From 27c2a9976ff0e382e52d092f88357ca98a6bf0be Mon Sep 17 00:00:00 2001
From: niki_main <niki_berman@bitbucket.com>
Date: Thu, 16 Nov 2017 11:20:44 +0200
Subject: [PATCH] adding y_axis scale function.
The function gives the option to ass full y axis scale to the tree in linear or log setting.
---
.gitignore | 6 +
ete3/treeview/main.py | 15 ++
ete3/treeview/qt4_render.py | 284 +++++++++++++++++++++++++++---------
3 files changed, 233 insertions(+), 72 deletions(-)
diff --git a/.gitignore b/.gitignore
index 110dfd05d..5f5f43d0c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,3 +22,9 @@ test_tmp/
# Coverage files
.coverage
htmlcov/
+.idea/workspace.xml
+bash_colors.sh
+.idea/ete.iml
+.idea/misc.xml
+.idea/modules.xml
+.idea/vcs.xml
diff --git a/ete3/treeview/main.py b/ete3/treeview/main.py
index 1c930fa97..12a29f0c0 100644
--- a/ete3/treeview/main.py
+++ b/ete3/treeview/main.py
@@ -248,6 +248,7 @@ def __setitem__(self, i, v):
#def clear(self):
# super(NodeStyle, self).__setitem__("_faces", {})
+
class TreeStyle(object):
""".. versionadded:: 2.1
@@ -362,6 +363,14 @@ class TreeStyle(object):
:param True show_scale: Include the scale legend in the tree
image
+ :param False y_axis['show']: Include calculated y scale legend in the tree
+ image (relative branch length)
+
+ :param linear y_axis['scale_type']: Defined the type of the y_axis scale log/linear
+
+ :param 1 y_axis['scale_length']: Sets the length of the y_axis scale
+ (recomended to set to: root.get_farthest_leaf()[1], the depth of the farthest leaf)
+
:param None scale_length: Scale length to be used as reference scale bar
when visualizing tree. None = automatically adjusted.
@@ -528,6 +537,12 @@ def __init__(self):
self.show_scale = True
self.scale_length = None
+ # Draw Y_axis scale
+ self.y_axis = dict()
+ self.y_axis['show'] = False
+ self.y_axis['scale_type'] = 'linear'
+ self.y_axis['scale_length'] = 1
+
# Initialize aligned face headers
self.aligned_header = FaceContainer()
self.aligned_foot = FaceContainer()
diff --git a/ete3/treeview/qt4_render.py b/ete3/treeview/qt4_render.py
index 10f30aed5..b2adf4e4c 100644
--- a/ete3/treeview/qt4_render.py
+++ b/ete3/treeview/qt4_render.py
@@ -39,6 +39,7 @@
import math
import re
import six
+import warnings
from .qt import *
from . import qt4_circular_render as crender
@@ -83,6 +84,7 @@ def __init__(self, node):
self.setBrush(QBrush(QColor(self.node.img_style["fgcolor"])))
self.setPen(QPen(QColor(self.node.img_style["fgcolor"])))
+
class _RectItem(QGraphicsRectItem, _ActionDelegator):
def __init__(self, node):
self.node = node
@@ -92,6 +94,7 @@ def __init__(self, node):
self.setBrush(QBrush(QColor(self.node.img_style["fgcolor"])))
self.setPen(QPen(QColor(self.node.img_style["fgcolor"])))
+
class _SphereItem(QGraphicsEllipseItem, _ActionDelegator):
def __init__(self, node):
self.node = node
@@ -107,6 +110,7 @@ def __init__(self, node):
self.setBrush(QBrush(gradient))
# self.setPen(Qt.NoPen)
+
class _EmptyItem(QGraphicsItem):
def __init__(self, parent=None):
QGraphicsItem.__init__(self)
@@ -124,6 +128,7 @@ def boundingRect(self):
def paint(self, *args, **kargs):
return
+
class _TreeItem(QGraphicsRectItem):
def __init__(self, parent=None):
QGraphicsRectItem.__init__(self)
@@ -131,6 +136,7 @@ def __init__(self, parent=None):
self.n2i = {}
self.n2f = {}
+
class _NodeItem(_EmptyItem):
def __init__(self, node, parent):
_EmptyItem.__init__(self, parent)
@@ -140,18 +146,22 @@ def __init__(self, node, parent):
self.fullRegion = QRectF()
self.highlighted = False
+
class _NodeLineItem(QGraphicsLineItem, _ActionDelegator):
def __init__(self, node, *args, **kargs):
self.node = node
QGraphicsLineItem.__init__(self, *args, **kargs)
_ActionDelegator.__init__(self)
+
def paint(self, painter, option, widget):
QGraphicsLineItem.paint(self, painter, option, widget)
+
class _LineItem(QGraphicsLineItem):
def paint(self, painter, option, widget):
QGraphicsLineItem.paint(self, painter, option, widget)
+
class _PointerItem(QGraphicsRectItem):
def __init__(self, parent=None):
QGraphicsRectItem.__init__(self,0,0,0,0, parent)
@@ -164,14 +174,14 @@ def paint(self, p, option, widget):
p.drawRect(self.rect())
return
# Draw info text
- font = QFont("Arial",13)
- text = "%d selected." % len(self.get_selected_nodes())
+ font = QFont("Arial", 13)
+ text = "%d selected." % len(self.get_selected_nodes())
textR = QFontMetrics(font).boundingRect(text)
if self.rect().width() > textR.width() and \
- self.rect().height() > textR.height()/2.0 and 0: # OJO !!!!
+ self.rect().height() > textR.height()/2.0 and 0: # OJO !!!!
p.setPen(QPen(self.color))
- p.setFont(QFont("Arial",13))
- p.drawText(self.rect().bottomLeft().x(),self.rect().bottomLeft().y(),text)
+ p.setFont(QFont("Arial", 13))
+ p.drawText(self.rect().bottomLeft().x(), self.rect().bottomLeft().y(),text)
def get_selected_nodes(self):
selPath = QPainterPath()
@@ -185,6 +195,7 @@ def setActive(self,bool):
def isActive(self):
return self._active
+
class _TreeScene(QGraphicsScene):
def __init__(self):
QGraphicsScene.__init__(self)
@@ -208,12 +219,13 @@ def draw(self):
tree_item.setParentItem(self.master_item)
self.setSceneRect(tree_item.rect())
-#@tracktime
+
+# @tracktime
def render(root_node, img, hide_root=False):
- '''main render function. hide_root option is used when render
+ """main render function. hide_root option is used when render
trees as Faces
- '''
+ """
mode = img.mode
orientation = img.orientation
@@ -222,10 +234,10 @@ def render(root_node, img, hide_root=False):
layout_fn = img._layout_handler
parent = _TreeItem()
- n2i = parent.n2i # node to items
- n2f = parent.n2f # node to faces
+ n2i = parent.n2i # node to items
+ n2f = parent.n2f # node to faces
- parent.bg_layer = _EmptyItem(parent)
+ parent.bg_layer = _EmptyItem(parent)
parent.tree_layer = _EmptyItem(parent)
parent.float_layer = _EmptyItem(parent)
parent.float_behind_layer = _EmptyItem(parent)
@@ -262,13 +274,13 @@ def render(root_node, img, hide_root=False):
if _leaf(n) and n.name and img.show_leaf_name:
faces.add_face_to_node(na_face, n, 0, position="branch-right")
- if _leaf(n):# or len(n.img_style["_faces"]["aligned"]):
+ if _leaf(n): # or len(n.img_style["_faces"]["aligned"]):
virtual_leaves += 1
update_node_faces(n, n2f, img)
rot_step = float(arc_span) / virtual_leaves
- #rot_step = float(arc_span) / len([n for n in root_node.traverse() if _leaf(n)])
+ # rot_step = float(arc_span) / len([n for n in root_node.traverse() if _leaf(n)])
# Calculate optimal branch length
if img._scale is not None:
@@ -286,7 +298,7 @@ def render(root_node, img, hide_root=False):
update_branch_lengths(root_node, n2i, n2f, img)
else:
img._scale = crender.calculate_optimal_scale(root_node, n2i, rot_step, img)
- #print "OPTIMAL circular scale", img._scale
+ # print "OPTIMAL circular scale", img._scale
update_branch_lengths(root_node, n2i, n2f, img)
init_items(root_node, parent, n2i, n2f, img, rot_step, hide_root)
else:
@@ -294,7 +306,7 @@ def render(root_node, img, hide_root=False):
img._scale = img.scale
init_items(root_node, parent, n2i, n2f, img, rot_step, hide_root)
- #print "USING scale", img._scale
+ # print "USING scale", img._scale
# Draw node content
for node in root_node.traverse(is_leaf_fn=_leaf):
if node is not root_node or not hide_root:
@@ -330,8 +342,8 @@ def render(root_node, img, hide_root=False):
if img.rotation:
rect = parent.boundingRect()
- x = rect.x() + (rect.width()/2.0)
- y = rect.y() + (rect.height()/2.0)
+ x = rect.x() + (rect.width()/2.0)
+ y = rect.y() + (rect.height()/2.0)
parent.setTransform(QTransform().translate(x, y).rotate(img.rotation).translate(-x, -y))
# Creates the main tree item that will act as frame for the whole image
@@ -351,9 +363,12 @@ def render(root_node, img, hide_root=False):
mainRect.adjust(_x, _y, _x, _y)
# Add extra components and adjust mainRect to them
- add_legend(img, mainRect, frame)
add_title(img, mainRect, frame)
+ add_legend(img, mainRect, frame)
add_scale(img, mainRect, frame)
+ add_y_scale(img, mainRect, frame, root_node)
+
+
frame.setRect(mainRect)
# Draws a border around the tree
@@ -364,6 +379,7 @@ def render(root_node, img, hide_root=False):
return frame, n2i, n2f
+
def adjust_faces_to_tranformations(img, mainRect, n2i, n2f, tree_layers):
if img.mode == "c":
rotate_inverted_faces(n2i, n2f, img)
@@ -375,6 +391,7 @@ def adjust_faces_to_tranformations(img, mainRect, n2i, n2f, tree_layers):
for pos, fb in six.iteritems(faceblock):
fb.flip_hz()
+
def add_legend(img, mainRect, parent):
if img.legend:
legend = _FaceGroupItem(img.legend, None)
@@ -398,6 +415,7 @@ def add_legend(img, mainRect, parent):
legend.setPos(pos.x()-lg_w, pos.y())
mainRect.adjust(0, 0, dw, lg_h)
+
def add_title(img, mainRect, parent):
if img.title:
title = _FaceGroupItem(img.title, None)
@@ -406,31 +424,9 @@ def add_title(img, mainRect, parent):
lg_w, lg_h = title.get_size()
dw = max(0, lg_w-mainRect.width())
title.setParentItem(parent)
- mainRect.adjust(0, -lg_h, dw, 0)
+ mainRect.adjust(0, -(lg_h+20), dw, 0)
title.setPos(mainRect.topLeft())
-def add_legend(img, mainRect, parent):
- if img.legend:
- legend = _FaceGroupItem(img.legend, None)
- legend.setup_grid()
- legend.render()
- lg_w, lg_h = legend.get_size()
- dw = max(0, lg_w-mainRect.width())
- legend.setParentItem(parent)
- if img.legend_position == 1:
- mainRect.adjust(0, -lg_h, dw, 0)
- legend.setPos(mainRect.topLeft())
- elif img.legend_position == 2:
- mainRect.adjust(0, -lg_h, dw, 0)
- pos = mainRect.topRight()
- legend.setPos(pos.x()-lg_w, pos.y())
- elif img.legend_position == 3:
- legend.setPos(mainRect.bottomLeft())
- mainRect.adjust(0, 0, dw, lg_h)
- elif img.legend_position == 4:
- pos = mainRect.bottomRight()
- legend.setPos(pos.x()-lg_w, pos.y())
- mainRect.adjust(0, 0, dw, lg_h)
def add_scale(img, mainRect, parent):
if img.show_scale:
@@ -476,13 +472,150 @@ def add_scale(img, mainRect, parent):
scaleItem.moveBy(img.margin_left, 0)
mainRect.adjust(0, 0, 0, length)
+
+def add_y_scale(img, mainRect, parent, root):
+
+ if img.y_axis['show']:
+
+ if img.scale is None:
+ scale_length = root.get_farthest_leaf()[1] * img._scale + \
+ int((root.get_farthest_leaf(topology_only=True)[1]+1)/img._scale)
+ # scale_length = img.y_axis['scale_length'] * img._scale + \
+ # int((root.get_farthest_leaf(topology_only=True)[1] + 1) / img._scale)
+ else:
+ scale_length = root.get_farthest_leaf()[1] * img.scale + \
+ int((root.get_farthest_leaf(topology_only=True)[1]+1)/img.scale)
+ # scale_length = img.y_axis['scale_length'] * img.scale + \
+ # int((root.get_farthest_leaf(topology_only=True)[1] + 1) / img.scale)
+
+
+ scale_item = _EmptyItem()
+ custom_pen = QtGui.QPen(QtGui.QColor("black"), 1)
+
+ line = QtGui.QGraphicsLineItem(scale_item)
+ line.setPen(custom_pen)
+
+ mark = {}
+ if img.y_axis['scale_type'] == 'log':
+ calculate_marks = int(math.ceil(math.log(root.get_farthest_leaf()[1], 10)))
+
+ for x in range(10*calculate_marks+1):
+ mark[x] = QtGui.QGraphicsLineItem(scale_item)
+ mark[x].setPen(custom_pen)
+
+ elif img.y_axis['scale_type'] == 'linear':
+ calculate_marks = int(root.get_farthest_leaf(topology_only=True)[1]+1)
+
+ for x in range(calculate_marks + 1):
+ mark[x] = QtGui.QGraphicsLineItem(scale_item)
+ mark[x].setPen(custom_pen)
+ else:
+ raise ValueError('The scale {} does not exist'.format(img.y_axis['scale_type']))
+
+ # scale line
+ if img.rotation == 0 or img.rotation == 180:
+ line.setLine(0, -10, scale_length, -10)
+ elif img.rotation == 90 or img.rotation == 270:
+ line.setLine(-10, 0, -10, scale_length)
+ else:
+ warnings.warn('The scale can\'t be rotated with the angle of the tree.'
+ 'Setting the scale in upright position')
+ line.setLine(0, -10, scale_length, -10)
+
+ # Adding markers
+ if img.y_axis['scale_type'] == 'log':
+ marker = scale_length/(math.log(root.get_farthest_leaf()[1], 10))
+
+ for x in range(10*calculate_marks):
+ if x % 10:
+ log_step = math.log(math.pow(10, int(x / 10)) * (x % 10), 10)
+ else:
+ log_step = math.log(math.pow(10, int(x / 10)), 10)
+
+ if (marker*log_step) > scale_length:
+ continue
+ if img.rotation == 0 or img.rotation == 180:
+ mark[x].setLine(marker*log_step, -15, marker*log_step, -10)
+ elif img.rotation == 90 or img.rotation == 270:
+ mark[x].setLine(-15, marker*log_step, -10, marker*log_step)
+ else:
+ mark[x].setLine(marker*log_step, -15, marker*log_step, -10)
+
+ elif img.y_axis['scale_type'] == 'linear':
+ marker = int(scale_length / (root.get_farthest_leaf(topology_only=True)[1]+1))
+ for x in range(calculate_marks):
+ if img.rotation == 0 or img.rotation == 180:
+ mark[x].setLine(x*marker, -15, x*marker, -10)
+ elif img.rotation == 90 or img.rotation == 270:
+ mark[x].setLine(-15, x*marker, -10, x*marker)
+ else:
+ mark[x].setLine(x * marker, -15, x * marker, -10)
+
+ if img.rotation == 0 or img.rotation == 180:
+ mark[calculate_marks].setLine(scale_length, -15, scale_length, -10)
+ elif img.rotation == 90 or img.rotation == 270:
+ mark[calculate_marks].setLine(-15, scale_length, -10, scale_length)
+ else:
+ mark[calculate_marks].setLine(scale_length, -15, scale_length, -10)
+
+ # adding text to scale
+ if img.y_axis['scale_type'] == 'linear':
+ if img.y_axis['scale_length'] != 1:
+ scale_mesure = img.y_axis['scale_length'] / calculate_marks
+ else:
+ scale_mesure = (root.get_farthest_leaf()[1] - root.dist)/calculate_marks
+
+ for x in range(calculate_marks+1):
+ if (x*marker) > scale_length:
+ break
+
+ if img.y_axis['scale_type'] == 'log':
+ scale_text = '10<sup>'+str(x)+'</sup>'
+
+ elif img.y_axis['scale_type'] == 'linear':
+ length_text = scale_mesure * x
+ if length_text < 1 and length_text != 0:
+ scale_text = "%0.4f" % length_text
+ else:
+ scale_text = "%0.1f" % length_text
+
+ font = QtGui.QFont('White Rabbit')
+ font.setPointSize(8)
+ scale = QtGui.QGraphicsTextItem()
+ scale.setHtml(scale_text)
+ scale.setFont(font)
+ # scale.setFlag(scale.ItemIgnoresTransformations, True)
+ scale.setParentItem(scale_item)
+
+ if img.rotation == 0 or img.rotation == 180:
+ scale.setPos(x*marker-5, -13)
+ elif img.rotation == 90 or img.rotation == 270:
+ scale.setPos(-13, x*marker-5)
+ else:
+ scale.setPos(x*marker-5, -13)
+
+ scale_item.setParentItem(parent)
+
+ x_pos = mainRect.topLeft().x()
+ y_pos = mainRect.topLeft().y()
+ if img.title:
+ title = _FaceGroupItem(img.title, None)
+ lg_w, lg_h = title.get_size()
+ root_pos = img.margin_top + lg_h + 15
+ else:
+ root_pos = img.margin_top
+ mainRect.adjust(0, -20, 0, 0)
+ scale_item.setPos(x_pos-10, y_pos+root_pos)
+
+
def rotate_inverted_faces(n2i, n2f, img):
for node, faceblock in six.iteritems(n2f):
item = n2i[node]
- if item.rotation > 90 and item.rotation < 270:
+ if 90 < item.rotation < 270:
for pos, fb in six.iteritems(faceblock):
fb.rotate(181)
+
def render_backgrounds(img, mainRect, bg_layer, n2i, n2f):
if img.mode == "c":
@@ -540,6 +673,7 @@ def render_backgrounds(img, mainRect, bg_layer, n2i, n2f):
bg.setParentItem(bg_layer)
bg.setZValue(item.zValue())
+
def set_node_size(node, n2i, n2f, img):
scale = img._scale
min_separation = img.min_leaf_separation
@@ -551,7 +685,7 @@ def set_node_size(node, n2i, n2f, img):
branch_length = item.branch_length = float(node.dist * scale)
# Organize faces by groups
- #faceblock = update_node_faces(node, n2f, img)
+ # faceblock = update_node_faces(node, n2f, img)
faceblock = n2f[node]
aligned_height = 0
if _leaf(node):
@@ -578,8 +712,8 @@ def set_node_size(node, n2i, n2f, img):
h1 = top_half_h + bottom_half_h
h2 = max(faceblock["branch-right"].h, \
- aligned_height, \
- min_separation )
+ aligned_height, \
+ min_separation )
h = max(h1, h2)
imbalance = abs(top_half_h - bottom_half_h)
if imbalance > h2/2.0:
@@ -597,7 +731,7 @@ def set_node_size(node, n2i, n2f, img):
)
# This breaks ultrametric tree visualization
- #w += node.img_style["vt_line_width"]
+ # w += node.img_style["vt_line_width"]
# rightside faces region
item.facesRegion.setRect(0, 0, faceblock["branch-right"].w, h)
@@ -608,6 +742,7 @@ def set_node_size(node, n2i, n2f, img):
# This is the node total region covered by the node
item.fullRegion.setRect(0, 0, w, h)
+
def render_node_content(node, n2i, n2f, img):
style = node.img_style
item = n2i[node]
@@ -621,7 +756,6 @@ def render_node_content(node, n2i, n2f, img):
# Node points
ball_size = style["size"]
-
vlw = style["vt_line_width"] if not _leaf(node) and len(node.children) > 1 else 0.0
# face_start_x = nodeR.width() - facesR.width() - vlw
@@ -638,10 +772,10 @@ def render_node_content(node, n2i, n2f, img):
node_ball.setPos(ball_start_x, center-(ball_size/2.0))
- #from qt4_gui import _BasicNodeActions
- #node_ball.delegate = _BasicNodeActions()
- #node_ball.setAcceptHoverEvents(True)
- #node_ball.setCursor(Qt.PointingHandCursor)
+ # from qt4_gui import _BasicNodeActions
+ # node_ball.delegate = _BasicNodeActions()
+ # node_ball.setAcceptHoverEvents(True)
+ # node_ball.setCursor(Qt.PointingHandCursor)
else:
node_ball = None
@@ -652,9 +786,9 @@ def render_node_content(node, n2i, n2f, img):
pen.setColor(QColor(style["hz_line_color"]))
pen.setWidth(style["hz_line_width"])
pen.setCapStyle(Qt.FlatCap)
- #pen.setCapStyle(Qt.RoundCap)
- #pen.setCapStyle(Qt.SquareCap)
- #pen.setJoinStyle(Qt.RoundJoin)
+ # pen.setCapStyle(Qt.RoundCap)
+ # pen.setCapStyle(Qt.SquareCap)
+ # pen.setJoinStyle(Qt.RoundJoin)
hz_line = _LineItem()
hz_line = _NodeLineItem(node)
hz_line.setPen(pen)
@@ -727,35 +861,34 @@ def render_node_content(node, n2i, n2f, img):
pen.setColor(QColor(style["vt_line_color"]))
pen.setWidth(style["vt_line_width"])
pen.setCapStyle(Qt.FlatCap)
- #pen.setCapStyle(Qt.RoundCap)
- #pen.setCapStyle(Qt.SquareCap)
+ # pen.setCapStyle(Qt.RoundCap)
+ # pen.setCapStyle(Qt.SquareCap)
vt_line.setPen(pen)
item.vt_line = vt_line
else:
vt_line = None
item.bg = QGraphicsItemGroup()
- item.movable_items = [] #QGraphicsItemGroup()
- item.static_items = [] #QGraphicsItemGroup()
+ item.movable_items = [] # QGraphicsItemGroup()
+ item.static_items = [] # QGraphicsItemGroup()
# Items fow which coordinates are exported in the image map
item.mapped_items = [node_ball, fblock_r, fblock_b, fblock_t]
-
for i in [vt_line, extra_line, hz_line]:
if i:
- #item.static_items.addToGroup(i)
+ # item.static_items.addToGroup(i)
item.static_items.append(i)
i.setParentItem(item.content)
for i in [node_ball, fblock_r, fblock_b, fblock_t]:
if i:
- #item.movable_items.addToGroup(i)
+ # item.movable_items.addToGroup(i)
item.movable_items.append(i)
i.setParentItem(item.content)
+ # item.movable_items.setParentItem(item.content)
+ # item.static_items.setParentItem(item.content)
- #item.movable_items.setParentItem(item.content)
- #item.static_items.setParentItem(item.content)
def set_pen_style(pen, line_style):
if line_style == 0:
@@ -765,8 +898,9 @@ def set_pen_style(pen, line_style):
elif line_style == 2:
pen.setStyle(Qt.DotLine)
+
def set_style(n, layout_func):
- #if not isinstance(getattr(n, "img_style", None), NodeStyle):
+ # if not isinstance(getattr(n, "img_style", None), NodeStyle):
# print "Style of", n.name ,"is None"
# n.set_style()
# n.img_style = NodeStyle()
@@ -776,8 +910,9 @@ def set_style(n, layout_func):
for func in layout_func:
func(n)
+
def render_floatings(n2i, n2f, img, float_layer, float_behind_layer):
- #floating_faces = [ [node, fb["float"]] for node, fb in n2f.iteritems() if "float" in fb]
+ # floating_faces = [ [node, fb["float"]] for node, fb in n2f.iteritems() if "float" in fb]
for node, faces in six.iteritems(n2f):
face_set = [ [float_layer, faces.get("float", None)],
@@ -799,10 +934,10 @@ def render_floatings(n2i, n2f, img, float_layer, float_behind_layer):
# Floatings are positioned over branches
crender.rotate_and_displace(fb, item.rotation, fb.h, item.radius - item.nodeRegion.width() + xtra)
# Floatings are positioned starting from the node circle
- #crender.rotate_and_displace(fb, item.rotation, fb.h, item.radius - item.nodeRegion.width())
+ # crender.rotate_and_displace(fb, item.rotation, fb.h, item.radius - item.nodeRegion.width())
elif img.mode == "r":
- start = item.branch_length + xtra - fb.w #if fb.w < item.branch_length else 0.0
+ start = item.branch_length + xtra - fb.w # if fb.w < item.branch_length else 0.0
fb.setPos(item.content.mapToScene(start, item.center - (fb.h/2.0)))
z = item.zValue()
@@ -813,6 +948,7 @@ def render_floatings(n2i, n2f, img, float_layer, float_behind_layer):
fb.update_columns_size()
fb.render()
+
def render_aligned_faces(img, mainRect, parent, n2i, n2f):
# Prepares and renders aligned face headers. Used to later
# place aligned faces
@@ -913,6 +1049,7 @@ def render_aligned_faces(img, mainRect, parent, n2i, n2f):
mainRect.adjust(0, 0, extra_width, 0)
return extra_width
+
def get_tree_img_map(n2i, x_scale=1, y_scale=1):
MOTIF_ITEMS = set([faces.QGraphicsTriangleItem,
faces.QGraphicsEllipseItem,
@@ -922,9 +1059,9 @@ def get_tree_img_map(n2i, x_scale=1, y_scale=1):
node_list = []
face_list = []
node_areas = {}
- #nid = 0
+ # nid = 0
for n, main_item in six.iteritems(n2i):
- #n.add_feature("_nid", str(nid))
+ # n.add_feature("_nid", str(nid))
nid = n._nid
rect = main_item.mapToScene(main_item.fullRegion).boundingRect()
@@ -957,7 +1094,7 @@ def get_tree_img_map(n2i, x_scale=1, y_scale=1):
if isinstance(f, _TextFaceItem):
face_list.append([x1, y1, x2, y2, nid, str(getattr(f, "face_label", f.text()))])
elif isinstance(f, faces.SeqMotifRectItem):
- #face_list.append([x1, y1, x2, y2, nid, str(getattr(f, "face_label", None))])
+ # face_list.append([x1, y1, x2, y2, nid, str(getattr(f, "face_label", None))])
for mf in f.childItems():
r = mf.boundingRect()
rect = mf.mapToScene(r).boundingRect()
@@ -976,7 +1113,8 @@ def get_tree_img_map(n2i, x_scale=1, y_scale=1):
return {"nodes": node_list, "faces": face_list, "node_areas": node_areas}
-#@tracktime
+
+# @tracktime
def init_items(root_node, parent, n2i, n2f, img, rot_step, hide_root):
# ::: Precalculate values :::
visited = set()
@@ -1091,7 +1229,7 @@ def init_node_dimensions(node, item, faceblock, img):
# Calculate total node size
total_w = sum([w0, w1, w2, w3, w4, item.xoff]) # do not count aligned faces
-
+
if img.mode == "c":
max_h = max(item.heights[:4] + [min_separation])
elif img.mode == "r":
@@ -1108,6 +1246,7 @@ def init_node_dimensions(node, item, faceblock, img):
item.nodeRegion.setRect(0, 0, total_w, max_h)
item.fullRegion.setRect(0, 0, total_w, max_h)
+
def update_branch_lengths(tree, n2i, n2f, img):
for node in tree.traverse("postorder", is_leaf_fn=_leaf):
item = n2i[node]
@@ -1128,6 +1267,7 @@ def update_branch_lengths(tree, n2i, n2f, img):
n2i[ch].moveBy(w0, 0)
item.fullRegion.setWidth(item.nodeRegion.width() + child_width)
+
def init_tree_style(t, ts):
custom_ts = True
if not ts: