def show(self):
sumtree.SumTree.show(self)
# set bindings
self.win.set_binding(input_key("g"), lambda: self.set_mode("gene"))
self.win.set_binding(input_key("e"), lambda: self.set_mode("events"))
self.win.set_binding(input_key("r"), lambda: self.set_mode("reroot"))
self.win.set_binding(input_key("s"), lambda: self.set_mode("swap"))
self.win.set_binding(input_key("S", "shift"),
lambda: self.swap(self.tree.root))
# build sidebar menu
if self.bar is None:
self.bar = hud.SideBar(self.win, width=150)
self.bar.add_item(
hud.MenuItem("gene mode (g)", lambda: self.set_mode("gene")))
self.bar.add_item(
hud.MenuItem("events mode (e)",
lambda: self.set_mode("events")))
self.bar.add_item(
hud.MenuItem("reroot mode (r)",
lambda: self.set_mode("reroot")))
self.bar.add_item(
hud.MenuItem("swap mode (s,S)", lambda: self.set_mode("swap")))
if self.events:
self.win.add_group(self.draw_events())
def show(self):
"""Make visualization window visible"""
# tree visualization
if self.vistree != None:
self.vistree.show()
#self.vistree.win.set_size(*self.tree_win_size)
self.windows.append(self.vistree.win)
self.coords.append(
max(node.y for node in self.current_tree.nodes.itervalues()))
# add additional menu options
self.vistree.bar.add_item(
hud.MenuItem("next tree (n)", self.next_tree))
self.vistree.bar.add_item(
hud.MenuItem("prev tree (p)", self.prev_tree))
# add additional key binding
self.vistree.win.set_binding(input_key("n"), self.next_tree)
self.vistree.win.set_binding(input_key("p"), self.prev_tree)
# distance matrix visualization
if self.visdist != None:
self.visdist.show()
self.visdist.win.set_name(self.distmat_names[0])
self.windows.append(self.visdist.win)
self.coords.append(0)
# add additional menu options
self.visdist.bar.add_item(
hud.MenuItem("next matrix (n)", self.next_matrix))
self.visdist.bar.add_item(
hud.MenuItem("prev matrix (p)", self.prev_matrix))
# add additional key binding
self.visdist.win.set_binding(input_key("n"), self.next_matrix)
self.visdist.win.set_binding(input_key("p"), self.prev_matrix)
# alignment visualization
if self.visalign != None:
self.visalign.show()
self.windows.append(self.visalign.vis.win)
self.coords.append(-1.5)
# add additional key binding
self.visalign.win.set_binding(input_key("n"), self.next_align)
self.visalign.win.set_binding(input_key("p"), self.prev_align)
# tie all windows by their y-coordinate
if len(self.windows) > 1:
self.ensembl = multiwindow.WindowEnsemble(self.windows,
stacky=True,
sameh=True,
tiey=True,
coordsy=self.coords)
def show(self):
matrix.MatrixViewer.show(self)
# build sidebar menu
self.bar = hud.SideBar(self.win, width=150)
self.bar.add_item(hud.MenuItem("align gene (a)", self.show_align))
self.bar.add_item(hud.MenuItem("clear genes (d)",
self.clear_selection))
self.bar.add_item(hud.MenuItem("show genes (s)", self.show_selection))
self.bar.add_item(
hud.MenuItem("toggle labels (l)", self.toggle_label_windows))
# register key bindings
self.win.set_binding(input_key("a"), self.show_align)
self.win.set_binding(input_key("d"), self.clear_selection)
self.win.set_binding(input_key("s"), self.show_selection)
def show(self):
newwin = (self.vis.win == None)
self.vis.show()
self.win = self.vis.win # for convenience
if newwin:
self.win.set_name(self.title)
self.win.set_size(*self.winsize)
if self.bar == None:
# build sidebar menu
self.bar = hud.SideBar(self.win, width=150)
self.bar.add_item(
hud.MenuItem("toggle color (c)", self.toggle_color_bases))
self.bar.add_item(
hud.MenuItem("toggle leftwin (l)", self.toggle_left_window))
self.bar.add_item(
hud.MenuItem("always color",
lambda: self.set_min_color_bases(0)))
# register key bindings
self.win.set_binding(input_key("c"), self.toggle_color_bases)
self.win.set_binding(input_key("l"), self.toggle_left_window)
def show(self):
"""Display browser"""
self.enable_updating(False)
# create window
if self.win == None or not self.win.is_open():
newwin = True
self.win = summon.Window(position=self.winpos, size=self.winsize)
self.win.set_bgcolor(1, 1, 1)
self.win.select.set_callback(self.on_select)
# zooming
self.win.set_binding(input_click("right", "down"), "focus")
self.win.set_binding(input_motion("right", "down"), "zoomx")
self.win.set_binding(input_click("right", "down", "shift"),
"focus")
self.win.set_binding(input_motion("right", "down", "shift"),
"zoomy")
# create left window
pos = self.win.get_position()
self.leftwin = summon.Window(
" ",
size=(150, self.win.get_size()[1]),
position=(pos[0] - 150 - self.win.get_decoration()[0], pos[1]))
self.leftwin.set_bgcolor(1, 1, 1)
self.left_ensemble = multiwindow.WindowEnsemble(
[self.leftwin, self.win],
stacky=True,
sameh=True,
tiey=True,
piny=True,
master=self.win)
# menu
self.sidebar = hud.SideBar(self.win, width=150)
self.sidebar.add_item(
hud.MenuItem("toggle ruler (r)", self.toggle_ruler))
self.win.set_binding(input_key("r"), self.toggle_ruler)
else:
newwin = False
self.win.clear_groups()
# determine largest chromosome size
maxchrom = max(x.length() for x in self.chroms)
# add line to left window
maxname = max(len(x.seqname) for x in self.chroms) * 20
self.leftwin.add_group(
lines(color(1, 1, 1), 0, 0, -maxname, 0, 0, 0, 0,
self.chrom_step * len(self.chroms), 0,
self.chrom_step * len(self.chroms), -maxname,
self.chrom_step * len(self.chroms)))
# draw chromosome labels
self.win.add_group(self.draw_chrom_labels())
self.leftwin.add_group(self.draw_chrom_labels())
# draw all tracks
for track in self._tracks:
self.win.add_group(track.draw())
if newwin:
# setup left window
self.leftwin.home()
# setup window
w, h = self.win.get_size()
bottom = float(
min(self.chrom_pos[i][1]
for i in self.chroms) + 2 * self.chrom_step)
self.win.set_visible(0, -2 * self.chrom_step, maxchrom, bottom)
self.win.focus(w / 2, h / 2)
self.win.zoom(1, maxchrom / abs(-2 * self.chrom_step - bottom))
self.win.zoom(.9, .9)
self.enable_updating(True)