def _paint(self, dst: QImage):
"""Retrieve QPainter for the given surface."""
p = QPainter(dst)
p.setPen(Qt.NoPen)
# Set the bounding rectangle if present.
if self.bounds:
x = self.bounds.left
y = self.bounds.top
w = self.bounds.right - x
h = self.bounds.bottom - y
p.setClipRect(x, y, w + 1, h + 1)
p.setClipping(True)
return p
def paintEvent(self, ev):
"""
Manually implemented paint event
:param ev: the QT paint event
:return:
"""
h = self.height()
w = self.width()
p = QPainter(self)
p.setClipRect(ev.region().boundingRect())
pen = QPen(QColor(0, 0, 0))
pen.setWidth(4)
ls = QFontMetricsF(p.font()).lineSpacing()
for idx, t in enumerate(sorted(list(self._loadData.keys()))):
y = 10 + idx * ls
pen.setColor(ThreadToColor.singleton.get(t))
p.setPen(pen)
p.drawLine(QLineF(15, y, 15 + 15, y))
pen.setColor(QColor(0, 0, 0))
p.setPen(pen)
p.drawText(QPointF(35, y), t)
if len(self._loadData) > 0:
right = max([
polygon[polygon.count() - 1].x()
for _, polygon in self._loadData.items()
])
else:
right = 0.0
p.translate(w - 10 - right * 20, h - 10)
p.scale(
20, -(h - 20)
) # x direction: 20 pixels per second, y direction: spread between 10 and h-10
topleft = p.transform().inverted()[0].map(QPointF(10, 10))
pen.setWidthF(0)
pen.setCosmetic(True)
left = topleft.x()
p.setRenderHint(QPainter.Antialiasing, True)
p.setPen(pen)
p.drawLine(QLineF(left, 0, right, 0))
p.drawLine(QLineF(left, 0, left, 1))
idx = 0
for t, polygon in self._loadData.items():
pen.setColor(ThreadToColor.singleton.get(t))
p.setPen(pen)
p.drawPolyline(polygon)
p.end()
def paint(self, painter: QPainter, option: QStyleOptionViewItem,
index: QModelIndex):
"""Apply graphical formatting to each item in each displayed column in the view"""
brush = QBrush()
pen = QPen()
font = QFont()
if option.state & QStyle.State_Selected:
text_color = option.palette.color(QPalette.Normal,
QPalette.BrightText)
else:
text_color = option.palette.color(QPalette.Normal, QPalette.Text)
is_selected = option.state & QStyle.State_Selected
# Default theme color
pen.setColor(text_color)
field_name = self.field_name(index).lower()
value = self.value(index)
# Colour bases (default color is the one of the current theme)
if (field_name == "ref"
or field_name == "alt") and (value in ("A", "C", "G", "T")
and not is_selected):
pen.setColor(
self.BASE_COLOR.get(value,
option.palette.color(QPalette.WindowText)))
if field_name == "impact" and not is_selected:
font.setBold(True)
pen.setColor(
self.IMPACT_COLOR.get(value, self.IMPACT_COLOR["MODIFIER"]))
if field_name == "gene" and not is_selected:
pen.setColor("#6a9fca")
if field_name == "classification":
icon = self.ACMG_ICON.get(str(value), self.ACMG_ICON["0"])
self.draw_icon(painter, option.rect, icon)
return
if field_name == "favorite":
icon = self.FAV_ICON.get(int(value), self.FAV_ICON[0])
self.draw_icon(painter, option.rect, icon)
return
if field_name == "hgvs_c":
font.setBold(True)
m = re.search(r"([cnm]\..+)", str(value))
if m:
value = m.group(1)
if field_name == "hgvs_p":
font.setBold(True)
m = re.search(r"(p\..+)", str(value))
if m:
value = m.group(1)
if re.match(r"sample\[.+\]\.gt", field_name):
icon = self.GENOTYPE_ICONS.get(int(value), self.GENOTYPE_ICONS[-1])
self.draw_icon(painter, option.rect, icon)
return
if field_name == "consequence":
values = str(self.value(index)).split("&")
metrics = QFontMetrics(font)
x = option.rect.x() + 5
# y = option.rect.center().y()
for value in values:
width = metrics.width(value)
height = metrics.height()
rect = QRect(x, 0, width + 15, height + 10)
rect.moveCenter(option.rect.center())
rect.moveLeft(x)
painter.setFont(font)
painter.setClipRect(option.rect, Qt.IntersectClip)
painter.setBrush(
QBrush(QColor(self.SO_COLOR.get(value, "#90d4f7"))))
painter.setPen(Qt.NoPen)
painter.drawRoundedRect(rect, 3, 3)
painter.setPen(QPen(QColor("white")))
painter.drawText(rect, Qt.AlignCenter | Qt.AlignVCenter, value)
x += width + 20
painter.setClipping(False)
return
if field_name == "rsid":
self.draw_url(painter, option.rect, value,
QUrl("http://www.google.fr"), index)
return
painter.setBrush(brush)
painter.setPen(pen)
painter.setFont(font)
painter.drawText(option.rect, option.displayAlignment, value)
def paintEvent(self, ev):
"""
Manually implemented paint event of the time / occupancy diagram.
:param ev: the qt paint event
:return:
"""
bgcolor = self.palette().color(self.backgroundRole())
h = self.height()
w = self.width()
p = QPainter(self)
p.setClipRect(ev.region().boundingRect())
pen = QPen(QColor(0, 0, 0))
pen.setWidth(0)
pen.setCosmetic(True)
ls = QFontMetricsF(p.font()).lineSpacing()
maxx = 0
minx = None
for t in sorted(list(self._spanData.keys())):
for port in sorted(list(self._spanData[t].keys())):
sd = self._spanData[t][port]
maxx = np.maximum(maxx, np.max(sd))
minx = np.minimum(
minx, np.min(sd)) if minx is not None else np.min(sd)
scalex = 1e-9 * 200 # 200 pixels / second
# (maxx-minx)*scalex + offx = w-10
if minx is None:
return
offx = w - 10 - (maxx - minx) * scalex
idx = 0
self.portYCoords = []
for t in sorted(list(self._spanData.keys())):
for port in sorted(list(self._spanData[t].keys())):
pen.setColor(QColor(0, 0, 0))
p.setPen(pen)
y = 10 + idx * ls
self.portYCoords.append((t, port, y - ls / 2, y))
idx += 1
sd = self._spanData[t][port]
for i in range(sd.shape[0]):
x1, x2 = sd[i, :]
x1 = (x1 - minx) * scalex + offx
x2 = (x2 - minx) * scalex + offx
color = ThreadToColor.singleton.get(t)
color.setAlpha(125)
p.fillRect(QRectF(x1, y - ls / 2, x2 - x1, ls / 2), color)
p.drawRect(QRectF(x1, y - ls / 2, x2 - x1, ls / 2))
pen = QPen(QColor(40, 40, 40))
pen.setWidth(0)
pen.setCosmetic(True)
pen.setStyle(Qt.DashLine)
p.setPen(pen)
for x in range(w - 10, -1, -20):
p.drawLine(x, 10, x, h - 10)
idx = 0
pen.setStyle(Qt.SolidLine)
p.setPen(pen)
for t in sorted(list(self._spanData.keys())):
for port in sorted(list(self._spanData[t].keys())):
y = 10 + idx * ls
idx += 1
br = QFontMetricsF(p.font()).boundingRect(port)
br.translate(10, y)
p.fillRect(br, bgcolor)
p.drawText(10, y, port)
p.end()