a44421a79fb36cc2036fe116b97ea3bc9590cd0c braney Fri Dec 2 09:34:39 2011 -0800 removed rcsid (#295) diff --git src/hg/hgTracks/bedGraph.c src/hg/hgTracks/bedGraph.c index 5fc7d51..06365e1 100644 --- src/hg/hgTracks/bedGraph.c +++ src/hg/hgTracks/bedGraph.c @@ -1,283 +1,282 @@ /* bedGraph - stuff to handle loading and display of * bedGraph type tracks in browser. Will be graphing a specified * column of a bed file. */ #include "common.h" #include "hash.h" #include "linefile.h" #include "jksql.h" #include "hdb.h" #include "hgTracks.h" #include "wiggle.h" #include "scoredRef.h" #include "customTrack.h" #include "wigCommon.h" -static char const rcsid[] = "$Id: bedGraph.c,v 1.24 2010/05/20 19:53:22 kent Exp $"; /* 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. */ static char *bedGraphName(struct track *tg, void *item) /* Return name of bedGraph level track. */ { struct bedGraphItem *bg = item; return bg->name; } void ctBedGraphLoadItems(struct track *tg) { /* load custom bedGraph track data */ /* Verify this is a custom track */ if (! (isCustomTrack(tg->table) && tg->customPt)) errAbort("ctBedGraphLoadItems: did not find a custom wiggle track: %s", tg->track); errAbort("custom track bedGraph load items not yet implemented"); } /* bedGraphLoadItems - an ordinary bed load, but we are interested * in only the chrom, start, end, and the graphColumn */ static void bedGraphLoadItems(struct track *tg) { struct sqlConnection *conn; struct sqlResult *sr = (struct sqlResult *) NULL; char **row = (char **)NULL; int rowOffset = 0; struct bedGraphItem *bgList = NULL; int itemsLoaded = 0; int colCount = 0; struct wigCartOptions *wigCart = (struct wigCartOptions *) tg->extraUiData; int graphColumn = 5; char *tableName; if(sameString(tg->table, "affyTranscription")) wigCart->colorTrack = "affyTransfrags"; graphColumn = wigCart->graphColumn; #ifndef GBROWSE if (isCustomTrack(tg->table) && tg->customPt) { struct customTrack *ct = (struct customTrack *) tg->customPt; tableName = ct->dbTableName; conn = hAllocConn(CUSTOM_TRASH); } else #endif /* GBROWSE */ { tableName = tg->table; conn = hAllocConnTrack(database, tg->tdb); } sr = hRangeQuery(conn, tableName, chromName, winStart, winEnd, NULL, &rowOffset); colCount = sqlCountColumns(sr) - rowOffset; /* Must have at least four good columns */ if (colCount < 4) errAbort("bedGraphLoadItems: table %s only has %d data columns, must be at least 4", tableName, colCount); if (colCount < graphColumn) errAbort("bedGraphLoadItems: table %s only has %d data columns, specified graph column %d does not exist", tableName, colCount, graphColumn); /* before loop, determine actual row[graphColumn] index */ graphColumn += (rowOffset - 1); while ((row = sqlNextRow(sr)) != NULL) { struct bedGraphItem *bg; struct bed *bed; ++itemsLoaded; /* load chrom, start, end */ bed = bedLoadN(row+rowOffset, 3); AllocVar(bg); bg->start = bed->chromStart; bg->end = bed->chromEnd; if ((colCount > 4) && ((graphColumn + rowOffset) != 4)) bg->name = cloneString(row[3+rowOffset]); else { char name[128]; safef(name,ArraySize(name),"%s.%d", bed->chrom, itemsLoaded); bg->name = cloneString(name); } bg->dataValue = sqlFloat(row[graphColumn]); /* filled in by DrawItems */ bg->graphUpperLimit = wigEncodeStartingUpperLimit; bg->graphLowerLimit = wigEncodeStartingLowerLimit; slAddHead(&bgList, bg); bedFree(&bed); } sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&bgList); tg->items = bgList; } /* bedGraphLoadItems() */ static void bedGraphFreeItems(struct track *tg) { #if defined(DEBUG) snprintf(dbgMsg, DBGMSGSZ, "I haven't seen bedGraphFreeItems ever called ?"); wigDebugPrint("bedGraphFreeItems"); #endif } struct preDrawContainer *bedGraphLoadPreDraw(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 bedGraphItem *wi; double pixelsPerBase = scaleForPixels(width); double basesPerPixel = 1.0; int i; /* an integer loop counter */ if (pixelsPerBase > 0.0) basesPerPixel = 1.0 / pixelsPerBase; /* 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 */ /* walk through all the data fill in the preDraw array */ for (wi = tg->items; wi != NULL; wi = wi->next) { double dataValue = wi->dataValue; /* the data value to graph */ /* Ready to draw, what do we know: * the feature being processed: * chrom coords: [wi->start : wi->end) * its data value: dataValue = wi->dataValue * * 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, * It is OK if these end up + or -, we do want to * keep track of pixels before and after the screen for * later smoothing operations */ int x1 = (wi->start - seqStart) * pixelsPerBase; int x2 = (wi->end - seqStart) * pixelsPerBase; if (x2 > x1) { for (i = x1; i <= x2; ++i) { int xCoord = preDrawZero + i; if ((xCoord >= 0) && (xCoord < preDrawSize)) { ++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; } } } 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 ((xCoord >= 0) && (xCoord < preDrawSize)) { ++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; } } } /* for (wi = tg->items; wi != NULL; wi = wi->next) */ return pre; } static void bedGraphDrawItems(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 *pre = bedGraphLoadPreDraw(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); } } /* * 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 bedGraphMethods(struct track *track, struct trackDb *tdb, int wordCount, char *words[]) { struct wigCartOptions *wigCart = wigCartOptionsNew(cart, tdb, wordCount, words); wigCart->bedGraph = TRUE; /* signal to left labels */ switch (wordCount) { case 2: wigCart->graphColumn = atoi(words[1]); /* protect against nonsense values */ if ( (wigCart->graphColumn < 2) || (wigCart->graphColumn > 100) ) wigCart->graphColumn = 5; /* default score column */ break; default: wigCart->graphColumn = 5; /* default score column */ break; } track->minRange = wigCart->minY; track->maxRange = wigCart->maxY; track->graphUpperLimit = wigEncodeStartingUpperLimit; track->graphLowerLimit = wigEncodeStartingLowerLimit; track->loadItems = bedGraphLoadItems; track->freeItems = bedGraphFreeItems; track->drawItems = bedGraphDrawItems; track->itemName = bedGraphName; track->mapItemName = bedGraphName; track->totalHeight = wigTotalHeight; track->itemHeight = tgFixedItemHeight; track->itemStart = tgItemNoStart; track->itemEnd = tgItemNoEnd; track->mapsSelf = TRUE; track->extraUiData = (void *) wigCart; track->colorShades = shadesOfGray; track->drawLeftLabels = wigLeftLabels; track->loadPreDraw = bedGraphLoadPreDraw; /* the lfSubSample type makes the image map function correctly */ track->subType = lfSubSample; /*make subType be "sample" (=2)*/ } /* bedGraphMethods() */