# #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 . # # # 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()