a8f93bb9c0961e8e3ac25a0168ad2d2eb6b66fad kent Wed Apr 25 23:30:45 2012 -0700 Fixing missing c=chromName in a lot of links. A bug Tim put in 2009 from what I can tell that manifests with an empty cart on IE. diff --git src/hg/hgTracks/chromGraphTrack.c src/hg/hgTracks/chromGraphTrack.c index 8be34e8..46faab3 100644 --- src/hg/hgTracks/chromGraphTrack.c +++ src/hg/hgTracks/chromGraphTrack.c @@ -1,334 +1,334 @@ /* chromGraphTrack - displays track that is just a line * connecting certain data points. This does not handle the * data volume that the wiggle track does. It's meant for * things like graphs for gene association studies. */ #include "common.h" #include "hash.h" #include "jksql.h" #include "trackDb.h" #include "hdb.h" #include "hgTracks.h" #include "hvGfx.h" #include "chromGraph.h" #include "imageV2.h" Color colorFromAscii(struct hvGfx *hvg, char *asciiColor) /* Get color index for a named color. */ /* Copy/pasted from hgGenome/mainPage.c ... should be in a library */ /* somewhere! */ { if (sameWord("red", asciiColor)) return MG_RED; else if (sameWord("blue", asciiColor)) return MG_BLUE; else if (sameWord("yellow", asciiColor)) return hvGfxFindColorIx(hvg, 220, 220, 0); else if (sameWord("purple", asciiColor)) return hvGfxFindColorIx(hvg, 150, 0, 200); else if (sameWord("orange", asciiColor)) return hvGfxFindColorIx(hvg, 230, 120, 0); else if (sameWord("green", asciiColor)) return hvGfxFindColorIx(hvg, 0, 180, 0); else if (sameWord("gray", asciiColor)) return MG_GRAY; else return MG_BLACK; } static Color cgColorLikeHgGenome(struct track *tg, struct hvGfx *hvg) /* Search the cart variables and use the colors corresponding to the hgGenome */ /* graph. */ { Color ret; struct hashEl *matchingCartSettings = NULL; struct hashEl *el; char cartGenomeWildStr[256]; char *graphCartVarName = NULL; char *colorCartVarSetting = "black"; safef(cartGenomeWildStr, sizeof(cartGenomeWildStr), "hgGenome_graph_%s_*", database); /* for ex. hgGenome_graph_hg18_1_1 */ matchingCartSettings = cartFindLike(cart, cartGenomeWildStr); for (el = matchingCartSettings; el != NULL; el = el->next) { char *val = (char *)el->val; if (val && sameString(val, tg->track)) { graphCartVarName = el->name; break; } } if (graphCartVarName) { char *colorCartVarName = replaceChars(graphCartVarName, "_graph_", "_graphColor_"); colorCartVarSetting = cartUsualString(cart, colorCartVarName, "black"); freeMem(colorCartVarName); } hashElFreeList(&matchingCartSettings); ret = colorFromAscii(hvg, colorCartVarSetting); return ret; } static void cgDrawEither(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis, char *binFileName) /* Draw chromosome graph - either built in or not. */ { struct chromGraphSettings *cgs = tg->customPt; int x,y,lastX=0,lastY=0, llastX = 0, llastY = 0; int height = tg->height; int maxGapToFill = cgs->maxGapToFill; int lastPos = -maxGapToFill-1; double minVal = cgs->minVal; double yScale = (height-1)/(cgs->maxVal - minVal); double xScale = scaleForPixels(width); Color myColor = cgColorLikeHgGenome(tg, hvg); /* Draw background lines in full mode. */ if (vis == tvFull && cgs->linesAtCount != 0) { int i; Color lightBlue = hvGfxFindRgb(hvg, &guidelineColor); for (i=0; i<cgs->linesAtCount; ++i) { y = height - 1 - (cgs->linesAt[i] - minVal)*yScale + yOff; hvGfxBox(hvg, xOff, y, width, 1, lightBlue); } } if (binFileName) { struct chromGraphBin *cgb = chromGraphBinOpen(binFileName); if (chromGraphBinSeekToChrom(cgb, chromName)) { int seqStartMinus = seqStart - cgs->maxGapToFill; while (chromGraphBinNextVal(cgb)) { int pos = cgb->chromStart; if (pos >= seqStartMinus) { double val = cgb->val; x = (pos - seqStart)*xScale + xOff; y = height - 1 - (val - minVal)*yScale + yOff; if (x >= xOff) { if (pos - lastPos <= maxGapToFill) { if (llastX != lastX || llastY != lastY || lastX != x || lastY != y) hvGfxLine(hvg, lastX, lastY, x, y, myColor); } else hvGfxDot(hvg, x, y, myColor); } llastX = lastX; llastY = lastY; lastX = x; lastY = y; lastPos = pos; if (pos >= seqEnd) break; } } } } else { struct sqlConnection *conn = hAllocConn(database); char query[512]; struct sqlResult *sr; char **row; /* Construct query. Set up a little more than window so that * we can draw connecting lines. */ safef(query, sizeof(query), "select chromStart,val from %s " "where chrom='%s' and chromStart>=%d and chromStart<%d", tg->table, chromName, seqStart - cgs->maxGapToFill, seqEnd + cgs->maxGapToFill); sr = sqlGetResult(conn, query); /* Loop through drawing lines from one point to another unless * the points are too far apart. */ while ((row = sqlNextRow(sr)) != NULL) { int pos = sqlUnsigned(row[0]); double val = atof(row[1]); x = (pos - seqStart)*xScale + xOff; y = height - 1 - (val - minVal)*yScale + yOff; if (x >= xOff) { if (pos - lastPos <= maxGapToFill) { if (llastX != lastX || llastY != lastY || lastX != x || lastY != y) hvGfxLine(hvg, lastX, lastY, x, y, myColor); } else hvGfxDot(hvg, x, y, myColor); } llastX = lastX; llastY = lastY; lastX = x; lastY = y; lastPos = pos; if (pos >= seqEnd) break; } sqlFreeResult(&sr); hFreeConn(&conn); } /* Do map box */ xOff = hvGfxAdjXW(hvg, xOff, width); char *encodedTrack = cgiEncode(tg->track); if(theImgBox && curImgTrack) { char link[512]; // FIXME: winStart/winEnd are not right when using a portal - safef(link,sizeof(link),"%s&o=%d&t=%d&g=%s", hgcNameAndSettings(), - winStart, winEnd, encodedTrack); + safef(link,sizeof(link),"%s&c=%s&o=%d&t=%d&g=%s", hgcNameAndSettings(), + chromName, winStart, winEnd, encodedTrack); #ifdef IMAGEv2_SHORT_MAPITEMS if(xOff < insideX && xOff+width > insideX) warn("cgDrawEither(%s) map item spanning slices. LX:%d TY:%d RX:%d BY:%d link:[%s]",encodedTrack,xOff, yOff, xOff+width, yOff+height, link); #endif//def IMAGEv2_SHORT_MAPITEMS imgTrackAddMapItem(curImgTrack,link,NULL,xOff,yOff,xOff+width,yOff+height,tg->track); } else { hPrintf("<AREA SHAPE=RECT COORDS=\"%d,%d,%d,%d\" ", xOff, yOff, xOff+width, yOff+height); hPrintf("HREF=\"%s&o=%d&t=%d&g=%s&c=%s&l=%d&r=%d&db=%s&pix=%d\">\n", hgcNameAndSettings(), winStart, winEnd, encodedTrack, chromName, winStart, winEnd, database, tl.picWidth); } } static void cgDrawItems(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) /* Draw chromosome graph for built-in track. */ { cgDrawEither(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis, NULL); } static void cgDrawItemsCt(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) /* Draw chromosome graph for customTrack. */ { cgDrawEither(tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis, trackDbRequiredSetting(tg->tdb, "binaryFile")); } int cgTotalHeight(struct track *tg, enum trackVisibility vis) /* Most fixed height track groups will use this to figure out the height * they use. */ { struct chromGraphSettings *cgs = tg->customPt; switch (vis) { case tvFull: case tvPack: tg->height = cgs->pixels; break; case tvDense: default: tg->height = tl.fontHeight; break; } return tg->height; } void wrapTextAndCenter(struct hvGfx *hvg, int xOff, int yOff, int width, int height, MgFont *font, Color color, char *text) /* Try and word-wrap text into box more or less. */ { struct slName *word, *wordList = slNameListFromString(text, ' '); int wordCount = slCount(wordList); int fontHeight = tl.fontHeight; int lineCount = height / fontHeight; int yUsed, y; if (lineCount > wordCount) lineCount = wordCount; yUsed = lineCount * fontHeight; y = (height - yUsed)/2 + yOff; for (word = wordList; word != NULL; word = word->next) { hvGfxText(hvg, xOff, y, color, font, word->name); y += fontHeight; } } void cgLeftLabels(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) /* Draw labels to the left. */ { struct chromGraphSettings *cgs = tg->customPt; if (vis == tvDense || cgs->linesAtCount == 0) { hvGfxTextRight(hvg, xOff, yOff, width - 1, height, color, font, tg->shortLabel); } else { int i; int realHeight = height; int realYoff = yOff; double minVal = cgs->minVal; double yScale; int tickSize = tl.nWidth; int numPos = tickSize * 1.25; if (withCenterLabels) { int centerLabelHeight = tl.fontHeight; realHeight -= centerLabelHeight; realYoff += centerLabelHeight; } yScale = (realHeight-1)/(cgs->maxVal - minVal); for (i=0; i<cgs->linesAtCount; ++i) { double val = cgs->linesAt[i]; int y = realHeight - 1 - (val - minVal)*yScale + realYoff; char numText[16]; hvGfxBox(hvg, xOff + width - tickSize, y, tickSize, 1, color); safef(numText, sizeof(numText), "%g", val); hvGfxTextRight(hvg, xOff, y - tl.fontHeight+2, width - numPos, tl.fontHeight, color, font, numText); } wrapTextAndCenter(hvg, xOff+1, yOff, width*5*tl.nWidth, height, font, color, tg->shortLabel); } } static void chromGraphMethodsCommon(struct track *tg) /* Get chromGraph methods common to built in and custom tracks. */ { tg->loadItems = tgLoadNothing; tg->totalHeight = cgTotalHeight; tg->freeItems = tgFreeNothing; tg->drawLeftLabels = cgLeftLabels; tg->mapsSelf = TRUE; } void chromGraphMethods(struct track *tg) /* Fill in chromGraph methods for built in track. */ { chromGraphMethodsCommon(tg); tg->drawItems = cgDrawItems; struct sqlConnection *conn = hAllocConn(database); tg->customPt = chromGraphSettingsGet(tg->track, conn, tg->tdb, cart); hFreeConn(&conn); } void chromGraphMethodsCt(struct track *tg) /* Fill in chromGraph methods for custom track. */ { tg->drawItems = cgDrawItemsCt; chromGraphMethodsCommon(tg); tg->customPt = chromGraphSettingsGet(tg->track, NULL, tg->tdb, cart); }