void ItemView::drawReminderIcon(const Cairo::RefPtr<Cairo::Context>& cr, const int width, const int height)
{
cr->save();
//draw reminder icon
cr->set_antialias(Cairo::ANTIALIAS_NONE);
if (data.isReminder())
{
Gtk::Image* image = Resources::res->imgReminderIcon;
if (getColorMode() == COLOR_ALARM)
image = Resources::res->imgReminderOnIcon;
const Glib::RefPtr<Gdk::Pixbuf> icon = image->get_pixbuf();
const int iconLeft = (TIME_WIDTH * 0.5) - (icon->get_width() * 0.5);
const int iconTop = (height - icon->get_height()) - (PADDING * 3);
Gdk::Cairo::set_source_pixbuf(cr, icon, iconLeft, iconTop);
cr->rectangle(iconLeft, iconTop, icon->get_width(), icon->get_height());
cr->fill();
}
cr->restore();
}
std::string ContextGen::printable(const SourceMap& val)
{
Color col(getColorMode());
std::string ret;
if(val.empty())
return "(empty map)";
else
ret = "(map)";
for(SourceMap::const_iterator it = val.begin(); it != val.end(); ++it)
{
ret.append("\n * ");
switch(it->second)
{
case LanguageAsssembler:
ret.append(col.blue("[ASM] "));
break;
case LanguageC:
ret.append(col.blue("[ C ] "));
break;
case LanguageCpp:
ret.append(col.blue("[C++] "));
break;
default:
throw Exception("disallowed source file type found in %s: %d", it->first.get().c_str(), it->second);
}
ret.append(it->first.get());
}
return ret;
}
std::string ContextGen::printable(const DefineMap& val)
{
std::string res;
if(val.empty())
return "(empty map)";
else {
res = "(map)";
}
Color col(getColorMode());
for(DefineMap::const_iterator it = val.begin(); it != val.end(); ++it)
{
res.append(col.red("\n * "));
res.append(col.cyan("<"));
res.append(it->first);
if(it->second.empty()) {
res.append(col.cyan(">"));
} else {
res.append(", ");
res.append(it->second);
res.append(col.cyan(">"));
}
}
return res;
}
GdkPixbuf * newPixbufFromSEXP (SEXP xx, int index) {
GdkPixbuf * pixbuf;
int width, height, rowstride, x, y;
numeric *dx,dr,dg,db;
unsigned char *dpixbuf,*data;
int colorMode;
int *ix,*idata;
int redstride=-1,greenstride=-1,bluestride=-1;
width=INTEGER(GET_DIM(xx))[0];
height=INTEGER(GET_DIM(xx))[1];
colorMode=getColorMode(xx);
pixbuf = gdk_pixbuf_new (GDK_COLORSPACE_RGB, TRUE, 8, width, height);
rowstride = gdk_pixbuf_get_rowstride (pixbuf);
dpixbuf=(unsigned char *)gdk_pixbuf_get_pixels(pixbuf);
// TrueColor
if (colorMode==MODE_TRUECOLOR) {
ix=INTEGER(xx);
for (y=0;y<height;y++) {
idata=(int *)(dpixbuf+y*rowstride);
for (x=0;x<width;x++) {
*idata=ix[x+y*width+index*width*height] | 0xff000000;
idata++;
}
}
} else {
dx=REAL(xx);
getColorStrides(xx,index,&redstride,&greenstride,&bluestride);
for (y=0;y<height;y++) {
data=dpixbuf+y*rowstride;
for (x=0;x<width;x++) {
if (redstride!=-1) dr=256*dx[x+y*width+redstride];
else dr=0;
if (greenstride!=-1) dg=256*dx[x+y*width+greenstride];
else dg=0;
if (bluestride!=-1) db=256*dx[x+y*width+bluestride];
else db=0;
if (dr<0.0) dr=0.0;
if (dr>255.0) dr=255.0;
if (dg<0.0) dg=0.0;
if (dg>255.0) dg=255.0;
if (db<0.0) db=0.0;
if (db>255.0) db=255.0;
*data++=(unsigned char)dr; // R
*data++=(unsigned char)dg; // G
*data++=(unsigned char)db; // B
*data++=255; // A
}
}
}
return pixbuf;
}
int caTable::qt_metacall(QMetaObject::Call _c, int _id, void **_a)
{
_id = QTableWidget::qt_metacall(_c, _id, _a);
if (_id < 0)
return _id;
if (_c == QMetaObject::InvokeMetaMethod) {
if (_id < 1)
qt_static_metacall(this, _c, _id, _a);
_id -= 1;
}
#ifndef QT_NO_PROPERTIES
else if (_c == QMetaObject::ReadProperty) {
void *_v = _a[0];
switch (_id) {
case 0: *reinterpret_cast< QString*>(_v) = getPVS(); break;
case 1: *reinterpret_cast< QString*>(_v) = getColumnSizes(); break;
case 2: *reinterpret_cast< colMode*>(_v) = getColorMode(); break;
case 3: *reinterpret_cast< int*>(_v) = getPrecision(); break;
case 4: *reinterpret_cast< SourceMode*>(_v) = getPrecisionMode(); break;
case 5: *reinterpret_cast< SourceMode*>(_v) = getLimitsMode(); break;
case 6: *reinterpret_cast< double*>(_v) = getMaxValue(); break;
case 7: *reinterpret_cast< double*>(_v) = getMinValue(); break;
}
_id -= 8;
} else if (_c == QMetaObject::WriteProperty) {
void *_v = _a[0];
switch (_id) {
case 0: setPVS(*reinterpret_cast< QString*>(_v)); break;
case 1: setColumnSizes(*reinterpret_cast< QString*>(_v)); break;
case 2: setColorMode(*reinterpret_cast< colMode*>(_v)); break;
case 3: setPrecision(*reinterpret_cast< int*>(_v)); break;
case 4: setPrecisionMode(*reinterpret_cast< SourceMode*>(_v)); break;
case 5: setLimitsMode(*reinterpret_cast< SourceMode*>(_v)); break;
case 6: setMaxValue(*reinterpret_cast< double*>(_v)); break;
case 7: setMinValue(*reinterpret_cast< double*>(_v)); break;
}
_id -= 8;
} else if (_c == QMetaObject::ResetProperty) {
_id -= 8;
} else if (_c == QMetaObject::QueryPropertyDesignable) {
_id -= 8;
} else if (_c == QMetaObject::QueryPropertyScriptable) {
_id -= 8;
} else if (_c == QMetaObject::QueryPropertyStored) {
_id -= 8;
} else if (_c == QMetaObject::QueryPropertyEditable) {
_id -= 8;
} else if (_c == QMetaObject::QueryPropertyUser) {
_id -= 8;
}
#endif // QT_NO_PROPERTIES
return _id;
}
void ItemView::drawBackground(const Cairo::RefPtr<Cairo::Context>& cr, const int width, const int height)
{
//fill background
if (isSelected())
{
cr->set_source_rgb(1, 1, 1);
cr->rectangle(0, 0, width, height);
cr->fill();
}
else
{
cr->set_source_rgb(0.98, 0.98, 0.98);
cr->rectangle(0, 0, width, height);
cr->fill();
}
//time area
Cairo::RefPtr<Cairo::LinearGradient> linearGradientTime = Cairo::LinearGradient::create(0, 0, 0, height);
//set color by status
ColorMode colorMode = getColorMode();
if (colorMode == COLOR_INACTIVE)
{
//gray
linearGradientTime->add_color_stop_rgb(0, 0.75, 0.75, 0.75);
linearGradientTime->add_color_stop_rgb(1, 0.65, 0.65, 0.65);
}
if (colorMode == COLOR_ALARM)
{
//orange
linearGradientTime->add_color_stop_rgb(0, 1.00, 0.60, 0.30);
linearGradientTime->add_color_stop_rgb(1, 0.90, 0.50, 0.20);
}
if (colorMode == COLOR_OK)
{
//green
linearGradientTime->add_color_stop_rgb(0, 0.40, 0.70, 0.45);
linearGradientTime->add_color_stop_rgb(1, 0.30, 0.60, 0.35);
}
cr->set_source(linearGradientTime);
cr->rectangle(0, 0, TIME_WIDTH, height);
cr->fill();
if (isSelected())
drawInnerShadow(cr, width, height);
}
int caClock::qt_metacall(QMetaObject::Call _c, int _id, void **_a)
{
_id = QwtAnalogClock::qt_metacall(_c, _id, _a);
if (_id < 0)
return _id;
if (_c == QMetaObject::InvokeMetaMethod) {
if (_id < 2)
qt_static_metacall(this, _c, _id, _a);
_id -= 2;
}
#ifndef QT_NO_PROPERTIES
else if (_c == QMetaObject::ReadProperty) {
void *_v = _a[0];
switch (_id) {
case 0: *reinterpret_cast< QString*>(_v) = getPV(); break;
case 1: *reinterpret_cast< timeType*>(_v) = getTimeType(); break;
case 2: *reinterpret_cast< QColor*>(_v) = getBaseColor(); break;
case 3: *reinterpret_cast< bool*>(_v) = getScaleDefaultColor(); break;
case 4: *reinterpret_cast< QColor*>(_v) = getScaleColor(); break;
case 5: *reinterpret_cast< colMode*>(_v) = getColorMode(); break;
}
_id -= 6;
} else if (_c == QMetaObject::WriteProperty) {
void *_v = _a[0];
switch (_id) {
case 0: setPV(*reinterpret_cast< QString*>(_v)); break;
case 1: setTimeType(*reinterpret_cast< timeType*>(_v)); break;
case 2: setBaseColor(*reinterpret_cast< QColor*>(_v)); break;
case 3: setScaleDefaultColor(*reinterpret_cast< bool*>(_v)); break;
case 4: setScaleColor(*reinterpret_cast< QColor*>(_v)); break;
case 5: setColorMode(*reinterpret_cast< colMode*>(_v)); break;
}
_id -= 6;
} else if (_c == QMetaObject::ResetProperty) {
_id -= 6;
} else if (_c == QMetaObject::QueryPropertyDesignable) {
_id -= 6;
} else if (_c == QMetaObject::QueryPropertyScriptable) {
_id -= 6;
} else if (_c == QMetaObject::QueryPropertyStored) {
_id -= 6;
} else if (_c == QMetaObject::QueryPropertyEditable) {
_id -= 6;
} else if (_c == QMetaObject::QueryPropertyUser) {
_id -= 6;
}
#endif // QT_NO_PROPERTIES
return _id;
}
void ItemView::drawTime(const Cairo::RefPtr<Cairo::Context>& cr, const int width, const int height)
{
int text_width;
int text_height;
Glib::RefPtr<Pango::Layout> layTime = Pango::Layout::create(cr);
layTime->set_font_description(fontTime);
layTime->set_text(data.getTimeText());
layTime->get_pixel_size(text_width, text_height);
rectTime.set_x((TIME_WIDTH * 0.5) - (text_width * 0.5));
rectTime.set_y((int)PADDING);
rectTime.set_width(text_width);
rectTime.set_height(text_height);
//highlight
const int highlightSize = 1;
cr->move_to(rectTime.get_x(), rectTime.get_y() - highlightSize);
//set colors
ColorMode colorMode = getColorMode();
if (colorMode == COLOR_INACTIVE)
{
//gray
cr->set_source_rgb(0.6, 0.6, 0.6);
}
if (colorMode == COLOR_ALARM)
{
//orange
cr->set_source_rgb(0.8, 0.40, 0.0);
}
if (colorMode == COLOR_OK)
{
//green
cr->set_source_rgb(0.0, 0.55, 0.0);
}
layTime->show_in_cairo_context(cr);
//inner color
cr->move_to(rectTime.get_x(), rectTime.get_y());
cr->set_source_rgb(1.0, 1.0, 1.0);
layTime->show_in_cairo_context(cr);
}
static int vcfHapClusterTotalHeight(struct track *tg, enum trackVisibility vis)
/* Return height of haplotype graph (2 * #samples * lineHeight);
* 2 because we're assuming diploid genomes here, no XXY, tetraploid etc. */
{
const struct vcfFile *vcff = tg->extraUiData;
if (vcff->records == NULL)
return 0;
int ploidy = sameString(chromName, "chrY") ? 1 : 2;
int simpleHeight = ploidy * vcff->genotypeCount * tg->lineHeight;
int defaultHeight = min(simpleHeight, VCF_DEFAULT_HAP_HEIGHT);
char *tdbHeight = trackDbSettingOrDefault(tg->tdb, VCF_HAP_HEIGHT_VAR, NULL);
if (isNotEmpty(tdbHeight))
defaultHeight = atoi(tdbHeight);
int cartHeight = cartOrTdbInt(cart, tg->tdb, VCF_HAP_HEIGHT_VAR, defaultHeight);
if (tg->visibility == tvSquish)
cartHeight /= 2;
int extraPixel = (getColorMode(tg->tdb) == altOnlyMode) ? 1 : 0;
int totalHeight = cartHeight + CLIP_PAD + 2*extraPixel;
tg->height = min(totalHeight, maximumTrackHeight(tg));
return tg->height;
}
std::string ContextGen::printable(const PathVector& val)
{
std::string res;
if(val.empty())
return "(empty vector)";
else
res = "(vector)";
Color col(getColorMode());
for(PathVector::const_iterator it = val.begin(); it != val.end(); ++it)
{
res.append(col.red("\n * "));
if(it->isNative()) res.append(col.yellow("[NATIVE] "));
else if(it->isForeign()) res.append(col.yellow("[FOREIGN] "));
else res.append(col.yellow("[NEITHER] ")); // is ok, if windows parity build and unix path with windows backend
res.append(it->get());
}
return res;
}
static void vcfHapClusterDraw(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Split samples' chromosomes (haplotypes), cluster them by center-weighted
* alpha similarity, and draw in the order determined by clustering. */
{
struct vcfFile *vcff = tg->extraUiData;
if (vcff->records == NULL)
return;
purple = hvGfxFindColorIx(hvg, 0x99, 0x00, 0xcc);
undefYellow = hvGfxFindRgb(hvg, &undefinedYellowColor);
enum hapColorMode colorMode = getColorMode(tg->tdb);
pushWarnHandler(ignoreEm);
struct vcfRecord *rec;
for (rec = vcff->records; rec != NULL; rec = rec->next)
vcfParseGenotypes(rec);
popWarnHandler();
unsigned short gtHapCount = 0;
int nRecords = slCount(vcff->records);
int centerIx = getCenterVariantIx(tg, seqStart, seqEnd, vcff->records);
// Limit the number of variants that we compare, to keep from timing out:
// (really what we should limit is the number of distinct haplo's passed to hacTree!)
// In the meantime, this should at least be a cart var...
int maxVariantsPerSide = 50;
int startIx = max(0, centerIx - maxVariantsPerSide);
int endIx = min(nRecords, centerIx+1 + maxVariantsPerSide);
struct hacTree *ht = NULL;
unsigned short *gtHapOrder = clusterHaps(vcff, centerIx, startIx, endIx, >HapCount, &ht);
struct vcfRecord *centerRec = NULL;
int ix;
// Unlike drawing order (last drawn is on top), the first mapBox gets priority,
// so map center variant before drawing & mapping other variants!
for (rec = vcff->records, ix=0; rec != NULL; rec = rec->next, ix++)
{
if (ix == centerIx)
{
centerRec = rec;
mapBoxForCenterVariant(rec, hvg, tg, xOff, yOff, width);
break;
}
}
for (rec = vcff->records, ix=0; rec != NULL; rec = rec->next, ix++)
{
boolean isClustered = (ix >= startIx && ix < endIx);
if (ix != centerIx)
drawOneRec(rec, gtHapOrder, gtHapCount, tg, hvg, xOff, yOff, width, isClustered, FALSE,
colorMode);
}
// Draw the center rec on top, outlined with black lines, to make sure it is very visible:
drawOneRec(centerRec, gtHapOrder, gtHapCount, tg, hvg, xOff, yOff, width, TRUE, TRUE,
colorMode);
// Draw as much of the tree as can fit in the left label area:
int extraPixel = (colorMode == altOnlyMode) ? 1 : 0;
int hapHeight = tg->height- CLIP_PAD - 2*extraPixel;
struct yFromNodeHelper yHelper = {0, NULL, NULL};
initYFromNodeHelper(&yHelper, yOff+extraPixel, hapHeight, gtHapCount, gtHapOrder,
vcff->genotypeCount);
struct titleHelper titleHelper = { NULL, 0, 0, 0, 0, NULL, NULL };
initTitleHelper(&titleHelper, tg->track, startIx, centerIx, endIx, nRecords, vcff);
char *treeAngle = cartOrTdbString(cart, tg->tdb, VCF_HAP_TREEANGLE_VAR, VCF_DEFAULT_HAP_TREEANGLE);
boolean drawRectangle = sameString(treeAngle, VCF_HAP_TREEANGLE_RECTANGLE);
drawTreeInLabelArea(ht, hvg, yOff+extraPixel, hapHeight+CLIP_PAD, &yHelper, &titleHelper,
drawRectangle);
}
