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# Copyright 2016 by Medical Research Council
# Author: Paul Emsley
#
# This program 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.
#
# This program 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 this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
# 02110-1301, USA
import gtk
import pango
import math
import string
import types
class ligand_validation_metrics_gui:
def __init__(self, ligand_validation_specs):
window = gtk.Window(gtk.WINDOW_TOPLEVEL)
title = "Ligand Validation Report for " # ...
title += ligand_validation_specs.title
window.set_title(title)
self.vbox = gtk.VBox(False, 0)
self.vbox.set_border_width(5)
h_sep = gtk.HSeparator()
self.bar_length = 300
self.bar_height = 10
self.abs_bar_height = int(self.bar_height * 1.6)
self.x_bar_offset = 160
self.y_bar_offset = 20
self.y_pixels_bar_spacing = 30
self.abs_bar_width = 6
da = gtk.DrawingArea()
da.set_size_request(560,280)
close_button = gtk.Button(" Close ")
hbox = gtk.HBox(False, 0)
self.vbox.append(da)
self.vbox.append(h_sep)
hbox.append(close_button)
self.vbox.pack_end(hbox, False, 6)
window.add(self.vbox)
window.show_all()
da.connect("expose-event", self.on_drawing_area_expose)
close_button.connect("clicked", lambda a : window.destroy())
self.pangolayout = da.create_pango_layout("")
style = da.get_style()
gc = style.fg_gc[gtk.STATE_NORMAL]
self.setup_colour_bar_buff()
self.lvs = ligand_validation_specs
def setup_colour_bar_buff(self):
c = 3*self.bar_length*self.bar_height*['\0']
for j in range(self.bar_length):
f_j = float(j)/float(self.bar_length)
# we need g to go 255:255:0
r = int(255*(1-math.pow(f_j, 5)))
# we need g to go 0:255:0
g_1 = f_j # 0 : 0.5 : 1
g_2 = 2 * (g_1 - 0.5) # -1 : 0. : 1
g_3 = g_2 * g_2 # 1 : 0. : 1
g_4 = 1 - g_3 # 0 : 1. : 0
g = int(240*g_4)
b = int(255*math.pow(f_j, 0.2))
for i in range(self.bar_height):
idx = 3*(self.bar_length*i + j)
c[idx ] = chr(r)
c[idx+1] = chr(g)
c[idx+2] = chr(b)
self.colour_bar_buff = string.join(c, '')
def draw_sliders(self, ligand_validation_specs, da, gc):
for idx in range(len(ligand_validation_specs.metrics)):
m = ligand_validation_specs.metrics[idx]
# print 'render metric', m.metric_name, m.percentile_abs
self.draw_slider(m.metric_name, 0, m.percentile_abs, m.percentile_rel, '{0:.3f}'.format(m.value), idx, da, gc)
values = [m.percentile_abs for m in ligand_validation_specs.metrics]
self.draw_connecting_lines(values, da, gc)
# perhaps we should check that the ligand metrics were (each good)?
return len(ligand_validation_specs.metrics)
# return True if the bar for the absolute percentile was drawn,
# otherwise return False (da is drawing_area, gc, is graphics_context (or something))
#
def draw_slider(self, name, x_for_rj, percentile_abs, percentile_rel_str, value_str, slider_no, da, gc):
print("debug:: draw_slider():", name, " ", x_for_rj, " percentile_abs:", percentile_abs,
"percentile_rel_str:", percentile_rel_str, "value_str", value_str, slider_no)
# if the percentile_abs is actually 0.0, then the block doesn't get drawn (it's off the canvas?)
if percentile_abs < 0.01:
percentile_abs = 0.01;
y = self.y_bar_offset + self.y_pixels_bar_spacing*(slider_no+1)
# colour bar
self.draw_rgb_image(da, gc, self.x_bar_offset, y)
local_gc = gc;
local_gc.set_foreground(local_gc.get_colormap().alloc_color("#888888"))
da.window.draw_rectangle(local_gc, False, self.x_bar_offset, y, self.bar_length, self.bar_height)
local_gc.set_foreground(local_gc.get_colormap().alloc_color("#000000"))
# Metric text
pangolayout = da.create_pango_layout("")
pangolayout.set_justify(1)
pangolayout.set_alignment(pango.ALIGN_RIGHT)
pangolayout.set_text(name)
pangolayout.context_changed()
da.window.draw_layout(gc, 4+x_for_rj, y-3, pangolayout)
# Values text
if isinstance(value_str, bytes):
x_for_value = self.x_bar_offset + self.bar_length + 12
pangolayout.set_text(value_str)
# print "Drawing Value value", x_for_value, y, value_str
da.window.draw_layout(gc, x_for_value, y-6, pangolayout)
# Bars for percentile scores
try:
if percentile_rel_str != False:
rel = float(percentile_rel_str)
self.arcs_for_rel(rel, y, da, gc)
if percentile_abs_str != False:
abs = float(percentile_abs_str)
self.bar_for_abs(abs, y, da, gc)
return True
rel = float(rel_str)
except TypeError as e:
print(e)
# hopefully we don't get here.
return False
# pass abs values
def draw_connecting_lines(self, pc_ranks, da, gc):
if len(pc_ranks) > 1:
for slider_no in range(len(pc_ranks)-1):
y_min_1 = 20 + 30*(slider_no+1)
y_min_2 = 20 + 30*(slider_no+2)
abs_1 = float(pc_ranks[slider_no])
abs_2 = float(pc_ranks[slider_no+1])
x_1 = int(self.x_bar_offset + 0.01 * abs_1 * self.bar_length)
y_1 = int(y_min_1 + self.bar_height + 1)
x_2 = int(self.x_bar_offset + 0.01 * abs_2 * self.bar_length)
y_2 = int(y_min_2 - self.bar_height * 0.25)
da.window.draw_line(gc, x_1, y_1, x_2, y_2)
def on_drawing_area_expose(self, drawing_area, event):
style = drawing_area.get_style()
gc = style.fg_gc[gtk.STATE_NORMAL]
n_sliders = self.draw_sliders(self.lvs, drawing_area, gc)
self.draw_top_labels(drawing_area, gc)
self.draw_bottom_labels(drawing_area, gc, n_sliders) # Worse, Better
self.draw_key(drawing_area, gc, n_sliders) # percentile box descriptions
def draw_rgb_image(self, da, gc, x, y):
da.window.draw_rgb_image(gc, x, y, self.bar_length, self.bar_height,
gtk.gdk.RGB_DITHER_NONE, self.colour_bar_buff, self.bar_length*3)
def bar_for_abs(self, abs_percent, y_min, da, gc):
x = int(self.x_bar_offset + 0.01 * abs_percent * self.bar_length - 0.5 * self.abs_bar_width)
y = int(y_min - self.bar_height * 0.25)
da.window.draw_rectangle(gc, True, x, y, self.abs_bar_width, self.abs_bar_height)
def arcs_for_rel(self, rel_percent, y_min, da, gc):
x = int(self.x_bar_offset + 0.01 * rel_percent * self.bar_length - 0.5 * self.abs_bar_width)
y = int(y_min - self.bar_height * 0.25)
da.window.draw_rectangle(gc, False, x, y, self.abs_bar_width, self.abs_bar_height)
def draw_top_labels(self, da, gc):
pangolayout = da.create_pango_layout("")
pangolayout = da.create_pango_layout("")
font_desc = pango.FontDescription('Sans 13')
pangolayout.set_font_description(font_desc)
pangolayout.set_text('Metric')
y_level = 15
da.window.draw_layout(gc, 80, y_level, pangolayout)
pangolayout.set_text('Percentile Ranks')
da.window.draw_layout(gc, 245, y_level, pangolayout)
pangolayout.set_text('Value')
da.window.draw_layout(gc, 470, y_level, pangolayout)
# Worse, Better
def draw_bottom_labels(self, da, gc, n_sliders):
x_worse = self.x_bar_offset
y_worse = self.y_bar_offset + self.y_pixels_bar_spacing * n_sliders + 18
x_better = self.x_bar_offset + self.bar_length - 32
y_better = y_worse
pl_wb = da.create_pango_layout("")
pl_wb.set_text('Worse')
font_desc = pango.FontDescription('Sans 8')
font_desc.set_style(pango.STYLE_ITALIC)
pl_wb.set_font_description(font_desc)
da.window.draw_layout(gc, x_worse, y_worse, pl_wb)
pl_wb.set_text('Better')
da.window.draw_layout(gc, x_better, y_better, pl_wb)
# percentile box descriptions
def draw_key(self, da, gc, n_sliders):
x_key_box_abs = self.x_bar_offset
y_key_box_abs = self.y_bar_offset + self.y_pixels_bar_spacing * (n_sliders + 1) + 10
x_key_box_rel = x_key_box_abs
y_key_box_rel = y_key_box_abs + 20
x_key_1 = x_key_box_abs + 10
y_key_1 = y_key_box_abs
x_key_2 = x_key_1
y_key_2 = y_key_1 + 20
da.window.draw_rectangle(gc, True, x_key_box_abs, y_key_box_abs,
self.abs_bar_width, self.abs_bar_height)
pl = da.create_pango_layout("")
font_desc = pango.FontDescription('Sans 9')
pl.set_font_description(font_desc)
pl.set_text('Percentile relative to all x-ray structures')
da.window.draw_layout(gc, x_key_1, y_key_1, pl)
#da.window.draw_rectangle(gc, False, x_key_box_rel, y_key_box_rel,
# self.abs_bar_width, self.abs_bar_height)
# pl.set_text('Percentile relative to x-ray structures of similar resolution')
# da.window.draw_layout(gc, x_key_2, y_key_2, pl)
class ligand_stats:
class stat_t:
# percentile is in 0-100 range, can be strings,
def __init__(self, metric_name, pc_metric_value_abs, pc_metric_value_rel, value):
self.metric_name = metric_name
self.percentile_abs = pc_metric_value_abs
self.percentile_rel = pc_metric_value_rel
self.value = value
def __init__(self):
self.title = 'Test-ligand'
self.metrics = []
def add_metric(self, metric_name, pc_value_abs, pc_value_rel, value):
s = self.stat_t(metric_name, pc_value_abs, pc_value_rel, value)
self.metrics.append(s)
# ligand stats are not very resolution dependent, so a
# ligand_stats metric can be generated without
# resolution-dependent (relative) percentiles
#
def add_metric(self, metric_name, pc_value_abs, value):
s = self.stat_t(metric_name, pc_value_abs, False, value)
self.metrics.append(s)
# we want to be able to call this function from scheme. So pass a list of stats
#
def ligand_validation_metrics_gui_list_wrapper(stats_list):
ls = ligand_stats()
for metric in stats_list:
metric_name = metric[0]
percentile = metric[1]
value = metric[2]
ls.add_metric(metric_name, percentile, value)
ligand_validation_metrics_gui(ls)
# if __name__ == '__main__':
# ls = ligand_stats()
# ls.add_metric("metric-name-1", 33, 45, '0.78')
# ls.add_metric("metric-name-2", 30, 66, '0.93')
# ls.add_metric("metric-name-3", 53, 45, '22.78')
# ls.add_metric("metric-name-4", 23, 25, '1.78')
# ligand_validation_metrics_gui(ls)
# gtk.main()
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