/* Copyright (C) 2010 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "jksql.h" #include "hgTracks.h" #include "rnaPLFoldTrack.h" /* ------ BEGIN RNAplfold ------ */ /*******************************************************************/ #define RNAPLFOLD_DATA_SHADES 10 /* Declare our color gradients and the the number of colors in them */ Color plShadesPos[RNAPLFOLD_DATA_SHADES * 3]; Color plOutlineColor; Color plHighDprimeLowLod; /* blue */ double basePairSpan=0; int maxBasePairSpan=5000; boolean rnaPLFoldInv=FALSE; // default is inverted = sequence on buttom double scaleHeight=0; void plShadesInit(struct track *tg, struct hvGfx *hvg, boolean isDprime) /* Allocate the LD for positive and negative values, and error cases */ { static struct rgbColor white = {255, 255, 255, 255}; static struct rgbColor red = {255, 0, 0, 255}; static struct rgbColor green = {0 , 255, 0, 255}; static struct rgbColor blue = { 0, 0, 255, 255}; plOutlineColor = hvGfxFindColorIx(hvg, 0, 0, 0); /* black */ plHighDprimeLowLod = hvGfxFindColorIx(hvg, 192, 192, 240); /* blue */ hvGfxMakeColorGradient(hvg, &white, &blue, RNAPLFOLD_DATA_SHADES, plShadesPos); hvGfxMakeColorGradient(hvg, &white, &red, RNAPLFOLD_DATA_SHADES, plShadesPos + RNAPLFOLD_DATA_SHADES); hvGfxMakeColorGradient(hvg, &white, &green, RNAPLFOLD_DATA_SHADES, plShadesPos + 2 * RNAPLFOLD_DATA_SHADES); char *cartString = cartCgiUsualString(cart, RNAPLFOLD_INVERT, RNAPLFOLD_INVERT_DEF); rnaPLFoldInv = sameString(cartString,RNAPLFOLD_INVERT_BUTTOM) ? FALSE : TRUE; } void plInitColorLookup(struct track *tg, struct hvGfx *hvg, boolean isDprime) { plShadesInit(tg, hvg, isDprime); colorLookup[(int)'a'] = plShadesPos[0]; colorLookup[(int)'b'] = plShadesPos[1]; colorLookup[(int)'c'] = plShadesPos[2]; colorLookup[(int)'d'] = plShadesPos[3]; colorLookup[(int)'e'] = plShadesPos[4]; colorLookup[(int)'f'] = plShadesPos[5]; colorLookup[(int)'g'] = plShadesPos[6]; colorLookup[(int)'h'] = plShadesPos[7]; colorLookup[(int)'i'] = plShadesPos[8]; colorLookup[(int)'j'] = plShadesPos[9]; colorLookup[(int)'A'] = plShadesPos[10]; colorLookup[(int)'B'] = plShadesPos[11]; colorLookup[(int)'C'] = plShadesPos[12]; colorLookup[(int)'D'] = plShadesPos[13]; colorLookup[(int)'E'] = plShadesPos[14]; colorLookup[(int)'F'] = plShadesPos[15]; colorLookup[(int)'G'] = plShadesPos[16]; colorLookup[(int)'H'] = plShadesPos[17]; colorLookup[(int)'I'] = plShadesPos[18]; colorLookup[(int)'J'] = plShadesPos[19]; colorLookup[(int)'K'] = plShadesPos[20]; colorLookup[(int)'L'] = plShadesPos[21]; colorLookup[(int)'M'] = plShadesPos[22]; colorLookup[(int)'N'] = plShadesPos[23]; colorLookup[(int)'O'] = plShadesPos[24]; colorLookup[(int)'P'] = plShadesPos[25]; colorLookup[(int)'Q'] = plShadesPos[26]; colorLookup[(int)'R'] = plShadesPos[27]; colorLookup[(int)'S'] = plShadesPos[28]; colorLookup[(int)'T'] = plShadesPos[29]; //colorLookup[(int)'y'] = plHighLodLowDprime; /* LOD error case */ //colorLookup[(int)'z'] = plHighDprimeLowLod; /* LOD error case */ } void bedLoadRnaLpFoldItemByQuery(struct track *tg, char *table, char *query, ItemLoader loader) /* RNALPFOLD specific tg->item loader, as we need to load items beyond the current window to load the chromEnd positions for RNALPFOLD values. */ { struct sqlConnection *conn = hAllocConn(database); int rowOffset = 0; //int chromEndOffset = min(winEnd-winStart, 250000); /* extended chromEnd range */ struct sqlResult *sr = NULL; char **row = NULL; struct slList *itemList = NULL, *item = NULL; char altTable[64]; if(winEnd-winStart < maxBasePairSpan) { // test if another base-pair span as default is set char *tableSuffix = cartCgiUsualString(cart, RNAPLFOLD_MAXBPDISTANCE, RNAPLFOLD_MAXBPDISTANCE_DEF); basePairSpan=atoi(tableSuffix); //if(strcmp(tableSuffix,RNAPLFOLD_MAXBPDISTANCE_DEF) != 0) // { strcpy(altTable,table); strcat(altTable,tableSuffix); table=altTable; // } if(query == NULL) sr = hRangeQuery(conn, table, chromName, winStart, winEnd/*+chromEndOffset*/, NULL, &rowOffset); else sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { item = loader(row + rowOffset); slAddHead(&itemList, item); } } //slSort(&itemList, bedCmp); sqlFreeResult(&sr); tg->items = itemList; hFreeConn(&conn); } void bedLoadRnaLpFoldItem(struct track *tg, char *table, ItemLoader loader) /* RNALPFOLD specific tg->item loader. */ { bedLoadRnaLpFoldItemByQuery(tg, table, NULL, loader); } void rnaPLFoldLoadItems(struct track *tg) /* loadItems loads up items for the chromosome range indicated. */ { bedLoadRnaLpFoldItem(tg, tg->table, (ItemLoader)rnaPLFoldLoad); tg->canPack = FALSE; } int rnaPLFoldTotalHeight(struct track *tg, enum trackVisibility vis) /* Return total height. Called before and after drawItems. * Must set height, lineHeight, heightPer */ { tg->lineHeight = tl.fontHeight + 1; tg->heightPer = tg->lineHeight - 1; if ( vis==tvDense || ( tg->limitedVisSet && tg->limitedVis==tvDense ) ) tg->height = tg->lineHeight; else { tg->height = max((int)(insideWidth*(basePairSpan/2.0)/(winEnd-winStart)),tg->lineHeight); if(tg->height > 200) { scaleHeight = 200.0 / (double)tg->height; tg->height = 200; // test !! } else scaleHeight = 1; } return tg->height; } void lpDrawDiamond(struct hvGfx *hvg, int xl, int yl, int xt, int yt, int xr, int yr, int xb, int yb, Color fillColor, Color outlineColor) /* Draw diamond shape. */ { struct gfxPoly *poly = gfxPolyNew(); gfxPolyAddPoint(poly, xl, yl); gfxPolyAddPoint(poly, xt, yt); gfxPolyAddPoint(poly, xr, yr); gfxPolyAddPoint(poly, xb, yb); hvGfxDrawPoly(hvg, poly, fillColor, TRUE); gfxPolyFree(&poly); } void rnaPLFoldDrawDiamond(struct hvGfx *hvg, struct track *tg, int width, int xOff, int yOff, int a, int b, int c, int d, Color shade, Color outlineColor, double scale, boolean drawMap, char *name, enum trackVisibility vis, boolean trim) /* Draw and map a single pairwise RNALPFOLD box */ { int yMax = rnaPLFoldTotalHeight(tg, vis)+yOff; /* convert from genomic coordinates to hvg coordinates */ /* multiple coordinates by 10 to avoid integer division rounding errors */ a*=10; b*=10; c*=10; d*=10; int xl = round((double)(scale*((c+a)/2-winStart*10)))/10 + xOff; int xt = round((double)(scale*((d+a)/2-winStart*10)))/10 + xOff; int xr = round((double)(scale*((d+b)/2-winStart*10)))/10 + xOff; int xb = round((double)(scale*((c+b)/2-winStart*10)))/10 + xOff; int yl = round((double)(scaleHeight * scale*(c-a)/2))/10 + yOff; int yt = round((double)(scaleHeight * scale*(d-a)/2))/10 + yOff; int yr = round((double)(scaleHeight * scale*(d-b)/2))/10 + yOff; int yb = round((double)(scaleHeight * scale*(c-b)/2))/10 + yOff; if (!rnaPLFoldInv) { yl = yMax - yl + yOff; yt = yMax - yt + yOff; yr = yMax - yr + yOff; yb = yMax - yb + yOff; } /* correct bottom coordinate if necessary */ if (yb<=0) yb=1; if (yt>yMax && trim) yt=yMax; lpDrawDiamond(hvg, xl, yl, xt, yt, xr, yr, xb, yb, shade, outlineColor); return; /* mapDiamondUI is working well, but there is a bug with AREA=POLY on the Mac browsers, so this will be postponed for now by not using this code */ /* also, since it only goes to hgTrackUi, it is redundant with mapTrackBackground. * so keep this disabled until there is something more specific like an hgc * handler for diamonds. */ if (drawMap && xt-xl>5 && xb-xl>5) mapDiamondUi(hvg, xl, yl, xt, yt, xr, yr, xb, yb, name, tg->track, tg->tdb->track); } void rnaPLFoldAddToDenseValueHash(struct hash *rnaPLFoldHash, unsigned a, char rnaPLFoldVal) /* Add new values to rnaFoldLp hash or update existing values. Values are averaged along the diagonals. */ { ldAddToDenseValueHash(rnaPLFoldHash, a, rnaPLFoldVal); } void rnaPLFoldDrawDenseValueHash(struct hvGfx *hvg, struct track *tg, int xOff, int yOff, double scale, Color outlineColor, struct hash *ldHash) { ldDrawDenseValueHash(hvg, tg, xOff, yOff, scale, outlineColor, ldHash); } /* rnaPLFoldDrawItems -- lots of disk and cpu optimizations here. * Based on rnaPLFoldDrawItems */ void rnaPLFoldDrawItems(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg, int xOff, int yOff, int width, MgFont *font, Color color, enum trackVisibility vis) /* Draw item list, one per track. */ { struct rnaPLFold *dPtr = NULL; // *sPtr = NULL; /* pointers to 5' and 3' ends */ double scale = scaleForPixels(insideWidth); //int itemCount = slCount((struct slList *)tg->items); Color shade = 0, outlineColor = plOutlineColor; //getOutlineColor(tg, itemCount); int a=0, b, c, d=0, i; /* chromosome coordinates and counter */ boolean drawMap = FALSE; /* ( itemCount<1000 ? TRUE : FALSE ); */ //struct hash *rnaPLFoldHash = newHash(20); Color yellow = hvGfxFindRgb(hvg, &undefinedYellowColor); char *rnaPLFoldVal = NULL; boolean rnaPLFoldTrm = FALSE; int basePairOffset; if ( vis==tvDense || ( tg->limitedVisSet && tg->limitedVis==tvDense ) ) hvGfxBox(hvg, insideX, yOff, insideWidth, tg->height-1, yellow); mapTrackBackground(tg, hvg, xOff, yOff); /*nothing to do? */ if (tg->items==NULL) return; /* initialize arrays to convert from ascii encoding to color values */ plInitColorLookup(tg, hvg, FALSE); /* Loop through all items to get values and initial coordinates (a and b) */ for (dPtr=tg->items; dPtr!=NULL && dPtr->next!=NULL; dPtr=dPtr->next) { a = dPtr->chromStart; b = a+1; //dPtr->next->chromStart; rnaPLFoldVal = dPtr->colorIndex; i = 0; c = a/*+1*/; d = b/*+1*/; while(rnaPLFoldVal[i] != 'Z') { /* Loop through all items again to get end coordinates (c and d): used to be 'drawNecklace' */ while(rnaPLFoldVal[i] != 'Y' && rnaPLFoldVal[i] != 'Z') // for ( sPtr=dPtr; iscore && sPtr!=NULL && sPtr->next!=NULL; sPtr=sPtr->next ) { basePairOffset = 16 * (rnaPLFoldVal[i]-'A') + (rnaPLFoldVal[i+1]-'A'); //basePairOffset = (int)rnaPLFoldVal[i+1]-(int)'A'; // if(basePairOffset > 70) // errAbort("Invalid Offset %d, %c, %d, %s",i+1,rnaPLFoldVal[i+1],basePairOffset,rnaPLFoldVal); i+=2; // c = sPtr->chromStart; // d = sPtr->next->chromStart; c+=basePairOffset; d+=basePairOffset; shade = colorLookup[(int)rnaPLFoldVal[i]]; if(b-a >1 || d-c>1) errAbort("Invalid distance: a:%d, b:%d, c:%d, d:%d",a,b,c,d); //if(c-a>70) // shade = plHighLodLowDprime; // if ( vis==tvFull && ( !tg->limitedVisSet || ( tg->limitedVisSet && tg->limitedVis==tvFull ) ) ) // emphasize stable base-pairs if(shade == plShadesPos[9] || shade == plShadesPos[19] || shade == plShadesPos[29]) outlineColor=plOutlineColor; else outlineColor=0; rnaPLFoldDrawDiamond(hvg, tg, width, xOff, yOff, a, b, c, d, shade, outlineColor, scale, drawMap, "", vis, rnaPLFoldTrm); // else if ( vis==tvDense || ( tg->limitedVisSet && tg->limitedVis==tvDense ) ) // { // rnaPLFoldAddToDenseValueHash(rnaPLFoldHash, a, rnaPLFoldVal[i]); // rnaPLFoldAddToDenseValueHash(rnaPLFoldHash, d, rnaPLFoldVal[i]); // } // else // errAbort("Visibility '%s' is not supported for the RNALPFOLD track yet.", hStringFromTv(vis)); i++; } if(rnaPLFoldVal[i] == 'Y') { a++; b++; i++; c=a/*+1*/; d=b/*+1*/; } } } // draw diagonals Color pColorDarkGray; Color pColorLightGray; pColorDarkGray = hvGfxFindColorIx(hvg, 128, 128, 128); /* dark gray */ pColorLightGray = hvGfxFindColorIx(hvg, 200, 200, 200); /* light gray */ int diagDark = atoi(cartCgiUsualString(cart, RNAPLFOLD_DIAGDARK, RNAPLFOLD_DIAGDARK_DEF)); int diagLight = atoi(cartCgiUsualString(cart, RNAPLFOLD_DIAGLIGHT, RNAPLFOLD_DIAGLIGHT_DEF)); int x,r; if(winEnd-winStart<1500) // do not show diags when zoom out too far { double xAdd; xAdd=(double)insideWidth / (double)(winEnd-winStart); x=xOff; // for(i=winStart-(winEnd-winStart),r=winStart-winEnd;iheight, x+(int)(xAdd*(double)r+(basePairSpan*xAdd)), yOff-tg->height, pColorDarkGray); hvGfxLine(hvg, x+(int)(xAdd*(double)r), yOff-tg->height, x+(int)(xAdd*(double)r+(basePairSpan*xAdd)), yOff+tg->height , pColorDarkGray); } else { if(diagLight && i%diagLight == 0) { hvGfxLine(hvg, x+(int)(xAdd*(double)r), yOff+tg->height, x+(int)(xAdd*(double)r+(basePairSpan*xAdd)), yOff-tg->height, pColorLightGray); hvGfxLine(hvg, x+(int)(xAdd*(double)r), yOff-tg->height, x+(int)(xAdd*(double)r+(basePairSpan*xAdd)), yOff+tg->height, pColorLightGray); } } } } //if ( vis==tvDense || ( tg->limitedVisSet && tg->limitedVis==tvDense ) ) // rnaPLFoldDrawDenseValueHash(hvg, tg, xOff, yOff, scale, outlineColor, rnaPLFoldHash); } void rnaPLFoldDrawLeftLabels(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 left labels. */ { char label[16]; int yVisOffset = 0 + tl.fontHeight; // ( vis == tvDense ? 0 : tg->heightPer + height/2 ); safecpy(label, sizeof(label), tg->shortLabel); hvGfxUnclip(hvg); hvGfxSetClip(hvg, leftLabelX, yOff+yVisOffset, leftLabelWidth, tg->heightPer); hvGfxTextRight(hvg, leftLabelX, yOff+yVisOffset, leftLabelWidth, tg->heightPer, color, font, label); hvGfxUnclip(hvg); hvGfxSetClip(hvg, insideX, yOff, insideWidth, tg->height); } void rnaPLFoldMethods(struct track *tg) /* setup special methods for the RNA LP FOLD track */ { if(tg->subtracks != 0) /* Only load subtracks, not top level track. */ return; tg->loadItems = rnaPLFoldLoadItems; tg->totalHeight = rnaPLFoldTotalHeight; tg->drawItems = rnaPLFoldDrawItems; tg->freeItems = ldFreeItems; tg->drawLeftLabels = rnaPLFoldDrawLeftLabels; tg->mapsSelf = TRUE; tg->canPack = FALSE; } /* ------ END RNA LP FOLD ------ */