def scientific_name_face(node, *args, **kwargs):
scientific_name_text = QGraphicsTextItem()
#underscore = node.name.replace("_", " ")
words = node.name.split("_")
text = []
if len(words) < 2:
# some sort of acronym or bin name, leave it alone
text = words
elif len(words) > 2:
if len(words) >= 5:
text.extend(
['<b>' + words[0] + ' <i> ' + words[1], words[2] + ' </i> '])
text.extend(words[3:] + ['</b>'])
elif len(words) == 3:
text.extend([
' <span style="color:grey"><i> ' + words[0],
words[1] + words[2] + ' </i></span>'
])
else:
# assume that everything after the
# second word is strain name
# which should not get italicized
text.extend([
' <span style="color:grey"><i> ' + words[0],
words[1] + ' </i></span>'
])
text.extend(words[2:])
else:
text.extend([
' <span style="color:grey"><i> ' + words[0],
words[1] + ' </i></span> '
])
scientific_name_text.setHtml(' '.join(text))
# below is a bit of a hack - I've found that the height of the bounding
# box gives a bit too much padding around the name, so I just minus 10
# from the height and recenter it. Don't know whether this is a generally
# applicable number to use
#myFont = QFont()
masterItem = QGraphicsRectItem(
0, 0,
scientific_name_text.boundingRect().width(),
scientific_name_text.boundingRect().height() - 10)
scientific_name_text.setParentItem(masterItem)
center = masterItem.boundingRect().center()
scientific_name_text.setPos(
masterItem.boundingRect().x(),
center.y() - scientific_name_text.boundingRect().height() / 2)
# I don't want a border around the masterItem
masterItem.setPen(QPen(QtCore.Qt.NoPen))
return masterItem
def scientific_name_face(node, *args, **kwargs):
scientific_name_text = QGraphicsTextItem()
words = node.visual_label.split()
text = []
if hasattr(node, 'bg_col'):
container_div = '<div style="background-color:{};">'.format(node.bgcolor)
text.append(container_div)
if len(words) < 2:
# some sort of acronym or bin name, leave it alone
text.extend(words)
elif len(words) > 2:
if words[0] == 'Candidatus':
# for candidatus names, only the Candidatus part is italicised
# name shortening it for brevity
text.append('<i>Ca.</i>')
text.extend(words[1:])
elif re.match('^[A-Z]+$', words[0]):
# If the first word is in all caps then it is an abreviation
# so we don't want to italicize that at all
text.extend(words)
else:
# assume that everything after the second word is strain name
# which should not get italicised
text.extend(['<i>'+words[0],words[1]+'</i>'])
text.extend(words[2:])
else:
text.extend(['<i>'+words[0],words[1]+'</i>'])
if hasattr(node, 'bg_col'):
text.append('</div>')
scientific_name_text.setHtml(' '.join(text))
#print(scientific_name_text.boundingRect().width(), scientific_name_text.boundingRect().height())
# below is a bit of a hack - I've found that the height of the bounding
# box gives a bit too much padding around the name, so I just minus 10
# from the height and recenter it. Don't know whether this is a generally
# applicable number to use
masterItem = QGraphicsRectItem(0, 0, scientific_name_text.boundingRect().width(), scientific_name_text.boundingRect().height() - 10)
scientific_name_text.setParentItem(masterItem)
center = masterItem.boundingRect().center()
scientific_name_text.setPos(masterItem.boundingRect().x(), center.y() - scientific_name_text.boundingRect().height()/2)
# I dont want a border around the masterItem
masterItem.setPen(QPen(QtCore.Qt.NoPen))
return masterItem
def trinomial_face(binom,
spp,
ftype="Verdana",
fsize=10,
fgcolor="black",
fstyle="normal",
bold=False):
"""
Stolen from:
https://connorskennerton.wordpress.com/2016/11/16/python-ete3-formatting-organism-names-the-way-i-want/
"""
font = QFont(ftype, fsize)
font.setBold(bold)
if fstyle == "italic":
font.setStyle(QFont.StyleItalic)
elif fstyle == "oblique":
font.setStyle(QFont.StyleOblique)
text = QGraphicsTextItem()
text.setFont(font)
if spp is None:
text.setHtml("<i>{}</i>".format(binom))
else:
text.setHtml("<i>{}</i> {}".format(binom, spp))
rect = QGraphicsRectItem(0, 0,
text.boundingRect().width(),
text.boundingRect().height() - 10)
text.setParentItem(rect)
center = rect.boundingRect().center()
text.setPos(rect.boundingRect().x(),
center.y() - text.boundingRect().height() / 2)
# no border
rect.setPen(QPen(QtCore.Qt.NoPen))
return ete3.faces.StaticItemFace(rect)
def polygon_name_face(node, *args, **kwargs):
"""create a wedge shaped face in the style of ARB
Args:
width (int): size in pixels for the width of the wedge
height (int): size in pixels for the height of the wedge
width_percent (float): change the angle of the point of the wedge.
This must be a number between 0 and 1
Returns:
QGraphicsRectItem: The Qt graphics item of the polygon
"""
n_leaves = len(node.get_leaves())
closest_leaf_dist = node.get_closest_leaf()[1]
farthest_leaf_dist = node.get_farthest_leaf()[1]
base_height = 30
width = 60
height = math.log(n_leaves, 2) + base_height
width_percent = closest_leaf_dist / farthest_leaf_dist
#print(width, height, width_percent)
points = [
(0.0, 0.0), # top left point
(width, 0.0), # top right point
(width * width_percent, height), # bottom right point
(0.0, height), # bottom left point
(0.0, 0.0) # back to the beginning
]
shape = QPolygonF()
for i in points:
shape << QtCore.QPointF(*i)
## Creates a main master Item that will contain all other elements
## Items can be standard QGraphicsItem
masterItem = QGraphicsRectItem(0, 0, width, height)
# Keep a link within the item to access node info
masterItem.node = node
# I dont want a border around the masterItem
masterItem.setPen(QPen(QtCore.Qt.NoPen))
polygon = QGraphicsPolygonItem(shape, masterItem)
# Make the wedge grey in color
polygon.setBrush(QBrush(QColor( '#D3D3D3')))
# Print the name of the node
# Center text according to masterItem size
center = masterItem.boundingRect().center()
text = QGraphicsSimpleTextItem(node.name)
text.setParentItem(polygon)
tw = text.boundingRect().width()
th = text.boundingRect().height()
text.setPos(center.x() + tw/2, center.y() - th/2)
# this is a hack to prevent the name being printed twice
# we set the node name to blank after we write it with the QGraphicsSimpleTextItem
# it must be set to a blank string for it not to be printed later
node.name = ''
# print the number of collapsed leaves in the polygon
leaves_count_text = QGraphicsSimpleTextItem('('+str(n_leaves)+')')
leaves_count_text.setParentItem(polygon)
leaves_count_text.setFont(QFont('Veranda', 6))
leaves_count_text.setPos(masterItem.boundingRect().x() + 5, center.y() - leaves_count_text.boundingRect().height()/2)
polygon.setPos(0, masterItem.boundingRect().y()/1.5)
return masterItem
class GradientLegendItem(QGraphicsObject, GraphicsWidgetAnchor):
gradient_width = 20
def __init__(self, title, palette, values, parent):
QGraphicsObject.__init__(self, parent)
GraphicsWidgetAnchor.__init__(self)
self.parent = self.legend = parent
self.palette = palette
self.values = values
self.title = QGraphicsTextItem('%s:' % title, self)
f = self.title.font()
f.setBold(True)
self.title.setFont(f)
self.title_item = QGraphicsRectItem(self.title.boundingRect(), self)
self.title_item.setPen(QPen(Qt.NoPen))
self.title_item.stackBefore(self.title)
self.label_items = [QGraphicsTextItem(text, self) for text in values]
for i in self.label_items:
i.setTextWidth(50)
self.rect = QRectF()
self.gradient_item = QGraphicsRectItem(self)
self.gradient = QLinearGradient()
self.gradient.setStops([(v * 0.1, self.palette[v * 0.1])
for v in range(11)])
self.orientation = Qt.Horizontal
self.set_orientation(Qt.Vertical)
self.setFlag(QGraphicsItem.ItemIgnoresTransformations, True)
self.setFlag(QGraphicsItem.ItemIsMovable, True)
def set_orientation(self, orientation):
return
if self.orientation == orientation:
return
self.orientation = orientation
if self.orientation == Qt.Vertical:
height = max(item.boundingRect().height()
for item in self.label_items)
total_height = height * max(5, len(self.label_items))
interval = (total_height -
self.label_items[-1].boundingRect().height()
) / (len(self.label_items) - 1)
self.gradient_item.setRect(10, 0, self.gradient_width, total_height)
self.gradient.setStart(10, 0)
self.gradient.setFinalStop(10, total_height)
self.gradient_item.setBrush(QBrush(self.gradient))
self.gradient_item.setPen(QPen(Qt.NoPen))
y = -20 # hja, no; dela --> pri boundingRect() zato pristejem +20
x = 0
move_item_xy(self.title, x, y, False)
y = 10
x = 30
for item in self.label_items:
move_item_xy(item, x, y, False)
# self.parent.graph.animate_plot)
y += interval
self.rect = QRectF(10, 0,
self.gradient_width +
max(item.boundingRect().width()
for item in self.label_items),
self.label_items[0].boundingRect().height() *
max(5, len(self.label_items)))
else:
# za horizontalno orientacijo nisem dodajal title-a
width = 50
height = max(item.boundingRect().height()
for item in self.label_items)
total_width = width * max(5, len(self.label_items))
interval = (total_width -
self.label_items[-1].boundingRect().width()
) / (len(self.label_items) - 1)
self.gradient_item.setRect(0, 0, total_width, self.gradient_width)
self.gradient.setStart(0, 0)
self.gradient.setFinalStop(total_width, 0)
self.gradient_item.setBrush(QBrush(self.gradient))
self.gradient_item.setPen(QPen(Qt.NoPen))
x = 0
y = 30
for item in self.label_items:
move_item_xy(item, x, y, False)
# self.parent.graph.animate_plot)
x += interval
self.rect = QRectF(0, 0, total_width, self.gradient_width + height)
# noinspection PyPep8Naming
def boundingRect(self):
width = max(self.rect.width(), self.title_item.boundingRect().width())
height = self.rect.height() + self.title_item.boundingRect().height()
return QRectF(self.rect.left(), self.rect.top(), width, height)
def paint(self, painter, option, widget):
pass
