static struct memGfx *altColorLabels(char **labels, int labelCount, int width)
/* Return a memory image with alternating colors. */
{
struct memGfx *mg = NULL;
Color c1,c2;
MgFont *font = mgMediumFont();
int lineHeight = mgFontLineHeight(font)-1;
int height = lineHeight * labelCount, i;
int y = 0;
/* Allocate picture and set up colors. */
mg = mgNew(width, height);
c1 = mgFindColor(mg, 0xE0, 0xE0, 0xFF);
c2 = mgFindColor(mg, 0xFF, 0xC8, 0xC8);
/* Draw text. */
for (i=labelCount-1; i >= 0; --i)
{
Color c = ((i&1) ? c2 : c1);
mgDrawBox(mg, 0, y, width, lineHeight, c);
mgTextRight(mg, 0+1, y+1, width-1, lineHeight, MG_BLACK, font, labels[i]);
y += lineHeight;
}
return mg;
}
static void doMapBoxPerRow(struct track *tg,
int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
{
int fontHeight = mgFontLineHeight(font);
int numRows = tg->height / fontHeight;
struct customTrack *ct = tg->customPt;
char itemBuffer[1024];
if (ct)
// this should have the trash file name instead of spacer
// but the click handler doesn't use it anyway
safef(itemBuffer, sizeof itemBuffer, "%s %s","spacer","zoom in");
else
safef(itemBuffer, sizeof itemBuffer, "zoom in");
while(numRows--)
{
char buffer[1024];
safef(buffer, sizeof buffer,
"Too many items in display. Zoom in to click on items. (%d)",numRows);
mapBoxHc(hvg, seqStart, seqEnd, xOff, yOff, width, fontHeight,
tg->track, itemBuffer,
buffer);
yOff += fontHeight;
}
// just do this once
tg->customInt = 0;
}
static void maybeDrawLeftLabels(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)
/* If this is invoked, we are hiding item labels. In full mode, that means no left labels.
* In dense mode, we do need the left label to show shortLabel. */
{
if (tg->limitedVis == tvDense)
{
int fontHeight = mgFontLineHeight(font);
if (isCenterLabelIncluded(tg))
yOff += fontHeight;
hvGfxTextRight(hvg, xOff, yOff, width, tg->lineHeight, color, font, tg->shortLabel);
}
return;
}
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);
}
}
}
char *altGraphXMakeImage(struct altGraphX *ag)
/* create a drawing of splicing pattern */
{
MgFont *font = mgSmallFont();
int fontHeight = mgFontLineHeight(font);
struct spaceSaver *ssList = NULL;
struct hash *heightHash = NULL;
int rowCount = 0;
struct tempName gifTn;
int pixWidth = atoi(cartUsualString(cart, "pix", DEFAULT_PIX_WIDTH ));
int pixHeight = 0;
struct hvGfx *hvg;
int lineHeight = 0;
double scale = 0;
Color shadesOfGray[9];
int maxShade = ArraySize(shadesOfGray)-1;
scale = (double)pixWidth/(ag->tEnd - ag->tStart);
lineHeight = 2 * fontHeight +1;
altGraphXLayout(ag, ag->tStart, ag->tEnd, scale, 100, &ssList, &heightHash, &rowCount);
hashFree(&heightHash);
pixHeight = rowCount * lineHeight;
makeTempName(&gifTn, "hgc", ".png");
hvg = hvGfxOpenPng(pixWidth, pixHeight, gifTn.forCgi, FALSE);
makeGrayShades(hvg, maxShade, shadesOfGray);
hvGfxSetClip(hvg, 0, 0, pixWidth, pixHeight);
altGraphXDrawPack(ag, ssList, hvg, 0, 0, pixWidth, lineHeight, lineHeight-1,
ag->tStart, ag->tEnd, scale,
font, MG_BLACK, shadesOfGray, "Dummy", NULL);
hvGfxUnclip(hvg);
hvGfxClose(&hvg);
printf(
"<IMG SRC = \"%s\" BORDER=1 WIDTH=%d HEIGHT=%d><BR>\n",
gifTn.forHtml, pixWidth, pixHeight);
return cloneString(gifTn.forHtml);
}
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;
}
