def drawTimeLine(self, width=None): if width == None: width = 3.0 tl = self.timeLine for item in tl.find_all(): tl.delete(item) for c in self.clusters: c.canvasItems = [] c.canvas = tl frameNums = range(self.startFrame, self.endFrame+1, self.stride) cluster = startFrame = None f2x = self._frame2x height = 22 for fn in frameNums: c = self.clusterMap[fn] if c == cluster: continue if cluster != None: tkColor = rgba2tk(cluster.color) cluster.canvasItems.append(tl.create_rectangle( f2x(startFrame), 0, f2x(fn)-1, height, fill=tkColor, outline=tkColor)) cluster = c startFrame = fn tkColor = rgba2tk(cluster.color) cluster.canvasItems.append(tl.create_rectangle(f2x(startFrame), 0, f2x(frameNums[-1]+self.stride)-1, height, fill=tkColor, outline=tkColor)) for c in self.clusters: rep = c.representative tkColor = rgba2tk(c.color) c.canvasItems.append(tl.create_rectangle( f2x(rep), 0, f2x(rep+self.stride)-1, -0.5*height, fill=tkColor, outline=tkColor)) tl.resizescrollregion()
def _rectKw(self):
kw = {}
if self.interiorRGBA:
kw['fill'] = rgba2tk(self.interiorRGBA)
if self._borderRGBA():
kw['outline'] = rgba2tk(self._borderRGBA())
if self.highlighted:
kw['dash'] = '-'
else:
kw['width'] = 0
kw['outline'] = ""
return kw
def setColor(self, color): self.__color = color if hasattr(self, 'canvasItems'): tkColor = rgba2tk(color) for i in self.canvasItems: self.canvas.itemconfigure(i, fill=tkColor, outline=tkColor)
def drawTimeLine(self, width=None):
if width == None:
width = 3.0
tl = self.timeLine
for item in tl.find_all():
tl.delete(item)
for c in self.clusters:
c.canvasItems = []
c.canvas = tl
frameNums = range(self.startFrame, self.endFrame + 1, self.stride)
cluster = startFrame = None
f2x = self._frame2x
height = 22
for fn in frameNums:
c = self.clusterMap[fn]
if c == cluster:
continue
if cluster != None:
tkColor = rgba2tk(cluster.color)
cluster.canvasItems.append(
tl.create_rectangle(f2x(startFrame),
0,
f2x(fn) - 1,
height,
fill=tkColor,
outline=tkColor))
cluster = c
startFrame = fn
tkColor = rgba2tk(cluster.color)
cluster.canvasItems.append(
tl.create_rectangle(f2x(startFrame),
0,
f2x(frameNums[-1] + self.stride) - 1,
height,
fill=tkColor,
outline=tkColor))
for c in self.clusters:
rep = c.representative
tkColor = rgba2tk(c.color)
c.canvasItems.append(
tl.create_rectangle(f2x(rep),
0,
f2x(rep + self.stride) - 1,
-0.5 * height,
fill=tkColor,
outline=tkColor))
tl.resizescrollregion()
def setInteriorRGBA(self, rgba): if rgba: fill = rgba2tk(rgba) else: fill = "" for item in self._items: self.canvas.itemconfigure(item, fill=fill) self.interiorRGBA = rgba
def alternateColors(parent):
"Generate an alternate color to the default background color"
import Tkinter
from CGLtk.color import rgba2tk
from CGLtk.color.ColorWell import _tkrgb2rgba
w = Tkinter.Button(parent, text="Hello")
bg = w.cget("bg")
fg = w.cget("fg")
disabledColor = w.cget("disabledforeground")
b_r, b_g, b_b, b_a = _tkrgb2rgba(w.winfo_rgb(bg))
f_r, f_g, f_b, f_a = _tkrgb2rgba(w.winfo_rgb(fg))
w.destroy()
r = b_r + (f_r - b_r) / 10.0
g = b_g + (f_g - b_g) / 10.0
b = b_b + (f_b - b_b) / 10.0
alt_bg = rgba2tk((r, g, b, b_a))
return (bg, alt_bg), disabledColor
def alternateColors(parent):
"Generate an alternate color to the default background color"
import Tkinter
from CGLtk.color import rgba2tk
from CGLtk.color.ColorWell import _tkrgb2rgba
w = Tkinter.Button(parent, text="Hello")
bg = w.cget("bg")
fg = w.cget("fg")
disabledColor = w.cget("disabledforeground")
b_r, b_g, b_b, b_a = _tkrgb2rgba(w.winfo_rgb(bg))
f_r, f_g, f_b, f_a = _tkrgb2rgba(w.winfo_rgb(fg))
w.destroy()
r = b_r + (f_r - b_r) / 10.0
g = b_g + (f_g - b_g) / 10.0
b = b_b + (f_b - b_b) / 10.0
alt_bg = rgba2tk((r, g, b, b_a))
return (bg, alt_bg), disabledColor
def _plotMarkers(self): canvas = self._canvas br = self['boxradius'] markerType = self['markertype'] if markerType == 'line': x1, y1, x2, y2 = self._dragRegion() for m in self.markers: if m['id'] != None: continue x, y = self._canvasXY(m['xy']) color = rgba2tk(m['rgba']) if markerType == 'line': m['id'] = canvas.create_rectangle(x-br, y1, x+br, y2, fill=color) else: m['id'] = canvas.create_rectangle(x-br, y-br, x+br, y+br, fill=color)
def _updateConnections(self):
cxy_list = map(lambda m: self._canvasXY(m['xy']), self.markers)
canvas = self._canvas
color = rgba2tk(self._rgba(self['connectcolor']))
ids = []
for k in range(len(cxy_list) - 1):
x0, y0 = cxy_list[k]
x1, y1 = cxy_list[k + 1]
id = canvas.create_line(x0, y0, x1, y1, fill=color)
ids.append(id)
for id in self.connectIds:
c.delete(id)
self.connectIds = ids
for m in self.markers:
canvas.tag_raise(m['id'])
def _updateConnections(self): cxy_list = map(lambda m: self._canvasXY(m['xy']), self.markers) canvas = self._canvas color = rgba2tk(self._rgba(self['connectcolor'])) ids = [] for k in range(len(cxy_list) - 1): x0, y0 = cxy_list[k] x1, y1 = cxy_list[k+1] id = canvas.create_line(x0, y0, x1, y1, fill=color) ids.append(id) for id in self.connectIds: c.delete(id) self.connectIds = ids for m in self.markers: canvas.tag_raise(m['id'])
def _plotMarkers(self):
canvas = self._canvas
br = self['boxradius']
markerType = self['markertype']
if markerType == 'line':
x1, y1, x2, y2 = self._dragRegion()
for m in self.markers:
if m['id'] != None:
continue
x, y = self._canvasXY(m['xy'])
color = rgba2tk(m['rgba'])
if markerType == 'line':
m['id'] = canvas.create_rectangle(x - br,
y1,
x + br,
y2,
fill=color)
else:
m['id'] = canvas.create_rectangle(x - br,
y - br,
x + br,
y + br,
fill=color)
def _setRgba(self):
if self['id'] == None:
return
self._canvas.itemconfigure(self['id'], fill=rgba2tk(self['rgba']))
def _hlistKw(self, model, colNum):
vt = _valueTypes[self.columnMap[colNum]]
vf = _valueFuncs[self.columnMap[colNum]]
kw = {'itemtype': vt}
txt = None
img = None
if vt == 'text':
txt = vf(model)
if not isinstance(txt, basestring):
txt, bcolor = txt
if bcolor is not None:
if not isinstance(bcolor, basestring):
if hasattr(bcolor, 'rgba'):
rgba = bcolor.rgba()
else:
rgba = bcolor
from CGLtk.color import rgba2tk
bcolor = rgba2tk(rgba)
fcolor = CGLtk.textForeground(
bcolor, self.modelTable)
kw['style'] = Tix.DisplayStyle("text",
refwindow=self.modelTable,
background=bcolor,
foreground=fcolor,
selectforeground=bcolor)
else:
kw['style'] = self.textStyle
elif vt == 'image':
img = vf(model)
elif vt == 'imagetext':
img, txt = vf(model)
elif vt == 'toggle':
kw['itemtype'] = 'window'
bool, cb = vf(model)
togKw = {'command':
# avoid holding references to model
lambda cb=cb, i=self.models.index(model),
b=not bool: cb(self.models[i], b),
'indicatoron': 0,
'borderwidth': 0}
if bool:
togKw['image'] = self.modelTable.tk.call(
'tix', 'getimage', 'ck_on')
else:
togKw['image'] = self.modelTable.tk.call(
'tix', 'getimage', 'ck_off')
toggle = Tkinter.Checkbutton(
self.modelTable.hlist, **togKw)
kw['window'] = toggle
kw['style'] = self.checkButtonStyle
elif vt == 'well':
color, noneOkay, alphaOkay, cb = vf(model)
if color is False:
kw['itemtype'] = 'text'
txt = ""
else:
kw['itemtype'] = 'window'
if isinstance(color, chimera.MaterialColor):
color = color.rgba()
def wellCB(clr, cb=cb, mdl=model):
if clr is not None:
clr = chimera.MaterialColor(
*clr)
cb(mdl, clr)
from CGLtk.color.ColorWell import ColorWell
kw['window'] = ColorWell(self.modelTable.hlist,
color, callback=wellCB,
width=18, height=18,
noneOkay=noneOkay, wantAlpha=alphaOkay)
kw['style'] = self.colorWellStyle
else:
raise ValueError("Unknown column type: '%s'" % vt)
if txt != None:
kw['text'] = str(txt)
if img != None:
kw['image'] = self.modelTable.tk.call(
'tix', 'getimage', img)
return kw
def writeDemo(self, save_path, tempMode=False):
from CGLtk.color import rgba2tk
from multiloader2 import Multiloader
m = Multiloader()
## GLOBAL options
demo = XMLDemo()
title = self.gTitleOption.get()
if title:
demo.title = title
else:
demo.title = "Chimera Demo"
autodelay = self.gAutoDelayOption.get()
if autodelay:
demo.autodelay = autodelay
image = self.gImageOption.get()
if image:
demo.image = image
datadir = self.gDataDirOption.get()
if datadir:
demo.datadir = datadir
else:
if tempMode and self.save_path:
demo.datadir = os.path.split(self.save_path)[0]
bg_color = self.gBgColorOption.get()
if bg_color:
demo.bg_color = rgba2tk(bg_color.rgba())
autorun_on = self.gAutoRunOption.get()
if autorun_on:
demo.autorun_on = autorun_on
demo.description = ''
panel_list = []
panel_id = 0
##PANEL information
for p in self.panels:
panel_id += 1
panel = XMLPanel()
panel.id = panel_id
delay = p.getDelayVar().get()
if delay:
panel.autodelay = delay
title = p.getNameVar().get()
if title:
if not title[0:9] == "<untitled":
panel.title = title
if p == self.getCurrentPanel():
panel.text = self.getCurrentText()
else:
panel.text = p.getText().strip()
panel.command = []
for var,entry in p.getCmds():
xmlc = XMLCommand()
xmlc.active = ["False","True"][var]
xmlc.item = entry
panel.command.append(xmlc)
panel.undo = []
for var,entry in p.getUndos():
xmlu = XMLUndo()
xmlu.active = ["False","True"][var]
xmlu.item = entry
panel.undo.append(xmlu)
panel_list.append(panel)
demo.panels = panel_list
m.save(save_path, {'Demo':[demo]})
def _setRgba(self): if self['id'] == None: return self._canvas.itemconfigure(self['id'], fill=rgba2tk(self['rgba']))
def setColor(self, color):
self.__color = color
if hasattr(self, 'canvasItems'):
tkColor = rgba2tk(color)
for i in self.canvasItems:
self.canvas.itemconfigure(i, fill=tkColor, outline=tkColor)
# --- UCSF Chimera Copyright ---
# Copyright (c) 2000 Regents of the University of California.
# All rights reserved. This software provided pursuant to a
# license agreement containing restrictions on its disclosure,
# duplication and use. This notice must be embedded in or
# attached to all copies, including partial copies, of the
# software or any revisions or derivations thereof.
# --- UCSF Chimera Copyright ---
#
# $Id: clustalX.py 26655 2009-01-07 22:02:30Z gregc $
from CGLtk.color import rgba2tk
_clustalRed = rgba2tk((0.9, 0.2, 0.1))
_clustalBlue = rgba2tk((0.1, 0.5, 0.9))
_clustalGreen = rgba2tk((0.1, 0.8, 0.1))
_clustalCyan = rgba2tk((0.1, 0.7, 0.7))
_clustalPink = rgba2tk((0.9, 0.5, 0.5))
_clustalMagenta = rgba2tk((0.8, 0.3, 0.8))
#_clustalYellow = rgba2tk((0.8, 0.8, 0.0))
# above is very hard to see on the gray background, so...
_clustalYellow = rgba2tk((0.69, 0.69, 0.0))
_clustalOrange = rgba2tk((0.9, 0.6, 0.3))
_clustalCategories = [("wlvimafcyhp", 0.6, '%'),
("wlvimafcyhp", 0.8, '#'), ("ed", 0.5, '-'),
("kr", 0.6, "+"), ("g", 0.5, 'g'), ("n", 0.5, 'n'),
("qe", 0.5, 'q'), ("p", 0.5, 'p'), ("ts", 0.5, 't')]
for c in "acdefghiklmnpqrstvwy":
_clustalCategories.append((c, 0.85, c.upper()))
_clustalColorings = {
'G': [(_clustalOrange, None)],
'P': [(_clustalYellow, None)],
def _hlistKw(self, model, colNum):
vt = _valueTypes[self.columnMap[colNum]]
vf = _valueFuncs[self.columnMap[colNum]]
kw = {'itemtype': vt}
txt = None
img = None
if vt == 'text':
txt = vf(model)
if not isinstance(txt, basestring):
txt, bcolor = txt
if bcolor is not None:
if not isinstance(bcolor, basestring):
if hasattr(bcolor, 'rgba'):
rgba = bcolor.rgba()
else:
rgba = bcolor
from CGLtk.color import rgba2tk
bcolor = rgba2tk(rgba)
fcolor = CGLtk.textForeground(bcolor, self.modelTable)
kw['style'] = Tix.DisplayStyle("text",
refwindow=self.modelTable,
background=bcolor,
foreground=fcolor,
selectforeground=bcolor)
else:
kw['style'] = self.textStyle
elif vt == 'image':
img = vf(model)
elif vt == 'imagetext':
img, txt = vf(model)
elif vt == 'toggle':
kw['itemtype'] = 'window'
bool, cb = vf(model)
togKw = {
'command':
# avoid holding references to model
lambda cb=cb, i=self.models.index(model), b=not bool: cb(
self.models[i], b),
'indicatoron':
0,
'borderwidth':
0
}
if bool:
togKw['image'] = self.modelTable.tk.call(
'tix', 'getimage', 'ck_on')
else:
togKw['image'] = self.modelTable.tk.call(
'tix', 'getimage', 'ck_off')
toggle = Tkinter.Checkbutton(self.modelTable.hlist, **togKw)
kw['window'] = toggle
kw['style'] = self.checkButtonStyle
elif vt == 'well':
color, noneOkay, alphaOkay, cb = vf(model)
if color is False:
kw['itemtype'] = 'text'
txt = ""
else:
kw['itemtype'] = 'window'
if isinstance(color, chimera.MaterialColor):
color = color.rgba()
def wellCB(clr, cb=cb, mdl=model):
if clr is not None:
clr = chimera.MaterialColor(*clr)
cb(mdl, clr)
from CGLtk.color.ColorWell import ColorWell
kw['window'] = ColorWell(self.modelTable.hlist,
color,
callback=wellCB,
width=18,
height=18,
noneOkay=noneOkay,
wantAlpha=alphaOkay)
kw['style'] = self.colorWellStyle
else:
raise ValueError("Unknown column type: '%s'" % vt)
if txt != None:
kw['text'] = str(txt)
if img != None:
kw['image'] = self.modelTable.tk.call('tix', 'getimage', img)
return kw
def clustalInfo(fileName=None):
if fileName is None:
return _clustalCategories, _clustalColorings
from prefs import RC_HYDROPHOBICITY
if fileName == RC_HYDROPHOBICITY:
import os.path
fileName = os.path.join(os.path.dirname(__file__),
"kdHydrophob.par")
colorInfo = {}
for colorName in [ "RED", "BLUE", "GREEN", "CYAN",
"PINK", "MAGENTA", "YELLOW", "ORANGE"]:
colorInfo[colorName] = eval("_clustal%s"
% colorName.capitalize())
from OpenSave import osOpen
from chimera import UserError
f = osOpen(fileName)
section = None
colorSeen = False
categories = []
colorings = {}
for line in f:
line = line.strip()
if line.startswith("@"):
section = line[1:].lower()
continue
if not line:
continue
if section == "rgbindex":
try:
name, sr, sg, sb = line.split()
except ValueError:
raise UserError("Line in @rgbindex section of"
" %s is not color name followed by"
" red, green and blue values: '%s'"
% (fileName, line))
try:
r, g, b = [float(x) for x in [sr, sg, sb]]
except ValueError:
raise UserError("Line in @rgbindex section of"
" %s has non-floating-point"
" red, green or blue value: '%s'"
% (fileName, line))
if r>1 or g>1 or b>1 or r<0 or g<0 or b<0:
raise UserError("Line in @rgbindex section of"
" %s has red, green or blue value"
" not in the range 0-1: '%s'"
% (fileName, line))
colorInfo[name] = rgba2tk((r, g, b))
elif section == "consensus":
try:
symbol, eq, percent, composition = line.split()
except ValueError:
raise UserError("Line in @consensus section of"
" %s is not of the form 'symbol = "
" percentage%% res-list: '%s'"
% (fileName, line))
if eq != '=':
raise UserError("Line in @consensus section of"
" %s doesn't have '=' as second"
" component: '%s'" % (fileName, line))
if percent[-1] != '%':
raise UserError("Line in @consensus section of"
" %s doesn't have '%' as last character"
" of third component: '%s'"
% (fileName, line))
try:
percentage = float(percent[:-1])
except ValueError:
raise UserError("Line in @consensus section of"
" %s doesn't have a number before the"
" '%' of third component: '%s'"
% (fileName, line))
if percentage < 0 or percentage > 100:
raise UserError("Line in @consensus section of"
" %s has a percentage not in the range"
" 0-100: '%s'" % (fileName, line))
composition = composition.replace(":", "")
categories.append((composition, percentage/100.0,
symbol))
elif section == "color":
colorSeen = True
fields = line.split()
if len(fields) not in [3,5]:
raise UserError("Line in @color section of"
" %s not of the form AA = color"
" [if consensus-list]: '%s'"
% (fileName, line))
aa, eq, color = fields[:3]
if len(aa) > 1 or not aa.islower():
raise UserError("Line in @color section of"
" %s uses amino-acid code that is not"
" a single lowercase character: '%s'"
% (fileName, line))
if eq != '=':
raise UserError("Line in @color section of"
" %s doesn't have '=' as second"
" component: '%s'" % (fileName, line))
if color not in colorInfo:
raise UserError("Line in @color section of"
" %s uses an unknown color:"
" '%s'" % (fileName, line))
if len(fields) == 3:
colorings.setdefault(aa.upper(), []).append(
(colorInfo[color], None))
continue
if fields[3] != 'if':
raise UserError("Line in @color section of"
" %s doesn't have 'if' as fourth"
" component: '%s'" % (fileName, line))
colorings.setdefault(aa.upper(), []).append(
(colorInfo[color], fields[-1].replace(":", "")))
f.close()
if not colorSeen:
raise UserError("'%s' has missing or empty @color section"
% fileName)
return categories, colorings
def writeDemo(self, save_path, tempMode=False):
from CGLtk.color import rgba2tk
from multiloader2 import Multiloader
m = Multiloader()
## GLOBAL options
demo = XMLDemo()
title = self.gTitleOption.get()
if title:
demo.title = title
else:
demo.title = "Chimera Demo"
autodelay = self.gAutoDelayOption.get()
if autodelay:
demo.autodelay = autodelay
image = self.gImageOption.get()
if image:
demo.image = image
datadir = self.gDataDirOption.get()
if datadir:
demo.datadir = datadir
else:
if tempMode and self.save_path:
demo.datadir = os.path.split(self.save_path)[0]
bg_color = self.gBgColorOption.get()
if bg_color:
demo.bg_color = rgba2tk(bg_color.rgba())
autorun_on = self.gAutoRunOption.get()
if autorun_on:
demo.autorun_on = autorun_on
demo.description = ''
panel_list = []
panel_id = 0
##PANEL information
for p in self.panels:
panel_id += 1
panel = XMLPanel()
panel.id = panel_id
delay = p.getDelayVar().get()
if delay:
panel.autodelay = delay
title = p.getNameVar().get()
if title:
if not title[0:9] == "<untitled":
panel.title = title
if p == self.getCurrentPanel():
panel.text = self.getCurrentText()
else:
panel.text = p.getText().strip()
panel.command = []
for var, entry in p.getCmds():
xmlc = XMLCommand()
xmlc.active = ["False", "True"][var]
xmlc.item = entry
panel.command.append(xmlc)
panel.undo = []
for var, entry in p.getUndos():
xmlu = XMLUndo()
xmlu.active = ["False", "True"][var]
xmlu.item = entry
panel.undo.append(xmlu)
panel_list.append(panel)
demo.panels = panel_list
m.save(save_path, {'Demo': [demo]})
