def body(self, guiParent):
self.geometry('900x750')
# Ensure that the first row and column in popup expand
guiParent.expandGrid(0,0)
self.eciFrame = EntryCompletionFrame(guiParent, basePopup=self, grid=(0,0))
# Add help, close buttons
#buttonList = UtilityButtonList(self.eciFrame.tabbedFrame.sideFrame,
# grid=(0,0), sticky='e')
# Dictionary to store popups opened by this application - e.g. need to close upon quit
self.popups = {}
# Default font
self.font = 'Helvetica 10'
# Closing the window from the desktop environment calls the proper quit
self.protocol('WM_DELETE_WINDOW', self.quit)
self.mainMenu = Menu(self)
self.projectMenu = self.makeProjectMenu()
self.ccpNmrMenu = self.makeCcpNmrMenu()
self.otherMenu = self.makeOtherMenu()
# Put the main menu
self.config(menu=self.mainMenu)
self.initProject()
def body(self, guiParent):
# Ensure that the first row and column in popup expand
guiParent.grid_rowconfigure(0, weight=1)
guiParent.grid_columnconfigure(0, weight=1, minsize=200)
frame = Frame(guiParent) # Body widgets can be put in this frame
frame.grid()
buttons = createDismissHelpButtonList(frame,
dismiss_text='Quit',
dismiss_cmd=self.quit,
help_url=self.help_url,
expands=1)
buttons.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.helpButton = buttons.buttons[-1]
self.helpButtonCommand = self.helpButton.buttonCommand # the command with no project
# Dictionary to store popups opened by this application - e.g. need to close upon quit
self.popups = {}
# Default font
self.font = 'Helvetica 10'
# Closing the window from the desktop environment calls the proper quit
self.protocol('WM_DELETE_WINDOW', self.quit)
self.mainMenu = Menu(self)
self.projectMenu = self.makeProjectMenu()
self.otherMenu = self.makeOtherMenu()
# Put the main menu
self.config(menu=self.mainMenu)
self.initProject()
def __init__(self, parent, resizeCallback = None, width=600, height=600, *args, **kw):
self.bbox = None
self.busy = 0
self.initialX = None
self.initialY = None
self.resizeCallback = resizeCallback
apply(Frame.__init__, (self, parent) + args, kw)
self.grid_rowconfigure(0, weight=1)
self.grid_columnconfigure(0, weight=1)
self.menu = Menu(self, tearoff=0, include_event=True)
self.configMenu()
self.canvas = Canvas(self, relief='flat', borderwidth=0, width=width, height=height)
self.canvas.configure(xscrollincrement=2, yscrollincrement=2)
self.canvas.grid(row = 0, column = 0, sticky = Tkinter.NSEW )
self.horizScrollbar = Tkinter.Scrollbar(self, bg=self.cget('bg'), command=self.canvas.xview, orient=Tkinter.HORIZONTAL, borderwidth=1)
self.vertScrollbar = Tkinter.Scrollbar(self, bg=self.cget('bg'), command=self.canvas.yview, orient=Tkinter.VERTICAL, borderwidth=1)
self.canvas.configure(xscrollcommand=self.horizScrollbar.set,yscrollcommand=self.vertScrollbar.set)
self.canvas.bind('<Configure>', self.resizeAfter)
self.canvas.bind('<Button-1>', self.mouseButton1)
self.canvas.bind('<Button-2>', self.mouseButton2)
self.canvas.bind('<Button-3>', self.mouseButton3)
self.canvas.bind('<ButtonRelease-1>', self.mouseButtonRelease1)
self.canvas.bind('<ButtonRelease-2>', self.mouseButtonRelease2)
self.canvas.bind('<B2-Motion>', self.mouseScroll)
self.canvas.bind('<B3-Motion>', self.doNothing)
self.canvas.bind('<Motion>', self.mouseEnter)
self.canvas.bind('<Enter>', self.mouseEnter)
def body(self, guiParent):
# Ensure that the first row and column in popup expand
guiParent.grid_rowconfigure(1, weight=1)
guiParent.grid_columnconfigure(0, weight=1, minsize=200)
frame = Frame(guiParent) # Body widgets can be put in this frame
frame.grid(row=1, column=0, sticky='nsew')
frame.grid_rowconfigure(0, weight=1)
frame.grid_columnconfigure(0, weight=1, minsize=200)
self.dangleFrame = DangleFrame(frame, self, project=self.project)
self.dangleFrame.grid(row=0, column=0, sticky='nsew')
# Dictionary to store popups opened by this application - e.g. need to close upon quit
self.popups = {}
# Default font
self.font = 'Helvetica 10'
# Closing the window from the desktop environment calls the proper quit
self.protocol('WM_DELETE_WINDOW', self.quit)
self.mainMenu = Menu(self)
self.projectMenu = self.makeProjectMenu()
self.viewMenu = self.viewFileMenu()
self.otherMenu = self.makeAppearanceMenu()
# Put the main menu
self.config(menu=self.mainMenu)
self.initProject()
def __init__(self, parent, setFunc, sizes=(8,10,12,14), doBold=1, doItalic=1, doBoldItalic=0, *args, **kw):
Menu.__init__(self, parent, *args, **kw)
subMenus = {}
for fontName in fontNames:
subMenus[fontName] = Menu(self, tearoff=0)
for s in sizes:
spec = '%s %d' % (fontName,s)
subMenus[fontName].add_command(label='%dpt' % s, font=spec, command=lambda s=spec: setFunc(s) )
if doBold:
for s in sizes:
spec = '%s %d bold' % (fontName,s)
subMenus[fontName].add_command(label='%dpt bold' % s, font=spec, command=lambda s=spec: setFunc(s) )
if doItalic:
for s in sizes:
spec = '%s %d italic' % (fontName,s)
subMenus[fontName].add_command(label='%dpt italic' % s, font=spec, command=lambda s=spec: setFunc(s) )
if doBoldItalic:
for s in sizes:
spec = '%s %d bold italic' % (fontName,s)
subMenus[fontName].add_command(label='%dpt bold italic' % s, font=spec, command=lambda s=spec: setFunc(s) )
self.add_cascade(label=fontName, shortcut=fontName[0], menu=subMenus[fontName])
def body(self, guiParent):
self.geometry('600x350')
# Ensure that the first row and column in popup expand
guiParent.expandGrid(0, 0)
self.importFrame = DataFileImportFrame(guiParent,
basePopup=self,
grid=(0, 0))
# Dictionary to store popups opened by this application - e.g. need to close upon quit
self.popups = {}
# Default font
self.font = DEFAULT_FONT
# Closing the window from the desktop environment calls the proper quit
self.protocol('WM_DELETE_WINDOW', self.quit)
self.mainMenu = Menu(self)
self.projectMenu = self.makeProjectMenu()
self.mainMenu.add_command(label='Formats',
shortcut='F',
command=self.importFrame.showFormats)
self.mainMenu.add_command(
label='Help',
shortcut='H',
command=self.importFrame.showMainInstructions)
# Put the main menu
self.config(menu=self.mainMenu)
self.setMenuState()
def viewFileMenu(self):
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
# Add various options to the menu and state the functions they call
menu.add_command(label='Prediction Graph', shortcut='G', command=self.viewGraph,
tipText='Show a graphical view of the poredicted backbone dihedral angles')
self.mainMenu.add_cascade(label='View', shortcut='V', menu=menu)
menu.options = ['Prediction Graph']
return menu
def makeOtherMenu(self):
# The fonts menu is a pre-created widget
fontsMenu = FontMenu(self.mainMenu, self.setFont, sizes=(8,10,12),
doItalic=0, doBoldItalic=0, tearoff=0)
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
# Only Fonts option so far
menu.add_cascade(label='Fonts', shortcut='F', menu=fontsMenu)
self.mainMenu.add_cascade(label='Options', shortcut='O', menu=menu)
menu.options = ['Fonts',]
return menu
def __init__(self, parent, callback=None, texts=None, objects=None,
categories=None, colors=None, index=0, prefix='', indent='',
initCallback=False, forceCallback=False, numbering=False,
arrowLine='#602000', arrowFill='#B05848', labelColor='#501000',
menuBg='#F0F0FF', sticky='w', docKey=None, tipText=None,
categoriesLast=True, *args, **kw):
Frame.__init__(self, parent, sticky=sticky, docKey=docKey, tipText=tipText, createToolTip=True, *args, **kw)
self.callback = callback
self.texts = texts or []
self.objects = objects or []
self.categories = categories or []
self.colors = colors or []
self.prefix = prefix
self.indent = indent
self.initCallback = initCallback
self.numbering = numbering
self.arrowLine = arrowLine
self.arrowFill = arrowFill
self.labelColor = labelColor
self.active = True
self.categoriesLast = categoriesLast
# Current selection
self.index = None
self.object = NullText
self.rows = []
self.bg = self.cget('bg')
self.label = Label(self, foreground=labelColor)
self.canvas = Canvas(self, width=12, height=12, background=self.bg)
self.menu = Menu(self.canvas, tearoff=False, bg=menuBg, relief='solid',
borderwidth=1, activeborderwidth=1)
self.menu.images = [] # Photoimage has to remain referenced
self.setup(self.texts, self.objects, index,
self.colors, self.categories)
self.label.bind( "<Button-1>", self._labelClick)
self.menu.bind( "<Leave>", self._leave)
self.canvas.bind("<Button-1>", self._canvasClick)
self.canvas.bind("<Configure>", self._resizeCallback)
self.grid_columnconfigure(0, weight=1)
self.label.grid(row=0, column=0, sticky='w')
self.canvas.grid(row=0, column=1, sticky='w', padx=2)
def makeRepositoryMenu(self):
self.repMenu = Menu(self.mainMenu, tearoff=0)
# Add various options to the menu and state the functions they call
self.repMenu.add_command(label='Manager',
shortcut='M',
command=self.tmpCall)
self.repMenu.add_command(label='Connect',
shortcut='C',
command=self.openRepository)
# doesn't really work to have a disconnect; we do not have a list
# of repositories and so would it refer to? Better to do this from
# within the RepositoryFrame
self.repMenu.add_command(label='Disconnect',
shortcut='D',
command=self.tmpCall)
# again, this is functionality that would make sense but which it is hard to put
# in the top level menu because it is not obvious which repository it refers
# to
self.repMenu.add_command(label='Import Project',
shortcut='I',
command=self.tmpCall)
self.repMenu.add_command(label='Export Project',
shortcut='E',
command=self.tmpCall)
# FIXME JMCI
# the quit option needs to be tied to a dialogue box that asks whether
# the current connection state should be saved. This will have to be
# secured and so means that the GUI should have a login itself (beyond
# the logins for the various resources).
self.repMenu.add_command(label='Quit', shortcut='Q', command=self.quit)
self.mainMenu.add_cascade(label='Repository',
shortcut='R',
menu=self.repMenu)
self.repMenu.options = [
'Connect', 'Disconnect', 'Import Project', 'Export Project', 'Quit'
]
return self.repMenu
def makeProjectMenu(self):
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
# Add various options to the menu and state the functions they call
menu.add_command(label='New', shortcut='N', command=self.newProject,
tipText='Make a new, blank CCPN project. Closes any existing project')
menu.add_command(label='Open', shortcut='O', command=self.openProject,
tipText='Open a new CCPN project from disk, closing any existing project')
menu.add_command(label='Close', shortcut='C', command=self.closeProject,
tipText='Close the current CCPN project')
menu.add_command(label='Save', shortcut='S', command=self.saveProject,
tipText='Save the current CCPN prjoject at its pre-specified location')
menu.add_command(label='Save As', shortcut='A', command=self.saveAsProject,
tipText='Save the current CCPN project at a new location')
menu.add_command(label='Backup', shortcut='B', command=self.backupProject,
tipText='Manage options for automatic CCPN project backup')
menu.add_command(label='Quit', shortcut='Q', command=self.quit,
tipText='Exit from the DANGLE program')
menu.add_command(label='Version', shortcut='V', command=self.showVersion)
self.mainMenu.add_cascade(label='Project', shortcut='P', menu=menu)
menu.options = ['New','Open','Close','Save','Save As','Backup','Quit','Version']
return menu
class CingGui(BasePopup):
def __init__(self, parent, options, *args, **kw):
# Fill in below variable once run generates some results
self.haveResults = None
# store the options
self.options = options
BasePopup.__init__(self, parent=parent, title='CING Setup', **kw)
# self.setGeometry(850, 750, 50, 50)
self.project = None
# self.tk_strictMotif( True)
self.updateGui()
# end def __init__
def body(self, guiFrame):
row = 0
col = 0
# frame = Frame( guiFrame )
# frame.grid(row=row, column=col, sticky='news')
self.menuBar = Menu(guiFrame)
self.menuBar.grid(row=row, column=col, sticky='ew')
#----------------------------------------------------------------------------------
# Project frame
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(row, weight=1)
# frame = LabelFrame(guiFrame, text='Project', font=medFont)
row = +1
col = 0
frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes)
print '>', frame.keys()
frame.grid(row=row, column=col, sticky='nsew')
frame.grid_columnconfigure(2, weight=1)
# frame.grid_rowconfigure(0, weight=1)
srow = 0
self.projectOptions = [
'old', 'new from PDB', 'new from CCPN', 'new from CYANA'
]
self.projOptionsSelect = RadioButtons(frame,
selected_index=0,
entries=self.projectOptions,
direction='vertical',
select_callback=self.updateGui)
self.projOptionsSelect.grid(row=srow,
column=0,
rowspan=len(self.projectOptions),
columnspan=2,
sticky='w')
if self.options.name:
text = self.options.name
else:
text = ''
# end if
self.projEntry = Entry(frame,
bd=1,
text=text,
returnCallback=self.updateGui)
self.projEntry.grid(row=srow, column=2, columnspan=2, sticky='ew')
# self.projEntry.bind('<Key>', self.updateGui)
self.projEntry.bind('<Leave>', self.updateGui)
projButton = Button(frame,
bd=1,
command=self.chooseOldProjectFile,
text='browse')
projButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.pdbEntry = Entry(frame, bd=1, text='')
self.pdbEntry.grid(row=srow, column=2, sticky='ew')
self.pdbEntry.bind('<Leave>', self.updateGui)
pdbButton = Button(frame,
bd=1,
command=self.choosePdbFile,
text='browse')
pdbButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.ccpnEntry = Entry(frame, bd=1, text='')
self.ccpnEntry.grid(row=srow, column=2, sticky='ew')
self.ccpnEntry.bind('<Leave>', self.updateGui)
ccpnButton = Button(frame,
bd=1,
command=self.chooseCcpnFile,
text='browse')
ccpnButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.cyanaEntry = Entry(frame, bd=1, text='')
self.cyanaEntry.grid(row=srow, column=2, sticky='ew')
self.cyanaEntry.bind('<Leave>', self.updateGui)
cyanaButton = Button(frame,
bd=1,
command=self.chooseCyanaFile,
text='browse')
cyanaButton.grid(row=srow, column=3, sticky='ew')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
label = Label(frame, text='Project name:')
label.grid(row=srow, column=0, sticky='nw')
self.nameEntry = Entry(frame, bd=1, text='')
self.nameEntry.grid(row=srow, column=2, sticky='w')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
self.openProjectButton = Button(frame,
command=self.openProject,
text='Open Project',
**actionButtonAttributes)
self.openProjectButton.grid(row=srow,
column=0,
columnspan=4,
sticky='ew')
#----------------------------------------------------------------------------------
# status
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(1, weight=0)
srow = 0
frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes)
frame.grid(row=srow, column=1, sticky='wnes')
self.projectStatus = Text(frame,
height=11,
width=70,
borderwidth=0,
relief='flat')
self.projectStatus.grid(row=0, column=0, sticky='wen')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
self.closeProjectButton = Button(frame,
command=self.closeProject,
text='Close Project',
**actionButtonAttributes)
self.closeProjectButton.grid(row=srow,
column=0,
columnspan=4,
sticky='ew')
#----------------------------------------------------------------------------------
# Validate frame
#----------------------------------------------------------------------------------
row += 1
col = 0
frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes)
# frame = LabelFrame(guiFrame, text='Validate', font=medFont)
frame.grid(row=row, column=col, sticky='nsew')
# frame.grid_columnconfigure(2, weight=1)
frame.grid_rowconfigure(0, weight=1)
srow = 0
# label = Label(frame, text='validation')
# label.grid(row=srow,column=0,sticky='nw')
#
# self.selectDoValidation = CheckButton(frame)
# self.selectDoValidation.grid(row=srow, column=1,sticky='nw' )
# self.selectDoValidation.set(True)
#
# srow += 1
# label = Label(frame, text='')
# label.grid(row=srow,column=0,sticky='nw')
#
# srow += 1
label = Label(frame, text='checks')
label.grid(row=srow, column=0, sticky='nw')
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=1, sticky='nw')
self.selectCheckAssign.set(True)
label = Label(frame, text='assignments and shifts')
label.grid(row=srow, column=2, sticky='nw')
# srow += 1
# self.selectCheckQueen = CheckButton(frame)
# self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' )
# self.selectCheckQueen.set(False)
# label = Label(frame, text='QUEEN')
# label.grid(row=srow,column=5,sticky='nw')
#
# queenButton = Button(frame, bd=1,command=None, text='setup')
# queenButton.grid(row=srow,column=6,sticky='ew')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=1, sticky='nw')
self.selectCheckResraint.set(True)
label = Label(frame, text='restraints')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectCheckStructure = CheckButton(frame)
self.selectCheckStructure.grid(row=srow, column=1, sticky='nw')
self.selectCheckStructure.set(True)
label = Label(frame, text='structural')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectMakeHtml = CheckButton(frame)
self.selectMakeHtml.grid(row=srow, column=1, sticky='nw')
self.selectMakeHtml.set(True)
label = Label(frame, text='generate HTML')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=1, sticky='nw')
self.selectCheckScript.set(False)
label = Label(frame, text='user script')
label.grid(row=srow, column=0, sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,
column=2,
columnspan=3,
sticky='ew')
scriptButton = Button(frame,
bd=1,
command=self.chooseValidScript,
text='browse')
scriptButton.grid(row=srow, column=5, sticky='ew')
srow += 1
label = Label(frame, text='ranges')
label.grid(row=srow, column=0, sticky='nw')
self.rangesEntry = Entry(frame, text='')
self.rangesEntry.grid(row=srow, column=2, columnspan=3, sticky='ew')
# self.validScriptEntry = Entry(frame, bd=1, text='')
# self.validScriptEntry.grid(row=srow,column=3,sticky='ew')
#
# scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
# scriptButton.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Run Validation', 'View Results', 'Setup QUEEN']
commands = [self.runCing, None, None]
buttonBar = ButtonList(frame,
texts=texts,
commands=commands,
expands=True)
buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.runButton = buttonBar.buttons[0]
self.viewResultButton = buttonBar.buttons[1]
self.queenButton = buttonBar.buttons[2]
#----------------------------------------------------------------------------------
# Miscellaneous frame
#----------------------------------------------------------------------------------
row += 0
col = 1
# frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont)
frame = LabelFrame(guiFrame,
text='Miscellaneous',
**labelFrameAttributes)
frame.grid(row=row, column=col, sticky='news')
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(4, weight=1, minsize=30)
frame.grid_rowconfigure(0, weight=1)
# Exports
srow = 0
label = Label(frame, text='export to')
label.grid(row=srow, column=0, sticky='nw')
self.selectExportXeasy = CheckButton(frame)
self.selectExportXeasy.grid(row=srow, column=1, sticky='nw')
self.selectExportXeasy.set(True)
label = Label(frame, text='Xeasy, Sparky, TALOS, ...')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportCcpn = CheckButton(frame)
self.selectExportCcpn.grid(row=srow, column=1, sticky='nw')
self.selectExportCcpn.set(True)
label = Label(frame, text='CCPN')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportQueen = CheckButton(frame)
self.selectExportQueen.grid(row=srow, column=1, sticky='nw')
self.selectExportQueen.set(True)
label = Label(frame, text='QUEEN')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportRefine = CheckButton(frame)
self.selectExportRefine.grid(row=srow, column=1, sticky='nw')
self.selectExportRefine.set(True)
label = Label(frame, text='refine')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
# User script
srow += 1
label = Label(frame, text='user script')
label.grid(row=srow, column=0, sticky='nw')
self.selectMiscScript = CheckButton(frame)
self.selectMiscScript.grid(row=srow, column=1, sticky='nw')
self.selectMiscScript.set(False)
self.miscScriptEntry = Entry(frame, bd=1, text='')
self.miscScriptEntry.grid(row=srow, column=3, sticky='ew')
script2Button = Button(frame,
bd=1,
command=self.chooseMiscScript,
text='browse')
script2Button.grid(row=srow, column=4, sticky='ew')
srow += 1
texts = ['Export', 'Run Script']
commands = [None, None]
buttonBar = ButtonList(frame,
texts=texts,
commands=commands,
expands=True)
buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.exportButton = buttonBar.buttons[0]
self.scriptButton = buttonBar.buttons[1]
#----------------------------------------------------------------------------------
# Textarea
#----------------------------------------------------------------------------------
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.outputTextBox = ScrolledText(guiFrame)
self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.redirectConsole()
#----------------------------------------------------------------------------------
# Buttons
#----------------------------------------------------------------------------------
row += 1
col = 0
texts = ['Quit', 'Help']
commands = [self.close, None]
self.buttonBar = ButtonList(guiFrame,
texts=texts,
commands=commands,
expands=True)
self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew')
# self.openProjectButton = self.buttonBar.buttons[0]
# self.closeProjectButton = self.buttonBar.buttons[1]
# self.runButton = self.buttonBar.buttons[0]
# self.viewResultButton = self.buttonBar.buttons[1]
for button in self.buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
# end def body
def getGuiOptions(self):
projectName = self.projEntry.get()
index = self.projOptionsSelect.getIndex()
if index > 0:
makeNewProject = True
projectImport = None
if index > 1:
i = index - 2
format = ['PDB', 'CCPN', 'CYANA'][i]
file = [self.pdbEntry, self.ccpnEntry,
self.cyanaEntry][i].get()
if not file:
showWarning('Failure', 'No %s file selected' % format)
return
# end if
projectImport = (format, file)
# end if
else:
# Chould also check that any old project file exists
makeNewProject = False
projectImport = None
# end if
doValidation = self.selectDoValidation.get()
checks = []
if doValidation:
if self.selectCheckAssign.get():
checks.append('assignments')
# end if
if self.selectCheckResraint.get():
checks.append('restraints')
# end if
if self.selectCheckStructure.get():
checks.append('structural')
# end if
if self.selectMakeHtml.get():
checks.append('HTML')
# end if
if self.selectCheckScript.get():
script = self.validScriptEntry.get()
if script:
checks.append(('script', script))
# end if
# end if
if self.selectCheckQueen.get():
checks.append('queen')
# end if
# end if
exports = []
if self.selectExportXeasy.get():
exports.append('Xeasy')
# end if
if self.selectExportCcpn.get():
exports.append('CCPN')
# end if
if self.selectExportQueen.get():
exports.append('QUEEN')
# end if
if self.selectExportRefine.get():
exports.append('refine')
# end if
miscScript = None
if self.selectMiscScript.get():
script = self.miscScriptEntry.get()
if script:
miscScript = script
# end if
# end if
return projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript
# end def getGuiOptions
def runCing(self):
options = self.getGuiOptions()
if options:
projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript = options
print 'Project name:', projectName
print 'Make new project?', makeNewProject
print 'Import source:', projectImport
print 'Do vailidation?', doValidation
print 'Validation checks:', ','.join(checks)
print 'Export to:', ','.join(exports)
print 'User script:', miscScript
# end if
# end def runCing
# else there was already an error message
def chooseOldProjectFile(self):
fileTypes = [FileType('CING', ['project.xml']), FileType('All', ['*'])]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='Select CING project file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
# dirName = popup.getDirectory()
if len(fileName) > 0:
# Put text into entry,name widgets
dummy, name = cing.Project.rootPath(fileName)
self.projEntry.configure(state='normal')
self.projEntry.set(fileName)
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
self.nameEntry.configure(state='disabled')
# choose the correct radiobutton
self.projOptionsSelect.setIndex(0)
self.updateGui()
# end if
#nd if
popup.destroy()
# end def chooseOldProjectFile
def choosePdbFile(self):
fileTypes = [FileType('PDB', ['*.pdb']), FileType('All', ['*'])]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='PDB file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
if len(fileName) > 0:
# Put text into entry widget
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
# Put text into name widget
_dir, name, dummy = nTpath(fileName)
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
# choose the correct radiobutton
self.projOptionsSelect.setIndex(1)
self.updateGui()
#end if
popup.destroy()
# end def choosePdbFile
def chooseCcpnFile(self):
fileTypes = [FileType('XML', ['*.xml']), FileType('All', ['*'])]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='CCPN project XML file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
if len(fileName) > 0:
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
self.projOptionsSelect.setIndex(1)
_dir, name, dummy = nTpath(fileName)
self.nameEntry.set(name)
#end if
self.ccpnEntry.set(fileName)
self.projOptionsSelect.setIndex(2)
popup.destroy()
# end def chooseCcpnFile
def chooseCyanaFile(self):
# Prepend default Cyana file extension below
fileTypes = [
FileType('All', ['*']),
]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='CYANA fproject file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
self.cyanaEntry.set(fileName)
self.projOptionsSelect.setIndex(3)
popup.destroy()
# end def chooseCyanaFile
def chooseValidScript(self):
# Prepend default Cyana file extension below
fileTypes = [
FileType('All', ['*']),
]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='Script file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
self.validScriptEntry.set(fileName)
popup.destroy()
# end def chooseValidScript
def chooseMiscScript(self):
# Prepend default Cyana file extension below
fileTypes = [
FileType('All', ['*']),
]
popup = FileSelectPopup(self,
file_types=fileTypes,
title='Script file',
dismiss_text='Cancel',
selected_file_must_exist=True)
fileName = popup.getFile()
self.miscScriptEntry.set(fileName)
popup.destroy()
# end def chooseMiscScript
def openProject(self):
projOption = self.projOptionsSelect.get()
if projOption == self.projectOptions[0]:
self.openOldProject()
elif projOption == self.projectOptions[1]:
self.initPdb()
# end if
if self.project:
self.project.gui = self
# end if
self.updateGui()
#end def
def openOldProject(self):
fName = self.projEntry.get()
if not os.path.exists(fName):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
if self.project:
self.closeProject()
# end if
self.project = cing.Project.open(name=fName,
status='old',
verbose=False)
#end def
def initPdb(self):
fName = self.pdbEntry.get()
if not os.path.exists(fName):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
self.project = cing.Project.open(self.nameEntry.get(), status='new')
self.project.initPDB(pdbFile=fName, convention='PDB')
#end def
def closeProject(self):
if self.project:
self.project.close()
# end if
self.project = None
self.updateGui()
#end def
def updateGui(self, event=None):
projOption = self.projOptionsSelect.get()
buttons = self.buttonBar.buttons
# Disable entries
for e in [
self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry,
self.nameEntry
]:
e.configure(state='disabled')
#end for
if projOption == self.projectOptions[0]:
# Enable entries
self.projEntry.configure(state='normal')
if (len(self.projEntry.get()) > 0):
self.openProjectButton.enable()
self.runButton.enable()
else:
self.openProjectButton.disable()
self.runButton.disable()
#end if
elif projOption == self.projectOptions[1]:
# Enable entries
self.pdbEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.pdbEntry.get()) > 0
and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[2]:
# Enable entries
self.ccpnEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.ccpnEntry.get()) > 0
and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[3]:
# Enable entries
self.cyanaEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.cyanaEntry.get()) > 0
and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
self.projectStatus.clear()
if not self.project:
self.projectStatus.setText('No open project')
self.closeProjectButton.setText('Close Project')
self.closeProjectButton.disable()
else:
self.projectStatus.setText(self.project.format())
self.closeProjectButton.enable()
self.closeProjectButton.setText(
sprintf('Close Project "%s"', self.project.name))
#end if
#end def
def redirectConsole(self):
#pipe = TextPipe(self.inputTextBox.text_area)
#sys.stdin = pipe
pipe = TextPipe(self.outputTextBox.text_area)
sys.stdout = pipe
nTmessage.stream = pipe
# end def redirectConsole
# sys.stderr = pipe
def resetConsole(self):
#sys.stdin = stdin
nTmessage.stream = stdout
sys.stdout = stdout
sys.stderr = stderr
# end def resetConsole
def open(self):
self.redirectConsole()
BasePopup.open(self)
# end def open
def close(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.close(self)
print 'close:', geometry
sys.exit(0) # remove later
# end def close
def destroy(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.destroy(self)
print 'destroy:', geometry
sys.exit(0) # remove later
def body(self, guiFrame):
row = 0
col =0
# frame = Frame( guiFrame )
# frame.grid(row=row, column=col, sticky='news')
self.menuBar = Menu( guiFrame)
self.menuBar.grid( row=row, column=col, sticky='ew')
#----------------------------------------------------------------------------------
# Project frame
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(row, weight=1)
# frame = LabelFrame(guiFrame, text='Project', font=medFont)
row = +1
col =0
frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes )
print '>', frame.keys()
frame.grid(row=row, column=col, sticky='nsew' )
frame.grid_columnconfigure(2, weight=1)
# frame.grid_rowconfigure(0, weight=1)
srow = 0
self.projectOptions = ['old','new from PDB','new from CCPN','new from CYANA']
self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical',
select_callback=self.updateGui
)
self.projOptionsSelect.grid(row=srow,column=0,rowspan=len(self.projectOptions),columnspan=2, sticky='w')
if self.options.name:
text = self.options.name
else:
text=''
# end if
self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui)
self.projEntry.grid(row=srow,column=2,columnspan=2,sticky='ew')
# self.projEntry.bind('<Key>', self.updateGui)
self.projEntry.bind('<Leave>', self.updateGui)
projButton = Button(frame, bd=1,command=self.chooseOldProjectFile, text='browse')
projButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.pdbEntry = Entry(frame, bd=1, text='')
self.pdbEntry.grid(row=srow,column=2,sticky='ew')
self.pdbEntry.bind('<Leave>', self.updateGui)
pdbButton = Button(frame, bd=1,command=self.choosePdbFile, text='browse')
pdbButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.ccpnEntry = Entry(frame, bd=1, text='')
self.ccpnEntry.grid(row=srow,column=2,sticky='ew')
self.ccpnEntry.bind('<Leave>', self.updateGui)
ccpnButton = Button(frame, bd=1,command=self.chooseCcpnFile, text='browse')
ccpnButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.cyanaEntry = Entry(frame, bd=1, text='')
self.cyanaEntry.grid(row=srow,column=2,sticky='ew')
self.cyanaEntry.bind('<Leave>', self.updateGui)
cyanaButton = Button(frame, bd=1,command=self.chooseCyanaFile, text='browse')
cyanaButton.grid(row=srow,column=3,sticky='ew')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
label = Label(frame, text='Project name:')
label.grid(row=srow,column=0,sticky='nw')
self.nameEntry = Entry(frame, bd=1, text='')
self.nameEntry.grid(row=srow,column=2,sticky='w')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes )
self.openProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew')
#----------------------------------------------------------------------------------
# status
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(1, weight=0)
srow = 0
frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes)
frame.grid( row=srow, column=1, sticky='wnes')
self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat')
self.projectStatus.grid(row=0, column=0, sticky='wen')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes)
self.closeProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew')
#----------------------------------------------------------------------------------
# Validate frame
#----------------------------------------------------------------------------------
row +=1
col=0
frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes)
# frame = LabelFrame(guiFrame, text='Validate', font=medFont)
frame.grid(row=row, column=col, sticky='nsew')
# frame.grid_columnconfigure(2, weight=1)
frame.grid_rowconfigure(0, weight=1)
srow = 0
# label = Label(frame, text='validation')
# label.grid(row=srow,column=0,sticky='nw')
#
# self.selectDoValidation = CheckButton(frame)
# self.selectDoValidation.grid(row=srow, column=1,sticky='nw' )
# self.selectDoValidation.set(True)
#
# srow += 1
# label = Label(frame, text='')
# label.grid(row=srow,column=0,sticky='nw')
#
# srow += 1
label = Label(frame, text='checks')
label.grid(row=srow,column=0,sticky='nw')
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=1,sticky='nw' )
self.selectCheckAssign.set(True)
label = Label(frame, text='assignments and shifts')
label.grid(row=srow,column=2,sticky='nw')
# srow += 1
# self.selectCheckQueen = CheckButton(frame)
# self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' )
# self.selectCheckQueen.set(False)
# label = Label(frame, text='QUEEN')
# label.grid(row=srow,column=5,sticky='nw')
#
# queenButton = Button(frame, bd=1,command=None, text='setup')
# queenButton.grid(row=srow,column=6,sticky='ew')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=1,sticky='nw' )
self.selectCheckResraint.set(True)
label = Label(frame, text='restraints')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectCheckStructure = CheckButton(frame)
self.selectCheckStructure.grid(row=srow, column=1,sticky='nw' )
self.selectCheckStructure.set(True)
label = Label(frame, text='structural')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectMakeHtml = CheckButton(frame)
self.selectMakeHtml.grid(row=srow, column=1,sticky='nw' )
self.selectMakeHtml.set(True)
label = Label(frame, text='generate HTML')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=1,sticky='nw' )
self.selectCheckScript.set(False)
label = Label(frame, text='user script')
label.grid(row=srow,column=0,sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,column=2,columnspan=3, sticky='ew')
scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
scriptButton.grid(row=srow,column=5,sticky='ew')
srow += 1
label = Label(frame, text='ranges')
label.grid(row=srow,column=0,sticky='nw')
self.rangesEntry = Entry( frame, text='' )
self.rangesEntry.grid( row=srow, column=2, columnspan=3, sticky='ew')
# self.validScriptEntry = Entry(frame, bd=1, text='')
# self.validScriptEntry.grid(row=srow,column=3,sticky='ew')
#
# scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
# scriptButton.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Run Validation','View Results','Setup QUEEN']
commands = [self.runCing, None, None]
buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True)
buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.runButton = buttonBar.buttons[0]
self.viewResultButton = buttonBar.buttons[1]
self.queenButton = buttonBar.buttons[2]
#----------------------------------------------------------------------------------
# Miscellaneous frame
#----------------------------------------------------------------------------------
row +=0
col=1
# frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont)
frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes)
frame.grid(row=row, column=col, sticky='news')
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(4, weight=1,minsize=30)
frame.grid_rowconfigure(0, weight=1)
# Exports
srow = 0
label = Label(frame, text='export to')
label.grid(row=srow,column=0,sticky='nw')
self.selectExportXeasy = CheckButton(frame)
self.selectExportXeasy.grid(row=srow, column=1,sticky='nw' )
self.selectExportXeasy.set(True)
label = Label(frame, text='Xeasy, Sparky, TALOS, ...')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportCcpn = CheckButton(frame)
self.selectExportCcpn.grid(row=srow, column=1,sticky='nw' )
self.selectExportCcpn.set(True)
label = Label(frame, text='CCPN')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportQueen = CheckButton(frame)
self.selectExportQueen.grid(row=srow, column=1,sticky='nw' )
self.selectExportQueen.set(True)
label = Label(frame, text='QUEEN')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportRefine = CheckButton(frame)
self.selectExportRefine.grid(row=srow, column=1,sticky='nw' )
self.selectExportRefine.set(True)
label = Label(frame, text='refine')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
# User script
srow += 1
label = Label(frame, text='user script')
label.grid(row=srow,column=0,sticky='nw')
self.selectMiscScript = CheckButton(frame)
self.selectMiscScript.grid(row=srow, column=1,sticky='nw' )
self.selectMiscScript.set(False)
self.miscScriptEntry = Entry(frame, bd=1, text='')
self.miscScriptEntry.grid(row=srow,column=3,sticky='ew')
script2Button = Button(frame, bd=1,command=self.chooseMiscScript, text='browse')
script2Button.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Export','Run Script']
commands = [None, None]
buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True)
buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.exportButton = buttonBar.buttons[0]
self.scriptButton = buttonBar.buttons[1]
#----------------------------------------------------------------------------------
# Textarea
#----------------------------------------------------------------------------------
row +=1
guiFrame.grid_rowconfigure(row, weight=1)
self.outputTextBox = ScrolledText(guiFrame)
self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.redirectConsole()
#----------------------------------------------------------------------------------
# Buttons
#----------------------------------------------------------------------------------
row +=1
col=0
texts = ['Quit', 'Help']
commands = [self.close, None]
self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands,expands=True)
self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew')
# self.openProjectButton = self.buttonBar.buttons[0]
# self.closeProjectButton = self.buttonBar.buttons[1]
# self.runButton = self.buttonBar.buttons[0]
# self.viewResultButton = self.buttonBar.buttons[1]
for button in self.buttonBar.buttons:
button.config(**actionButtonAttributes)
class CingGui(BasePopup):
def __init__(self, parent, options, *args, **kw):
# Fill in below variable once run generates some results
self.haveResults = None
# store the options
self.options = options
BasePopup.__init__(self, parent=parent, title='CING Setup', **kw)
# self.setGeometry(850, 750, 50, 50)
self.project = None
# self.tk_strictMotif( True)
self.updateGui()
# end def __init__
def body(self, guiFrame):
row = 0
col =0
# frame = Frame( guiFrame )
# frame.grid(row=row, column=col, sticky='news')
self.menuBar = Menu( guiFrame)
self.menuBar.grid( row=row, column=col, sticky='ew')
#----------------------------------------------------------------------------------
# Project frame
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(row, weight=1)
# frame = LabelFrame(guiFrame, text='Project', font=medFont)
row = +1
col =0
frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes )
print '>', frame.keys()
frame.grid(row=row, column=col, sticky='nsew' )
frame.grid_columnconfigure(2, weight=1)
# frame.grid_rowconfigure(0, weight=1)
srow = 0
self.projectOptions = ['old','new from PDB','new from CCPN','new from CYANA']
self.projOptionsSelect = RadioButtons(frame, selected_index=0, entries=self.projectOptions, direction='vertical',
select_callback=self.updateGui
)
self.projOptionsSelect.grid(row=srow,column=0,rowspan=len(self.projectOptions),columnspan=2, sticky='w')
if self.options.name:
text = self.options.name
else:
text=''
# end if
self.projEntry = Entry(frame, bd=1, text=text, returnCallback=self.updateGui)
self.projEntry.grid(row=srow,column=2,columnspan=2,sticky='ew')
# self.projEntry.bind('<Key>', self.updateGui)
self.projEntry.bind('<Leave>', self.updateGui)
projButton = Button(frame, bd=1,command=self.chooseOldProjectFile, text='browse')
projButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.pdbEntry = Entry(frame, bd=1, text='')
self.pdbEntry.grid(row=srow,column=2,sticky='ew')
self.pdbEntry.bind('<Leave>', self.updateGui)
pdbButton = Button(frame, bd=1,command=self.choosePdbFile, text='browse')
pdbButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.ccpnEntry = Entry(frame, bd=1, text='')
self.ccpnEntry.grid(row=srow,column=2,sticky='ew')
self.ccpnEntry.bind('<Leave>', self.updateGui)
ccpnButton = Button(frame, bd=1,command=self.chooseCcpnFile, text='browse')
ccpnButton.grid(row=srow,column=3,sticky='ew')
srow += 1
self.cyanaEntry = Entry(frame, bd=1, text='')
self.cyanaEntry.grid(row=srow,column=2,sticky='ew')
self.cyanaEntry.bind('<Leave>', self.updateGui)
cyanaButton = Button(frame, bd=1,command=self.chooseCyanaFile, text='browse')
cyanaButton.grid(row=srow,column=3,sticky='ew')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
label = Label(frame, text='Project name:')
label.grid(row=srow,column=0,sticky='nw')
self.nameEntry = Entry(frame, bd=1, text='')
self.nameEntry.grid(row=srow,column=2,sticky='w')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
self.openProjectButton = Button(frame, command=self.openProject, text='Open Project', **actionButtonAttributes )
self.openProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew')
#----------------------------------------------------------------------------------
# status
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(1, weight=0)
srow = 0
frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes)
frame.grid( row=srow, column=1, sticky='wnes')
self.projectStatus = Text(frame, height=11, width=70, borderwidth=0, relief='flat')
self.projectStatus.grid(row=0, column=0, sticky='wen')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
srow += 1
self.closeProjectButton = Button(frame, command=self.closeProject, text='Close Project', **actionButtonAttributes)
self.closeProjectButton.grid(row=srow,column=0, columnspan=4, sticky='ew')
#----------------------------------------------------------------------------------
# Validate frame
#----------------------------------------------------------------------------------
row +=1
col=0
frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes)
# frame = LabelFrame(guiFrame, text='Validate', font=medFont)
frame.grid(row=row, column=col, sticky='nsew')
# frame.grid_columnconfigure(2, weight=1)
frame.grid_rowconfigure(0, weight=1)
srow = 0
# label = Label(frame, text='validation')
# label.grid(row=srow,column=0,sticky='nw')
#
# self.selectDoValidation = CheckButton(frame)
# self.selectDoValidation.grid(row=srow, column=1,sticky='nw' )
# self.selectDoValidation.set(True)
#
# srow += 1
# label = Label(frame, text='')
# label.grid(row=srow,column=0,sticky='nw')
#
# srow += 1
label = Label(frame, text='checks')
label.grid(row=srow,column=0,sticky='nw')
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=1,sticky='nw' )
self.selectCheckAssign.set(True)
label = Label(frame, text='assignments and shifts')
label.grid(row=srow,column=2,sticky='nw')
# srow += 1
# self.selectCheckQueen = CheckButton(frame)
# self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' )
# self.selectCheckQueen.set(False)
# label = Label(frame, text='QUEEN')
# label.grid(row=srow,column=5,sticky='nw')
#
# queenButton = Button(frame, bd=1,command=None, text='setup')
# queenButton.grid(row=srow,column=6,sticky='ew')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=1,sticky='nw' )
self.selectCheckResraint.set(True)
label = Label(frame, text='restraints')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectCheckStructure = CheckButton(frame)
self.selectCheckStructure.grid(row=srow, column=1,sticky='nw' )
self.selectCheckStructure.set(True)
label = Label(frame, text='structural')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectMakeHtml = CheckButton(frame)
self.selectMakeHtml.grid(row=srow, column=1,sticky='nw' )
self.selectMakeHtml.set(True)
label = Label(frame, text='generate HTML')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=1,sticky='nw' )
self.selectCheckScript.set(False)
label = Label(frame, text='user script')
label.grid(row=srow,column=0,sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,column=2,columnspan=3, sticky='ew')
scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
scriptButton.grid(row=srow,column=5,sticky='ew')
srow += 1
label = Label(frame, text='ranges')
label.grid(row=srow,column=0,sticky='nw')
self.rangesEntry = Entry( frame, text='' )
self.rangesEntry.grid( row=srow, column=2, columnspan=3, sticky='ew')
# self.validScriptEntry = Entry(frame, bd=1, text='')
# self.validScriptEntry.grid(row=srow,column=3,sticky='ew')
#
# scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
# scriptButton.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Run Validation','View Results','Setup QUEEN']
commands = [self.runCing, None, None]
buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True)
buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.runButton = buttonBar.buttons[0]
self.viewResultButton = buttonBar.buttons[1]
self.queenButton = buttonBar.buttons[2]
#----------------------------------------------------------------------------------
# Miscellaneous frame
#----------------------------------------------------------------------------------
row +=0
col=1
# frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont)
frame = LabelFrame(guiFrame, text='Miscellaneous', **labelFrameAttributes)
frame.grid(row=row, column=col, sticky='news')
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(4, weight=1,minsize=30)
frame.grid_rowconfigure(0, weight=1)
# Exports
srow = 0
label = Label(frame, text='export to')
label.grid(row=srow,column=0,sticky='nw')
self.selectExportXeasy = CheckButton(frame)
self.selectExportXeasy.grid(row=srow, column=1,sticky='nw' )
self.selectExportXeasy.set(True)
label = Label(frame, text='Xeasy, Sparky, TALOS, ...')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportCcpn = CheckButton(frame)
self.selectExportCcpn.grid(row=srow, column=1,sticky='nw' )
self.selectExportCcpn.set(True)
label = Label(frame, text='CCPN')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportQueen = CheckButton(frame)
self.selectExportQueen.grid(row=srow, column=1,sticky='nw' )
self.selectExportQueen.set(True)
label = Label(frame, text='QUEEN')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
self.selectExportRefine = CheckButton(frame)
self.selectExportRefine.grid(row=srow, column=1,sticky='nw' )
self.selectExportRefine.set(True)
label = Label(frame, text='refine')
label.grid(row=srow,column=2,sticky='nw')
srow += 1
label = Label(frame, text='')
label.grid(row=srow,column=0,sticky='nw')
# User script
srow += 1
label = Label(frame, text='user script')
label.grid(row=srow,column=0,sticky='nw')
self.selectMiscScript = CheckButton(frame)
self.selectMiscScript.grid(row=srow, column=1,sticky='nw' )
self.selectMiscScript.set(False)
self.miscScriptEntry = Entry(frame, bd=1, text='')
self.miscScriptEntry.grid(row=srow,column=3,sticky='ew')
script2Button = Button(frame, bd=1,command=self.chooseMiscScript, text='browse')
script2Button.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Export','Run Script']
commands = [None, None]
buttonBar = ButtonList(frame, texts=texts, commands=commands,expands=True)
buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.exportButton = buttonBar.buttons[0]
self.scriptButton = buttonBar.buttons[1]
#----------------------------------------------------------------------------------
# Textarea
#----------------------------------------------------------------------------------
row +=1
guiFrame.grid_rowconfigure(row, weight=1)
self.outputTextBox = ScrolledText(guiFrame)
self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.redirectConsole()
#----------------------------------------------------------------------------------
# Buttons
#----------------------------------------------------------------------------------
row +=1
col=0
texts = ['Quit', 'Help']
commands = [self.close, None]
self.buttonBar = ButtonList(guiFrame, texts=texts, commands=commands,expands=True)
self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew')
# self.openProjectButton = self.buttonBar.buttons[0]
# self.closeProjectButton = self.buttonBar.buttons[1]
# self.runButton = self.buttonBar.buttons[0]
# self.viewResultButton = self.buttonBar.buttons[1]
for button in self.buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
# end def body
def getGuiOptions(self):
projectName = self.projEntry.get()
index = self.projOptionsSelect.getIndex()
if index > 0:
makeNewProject = True
projectImport = None
if index > 1:
i = index-2
format = ['PDB','CCPN','CYANA'][i]
file = [self.pdbEntry, self.ccpnEntry, self.cyanaEntry][i].get()
if not file:
showWarning('Failure','No %s file selected' % format)
return
# end if
projectImport = (format, file)
# end if
else:
# Chould also check that any old project file exists
makeNewProject = False
projectImport = None
# end if
doValidation = self.selectDoValidation.get()
checks = []
if doValidation:
if self.selectCheckAssign.get():
checks.append('assignments')
# end if
if self.selectCheckResraint.get():
checks.append('restraints')
# end if
if self.selectCheckStructure.get():
checks.append('structural')
# end if
if self.selectMakeHtml.get():
checks.append('HTML')
# end if
if self.selectCheckScript.get():
script = self.validScriptEntry.get()
if script:
checks.append( ('script',script) )
# end if
# end if
if self.selectCheckQueen.get():
checks.append('queen')
# end if
# end if
exports = []
if self.selectExportXeasy.get():
exports.append('Xeasy')
# end if
if self.selectExportCcpn.get():
exports.append('CCPN')
# end if
if self.selectExportQueen.get():
exports.append('QUEEN')
# end if
if self.selectExportRefine.get():
exports.append('refine')
# end if
miscScript = None
if self.selectMiscScript.get():
script = self.miscScriptEntry.get()
if script:
miscScript = script
# end if
# end if
return projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript
# end def getGuiOptions
def runCing(self):
options = self.getGuiOptions()
if options:
projectName, makeNewProject, projectImport, doValidation, checks, exports, miscScript = options
print 'Project name:', projectName
print 'Make new project?', makeNewProject
print 'Import source:', projectImport
print 'Do vailidation?', doValidation
print 'Validation checks:', ','.join(checks)
print 'Export to:', ','.join(exports)
print 'User script:', miscScript
# end if
# end def runCing
# else there was already an error message
def chooseOldProjectFile(self):
fileTypes = [ FileType('CING', ['project.xml']),
FileType('All', ['*'])
]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'Select CING project file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
# dirName = popup.getDirectory()
if len(fileName) > 0:
# Put text into entry,name widgets
dummy,name = cing.Project.rootPath(fileName)
self.projEntry.configure(state='normal')
self.projEntry.set(fileName)
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
self.nameEntry.configure(state='disabled')
# choose the correct radiobutton
self.projOptionsSelect.setIndex(0)
self.updateGui()
# end if
#nd if
popup.destroy()
# end def chooseOldProjectFile
def choosePdbFile(self):
fileTypes = [ FileType('PDB', ['*.pdb']), FileType('All', ['*'])]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'PDB file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
if len(fileName)>0:
# Put text into entry widget
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
# Put text into name widget
_dir,name,dummy = nTpath( fileName )
self.nameEntry.configure(state='normal')
self.nameEntry.set(name)
# choose the correct radiobutton
self.projOptionsSelect.setIndex(1)
self.updateGui()
#end if
popup.destroy()
# end def choosePdbFile
def chooseCcpnFile(self):
fileTypes = [ FileType('XML', ['*.xml']), FileType('All', ['*'])]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'CCPN project XML file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
if len(fileName)>0:
self.pdbEntry.configure(state='normal')
self.pdbEntry.set(fileName)
self.projOptionsSelect.setIndex(1)
_dir,name,dummy = nTpath( fileName )
self.nameEntry.set(name)
#end if
self.ccpnEntry.set(fileName)
self.projOptionsSelect.setIndex(2)
popup.destroy()
# end def chooseCcpnFile
def chooseCyanaFile(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('All', ['*']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'CYANA fproject file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.cyanaEntry.set(fileName)
self.projOptionsSelect.setIndex(3)
popup.destroy()
# end def chooseCyanaFile
def chooseValidScript(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('All', ['*']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'Script file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.validScriptEntry.set(fileName)
popup.destroy()
# end def chooseValidScript
def chooseMiscScript(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('All', ['*']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title = 'Script file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.miscScriptEntry.set(fileName)
popup.destroy()
# end def chooseMiscScript
def openProject(self ):
projOption = self.projOptionsSelect.get()
if projOption == self.projectOptions[0]:
self.openOldProject()
elif projOption == self.projectOptions[1]:
self.initPdb()
# end if
if self.project:
self.project.gui = self
# end if
self.updateGui()
#end def
def openOldProject(self ):
fName = self.projEntry.get()
if not os.path.exists( fName ):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
if self.project:
self.closeProject()
# end if
self.project = cing.Project.open( name=fName, status='old', verbose=False )
#end def
def initPdb(self ):
fName = self.pdbEntry.get()
if not os.path.exists( fName ):
nTerror('Error: file "%s" does not exist\n', fName)
#end if
self.project = cing.Project.open( self.nameEntry.get(), status='new' )
self.project.initPDB( pdbFile=fName, convention = 'PDB' )
#end def
def closeProject(self):
if self.project:
self.project.close()
# end if
self.project = None
self.updateGui()
#end def
def updateGui(self, event=None):
projOption = self.projOptionsSelect.get()
buttons = self.buttonBar.buttons
# Disable entries
for e in [self.projEntry, self.pdbEntry, self.ccpnEntry, self.cyanaEntry, self.nameEntry]:
e.configure(state='disabled')
#end for
if projOption == self.projectOptions[0]:
# Enable entries
self.projEntry.configure(state='normal')
if (len(self.projEntry.get()) > 0):
self.openProjectButton.enable()
self.runButton.enable()
else:
self.openProjectButton.disable()
self.runButton.disable()
#end if
elif projOption == self.projectOptions[1]:
# Enable entries
self.pdbEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.pdbEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[2]:
# Enable entries
self.ccpnEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.ccpnEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
elif projOption == self.projectOptions[3]:
# Enable entries
self.cyanaEntry.configure(state='normal')
self.nameEntry.configure(state='normal')
if (len(self.cyanaEntry.get()) > 0 and len(self.nameEntry.get()) > 0):
buttons[0].enable()
buttons[1].enable()
else:
buttons[0].disable()
buttons[1].disable()
#end if
#end if
self.projectStatus.clear()
if not self.project:
self.projectStatus.setText('No open project')
self.closeProjectButton.setText('Close Project')
self.closeProjectButton.disable()
else:
self.projectStatus.setText(self.project.format())
self.closeProjectButton.enable()
self.closeProjectButton.setText(sprintf('Close Project "%s"', self.project.name))
#end if
#end def
def redirectConsole(self):
#pipe = TextPipe(self.inputTextBox.text_area)
#sys.stdin = pipe
pipe = TextPipe(self.outputTextBox.text_area)
sys.stdout = pipe
nTmessage.stream = pipe
# end def redirectConsole
# sys.stderr = pipe
def resetConsole(self):
#sys.stdin = stdin
nTmessage.stream = stdout
sys.stdout = stdout
sys.stderr = stderr
# end def resetConsole
def open(self):
self.redirectConsole()
BasePopup.open(self)
# end def open
def close(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.close(self)
print 'close:',geometry
sys.exit(0) # remove later
# end def close
def destroy(self):
geometry = self.getGeometry()
self.resetConsole()
BasePopup.destroy(self)
print 'destroy:',geometry
sys.exit(0) # remove later
def makeCcpNmrMenu(self):
try:
from ccpnmr.analysis.AnalysisPopup import AnalysisPopup
haveAnalysis = True
except ImportError:
haveAnalysis = False
try:
from ccpnmr.format.gui.FormatConverter import FormatConverter
from ccpnmr.format.gui.DataShifter import DataShifter
haveFormatConv = True
except ImportError:
haveFormatConv = False
menu = Menu(self.mainMenu, tearoff=0)
if haveAnalysis:
menu.add_command(label='Analysis',
shortcut='A',
command=self.ccpNmrAnalysis)
else:
menu.add_command(label='Analysis ** NOT INSTALLED **',
shortcut='A',
command=None)
if haveFormatConv:
menu.add_command(label='Format Converter',
shortcut='F',
command=self.ccpNmrFormatConverter)
menu.add_command(label='Data Shifter',
shortcut='D',
command=self.ccpNmrDataShifter)
else:
menu.add_command(label='Format Converter ** NOT INSTALLED **',
shortcut='F',
command=None)
menu.add_command(label='Data Shifter ** NOT INSTALLED **',
shortcut='D',
command=None)
self.mainMenu.add_cascade(label='CcpNmr', shortcut='C', menu=menu)
menu.options = ['Analysis', 'Format Converter', 'Data Shifter']
return menu
class EntryCompletionGui(BasePopup):
'''
The standalone version of CcpNmr Entry Completion Interface (ECI). With it, you can complete all the necessary information required for PDB and BMRB data depositions by adding an "Entry" object to your CCPN project. An "Entry" object contains all the information that you wish to deposit with your submission. You can also select chemical shift lists, peak lists, structural restraints, ensembles, etc. and all at the click of a button. In addition, you can add all the meta data that is required for submissions to the PDB and BMRB. This can be done securely on your desktop computer over the duration of your NMR project.
'''
help_url = 'http://www.ccpn.ac.uk'
def __init__(self, root):
self.root = root
self.font = DEFAULT_FONT
# Application object needed to store application-specific data with project
self.application = Application(name=PROGRAM_NAME)
self.versionInfo = VERSION
# Application popup is a superclass of memops.editor.BasePoup
BasePopup.__init__(self, parent=root, title=PROGRAM_NAME,
location='+100+100', class_=self.application.name)
#self.setTitle(PROGRAM_NAME)
def body(self, guiParent):
self.geometry('900x750')
# Ensure that the first row and column in popup expand
guiParent.expandGrid(0,0)
self.eciFrame = EntryCompletionFrame(guiParent, basePopup=self, grid=(0,0))
# Add help, close buttons
#buttonList = UtilityButtonList(self.eciFrame.tabbedFrame.sideFrame,
# grid=(0,0), sticky='e')
# Dictionary to store popups opened by this application - e.g. need to close upon quit
self.popups = {}
# Default font
self.font = 'Helvetica 10'
# Closing the window from the desktop environment calls the proper quit
self.protocol('WM_DELETE_WINDOW', self.quit)
self.mainMenu = Menu(self)
self.projectMenu = self.makeProjectMenu()
self.ccpNmrMenu = self.makeCcpNmrMenu()
self.otherMenu = self.makeOtherMenu()
# Put the main menu
self.config(menu=self.mainMenu)
self.initProject()
def makeProjectMenu(self):
importsMenu = Menu(self.mainMenu, tearoff=False)
importsMenu.add_command(label='Fasta Sequence',command=self.importFastaSeq)
importsMenu.add_command(label='NMR-STAR 2.1.1', command=self.importNmrStar211)
importsMenu.add_command(label='NMR-STAR 3.1', command=self.importNmrStar31)
importsMenu.add_command(label='PDB 3.20',command=self.importPdb)
importsMenu.add_command(label='PDB Coords',command=self.importPdbCoords)
#importsMenu.add_command(label='CNS Distance Restraints',command=self.importCnsDistance)
exportsMenu = Menu(self.mainMenu, tearoff=False)
exportsMenu.add_command(label='NMR-STAR 3.1', command=self.eciFrame.exportNmrStar31)
exportsMenu.add_command(label='PDB Coords',command=self.eciFrame.exportPdb)
#exportsMenu.add_command(label='CNS Distance Restraints',command=self.eciFrame.exportCnsDistance)
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
# Add various options to the menu and state the functions they call
menu.add_command(label='New', shortcut='N', command=self.newProject)
menu.add_command(label='Open', shortcut='O', command=self.openProject)
menu.add_command(label='Close', shortcut='C', command=self.closeProject)
menu.add_command(label='Save', shortcut='S', command=self.saveProject)
menu.add_command(label='Save As', shortcut='A', command=self.saveAsProject)
menu.add_cascade(label='Import', shortcut='I', menu=importsMenu)
menu.add_cascade(label='Export', shortcut='E', menu=exportsMenu)
menu.add_command(label='Quit', shortcut='Q', command=self.quit)
menu.add_command(label='Version', shortcut='V', command=self.showVersion)
self.mainMenu.add_cascade(label='Project', shortcut='P', menu=menu)
menu.options = ['New','Open','Close','Save','Save As','Import','Export','Quit','Version']
return menu
def makeOtherMenu(self):
# The fonts menu is a pre-created widget
fontsMenu = FontMenu(self.mainMenu, self.setFont, sizes=(8,10,12),
doItalic=0, doBoldItalic=0, tearoff=0)
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
# Only Fonts option so far
menu.add_cascade(label='Fonts', shortcut='F', menu=fontsMenu)
self.mainMenu.add_cascade(label='Options', shortcut='O', menu=menu)
menu.options = ['Fonts',]
return menu
def makeCcpNmrMenu(self):
try:
from ccpnmr.analysis.AnalysisPopup import AnalysisPopup
haveAnalysis = True
except ImportError:
haveAnalysis = False
try:
from ccpnmr.format.gui.FormatConverter import FormatConverter
from ccpnmr.format.gui.DataShifter import DataShifter
haveFormatConv = True
except ImportError:
haveFormatConv = False
menu = Menu(self.mainMenu, tearoff=0)
if haveAnalysis:
menu.add_command(label='Analysis', shortcut='A', command=self.ccpNmrAnalysis)
else:
menu.add_command(label='Analysis ** NOT INSTALLED **', shortcut='A', command=None)
if haveFormatConv:
menu.add_command(label='Format Converter', shortcut='F', command=self.ccpNmrFormatConverter)
menu.add_command(label='Data Shifter', shortcut='D', command=self.ccpNmrDataShifter)
else:
menu.add_command(label='Format Converter ** NOT INSTALLED **', shortcut='F', command=None)
menu.add_command(label='Data Shifter ** NOT INSTALLED **', shortcut='D', command=None)
self.mainMenu.add_cascade(label='CcpNmr', shortcut='C', menu=menu)
menu.options = ['Analysis','Format Converter','Data Shifter']
return menu
def ccpNmrAnalysis(self, cacheSize=64):
from ccpnmr.analysis.AnalysisPopup import AnalysisPopup
analysis = AnalysisPopup(self, cache_size=cacheSize, glDirect=None)
analysis.update_idletasks() # fast
if self.project:
analysis.initProject(self.project)
def ccpNmrFormatConverter(self):
from ccpnmr.format.gui.FormatConverter import FormatConverter
fc = FormatConverter(self,threading=False,project=self.project)
fc.open()
if self.project:
fc.initProject(self.project)
def ccpNmrDataShifter(self):
from ccpnmr.format.gui.DataShifter import DataShifter
ds = DataShifter(self)
ds.open()
def newProject(self):
if self.project:
# Project already present
if not self.closeProject():
# If we don't close the current project do nothing
return
name = askString(title='Project name', prompt='Enter project name:',parent=self)
if name:
# Make the API Project object
project = Implementation.MemopsRoot(name=name)
nmrProject = project.newNmrProject(name=name)
self.initProject(project)
def openProject(self):
if self.project:
if not self.closeProject():
return
self.openPopup('open_project', OpenProjectPopup,
callback=self.initProject)
def openPopup(self, popup_name, clazz, oldStyle=False, *args, **kw):
popup = self.popups.get(popup_name)
if (popup):
popup.open()
else:
if self.project:
analysisProfile = self.analysisProfile
else:
analysisProfile = None
if analysisProfile:
transient = analysisProfile.transientDialogs
else:
transient = True
name = popup_name
if (oldStyle):
popup = self.popups[popup_name] = clazz(self, transient=transient, *args, **kw)
else:
popup = self.popups[popup_name] = clazz(self, project=self.project, popup_name=name,
transient=transient, *args, **kw)
# above automatically opens popup
return popup
def closeProject(self, queryClose = True, querySave = True):
if queryClose:
if not showYesNo('Close project', 'Close current project?', parent=self):
return False
if querySave:
if not self.checkSaving():
return False
self.destroyPopups()
self.initProject()
return True
def saveProject(self):
self.saveFile()
def saveAsProject(self):
self.askSaveFile()
def importNmrStar211(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('STAR', ['*.str']),
FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import NMR-STAR 2.1.1 file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
nmrStarObj = NmrStarFormat(self.project, self, verbose=True)
nmrStarObj.readProject(fileName, minimalPrompts=True, version='2.1.1')
self.eciFrame.updateAll()
return nmrStarObj
def importNmrStar31(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('STAR', ['*.str']),
FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import NMR-STAR 3.1 file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
nmrStarObj = NmrStarFormat(self.project, self, verbose=True)
nmrStarObj.readProject(fileName, minimalPrompts=True, version='3.1')
self.eciFrame.updateAll()
return nmrStarObj
def importPdb(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('PDB', ['*.pdb']),
FileType('PDB Entry', ['*.ent']),
FileType('All', ['*']) ]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import PDB 3.20 file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
name = os.path.split(fileName)[1]
if '.' in name:
name = name.split('.')[0]
pdbObj = ReadPdb(fileName, self.project, 'PDB_'+ name, self)
self.eciFrame.updateAll()
return pdbObj
def importCnsDistance(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('CNS', ['*.tbl']),
FileType('All', ['*']) ]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import CNS distance restraints file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
name = os.path.split(fileName)[1]
if '.' in name:
name = name.split('.')[0]
cnsObj = CnsFormat(self.project, self, verbose=True)
cnsObj.readDistanceConstraints(fileName, minimalPrompts=True)
self.eciFrame.updateAll()
return cnsObj
def importFastaSeq(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('Fasta', ['*.fsa']),
FileType('All', ['*']) ]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import Fasta sequence file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
name = os.path.split(fileName)[1]
if '.' in name:
name = name.split('.')[0]
fastaObj = FastaFormat(self.project, self, verbose=True)
fastaObj.readSequence(fileName, minimalPrompts=True)
self.eciFrame.updateAll()
return fastaObj
def importPdbCoords(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('PDB', ['*.pdb']),
FileType('PDB Entry', ['*.ent']),
FileType('All', ['*']) ]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import PDB coordinates file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
name = os.path.split(fileName)[1]
if '.' in name:
name = name.split('.')[0]
pdbObj = PseudoPdbFormat(self.project, self, verbose=True)
pdbObj.readCoordinates(fileName, minimalPrompts=True)
self.eciFrame.updateAll()
return pdbObj
def showVersion(self):
showInfo('Version', 'Version ' + self.versionInfo, parent=self)
def changeFont(self, analysisProfile):
if analysisProfile is self.analysisProfile:
if self.font != analysisProfile.font:
self.font = analysisProfile.font or DEFAULT_FONT
self.setFont()
def selectFont(self, font): # Only called from main menu option
if self.project:
self.analysisProfile.font = font
def setFont(self, font=None, popup=None):
if font is None:
font = self.font or DEFAULT_FONT
else:
self.font = font
if not popup:
popup = self
childList = popup.children.values()
classes = [Tkinter.Button,
Tkinter.Label,
Tkinter.Menu,
Tkinter.Entry,
Tkinter.Checkbutton,
Tkinter.Radiobutton]
for child in childList:
for clazz in classes:
if isinstance(child, clazz):
if hasattr(child, 'font'):
if not child.font:
child.config( font=font)
else:
child.config( font=font )
break
if isinstance(child, Tkinter.Frame):
child.font = font
elif isinstance(child, ScrolledMatrix):
child.setFont(font)
if hasattr(child, 'children'):
childList.extend( child.children.values() )
def initProject(self, project=None):
self.project = project
if project:
self.initTopObjects(self.project)
self.project.application = self.application
self.setFont()
webBrowser = ProjectWebBrowser(self.top, popup=self, project=project)
self.setupSoftware()
self.eciFrame.updateAll(project)
self.setMenuState()
def setupSoftware(self):
project = self.project
methodStore = project.currentMethodStore or \
project.findFirstMethodStore() or \
project.newMethodStore(name=project.name)
software = methodStore.findFirstSoftware(name=PROGRAM_NAME, version=VERSION)
if not software:
software = methodStore.newSoftware(name=PROGRAM_NAME, version=VERSION)
software.vendorName = 'PDBe & CCPN'
#software.vendorAddress = ''
software.vendorWebAddress = 'http://www.ebi.ac.uk/pdbe/'
software.details = 'The PDBe & CCPN Entry Completion Interface'
software.tasks = ['data deposition']
def setMenuState(self):
if self.project:
state = Tkinter.NORMAL
else:
state = Tkinter.DISABLED
# Disable bits of the project menu if there's no project
for option in ('Close','Save','Save As',):
i = self.projectMenu.options.index(option)
self.projectMenu.entryconfig(i, state=state)
# Disable other menus if there's no project
for menu in [self.otherMenu,]: # Include more menus in this list
for i in range(len(menu.options)):
menu.entryconfig(i, state=state)
def askSaveFile(self):
popup = self.openPopup('save_project', SaveProjectPopup)
popup.refresh()
def modalAskSaveFile(self):
popup = SaveProjectPopup(self, project=self.project, dismiss_text='Cancel Quit',
modal=True)
did_save = popup.did_save
popup.destroy()
return did_save
def quitSaveProject(self):
if (self.project.activeRepositories):
return self.saveFile()
else:
return self.modalAskSaveFile()
def destroyPopups(self):
for key in self.popups.keys():
popup = self.popups[key]
popup.destroy()
self.popups = {}
def copyModifiedStorages(self):
modifiedStorages = [storage for storage in self.project.storages if storage.isModified]
if (self.project.isModified):
modifiedStorages.append(self.project)
for storage in modifiedStorages:
self.copyStorage(storage)
def saveFile(self):
if not self.project:
return False
try:
saveProject(self.project, createFallback=True)
print 'successfully saved project'
return True
except IOError, e:
showError('Saving file', str(e), parent=self)
return False
class DangleGui(BasePopup):
"""
**A Bayesian inferential prediction method for protein backbone dihedral angles**
DANGLE (Dihedral ANgles from Global Likelihood Estimates) predicts protein
backbone Phi and Psi angles and secondary structure assignments solely from
amino acid sequence information, experimental chemical shifts and a database
of known protein structures and their associated shifts. This approach
uses Bayesian inferential logic to analyse the likelihood of conformations
throughout Ramachandran space, paying explicit attention to the population
distributions expected for different amino acid residue types.
Simple filtering procedures can identify the most "predictable" residues,
yielding 92% of all Phi and Psi predictions accurate to within +/-30 degrees.
In contrast to previous approaches, more than 80% of Phi or Psi predictions
for glycine and pre-proline are reliable. Furthermore, DANGLE provides
meaningful upper and lower bounds for the predictions which are shown to
represent the precision of the prediction. Over 90% of the experimental
dihedral angles in the set of test proteins are within the boundary ranges
suggested by DANGLE. At a lower resolution level, the program correctly
assigns each residue to one of three secondary structure states (H, E or C) in
85% of cases.
DANGLE also provides an indication of the degeneracy in the relationship
between shift measurements and conformation at each site.
For more documentation see the `DANGLE web site`_ at SourceForge.
.. _`DANGLE web site`: http://dangle.sourceforge.net/
**Reference**
*Ming-Sin Cheung, Mahon L. Maguire, Tim J. Stevens, and R. William Broadhurst.
"DANGLE: A Bayesian inferential method for predicting protein backbone
dihedral angles and secondary structure." Journal of Magnetic Resonance Volume
202, Issue 2, February 2010, Pages 223-233*
"""
def __init__(self, root, programName=PROGRAM_NAME, **kw):
self.parent = root
self.programName = programName
# Application object needed to store application-specific data with project
self.application = Application(name=PROGRAM_NAME)
self.versionInfo = 'Version ' + VERSION
self.graphPopup = None
self.analysisProfile = None
# Application popup is a superclass of memops.editor.BasePoup
BasePopup.__init__(self, parent=root, title=PROGRAM_NAME,
location='+100+100', class_=self.application.name, **kw)
def body(self, guiParent):
# Ensure that the first row and column in popup expand
guiParent.grid_rowconfigure(1, weight=1)
guiParent.grid_columnconfigure(0, weight=1, minsize=200)
frame = Frame(guiParent) # Body widgets can be put in this frame
frame.grid(row=1, column=0, sticky='nsew')
frame.grid_rowconfigure(0, weight=1)
frame.grid_columnconfigure(0, weight=1, minsize=200)
self.dangleFrame = DangleFrame(frame, self, project=self.project)
self.dangleFrame.grid(row=0, column=0, sticky='nsew')
# Dictionary to store popups opened by this application - e.g. need to close upon quit
self.popups = {}
# Default font
self.font = 'Helvetica 10'
# Closing the window from the desktop environment calls the proper quit
self.protocol('WM_DELETE_WINDOW', self.quit)
self.mainMenu = Menu(self)
self.projectMenu = self.makeProjectMenu()
self.viewMenu = self.viewFileMenu()
self.otherMenu = self.makeAppearanceMenu()
# Put the main menu
self.config(menu=self.mainMenu)
self.initProject()
def makeProjectMenu(self):
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
# Add various options to the menu and state the functions they call
menu.add_command(label='New', shortcut='N', command=self.newProject,
tipText='Make a new, blank CCPN project. Closes any existing project')
menu.add_command(label='Open', shortcut='O', command=self.openProject,
tipText='Open a new CCPN project from disk, closing any existing project')
menu.add_command(label='Close', shortcut='C', command=self.closeProject,
tipText='Close the current CCPN project')
menu.add_command(label='Save', shortcut='S', command=self.saveProject,
tipText='Save the current CCPN prjoject at its pre-specified location')
menu.add_command(label='Save As', shortcut='A', command=self.saveAsProject,
tipText='Save the current CCPN project at a new location')
menu.add_command(label='Backup', shortcut='B', command=self.backupProject,
tipText='Manage options for automatic CCPN project backup')
menu.add_command(label='Quit', shortcut='Q', command=self.quit,
tipText='Exit from the DANGLE program')
menu.add_command(label='Version', shortcut='V', command=self.showVersion)
self.mainMenu.add_cascade(label='Project', shortcut='P', menu=menu)
menu.options = ['New','Open','Close','Save','Save As','Backup','Quit','Version']
return menu
def viewFileMenu(self):
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
# Add various options to the menu and state the functions they call
menu.add_command(label='Prediction Graph', shortcut='G', command=self.viewGraph,
tipText='Show a graphical view of the poredicted backbone dihedral angles')
self.mainMenu.add_cascade(label='View', shortcut='V', menu=menu)
menu.options = ['Prediction Graph']
return menu
def makeAppearanceMenu(self):
# The fonts menu is a pre-created widget
fontsMenu = FontMenu(self.mainMenu, self.setFont, sizes=(8,10,12),
doItalic=0, doBoldItalic=0, tearoff=0)
# Plot color schemes
colorMenu = Menu(self.mainMenu, tearoff=0)
colorMenu.add_radiobutton(label='Red', command=self.colorSchemeRed,)
colorMenu.add_radiobutton(label='Rainbow', command=self.colorSchemeRainbow,)
#colorMenu.add_radiobutton(label='Black', shortcut='B', command=self.colorSchemeBlack)
#colorMenu.add_radiobutton(label='White', shortcut='W', command=self.colorSchemeWhite)
# Submenu of the main menu
menu = Menu(self.mainMenu, tearoff=0)
# Only Fonts option so far
menu.add_cascade(label='Plot Colour Scheme',shortcut='C', menu=colorMenu)
menu.add_cascade(label='Fonts', shortcut='F', menu=fontsMenu)
self.mainMenu.add_cascade(label='Appearance', shortcut='A', menu=menu)
menu.options = ['Plot Colour Scheme','Fonts']
return menu
def colorSchemeRed(self):
self.dangleFrame.colorScheme = 'red'
def colorSchemeRainbow(self):
self.dangleFrame.colorScheme = 'rainbow'
def colorSchemeBlack(self):
self.dangleFrame.colorScheme = 'black'
def colorSchemeWhite(self):
self.dangleFrame.colorScheme = 'white'
def viewGraph(self):
phiData, psiData = self.dangleFrame.getPhiPsiPredictions()
if self.graphPopup:
self.graphPopup.open()
else:
self.graphPopup = DangleGraphPopup(self)
dangleChain = self.dangleFrame.dangleChain
good = []
med = []
bad = []
if dangleChain:
resNum = 0 # In case no residues
for dResidue in dangleChain.dangleResidues:
resNum = dResidue.residue.seqCode
nIslands = dResidue.numIslands
if nIslands < 2:
good.append((resNum, nIslands))
elif nIslands < 4:
med.append((resNum, nIslands))
else:
bad.append((resNum, nIslands))
good.append((resNum, 0)) # To bias the graph
islandData = [good, med, bad]
self.graphPopup.update(phiData,psiData,islandData)
def newProject(self):
if self.project:
# Project already present
if not self.closeProject():
# If we don't close the current project do nothing
return
name = askString(title='Project name', prompt='Enter project name:',parent=self)
if name:
# Make the API Project object
project = Implementation.MemopsRoot(name=name)
nmrProject = project.newNmrProject(name = project.name)
self.initProject(project)
def openProject(self):
if self.project:
if not self.closeProject():
return
self.openPopup('open_project', OpenProjectPopup, callback=self.initProject)
def openPopup(self, popup_name, clazz, *args, **kw):
popup = self.popups.get(popup_name)
if popup:
popup.open()
else:
if self.analysisProfile:
transient = self.analysisProfile.transientWindows
else:
transient = True
# Below automatically opens popup
popup = self.popups[popup_name] = clazz(self, project=self.project, transient=transient, *args, **kw)
return popup
def closeProject(self, queryClose=True, querySave=True):
if queryClose:
if (not showYesNo('Close project', 'Close current project?')):
return False
if querySave:
if (not self.checkSaving()):
return False
self.destroyPopups()
self.initProject()
return True
def saveProject(self):
#if (self.project.isStored):
self.saveFile()
#else:
# self.askSaveFile()
def saveAsProject(self):
self.askSaveFile()
def backupProject(self):
pass
#self.openPopup('backup_project', BackupProjectPopup)
def showVersion(self):
showInfo('Version', self.versionInfo, parent=self)
def setFont(self, fontName=None, popup=None):
if fontName is None:
if self.analysisProfile:
# Get font specification saved as project application data
self.font = self.analysisProfile.font
else:
self.font = fontName
if self.analysisProfile:
# Set font specification as project application data
self.analysisProfile.font = fontName
if not popup:
popup = self
childList = popup.children.values()
classes = [Tkinter.Button,
Tkinter.Label,
Tkinter.Menu,
Tkinter.Entry,
Tkinter.Checkbutton,
Tkinter.Radiobutton]
for child in childList:
for clazz in classes:
if isinstance(child, clazz):
if hasattr(child, 'font'):
if not child.font:
child.config( font=self.font)
else:
child.config( font=self.font )
break
if hasattr(child, 'children'):
childList.extend( child.children.values() )
def initProject(self, project=None):
if project:
self.project = project
else:
project = self.project
self.setTitle(self.programName)
if project:
self.project.application = self.application
self.setFont()
self.dangleFrame.updateProject(project)
self.setupSoftware()
if not project.currentAnalysisProfile:
analysisProfiles = project.sortedAnalysisProfiles()
if analysisProfiles:
project.currentAnalysisProfile = analysisProfiles[0]
else:
project.newAnalysisProfile(name=project.name)
self.analysisProfile = project.currentAnalysisProfile
self.setMenuState()
def setupSoftware(self):
project = self.project
methodStore = project.currentMethodStore or \
project.findFirstMethodStore() or \
project.newMethodStore(name=project.name)
software = methodStore.findFirstSoftware(name=PROGRAM_NAME, version=VERSION)
if not software:
software = methodStore.newSoftware(name=PROGRAM_NAME, version=VERSION)
#software.vendorName = 'Nicole Cheung'
#software.vendorAddress = ''
#software.vendorWebAddress = 'http:'
#software.details = ''
def setMenuState(self):
if self.project:
state = Tkinter.NORMAL
else:
state = Tkinter.DISABLED
# Disable bits of the project menu if there's no project
for option in ('Save','Save As','Backup','Close'):
i = self.projectMenu.options.index(option)
self.projectMenu.entryconfig(i, state=state)
# Disable bits of the project menu if not stand-alone
if hasattr(self.parent, 'project'):
for option in ('New','Open','Close'):
i = self.projectMenu.options.index(option)
self.projectMenu.entryconfig(i, state=Tkinter.DISABLED)
# Disable other manus and view menu if there's no project
for menu in [self.otherMenu,self.viewMenu]: # Include more menus in this list
for i in range(len(menu.options)):
menu.entryconfig(i, state=state)
def askSaveFile(self):
popup = self.openPopup('save_project', SaveProjectPopup)
def modalAskSaveFile(self):
popup = SaveProjectPopup(self, project=self.project, dismiss_text='Cancel Quit',
modal=True)
did_save = popup.did_save
popup.destroy()
return did_save
def quitSaveProject(self):
if self.project.activeRepositories:
return self.saveFile()
else:
return self.modalAskSaveFile()
def destroyPopups(self):
for key in self.popups.keys():
popup = self.popups[key]
popup.destroy()
self.popups = {}
def saveFile(self):
if (not self.project):
return False
try:
self.project.saveModified()
print 'Successfully saved project'
return True
except IOError, e:
showError('Saving file', str(e))
return False
def body(self, guiFrame):
row = 0
col = 0
# frame = Frame( guiFrame )
# frame.grid(row=row, column=col, sticky='news')
self.menuBar = Menu(guiFrame)
self.menuBar.grid(row=row, column=col, sticky='ew')
#----------------------------------------------------------------------------------
# Project frame
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(row, weight=1)
# frame = LabelFrame(guiFrame, text='Project', font=medFont)
row = +1
col = 0
frame = LabelFrame(guiFrame, text='Project', **labelFrameAttributes)
print '>', frame.keys()
frame.grid(row=row, column=col, sticky='nsew')
frame.grid_columnconfigure(2, weight=1)
# frame.grid_rowconfigure(0, weight=1)
srow = 0
self.projectOptions = [
'old', 'new from PDB', 'new from CCPN', 'new from CYANA'
]
self.projOptionsSelect = RadioButtons(frame,
selected_index=0,
entries=self.projectOptions,
direction='vertical',
select_callback=self.updateGui)
self.projOptionsSelect.grid(row=srow,
column=0,
rowspan=len(self.projectOptions),
columnspan=2,
sticky='w')
if self.options.name:
text = self.options.name
else:
text = ''
# end if
self.projEntry = Entry(frame,
bd=1,
text=text,
returnCallback=self.updateGui)
self.projEntry.grid(row=srow, column=2, columnspan=2, sticky='ew')
# self.projEntry.bind('<Key>', self.updateGui)
self.projEntry.bind('<Leave>', self.updateGui)
projButton = Button(frame,
bd=1,
command=self.chooseOldProjectFile,
text='browse')
projButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.pdbEntry = Entry(frame, bd=1, text='')
self.pdbEntry.grid(row=srow, column=2, sticky='ew')
self.pdbEntry.bind('<Leave>', self.updateGui)
pdbButton = Button(frame,
bd=1,
command=self.choosePdbFile,
text='browse')
pdbButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.ccpnEntry = Entry(frame, bd=1, text='')
self.ccpnEntry.grid(row=srow, column=2, sticky='ew')
self.ccpnEntry.bind('<Leave>', self.updateGui)
ccpnButton = Button(frame,
bd=1,
command=self.chooseCcpnFile,
text='browse')
ccpnButton.grid(row=srow, column=3, sticky='ew')
srow += 1
self.cyanaEntry = Entry(frame, bd=1, text='')
self.cyanaEntry.grid(row=srow, column=2, sticky='ew')
self.cyanaEntry.bind('<Leave>', self.updateGui)
cyanaButton = Button(frame,
bd=1,
command=self.chooseCyanaFile,
text='browse')
cyanaButton.grid(row=srow, column=3, sticky='ew')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
label = Label(frame, text='Project name:')
label.grid(row=srow, column=0, sticky='nw')
self.nameEntry = Entry(frame, bd=1, text='')
self.nameEntry.grid(row=srow, column=2, sticky='w')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
self.openProjectButton = Button(frame,
command=self.openProject,
text='Open Project',
**actionButtonAttributes)
self.openProjectButton.grid(row=srow,
column=0,
columnspan=4,
sticky='ew')
#----------------------------------------------------------------------------------
# status
#----------------------------------------------------------------------------------
# guiFrame.grid_columnconfigure(1, weight=0)
srow = 0
frame = LabelFrame(guiFrame, text='Status', **labelFrameAttributes)
frame.grid(row=srow, column=1, sticky='wnes')
self.projectStatus = Text(frame,
height=11,
width=70,
borderwidth=0,
relief='flat')
self.projectStatus.grid(row=0, column=0, sticky='wen')
#Empty row
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
srow += 1
self.closeProjectButton = Button(frame,
command=self.closeProject,
text='Close Project',
**actionButtonAttributes)
self.closeProjectButton.grid(row=srow,
column=0,
columnspan=4,
sticky='ew')
#----------------------------------------------------------------------------------
# Validate frame
#----------------------------------------------------------------------------------
row += 1
col = 0
frame = LabelFrame(guiFrame, text='Validate', **labelFrameAttributes)
# frame = LabelFrame(guiFrame, text='Validate', font=medFont)
frame.grid(row=row, column=col, sticky='nsew')
# frame.grid_columnconfigure(2, weight=1)
frame.grid_rowconfigure(0, weight=1)
srow = 0
# label = Label(frame, text='validation')
# label.grid(row=srow,column=0,sticky='nw')
#
# self.selectDoValidation = CheckButton(frame)
# self.selectDoValidation.grid(row=srow, column=1,sticky='nw' )
# self.selectDoValidation.set(True)
#
# srow += 1
# label = Label(frame, text='')
# label.grid(row=srow,column=0,sticky='nw')
#
# srow += 1
label = Label(frame, text='checks')
label.grid(row=srow, column=0, sticky='nw')
self.selectCheckAssign = CheckButton(frame)
self.selectCheckAssign.grid(row=srow, column=1, sticky='nw')
self.selectCheckAssign.set(True)
label = Label(frame, text='assignments and shifts')
label.grid(row=srow, column=2, sticky='nw')
# srow += 1
# self.selectCheckQueen = CheckButton(frame)
# self.selectCheckQueen.grid(row=srow, column=4,sticky='nw' )
# self.selectCheckQueen.set(False)
# label = Label(frame, text='QUEEN')
# label.grid(row=srow,column=5,sticky='nw')
#
# queenButton = Button(frame, bd=1,command=None, text='setup')
# queenButton.grid(row=srow,column=6,sticky='ew')
srow += 1
self.selectCheckResraint = CheckButton(frame)
self.selectCheckResraint.grid(row=srow, column=1, sticky='nw')
self.selectCheckResraint.set(True)
label = Label(frame, text='restraints')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectCheckStructure = CheckButton(frame)
self.selectCheckStructure.grid(row=srow, column=1, sticky='nw')
self.selectCheckStructure.set(True)
label = Label(frame, text='structural')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectMakeHtml = CheckButton(frame)
self.selectMakeHtml.grid(row=srow, column=1, sticky='nw')
self.selectMakeHtml.set(True)
label = Label(frame, text='generate HTML')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectCheckScript = CheckButton(frame)
self.selectCheckScript.grid(row=srow, column=1, sticky='nw')
self.selectCheckScript.set(False)
label = Label(frame, text='user script')
label.grid(row=srow, column=0, sticky='nw')
self.validScriptEntry = Entry(frame, bd=1, text='')
self.validScriptEntry.grid(row=srow,
column=2,
columnspan=3,
sticky='ew')
scriptButton = Button(frame,
bd=1,
command=self.chooseValidScript,
text='browse')
scriptButton.grid(row=srow, column=5, sticky='ew')
srow += 1
label = Label(frame, text='ranges')
label.grid(row=srow, column=0, sticky='nw')
self.rangesEntry = Entry(frame, text='')
self.rangesEntry.grid(row=srow, column=2, columnspan=3, sticky='ew')
# self.validScriptEntry = Entry(frame, bd=1, text='')
# self.validScriptEntry.grid(row=srow,column=3,sticky='ew')
#
# scriptButton = Button(frame, bd=1,command=self.chooseValidScript, text='browse')
# scriptButton.grid(row=srow,column=4,sticky='ew')
srow += 1
texts = ['Run Validation', 'View Results', 'Setup QUEEN']
commands = [self.runCing, None, None]
buttonBar = ButtonList(frame,
texts=texts,
commands=commands,
expands=True)
buttonBar.grid(row=srow, column=0, columnspan=6, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.runButton = buttonBar.buttons[0]
self.viewResultButton = buttonBar.buttons[1]
self.queenButton = buttonBar.buttons[2]
#----------------------------------------------------------------------------------
# Miscellaneous frame
#----------------------------------------------------------------------------------
row += 0
col = 1
# frame = LabelFrame(guiFrame, text='Miscellaneous', font=medFont)
frame = LabelFrame(guiFrame,
text='Miscellaneous',
**labelFrameAttributes)
frame.grid(row=row, column=col, sticky='news')
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(4, weight=1, minsize=30)
frame.grid_rowconfigure(0, weight=1)
# Exports
srow = 0
label = Label(frame, text='export to')
label.grid(row=srow, column=0, sticky='nw')
self.selectExportXeasy = CheckButton(frame)
self.selectExportXeasy.grid(row=srow, column=1, sticky='nw')
self.selectExportXeasy.set(True)
label = Label(frame, text='Xeasy, Sparky, TALOS, ...')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportCcpn = CheckButton(frame)
self.selectExportCcpn.grid(row=srow, column=1, sticky='nw')
self.selectExportCcpn.set(True)
label = Label(frame, text='CCPN')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportQueen = CheckButton(frame)
self.selectExportQueen.grid(row=srow, column=1, sticky='nw')
self.selectExportQueen.set(True)
label = Label(frame, text='QUEEN')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
self.selectExportRefine = CheckButton(frame)
self.selectExportRefine.grid(row=srow, column=1, sticky='nw')
self.selectExportRefine.set(True)
label = Label(frame, text='refine')
label.grid(row=srow, column=2, sticky='nw')
srow += 1
label = Label(frame, text='')
label.grid(row=srow, column=0, sticky='nw')
# User script
srow += 1
label = Label(frame, text='user script')
label.grid(row=srow, column=0, sticky='nw')
self.selectMiscScript = CheckButton(frame)
self.selectMiscScript.grid(row=srow, column=1, sticky='nw')
self.selectMiscScript.set(False)
self.miscScriptEntry = Entry(frame, bd=1, text='')
self.miscScriptEntry.grid(row=srow, column=3, sticky='ew')
script2Button = Button(frame,
bd=1,
command=self.chooseMiscScript,
text='browse')
script2Button.grid(row=srow, column=4, sticky='ew')
srow += 1
texts = ['Export', 'Run Script']
commands = [None, None]
buttonBar = ButtonList(frame,
texts=texts,
commands=commands,
expands=True)
buttonBar.grid(row=srow, column=0, columnspan=5, sticky='ew')
for button in buttonBar.buttons:
button.config(**actionButtonAttributes)
# end for
self.exportButton = buttonBar.buttons[0]
self.scriptButton = buttonBar.buttons[1]
#----------------------------------------------------------------------------------
# Textarea
#----------------------------------------------------------------------------------
row += 1
guiFrame.grid_rowconfigure(row, weight=1)
self.outputTextBox = ScrolledText(guiFrame)
self.outputTextBox.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.redirectConsole()
#----------------------------------------------------------------------------------
# Buttons
#----------------------------------------------------------------------------------
row += 1
col = 0
texts = ['Quit', 'Help']
commands = [self.close, None]
self.buttonBar = ButtonList(guiFrame,
texts=texts,
commands=commands,
expands=True)
self.buttonBar.grid(row=row, column=col, columnspan=2, sticky='ew')
# self.openProjectButton = self.buttonBar.buttons[0]
# self.closeProjectButton = self.buttonBar.buttons[1]
# self.runButton = self.buttonBar.buttons[0]
# self.viewResultButton = self.buttonBar.buttons[1]
for button in self.buttonBar.buttons:
button.config(**actionButtonAttributes)
class PulldownMenu(Frame):
# if using indentation then should use list as stack only
# in other words only delete or insert at end
# entries entries must have attribute text_attr or if this is
# None then assume that entries entries themselves provide name
def __init__(self,
parent,
callback=None,
entries=None,
text_attr=None,
colors=None,
outline='#602000',
fill='#B05848',
label_color='#501000',
selected_index=-1,
indent='',
extra='',
sticky='w',
do_initial_callback=True,
force_callback=False,
*args,
**kw):
if (entries is None):
entries = []
Frame.__init__(self, parent, sticky=sticky, *args, **kw)
self.text_attr = text_attr
#indentation and extra string for popup information
self.indent = indent
self.extra = extra
self.callback = callback
self.do_initial_callback = do_initial_callback
self.force_callback = force_callback
frame = Frame(self)
#frame = parent
self.frame = frame
self.bg = frame.cget('bg')
self.outline = outline
self.fill = fill
self.label_color = label_color
self.menu = Menu(parent, tearoff=0, borderwidth=1, activeborderwidth=1)
self.menu.images = []
self.label = Label(self, foreground=label_color)
self.first_pass = True
#self.entries = entries
self.entries = []
self.colors = []
self.setup(entries, selected_index, colors=colors)
s = 10
self.canvas = Canvas(self, width=s, height=s, background=self.bg)
self.label.bind("<Button-1>", self.labelPopup)
# below does not work for some reason
#self.bind("<Button-1>", self.labelPopup)
# below does not work any more since can have submenus and
# no way to reach those with below since involves leaving menu
#self.menu.bind("<Leave>", self.popdown)
self.menu.bind("<Leave>", self.leave)
self.menu.bind("<Button-1>", self.buttonPress)
self.poppedUpSubmenu = False
self.canvas.bind("<Button-1>", self.canvasPopup)
self.canvas.bind("<Configure>", self.resizeCallback)
self.label.grid(row=0, column=0, sticky=Tkinter.W)
self.canvas.grid(row=0, column=1, sticky=Tkinter.E, padx=2)
def leave(self, event):
if (not self.poppedUpSubmenu):
x = event.x
y = event.y
x1 = self.menu.winfo_width()
y1 = self.menu.winfo_height()
if (x < 0) or (y < 0) or (x >= x1) or (y >= y1):
self.popdown()
def buttonPress(self, event):
if (event.widget != self.menu):
return
for n in range(len(self.entries) - 1, -1, -1):
if event.y >= self.menu.yposition(n):
break
else:
return
item = self.entries[n]
if (isinstance(item, {}.__class__) and item['kind'] == 'cascade'):
self.poppedUpSubmenu = True
else:
self.poppedUpSubmenu = False
def resizeCallback(self, *event):
w = self.canvas.winfo_width() / 2
h = self.canvas.winfo_height() / 2
self.canvas.delete('all')
self.canvas.create_polygon(1,
1,
w,
2 * h - 1,
2 * w - 1,
1,
fill=self.fill,
outline=self.outline)
def getEntry(self, entry_index, entries=None):
if not entries:
entries = self.entries
if type(entry_index) == types.TupleType:
e = entry_index[0]
if len(entry_index) > 1:
items = entries[e]['submenu']
entry = self.getEntry(entry_index[1:], items)
else:
entry = entries[e]['label']
elif (entry_index >= 0):
entry = entries[entry_index]
else:
entry = None
return entry
def getEntryText(self, entry_index, entries=None):
if not entries:
entries = self.entries
if type(entry_index) in (types.TupleType, types.ListType):
e = entry_index[0]
if len(entry_index) > 1:
items = entries[e]['submenu']
text = self.getEntryText(entry_index[1:], items)
else:
text = entries[e]['label']
elif (entry_index != -1):
#print 'getEntryText', entry_index, entries
entry = entries[entry_index]
if (self.text_attr):
text = getattr(entry, self.text_attr)
else:
text = entry
else:
text = ''
# TBD: for now text returned should not be unicode
text = str(text)
# below did not work for one person (Chinese characters??) but above did
###text = text.encode('utf-8')
return text
def setup(self, entries, selected_index, first_pass=True, colors=None):
#print 'setup', entries, selected_index
if first_pass is not None:
self.first_pass = first_pass
self.clearMenuItems()
if (entries):
e = list(entries)
else:
e = [No_entries_label]
self.entries = e
self.colors = colors or [None] * len(e)
if type(selected_index) in (types.TupleType, types.ListType):
if (not selected_index or selected_index[0] >= len(entries)):
selected_index = -1
else:
if (selected_index >= len(entries)):
selected_index = -1
if (selected_index == -1):
selected_index = 0
self.selected_index = -1 # changed in setSelectedIndex()
self.setMenuItems()
self.setSelectedIndex(selected_index)
def substituteCascadeCallbacks(self, item, selected_index):
if (item['kind'] == 'cascade'):
n = 0
for subitem in item['submenu']:
self.substituteCascadeCallbacks(subitem, selected_index + [n])
n = n + 1
else:
callback = item.get('command')
if (callback):
label = item['label']
item['command'] = lambda: self.cascadeCallback(
callback, label, tuple(selected_index))
def cascadeCallback(self, callback, label, selected_index):
self.selected_index = selected_index
self.setLabel(selected_index)
callback(selected_index, label)
def setMenuItems(self):
self.menu.images = []
for n in range(len(self.entries)):
columnbreak = 0
if n and n % 20 == 0:
columnbreak = 1
item = self.entries[n]
color = None
if n < len(self.colors):
color = self.colors[n]
if isinstance(item, {}.__class__):
if (item['kind'] == 'cascade'):
self.substituteCascadeCallbacks(item, [n])
else:
t = (self.indent * n) + self.extra + str(self.getEntryText(n))
command = lambda n=n: self.setSelectedIndex(n)
if color:
image = self.makeColorTile(color)
item = {
'kind': 'command',
'accelerator': t,
'command': command,
'image': image,
'columnbreak': columnbreak
}
else:
item = {
'kind': 'command',
'label': t,
'command': command,
'columnbreak': columnbreak
}
self.menu.addMenuItem(item)
def clearMenuItems(self):
if self.entries:
self.menu.delete(0, len(self.entries))
# below assumes entry_index is integer not tuple
def insert(self, entry_index, entry, make_selected=False, color=None):
if (self.haveNoEntries()):
if (entry_index != 0):
return
elif ((entry_index < 0) or (entry_index >= len(self.entries))):
return
self.clearMenuItems()
self.checkForNone()
self.entries.insert(entry_index, entry)
self.colors.insert(entry_index, color)
self.setMenuItems()
if (make_selected or (self.selected_index == -1)):
self.setSelectedIndex(entry_index, force_callback=True)
else:
self.setSelectedIndex(self.selected_index)
# below assumes entry is integer not tuple
def append(self, entry, make_selected=False, color=None):
self.clearMenuItems()
self.checkForNone()
self.entries.append(entry)
self.colors.append(color)
self.setMenuItems()
if (make_selected or (self.selected_index == -1)):
self.setSelectedIndex(len(self.entries) - 1, force_callback=True)
else:
self.setSelectedIndex(self.selected_index)
def checkForNone(self):
if (self.haveNoEntries()):
self.entries = []
self.colors = []
self.menu.delete(0)
def haveNoEntries(self):
if (len(self.entries) == 1 and self.entries[0] == No_entries_label):
return True
else:
return False
def baseIndex(self, ind):
if type(ind) == types.TupleType:
ind = ind[0]
return ind
# below assumes entry_index is integer not tuple
def delete(self, entry_index, n=1):
if (self.haveNoEntries()):
return
if ((entry_index < 0) or (entry_index >= len(self.entries))):
return
self.clearMenuItems()
n1 = entry_index
n2 = n1 + n
m = self.baseIndex(self.selected_index)
del self.entries[n1:n2]
del self.colors[n1:n2]
if (not self.entries):
self.entries = [No_entries_label]
self.colors = [None]
self.setMenuItems()
if ((m >= n1) and (m < n2)):
if (n1 == 0):
selected_index = 0
else:
selected_index = n1 - 1
self.setSelectedIndex(selected_index, force_callback=True)
def replace(self, entries, selected_index=-1, colors=None):
self.menu.delete(0, len(self.entries))
self.setup(entries, selected_index, first_pass=False, colors=colors)
def popdown(self, *event):
self.menu.unpost()
def setLabel(self, selected_index):
text = self.getEntryText(selected_index)
if (not text):
text = self.extra # arbitrary
self.label.set(text=text)
def labelPopup(self, event):
self.poppedUpSubmenu = False
s = self.baseIndex(self.selected_index)
x = event.x_root - event.x + 2
y = event.y_root - event.y - \
max(0, s) * (self.label.winfo_height() + 1)
self.menu.post(x, y)
def canvasPopup(self, event):
s = self.baseIndex(self.selected_index)
x = event.x_root - event.x - self.label.winfo_width() + 2
y = event.y_root - event.y - \
max(0, s) * (self.label.winfo_height() + 1) + \
self.canvas.winfo_height() - self.label.winfo_height()
self.menu.post(x, y)
def getSelectedIndex(self):
return self.selected_index
def setSelectedIndex(self, selected_index, force_callback=False):
if (force_callback or self.force_callback or \
(selected_index != self.selected_index)):
#print 'setSelectedIndex', self.entries, selected_index, self.selected_index, self.first_pass
self.selected_index = selected_index
self.setLabel(selected_index)
if (self.callback):
if (self.haveNoEntries()):
if (not self.first_pass):
self.callback(-1, None)
elif (selected_index != -1):
if (not self.first_pass or self.do_initial_callback):
self.callback(selected_index,
self.entries[selected_index])
self.first_pass = False
def get(self):
return self.getSelected()
def getSelected(self):
ind = self.getSelectedIndex()
if (ind == -1):
return None
else:
return self.getEntry(ind)
def set(self, selected):
self.setSelected(selected)
def findEntryIndex(self, entry, entries=None):
#print 'findEntryIndex1', entry, entries
if (entries):
noEntries = True
else:
noEntries = False
entries = self.entries
try:
ind = entries.index(entry)
return ind
except:
pass
#print 'findEntryIndex2', entry, entries
for n in range(len(entries)):
e = entries[n]
#print 'findEntryIndex3', entry, e
if e == entry:
if noEntries:
return [n]
else:
return n
elif type(e) == types.DictType:
if (len(entries) > 1):
try:
ind = self.findEntryIndex(entry, e['submenu'])
return [n] + ind
except:
pass
else:
if (entry == e['label']):
return [n]
raise 'unknown entry "%s"' % entry
# selects first item found in entries which matches
def setSelected(self, selected):
#print 'setSelected1', selected, type(selected), self.entries
try:
selected_index = self.findEntryIndex(selected)
except:
#selected_index = -1
return
#print 'setSelected2', selected_index
self.setSelectedIndex(selected_index)
def makeColorTile(self, color):
image = Tkinter.PhotoImage()
self.menu.images.append(image)
if type(color) == type([]):
colors = [scaleColor(self.menu, c, 1.0) for c in color]
else:
colors = [
scaleColor(self.menu, color, 1.0),
]
cols = max(8, len(colors))
for x in range(cols):
i = x % len(colors)
c = colors[i]
for y in range(16):
image.put('{%s %s}' % (c, c), to=(2 * x, y))
return image
def makeProjectMenu(self):
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
menu.add_command(label='Save', shortcut='S', command=self.saveProject)
menu.add_command(label='Save As',
shortcut='A',
command=self.saveAsProject)
menu.add_command(label='Quit', shortcut='Q', command=self.quit)
menu.add_command(label='Version',
shortcut='V',
command=self.showVersion)
self.mainMenu.add_cascade(label='Project', shortcut='P', menu=menu)
menu.options = ['Save', 'Save As', 'Quit', 'Version']
return menu
class ScrolledCanvas(Frame):
def __init__(self,
parent,
resizeCallback=None,
width=600,
height=600,
*args,
**kw):
self.bbox = None
self.busy = 0
self.initialX = None
self.initialY = None
self.resizeCallback = resizeCallback
apply(Frame.__init__, (self, parent) + args, kw)
self.grid_rowconfigure(0, weight=1)
self.grid_columnconfigure(0, weight=1)
self.menu = Menu(self, tearoff=0, include_event=True)
self.configMenu()
self.canvas = Canvas(self,
relief='flat',
borderwidth=0,
width=width,
height=height)
self.canvas.configure(xscrollincrement=2, yscrollincrement=2)
self.canvas.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.horizScrollbar = Tkinter.Scrollbar(self,
bg=self.cget('bg'),
command=self.canvas.xview,
orient=Tkinter.HORIZONTAL,
borderwidth=1)
self.vertScrollbar = Tkinter.Scrollbar(self,
bg=self.cget('bg'),
command=self.canvas.yview,
orient=Tkinter.VERTICAL,
borderwidth=1)
self.canvas.configure(xscrollcommand=self.horizScrollbar.set,
yscrollcommand=self.vertScrollbar.set)
self.canvas.bind('<Configure>', self.resizeAfter)
self.canvas.bind('<Button-1>', self.mouseButton1)
self.canvas.bind('<Button-2>', self.mouseButton2)
self.canvas.bind('<Button-3>', self.mouseButton3)
self.canvas.bind('<ButtonRelease-1>', self.mouseButtonRelease1)
self.canvas.bind('<ButtonRelease-2>', self.mouseButtonRelease2)
self.canvas.bind('<B2-Motion>', self.mouseScroll)
self.canvas.bind('<B3-Motion>', self.doNothing)
self.canvas.bind('<Motion>', self.mouseEnter)
self.canvas.bind('<Enter>', self.mouseEnter)
def doNothing(self, event):
pass
def mouseEnter(self, event):
if self.menu.winfo_ismapped():
self.removeMenu()
def refresh(self):
self.bbox = self.canvas.bbox('all')
bbox = self.bbox
if not bbox:
self.busy = 0
return
cWidth = int(self.canvas.cget('width'))
cHeight = int(self.canvas.cget('height'))
if cHeight > bbox[3] - bbox[1]:
self.vertScrollbar.grid_forget()
else:
self.vertScrollbar.grid(row=0, column=1, sticky=Tkinter.NS)
if cWidth > bbox[2] - bbox[0]:
self.horizScrollbar.grid_forget()
else:
self.horizScrollbar.grid(row=1, column=0, sticky=Tkinter.EW)
x1 = bbox[0]
y1 = bbox[1]
x2 = max(bbox[0] + cWidth, bbox[2])
y2 = max(bbox[1] + cHeight, bbox[3])
self.canvas.configure(scrollregion=(x1, y1, x2, y2))
self.update_idletasks()
self.busy = 0
def printCanvas(self, *event):
fileTypes = [FileType('PostScript', ['*.ps']), FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(self,
file_types=fileTypes,
title='Print canvas to file',
dismiss_text='Cancel',
selected_file_must_exist=False)
fileName = fileSelectPopup.getFile()
self.bbox = bbox = self.canvas.bbox('all')
w = bbox[2] - bbox[0]
h = bbox[3] - bbox[1]
self.canvas.postscript(colormode='color',
file=fileName,
x=bbox[0],
y=bbox[1],
width=w + 2,
pagewidth='21.c',
height=h + 2)
def configMenu(self):
items = [
{
'kind': 'command',
'label': 'Print to file',
'command': self.printCanvas
},
]
self.menu.setMenuItems(items)
def removeMenu(self, *event):
self.menu.unpost()
def mouseButton3(self, event):
self.menu.popupMenu(event)
def mouseButton1(self, event):
self.removeMenu()
if not self.initialX:
self.initialX = event.x
self.initialY = event.y
def mouseButton2(self, event):
self.removeMenu()
if not self.initialX:
self.initialX = event.x
self.initialY = event.y
self.initialPX = self.horizScrollbar.get()[0]
self.initialPY = self.vertScrollbar.get()[0]
def mouseButtonRelease1(self, event):
self.initialX = None
self.initialY = None
def mouseButtonRelease2(self, event):
self.initialX = None
self.initialY = None
self.initialPX = None
self.initialPY = None
def mouseScroll(self, event):
self.menu.unpost()
bbox = self.bbox
if not bbox:
return
bW = float(bbox[2] - bbox[0])
bH = float(bbox[3] - bbox[1])
cWidth = int(self.canvas.cget('width'))
cHeight = int(self.canvas.cget('height'))
if cWidth < bW:
dx = self.initialX - event.x
prop = self.initialPX + (dx / bW)
self.canvas.xview('moveto', prop)
if cHeight < bH:
dy = self.initialY - event.y
prop = self.initialPY + (dy / bH)
self.canvas.yview('moveto', prop)
def resizeAfter(self, event):
if self.busy:
return
else:
self.busy = 1
self.removeMenu()
self.after_idle(lambda: self.resize(event))
def resize(self, event):
if self.resizeCallback:
self.after_idle(
lambda: self.resizeCallback(event.width, event.height))
self.canvas.configure(width=event.width, height=event.height)
self.after_idle(self.refresh)
class LinkChart(Frame):
def __init__(self, parent, scrollX=True, scrollY=True, *args, **kw):
self.parent = parent
self.scrollX = scrollX
self.scrollY = scrollY
self.prototypes = []
self.nodes = []
self.node = None # Selected
self.links = []
self.link = None # Selected
self.objDict = {} # Map canvas to nodes, links
self.cornerDict = {}
self.editWidget = None
self.mouseOver = None
self.inMotion = None
self.inMotion2 = None
self.inMotion3 = None
self.dragRegion = None
self._resizeBusy = False
self.selectedNodes = []
self.selectedLinks = []
self.highlightNodes = []
self.highlightLinks = []
kw['relief'] = 'flat'
kw['borderwidth'] = 0
Frame.__init__(self, parent, *args, **kw)
self.canvas = canvas = Canvas(self, relief='flat', borderwidth=0)
self.canvas.configure(xscrollincrement=2,
yscrollincrement=2,
bg=self.cget('bg'))
self.canvas.grid(row=0, column=0, sticky='nsew')
if scrollX:
self.horizScrollbar = Tkinter.Scrollbar(self,
bg=self.cget('bg'),
command=self.canvas.xview,
orient=Tkinter.HORIZONTAL,
borderwidth=1)
self.canvas.configure(xscrollcommand=self.horizScrollbar.set)
if scrollY:
self.vertScrollbar = Tkinter.Scrollbar(self,
bg=self.cget('bg'),
command=self.canvas.yview,
orient=Tkinter.VERTICAL,
borderwidth=1)
self.canvas.configure(yscrollcommand=self.vertScrollbar.set)
canvas.bind('<Button-1>', self._mouseSingleClick)
if not isWindowsOS():
canvas.bind('<Button-4>', self.scrollUp)
canvas.bind('<Button-5>', self.scrollDown)
else:
canvas.bind('<MouseWheel>', self._windowsOsScroll)
canvas.bind('<Double-1>', self._mouseDoubleClick)
canvas.bind('<B1-Motion>', self._mouseDrag)
canvas.bind('<ButtonRelease-1>', self._mouseRelease)
canvas.bind('<Motion>', self._mouseEnter)
canvas.bind('<Enter>', self._mouseEnter)
canvas.bind('<Leave>', self._mouseLeave)
canvas.bind('<KeyPress-Up>', self._moveUp)
canvas.bind('<KeyPress-Down>', self._moveDown)
canvas.bind('<KeyPress-Right>', self._moveRight)
canvas.bind('<KeyPress-Left>', self._moveLeft)
canvas.bind('<KeyPress-Delete>', self.deleteSelected)
self.bind('<Configure>', self._resizeAfter)
self.menu = Menu(self, tearoff=False)
alignItems = [{
'kind': 'command',
'label': 'Y axis',
'command': self._alignHorizontal
}, {
'kind': 'command',
'label': 'X axis',
'command': self._alignVertical
}]
distributeItems = [{
'kind': 'command',
'label': 'Horizontal',
'command': self._distributeHorizontal
}, {
'kind': 'command',
'label': 'Verical',
'command': self._distributeVertical
}]
menuItems = [
{
'kind': 'cascade',
'label': 'Align',
'submenu': alignItems
}, #0
{
'kind': 'cascade',
'label': 'Distribute',
'submenu': distributeItems
}, #1
{
'kind': 'command',
'label': 'Link Selected',
'command': self.linkSelected
}, #2
{
'kind': 'command',
'label': 'Reset Links',
'command': self._resetLinks
}, #3
{
'kind': 'separator'
},
{
'kind': 'command',
'label': 'Delete Links', #5
'command': self.deleteLinks
},
{
'kind': 'command',
'label': 'Delete Items', #6
'command': self.deleteNodes
},
{
'kind': 'separator'
},
{
'kind': 'command',
'label': 'Save PostScript File',
'command': self.printCanvas
},
]
self.menuItems = menuItems
self.menu.setMenuItems(menuItems)
canvas.bind('<ButtonPress-3>', self._popupMenu)
self._drawAfter()
def _resizeAfter(self, event):
if self._resizeBusy:
return
self._resizeBusy = True
self._popdownMenu(event)
self.after_idle(lambda: self._refreshScrollbars(event))
def _refreshScrollbars(self, event):
bbox = self.canvas.bbox('all')
if not bbox:
self._resizeBusy = False
return
cWidth = event.width
cHeight = event.height
vertScrollbar = self.vertScrollbar
horizScrollbar = self.horizScrollbar
xSpace = bbox[2] + bbox[0] # Symmetric space
ySpace = bbox[3] + bbox[1]
horizHeight = int(horizScrollbar.winfo_height())
vertWidth = int(vertScrollbar.winfo_width())
if cHeight < ySpace + horizHeight:
vertScrollbar.grid(row=0, column=1, sticky='ns')
cWidth -= vertWidth
else:
vertScrollbar.grid_forget()
if cWidth < xSpace + vertWidth:
horizScrollbar.grid(row=1, column=0, sticky='ew')
cHeight -= horizHeight
else:
horizScrollbar.grid_forget()
x1 = 0
y1 = 0
x2 = max(cWidth, xSpace)
y2 = max(cHeight, ySpace)
self.canvas.configure(width=cWidth, height=cHeight)
self.canvas.configure(scrollregion=(x1, y1, x2, y2))
self.update_idletasks()
self._resizeBusy = False
def _popupMenu(self, event):
self._finishEdit()
self._configMenu()
self.menu.popupMenu(event)
def _popdownMenu(self, event):
self._finishEdit()
self.menu.unpost()
def _configMenu(self):
if self.selectedLinks:
self.menu.entryconfig(5, state=ACTIVE)
self.menu.entryconfig(3, state=ACTIVE)
else:
self.menu.entryconfig(5, state=INACTIVE)
self.menu.entryconfig(3, state=INACTIVE)
if self.selectedNodes:
self.menu.entryconfig(2, state=ACTIVE)
self.menu.entryconfig(6, state=ACTIVE)
else:
self.menu.entryconfig(2, state=INACTIVE)
self.menu.entryconfig(6, state=INACTIVE)
if self.selectedNodes or self.selectedLinks:
self.menu.entryconfig(0, state=ACTIVE)
self.menu.entryconfig(1, state=ACTIVE)
else:
self.menu.entryconfig(0, state=INACTIVE)
self.menu.entryconfig(1, state=INACTIVE)
def _resetLinks(self):
for link in self.selectedLinks:
link.resetCoords()
def _alignSelected(self, vertical=False, horizontal=False):
obj = self.node or self.link
if not obj:
return
x0, y0 = obj.coords
objs = self.selectedNodes + self.selectedLinks
n = len(objs)
if n < 2:
return
if horizontal:
for obj in objs:
obj.move(obj.coords[0], y0)
if vertical:
for obj in objs:
obj.move(x0, obj.coords[1])
def _distributeSelected(self, vertical=False, horizontal=False):
xCoords = []
yCoords = []
objs = self.selectedNodes + self.selectedLinks
n = len(objs)
if n < 3:
return
for obj in objs:
x, y = obj.coords
xCoords.append((x, obj))
yCoords.append((y, obj))
if horizontal:
xCoords.sort()
xA = xCoords[0][0]
dx = (xCoords[-1][0] - xA) / float(n - 1)
for i, (x0, obj) in enumerate(xCoords):
y = obj.coords[1]
x = xA + (i * dx)
obj.move(x, y)
if vertical:
yCoords.sort()
yA = yCoords[0][0]
dy = (yCoords[-1][0] - yA) / float(n - 1)
for i, (y0, obj) in enumerate(yCoords):
x = obj.coords[0]
y = yA + (i * dy)
obj.move(x, y)
def _alignHorizontal(self):
self._alignSelected(horizontal=True)
def _alignVertical(self):
self._alignSelected(vertical=True)
def _distributeHorizontal(self):
self._distributeSelected(horizontal=True)
def _distributeVertical(self):
self._distributeSelected(vertical=True)
def linkSelected(self):
nodes = self.selectedNodes
n = len(nodes)
if n > 1:
for i in range(n - 1):
nodeA = nodes[i]
for j in range(i + 1, n):
nodeB = nodes[j]
for link in nodeA.links:
if nodeB in link.nodes:
#print link, link.nodes, nodeA, nodeB
break
else:
link = Link(self, nodeA, nodeB, text='*')
#print link
def deleteNodes(self):
if self.selectedNodes:
msg = 'Really delete %d selected nodes?' % len(self.selectedNodes)
if showOkCancel('Confirm', msg, parent=self):
for node in self.selectedNodes[:]:
node.delete()
self.selectedNodes = []
self.node = None
def deleteLinks(self):
if self.selectedLinks:
msg = 'Really delete %d selected links?' % len(self.selectedLinks)
if showOkCancel('Confirm', msg, parent=self):
for link in self.selectedLinks[:]:
link.delete()
self.selectedLinks = []
self.link = None
def deleteSelected(self, event=None):
objs = self.selectedLinks + self.selectedNodes
if objs:
n1 = len(self.selectedNodes)
n2 = len(self.selectedLinks)
msg = 'Really delete %d selected objects?\n' % (n1 + n2)
msg += '(%d nodes, %d links)' % (n1, n2)
if showOkCancel('Confirm', msg, parent=self):
for obj in objs:
obj.delete()
self.selectedLinks = []
self.link = None
self.selectedNodes = []
self.node = None
def printCanvas(self, *event):
from memops.gui.FileSelect import FileType
from memops.gui.FileSelectPopup import FileSelectPopup
fileTypes = [FileType('PostScript', ['*.ps']), FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(self,
file_types=fileTypes,
title='Print canvas to file',
dismiss_text='Cancel',
selected_file_must_exist=False)
fileName = fileSelectPopup.getFile()
self.postscript(colormode='color', file=fileName)
def _clearSelection(self):
for node in self.selectedNodes:
node.isSelected = False
for link in self.selectedLinks:
link.isSelected = False
self.selectedNodes = []
self.selectedLinks = []
self.link = None
self.node = None
def _clearHighlights(self):
for node in self.highlightNodes:
node.highlight = False
for link in self.highlightLinks:
link.highlight = False
self.mouseOver = None
self.highlightNodes = []
self.highlightLinks = []
def _mouseSingleClick(self, event):
self._mouseClick(event)
def _mouseDoubleClick(self, event):
self._mouseClick(event, True)
def _mouseClick(self, event, edit=False):
#self.menu.popdownMenu(event)
self._finishEdit()
canvas = event.widget
canvas.focus_force()
x = canvas.canvasx(event.x)
y = canvas.canvasy(event.y)
items = canvas.find('overlapping', x - 1, y - 1, x + 1, y + 1)
#item = self.find('closest',x,y)[0]
if not items:
self._clearSelection()
self._clearHighlights()
self.draw()
return
objs = [
self.objDict.get(item) for item in items if self.objDict.get(item)
]
for obj in objs:
if isinstance(obj, Node):
if not (event.state & 4 or event.state & 1):
self._clearSelection()
obj.isSelected = True
self.node = obj
if obj not in self.selectedNodes:
self.selectedNodes.append(obj)
break
else:
self.node = None
for obj in objs:
if isinstance(obj, Link):
if not (event.state & 4 or event.state & 1):
self._clearSelection()
obj.isSelected = True
self.link = obj
if obj not in self.selectedLinks:
self.selectedLinks.append(obj)
break
else:
self.link = None
self._drawAfter()
if not obj:
return
if edit and obj.editWidget:
obj.edit()
self.editWidget = obj.editWidget
def _clearDragRegion(self, canvas):
if self.dragRegion:
canvas.delete(self.dragRegion[0])
self.dragRegion = None
def _mouseEnter(self, event):
self.menu.popdownMenu(event)
canvas = event.widget
canvas.focus_force()
x = canvas.canvasx(event.x)
y = canvas.canvasy(event.y)
items = canvas.find('overlapping', x - 1, y - 1, x + 1, y + 1)
#item = self.find('closest',x,y)[0]
if not items:
self._clearHighlights()
self.draw()
return
obj = self.objDict.get(items[0])
self._clearHighlights()
if obj is None:
self.draw()
return
if obj is self.mouseOver:
if self.inMotion2:
for item in items:
if self.cornerDict.has_key(item):
self.inMotion2 = None
break
return
objs = [
self.objDict.get(item) for item in items if self.objDict.get(item)
]
for obj in objs:
if isinstance(obj, Node):
self.highlightNodes = [
obj,
]
break
else:
for obj in objs:
if isinstance(obj, Link):
self.highlightLinks = [
obj,
]
obj.highlight = True
self.mouseOver = obj
self.draw()
def _mouseLeave(self, event):
#self._mouseRelease(event)
#self._finishEdit()
self._clearHighlights()
self.draw()
def _mouseDrag(self, event):
self.menu.popdownMenu(event)
canvas = event.widget
canvas.focus_force()
x = canvas.canvasx(event.x)
y = canvas.canvasy(event.y)
#width = int(canvas.winfo_width())
#height = int (canvas.winfo_height())
#
#if not (0 < x < width) or not (0 < y < height):
# self._mouseRelease(event)
# return
inMotion = self.inMotion
objs = self.selectedNodes + self.selectedLinks
if objs:
items = canvas.find('overlapping', x - 1, y - 1, x + 1, y + 1)
if not inMotion:
for item in items:
if self.inMotion2 or self.cornerDict.has_key(item):
obj = self.node
x1, y1 = obj.coords # offsets
dx = abs(x - x1)
dy = abs(y - y1)
size = max(dx, dy) + 1
obj.width = size
obj.draw()
self.inMotion2 = True
return
if inMotion:
offsets = inMotion # Get offsets
else:
offsets = []
for obj in objs:
x1, y1 = obj.coords # offsets
dx = x - x1 # Offset relative to centre
dy = y - y1
if isinstance(obj, Node) and obj.isPrototype:
obj = obj.copy()
offsets.append((dx, dy, obj))
self.inMotion = offsets # Store click offset and Node
#print event, event.widget._root()
for dx, dy, obj in offsets:
x2 = x - dx
y2 = y - dy
obj.move(x2, y2)
x0, y0 = event.x_root, event.y_root
under = self.winfo_containing(x0, y0)
if isinstance(under, Canvas):
under = under.parent
if isinstance(under, LinkChart) and (under is not self):
for dx, dy, obj in offsets:
if not isinstance(obj, Node):
continue
original = obj.original
if original and original.isPrototype:
xT = x0 - under.winfo_rootx() - dx
yT = y0 - under.winfo_rooty() - dy
if original.spawn:
original.spawn.move(xT, yT)
else:
original.spawn = original.copy(under,
coords=(xT, yT))
else:
for dx, dy, obj in offsets:
if not isinstance(obj, Node):
continue
original = obj.original
if original and original.spawn:
original.spawn.delete()
original.spawn = None
else:
if self.inMotion3:
x0, y0, = self.inMotion3
else:
#self._mouseRelease(event)
x0 = x
y0 = y
self.inMotion3 = (x, y)
if self.dragRegion:
item = self.dragRegion[0]
canvas.coords(item, x0, y0, x, y)
else:
item = canvas.create_rectangle(x0,
y0,
x,
y,
outline='#008000',
fill='#00E000',
stipple='gray25')
self.dragRegion = (item, x0, y0, x, y)
def _mouseRelease(self, event):
canvas = event.widget
if self.dragRegion:
item, x1, y1, x2, y2 = self.dragRegion
xCoords = [x1, x2]
yCoords = [y1, y2]
xCoords.sort()
yCoords.sort()
x1, x2 = xCoords
y1, y2 = yCoords
self.node = None
self.selectedNodes = []
for node in self.nodes:
x0, y0 = node.coords
if (x1 < x0 < x2) and (y1 < y0 < y2):
self.selectedNodes.append(node)
node.isSelected = True
self.node = node
else:
node.isSelected = False
self.link = None
self.selectedLinks = []
for link in self.links:
x0, y0 = link.coords
if (x1 < x0 < x2) and (y1 < y0 < y2):
self.selectedLinks.append(link)
link.isSelected = True
self.link = link
else:
link.isSelected = False
self._clearDragRegion(canvas)
self.draw()
if self.inMotion:
for dx, dy, obj in self.inMotion:
if isinstance(
obj,
Node) and obj.original and obj.original.isPrototype:
if obj.original.spawn:
obj.original.spawn.original = None
obj.original.spawn = None
obj.delete()
self.inMotion = None
self.inMotion2 = None
self.inMotion3 = None
def _finishEdit(self):
if self.editWidget:
self.focus_force()
self.editWidget.commit()
self.editWidget.hide()
self.editWidget = None
def _moveUp(self, event):
self._moveSelected(event, 0, -1)
def _moveDown(self, event):
self._moveSelected(event, 0, 1)
def _moveRight(self, event):
self._moveSelected(event, 1, 0)
def _moveLeft(self, event):
self._moveSelected(event, -1, 0)
def _moveSelected(self, event, dx, dy):
if not (event.state & 4 or event.state & 1):
dx *= MOVE_STEP
dy *= MOVE_STEP
for node in self.selectedNodes:
x0, y0 = node.coords
node.move(x0 + dx, y0 + dy)
for link in self.selectedLinks:
x0, y0 = link.coords
link.move(x0 + dx, y0 + dy)
def scrollUp(self, event=None):
pass
def scrollDown(self, event):
pass
def _windowsOsScroll(self, event=None):
delta = event.delta
if delta > 0:
self.scrollUp(event)
elif delta < 0:
self.scrollDown(event)
def _drawAfter(self):
self.after_idle(self.draw)
def draw(self):
for link in self.links:
link.draw()
for node in self.nodes:
node.draw()
def __init__(self, parent, scrollX=True, scrollY=True, *args, **kw):
self.parent = parent
self.scrollX = scrollX
self.scrollY = scrollY
self.prototypes = []
self.nodes = []
self.node = None # Selected
self.links = []
self.link = None # Selected
self.objDict = {} # Map canvas to nodes, links
self.cornerDict = {}
self.editWidget = None
self.mouseOver = None
self.inMotion = None
self.inMotion2 = None
self.inMotion3 = None
self.dragRegion = None
self._resizeBusy = False
self.selectedNodes = []
self.selectedLinks = []
self.highlightNodes = []
self.highlightLinks = []
kw['relief'] = 'flat'
kw['borderwidth'] = 0
Frame.__init__(self, parent, *args, **kw)
self.canvas = canvas = Canvas(self, relief='flat', borderwidth=0)
self.canvas.configure(xscrollincrement=2,
yscrollincrement=2,
bg=self.cget('bg'))
self.canvas.grid(row=0, column=0, sticky='nsew')
if scrollX:
self.horizScrollbar = Tkinter.Scrollbar(self,
bg=self.cget('bg'),
command=self.canvas.xview,
orient=Tkinter.HORIZONTAL,
borderwidth=1)
self.canvas.configure(xscrollcommand=self.horizScrollbar.set)
if scrollY:
self.vertScrollbar = Tkinter.Scrollbar(self,
bg=self.cget('bg'),
command=self.canvas.yview,
orient=Tkinter.VERTICAL,
borderwidth=1)
self.canvas.configure(yscrollcommand=self.vertScrollbar.set)
canvas.bind('<Button-1>', self._mouseSingleClick)
if not isWindowsOS():
canvas.bind('<Button-4>', self.scrollUp)
canvas.bind('<Button-5>', self.scrollDown)
else:
canvas.bind('<MouseWheel>', self._windowsOsScroll)
canvas.bind('<Double-1>', self._mouseDoubleClick)
canvas.bind('<B1-Motion>', self._mouseDrag)
canvas.bind('<ButtonRelease-1>', self._mouseRelease)
canvas.bind('<Motion>', self._mouseEnter)
canvas.bind('<Enter>', self._mouseEnter)
canvas.bind('<Leave>', self._mouseLeave)
canvas.bind('<KeyPress-Up>', self._moveUp)
canvas.bind('<KeyPress-Down>', self._moveDown)
canvas.bind('<KeyPress-Right>', self._moveRight)
canvas.bind('<KeyPress-Left>', self._moveLeft)
canvas.bind('<KeyPress-Delete>', self.deleteSelected)
self.bind('<Configure>', self._resizeAfter)
self.menu = Menu(self, tearoff=False)
alignItems = [{
'kind': 'command',
'label': 'Y axis',
'command': self._alignHorizontal
}, {
'kind': 'command',
'label': 'X axis',
'command': self._alignVertical
}]
distributeItems = [{
'kind': 'command',
'label': 'Horizontal',
'command': self._distributeHorizontal
}, {
'kind': 'command',
'label': 'Verical',
'command': self._distributeVertical
}]
menuItems = [
{
'kind': 'cascade',
'label': 'Align',
'submenu': alignItems
}, #0
{
'kind': 'cascade',
'label': 'Distribute',
'submenu': distributeItems
}, #1
{
'kind': 'command',
'label': 'Link Selected',
'command': self.linkSelected
}, #2
{
'kind': 'command',
'label': 'Reset Links',
'command': self._resetLinks
}, #3
{
'kind': 'separator'
},
{
'kind': 'command',
'label': 'Delete Links', #5
'command': self.deleteLinks
},
{
'kind': 'command',
'label': 'Delete Items', #6
'command': self.deleteNodes
},
{
'kind': 'separator'
},
{
'kind': 'command',
'label': 'Save PostScript File',
'command': self.printCanvas
},
]
self.menuItems = menuItems
self.menu.setMenuItems(menuItems)
canvas.bind('<ButtonPress-3>', self._popupMenu)
self._drawAfter()
def setProjectMenu(self):
ProjectMenu = 'Project'
# Imports submenu
importsMenu = Menu(self.menubar, tearoff=False)
importsMenu.add_command(label='Via Format Converter',
shortcut='F',
command=self.runFormatConverter)
importsMenu.add_command(label='NMR-STAR 2.1.1',
command=self.importNmrStar211)
importsMenu.add_command(label='NMR-STAR 3.1',
shortcut='N',
command=self.importNmrStar31)
importsMenu.add_command(label='PDB 3.20',
shortcut='P',
command=self.importPdb)
importsMenu.add_command(label='Coordinates (PDB-style)',
shortcut='C',
command=self.importCoordinates)
# Preferences submenu
fontsMenu = FontMenu(self.menubar,
self.selectFont,
sizes=(8, 10, 12),
doItalic=False,
doBoldItalic=False,
tearoff=0)
prefsMenu = Menu(self.menubar, tearoff=False)
prefsMenu.add_cascade(
label='Fonts',
shortcut='F',
image=self.iconFont,
compound='left',
menu=fontsMenu,
tipText='Select font to use in the graphical interface')
prefsMenu.add_command(label='Colour Schemes',
image=self.iconTable,
compound='left',
shortcut='C',
tipText='Edit and create colour schemes',
command=self.editColorSchemes)
prefsMenu.add_command(
label='Residue Codes',
image=self.iconTable,
compound='left',
shortcut='R',
tipText=
'User-specified codes that override the standard residue names',
command=self.editResidueCodes)
prefsMenu.add_command(label='User Options',
image=self.iconTable,
compound='left',
shortcut='U',
tipText='General options for Analysis behaviour',
command=self.editProfiles)
#
menu = Menu(self.menubar, tearoff=0)
menu.add_command(
label='New',
shortcut='N',
image=self.iconNewWindow,
compound='left',
command=self.newProject,
tipText='Create a new, blank CCPN project (closes any open project)'
)
menu.add_command(
label='Open Project',
shortcut='O',
image=self.iconOpen,
compound='left',
command=self.openProject,
tipText=
'Open a new CCPN project by selecting a project directory on disk')
menu.add_command(
label='Open Spectra',
shortcut='p',
image=self.iconOpenFile,
compound='left',
command=self.openSpectrum,
tipText=
'Open spectrum data fom disk, creating a default CCPN project if needed'
)
menu.add_command(label='Save',
shortcut='S',
image=self.iconSave,
compound='left',
command=self.saveProject,
tipText='Save the current CCPN project on disk')
menu.add_command(
label='Save As',
shortcut='A',
image=self.iconSaveAs,
compound='left',
command=self.saveAsProject,
tipText=
'Save the current CCPN project under a different name (project directory)'
)
menu.add_cascade(label='Import',
shortcut='I',
image=self.iconImport,
compound='left',
menu=importsMenu)
menu.add_command(label='Close',
shortcut='C',
image=self.iconClose,
compound='left',
command=self.closeProject,
tipText='Close the current CCPN project')
menu.add_command(
label='Quit',
shortcut='Q',
image=self.iconQuit,
compound='left',
command=self.quit,
tipText='Quit Extend-NMR, closing any open CCPN project')
menu.add_separator()
menu.add_cascade(label='Preferences',
shortcut='P',
image=self.iconPrefs,
compound='left',
menu=prefsMenu)
menu.add_command(
label='Validate',
shortcut='V',
image=self.iconTool,
compound='left',
command=self.validateProject,
tipText=
'Check the current CCPN project for data model consistency errors')
menu.add_command(
label='Backup',
shortcut='B',
image=self.iconTool,
compound='left',
command=self.backupProject,
tipText='Setup options for automated backup of CCPN project data')
menu.add_command(
label='Archive',
shortcut='r',
image=self.iconTool,
compound='left',
command=self.archiveProject,
tipText=
'Save the current CCPN project in an archived form, e.g. tar gzipped'
)
self.menubar.add_cascade(label=ProjectMenu, shortcut='j', menu=menu)
self.menus[ProjectMenu] = menu
self.menu_items[ProjectMenu] = [
'New',
'Open Project',
'Open Spectra',
'Save',
'Save As',
'Import',
'Close',
'Quit',
'Preferences',
'Validate',
'Backup',
'Archive',
]
# Menus that area ctive in absence of a project
#for ii in (0,1,2,7,13,15):
for ii in (
0,
1,
2,
7,
):
self.fixedActiveMenus[(ProjectMenu, ii)] = True
def makeAppearanceMenu(self):
# The fonts menu is a pre-created widget
fontsMenu = FontMenu(self.mainMenu, self.setFont, sizes=(8,10,12),
doItalic=0, doBoldItalic=0, tearoff=0)
# Plot color schemes
colorMenu = Menu(self.mainMenu, tearoff=0)
colorMenu.add_radiobutton(label='Red', command=self.colorSchemeRed,)
colorMenu.add_radiobutton(label='Rainbow', command=self.colorSchemeRainbow,)
#colorMenu.add_radiobutton(label='Black', shortcut='B', command=self.colorSchemeBlack)
#colorMenu.add_radiobutton(label='White', shortcut='W', command=self.colorSchemeWhite)
# Submenu of the main menu
menu = Menu(self.mainMenu, tearoff=0)
# Only Fonts option so far
menu.add_cascade(label='Plot Colour Scheme',shortcut='C', menu=colorMenu)
menu.add_cascade(label='Fonts', shortcut='F', menu=fontsMenu)
self.mainMenu.add_cascade(label='Appearance', shortcut='A', menu=menu)
menu.options = ['Plot Colour Scheme','Fonts']
return menu
def makeProjectMenu(self):
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
# Add various options to the menu and state the functions they call
menu.add_command(label='New', shortcut='N', command=self.newProject)
menu.add_command(label='Open', shortcut='O', command=self.openProject)
menu.add_command(label='Close',
shortcut='C',
command=self.closeProject)
menu.add_command(label='Save', shortcut='S', command=self.saveProject)
menu.add_command(label='Save As',
shortcut='A',
command=self.saveAsProject)
menu.add_command(label='Quit', shortcut='Q', command=self.quit)
menu.add_command(label='Version',
shortcut='V',
command=self.showVersion)
self.mainMenu.add_cascade(label='Project', shortcut='P', menu=menu)
menu.options = [
'New', 'Open', 'Close', 'Save', 'Save As', 'Quit', 'Version'
]
return menu
class ApplicationPopup(BasePopup):
help_url = 'http://www.ccpn.ac.uk'
def __init__(self, root, programName='Ccpn Workflow Management System'):
self.programName = programName
self.font = DEFAULT_FONT
# Application object needed to store application-specific data with project
self.application = Application(name=PROGRAM_NAME)
self.versionInfo = 'Version ' + VERSION
self.ariaProjectFile = None
self.username = None
# what do these do??
self.updateFuncs = []
self.projButtons = []
# may need these in the end
self.ariaPaths = []
self.isdPaths = []
# FIXME JMCI
# hard code this for now. this should be initialised from file
# read during GUI login and then extended using the menu options
# should set a placeholder. In fact, this placeholder will also have
# a default user (guest) so that there is always a structure to
# extend should the user wish to start from scratch and not log in
self.repList = RepositoryList()
self.currentTask = None
# going to stick in shortcuts to frames for quick access
self.frameShortcuts = {}
# Application popup is a superclass of memops.editor.BasePoup
BasePopup.__init__(self,
parent=root,
title=PROGRAM_NAME,
location='+100+100',
class_=self.application.name)
self.setTitle(PROGRAM_NAME)
def body(self, guiParent):
self.geometry('700x600')
# Ensure that the first row and column in popup expand
guiParent.grid_rowconfigure(0, weight=1)
guiParent.grid_columnconfigure(0, weight=1, minsize=200)
frame = Frame(guiParent) # Body widgets can be put in this frame
frame.grid()
# this is going to set up the options on the tabs. Really we need
# stronger bookeeping between the options and the frames. it
# might make sense to define a master dictionary with option_name
# => index. We can use this dictionary to build up the software
# options and can also use it to define any refreshes etc (although
# these would be better done through notifiers)
softwareOpts = [
'Repository', 'Project', 'Process', 'Client Tasks', 'Server Tasks',
'Data Exchange', 'Workflow', 'Protocols', 'User'
]
# FIXME JMCI
# we should have a tidier tabbed frame. ned to discuss rules with
# tjs but it would seem to make sense to have the tabs stretch
# across the entire top of the frame. Check the existing options
# first, though
self.tabbedFrame = TabbedFrame(guiParent,
options=softwareOpts,
toggleOff=False,
selected=0)
self.tabbedFrame.grid(row=0, column=0, sticky='nsew')
frames = self.tabbedFrame.frames
# Logos
ccpnDir = getTopDirectory()
imageDir = os.path.join(ccpnDir, 'python', 'extendNmr', 'images')
imageFile = os.path.join(imageDir, 'CcpnLogo.gif')
self.ccpnLogo = Tkinter.PhotoImage(file=imageFile)
# Dictionary to store popups opened by this application - e.g. need to close upon quit
self.popups = {}
# Default font
self.font = 'Helvetica 10'
# Closing the window from the desktop environment calls the proper quit
self.protocol('WM_DELETE_WINDOW', self.quit)
# jmci we are going to have to change these drastically
self.mainMenu = Menu(self)
self.userMenu = self.makeUserMenu()
self.repositoryMenu = self.makeRepositoryMenu()
self.otherMenu = self.makeOtherMenu()
# Put the top level menu
self.config(menu=self.mainMenu)
self.initRepository(frames[0])
self.initProjectFrame(frames[1])
self.initWms(frames[2])
self.initTasks(frames[3])
self.initDataExch(frames[5])
self.initWorkflow(frames[6])
self.initProtocol(frames[7])
self.initUserFrame(frames[8])
self.initProject()
if not self.project:
for button in self.projButtons:
button.disable()
# the main client side daemon. This is going to run in the background
# and control the task processing
self.taskDaemon = TaskManager(self)
self.taskDaemon.active = False
self.taskDaemon.start()
## THE TABBED FRAMES ##
def initRepository(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
repositoryFrame = RepositoryFrame(frame, basePopup=self)
repositoryFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(repositoryFrame.updateAll)
def initProjectFrame(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
self.projectFrame = ProjectFrame(frame, basePopup=self)
self.projectFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(self.projectFrame.updateAll)
def initWms(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
extendNmrFrame = ExtendNmrFrame(frame, basePopup=self)
extendNmrFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(extendNmrFrame.updateAll)
def initTasks(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
tasksFrame = TasksFrame(frame, self)
tasksFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(tasksFrame.updateAll)
def initDataExch(self, frame):
row = 0
frame.config(bg='#E6E6E6')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
dataExchFrame = DataExchFrame(frame, basePopup=self)
dataExchFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(dataExchFrame.updateAll)
def initWorkflow(self, frame):
row = 0
frame.config(bg='#FFFFFF')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
workflowFrame = WorkflowFrame(frame, basePopup=self)
workflowFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(workflowFrame.updateAll)
def initProtocol(self, frame):
row = 0
frame.config(bg='#FFFFFF')
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
protocolFrame = ProtocolFrame(frame, basePopup=self)
protocolFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(protocolFrame.updateAll)
def initUserFrame(self, frame):
frame.grid_columnconfigure(0, weight=1)
frame.grid_rowconfigure(1, weight=1)
row = 0
frame.config(bg='#FFFFFF')
userFrame = UserFrame(frame, basePopup=self)
userFrame.grid(row=1, column=0, sticky='nsew')
self.updateFuncs.append(userFrame.updateAll)
## The Menu ##
def makeUserMenu(self):
menu = Menu(self.mainMenu, tearoff=0)
menu.add_command(label='Log In',
shortcut='I',
command=self.openLoginPopup)
menu.add_command(label='Log Out', shortcut='O', command=self.logout)
menu.add_command(label='Save Profile',
shortcut='S',
command=self.tmpCall)
menu.add_command(label='View Profile',
shortcut='V',
command=self.tmpCall)
menu.add_command(label='Create Profile',
shortcut='C',
command=self.tmpCall)
menu.add_command(label='Edit Profile',
shortcut='E',
command=self.tmpCall)
self.mainMenu.add_cascade(label='User', shortcut='U', menu=menu)
menu.options = [
'Log In', 'Log Out', 'Save Profile', 'View Profile',
'Create Profile', 'Edit Profile'
]
return menu
def makeRepositoryMenu(self):
self.repMenu = Menu(self.mainMenu, tearoff=0)
# Add various options to the menu and state the functions they call
self.repMenu.add_command(label='Manager',
shortcut='M',
command=self.tmpCall)
self.repMenu.add_command(label='Connect',
shortcut='C',
command=self.openRepository)
# doesn't really work to have a disconnect; we do not have a list
# of repositories and so would it refer to? Better to do this from
# within the RepositoryFrame
self.repMenu.add_command(label='Disconnect',
shortcut='D',
command=self.tmpCall)
# again, this is functionality that would make sense but which it is hard to put
# in the top level menu because it is not obvious which repository it refers
# to
self.repMenu.add_command(label='Import Project',
shortcut='I',
command=self.tmpCall)
self.repMenu.add_command(label='Export Project',
shortcut='E',
command=self.tmpCall)
# FIXME JMCI
# the quit option needs to be tied to a dialogue box that asks whether
# the current connection state should be saved. This will have to be
# secured and so means that the GUI should have a login itself (beyond
# the logins for the various resources).
self.repMenu.add_command(label='Quit', shortcut='Q', command=self.quit)
self.mainMenu.add_cascade(label='Repository',
shortcut='R',
menu=self.repMenu)
self.repMenu.options = [
'Connect', 'Disconnect', 'Import Project', 'Export Project', 'Quit'
]
return self.repMenu
def makeProjectMenu(self):
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
# Add various options to the menu and state the functions they call
menu.add_command(label='New', shortcut='N', command=self.newProject)
menu.add_command(label='Open', shortcut='O', command=self.openProject)
menu.add_command(label='Close',
shortcut='C',
command=self.closeProject)
menu.add_command(label='Save', shortcut='S', command=self.saveProject)
menu.add_command(label='Save As',
shortcut='A',
command=self.saveAsProject)
menu.add_command(label='Quit', shortcut='Q', command=self.quit)
menu.add_command(label='Version',
shortcut='V',
command=self.showVersion)
self.mainMenu.add_cascade(label='Project', shortcut='P', menu=menu)
menu.options = [
'New', 'Open', 'Close', 'Save', 'Save As', 'Quit', 'Version'
]
return menu
def makeOtherMenu(self):
# The fonts menu is a pre-created widget
fontsMenu = FontMenu(self.mainMenu,
self.setFont,
sizes=(8, 10, 12),
doItalic=0,
doBoldItalic=0,
tearoff=0)
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
# Only Fonts option so far
menu.add_cascade(label='Fonts', shortcut='F', menu=fontsMenu)
self.mainMenu.add_cascade(label='Options', shortcut='O', menu=menu)
menu.options = [
'Fonts',
]
return menu
def makeCcpNmrMenu(self):
try:
from ccpnmr.analysis.AnalysisPopup import AnalysisPopup
haveAnalysis = True
except ImportError:
haveAnalysis = False
try:
from ccpnmr.format.gui.FormatConverter import FormatConverter
from ccpnmr.format.gui.DataShifter import DataShifter
haveFormatConv = True
except ImportError:
haveFormatConv = False
menu = Menu(self.mainMenu, tearoff=0)
if haveAnalysis:
menu.add_command(label='Analysis',
shortcut='A',
command=self.ccpNmrAnalysis)
else:
menu.add_command(label='Analysis ** NOT INSTALLED **',
shortcut='A',
command=None)
if haveFormatConv:
menu.add_command(label='Format Converter',
shortcut='F',
command=self.ccpNmrFormatConverter)
menu.add_command(label='Data Shifter',
shortcut='D',
command=self.ccpNmrDataShifter)
else:
menu.add_command(label='Format Converter ** NOT INSTALLED **',
shortcut='F',
command=None)
menu.add_command(label='Data Shifter ** NOT INSTALLED **',
shortcut='D',
command=None)
self.mainMenu.add_cascade(label='CcpNmr', shortcut='C', menu=menu)
menu.options = ['Analysis', 'Format Converter', 'Data Shifter']
return menu
def ccpNmrAnalysis(self, cacheSize=64):
from ccpnmr.analysis.AnalysisPopup import AnalysisPopup
analysis = AnalysisPopup(self, cache_size=cacheSize, glDirect=None)
analysis.update_idletasks() # fast
if self.project:
analysis.initProject(self.project)
def ccpNmrFormatConverter(self):
from ccpnmr.format.gui.FormatConverter import FormatConverter
fc = FormatConverter(self, threading=False, project=self.project)
fc.open()
if self.project:
fc.initProject(self.project)
def ccpNmrDataShifter(self):
from ccpnmr.format.gui.DataShifter import DataShifter
ds = DataShifter(self)
ds.open()
def newProject(self):
if self.project:
# Project already present
if not self.closeProject():
# If we don't close the current project do nothing
return
name = askString(title='Project name',
prompt='Enter project name:',
parent=self)
if name:
# Make the API Project object
project = Implementation.MemopsRoot(name=name)
nmrProject = project.newNmrProject(name=name)
self.initProject(project)
# placeholder method until we write code
def tmpCall(self):
return
def openProject(self):
if self.project:
if not self.closeProject():
return
self.openPopup('open_project',
OpenProjectPopup,
callback=self.initProject)
def openLoginPopup(self):
# at the moment we do this through methods in the popup. It
# would be much more sensible to do this through some
# sort of callback.
login_popup = LoginPopup(self)
# really we want to imoblise the rest. how to do?
def setRepository(self, rep):
self.repList.currentRepository = rep
if self.frameShortcuts.has_key('Repository'):
self.frameShortcuts['Repository'].drawFrame()
if self.frameShortcuts.has_key('Tasks'):
self.frameShortcuts['Tasks'].drawFrame()
#for ff in self.tabbedFrame.frames[0].children.values():
# ff.draw()
#for ff in self.tabbedFrame.frames[3].children.values():
# ff.draw()
for ff in self.tabbedFrame.frames[8].children.values():
ff.draw()
def openRepository(self):
rep_popup = RepositoryPropertiesPopup(self)
def closeRepository(self):
pass
def logout(self):
self.setUsername(None)
self.repList = RepositoryList()
print 'in logout ', self.repList
print '#########################'
print self.tabbedFrame.frames[0].__dict__
print '#########################'
if self.frameShortcuts.has_key('Repository'):
self.frameShortcuts['Repository'].drawFrame()
#for ff in self.tabbedFrame.frames[0].children.values():
# ff.draw()
for ff in self.tabbedFrame.frames[8].children.values():
ff.draw()
def openPopup(self, popup_name, clazz, oldStyle=False, *args, **kw):
popup = self.popups.get(popup_name)
if (popup):
popup.open()
else:
if self.project:
analysisProfile = self.analysisProfile
else:
analysisProfile = None
if analysisProfile:
transient = analysisProfile.transientDialogs
else:
transient = True
name = popup_name
if (oldStyle):
popup = self.popups[popup_name] = clazz(self,
transient=transient,
*args,
**kw)
else:
popup = self.popups[popup_name] = clazz(self,
project=self.project,
popup_name=name,
transient=transient,
*args,
**kw)
# above automatically opens popup
return popup
def closeProject(self, queryClose=True, querySave=True):
if queryClose:
if not showYesNo(
'Close project', 'Close current project?', parent=self):
return False
if querySave:
if not self.checkSaving():
return False
self.destroyPopups()
self.initProject()
return True
def saveProject(self):
self.saveFile()
# NBNB Rasmus 22/8/08 changed to fit AnalysisPopup (and removed 'isStored' bug)
#if (self.project.isStored):
# self.saveFile()
#else:
# self.askSaveFile()
def saveAsProject(self):
self.askSaveFile()
def showVersion(self):
showInfo('Version', self.versionInfo, parent=self)
def changeFont(self, analysisProfile):
if analysisProfile is self.analysisProfile:
if self.font != analysisProfile.font:
self.font = analysisProfile.font or DEFAULT_FONT
self.setFont()
def selectFont(self, font): # Only called from main menu option
if self.project:
self.analysisProfile.font = font
def setFont(self, font=None, popup=None):
if font is None:
font = self.font or DEFAULT_FONT
else:
self.font = font
if not popup:
popup = self
childList = popup.children.values()
classes = [
Tkinter.Button, Tkinter.Label, Tkinter.Menu, Tkinter.Entry,
Tkinter.Checkbutton, Tkinter.Radiobutton
]
for child in childList:
for clazz in classes:
if isinstance(child, clazz):
if hasattr(child, 'font'):
if not child.font:
child.config(font=font)
else:
child.config(font=font)
break
if isinstance(child, Tkinter.Frame):
child.font = font
elif isinstance(child, ScrolledMatrix):
child.setFont(font)
if hasattr(child, 'children'):
childList.extend(child.children.values())
def initProject(self, project=None):
self.project = project
if project:
self.initTopObjects(self.project)
self.project.application = self.application
self.setFont()
webBrowser = ProjectWebBrowser(self.top,
popup=self,
project=project)
#self.helpButton.config(command = lambda url=self.help_url: webBrowser.open(url) )
for i, func in enumerate(self.updateFuncs):
func(project)
for button in self.projButtons:
button.enable()
self.setupSoftware()
else:
for button in self.projButtons:
button.disable()
self.setMenuState()
def setUsername(self, name):
self.username = name
print 'set username ', self.username
# jmci FIXME
# need to look into this carefully and analyse the possible
# states
def setMenuState(self):
if self.project:
state = Tkinter.NORMAL
else:
state = Tkinter.DISABLED
# Disable bits of the project menu if there's no project
#for option in ('Save','Save As','Close'):
# i = self.projectMenu.options.index(option)
# self.projectMenu.entryconfig(i, state=state)
# Disable other manus if there's no project
#for menu in [self.otherMenu,]: # Include more menus in this list
# for i in range(len(menu.options)):
# menu.entryconfig(i, state=state)
def setupSoftware(self):
project = self.project
methodStore = project.currentMethodStore or \
project.findFirstMethodStore() or \
project.newMethodStore(name=project.name)
software = methodStore.findFirstSoftware(name=PROGRAM_NAME,
version=VERSION)
if not software:
software = methodStore.newSoftware(name=PROGRAM_NAME,
version=VERSION)
#software.vendorName = 'PDBe & CCPN'
#software.vendorAddress = ''
#software.vendorWebAddress = 'http:'
#software.details = ''
def askSaveFile(self):
popup = self.openPopup('save_project', SaveProjectPopup)
popup.refresh()
def modalAskSaveFile(self):
popup = SaveProjectPopup(self,
project=self.project,
dismiss_text='Cancel Quit',
modal=True)
did_save = popup.did_save
popup.destroy()
return did_save
def quitSaveProject(self):
if (self.project.activeRepositories):
return self.saveFile()
else:
return self.modalAskSaveFile()
def destroyPopups(self):
for key in self.popups.keys():
popup = self.popups[key]
popup.destroy()
self.popups = {}
## WMS methods
# should maybe merge this with setUsername
# this will read a config file that stores user setups. How this
# is done TBD so hack for now and just return
def readConfig(self, userName):
# this should return the full RepositoryList structure. In reality this
# will parse from file. set it by hand from here for now for speed
repList = RepositoryList(userName)
rep1 = repList.newRepository('remote', 'localhost:8080/HalxService',
'ccpn', 'remote')
repList.currentRepository = rep1
# should these be directory objects?
repList.current_export_dir = '/home/jionides/work/CCPN/test_JMCI_data'
repList.current_import_dir = '/home/jionides/work/CCPN/test_EXP_data'
self.repList = repList
print 'in readconfig '
self.setRepository(rep1)
# really should be done through notifiers
if self.frameShortcuts.has_key('Repository'):
self.frameShortcuts['Repository'].drawFrame()
if self.frameShortcuts.has_key('Tasks'):
self.frameShortcuts['Tasks'].drawFrame()
if self.frameShortcuts.has_key('DataExch'):
self.frameShortcuts['DataExch'].drawFrame()
for ff in self.tabbedFrame.frames[8].children.values():
ff.draw()
# want to update the top menu. The idea should be to add a bar item
# and then to list all the repositories underneath. Clicking on a given
# repository will set the home repository as current. That seems to
# be a good sensible way of simplifying the interface in a expected
# way. We could, alternatively, use tabs.
opts = {}
self.repMenu.add('separator', **opts)
for rep in repList.repositories:
item = {
'command': lambda rep=rep: self.setRepository(rep),
'label': rep.name
}
self.repMenu.add('comman', **item)
self.repMenu.config()
## end WMS methods
def copyModifiedStorages(self):
modifiedStorages = [
storage for storage in self.project.storages if storage.isModified
]
if (self.project.isModified):
modifiedStorages.append(self.project)
for storage in modifiedStorages:
self.copyStorage(storage)
def saveFile(self):
if not self.project:
return False
try:
saveProject(self.project, createFallback=True)
print 'successfully saved project'
return True
except IOError, e:
showError('Saving file', str(e), parent=self)
return False
def makeProjectMenu(self):
importsMenu = Menu(self.mainMenu, tearoff=False)
importsMenu.add_command(label='Fasta Sequence',command=self.importFastaSeq)
importsMenu.add_command(label='NMR-STAR 2.1.1', command=self.importNmrStar211)
importsMenu.add_command(label='NMR-STAR 3.1', command=self.importNmrStar31)
importsMenu.add_command(label='PDB 3.20',command=self.importPdb)
importsMenu.add_command(label='PDB Coords',command=self.importPdbCoords)
#importsMenu.add_command(label='CNS Distance Restraints',command=self.importCnsDistance)
exportsMenu = Menu(self.mainMenu, tearoff=False)
exportsMenu.add_command(label='NMR-STAR 3.1', command=self.eciFrame.exportNmrStar31)
exportsMenu.add_command(label='PDB Coords',command=self.eciFrame.exportPdb)
#exportsMenu.add_command(label='CNS Distance Restraints',command=self.eciFrame.exportCnsDistance)
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
# Add various options to the menu and state the functions they call
menu.add_command(label='New', shortcut='N', command=self.newProject)
menu.add_command(label='Open', shortcut='O', command=self.openProject)
menu.add_command(label='Close', shortcut='C', command=self.closeProject)
menu.add_command(label='Save', shortcut='S', command=self.saveProject)
menu.add_command(label='Save As', shortcut='A', command=self.saveAsProject)
menu.add_cascade(label='Import', shortcut='I', menu=importsMenu)
menu.add_cascade(label='Export', shortcut='E', menu=exportsMenu)
menu.add_command(label='Quit', shortcut='Q', command=self.quit)
menu.add_command(label='Version', shortcut='V', command=self.showVersion)
self.mainMenu.add_cascade(label='Project', shortcut='P', menu=menu)
menu.options = ['New','Open','Close','Save','Save As','Import','Export','Quit','Version']
return menu
class DataFileImportGui(BasePopup):
# TODO CHANGE
help_url = 'http://www.ebi.ac.uk/pdbe'
def __init__(self, root):
self.root = root
self.font = DEFAULT_FONT
# Application object needed to store application-specific data with project
self.application = Application(name=PROGRAM_NAME)
self.versionInfo = VERSION
ccpnProjectName = askString(
"CCPN project name", 'Please give a name to this import session:')
self.fcWrapper = FormatConverterWrapper(
ccpnProjectName=ccpnProjectName, guiRoot=self)
self.project = self.fcWrapper.formatConversion.ccpnProject
# Application popup is a superclass of memops.editor.BasePoup
BasePopup.__init__(self,
parent=root,
title=PROGRAM_NAME,
location='+100+100',
class_=self.application.name)
self.setTitle(PROGRAM_NAME)
def body(self, guiParent):
self.geometry('600x350')
# Ensure that the first row and column in popup expand
guiParent.expandGrid(0, 0)
self.importFrame = DataFileImportFrame(guiParent,
basePopup=self,
grid=(0, 0))
# Dictionary to store popups opened by this application - e.g. need to close upon quit
self.popups = {}
# Default font
self.font = DEFAULT_FONT
# Closing the window from the desktop environment calls the proper quit
self.protocol('WM_DELETE_WINDOW', self.quit)
self.mainMenu = Menu(self)
self.projectMenu = self.makeProjectMenu()
self.mainMenu.add_command(label='Formats',
shortcut='F',
command=self.importFrame.showFormats)
self.mainMenu.add_command(
label='Help',
shortcut='H',
command=self.importFrame.showMainInstructions)
# Put the main menu
self.config(menu=self.mainMenu)
self.setMenuState()
def makeProjectMenu(self):
# Submenu of the min menu
menu = Menu(self.mainMenu, tearoff=0)
menu.add_command(label='Save', shortcut='S', command=self.saveProject)
menu.add_command(label='Save As',
shortcut='A',
command=self.saveAsProject)
menu.add_command(label='Quit', shortcut='Q', command=self.quit)
menu.add_command(label='Version',
shortcut='V',
command=self.showVersion)
self.mainMenu.add_cascade(label='Project', shortcut='P', menu=menu)
menu.options = ['Save', 'Save As', 'Quit', 'Version']
return menu
def saveProject(self):
self.saveFile()
def saveAsProject(self):
self.askSaveFile()
def showVersion(self):
showInfo('Version', 'Version ' + self.versionInfo, parent=self)
def setMenuState(self):
state = Tkinter.NORMAL
for option in ('Save', 'Save As', 'Quit', 'Version'):
i = self.projectMenu.options.index(option)
self.projectMenu.entryconfig(i, state=state)
def askSaveFile(self):
popup = self.openPopup('save_project', SaveProjectPopup)
popup.refresh()
def modalAskSaveFile(self):
popup = SaveProjectPopup(self,
project=self.project,
dismiss_text='Cancel Quit',
modal=True)
did_save = popup.did_save
popup.destroy()
return did_save
def quitSaveProject(self):
if (self.project.activeRepositories):
return self.saveFile()
else:
return self.modalAskSaveFile()
"""
def destroyPopups(self):
for key in self.popups.keys():
popup = self.popups[key]
popup.destroy()
self.popups = {}
"""
def saveFile(self):
if not self.project:
return False
try:
saveProject(self.project, createFallback=True)
print 'successfully saved project'
return True
except IOError, e:
showError('Saving file', str(e), parent=self)
return False
def body(self, guiParent):
self.geometry('700x600')
# Ensure that the first row and column in popup expand
guiParent.grid_rowconfigure(0, weight=1)
guiParent.grid_columnconfigure(0, weight=1, minsize=200)
frame = Frame(guiParent) # Body widgets can be put in this frame
frame.grid()
# this is going to set up the options on the tabs. Really we need
# stronger bookeeping between the options and the frames. it
# might make sense to define a master dictionary with option_name
# => index. We can use this dictionary to build up the software
# options and can also use it to define any refreshes etc (although
# these would be better done through notifiers)
softwareOpts = [
'Repository', 'Project', 'Process', 'Client Tasks', 'Server Tasks',
'Data Exchange', 'Workflow', 'Protocols', 'User'
]
# FIXME JMCI
# we should have a tidier tabbed frame. ned to discuss rules with
# tjs but it would seem to make sense to have the tabs stretch
# across the entire top of the frame. Check the existing options
# first, though
self.tabbedFrame = TabbedFrame(guiParent,
options=softwareOpts,
toggleOff=False,
selected=0)
self.tabbedFrame.grid(row=0, column=0, sticky='nsew')
frames = self.tabbedFrame.frames
# Logos
ccpnDir = getTopDirectory()
imageDir = os.path.join(ccpnDir, 'python', 'extendNmr', 'images')
imageFile = os.path.join(imageDir, 'CcpnLogo.gif')
self.ccpnLogo = Tkinter.PhotoImage(file=imageFile)
# Dictionary to store popups opened by this application - e.g. need to close upon quit
self.popups = {}
# Default font
self.font = 'Helvetica 10'
# Closing the window from the desktop environment calls the proper quit
self.protocol('WM_DELETE_WINDOW', self.quit)
# jmci we are going to have to change these drastically
self.mainMenu = Menu(self)
self.userMenu = self.makeUserMenu()
self.repositoryMenu = self.makeRepositoryMenu()
self.otherMenu = self.makeOtherMenu()
# Put the top level menu
self.config(menu=self.mainMenu)
self.initRepository(frames[0])
self.initProjectFrame(frames[1])
self.initWms(frames[2])
self.initTasks(frames[3])
self.initDataExch(frames[5])
self.initWorkflow(frames[6])
self.initProtocol(frames[7])
self.initUserFrame(frames[8])
self.initProject()
if not self.project:
for button in self.projButtons:
button.disable()
# the main client side daemon. This is going to run in the background
# and control the task processing
self.taskDaemon = TaskManager(self)
self.taskDaemon.active = False
self.taskDaemon.start()
def __init__(self,
parent,
callback=None,
entries=None,
text_attr=None,
colors=None,
outline='#602000',
fill='#B05848',
label_color='#501000',
selected_index=-1,
indent='',
extra='',
sticky='w',
do_initial_callback=True,
force_callback=False,
*args,
**kw):
if (entries is None):
entries = []
Frame.__init__(self, parent, sticky=sticky, *args, **kw)
self.text_attr = text_attr
#indentation and extra string for popup information
self.indent = indent
self.extra = extra
self.callback = callback
self.do_initial_callback = do_initial_callback
self.force_callback = force_callback
frame = Frame(self)
#frame = parent
self.frame = frame
self.bg = frame.cget('bg')
self.outline = outline
self.fill = fill
self.label_color = label_color
self.menu = Menu(parent, tearoff=0, borderwidth=1, activeborderwidth=1)
self.menu.images = []
self.label = Label(self, foreground=label_color)
self.first_pass = True
#self.entries = entries
self.entries = []
self.colors = []
self.setup(entries, selected_index, colors=colors)
s = 10
self.canvas = Canvas(self, width=s, height=s, background=self.bg)
self.label.bind("<Button-1>", self.labelPopup)
# below does not work for some reason
#self.bind("<Button-1>", self.labelPopup)
# below does not work any more since can have submenus and
# no way to reach those with below since involves leaving menu
#self.menu.bind("<Leave>", self.popdown)
self.menu.bind("<Leave>", self.leave)
self.menu.bind("<Button-1>", self.buttonPress)
self.poppedUpSubmenu = False
self.canvas.bind("<Button-1>", self.canvasPopup)
self.canvas.bind("<Configure>", self.resizeCallback)
self.label.grid(row=0, column=0, sticky=Tkinter.W)
self.canvas.grid(row=0, column=1, sticky=Tkinter.E, padx=2)
def makeUserMenu(self):
menu = Menu(self.mainMenu, tearoff=0)
menu.add_command(label='Log In',
shortcut='I',
command=self.openLoginPopup)
menu.add_command(label='Log Out', shortcut='O', command=self.logout)
menu.add_command(label='Save Profile',
shortcut='S',
command=self.tmpCall)
menu.add_command(label='View Profile',
shortcut='V',
command=self.tmpCall)
menu.add_command(label='Create Profile',
shortcut='C',
command=self.tmpCall)
menu.add_command(label='Edit Profile',
shortcut='E',
command=self.tmpCall)
self.mainMenu.add_cascade(label='User', shortcut='U', menu=menu)
menu.options = [
'Log In', 'Log Out', 'Save Profile', 'View Profile',
'Create Profile', 'Edit Profile'
]
return menu