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# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ETE is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
# License for more details.
#
# You should have received a copy of the GNU General Public License
# along with ETE. If not, see <http://www.gnu.org/licenses/>.
#
#
# ABOUT THE ETE PACKAGE
# =====================
#
# ETE is distributed under the GPL copyleft license (2008-2015).
#
# If you make use of ETE in published work, please cite:
#
# Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon.
# ETE: a python Environment for Tree Exploration. Jaime BMC
# Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24
#
# Note that extra references to the specific methods implemented in
# the toolkit may be available in the documentation.
#
# More info at http://etetoolkit.org. Contact: huerta@embl.de
#
#
# #END_LICENSE#############################################################
from __future__ import absolute_import
from functools import partial
from six.moves import range
from .qt import Qt, QDialog, QMenu, QCursor, QInputDialog
from .svg_colors import random_color
from . import _show_newick
from ..evol import EvolTree
class NewickDialog(QDialog):
def __init__(self, node, *args):
QDialog.__init__(self, *args)
self.node = node
def update_newick(self):
f = int(self._conf.nwFormat.currentText())
if self._conf.useAllFeatures.isChecked():
features = []
elif self._conf.features_list.count() == 0:
features = None
else:
features = set()
for i in range(self._conf.features_list.count()):
features.add(str(self._conf.features_list.item(i).text()))
nw = self.node.write(format=f, features=features)
self._conf.newickBox.setText(nw)
def add_feature(self):
aName = str(self._conf.attrName.text()).strip()
if aName != '' and not self._conf.features_list.findItems(aName, Qt.MatchCaseSensitive):
self._conf.features_list.addItem(aName)
self.update_newick()
def del_feature(self):
r = self._conf.features_list.currentRow()
self._conf.features_list.takeItem(r)
self.update_newick()
def set_custom_features(self):
state = self._conf.useAllFeatures.isChecked()
self._conf.features_list.setDisabled(state)
self._conf.attrName.setDisabled(state)
self.update_newick()
class _NodeActions(object):
""" Used to extend QGraphicsItem features """
def __init__(self):
self.setCursor(Qt.PointingHandCursor)
self.setAcceptHoverEvents(True)
def mouseReleaseEvent(self, e):
if not self.node:
return
if e.button() == Qt.RightButton:
self.showActionPopup()
elif e.button() == Qt.LeftButton:
self.scene().view.set_focus(self.node)
if isinstance(self.node, EvolTree) and self.node.get_tree_root()._is_mark_mode():
root = self.node.get_tree_root()
all_marks = set([getattr(n, "mark", '').replace('#', '').strip()
for n in root.traverse() if n is not self.node])
all_marks.discard('')
max_value = max(map(int, all_marks)) if all_marks else 0
current_mark = getattr(self.node, "mark", "")
try:
current_mark = int(current_mark.replace('#', ''))
except:
current_mark = 0
if current_mark > max_value:
self._gui_unmark_node()
else:
self._gui_mark_node('#%d'% (current_mark + 1))
#self.scene().view.prop_table.update_properties(self.node)
def hoverEnterEvent (self, e):
if self.node:
if self.node in self.scene().view.n2hl:
pass
else:
self.scene().view.highlight_node(self.node, fullRegion=True)
def hoverLeaveEvent(self,e):
if self.node:
if self.node in self.scene().view.n2hl:
self.scene().view.unhighlight_node(self.node, reset=False)
def mousePressEvent(self,e):
pass
def mouseDoubleClickEvent(self,e):
if self.node:
item = self.scene().n2i[self.node]
if item.highlighted:
self.scene().view.unhighlight_node(self.node, reset=True)
else:
self.scene().view.highlight_node(self.node, fullRegion=True,
bg=random_color(l=0.5, s=0.5), permanent=True)
def showActionPopup(self):
contextMenu = QMenu()
contextMenu.addAction( "Set as outgroup", self.set_as_outgroup)
contextMenu.addAction( "Copy partition", self.copy_partition)
contextMenu.addAction( "Cut partition", self.cut_partition)
if self.scene().view.buffer_node:
contextMenu.addAction( "Paste partition", self.paste_partition)
contextMenu.addAction( "Delete node (collapse children)", self.delete_node)
contextMenu.addAction( "Delete partition", self.detach_node)
contextMenu.addAction( "Populate subtree", self.populate_partition)
contextMenu.addAction( "Add children", self.add_children)
contextMenu.addAction( "Swap branches", self.swap_branches)
if self.node.img_style["draw_descendants"] == False:
contextMenu.addAction( "Open", self.toggle_collapse)
else:
contextMenu.addAction( "Close", self.toggle_collapse)
if self.node.up is not None and\
self.scene().tree == self.node:
contextMenu.addAction( "Back to parent", self.back_to_parent_node)
else:
contextMenu.addAction( "Extract", self.set_start_node)
if isinstance(self.node, EvolTree):
root = self.node.get_tree_root()
all_marks = set([getattr(n, "mark", '').replace('#', '').strip()
for n in root.traverse() if n is not self.node])
all_marks.discard('')
max_value = max(map(int, all_marks)) if all_marks else 1
current_mark = getattr(self.node, "mark", '').replace('#', '').strip()
current_mark = int(current_mark) if current_mark != '' else 0
if current_mark <= max_value:
mark = "#%d" %(current_mark + 1)
contextMenu.addAction("ETE-evol: mark node as " + mark, partial(
self._gui_mark_node, mark))
contextMenu.addAction("ETE-evol: mark group as " + mark, partial(
self._gui_mark_group, mark))
if getattr(self.node, "mark", None):
contextMenu.addAction("ETE-evol: clear mark in node", partial(
self._gui_unmark_node))
contextMenu.addAction("ETE-evol: clear mark in group", partial(
self._gui_unmark_group))
contextMenu.addAction( "Show newick", self.show_newick)
contextMenu.exec_(QCursor.pos())
def _gui_mark_node(self, mark=None):
if not mark:
if self.node.mark:
mark = '#' + str(int(self.node.mark.replace('#', '')) + 1)
else:
mark = '#1'
self.node.mark_tree([self.node.node_id], marks=[mark])
self.scene().GUI.redraw()
def _gui_unmark_node(self):
self.node.mark = ""
self.scene().GUI.redraw()
def _gui_mark_group(self, mark=None):
self.node.mark_tree([self.node.node_id], marks=[mark])
for leaf in self.node.iter_descendants():
leaf.mark_tree([leaf.node_id], marks=[mark])
self.scene().GUI.redraw()
def _gui_unmark_group(self):
self.node.mark = ""
for leaf in self.node.iter_descendants():
leaf.mark = ""
self.scene().GUI.redraw()
def show_newick(self):
d = NewickDialog(self.node)
d._conf = _show_newick.Ui_Newick()
d._conf.setupUi(d)
d.update_newick()
d.exec_()
return False
def delete_node(self):
self.node.delete()
self.scene().GUI.redraw()
def detach_node(self):
self.node.detach()
self.scene().GUI.redraw()
def swap_branches(self):
self.node.swap_children()
self.scene().GUI.redraw()
def add_children(self):
n,ok = QInputDialog.getInteger(None,"Add childs","Number of childs to add:",1,1)
if ok:
for i in range(n):
ch = self.node.add_child()
self.scene().GUI.redraw()
def void(self):
return True
def set_as_outgroup(self):
self.scene().tree.set_outgroup(self.node)
self.scene().GUI.redraw()
def toggle_collapse(self):
self.node.img_style["draw_descendants"] ^= True
self.scene().GUI.redraw()
def cut_partition(self):
self.scene().view.buffer_node = self.node
self.node.detach()
self.scene().GUI.redraw()
def copy_partition(self):
self.scene().view.buffer_node = self.node.copy('deepcopy')
def paste_partition(self):
if self.scene().view.buffer_node:
self.node.add_child(self.scene().view.buffer_node)
self.scene().view.buffer_node= None
self.scene().GUI.redraw()
def populate_partition(self):
n, ok = QInputDialog.getInteger(None,"Populate partition","Number of nodes to add:",2,1)
if ok:
self.node.populate(n)
#self.scene().set_style_from(self.scene().tree,self.scene().layout_func)
self.scene().GUI.redraw()
def set_start_node(self):
self.scene().start_node = self.node
self.scene().GUI.redraw()
def back_to_parent_node(self):
self.scene().start_node = self.node.up
self.scene().GUI.redraw()
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