static char *abbreviatedBandName(struct cytoBand *band,
MgFont *font, int width, boolean isDmel)
/* Return a string abbreviated enough to fit into space. */
{
int textWidth;
static char string[32];
/* If have enough space, return original chromosome/band. */
sprintf(string, "%s%s", (isDmel ? "" : skipChr(band->chrom)), band->name);
textWidth = mgFontStringWidth(font, string);
if (textWidth <= width)
return string;
/* Try leaving off chromosome */
sprintf(string, "%s", band->name);
textWidth = mgFontStringWidth(font, string);
if (textWidth <= width)
return string;
/* Try leaving off initial letter */
sprintf(string, "%s", band->name+1);
textWidth = mgFontStringWidth(font, string);
if (textWidth <= width)
return string;
return NULL;
}
static char *abbreviateContig(char *string, MgFont *font, int width)
/* Return a string abbreviated enough to fit into space. */
{
int textWidth;
/* If have enough space, return original unabbreviated string. */
textWidth = mgFontStringWidth(font, string);
if (textWidth <= width)
return string;
/* Try skipping over 'ctg' */
string += 3;
textWidth = mgFontStringWidth(font, string);
if (textWidth <= width)
return string;
return NULL;
}
void vgDrawRulerBumpText(struct vGfx *vg, 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[14];
int numWid;
int goodNumTicks;
int niceNumTicks = width/35;
numLabelString(startNum+range, tbuf);
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)
{
numLabelString(tickPos, tbuf);
numWid = mgFontStringWidth(font, tbuf)+4;
x = (int)((tickPos-startNum) * scale) + xOff;
vgBox(vg, x, yOff, 1, height, color);
if (x - numWid >= xOff)
{
vgTextCentered(vg, x-numWid + bumpX, yOff + bumpY, numWid,
height, color, font, tbuf);
}
}
}
static void midLabel(struct hvGfx *hvg, struct genoLay *gl,
struct genoLayChrom *chrom, int yOffset, int fontHeight,
int color)
/* Draw a chromosome with label on left. */
{
MgFont *font = gl->font;
int textWidth = mgFontStringWidth(font, chrom->shortName);
hvGfxTextRight(hvg, chrom->x - textWidth - gl->spaceWidth,
chrom->y + yOffset,
textWidth, fontHeight, color,
font, chrom->shortName);
}
int ggLabelWidth(struct genoGraph *gg, MgFont *font)
/* Return width used by graph labels. */
{
struct chromGraphSettings *cgs = gg->settings;
int i;
int minLabelWidth = 0, labelWidth;
char buf[24];
fakeEmptyLabels(cgs);
for (i=0; i<cgs->linesAtCount; ++i)
{
safef(buf, sizeof(buf), "%g ", cgs->linesAt[i]);
labelWidth = mgFontStringWidth(font, buf);
if (labelWidth > minLabelWidth)
minLabelWidth = labelWidth;
}
return minLabelWidth;
}
int gifLabelMaxWidth(char **labels, int labelCount)
/* Return maximum pixel width of labels. It's ok to have
* NULLs in labels array. */
{
int width = 0, w, i;
MgFont *font = mgMediumFont();
for (i=0; i<labelCount; ++i)
{
char *label = labels[i];
if (label != NULL)
{
w = mgFontStringWidth(font, labels[i]);
if (w > width)
width = w;
}
}
width += 2;
return width;
}
struct genoLay *genoLayNew(struct genoLayChrom *chromList,
MgFont *font, int picWidth, int betweenChromHeight,
int minLeftLabelWidth, int minRightLabelWidth,
char *how)
/* Figure out layout. For human and most mammals this will be
* two columns with sex chromosomes on bottom. This is complicated
* by the platypus having a bunch of sex chromosomes. */
{
int margin = 3;
struct slRef *refList = NULL, *ref, *left, *right;
struct genoLayChrom *chrom;
struct genoLay *gl;
int autoCount, halfCount, bases, chromInLine;
int leftLabelWidth=0, rightLabelWidth=0, labelWidth;
int spaceWidth = mgFontCharWidth(font, ' ');
int extraLabelPadding = 0;
int autosomeOtherPixels=0, sexOtherPixels=0;
int autosomeBasesInLine=0; /* Maximum bases in a line for autosome. */
int sexBasesInLine=0; /* Bases in line for sex chromsome. */
double sexBasesPerPixel, autosomeBasesPerPixel, basesPerPixel;
int pos = margin;
int y = 0;
int fontHeight = mgFontLineHeight(font);
int chromHeight = fontHeight;
int lineHeight = chromHeight + betweenChromHeight;
boolean allOneLine = FALSE;
refList = refListFromSlList(chromList);
/* Allocate genoLay object and fill in simple fields. */
AllocVar(gl);
gl->chromList = chromList;
gl->chromHash = hashNew(0);
gl->font = font;
gl->picWidth = picWidth;
gl->margin = margin;
gl->spaceWidth = spaceWidth;
gl->lineHeight = lineHeight;
gl->betweenChromHeight = betweenChromHeight;
gl->betweenChromOffsetY = 0;
gl->chromHeight = chromHeight;
gl->chromOffsetY = lineHeight - chromHeight;
/* Save chromosomes in hash too, for easy access */
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
hashAdd(gl->chromHash, chrom->fullName, chrom);
if (sameString(how, genoLayOnePerLine))
{
gl->leftList = refList;
}
else if (sameString(how, genoLayAllOneLine))
{
gl->bottomList = refList;
allOneLine = TRUE;
}
else
{
/* Put sex chromosomes on bottom, and rest on left. */
separateSexChroms(refList, &refList, &gl->bottomList);
autoCount = slCount(refList);
gl->leftList = refList;
/* If there are a lot of chromosomes, then move later
* (and smaller) chromosomes to a new right column */
if (autoCount > 12)
{
halfCount = (autoCount+1)/2;
ref = slElementFromIx(refList, halfCount-1);
gl->rightList = ref->next;
ref->next = NULL;
slReverse(&gl->rightList);
}
}
if (allOneLine)
{
unsigned long totalBases = 0, bStart=0, bEnd;
int chromCount = 0, chromIx=0;
for (ref = gl->bottomList; ref != NULL; ref = ref->next)
{
chrom = ref->val;
totalBases += chrom->size;
chromCount += 1;
}
int availablePixels = picWidth - minLeftLabelWidth - minRightLabelWidth
- 2*margin - (chromCount-1);
double basesPerPixel = (double)totalBases/availablePixels;
gl->picHeight = 2*margin + lineHeight + fontHeight;
for (ref = gl->bottomList; ref != NULL; ref = ref->next)
{
chrom = ref->val;
bEnd = bStart + chrom->size;
int pixStart = round(bStart / basesPerPixel);
int pixEnd = round(bEnd / basesPerPixel);
chrom->width = pixEnd - pixStart;
chrom->height = lineHeight;
chrom->x = pixStart + margin + chromIx + minLeftLabelWidth;
chrom->y = 0;
chromIx += 1;
bStart = bEnd;
}
gl->lineCount = 1;
gl->picHeight = 2*margin + lineHeight + fontHeight + 1;
gl->allOneLine = TRUE;
gl->leftLabelWidth = minLeftLabelWidth;
gl->rightLabelWidth = minRightLabelWidth;
gl->basesPerPixel = basesPerPixel;
gl->pixelsPerBase = 1.0/basesPerPixel;
}
else
{
/* Figure out space needed for autosomes. */
left = gl->leftList;
right = gl->rightList;
while (left || right)
{
bases = 0;
chromInLine = 0;
if (left)
{
chrom = left->val;
labelWidth = mgFontStringWidth(font, chrom->shortName) + spaceWidth;
if (leftLabelWidth < labelWidth)
leftLabelWidth = labelWidth;
bases = chrom->size;
left = left->next;
}
if (right)
{
chrom = right->val;
labelWidth = mgFontStringWidth(font, chrom->shortName) + spaceWidth;
if (rightLabelWidth < labelWidth)
rightLabelWidth = labelWidth;
bases += chrom->size;
right = right->next;
}
if (autosomeBasesInLine < bases)
autosomeBasesInLine = bases;
gl->lineCount += 1;
}
/* Figure out space needed for bottom chromosomes. */
if (gl->bottomList)
{
gl->lineCount += 1;
sexOtherPixels = spaceWidth + 2*margin;
for (ref = gl->bottomList; ref != NULL; ref = ref->next)
{
chrom = ref->val;
sexBasesInLine += chrom->size;
labelWidth = mgFontStringWidth(font, chrom->shortName) + spaceWidth;
if (ref == gl->bottomList )
{
if (leftLabelWidth < labelWidth)
leftLabelWidth = labelWidth;
sexOtherPixels = leftLabelWidth;
}
else if (ref->next == NULL)
{
if (rightLabelWidth < labelWidth)
rightLabelWidth = labelWidth;
sexOtherPixels += rightLabelWidth + spaceWidth;
}
else
{
sexOtherPixels += labelWidth + spaceWidth;
}
}
}
/* Do some adjustments if side labels are bigger than needed for
* chromosome names. */
if (leftLabelWidth < minLeftLabelWidth)
{
extraLabelPadding += (minLeftLabelWidth - leftLabelWidth);
leftLabelWidth = minLeftLabelWidth;
}
if (rightLabelWidth < minRightLabelWidth)
{
extraLabelPadding += (minRightLabelWidth - rightLabelWidth);
rightLabelWidth = minRightLabelWidth;
}
sexOtherPixels += extraLabelPadding;
/* Figure out the number of bases needed per pixel. */
autosomeOtherPixels = 2*margin + spaceWidth + leftLabelWidth + rightLabelWidth;
basesPerPixel = autosomeBasesPerPixel
= autosomeBasesInLine/(picWidth-autosomeOtherPixels);
if (gl->bottomList)
{
sexBasesPerPixel = sexBasesInLine/(picWidth-sexOtherPixels);
if (sexBasesPerPixel > basesPerPixel)
basesPerPixel = sexBasesPerPixel;
}
/* Save positions and sizes of some things in layout structure. */
gl->leftLabelWidth = leftLabelWidth;
gl->rightLabelWidth = rightLabelWidth;
gl->basesPerPixel = basesPerPixel;
gl->pixelsPerBase = 1.0/basesPerPixel;
/* Set pixel positions for left autosomes */
for (ref = gl->leftList; ref != NULL; ref = ref->next)
{
chrom = ref->val;
chrom->x = leftLabelWidth + margin;
chrom->y = y;
chrom->width = round(chrom->size/basesPerPixel);
chrom->height = lineHeight;
y += lineHeight;
}
/* Set pixel positions for right autosomes */
y = 0;
for (ref = gl->rightList; ref != NULL; ref = ref->next)
{
chrom = ref->val;
chrom->width = round(chrom->size/basesPerPixel);
chrom->height = lineHeight;
chrom->x = picWidth - margin - rightLabelWidth - chrom->width;
chrom->y = y;
y += lineHeight;
}
gl->picHeight = 2*margin + lineHeight * gl->lineCount;
y = gl->picHeight - margin - lineHeight;
/* Set pixel positions for sex chromosomes */
for (ref = gl->bottomList; ref != NULL; ref = ref->next)
{
chrom = ref->val;
chrom->y = y;
chrom->width = round(chrom->size/basesPerPixel);
chrom->height = lineHeight;
if (ref == gl->bottomList)
chrom->x = leftLabelWidth + margin;
else if (ref->next == NULL)
chrom->x = picWidth - margin - rightLabelWidth - chrom->width;
else
chrom->x = 2*spaceWidth+mgFontStringWidth(font,chrom->shortName) + pos;
pos = chrom->x + chrom->width;
}
}
return gl;
}
static void altGraphXDrawAt(struct track *tg, void *item, struct hvGfx *hvg,
int xOff, int yOff, double scale,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw an altGraphX at the specified location. */
{
int i = 0;
int s =0, e=0;
int heightPer = tg->heightPer;
int start = 0, end = 0;
struct altGraphX *ag = item;
int width = 0;
int x1, x2;
/* Create a link to hgc. */
if(tg->mapsSelf && tg->mapItem)
{
char name[256];
int nameWidth = 0;
int textX = 0;
start = max(winStart, ag->tStart);
end = min(winEnd, ag->tEnd);
width = (end - start) * scale;
x1 = round((double)((int) start - winStart)*scale) + xOff;
textX = x1;
if(width == 0)
width = 1;
/* If there isn't enough room on before the left edge snap the
label to the left edge. */
if(withLeftLabels && tg->limitedVis == tvPack)
{
safef(name, sizeof(name), "%s", tg->itemName(tg, ag));
nameWidth = mgFontStringWidth(font, name);
textX = textX - (nameWidth + tl.nWidth/2);
if(textX < insideX)
textX = insideX - nameWidth;
width = width + (x1 - textX);
}
tg->mapItem(tg, hvg, ag, "notUsed", "notUsed", ag->tStart, ag->tEnd, textX, yOff, width, heightPer);
}
/* Draw the edges (exons and introns). */
for(i= 0; i < ag->edgeCount; i++)
{
Color color2;
s = ag->vPositions[ag->edgeStarts[i]];
e = ag->vPositions[ag->edgeEnds[i]];
color2 = MG_BLACK;
/* If you want to shade by number of transcripts uncomment next line. */
/* color2 = altGraphXColorForEdge(hvg, ag, i); */
if(isExon(ag, i))
{
if(vis == tvPack)
drawScaledBox(hvg, s, e, scale, xOff, yOff+heightPer/2, heightPer/2, color2);
else
drawScaledBox(hvg, s, e, scale, xOff, yOff, heightPer, color2);
}
else
{
int midX;
s = ag->vPositions[ag->edgeStarts[i]];
e = ag->vPositions[ag->edgeEnds[i]];
x1 = round((double)((int) s - winStart)*scale) + xOff;
x2 = round((double)((int) e - winStart)*scale) + xOff;
if(vis == tvPack)
{
midX = (x1+x2)/2;
hvGfxLine(hvg, x1, yOff+heightPer/2, midX, yOff, color2);
hvGfxLine(hvg, midX, yOff, x2, yOff+heightPer/2, color2);
}
else
hvGfxLine(hvg, x1, yOff+heightPer/2, x2, yOff+heightPer/2, color2);
}
}
}
