in loaded rows. On a 250 Mbase chromosome * there would be 256,000 rows at the 1 base level and only * 256 rows at the 1K zoom level. Otherwise, we go back to the * regular query which will give us all rows. */ /* JK - Can't we figure out here one, and only one span to load? This * would simplify drawing logic. */ if (itemsLoaded) { sr = hRangeQuery(conn, dbTableName, chromName, loadStart, loadEnd, spanOver1K, &rowOffset); } else { sr = hRangeQuery(conn, dbTableName, chromName, loadStart, loadEnd, whereNULL, &rowOffset); } /* Allocate trackSpans one time only */ if (! trackSpans) trackSpans = newHash(4); /* Each instance of this LoadItems will create a new spans hash * It will be the value included in the trackSpans hash */ spans = newHash(4); /* Each row read will be turned into an instance of a wigItem * A growing list of wigItems will be the items list to return */ previousFileName = ""; itemsLoaded = 0; while ((row = sqlNextRow(sr)) != NULL) { struct wigItem *wi; ++itemsLoaded; wiggleStaticLoad(row + rowOffset, &wiggle); AllocVar(wi); wigSetItemData(tg, wi, &wiggle, spans); slAddHead(&wiList, wi); } sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&wiList); tg->items = wiList; } /* wigLoadItems() */ static void wigFreeItems(struct track *tg) { #if defined(DEBUG) safef(dbgMsg, DBGMSGSZ, "I haven't seen wigFreeItems ever called ?"); wigDebugPrint("wigFreeItems"); #endif } struct preDrawContainer *initPreDrawContainer(int width) /* Initialize preDraw of given size */ { struct preDrawContainer *pre; AllocVar(pre); int size = pre->preDrawSize = width + 2*wiggleSmoothingMax; pre->preDrawZero = wiggleSmoothingMax; pre->width = width; struct preDrawElement *preDraw = AllocArray(pre->preDraw, pre->preDrawSize); int i; for (i = 0; i < size; ++i) { preDraw[i].count = 0; preDraw[i].max = wigEncodeStartingUpperLimit; preDraw[i].min = wigEncodeStartingLowerLimit; } return pre; } double wiggleLogish(double x) /* Return log-like transform without singularity at 0. */ { if (x >= 0) return log(1+x); else return -log(1-x); } static double doTransform(double x, enum wiggleTransformFuncEnum transformFunc) /* Do log-type transformation if asked. */ { if (transformFunc == wiggleTransformFuncLog) { x = wiggleLogish(x); } return x; } void preDrawWindowFunction(struct preDrawElement *preDraw, int preDrawSize, enum wiggleWindowingEnum windowingFunction, enum wiggleTransformFuncEnum transformFunc) /* apply windowing function to the values in preDraw array */ { int i; /* Determine the raw plotting value */ for (i = 0; i < preDrawSize; ++i) { double dataValue; if (preDraw[i].count) { switch (windowingFunction) { case wiggleWindowingMin: if (fabs(preDraw[i].min) < fabs(preDraw[i].max)) dataValue = preDraw[i].min; else dataValue = preDraw[i].max; break; case wiggleWindowingMean: case wiggleWindowingWhiskers: dataValue = preDraw[i].sumData / preDraw[i].count; break; default: case wiggleWindowingMax: if (fabs(preDraw[i].min) > fabs(preDraw[i].max)) dataValue = preDraw[i].min; else dataValue = preDraw[i].max; break; } dataValue = doTransform(dataValue, transformFunc); preDraw[i].plotValue = dataValue; preDraw[i].smooth = dataValue; } } } void preDrawSmoothing(struct preDrawElement *preDraw, int preDrawSize, enum wiggleSmoothingEnum smoothingWindow) /* apply smoothing function to preDraw array */ { /* Are we perhaps doing smoothing ? smoothingWindow is 1 off due * to enum funny business in inc/hui.h and lib/hui.c */ if (smoothingWindow > 0) { int winSize = smoothingWindow + 1; /* enum funny business */ int winBegin = 0; int winMiddle = -(winSize/2); int winEnd = -winSize; double sum = 0.0; unsigned long long points = 0LL; for (winBegin = 0; winBegin < preDrawSize; ++winBegin) { if (winEnd >=0) { if (preDraw[winEnd].count) { points -= preDraw[winEnd].count; sum -= preDraw[winEnd].plotValue * preDraw[winEnd].count; } } if (preDraw[winBegin].count) { points += preDraw[winBegin].count; sum += preDraw[winBegin].plotValue * preDraw[winBegin].count; } if ((winMiddle >= 0) && points && preDraw[winMiddle].count) preDraw[winMiddle].smooth = sum / points; ++winEnd; ++winMiddle; } } } double preDrawLimits(struct preDrawElement *preDraw, int preDrawZero, int width, double *overallUpperLimit, double *overallLowerLimit) /* scan preDraw array and determine graph limits */ { int i; /* Just in case they haven't been initialized before */ *overallUpperLimit = wigEncodeStartingUpperLimit; *overallLowerLimit = wigEncodeStartingLowerLimit; for (i = preDrawZero; i < preDrawZero+width; ++i) { /* count is non-zero meaning valid data exists here */ if (preDraw[i].count) { if (preDraw[i].max > *overallUpperLimit) *overallUpperLimit = preDraw[i].max; if (preDraw[i].min < *overallLowerLimit) *overallLowerLimit = preDraw[i].min; } } return (overallUpperLimit - overallLowerLimit); } double preDrawAutoScale(struct preDrawElement *preDraw, int preDrawZero, int width, enum wiggleScaleOptEnum autoScale, double *overallUpperLimit, double *overallLowerLimit, double *graphUpperLimit, double *graphLowerLimit, double *overallRange, double *epsilon, int lineHeight, double maxY, double minY, enum wiggleAlwaysZeroEnum alwaysZero) /* if autoScaling, scan preDraw array and determine limits */ { double graphRange; if (autoScale == wiggleScaleAuto) { int i, lastI = preDrawZero+width; /* reset limits for auto scale */ for (i = preDrawZero; i < lastI; ++i) { /* count is non-zero meaning valid data exists here */ if (preDraw[i].count) { if (preDraw[i].smooth > *overallUpperLimit) *overallUpperLimit = preDraw[i].smooth; if (preDraw[i].smooth < *overallLowerLimit) *overallLowerLimit = preDraw[i].smooth; } } if (alwaysZero == wiggleAlwaysZeroOn) { if ( *overallUpperLimit < 0) *overallUpperLimit = 0.0; else if ( *overallLowerLimit > 0) *overallLowerLimit = 0.0; } *overallRange = *overallUpperLimit - *overallLowerLimit; if (*overallRange == 0.0) { if (*overallUpperLimit > 0.0) { *graphUpperLimit = *overallUpperLimit; *graphLowerLimit = 0.0; } else if (*overallUpperLimit < 0.0) { *graphUpperLimit = 0.0; *graphLowerLimit = *overallUpperLimit; } else { *graphUpperLimit = 1.0; *graphLowerLimit = -1.0; } } else { *graphUpperLimit = *overallUpperLimit; *graphLowerLimit = *overallLowerLimit; } } else { *graphUpperLimit = maxY; *graphLowerLimit = minY; } graphRange = *graphUpperLimit - *graphLowerLimit; *epsilon = graphRange / lineHeight; return(graphRange); } static Color * makeColorArray(struct preDrawElement *preDraw, int width, int preDrawZero, struct wigCartOptions *wigCart, struct track *tg, struct hvGfx *hvg) /* allocate and fill in a coloring array based on another track */ { char *colorTrack = wigCart->colorTrack; int x1; Color *colorArray = NULL; /* Array of pixels to be drawn. */ /* Set up the color by array. Determine color of each pixel * based initially on the sign of the data point. If a colorTrack * is specified also fill in the color array with that. */ AllocArray(colorArray, width); for(x1 = 0; x1 < width; ++x1) { int preDrawIndex = x1 + preDrawZero; if (preDraw[preDrawIndex].count) { double dataValue; /* the data value in data space */ dataValue = preDraw[preDrawIndex].smooth; /* negative data is the alternate color */ if (dataValue < 0.0) colorArray[x1] = tg->ixAltColor; else colorArray[x1] = tg->ixColor; } } /* Fill in colors from alternate track if necessary. */ if(colorTrack != NULL) { struct track *cTrack = hashMustFindVal(trackHash, colorTrack); wigFillInColorArray(tg, hvg, colorArray, width, cTrack); } return colorArray; } void graphPreDraw(struct preDrawElement *preDraw, int preDrawZero, int width, struct track *tg, struct hvGfx *hvg, int xOff, int yOff, double graphUpperLimit, double graphLowerLimit, double graphRange, double epsilon, Color *colorArray, enum trackVisibility vis, struct wigCartOptions *wigCart) /* graph the preDraw array */ { int x1; int h = tg->lineHeight; /* the height of our drawing window */ double scaleFactor = h/graphRange; Color oldDrawColor = colorArray[0] + 1; /* Just to be different from 1st drawColor. */ Color mediumColor = MG_BLACK; // Will be overriden Color lightColor = MG_BLACK; // Will be overriden Color clipColor = MG_MAGENTA; enum wiggleTransformFuncEnum transformFunc = wigCart->transformFunc; enum wiggleGraphOptEnum lineBar = wigCart->lineBar; boolean whiskers = (wigCart->windowingFunction == wiggleWindowingWhiskers && width < winEnd-winStart); /* right now this is a simple pixel by pixel loop. Future * enhancements could draw boxes where pixels * are all the same height in a run. */ for (x1 = 0; x1 < width; ++x1) { int x = x1 + xOff; int preDrawIndex = x1 + preDrawZero; struct preDrawElement *p = &preDraw[preDrawIndex]; Color drawColor = colorArray[x1]; if (drawColor != oldDrawColor) { mediumColor = somewhatLighterColor(hvg, drawColor); lightColor = somewhatLighterColor(hvg, mediumColor); oldDrawColor = drawColor; } /* count is non-zero meaning valid data exists here */ if (p->count) { /* data value has been picked by previous scanning. * Could be smoothed, maybe not. */ double dataValue = p->smooth; /* The graphing coordinate conversion situation is: * graph coordinate y = 0 is graphUpperLimit data space * and total graph height is h which is graphRange in data space * The Y axis is positive down, negative up. * * Taking a simple coordinate conversion from data space * to the graphing space, the data value is at: * h * ((graphUpperLimit - dataValue)/graphRange) * and a data value zero line is at: * h * (graphUpperLimit/graphRange) * These may end up to be negative meaning they are above * the upper graphing limit, or be very large, meaning they * are below the lower graphing limit. This is OK, the * clipping will be taken care of by the vgBox() function. */ if (vis == tvFull || vis == tvPack) { #define scaleHeightToPixels(val) (min(BIGNUM,(scaleFactor * (graphUpperLimit - (val)) + yOff))) if (lineBar == wiggleGraphBar) { if (whiskers) { int zeroPos = max(0,scaleHeightToPixels(0)); int scaledVal = scaleHeightToPixels(dataValue); double std = calcStdFromSums(p->sumData, p->sumSquares, p->count); double mean = p->sumData/p->count; if (dataValue < 0) { int scaledMin = scaleHeightToPixels(doTransform(p->min, transformFunc)); int lightHeight = max(1,scaledMin-zeroPos); int mediumHeight = lightHeight; if (!isnan(std)) { // Test needed due to bug in version 1.5 bigWiles double minus = doTransform(mean - std, transformFunc); int scaledMinus = scaleHeightToPixels(minus); mediumHeight = max(1,scaledMinus-zeroPos); } int darkHeight = max(1,scaledVal-zeroPos); if (zeroPos == (yOff+h)) // bottom pixel special case zeroPos -= 1; if (((zeroPos-yOff)+darkHeight) == 0) darkHeight += 1; // top pixel special case hvGfxBox(hvg, x,zeroPos,1, darkHeight, drawColor); hvGfxBox(hvg, x, zeroPos+darkHeight, 1, mediumHeight-darkHeight, mediumColor); hvGfxBox(hvg, x, zeroPos+mediumHeight,1, lightHeight-mediumHeight, lightColor); } else { /* The calculations here are a little convoluted because * of the history. Originally it drew from the baseline * up to the max first in the lightest color, then from the * baseline to the mean+std in medium color, and finally * from baseline to mean in dark color. This ended up * drawing the same pixels up to three times which messed * things up in transparent overlay mode. The code was * refactored to accomplish this without having to worry * about +/- 1 differences. In particular be aware the * xyzHeight calculations are done assuming the other end is * the baseline. */ /* Calculate dark part from smoothed mean. */ int boxHeight = max(1,zeroPos - scaledVal); if (scaledVal == (yOff+h)) // bottom pixel special case scaledVal -= 1; if (((scaledVal-yOff)+boxHeight) == 0) boxHeight += 1; // top pixel special case int darkTop = scaledVal, darkHeight = boxHeight; /* Calculate medium part from smoothed mean + std */ int mediumTop = darkTop, mediumHeight = darkHeight; if (!isnan(std)) { // Test needed due to bug in version 1.5 bigWiles double plus = doTransform(mean + std, transformFunc); int scaledPlus = scaleHeightToPixels(plus); int boxHeight = max(1,zeroPos-scaledPlus); mediumTop = scaledPlus, mediumHeight = boxHeight; } /* Calculate light part from max. */ int scaledMax = scaleHeightToPixels(doTransform(p->max, transformFunc)); if (scaledMax == (h+yOff)) scaledMax = (h+yOff) - 1; boxHeight = max(1,zeroPos-scaledMax); int lightTop = scaledMax, lightHeight = boxHeight; /* Draw, making sure not to overwrite pixels since * would mess up transparent drawing. */ hvGfxBox(hvg,x,darkTop,1, darkHeight, drawColor); hvGfxBox(hvg, x, mediumTop, 1, mediumHeight-darkHeight, mediumColor); hvGfxBox(hvg,x,lightTop,1,lightHeight-mediumHeight, lightColor); } } else { int y0 = graphUpperLimit * scaleFactor; int y1 = (graphUpperLimit - dataValue)*scaleFactor; int boxHeight = max(1,abs(y1 - y0)); int boxTop = min(y1,y0); // positive data value exactly equal to Bottom pixel // make sure it draws at least a pixel there if (boxTop == h) boxTop = h - 1; // negative data value exactly equal to top pixel // make sure it draws something if ((boxTop+boxHeight) == 0) boxHeight += 1; hvGfxBox(hvg,x, yOff+boxTop, 1, boxHeight, drawColor); } } else { /* draw a 3 pixel height box */ if (whiskers) { int scaledMin = scaleHeightToPixels(doTransform(p->min, transformFunc)); int scaledMax = scaleHeightToPixels(doTransform(p->max, transformFunc)); double mean = p->sumData/p->count; int boxHeight = max(1,scaledMin - scaledMax); hvGfxBox(hvg, x, scaledMax, 1, boxHeight, lightColor); int scaledMean = scaleHeightToPixels(dataValue); double std = calcStdFromSums(p->sumData, p->sumSquares, p->count); if (!isnan(std)) // Test needed because of bug in version 1.5 bigWiles { int scaledPlus = scaleHeightToPixels(doTransform(mean+std, transformFunc)); int scaledMinus = scaleHeightToPixels(doTransform(mean-std, transformFunc)); int boxHeight = max(1,scaledMinus - scaledPlus); hvGfxBox(hvg, x, scaledPlus, 1, boxHeight, mediumColor); } hvGfxBox(hvg, x, scaledMean, 1, 1, drawColor); } else { int yPointGraph = scaleHeightToPixels(dataValue) - 1; hvGfxBox(hvg, x, yPointGraph, 1, 3, drawColor); } } if (dataValue > graphUpperLimit) hvGfxBox(hvg, x, yOff, 1, 2, clipColor); else if (dataValue < graphLowerLimit) hvGfxBox(hvg, x, yOff + h - 1, 1, 2, clipColor); #undef scaleHeightToPixels /* No longer use this symbol */ } /* vis == tvFull || vis == tvPack */ else if (vis == tvDense || vis == tvSquish) { double grayValue; int grayIndex; /* honor the viewLimits, data below is white, data above is black */ grayValue = max(dataValue,graphLowerLimit); grayValue = min(grayValue,graphUpperLimit); grayIndex = ((grayValue-graphLowerLimit)/graphRange)*MAX_WIG_VALUE; drawColor = tg->colorShades[grayInRange(grayIndex, 0, MAX_WIG_VALUE)]; hvGfxBox(hvg, x, yOff, 1, tg->lineHeight, drawColor); } /* vis == tvDense || vis == tvSquish */ } /* if (preDraw[].count) */ } /* for (x1 = 0; x1 < width; ++x1) */ } /* graphPreDraw() */ void drawZeroLine(enum trackVisibility vis, enum wiggleGridOptEnum horizontalGrid, double graphUpperLimit, double graphLowerLimit, struct hvGfx *hvg, int xOff, int yOff, int width, int lineHeight) /* draw a line at y=0 on the graph */ { /* Do we need to draw a zero line ? * This is to be generalized in the future to allow horizontal grid * lines, perhaps user specified to indicate thresholds. */ if ((vis == tvFull) && (horizontalGrid == wiggleHorizontalGridOn)) { Color black = hvGfxFindColorIx(hvg, 0, 0, 0); int x1, x2, y1, y2; x1 = xOff; x2 = x1 + width; /* Let's see if the zero line can be drawn */ if ((0.0 <= graphUpperLimit) && (0.0 >= graphLowerLimit)) { int zeroOffset; zeroOffset = (int)((graphUpperLimit * lineHeight) / (graphUpperLimit - graphLowerLimit)); y1 = yOff + zeroOffset; if (y1 >= (yOff + lineHeight)) y1 = yOff + lineHeight - 1; y2 = y1; hvGfxLine(hvg,x1,y1,x2,y2,black); } } /* drawing horizontalGrid */ } /* drawZeroLine() */ void drawArbitraryYLine(enum trackVisibility vis, enum wiggleGridOptEnum horizontalGrid, double graphUpperLimit, double graphLowerLimit, struct hvGfx *hvg, int xOff, int yOff, int width, int lineHeight, double yLineMark, double graphRange, enum wiggleYLineMarkEnum yLineOnOff) /* draw a line at y=yLineMark on the graph */ { /* Optionally, a user requested Y marker line at some value */ if ((vis == tvFull) && (yLineOnOff == wiggleYLineMarkOn)) { int x1, x2, y1, y2; Color black = hvGfxFindColorIx(hvg, 0, 0, 0); x1 = xOff; x2 = x1 + width; /* Let's see if this marker line can be drawn */ if ((yLineMark <= graphUpperLimit) && (yLineMark >= graphLowerLimit)) { int Offset; Offset = lineHeight * ((graphUpperLimit - yLineMark)/graphRange); y1 = yOff + Offset; if (y1 >= (yOff + lineHeight)) y1 = yOff + lineHeight - 1; y2 = y1; hvGfxLine(hvg,x1,y1,x2,y2,black); } } /* drawing y= line marker */ } /* drawArbitraryYLine() */ void wigMapSelf(struct track *tg, struct hvGfx *hvg, int seqStart, int seqEnd, int xOff, int yOff, int width) /* if self mapping, create the mapping box */ { /* Map this wiggle area if we are self mapping */ if (tg->mapsSelf) { char *itemName; #ifndef GBROWSE if (isCustomTrack(tg->table) && tg->customPt) { struct customTrack *ct = tg->customPt; itemName = (char *)needMem(LARGEBUF * sizeof(char)); safef(itemName, LARGEBUF, "%s %s", ct->wigFile, tg->track); } else #endif /* GBROWSE */ itemName = cloneString(tg->track); // Don't bother if we are imageV2 and a dense child. if(!theImgBox || tg->limitedVis != tvDense || !tdbIsCompositeChild(tg->tdb)) mapBoxHc(hvg, seqStart, seqEnd, xOff, yOff, width, tg->height, tg->track, itemName, NULL); freeMem(itemName); } } int wigFindSpan(struct track *tg, double basesPerPixel) /* Return span to use at this scale */ { int usingDataSpan = 1; int minimalSpan = 100000000; /* a lower limit safety check */ struct hashEl *el, *elList; /* Take a look through the potential spans, and given what we have * here for basesPerPixel, pick the largest usingDataSpan that is * not greater than the basesPerPixel */ el = hashLookup(trackSpans, tg->track); /* What Spans do we have */ elList = hashElListHash(el->val); /* Our pointer to spans hash */ for (el = elList; el != NULL; el = el->next) { int Span; Span = ptToInt(el->val); if ((Span < basesPerPixel) && (Span > usingDataSpan)) usingDataSpan = Span; if (Span < minimalSpan) minimalSpan = Span; } hashElFreeList(&elList); /* There may not be a span of 1, use whatever is lowest */ if (minimalSpan > usingDataSpan) usingDataSpan = minimalSpan; return usingDataSpan; } void wigDrawPredraw(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis, struct preDrawContainer *preDrawList, int preDrawZero, int preDrawSize, double *retGraphUpperLimit, double *retGraphLowerLimit) /* Draw once we've figured out predraw... */ { enum wiggleYLineMarkEnum yLineOnOff; double yLineMark; /* determined from data */ double overallUpperLimit = wigEncodeStartingUpperLimit; double overallLowerLimit = wigEncodeStartingLowerLimit; double overallRange=0; /* determined from data */ double graphUpperLimit=0; /* scaling choice will set these */ double graphLowerLimit=0; /* scaling choice will set these */ double graphRange=0; /* scaling choice will set these */ double epsilon; /* range of data in one pixel */ Color *colorArray = NULL; /* Array of pixels to be drawn. */ struct wigCartOptions *wigCart = (struct wigCartOptions *) tg->extraUiData; yLineOnOff = wigCart->yLineOnOff; yLineMark = wigCart->yLineMark; /* width - width of drawing window in pixels * pixelsPerBase - pixels per base * basesPerPixel - calculated as 1.0/pixelsPerBase */ struct preDrawContainer *preContainer; /* loop through all the preDraw containers */ for(preContainer = preDrawList; preContainer; preContainer = preContainer->next) { struct preDrawElement *preDraw = preContainer->preDraw; double thisOverallUpperLimit; double thisOverallLowerLimit; double thisGraphUpperLimit; double thisGraphLowerLimit; preDrawWindowFunction(preDraw, preDrawSize, wigCart->windowingFunction, wigCart->transformFunc); preDrawSmoothing(preDraw, preDrawSize, wigCart->smoothingWindow); overallRange = preDrawLimits(preDraw, preDrawZero, width, &thisOverallUpperLimit, &thisOverallLowerLimit); graphRange = preDrawAutoScale(preDraw, preDrawZero, width, wigCart->autoScale, &thisOverallUpperLimit, &thisOverallLowerLimit, &thisGraphUpperLimit, &thisGraphLowerLimit, &overallRange, &epsilon, tg->lineHeight, wigCart->maxY, wigCart->minY, wigCart->alwaysZero); if (preContainer == preDrawList) // first time through { overallUpperLimit = thisOverallUpperLimit; overallLowerLimit = thisOverallLowerLimit; graphUpperLimit = thisGraphUpperLimit; graphLowerLimit = thisGraphLowerLimit; } else { if (overallUpperLimit < thisOverallUpperLimit) overallUpperLimit = thisOverallUpperLimit; if (overallLowerLimit > thisOverallLowerLimit) overallLowerLimit = thisOverallLowerLimit; if (graphUpperLimit < thisGraphUpperLimit) graphUpperLimit = thisGraphUpperLimit; if (graphLowerLimit > thisGraphLowerLimit) graphLowerLimit = thisGraphLowerLimit; } } overallRange = overallUpperLimit - overallLowerLimit; /* if we're autoscaling and the range is 0 this implies that all values * in the given range are the same. We create a bottom of the scale * by subtracting one from the only value. * This results in drawing a box that fills the range. */ if ((graphUpperLimit == graphLowerLimit)) { graphRange = 1.0; graphLowerLimit = graphUpperLimit - 1; } else { graphRange = graphUpperLimit - graphLowerLimit; } epsilon = graphRange / tg->lineHeight; struct preDrawElement *preDraw = preDrawList->preDraw; colorArray = makeColorArray(preDraw, width, preDrawZero, wigCart, tg, hvg); /* now draw all the containers */ for(preContainer = preDrawList; preContainer; preContainer = preContainer->next) { struct preDrawElement *preDraw = preContainer->preDraw; graphPreDraw(preDraw, preDrawZero, width, tg, hvg, xOff, yOff, graphUpperLimit, graphLowerLimit, graphRange, epsilon, colorArray, vis, wigCart); } drawZeroLine(vis, wigCart->horizontalGrid, graphUpperLimit, graphLowerLimit, hvg, xOff, yOff, width, tg->lineHeight); drawArbitraryYLine(vis, wigCart->yLineOnOff, graphUpperLimit, graphLowerLimit, hvg, xOff, yOff, width, tg->lineHeight, wigCart->yLineMark, graphRange, wigCart->yLineOnOff); wigMapSelf(tg, hvg, seqStart, seqEnd, xOff, yOff, width); freez(&colorArray); if (retGraphUpperLimit != NULL) *retGraphUpperLimit = graphUpperLimit; if (retGraphLowerLimit != NULL) *retGraphLowerLimit = graphLowerLimit; } struct preDrawContainer *wigLoadPreDraw(struct track *tg, int seqStart, int seqEnd, int width) /* Do bits that load the predraw buffer tg->preDrawContainer. */ { /* Just need to do this once... */ if (tg->preDrawContainer) return tg->preDrawContainer; struct wigItem *wi; double pixelsPerBase = scaleForPixels(width); double basesPerPixel = 1.0; int itemCount = 0; char currentFile[PATH_LEN]; int wibFH = 0; /* file handle to binary file */ int i; /* an integer loop counter */ int x1 = 0; /* screen coordinates */ int x2 = 0; /* screen coordinates */ int usingDataSpan = 1; /* will become larger if possible */ if (tg->items == NULL) return NULL; currentFile[0] = '\0'; if (pixelsPerBase > 0.0) basesPerPixel = 1.0 / pixelsPerBase; /* width - width of drawing window in pixels * pixelsPerBase - pixels per base * basesPerPixel - calculated as 1.0/pixelsPerBase */ itemCount = 0; /* Allocate predraw and save it and related info in the track. */ struct preDrawContainer *pre = tg->preDrawContainer = initPreDrawContainer(width); struct preDrawElement *preDraw = pre->preDraw; /* to accumulate everything in prep for draw */ int preDrawZero = pre->preDrawZero; /* location in preDraw where screen starts */ int preDrawSize = pre->preDrawSize; /* size of preDraw array */ usingDataSpan = wigFindSpan(tg, basesPerPixel); /* walk through all the data and prepare the preDraw array */ for (wi = tg->items; wi != NULL; wi = wi->next) { size_t bytesRead; /* to check fread being OK */ int dataOffset = 0; /* within data block during drawing */ ++itemCount; /* Now that we know what Span to draw, see if this item should be * drawn at all. */ if (usingDataSpan == wi->span) { /* Check our data file, see if we need to open a new one */ if (differentString(currentFile,"")) { if (differentString(currentFile,wi->file)) { if (wibFH > 0) { close(wibFH); freeMem(currentFile); } strncpy(currentFile, wi->file, PATH_LEN); currentFile[PATH_LEN-1] = '\0'; wibFH = open(currentFile, O_RDONLY); if (-1 == wibFH) errAbort("openWibFile: failed to open %s", currentFile); } } else { strncpy(currentFile, wi->file, PATH_LEN-1); currentFile[PATH_LEN-1] = '\0'; wibFH = open(currentFile, O_RDONLY); if (-1 == wibFH) errAbort("openWibFile: failed to open %s", currentFile); } /* Ready to draw, what do we know: * the feature being processed: * chrom coords: [wi->start : wi-end) * * The data to be drawn: to be read from file f at offset wi->Offset * data points available: wi->Count, representing wi->Span bases * for each data point * * The drawing window, in pixels: * xOff = left margin, yOff = top margin, h = height of drawing window * drawing window in chrom coords: seqStart, seqEnd * 'basesPerPixel' is known, 'pixelsPerBase' is known */ /* let's check end point screen coordinates. If they are * the same, then this entire data block lands on one pixel, * no need to walk through it, just use the block's specified * max/min. It is OK if these end up + or - values, we do want to * keep track of pixels before and after the screen for * later smoothing operations. */ double x1d = (double)(wi->start - seqStart) * pixelsPerBase; x1 = round(x1d); double x2d = (double)((wi->start+(wi->count * usingDataSpan))-seqStart) * pixelsPerBase; x2 = round(x2d); /* this used to be if (x2 > x1) which often caused reading of blocks * when they were merely x2 = x1 + 1 due to rounding errors as * they became integers. This double comparison for something over * 0.5 will account for rounding errors that are really small, but * still handle a slipping window size as it walks across the screen */ if ((x2d - x1d) > 0.5) { unsigned char *readData; /* the bytes read in from the file */ lseek(wibFH, wi->offset, SEEK_SET); readData = (unsigned char *) needMem((size_t) (wi->count + 1)); bytesRead = read(wibFH, readData, (size_t) wi->count * (size_t) sizeof(unsigned char)); /* walk through all the data in this block */ for (dataOffset = 0; dataOffset < wi->count; ++dataOffset) { unsigned char datum = readData[dataOffset]; if (datum != WIG_NO_DATA) { x1 = ((wi->start-seqStart) + (dataOffset * usingDataSpan)) * pixelsPerBase; x2 = x1 + (usingDataSpan * pixelsPerBase); for (i = x1; i <= x2; ++i) { int xCoord = preDrawZero + i; if ((xCoord >= 0) && (xCoord < preDrawSize)) { double dataValue = BIN_TO_VALUE(datum,wi->lowerLimit,wi->dataRange); ++preDraw[xCoord].count; if (dataValue > preDraw[xCoord].max) preDraw[xCoord].max = dataValue; if (dataValue < preDraw[xCoord].min) preDraw[xCoord].min = dataValue; preDraw[xCoord].sumData += dataValue; preDraw[xCoord].sumSquares += dataValue * dataValue; } } } } freeMem(readData); } else { /* only one pixel for this block of data */ int xCoord = preDrawZero + x1; /* if the point falls within our array, record it. * the (wi->validCount > 0) is a safety check. It * should always be true unless the data was * prepared incorrectly. */ if ((wi->validCount > 0) && (xCoord >= 0) && (xCoord < preDrawSize)) { double upperLimit; preDraw[xCoord].count += wi->validCount; upperLimit = wi->lowerLimit + wi->dataRange; if (upperLimit > preDraw[xCoord].max) preDraw[xCoord].max = upperLimit; if (wi->lowerLimit < preDraw[xCoord].min) preDraw[xCoord].min = wi->lowerLimit; preDraw[xCoord].sumData += wi->sumData; preDraw[xCoord].sumSquares += wi->sumSquares; } } } /* Draw if span is correct */ } /* for (wi = tg->items; wi != NULL; wi = wi->next) */ if (wibFH > 0) { close(wibFH); wibFH = 0; } return pre; } static void wigDrawItems(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) /* Draw wiggle items that resolve to doing a box for each pixel. */ { struct preDrawContainer *pre = wigLoadPreDraw(tg, seqStart, seqEnd, width); if (pre != NULL) { wigDrawPredraw(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis, pre, pre->preDrawZero, pre->preDrawSize, &tg->graphUpperLimit, &tg->graphLowerLimit); } } void wigLeftAxisLabels(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, int height, boolean withCenterLabels, MgFont *font, Color color, enum trackVisibility vis, char *shortLabel, double graphUpperLimit, double graphLowerLimit, boolean showNumbers) /* Draw labels on left for a wiggle-type track. */ { int fontHeight = tl.fontHeight+1; int centerOffset = 0; double lines[2]; /* lines to label */ int numberOfLines = 1; /* at least one: 0.0 */ int i; /* loop counter */ struct wigCartOptions *wigCart = (struct wigCartOptions *) tg->extraUiData; lines[0] = 0.0; lines[1] = wigCart->yLineMark; if (wigCart->yLineOnOff == wiggleYLineMarkOn) ++numberOfLines; if (withCenterLabels) centerOffset = fontHeight; /* We only do Dense and Full */ if (tg->limitedVis == tvDense) { hvGfxTextRight(hvg, xOff, yOff+centerOffset, width - 1, height-centerOffset, tg->ixColor, font, shortLabel); } else if (tg->limitedVis == tvFull) { int centerLabel = (height/2)-(fontHeight/2); int labelWidth = mgFontStringWidth(font, shortLabel); /* track label is centered in the whole region */ hvGfxText(hvg, xOff, yOff+centerLabel, tg->ixColor, font, shortLabel); /* Is there room left to draw the min, max ? */ if (showNumbers && height >= (3 * fontHeight)) { boolean zeroOK = TRUE; char upper[SMALLBUF]; char lower[SMALLBUF]; char upperTic = '-'; /* as close as we can get with ASCII */ /* the ideal here would be to draw tic marks in * exactly the correct location. */ Color drawColor; if (withCenterLabels) { centerOffset = fontHeight; upperTic = '_'; /* this is correct */ } /* In areas where there is no data, these limits do not change */ if (graphUpperLimit < graphLowerLimit) { double d = graphLowerLimit; graphLowerLimit = graphUpperLimit; graphUpperLimit = d; if (hvg->rc) { safef(upper, sizeof(upper), " %c No data", upperTic); safef(lower, sizeof(lower), "_ No data"); } else { safef(upper, sizeof(upper), "No data %c", upperTic); safef(lower, sizeof(lower), "No data _"); } zeroOK = FALSE; } else { enum wiggleTransformFuncEnum transformFunc = wigCart->transformFunc; boolean gotLog = (transformFunc == wiggleTransformFuncLog); char *transform = (gotLog ? "ln(x+1) " : ""); if (hvg->rc) { safef(upper, sizeof(upper), "%c %s%g", upperTic, transform, graphUpperLimit); safef(lower, sizeof(lower), "_ %g", graphLowerLimit); } else { safef(upper, sizeof(upper), "%s%g %c", transform, graphUpperLimit, upperTic); safef(lower, sizeof(lower), "%g _", graphLowerLimit); } } drawColor = tg->ixColor; if (graphUpperLimit < 0.0) drawColor = tg->ixAltColor; hvGfxTextRight(hvg, xOff, yOff, width - 1, fontHeight, drawColor, font, upper); drawColor = tg->ixColor; if (graphLowerLimit < 0.0) drawColor = tg->ixAltColor; hvGfxTextRight(hvg, xOff, yOff+height-fontHeight, width - 1, fontHeight, drawColor, font, lower); for (i = 0; i < numberOfLines; ++i ) { double lineValue = lines[i]; /* Maybe zero can be displayed */ /* It may overwrite the track label ... */ if (zeroOK && (lineValue < graphUpperLimit) && (lineValue > graphLowerLimit)) { int offset; int Width; drawColor = hvGfxFindColorIx(hvg, 0, 0, 0); offset = centerOffset + (int)(((graphUpperLimit - lineValue) * (height - centerOffset)) / (graphUpperLimit - graphLowerLimit)); /* reusing the lower string here */ if (hvg->rc) safef(lower, sizeof(lower), "- %g", ((i == 0) ? 0.0 : lineValue)); else safef(lower, sizeof(lower), "%g -", ((i == 0) ? 0.0 : lineValue)); /* only draw if it is far enough away from the * upper and lower labels, and it won't overlap with * the center label. */ Width = mgFontStringWidth(font,lower); if ( !( (offset < centerLabel+fontHeight) && (offset > centerLabel-(fontHeight/2)) && (Width+labelWidth >= width) ) && (offset > (fontHeight*2)) && (offset < height-(fontHeight*2)) ) { hvGfxTextRight(hvg, xOff, yOff+offset-(fontHeight/2), width - 1, fontHeight, drawColor, font, lower); } } /* drawing a zero label */ } /* drawing 0.0 and perhaps yLineMark */ } /* if (height >= (3 * fontHeight)) */ } /* if (tg->visibility == tvFull) */ } /* wigAxisLeftLabels */ void wigLeftLabels(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, int height, boolean withCenterLabels, MgFont *font, Color color, enum trackVisibility vis) /* drawing left labels */ { wigLeftAxisLabels(tg, seqStart, seqEnd, hvg, xOff, yOff, width, height, withCenterLabels, font, color, vis, tg->shortLabel, tg->graphUpperLimit, tg->graphLowerLimit, TRUE); } struct wigCartOptions *wigCartOptionsNew(struct cart *cart, struct trackDb *tdb, int wordCount, char *words[]) /* Create a wigCartOptions from cart contents and tdb. */ { struct wigCartOptions *wigCart; int defaultHeight; /* truncated by limits */ double yLineMark; /* from trackDb or cart */ int maxHeight = atoi(DEFAULT_HEIGHT_PER); int minHeight = MIN_HEIGHT_PER; AllocVar(wigCart); /* These Fetch functions look for variables in the cart bounded by * limits specified in trackDb or returning defaults */ wigCart->lineBar = wigFetchGraphTypeWithCart(cart,tdb,tdb->track, (char **) NULL); wigCart->horizontalGrid = wigFetchHorizontalGridWithCart(cart,tdb,tdb->track, (char **) NULL); wigCart->autoScale = wigFetchAutoScaleWithCart(cart,tdb,tdb->track, (char **) NULL); wigCart->windowingFunction = wigFetchWindowingFunctionWithCart(cart,tdb,tdb->track, (char **) NULL); wigCart->smoothingWindow = wigFetchSmoothingWindowWithCart(cart,tdb,tdb->track, (char **) NULL); wigFetchMinMaxPixelsWithCart(cart,tdb,tdb->track, &minHeight, &maxHeight, &defaultHeight); wigFetchYLineMarkValueWithCart(cart,tdb,tdb->track, &yLineMark); wigCart->yLineMark = yLineMark; wigCart->yLineOnOff = wigFetchYLineMarkWithCart(cart,tdb,tdb->track, (char **) NULL); wigCart->alwaysZero = wigFetchAlwaysZeroWithCart(cart,tdb,tdb->track, (char **) NULL); wigCart->transformFunc = wigFetchTransformFuncWithCart(cart,tdb,tdb->track, (char **) NULL); wigCart->maxHeight = maxHeight; wigCart->defaultHeight = defaultHeight; wigCart->minHeight = minHeight; wigFetchMinMaxYWithCart(cart,tdb,tdb->track, &wigCart->minY, &wigCart->maxY, NULL, NULL, wordCount, words); wigCart->colorTrack = trackDbSetting(tdb, "wigColorBy"); char *containerType = trackDbSetting(tdb, "container"); if (containerType != NULL && sameString(containerType, "multiWig")) wigCart->isMultiWig = TRUE; char *aggregate = wigFetchAggregateValWithCart(cart, tdb); if (aggregate != NULL) wigCart->overlay = wigIsOverlayTypeAggregate(aggregate); return wigCart; } /* Make track group for wig multiple alignment. * WARNING ! - track->visibility is merely the default value * from the trackDb entry at this time. It will be set after this * by hgTracks from its cart UI setting. When called in * TotalHeight it will then be the requested visibility. */ void wigMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]) { struct wigCartOptions *wigCart = wigCartOptionsNew(cart, tdb, wordCount, words); track->minRange = wigCart->minY; track->maxRange = wigCart->maxY; track->graphUpperLimit = wigEncodeStartingUpperLimit; track->graphLowerLimit = wigEncodeStartingLowerLimit; wigCart->bedGraph = FALSE; /* signal to left labels */ track->loadItems = wigLoadItems; track->freeItems = wigFreeItems; track->drawItems = wigDrawItems; track->itemName = wigNameCallback; track->mapItemName = wigNameCallback; track->totalHeight = wigTotalHeight; track->itemHeight = tgFixedItemHeight; track->itemStart = tgItemNoStart; track->itemEnd = tgItemNoEnd; /* the wigMaf parent will turn mapsSelf off */ track->mapsSelf = TRUE; track->extraUiData = (void *) wigCart; track->colorShades = shadesOfGray; track->drawLeftLabels = wigLeftLabels; track->loadPreDraw = wigLoadPreDraw; /* the lfSubSample type makes the image map function correctly */ track->subType = lfSubSample; /*make subType be "sample" (=2)*/ } /* wigMethods() */