void drawUseBamWarning(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg,
int xOff, int yOff, int width, MgFont *font, Color color,
enum trackVisibility vis)
/* Draw a message saying that the code needs to be built with USE_BAM=1. */
{
char message[512];
safef(message, sizeof(message),
"Get samtools(.sourceforge.net) and recompile kent/src with USE_BAM=1");
Color yellow = hvGfxFindRgb(hvg, &undefinedYellowColor);
hvGfxBox(hvg, xOff, yOff, width, tg->heightPer, yellow);
hvGfxTextCentered(hvg, xOff, yOff, width, tg->heightPer, MG_BLACK, font, message);
}
void bigDrawWarning(struct track *tg, int seqStart, int seqEnd, struct hvGfx *hvg,
int xOff, int yOff, int width, MgFont *font, Color color,
enum trackVisibility vis)
/* Draw the network error message */
{
char message[1024];
Color yellow = hvGfxFindRgb(hvg, &undefinedYellowColor);
char *errMsg = bigWarnReformat(tg->networkErrMsg);
char *nl = errMsg;
int sl = strlen(errMsg);
// in some cases, cannot use tg-> values, so recalc local equivalents.
int heightPer = tl.fontHeight; /* Height per item line minus border. */
int lineHeight = heightPer+4; /* Height per item line including border. */
if (lineHeight > tg->height)
lineHeight = tg->height;
int n = bigWarnNumLines(errMsg); /* Lines of warning text */
int m = tg->height / lineHeight; /* Lines of text space available */
if (m < 1)
m = 1;
// make yellow background to draw user's attention to the err msg
if (!sameOk(parentContainerType(tg), "multiWig")) // unless multiwig has already done it.
hvGfxBox(hvg, xOff, yOff, width, tg->height, yellow);
// leading blank lines if any
int bl = (m-n)/2;
int i;
for(i=0;i<bl;++i)
yOff += lineHeight;
int l = 0;
while (TRUE)
{
char *msg = nl;
nl = strchr(nl,'\n');
if (nl)
nl[0] = 0;
if (nl || ((sl > 0) && (errMsg[sl-1]!='\n')))
{
safef(message, sizeof(message), "%s", msg);
hvGfxTextCentered(hvg, xOff, yOff, width, lineHeight, MG_BLACK, font, message);
yOff += lineHeight;
++l;
if (l > n)
break;
if (l > m)
break;
}
if (!nl)
break;
++nl;
}
freeMem(errMsg);
}
void hvGfxDrawRulerBumpText(struct hvGfx *hvg, int xOff, int yOff,
int height, int width,
Color color, MgFont *font,
int startNum, int range, int bumpX, int bumpY)
/* Draw a ruler inside the indicated part of mg with numbers that start at
* startNum and span range. Bump text positions slightly. */
{
int tickSpan;
int tickPos;
double scale;
int firstTick;
int remainder;
int end = startNum + range;
int x;
char tbuf[18];
int numWid;
int goodNumTicks;
int niceNumTicks = width/35;
sprintLongWithCommas(tbuf, startNum+range);
numWid = mgFontStringWidth(font, tbuf)+4+bumpX;
goodNumTicks = width/numWid;
if (goodNumTicks < 1) goodNumTicks = 1;
if (goodNumTicks > niceNumTicks) goodNumTicks = niceNumTicks;
tickSpan = figureTickSpan(range, goodNumTicks);
scale = (double)width / range;
firstTick = startNum + tickSpan;
remainder = firstTick % tickSpan;
firstTick -= remainder;
for (tickPos=firstTick; tickPos<end; tickPos += tickSpan)
{
sprintLongWithCommas(tbuf, tickPos);
numWid = mgFontStringWidth(font, tbuf)+4;
x = (int)((tickPos-startNum) * scale) + xOff;
hvGfxBox(hvg, x, yOff, 1, height, color);
if (x - numWid >= xOff)
{
hvGfxTextCentered(hvg, x-numWid + bumpX, yOff + bumpY, numWid,
height, color, font, tbuf);
}
}
}
void hCytoBandDrawAt(struct cytoBand *band, struct hvGfx *hvg,
int x, int y, int width, int height, boolean isDmel,
MgFont *font, int fontPixelHeight, Color aColor, Color bColor,
Color *shades, int maxShade)
/* Draw a single band in appropriate color at given position. If there's
* room put in band label. */
{
Color col = hCytoBandColor(band, hvg, isDmel, aColor, bColor, shades, maxShade);
hvGfxBox(hvg, x, y, width, height, col);
if (height >= mgFontLineHeight(font))
{
char *s = abbreviatedBandName(band, font, width, isDmel);
if (s != NULL)
{
Color textCol = hvGfxContrastingColor(hvg, col);
hvGfxTextCentered(hvg, x, y, width, height, textCol, font, s);
}
}
}
static void contigDraw(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw contig items. */
{
struct ctgPos *ctg;
int y = yOff;
int heightPer = tg->heightPer;
int lineHeight = tg->lineHeight;
int x1,x2,w;
boolean isFull = (vis == tvFull);
int ix = 0;
char *s;
double scale = scaleForPixels(width);
for (ctg = tg->items; ctg != NULL; ctg = ctg->next)
{
x1 = round((double)((int)ctg->chromStart-winStart)*scale) + xOff;
x2 = round((double)((int)ctg->chromEnd-winStart)*scale) + xOff;
/* Clip here so that text will tend to be more visible... */
if (x1 < xOff)
x1 = xOff;
if (x2 > xOff + width)
x2 = xOff + width;
w = x2-x1;
if (w < 1)
w = 1;
hvGfxBox(hvg, x1, y, w, heightPer, color);
s = abbreviateContig(ctg->contig, tl.font, w);
if (s != NULL)
hvGfxTextCentered(hvg, x1, y, w, heightPer, MG_WHITE, tl.font, s);
if (isFull)
y += lineHeight;
else
{
mapBoxHc(hvg, ctg->chromStart, ctg->chromEnd, x1,y,w,heightPer, tg->track,
tg->mapItemName(tg, ctg),
tg->itemName(tg, ctg));
}
++ix;
}
}
void genoLayDrawChromLabels(struct genoLay *gl, struct hvGfx *hvg, int color)
/* Draw chromosomes labels in image */
{
struct slRef *ref;
struct genoLayChrom *chrom;
int pixelHeight = mgFontPixelHeight(gl->font);
if (gl->allOneLine)
{
int yOffset = gl->chromOffsetY + gl->chromHeight + 1;
for (ref = gl->bottomList; ref != NULL; ref = ref->next)
{
chrom = ref->val;
hvGfxTextCentered(hvg, chrom->x, yOffset, chrom->width, pixelHeight, color, gl->font,
chrom->shortName);
}
}
else
{
int yOffset = gl->chromOffsetY + gl->chromHeight - pixelHeight;
/* Draw chromosome labels. */
for (ref = gl->leftList; ref != NULL; ref = ref->next)
leftLabel(hvg, gl, ref->val, yOffset, pixelHeight, color);
for (ref = gl->rightList; ref != NULL; ref = ref->next)
rightLabel(hvg, gl, ref->val, yOffset, pixelHeight, color);
for (ref = gl->bottomList; ref != NULL; ref = ref->next)
{
chrom = ref->val;
if (ref == gl->bottomList)
leftLabel(hvg, gl, chrom, yOffset, pixelHeight, color);
else if (ref->next == NULL)
rightLabel(hvg, gl, chrom, yOffset, pixelHeight, color);
else
midLabel(hvg, gl, chrom, yOffset, pixelHeight, color);
}
}
}
static void longRangeDraw(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw a list of longTabix structures. */
{
double scale = scaleForWindow(width, seqStart, seqEnd);
struct bed *beds = tg->items;
unsigned int maxWidth;
struct longRange *longRange;
char buffer[1024];
char itemBuf[2048];
char statusBuf[2048];
safef(buffer, sizeof buffer, "%s.%s", tg->tdb->track, LONG_MINSCORE);
double minScore = sqlDouble(cartUsualString(cart, buffer, LONG_DEFMINSCORE));
struct longRange *longRangeList = parseLongTabix(beds, &maxWidth, minScore);
for(longRange=longRangeList; longRange; longRange=longRange->next)
{
safef(itemBuf, sizeof itemBuf, "%d", longRange->id);
safef(statusBuf, sizeof statusBuf, "%g %s:%d %s:%d", longRange->score, longRange->sChrom, longRange->s, longRange->eChrom, longRange->e);
boolean sOnScreen = (longRange->s >= seqStart) && (longRange->s < seqEnd);
unsigned sx = 0, ex = 0;
if (sOnScreen)
sx = (longRange->s - seqStart) * scale + xOff;
if (differentString(longRange->sChrom, longRange->eChrom))
{
if (!sOnScreen)
continue;
// draw the foot
int footWidth = scale * (longRange->sw / 2);
hvGfxLine(hvg, sx - footWidth, yOff, sx + footWidth, yOff, MG_BLUE);
int height = tg->height/2;
if (tg->visibility == tvDense)
height = tg->height;
unsigned yPos = yOff + height;
hvGfxLine(hvg, sx, yOff, sx, yPos, MG_BLUE);
if (tg->visibility == tvFull)
{
mapBoxHgcOrHgGene(hvg, longRange->s, longRange->s, sx - 2, yOff, 4, tg->height/2,
tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
safef(buffer, sizeof buffer, "%s:%d", longRange->eChrom, longRange->e);
hvGfxTextCentered(hvg, sx, yPos + 2, 4, 4, MG_BLUE, font, buffer);
int width = vgGetFontStringWidth(hvg->vg, font, buffer);
int height = vgGetFontPixelHeight(hvg->vg, font);
mapBoxHgcOrHgGene(hvg, longRange->s, longRange->s, sx - width/2, yPos, width, height,
tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
}
}
else
{
boolean eOnScreen = (longRange->e >= seqStart) && (longRange->e < seqEnd);
if (!(sOnScreen || eOnScreen))
continue;
if (eOnScreen)
ex = (longRange->e - seqStart) * scale + xOff;
double longRangeWidth = longRange->e - longRange->s;
int peak = (tg->height - 15) * ((double)longRangeWidth / maxWidth) + yOff + 10;
if (tg->visibility == tvDense)
peak = yOff + tg->height;
if (sOnScreen)
{
int footWidth = scale * (longRange->sw / 2);
hvGfxLine(hvg, sx - footWidth, yOff, sx + footWidth, yOff, color);
hvGfxLine(hvg, sx, yOff, sx, peak, color);
}
if (eOnScreen)
{
int footWidth = scale * (longRange->ew / 2);
hvGfxLine(hvg, ex - footWidth, yOff, ex + footWidth, yOff, color);
hvGfxLine(hvg, ex, yOff, ex, peak, color);
}
if (tg->visibility == tvFull)
{
unsigned sPeak = sOnScreen ? sx : xOff;
unsigned ePeak = eOnScreen ? ex : xOff + width;
hvGfxLine(hvg, sPeak, peak, ePeak, peak, color);
safef(statusBuf, sizeof statusBuf, "%g %s:%d %s:%d", longRange->score, longRange->sChrom, longRange->s, longRange->eChrom, longRange->e);
if (sOnScreen)
mapBoxHgcOrHgGene(hvg, longRange->s, longRange->e, sx - 2, yOff, 4, peak - yOff,
tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
if (eOnScreen)
mapBoxHgcOrHgGene(hvg, longRange->s, longRange->e, ex - 2, yOff, 4, peak - yOff,
tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
mapBoxHgcOrHgGene(hvg, longRange->s, longRange->e, sPeak, peak-2, ePeak - sPeak, 4,
tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
}
}
}
}