QtGui standalone and embedded. Minor tree changes in available tree drawing functions (ladderize nodes)

ete3/coretype/tree.py

@@ -68,6 +68,7 @@
 DEFAULT_DIST = 1.0
 DEFAULT_SUPPORT = 1.0
 DEFAULT_NAME = ""
+DEFAULT_TEXT_COLOR = "black"
 
 class TreeError(Exception):
     """
@@ -1353,16 +1354,17 @@ def unroot(self, mode='legacy'):
             else:
                 raise TreeError("Cannot unroot a tree with only two leaves")
 
-    def show(self, layout=None, tree_style=None, name="ETE"):
+    def show(self, layout=None, tree_style=None, name="ETE", child_app = False):
         """
         Starts an interactive session to visualize current node
         structure using provided layout and TreeStyle.
 
         """
         from ..treeview import drawer
         drawer.show_tree(self, layout=layout,
-                         tree_style=tree_style, win_name=name)
+                         tree_style=tree_style, win_name=name, child_app = child_app)
 
+
     def render(self, file_name, layout=None, w=None, h=None, \
                        tree_style=None, units="px", dpi=90):
         """
@@ -2586,6 +2588,13 @@ def phonehome(self):
         from .. import _ph
         _ph.call()
 
+    def add_leaf_text_color(self, color=None):
+        # Added the extra function to use the is_leaf() bool
+        if self.is_leaf():
+            if color == None:
+                color = "#000000"
+            self.add_feature("text_color",color)
+
 def _translate_nodes(root, *nodes):
     name2node = dict([ [n, None] for n in nodes if type(n) is str])
     if name2node:

ete3/treeview/drawer.py

@@ -56,23 +56,25 @@
 def exit_gui(a, b):
     _QApp.exit(0)
 
-def init_scene(t, layout, ts):
+def init_scene(t, layout, ts, child_app = False):
     global _QApp
 
     ts = init_tree_style(t, ts)
     if layout:
         ts.layout_fn  = layout
 
-    if not _QApp:
+    if not child_app:
         _QApp = QApplication(["ETE"])
+    else:
+        _QApp = QMainWindow()
 
     scene  = _TreeScene()
 	#ts._scale = None
     return scene, ts
 
-def show_tree(t, layout=None, tree_style=None, win_name=None):
+def show_tree(t, layout=None, tree_style=None, win_name=None, child_app=None):
     """ Interactively shows a tree."""
-    scene, img = init_scene(t, layout, tree_style)
+    scene, img = init_scene(t, layout, tree_style, child_app=child_app)
     tree_item, n2i, n2f = render(t, img)
     scene.init_values(t, img, n2i, n2f)
 
@@ -91,7 +93,10 @@ def show_tree(t, layout=None, tree_style=None, win_name=None):
         signal.signal(signal.SIGALRM, exit_gui)
         signal.alarm(GUI_TIMEOUT)
 
-    _QApp.exec_()
+    if not child_app:
+        _QApp.exec_()
+    else:
+        pass
 
 def render_tree(t, imgName, w=None, h=None, layout=None,
                 tree_style = None, header=None, units="px",
@@ -149,10 +154,13 @@ def run(self):
 
 
 def get_img(t, w=None, h=None, layout=None, tree_style = None,
-            header=None, units="px", dpi=90, return_format="%%return"):
+            header=None, units="px", dpi=90, return_format="%%return", child_app = False):
     global _QApp
-    if not _QApp:
+    if not child_app and not _QApp:
         _QApp = QApplication(["ETE"])
+    else:
+        _QApp = QMainWindow()
+
 
     r = RenderThread(t, layout, tree_style, w, h, dpi, units, return_format)
     r.start()

ete3/treeview/node_gui_actions.py

@@ -151,6 +151,8 @@ def mouseDoubleClickEvent(self,e):
 
     def showActionPopup(self):
         contextMenu = QMenu()
+        contextMenu.addAction( "Ladderize top to bottom", self.ladderize_top)
+        contextMenu.addAction( "Ladderize bottom to top", self.ladderize_bottom)
         contextMenu.addAction( "Set as outgroup", self.set_as_outgroup)
         contextMenu.addAction( "Copy partition", self.copy_partition)
         contextMenu.addAction( "Cut partition", self.cut_partition)
@@ -264,6 +266,14 @@ def toggle_collapse(self):
         self.node.img_style["draw_descendants"] ^= True
         self.scene().GUI.redraw()
 
+    def ladderize_top(self):
+        self.node.ladderize(1)
+        self.scene().GUI.redraw()
+
+    def ladderize_bottom(self):
+        self.node.ladderize(0)
+        self.scene().GUI.redraw()
+
     def cut_partition(self):
         self.scene().view.buffer_node = self.node
         self.node.detach()

ete3/treeview/qt4_gui.py

@@ -369,9 +369,9 @@ def on_actionOpen_triggered(self):
 
     @QtCore.pyqtSlot()
     def on_actionSave_newick_triggered(self):
-        fname = QFileDialog.getSaveFileName(self ,"Save File",
+        fname = QFileDialog.getSaveFileName(self ,"Save Newick File",
                                                  "/home",
-                                                 "Newick (*.nh *.nhx *.nw )")
+                                                 "Newick (*.nh *.nhx *.nw *.nwk *.newick)")
         nw = self.scene.tree.write()
         try:
             OUT = open(fname,"w")
@@ -383,27 +383,30 @@ def on_actionSave_newick_triggered(self):
 
     @QtCore.pyqtSlot()
     def on_actionRenderPDF_triggered(self):
-        F = QFileDialog(self)
-        if F.exec_():
-            imgName = str(F.selectedFiles()[0])
-            if not imgName.endswith(".pdf"):
-                imgName += ".pdf"
-            save(self.scene, imgName)
-
+        file_filter = "PDF file (*.PDF)"
+        response = QFileDialog.getSaveFileName(parent=self,
+        caption = "Save PDF file",
+        filter = file_filter
+        )
+        if response != "":
+            save(self.scene, response[0])
+        else:
+            return
 
     @QtCore.pyqtSlot()
     def on_actionRender_selected_region_triggered(self):
         if not self.scene.selector.isVisible():
             return QMessageBox.information(self, "!",\
                                               "You must select a region first")
-
-        F = QFileDialog(self)
-        if F.exec_():
-            imgName = str(F.selectedFiles()[0])
-            if not imgName.endswith(".pdf"):
-                imgName += ".pdf"
-            save(imgName, take_region=True)
-
+        file_filter = "PDF file (*.PDF)"
+        response = QFileDialog.getSaveFileName(parent=self,
+        caption = "Save PDF file",
+        filter = file_filter
+        )
+        if response != "":
+            save(self.scene, response[0])
+        else:
+            return
 
     @QtCore.pyqtSlot()
     def on_actionPaste_newick_triggered(self):

ete3/treeview/qt4_render.py

@@ -260,7 +260,12 @@ def render(root_node, img, hide_root=False):
             faces.add_face_to_node(su_face, n, 0, position="branch-bottom")
 
         if _leaf(n) and n.name and img.show_leaf_name:
-            faces.add_face_to_node(na_face, n, 0, position="branch-right")
+            if hasattr(n, "_faces") and 0 in n._faces.__dict__["branch-right"]:
+                pass
+                # If the node already has a text face in the position branch right in column 0
+                # the user already has already added a face in that position (node name with certain color)
+            else:
+                faces.add_face_to_node(na_face, n, 0, position="branch-right")
 
         if _leaf(n):# or len(n.img_style["_faces"]["aligned"]):
             virtual_leaves += 1