def __init__(self, title, message, texts, objects=None, parent=None):
if parent is None:
parent = Tkinter.Tk()
#parent.withdraw()
self.root = parent
parent.protocol('WM_DELETE_WINDOW', self.destroy)
else:
self.root = None
Tkinter.Toplevel.__init__(self, parent)
self.resizable(0, 0)
self.parent = parent
self.title(title)
self.var = Tkinter.IntVar()
self.objects = objects or range(len(texts))
assert len(self.objects) == len(texts)
x = parent.winfo_rootx() + parent.winfo_width() / 2
y = parent.winfo_rooty() + parent.winfo_height() / 2
location = '+%d+%d' % (x, y)
if hasattr(parent, 'font'):
self.font = parent.font
else:
self.font = None
Tkinter.Toplevel.geometry(self, location)
Tkinter.Toplevel.lift(self, parent)
self.update_idletasks()
self.transient(parent)
self.protocol('WM_DELETE_WINDOW', self._null)
self.focus_force()
self.grab_set()
self.grid_rowconfigure(0, weight=1)
self.grid_columnconfigure(1, weight=1)
label = Label(self, text=message, grid=(0, 0))
self.config(bg=label.cget('bg'))
frame = Frame(self, grid=(1, 0))
_buttons = []
for i, text in enumerate(texts):
button = Button(frame,
text=text,
command=lambda j=i: self._click(j))
button.grid(row=i + 1, column=0, padx=2, pady=2, sticky='ew')
if objects[i] is None:
button.config(bg='#B0FFB0')
_buttons.append(button)
self._wait()
def body(self, master):
self.geometry('600x130')
master.grid_columnconfigure(1, weight=1)
for n in range(5):
master.grid_rowconfigure(n, weight=1)
row = 0
label = Label(master, text='Spectrum: ')
label.grid(row=row, column=0, sticky='e')
tipText = 'The spectrum for which the contour file is being added'
self.expt_spectrum = PulldownList(master,
callback=self.updateContourDir,
tipText=tipText)
self.expt_spectrum.grid(row=row, column=1, sticky='w')
row = row + 1
tipText = 'The location of the directory where contour files are stored on disk'
label = Label(master, text='Contour dir: ')
label.grid(row=row, column=0, sticky='e')
self.dir_label = Label(master, text='', tipText=tipText)
self.dir_label.grid(row=row, column=1, sticky='w')
row = row + 1
label = Label(
master,
text=
'(file will be copied into Contour dir if it is not already in there)'
)
label.grid(row=row, column=1, sticky='w')
row = row + 1
tipText = 'Browse for a file store contour data'
button = Button(master,
text='File name: ',
command=self.selectFile,
tipText=tipText)
button.grid(row=row, column=0, sticky='e')
tipText = 'Enter the name of the file to store contour data'
self.file_entry = Entry(master, tipText=tipText)
self.file_entry.grid(row=row, column=1, sticky='ew')
row = row + 1
texts = ['Add File']
commands = [self.addFile]
tipTexts = [
'Use the selected contour file in the current project, copying it to the contour directory if required',
]
self.buttons = UtilityButtonList(master,
texts=texts,
doClone=False,
tipTexts=tipTexts,
commands=commands,
helpUrl=self.help_url)
self.buttons.grid(row=row, column=0, columnspan=2, sticky='ew')
self.curateNotifiers(self.registerNotify)
self.updateSpectrum()
def body(self, master):
label = Tkinter.Label(master, text='label 1')
label.grid(row=0, column=0, sticky=Tkinter.EW)
label = Tkinter.Label(master, text='label 2')
label.grid(row=1, column=0, sticky=Tkinter.EW)
button = Button(master, text='ok', command=self.ok)
button.grid(row=2, column=0, sticky=Tkinter.EW)
button = Button(master, text='cancel', command=self.close)
button.grid(row=2, column=1, sticky=Tkinter.EW)
def body(self, master):
master.grid_columnconfigure(2, weight=1)
row = 0
label = Label(master, text='Data to export:')
label.grid(row=row, column=0, columnspan=3, sticky=Tkinter.W)
self.check_buttons = {}
i = 0
for heading in self.headings:
row = row + 1
isSelected = self.exportSelection.get(row, True)
self.check_buttons[i] = c = CheckButton(
master, selected=isSelected, callback=self.toggleCheckButton)
c.grid(row=row, column=1)
label = Label(master, text=heading)
label.grid(row=row, column=2, sticky=Tkinter.W)
i += 1
row = row + 1
button = Button(master, text='File:', command=self.findFile)
button.grid(row=row, column=0, sticky=Tkinter.W)
self.file_entry = Entry(master, text=self.file, width=30)
self.file_entry.grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.EW)
row = row + 1
label = Label(master, text='Format:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.format_menu = PulldownMenu(master, entries=exportFormats)
self.format_menu.grid(row=row,
column=1,
columnspan=2,
sticky=Tkinter.W)
row = row + 1
master.grid_rowconfigure(row, weight=1)
texts = ['Save']
commands = [self.ok]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
dismiss_text='Cancel')
buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
class ToggleLabel(Frame):
def __init__(self, parent, arrowSize = 12, outline='#5050b0', fill='#a0a0ff', font=None,
isArrowClosed = True, callback = None, text = '', *args, **kw):
apply(Frame.__init__, (self, parent) + args, kw)
self.grid_rowconfigure(0, weight=1)
self.grid_columnconfigure(1, weight=1)
self.arrow = ToggleArrow(self, arrowSize=arrowSize, outline=outline, fill=fill,
isArrowClosed=isArrowClosed, callback=callback)
self.arrow.grid(row=0, column=0, sticky=Tkinter.W)
if font:
self.label = Button(self, relief='flat',borderwidth=0, padx=1, pady=1, text=text, font=font, command=self.arrow.flipState)
else:
self.label = Button(self, relief='flat',borderwidth=0, padx=1, pady=1, text=text, command=self.arrow.flipState)
self.label.grid(row=0, column=1, sticky=Tkinter.W)
def arrowOn(self):
if self.arrow.isArrowClosed:
self.arrow.isArrowClosed = 0
self.arrow.drawArrow()
def arrowOff(self):
if not self.arrow.isArrowClosed:
self.arrow.isArrowClosed = 1
self.arrow.drawArrow()
def __getattr__(self, name):
# dispatch everything not defined by ToggleLabel to arrow widget
try:
return getattr(self.__dict__['arrow'], name)
except:
raise AttributeError, "%s instance has no attribute '%s'" % (self.__class__.__name__, name)
def createFindFrame(self, master):
frame = Frame(master)
frame.grid(row=0, column=0, sticky=Tkinter.W)
arrow = ToggleArrow(frame, callback=self.toggleFindFrame)
arrow.grid(row=0, column=0)
button = Button(frame, text='find:', command=self.findPhrase)
button.grid(row=0, column=1)
self.find_entry = Entry(frame,
width=20,
returnCallback=self.findPhrase)
self.find_entry.grid(row=0, column=2)
self.find_frame = frame = Frame(master)
entries = ('search forwards', 'search backwards')
self.direction_buttons = PulldownMenu(frame, entries=entries)
self.direction_buttons.grid(row=0, column=0, sticky=Tkinter.W, padx=5)
self.forwards_entries = entries = ('wrap search', 'stop at end')
self.backwards_entries = ('wrap search', 'stop at beginning')
self.wrap_buttons = PulldownMenu(frame, entries=entries)
self.wrap_buttons.grid(row=0, column=1, sticky=Tkinter.W, padx=5)
self.direction_buttons.callback = self.setWrapText
entries = ('case insensitive', 'case sensitive')
self.case_buttons = PulldownMenu(frame, entries=entries)
self.case_buttons.grid(row=0, column=2, sticky=Tkinter.W, padx=5)
entries = ('literal search', 'regex search')
self.pattern_buttons = PulldownMenu(frame, entries=entries)
self.pattern_buttons.grid(row=0, column=3, sticky=Tkinter.W, padx=5)
self.countVar = Tkinter.IntVar()
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 DataFileImportFrame(Frame):
"""
TODO: should I also ask for sample conditions info with chemical shifts? Or do in ECI - possible? Check!
"""
# TODO should go where?
email = '*****@*****.**'
defaultSelectText = "Select file."
fontOkColor = 'green3'
fontCheckColor = 'orange3'
fontBadColor = 'red3'
fontDefaultColor = 'black'
def __init__(self, parent, basePopup, *args, **kw):
#
# Variable initialisation
#
self.fcWrapper = basePopup.fcWrapper
self.project = basePopup.project
self.basePopup = basePopup
# TODO necessary?
if self.project:
self.nmrProject = self.project.currentNmrProject
self.entry = self.project.currentNmrEntryStore.findFirstEntry()
if not self.entry:
self.entry = self.project.currentNmrEntryStore.newEntry(
name=self.project.name)
else:
self.nmrProject = None
self.sequenceCoordinatesLoaded = False
self.shiftsLoaded = False
self.linkResDone = False
self.currentShiftList = None
self.shiftListChainPairs = []
self.moleculeList = []
self.moleculeDict = {}
#
# Frame setup
#
Frame.__init__(self, parent, **kw)
self.grid_columnconfigure(1, weight=1)
self.grid_rowconfigure(1, weight=1)
options = ['Import', 'Deposition']
tabbedFrame = TabbedFrame(self,
options=options,
callback=self.selectTab)
tabbedFrame.grid(row=1, column=0, columnspan=2, sticky='nsew')
self.tabbedFrame = tabbedFrame
frameA, frameD = tabbedFrame.frames
#
# Main
#
frameA.grid_columnconfigure(0, weight=1)
#frameA.grid_columnconfigure(1, weight=1) # Change to 2 if want 2 columns
frameA.grid_rowconfigure(12, weight=1)
#frameA.grid_rowconfigure(12, weight=1)
row = 0
div = LabelDivider(
frameA,
text=
'Select the full coordinate file or a sequence file (with info for a single molecule).',
justify='center',
grid=(row, 0),
gridSpan=(1, 1))
row += 1
self.sequenceCoordinatesImport = Button(
frameA,
text=self.defaultSelectText,
command=self.importSequenceOrCoords,
foreground=self.fontDefaultColor)
self.sequenceCoordinatesImport.grid(row=row, column=0, sticky='ew')
row += 1
label = Label(frameA, text="")
label.grid(row=row, column=0, sticky='ew')
row += 1
div = LabelDivider(
frameA,
text='Select the molecule relevant for your chemical shift file.',
justify='center',
grid=(row, 0),
gridSpan=(1, 1))
row += 1
self.moleculeSelect = Label(
frameA,
text="None available yet - import valid file first",
foreground=self.fontBadColor)
self.moleculeSelect.grid(row=row, column=0, sticky='ew')
self.moleculeSelectRow = row
row += 1
label = Label(frameA, text="")
label.grid(row=row, column=0, sticky='ew')
row += 1
div = LabelDivider(
frameA,
text=
'Select a chemical shift file with values only for the above molecule.',
justify='center',
grid=(row, 0),
gridSpan=(1, 1))
row += 1
self.shiftImport = Button(frameA,
text=self.defaultSelectText,
command=self.importShifts,
foreground=self.fontDefaultColor)
self.shiftImport.grid(row=row, column=0, sticky='ew')
row += 1
label = Label(frameA, text="")
label.grid(row=row, column=0, sticky='ew')
row += 1
div = LabelDivider(
frameA,
text='Consistency check between molecule and shift information.',
justify='center',
grid=(row, 0),
gridSpan=(2, 1))
row += 1
self.linkResCheckInfo = Label(frameA, text='')
self.linkResCheckInfo.grid(row=row, column=0, sticky='ew')
row += 1
div = Separator(frameA, grid=(row, 0), gridSpan=(1, 1))
row += 1
texts = ['Import new sequence', 'Import new set of shifts']
commands = [self.resetSequenceImport, self.resetShiftImport]
self.mainButtons = ButtonList(frameA, texts=texts, commands=commands)
self.mainButtons.grid(row=row, column=0, columnspan=2, sticky='ew')
self.mainButtons.buttons[0].config(foreground=self.fontDefaultColor)
#print row
self.frameA = frameA
#
# Not in use...
#
#frameX.grid_columnconfigure(0, weight=1)
#frameX.grid_columnconfigure(1, weight=1)
#frameX.grid_rowconfigure(1, weight=1)
#frameX.grid_rowconfigure(3, weight=1)
#
# Deposition, is updated after each successful import run.
#
frameD.grid_columnconfigure(0, weight=1)
frameD.grid_rowconfigure(5, weight=1)
self.frameD = frameD
row = 0
div = LabelDivider(frameD,
text='Imported data.',
justify='center',
grid=(row, 0),
gridSpan=(1, 2))
row += 1
self.depositionImportText = "\nImported %d shift list(s) for a total of %d shifts.\n\nImported %d molecule(s) and %d chain(s).\n\nImported %d model(s) for a total of %d atom coordinates.\n\nLinked %.2f%% of imported NMR information to %d chain(s)."
self.depositionImportLoc = (row, 0)
# These used for setting text above...
self.depositionImportNums = [0, 0, 0, 0, 0, 0, 0.0, 0]
self.importedShiftLists = []
self.connectedChains = []
self.depositionImportLabel = Label(frameD,
text=self.depositionImportText %
tuple(self.depositionImportNums),
foreground=self.fontBadColor)
self.depositionImportLabel.grid(row=row, column=0, sticky='ew')
row += 1
label = Label(frameD, text="")
label.grid(row=row, column=0, sticky='ew')
#
# Finalize the import part, proceed to ECI.
#
row += 1
div = LabelDivider(
frameD,
text=
'Import completed, save project and start Entry Completion Interface.',
justify='center',
grid=(row, 0),
gridSpan=(1, 1))
row += 1
self.eciStart = Button(frameD,
text="Finalise import",
command=self.finaliseImport,
foreground=self.fontBadColor)
self.eciStart.grid(row=row, column=0, sticky='ew')
def finaliseImport(self):
if not self.depositionImportNums[6]:
showWarning('Failure',
'Need connected molecule and shift information first')
return
if showYesNo(
"Save project and continue annotation",
"Are you sure you want to save this project and continue?",
parent=self):
if self.depositionImportNums[5] or showYesNo(
"No coordinates",
"No coordinates are available - are you sure you want to continue?",
parent=self):
showInfo("Project name",
"Your project will be saved in the %s directory." %
self.project.name,
parent=self)
self.project.saveModified()
#userData = self.project.findFirstRepository(name='userData')
#currentPath = userData.url.path
#currentProjectName = self.project.name
#projectDir = os.path.join(currentPath,currentProjectName)
eci = EntryCompletionGui(self.basePopup.root)
eci.initProject(self.project)
#
# File type determination and import
#
def createFileTypes(self, dataTypes):
fileTypes = [FileType('all', ['*'])]
for dataType in dataTypes:
formatNames = fileTypeDict[dataType].keys()
formatNames.sort()
for formatName in formatNames:
if formatName in self.fcWrapper.formatNameLists[dataType]:
fileTypes.append(
FileType(formatName,
fileTypeDict[dataType][formatName]))
return fileTypes
def getFileName(self, title, fileTypes):
fileSelectPopup = FileSelectPopup(
self,
file_types=fileTypes,
title=title,
dismiss_text='Cancel',
selected_file_must_exist=True,
multiSelect=False,
)
self.fileName = fileSelectPopup.getFile()
if not self.fileName:
showWarning('Failure',
'Please select an existing file.',
parent=self)
return False
return True
def importSequenceOrCoords(self):
dataTypes = ['sequence', 'coordinates']
fileTypes = self.createFileTypes(dataTypes)
if self.getFileName('Import sequence or coordinate file', fileTypes):
formatNameSuggestions = {}
for dataType in dataTypes:
tmpList = self.fcWrapper.determineFormatNamesForFile(
dataType, self.fileName)
if tmpList:
formatNameSuggestions[dataType] = tmpList
if not formatNameSuggestions:
showWarning(
'Failure',
'This file cannot be read by this software.\nPlease send the file with an explanation to %s.'
% self.email,
parent=self)
return False
#
# Let user select if multiple options, otherwise take default
#
if len(formatNameSuggestions) == 1 and len(formatNameSuggestions[
formatNameSuggestions.keys()[0]]) == 1:
dataType = formatNameSuggestions.keys()[0]
formatName = formatNameSuggestions[dataType][0]
if not showYesNo(
'File type detected',
'Reading as %s file in %s format. Is this correct?' %
(dataType, formatName),
parent=self):
showWarning(
'Failure',
'This file cannot be read by this software.\nPlease send the file with an explanation to %s.'
% self.email,
parent=self)
return False
else:
#
# Create a selection (hopefully user-understandable)
#
selectionList = []
selectionDict = {}
for dataType in dataTypes:
dataTypeString = dataType
if formatNameSuggestions.has_key(dataType):
formatNames = formatNameSuggestions[dataType]
formatNames.sort()
for formatName in formatNames:
selectionString = "%s file in %s format." % (
dataTypeString, formatName)
selectionList.append(selectionString)
selectionDict[selectionString] = (dataType,
formatName)
interaction = SelectionListPopup(self,
selectionList,
title='File format selection',
text='This is a:',
selectionDict=selectionDict,
dismissButton=True,
modal=True)
#
# Check if anything was selected...
#
dataType = formatName = None
if interaction.isSelected:
(dataType, formatName) = interaction.selection
else:
showWarning(
'Failure',
'This file cannot by read without a format selection.\nIf the correct format is not available, please send the file with an explanation to %s'
% self.email,
parent=self)
return False
#
# Now read the file, need to do some field updates!
#
(fileRead, fileInformation) = self.fcWrapper.readFile(
dataType, formatName, self.fileName)
if not fileRead:
showWarning(
'Failure',
'This file cannot be read by this software:%s\nPlease send the file with an explanation to %s.'
% (fileInformation, self.email),
parent=self)
return False
(conversionInfo, conversionSuccess) = (
self.fcWrapper.formatConversion.conversionInfo,
self.fcWrapper.formatConversion.conversionSuccess)
if not conversionSuccess:
showWarning(
'Failure',
'This file was read by the software but contains invalid information.\nPlease send the file with an explanation to %s.'
% self.email,
parent=self)
return False
#
# Set info if import worked OK
#
conversionLines = conversionInfo.split(": ")
showInfo("Import coordinate and/or sequence information",
":\n".join(conversionLines),
parent=self)
if dataType == 'sequence':
chains = self.fcWrapper.importReturns[dataType]
models = []
elif dataType == 'coordinates':
models = self.fcWrapper.importReturns[dataType]
chains = [
cChain.chain
for cChain in models[0].structureEnsemble.coordChains
]
self.sequenceCoordinatesImport.setText(
self.fileName) # TODO change color or something?
self.sequenceCoordinatesImport.configure(
foreground=self.fontOkColor)
self.sequenceCoordinatesLoaded = True
#
# Reset to list selector for further use
#
moleculeName = None
for chain in chains:
if chain in self.moleculeDict.values():
continue
numResidues = len(chain.residues)
if numResidues == 1:
residueText = "%s residue" % chain.findFirstResidue(
).ccpCode
else:
residueText = "%d residues" % numResidues
moleculeName = "%s (chain '%s', %s)" % (
chain.molecule.name, chain.code, residueText)
self.moleculeList.append(moleculeName)
self.moleculeDict[moleculeName] = chain
self.moleculeList.sort()
self.moleculeSelect.destroy()
if len(chains) == 1 and moleculeName:
selectedIndex = self.moleculeList.index(moleculeName)
else:
selectedIndex = 0
self.moleculeSelect = PulldownList(self.frameA,
texts=self.moleculeList,
index=selectedIndex,
sticky='ew')
self.moleculeSelect.grid(row=self.moleculeSelectRow, column=0)
#
# Now update Deposition tab
#
molecules = []
for chain in chains:
if not chain.molecule in molecules:
molecules.append(chain.molecule)
numCoords = 0
for model in models:
numCoords += len(model.coords)
self.updateDepositionImportLabel(molecules=len(molecules),
chains=len(chains),
models=len(models),
coordinates=numCoords)
# Add the molSystem to the entry!
if chains and not chains[0].molSystem == self.entry.molSystem:
self.entry.molSystem = chains[0].molSystem
self.updateAll()
def importShifts(self):
currentChain = self.getCurrentChain()
if not currentChain:
showWarning(
'Failure',
'Please first read in a sequence or coordinate file and select the molecule relevant for this shift list.',
parent=self)
return
elif self.currentShiftList:
shiftListChainPair = (self.currentShiftList, currentChain)
if shiftListChainPair in self.shiftListChainPairs:
showWarning(
'Failure',
"You already read in chemical shifts for this chain.\nPlease read in related shifts for the other chain(s), if present, or press the 'Import new set of shifts' button to read in a new set of shifts.",
parent=self)
return
dataType = 'shifts'
fileTypes = self.createFileTypes([dataType])
if self.getFileName('Import chemical shift file', fileTypes):
formatNameSuggestions = self.fcWrapper.determineFormatNamesForFile(
dataType, self.fileName)
if not formatNameSuggestions:
showWarning(
'Failure',
'This file cannot be read by this software.\nPlease send the file with an explanation to %s.'
% self.email,
parent=self)
return False
#
# Let user select if multiple options, otherwise take default
#
if len(formatNameSuggestions) == 1:
formatName = formatNameSuggestions[0]
if not showYesNo(
'File type detected',
'Reading as a chemical shift file in %s format. Is this correct?'
% formatName,
parent=self):
showWarning(
'Failure',
'This file cannot be read by this software.\nPlease send the file with an explanation to %s.'
% self.email,
parent=self)
return False
else:
#
# Create a selection (hopefully user-understandable)
#
selectionList = []
selectionDict = {}
formatNameSuggestions.sort()
for formatName in formatNameSuggestions:
selectionString = "chemical shift file in %s format." % (
formatName)
selectionList.append(selectionString)
selectionDict[selectionString] = formatName
interaction = SelectionListPopup(self,
selectionList,
title='File format selection',
text='This is a:',
selectionDict=selectionDict,
dismissButton=True,
modal=True)
#
# Check if anything was selected...
#
formatName = None
if interaction.isSelected:
formatName = interaction.selection
else:
showWarning(
'Failure',
'This file cannot by read without a format selection.\nIf the correct format is not available, please send the file with an explanation to %s'
% self.email,
parent=self)
return False
#
# Now read the file, need to do some field updates! Also make sure to re-use shift list for other molecules...
#
(fileRead, fileInformation) = self.fcWrapper.readFile(
dataType,
formatName,
self.fileName,
addKeywords={'measurementList': self.currentShiftList})
if not fileRead:
showWarning(
'Failure',
'This file cannot be read by this software:%s\nPlease send the file with an explanation to %s.'
% (fileInformation, self.email),
parent=self)
return False
(conversionInfo, conversionSuccess) = (
self.fcWrapper.formatConversion.conversionInfo,
self.fcWrapper.formatConversion.conversionSuccess)
if not conversionSuccess:
showWarning(
'Failure',
'This file was read by the software but contains invalid information.\nPlease send the file with an explanation to %s.'
% self.email,
parent=self)
return False
#
# Set info if import worked OK
#
conversionLines = conversionInfo.split(": ")
showInfo("Import chemical shift information",
":\n".join(conversionLines),
parent=self)
self.shiftImport.setText(
self.fileName) # TODO change color or something?
self.shiftImport.configure(foreground=self.fontOkColor)
self.shiftsLoaded = True
self.shiftsFormatName = formatName
shiftList = self.fcWrapper.importReturns[dataType]
if not self.currentShiftList:
self.currentShiftList = shiftList
self.shiftListChainPairs.append(
(self.currentShiftList, currentChain))
self.updateDepositionImportLabel(shiftList=shiftList)
if not shiftList in self.entry.measurementLists:
print shiftList
self.entry.addMeasurementList(shiftList)
print self.entry.measurementLists
self.updateAll()
#
# Updaters
#
def selectTab(self, index):
funcsDict = {
0: (self.updateMain, ),
1: (self.updateCoordinates, ),
2: (self.updateDeposition, )
}
for func in funcsDict[index]:
func()
def updateMain(self):
pass
def updateCoordinates(self):
pass
def updateDeposition(self):
pass
def updateAll(self):
self.selectTab(self.tabbedFrame.selected)
if self.sequenceCoordinatesLoaded and self.shiftsLoaded:
if showYesNo(
'Connect shifts to sequence',
'You have to check whether the chemical shift information matches the sequence. Do you want to this now?',
parent=self):
self.connectShiftsSequence()
self.waiting = False
def getCurrentChain(self):
if len(self.moleculeList) == 1:
chain = self.moleculeDict.values()[0]
else:
try:
moleculeSelected = self.moleculeSelect.getText()
chain = self.moleculeDict[moleculeSelected]
except:
chain = None
return chain
def connectShiftsSequence(self):
if not self.linkResDone:
changeResetColor = False
#
# Get chain mapping and run linkResonances
#
chain = self.getCurrentChain()
forceChainMappings = self.fcWrapper.linkResonancesToSequence(
chain=chain)
self.fcWrapper.formatConversion.linkResonances(
forceChainMappings=forceChainMappings, guiParent=self)
#
# Get information about the linking process
#
# TODO Should only have an nmrProject (no restraint import, should be included?)
# In any case, is always the LAST info in numResonancesLinked info
numResonancesLinked = self.fcWrapper.formatConversion.numResonancesLinked
(origLinked, origUnlinked, linked,
unlinked) = (numResonancesLinked['origLinked'][-1],
numResonancesLinked['origUnlinked'][-1],
numResonancesLinked['linked'][-1],
numResonancesLinked['unlinked'][-1])
#
# Track number of new resonances, and reset for new import
#
if self.fcWrapper.formatConversion.allResonancesLinked:
status = 'All information matches (for all imports).'
foreground = self.fontOkColor
changeResetColor = True
else:
if origUnlinked - unlinked == self.fcWrapper.numNewResonances:
status = 'All information matches (for this import)'
foreground = self.fontOkColor
changeResetColor = True
else:
if origUnlinked != unlinked:
status = 'Not all information matches (for this and/or another import).'
foreground = self.fontCheckColor
changeResetColor = True
else:
status = 'No information matches (for this import).'
foreground = self.fontBadColor
otherUnlinked = (origUnlinked -
self.fcWrapper.numNewResonances)
notLinked = unlinked - otherUnlinked
status += "\nUnable to link %d out of %d imported shifts (%.2f%%)." % (
notLinked, self.fcWrapper.numNewResonances,
(notLinked * 100.0) / self.fcWrapper.numNewResonances)
self.linkResCheckInfo.set("Status: %s" % status)
self.linkResCheckInfo.config(foreground=foreground)
self.linkResDone = True
#
# Change the color of the reset button to indicate OK to do next one
#
if changeResetColor:
self.mainButtons.buttons[0].config(foreground=self.fontOkColor)
self.updateDepositionImportLabel(
shiftList=None,
percentageLinked=(linked * 100.0 / (unlinked + linked)),
connectedChain=chain)
def updateDepositionImportLabel(self,
shiftList=None,
molecules=0,
chains=0,
models=0,
coordinates=0,
percentageLinked=None,
connectedChain=None):
if shiftList and shiftList not in self.importedShiftLists:
self.importedShiftLists.append(shiftList)
self.depositionImportNums[0] += 1
shifts = 0
for shiftList in self.importedShiftLists:
shifts += len(shiftList.measurements)
self.depositionImportNums[1] += shifts
self.depositionImportNums[2] += molecules
self.depositionImportNums[3] += chains
self.depositionImportNums[4] += models
self.depositionImportNums[5] += coordinates
if percentageLinked != None:
self.depositionImportNums[6] = percentageLinked
if connectedChain and connectedChain not in self.connectedChains:
self.depositionImportNums[7] += 1
self.connectedChains.append(connectedChain)
self.depositionImportLabel.destroy()
finalForeground = self.fontBadColor
if self.depositionImportNums[0] == 0 and self.depositionImportNums[
2] == 0:
# Nothing imported
foreground = self.fontBadColor
elif self.depositionImportNums[6]:
# Linked shifts available - TODO base this on % of shifts linked?
foreground = self.fontOkColor
if self.depositionImportNums[5]:
finalForeground = self.fontOkColor
else:
finalForeground = self.fontCheckColor
else:
# Intermediate state
foreground = self.fontCheckColor
self.depositionImportLabel = Label(self.frameD,
text=self.depositionImportText %
tuple(self.depositionImportNums),
foreground=foreground)
self.depositionImportLabel.grid(row=self.depositionImportLoc[0],
column=self.depositionImportLoc[1],
sticky='ew')
self.eciStart.configure(foreground=finalForeground)
def resetSequenceImport(self):
doReset = True
if not self.linkResDone and self.sequenceCoordinatesLoaded and self.shiftsLoaded:
if showYesNo(
'Shifts not connected to sequence',
'You have not checked whether the imported chemical shift information matches the imported sequence. Do you want to this first? If not, the last imported data will be invalid.',
parent=self):
self.connectShiftsSequence()
doReset = False
if doReset:
self.mainButtons.buttons[0].config(
foreground=self.fontDefaultColor)
self.sequenceCoordinatesLoaded = self.shiftsLoaded = self.linkResDone = False
self.sequenceCoordinatesImport.setText(self.defaultSelectText)
self.sequenceCoordinatesImport.configure(
foreground=self.fontDefaultColor)
self.moleculeSelect.destroy()
self.moleculeSelect = Label(
self.frameA,
text="None available yet - import valid file first",
foreground=self.fontBadColor)
self.moleculeSelect.grid(row=self.moleculeSelectRow,
column=0,
sticky='ew')
self.shiftImport.setText(self.defaultSelectText)
self.shiftImport.configure(foreground=self.fontDefaultColor)
self.linkResCheckInfo.set("")
def resetShiftImport(self):
doReset = True
if not self.linkResDone and self.sequenceCoordinatesLoaded and self.shiftsLoaded:
if showYesNo(
'Shifts not connected to sequence',
'You have not checked whether the imported chemical shift information matches the imported sequence. Do you want to this first? If not, the last imported data will be invalid.',
parent=self):
self.connectShiftsSequence()
doReset = False
if doReset:
self.mainButtons.buttons[1].config(
foreground=self.fontDefaultColor)
self.shiftsLoaded = self.linkResDone = False
self.currentShiftList = None
self.shiftImport.setText(self.defaultSelectText)
self.shiftImport.configure(foreground=self.fontDefaultColor)
self.linkResCheckInfo.set("")
def destroy(self):
Frame.destroy(self)
#
# Instructions
#
def showMainInstructions(self):
popup = getPopup(self)
message = """Use this tab to import the chemical shifts and the coordinate and/or sequence information for your molecular chains.
The imported chemical shift file should contain information for only *one* molecular chain to make it easier to connect the molecule information to the chemical shift information. You therefore have to select a single chain for each shift list from the dropdown menu that will appear after you imported a coordinate or sequence file.
For example, when using sequence files for a dimer, import the information for the chemical shifts for each chain separately:
1. Import the sequence for the first molecular chain.
2. Import a chemical shift file with shifts only for this molecular chain.
3. Reset using the 'Import new sequence' button
4. Import the sequence for the second molecular chain
5. Import a chemical shift file with shifts only for this second chain
Alternatively, it is possible to read in the molecule information from a full coordinate file:
1. Import a coordinate file with all molecular information, including coordinates.
2. Select a molecular chain.
3. Import a chemical shift file with shifts only for the selected molecular chain.
4. Go back to step 2. if necessary.
You can also import multiple sets of chemical shifts (e.g. for the sample in different conditions). In this case, you have to import all chemical shift information that belongs together for all molecular chains, then press the 'Import new set of shifts' button.
Notes:
1. This application always creates a new CCPN project. It is not possible to import files into existing projects.
2. If your chemical shift file contains information for multiple chains, you have to edit it manually to split up the information per chain.
"""
showHelpText(self, message, popup=popup)
def showFormats(self):
popup = getPopup(self)
message = """For chemical shifts, the following formats are recognised:
*** Auremol ***
section_sequenzdefinition
_Residue_seq_code
_Atom_num_code
_Residue_label
_Atom_name
_Atom_type
_Atom_alias
_Atom_equivalent
_Atom_CSA
1 1 MET HN H - - 8.95
1 2 MET N N - - 157.00
1 3 MET CA C - - 40.00
*** Autoassign ***
AA HN N15 CO-1 CA-1 CB-1 HA-1 CO CA CB HA
A31 8.14 121.4 51.3 19.6 (GS178 115.HSQC)
D32 8.88 122.9 51.3 19.5 55.4 39.6 (GS271 22.HSQC)
*** CNS ***
do ( store1 = 53.13218 ) ( resid 78 and name CA )
do ( store1 = 0.7356673 ) ( resid 15 and name HD1# )
do ( store1 = 120.5381 ) ( resid 8 and name N )
do ( store1 = 121.1414 ) ( resid 78 and name N )
*** Cosmos ***
CS_VALUES 3
C_ALA 176.6
CA_ALA 51.66
CB_ALA 17.26
END
*** CSI ***
# A HA CA CO CB Consensus
#
1 MET 0 C 0 C NA 0 C 0 C
2 GLY 0 C 0 C NA 0 C 0 C
*** MARS ***
H N CO-1 CA CA-1
PR_2 8.900 123.220 170.540 55.080 54.450
PR_4 8.320 115.340 175.920 - 55.080
*** MONTE ***
1 102.544 8.211 45.853 54.925 0.000 18.069 180.112
2 103.276 8.580 45.334 54.154 0.000 35.650 175.087
3 103.997 7.407 45.165 0.000 0.000 0.000 0.000
*** NMR-STAR ***
data_test
save_shifts1
_Saveframe_category assigned_chemical_shifts
loop_
_Atom_shift_assign_ID
_Residue_seq_code
_Residue_label
_Atom_name
_Atom_type
_Chem_shift_value
_Chem_shift_value_error
_Chem_shift_ambiguity_code
1 1 ASP CA C 52.000 0.02 1
2 1 ASP HA H 4.220 0.02 1
stop_
save_
*** NMRVIEW ***
2.CG1 18.549 0
2.CG2 18.844 0
2.HG1# 0.800 0
2.HG2# 0.723 0
3.HG2 2.298 0
3.HG1 2.298 0
*** PIPP ***
RES_ID 1
RES_TYPE MET
SPIN_SYSTEM_ID 1
CA 55.9920
CB 33.1470
HA 4.1141
HB# 2.0492
HG# 2.4250
END_RES_DEF
*** PISTACHIO ***
1 1 GLY C C 172.621 1.000 0
2 1 GLY CA C 44.308 1.000 0
3 2 SER N N 122.241 1.000 0
*** PRONTO ***
Spin system HN HA Other:
1: Val-1 3.76 HB: 1.945, HG1: 0.770, HG2: 0.608
2: Ile-2 8.80 4.26 HB: 1.526, HG1: 1.278, HG2: 0.728, HD: 0.918
*** SHIFTX ***
NUM RES HA H N CA CB C
--- --- ------ ------ -------- ------- ------- --------
2 T 4.4161 8.1749 111.0443 61.8324 70.3867 172.5362
3 Y 4.9022 9.0239 120.2106 56.0493 41.4218 173.0761
NUM RES H HA HB HB2 HB3 HD1 HD2 HD21 HD22 HD3 HE HE1 HE2 HE21 HE22 HE3 HG HG1 HG12 HG13 HG2 HG3 HZ
2 T 8.17 4.42 4.24 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.21 0.00 0.00
3 Y 9.02 4.90 0.00 2.22 2.20 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
*** SPARKY ***
Group Atom Nuc Shift SDev Assignments
R2 CA 13C 56.539 0.003 3
R2 CB 13C 30.808 0.009 3
*** TALOS ***
VARS RESID RESNAME PHI PSI DPHI DPSI DIST COUNT CLASS
FORMAT %4d %s %8.3f %8.3f %8.3f %8.3f %8.3f %2d %s
1 Q 9999.000 9999.000 0.000 0.000 0.000 0 None
2 N -85.000 124.000 23.000 28.000 85.920 10 Good
***XEASY/CYANA:
1 117.803 0.000 N 1
2 8.208 0.002 HN 1
3 56.508 0.055 CA 1
4 999.000 0.000 HA 1
5 29.451 0.004 CB 1
"""
showHelpText(self, message, popup=popup)
class ResultsTab(object):
def __init__(self, parent, frame):
self.guiParent = parent
self.frame = frame
self.project = parent.project
self.nmrProject = parent.nmrProject
self.selectedLinkA = None
self.selectedLinkB = None
self.selectedResidueA = None
self.selectedResidueB = None
self.selectedLink = None
self.dataModel = self.guiParent.connector.results
self.body()
def body(self):
frame = self.frame
self.resultsResidueNumber = 1
frame.expandGrid(5, 0)
resultTopFrame = LabelFrame(frame, text='Which results to show')
resultTopFrame.grid(row=0, column=0, sticky='ew')
self.resultsResidueNumber = 3
texts = [' < ']
commands = [self.resultsPrevResidue]
self.resultsPreviousButton = ButtonList(resultTopFrame,
commands=commands,
texts=texts)
self.resultsPreviousButton.grid(row=0, column=1, sticky='nsew')
tipText = 'The Number of the residue in the sequence to display results for'
self.resultsResidueNumberEntry = IntEntry(
resultTopFrame,
grid=(0, 2),
width=7,
text=3,
returnCallback=self.resultsUpdateAfterEntry,
tipText=tipText)
#self.resultsResidueNumberEntry.bind('<Leave>', self.resultsUpdateAfterEntry, '+')
texts = [' > ']
commands = [self.resultsNextResidue]
self.resultsNextButton = ButtonList(resultTopFrame,
commands=commands,
texts=texts)
self.resultsNextButton.grid(row=0, column=3, sticky='nsew')
selectCcpCodes = ['residue'] + AMINO_ACIDS
self.resultsSelectedCcpCode = 'residue'
tipText = 'Instead of going through the sequence residue by residue, jump directly to next amino acid of a specific type.'
resultsSelectCcpCodeLabel = Label(
resultTopFrame,
text='Directly jump to previous/next:',
grid=(0, 4))
self.resultsSelectCcpCodePulldown = PulldownList(
resultTopFrame,
callback=self.resultsChangeSelectedCcpCode,
texts=selectCcpCodes,
index=selectCcpCodes.index(self.resultsSelectedCcpCode),
grid=(0, 5),
tipText=tipText)
self.selectedSolution = 1
runLabel = Label(resultTopFrame, text='run:')
runLabel.grid(row=0, column=6)
texts = [' < ']
commands = [self.resultsPrevSolution]
self.resultsPreviousSolutionButton = ButtonList(resultTopFrame,
commands=commands,
texts=texts)
self.resultsPreviousSolutionButton.grid(row=0, column=7, sticky='nsew')
tipText = 'If you ran the algorithm more than once, you can select the solution given by the different runs.'
self.resultsSolutionNumberEntry = IntEntry(
resultTopFrame,
grid=(0, 8),
width=7,
text=1,
returnCallback=self.solutionUpdateAfterEntry,
tipText=tipText)
#self.resultsSolutionNumberEntry.bind('<Leave>', self.solutionUpdateAfterEntry, '+')
texts = [' > ']
commands = [self.resultsNextSolution]
self.resultsNextSolutionButton = ButtonList(resultTopFrame,
commands=commands,
texts=texts)
self.resultsNextSolutionButton.grid(row=0, column=9, sticky='nsew')
self.energyLabel = Label(resultTopFrame, text='energy:')
self.energyLabel.grid(row=0, column=10)
texts = ['template for puzzling']
commands = [self.adoptSolution]
self.adoptButton = ButtonList(resultTopFrame,
commands=commands,
texts=texts)
self.adoptButton.grid(row=0, column=11, sticky='nsew')
# LabelFrame(frame, text='Spin Systems')
resultsSecondFrame = Frame(frame)
resultsSecondFrame.grid(row=2, column=0, sticky='nsew')
resultsSecondFrame.grid_columnconfigure(0, weight=1)
resultsSecondFrame.grid_columnconfigure(1, weight=1)
resultsSecondFrame.grid_columnconfigure(2, weight=1)
resultsSecondFrame.grid_columnconfigure(3, weight=1)
resultsSecondFrame.grid_columnconfigure(4, weight=1)
headingList = ['#', '%']
tipTexts = [
'Spinsystem number {} indicates serial of the spinsystem. If the spinsystem was already assigned to a residue, the residue number is shown aswell',
'percentage of the solutions that connected this spinsystem to this residue'
]
editWidgets = [None, None, None]
self.displayResultsTables = []
self.residueLabels = []
for i in range(5):
label = Label(resultsSecondFrame, text='residue')
label.grid(row=0, column=i)
#editGetCallbacks = [createCallbackFunction(i)]*3
displayResultsTable = ScrolledMatrix(
resultsSecondFrame,
headingList=headingList,
multiSelect=False,
tipTexts=tipTexts,
callback=self.selectSpinSystemForTable,
passSelfToCallback=True)
displayResultsTable.grid(row=2, column=i, sticky='nsew')
displayResultsTable.sortDown = False
self.residueLabels.append(label)
self.displayResultsTables.append(displayResultsTable)
# LabelFrame(frame, text='Sequence Fragment')
resultsFirstFrame = Frame(resultsSecondFrame)
resultsFirstFrame.grid(row=1, column=0, sticky='ew', columnspan=5)
resultsFirstFrame.grid_rowconfigure(0, weight=1)
resultsFirstFrame.grid_rowconfigure(1, weight=1)
resultsFirstFrame.grid_columnconfigure(0, weight=1)
texts = [
' res 1 ', ' links ', ' res 2 ', ' links ', ' res 3 ', ' links ',
' res 4 ', ' links ', ' res 5 '
]
commands = [
lambda: self.selectRelativeResidue(1, True),
lambda: self.selectLink(1, True),
lambda: self.selectRelativeResidue(2, True),
lambda: self.selectLink(2, True),
lambda: self.selectRelativeResidue(3, True),
lambda: self.selectLink(3, True),
lambda: self.selectRelativeResidue(4, True),
lambda: self.selectLink(4, True),
lambda: self.selectRelativeResidue(5, True)
]
self.sequenceButtons = ButtonList(resultsFirstFrame,
commands=commands,
texts=texts)
self.sequenceButtons.grid(row=0, column=0, sticky='nsew')
for n, button in enumerate(self.sequenceButtons.buttons):
if n % 2:
button.grid(column=n, sticky='ns')
self.sequenceButtons.grid_columnconfigure(n, weight=0)
else:
self.sequenceButtons.grid_columnconfigure(n, uniform=2)
spacer = Spacer(resultsFirstFrame)
spacer.grid(row=1, column=0, sticky='nsew')
texts = [
' res 1 ', ' links ', ' res 2 ', ' links ', ' res 3 ', ' links ',
' res 4 ', ' links ', ' res 5 '
]
commands = commands = [
lambda: self.selectRelativeResidue(1, False),
lambda: self.selectLink(1, False),
lambda: self.selectRelativeResidue(2, False),
lambda: self.selectLink(2, False),
lambda: self.selectRelativeResidue(3, False),
lambda: self.selectLink(3, False),
lambda: self.selectRelativeResidue(4, False),
lambda: self.selectLink(4, False),
lambda: self.selectRelativeResidue(5, False)
]
self.sequenceButtonsB = ButtonList(resultsFirstFrame,
commands=commands,
texts=texts)
self.sequenceButtonsB.grid(row=2, column=0, sticky='nsew')
for n, button in enumerate(self.sequenceButtonsB.buttons):
if n % 2:
button.grid(column=n, sticky='ns')
self.sequenceButtonsB.grid_columnconfigure(n, weight=0)
else:
self.sequenceButtonsB.grid_columnconfigure(n, uniform=2)
frame.grid_rowconfigure(3, weight=2)
resultsThirdFrame = Frame(frame)
resultsThirdFrame.grid(row=3, column=0, sticky='nsew')
resultsThirdFrame.grid_rowconfigure(0, weight=1)
resultsThirdFrame.grid_columnconfigure(0, weight=1)
tabbedFrameB = TabbedFrame(resultsThirdFrame,
options=['Peaks', 'Spin System'],
callback=self.toggleTab,
grid=(0, 0))
#self.tabbedFrameB = tabbedFrame
PeakFrame, SpinSystemFrame = tabbedFrameB.frames
SpinSystemFrame.grid_rowconfigure(0, weight=1)
PeakFrame.grid_rowconfigure(1, weight=1)
SpinSystemFrame.grid_columnconfigure(0, weight=1)
PeakFrame.grid_columnconfigure(0, weight=1)
headingList = [
'residue', 'assigned to in project', 'user defined sequence',
'selected annealing result', '%'
]
tipTexts = [None, None, None, None, None]
editWidgets = [None, None, None, None, None]
editGetCallbacks = [None, None, None, None, None]
editSetCallbacks = [None, None, None, None, None]
self.spinSysTable = ScrolledMatrix(SpinSystemFrame,
headingList=headingList,
editWidgets=editWidgets,
multiSelect=False,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
tipTexts=tipTexts)
self.spinSysTable.grid(row=0, column=0, sticky='nsew')
buttonFrameinPeakFrame = Frame(PeakFrame)
buttonFrameinPeakFrame.grid(sticky='ew')
self.findButton = Button(
buttonFrameinPeakFrame,
text=' Go to Peak ',
borderwidth=1,
padx=2,
pady=1,
command=self.findPeak,
tipText='Locate the currently selected peak in the specified window'
)
self.findButton.grid(row=0, column=0, sticky='e')
label = Label(buttonFrameinPeakFrame, text='in window:')
label.grid(row=0, column=1, sticky='w')
self.windowPulldown = PulldownList(
buttonFrameinPeakFrame,
callback=self.selectWindowPane,
tipText='Choose the spectrum window for locating peaks or strips')
self.windowPulldown.grid(row=0, column=2, sticky='w')
self.assignSelectedPeaksButton = Button(
buttonFrameinPeakFrame,
text='Assign Resonances to Peak(s)',
borderwidth=1,
padx=2,
pady=1,
command=self.assignSelectedPeaks,
tipText=
'Assign resonances to peak dimensions, this of course only works when the peak is found in the spectrum.'
)
self.assignSelectedPeaksButton.grid(row=0, column=3, sticky='ew')
self.assignSelectedSpinSystemsToResiduesButton = Button(
buttonFrameinPeakFrame,
text='Assign Spinsystems to Residues',
borderwidth=1,
padx=2,
pady=1,
command=self.assignSelectedSpinSystemsToResidues,
tipText='Assign spinsystems to residues')
self.assignSelectedSpinSystemsToResiduesButton.grid(row=0,
column=4,
sticky='ew')
headingList = [
'#', 'spectrum', 'Dim1', 'Dim2', 'Dim3', 'c.s. dim1', 'c.s. dim2',
'c.s. dim3', 'colabelling'
]
tipTexts = [
'Peak number, only present when the peak was actually found in the spectrum.',
'Name of the spectrum',
'Name of atomSet measured in this dimension. Dimension number corresponds to Ref Exp Dim as indicated by going in the main menu to Experiment-->Experiments-->Experiment Type',
'Name of atomSet measured in this dimension. Dimension number corresponds to Ref Exp Dim as indicated by going in the main menu to Experiment-->Experiments-->Experiment Type',
'Name of atomSet measured in this dimension. Dimension number corresponds to Ref Exp Dim as indicated by going in the main menu to Experiment-->Experiments-->Experiment Type',
'Chemical Shift', 'Chemical Shift', 'Chemical Shift',
'Colabbeling fraction over all nuclei that are on the magnetization transfer pathway during the experiment that gave rise to the peak, including visited nuclei that were not measured in any of the peak dimensions'
]
#editWidgets = [None, None, None, None, None, None, None, None, None]
editGetCallbacks = [
None, None, None, None, None, None, None, None, None
]
#editGetCallbacks = [self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak, self.selectPeak]
editSetCallbacks = [
None, None, None, None, None, None, None, None, None
]
self.displayPeakTable = ScrolledMatrix(PeakFrame,
headingList=headingList,
multiSelect=True,
tipTexts=tipTexts)
#editWidgets=editWidgets, multiSelect=True,
# editGetCallbacks=editGetCallbacks,
# editSetCallbacks=editSetCallbacks,
# tipTexts=tipTexts)
self.displayPeakTable.grid(row=1, column=0, sticky='nsew')
self.windowPane = None
self.updateWindows()
def selectSpinSystemForTable(self, spinSystem, row, column, table):
table_number = self.displayResultsTables.index(table)
self.selectSpinSystem(table_number, spinSystem)
@lockUntillResults
def showResults(self):
self.updateResultsTable()
@lockUntillResults
def selectLink(self, number, topRow):
if topRow:
self.selectedResidueA = None
self.selectedResidueB = None
self.selectedLinkA = number
self.selectedLinkB = None
else:
self.selectedResidueA = None
self.selectedResidueB = None
self.selectedLinkA = None
self.selectedLinkB = number
self.updateButtons()
self.updateLink()
@lockUntillResults
def selectRelativeResidue(self, number, topRow):
if topRow:
self.selectedResidueA = number
self.selectedResidueB = None
self.selectedLinkA = None
self.selectedLinkB = None
else:
self.selectedResidueA = None
self.selectedResidueB = number
self.selectedLinkA = None
self.selectedLinkB = None
self.updateButtons()
self.updateLink()
def updateLink(self):
'''
Checks for any selected link (self.selectedLinkA or self.selectedLinkB) and calls
updatePeakTable with the correct residue Object and spinsystem Objects.
'''
number = self.selectedLinkA or self.selectedLinkB or self.selectedResidueA or self.selectedResidueB
if not number:
self.emptyPeakTable()
return
dataModel = self.dataModel
resNumber = self.resultsResidueNumber
chain = dataModel.chain
residues = chain.residues
solutionNumber = self.selectedSolution - 1
if self.selectedResidueA:
res = residues[resNumber - 4 + number]
spinSystem = res.solutions[solutionNumber]
self.selectedLink = None
if res and spinSystem:
self.selectedLink = res.getIntraLink(spinSystem)
#self.updatePeakTableIntra(res, spinSystem)
self.updateSpinSystemTable(spinSystem)
elif self.selectedResidueB:
res = residues[resNumber - 4 + number]
spinSystem = res.userDefinedSolution
self.selectedLink = None
if res and spinSystem:
self.selectedLink = res.getIntraLink(spinSystem)
#self.updatePeakTableIntra(res, spinSystem)
self.updateSpinSystemTable(spinSystem)
elif self.selectedLinkA:
resA = residues[resNumber - 4 + number]
resB = residues[resNumber - 3 + number]
spinSystemA = resA.solutions[solutionNumber]
spinSystemB = resB.solutions[solutionNumber]
self.selectedLink = None
if resA and spinSystemA and spinSystemB:
self.selectedLink = resA.getLink(spinSystemA, spinSystemB)
#self.updatePeakTable(resA, spinSystemA, spinSystemB)
# and resA.userDefinedSolution and resB.userDefinedSolution:
elif self.selectedLinkB:
resA = residues[resNumber - 4 + number]
resB = residues[resNumber - 3 + number]
spinSystemA = resA.userDefinedSolution
spinSystemB = resB.userDefinedSolution
self.selectedLink = None
if resA and spinSystemA and spinSystemB:
self.selectedLink = resA.getLink(spinSystemA, spinSystemB)
#self.updatePeakTable(resA, spinSystemA, spinSystemB)
self.updatePeakTable()
def emptyPeakTable(self):
self.displayPeakTable.update(objectList=[],
textMatrix=[],
colorMatrix=[])
def updatePeakTable(self):
'''
Updates the peak table to show the peaks that are found for a sequencial pair of
spinsystems A and B. If there is not a linkobject found for spinsystems A and B the
table is emptied. Also sets the selected peak to None.
'''
link = self.selectedLink
if not link:
self.emptyPeakTable()
else:
resA, resB = link.getResidues()
spinSystemA, spinSystemB = link.getSpinSystems()
data = []
objectList = []
peakLinks = link.getAllPeakLinks()
if not peakLinks:
self.emptyPeakTable()
return
maxDimenionality = max([
len(peakLink.getSimulatedPeak().getContribs())
for peakLink in peakLinks
])
for peakLink in peakLinks:
serial = None
realPeak = peakLink.getPeak()
simPeak = peakLink.getSimulatedPeak()
atomTexts = [None] * maxDimenionality
chemicalShifts = [None] * maxDimenionality
for simulatedPeakContrib in simPeak.getContribs():
atomName = simulatedPeakContrib.getAtomName()
#ccpCode = simulatedPeakContrib.getCcpCode()
dimNumber = simulatedPeakContrib.getDimNumber()
if resA is simulatedPeakContrib.getResidue():
spinSystemDescription = spinSystemA.getDescription(
noSerialWhenSeqCodeIsPresent=True)
else:
spinSystemDescription = spinSystemB.getDescription(
noSerialWhenSeqCodeIsPresent=True)
atomTexts[dimNumber -
1] = '%s %s' % (spinSystemDescription, atomName)
if realPeak:
serial = realPeak.getSerial()
for dim in realPeak.getDimensions():
chemicalShifts[dim.getDimNumber() -
1] = dim.getChemicalShift()
else:
shiftListSerial = simPeak.getSpectrum().getShiftListSerial(
)
for resonance, simulatedPeakContrib in zip(
peakLink.getResonances(), simPeak.getContribs()):
if resonance:
chemicalShifts[simulatedPeakContrib.getDimNumber()
- 1] = resonance.getChemicalShift(
shiftListSerial)
else:
chemicalShifts[simulatedPeakContrib.getDimNumber()
- 1] = '?'
data.append([serial, simPeak.getSpectrum().name] + atomTexts +
chemicalShifts + [simPeak.colabelling])
objectList.append(peakLink)
headingList = ['#', 'spectrum'] + [
'dim%s' % a for a in range(1, maxDimenionality + 1)
] + ['c.s. dim%s' % a
for a in range(1, maxDimenionality + 1)] + ['colabbeling']
self.displayPeakTable.update(objectList=objectList,
textMatrix=data,
headingList=headingList)
def findPeak(self):
if not self.windowPane:
return
selectedPeakLinks = self.displayPeakTable.currentObjects
if not selectedPeakLinks:
self.guiParent.updateInfoText('Please select a peak first.')
return
if len(selectedPeakLinks) > 1:
self.guiParent.updateInfoText('Can only go to one peak at a time.')
return
selectedPeakLink = selectedPeakLinks[0]
selectedPeak = selectedPeakLink.getPeak()
if selectedPeak:
ccpnPeak = selectedPeak.getCcpnPeak()
createPeakMark(ccpnPeak, lineWidth=2.0)
windowFrame = self.windowPane.getWindowFrame()
windowFrame.gotoPeak(ccpnPeak)
else:
simPeak = selectedPeakLink.getSimulatedPeak()
spectrum = simPeak.getSpectrum()
ccpnSpectrum = spectrum.getCcpnSpectrum()
view = getSpectrumWindowView(self.windowPane, ccpnSpectrum)
if not view:
self.guiParent.updateInfoText(
'This peak cannot be displayed in the window you chose.')
axisMappingByRefExpDimNumber = {}
for axisMapping in view.axisMappings:
refExpDimNumber = axisMapping.analysisDataDim.dataDim.expDim.refExpDim.dim
axisMappingByRefExpDimNumber[refExpDimNumber] = axisMapping
positionToGoTo = {}
markPosition = []
axisTypes = []
for resonance, contrib in zip(selectedPeakLink.getResonances(),
simPeak.getContribs()):
dimNumber = contrib.getDimNumber()
axisMapping = axisMappingByRefExpDimNumber.get(dimNumber)
label = axisMapping.label
if resonance:
axisType = axisMapping.axisPanel.axisType
chemicalShift = resonance.getChemicalShift()
positionToGoTo[label] = chemicalShift
markPosition.append(chemicalShift)
axisTypes.append(axisType)
# Not drawing a mark at this chemical shift, just hoovering to
# the good region in the spectrum
else:
ccpCode = contrib.getResidue().getCcpCode()
atomName = contrib.getAtomName()
medianChemicalShift = self.getMedianChemicalShift(
ccpCode, atomName)
if medianChemicalShift:
positionToGoTo[label] = medianChemicalShift
if positionToGoTo:
windowFrame = self.windowPane.getWindowFrame()
windowFrame.gotoPosition(positionToGoTo)
if markPosition:
createNonPeakMark(markPosition, axisTypes)
def assignSelectedPeaks(self):
selectedPeakLinks = self.displayPeakTable.currentObjects
for pl in selectedPeakLinks:
peak = pl.getPeak()
if peak:
for resonance, dimension in zip(pl.getResonances(),
peak.getDimensions()):
ccpnResonance = resonance.getCcpnResonance()
ccpnDimension = dimension.getCcpnDimension()
if ccpnResonance and ccpnDimension:
assignResToDim(ccpnDimension, ccpnResonance)
def assignSelectedSpinSystemsToResidues(self):
link = self.selectedLink
if link:
residues = link.getResidues()
spinSystems = link.getSpinSystems()
ccpnSpinSystems = []
ccpnResidues = []
for spinSys, res in zip(spinSystems, residues):
if spinSys and res:
ccpnSpinSystems.append(spinSys.getCcpnResonanceGroup())
ccpnResidues.append(res.getCcpnResidue())
assignSpinSystemstoResidues(ccpnSpinSystems,
ccpnResidues,
guiParent=self.guiParent)
self.updateButtons()
self.updateButtons()
self.updateResultsTable()
self.updatePeakTable()
def getMedianChemicalShift(self, ccpCode, atomName):
nmrRefStore = self.project.findFirstNmrReferenceStore(
molType='protein', ccpCode=ccpCode)
chemCompNmrRef = nmrRefStore.findFirstChemCompNmrRef(
sourceName='RefDB')
chemCompVarNmrRef = chemCompNmrRef.findFirstChemCompVarNmrRef(
linking='any', descriptor='any')
if chemCompVarNmrRef:
chemAtomNmrRef = chemCompVarNmrRef.findFirstChemAtomNmrRef(
name=atomName)
if chemAtomNmrRef:
distribution = chemAtomNmrRef.distribution
maxIndex = max([
(value, index) for index, value in enumerate(distribution)
])[1]
return chemAtomNmrRef.refValue + chemAtomNmrRef.valuePerPoint * (
maxIndex - chemAtomNmrRef.refPoint)
return None
def selectWindowPane(self, windowPane):
if windowPane is not self.windowPane:
self.windowPane = windowPane
def updateWindows(self):
index = 0
windowPane = None
windowPanes = []
names = []
peakList = None
tryWindows = WindowBasic.getActiveWindows(self.project)
windowData = []
getName = WindowBasic.getWindowPaneName
for window in tryWindows:
for windowPane0 in window.spectrumWindowPanes:
# if WindowBasic.isSpectrumInWindowPane(windowPane0, spectrum):
windowData.append((getName(windowPane0), windowPane0))
windowData.sort()
names = [x[0] for x in windowData]
windowPanes = [x[1] for x in windowData]
if windowPanes:
if windowPane not in windowPanes:
windowPane = windowPanes[0]
index = windowPanes.index(windowPane)
else:
windowPane = None
self.selectWindowPane(windowPane)
self.windowPulldown.setup(names, windowPanes, index)
def selectSpinSystem(self, number, spinSystem):
res = self.dataModel.chain.residues[self.resultsResidueNumber - 3 +
number]
oldSpinSystemForResidue = res.userDefinedSolution
if oldSpinSystemForResidue and res.getSeqCode(
) in oldSpinSystemForResidue.userDefinedSolutions:
oldSpinSystemForResidue.userDefinedSolutions.remove(
res.getSeqCode())
res.userDefinedSolution = spinSystem
spinSystem.userDefinedSolutions.append(res.getSeqCode())
# self.updateSpinSystemTable(spinSystem)
self.updateLink()
self.updateButtons()
def updateSpinSystemTable(self, spinSystem):
if not spinSystem:
self.emptySpinSystemTable()
return
dataModel = self.dataModel
residues = dataModel.chain.residues
data = []
colorMatrix = []
for residue in spinSystem.allowedResidues:
oneRow = []
oneRowColor = []
string = str(residue.getSeqCode()) + ' ' + residue.getCcpCode()
oneRow.append(string)
resonanceGroup = spinSystem.getCcpnResonanceGroup()
ccpnResidue = residue.ccpnResidue
# Assigned in the project to this residue
if resonanceGroup and resonanceGroup.residue and resonanceGroup.residue is ccpnResidue:
oneRow.append('x')
else:
oneRow.append(None)
# The user selected this res for this spinsystem (could be more
# than one res for which this happens)
if residue.getSeqCode() in spinSystem.userDefinedSolutions:
oneRow.append('x')
else:
oneRow.append(None)
if residue.solutions[self.selectedSolution - 1] == spinSystem:
oneRow.append('x')
else:
oneRow.append(None)
if spinSystem.solutions:
percentage = spinSystem.solutions.count(
residue.getSeqCode()) / float(len(
spinSystem.solutions)) * 100.0
else:
percentage = 0
oneRow.append(int(percentage + 0.5))
color = pick_color_by_percentage(percentage)
oneRowColor = [color] * 5
data.append(oneRow)
colorMatrix.append(oneRowColor)
self.spinSysTable.update(objectList=data,
textMatrix=data,
colorMatrix=colorMatrix)
self.spinSysTable.sortDown = False
self.spinSysTable.sortLine(-1, noUpdate=True)
def emptySpinSystemTable(self):
self.spinSysTable.update(objectList=[], textMatrix=[], colorMatrix=[])
@lockUntillResults
def adoptSolution(self):
dataModel = self.dataModel
selectedSolution = self.selectedSolution
for res in dataModel.chain.residues:
spinSystem = res.solutions[selectedSolution - 1]
res.userDefinedSolution = spinSystem
spinSystem.userDefinedSolutions = [res.getSeqCode()]
self.updateLink()
self.updateButtons()
@lockUntillResults
def resultsPrevSolution(self):
if self.selectedSolution != 1:
self.selectedSolution = self.selectedSolution - 1
self.resultsSolutionNumberEntry.set(self.selectedSolution)
self.updateLink()
self.updateButtons()
self.updateEnergy()
@lockUntillResults
def resultsNextSolution(self):
amountOfRepeats = len(self.dataModel.chain.residues[0].solutions)
if self.selectedSolution < amountOfRepeats:
self.selectedSolution = self.selectedSolution + 1
self.resultsSolutionNumberEntry.set(self.selectedSolution)
self.updateLink()
self.updateButtons()
self.updateEnergy()
@lockUntillResults
def resultsPrevResidue(self):
residues = self.dataModel.chain.residues
#chainLength = len(residues)
new_value = self.resultsResidueNumber
if self.resultsSelectedCcpCode == 'residue':
if self.resultsResidueNumber != 3:
new_value = self.resultsResidueNumber - 1
else:
for res in residues:
if res.getSeqCode() == self.resultsResidueNumber:
break
elif res.getCcpCode() == self.resultsSelectedCcpCode:
new_value = res.getSeqCode()
if new_value < 3:
new_value = 3
if self.resultsResidueNumber != new_value:
self.resultsResidueNumber = new_value
self.resultsResidueNumberEntry.set(self.resultsResidueNumber)
self.updateLink()
self.updateButtons()
self.updateButtons()
self.updateResultsTable()
self.updateResidueLabels()
@lockUntillResults
def resultsNextResidue(self):
residues = self.dataModel.chain.residues
chainLength = len(residues)
new_value = self.resultsResidueNumber
if self.resultsSelectedCcpCode == 'residue':
if self.resultsResidueNumber != chainLength - 2:
new_value = self.resultsResidueNumber + 1
else:
for res in residues[(self.resultsResidueNumber):]:
if res.getCcpCode() == self.resultsSelectedCcpCode:
new_value = res.getSeqCode()
if new_value > chainLength - 2:
new_value = chainLength - 2
break
if self.resultsResidueNumber != new_value:
self.resultsResidueNumber = new_value
self.resultsResidueNumberEntry.set(self.resultsResidueNumber)
self.updateLink()
self.updateButtons()
self.updateButtons()
self.updateResultsTable()
self.updateResidueLabels()
def resultsChangeSelectedCcpCode(self, ccpCode):
self.resultsSelectedCcpCode = ccpCode
@lockUntillResults
def resultsUpdateAfterEntry(self, event=None):
'''
Update for entry of residue number in strip plots
'''
residues = self.dataModel.chain.residues
value = self.resultsResidueNumberEntry.get()
if value == self.resultsResidueNumber:
return
else:
self.resultsResidueNumber = value
if value < 3:
self.resultsResidueNumberEntry.set(3)
self.resultsResidueNumber = 3
elif value > len(residues) - 2:
self.resultsResidueNumber = len(residues) - 2
self.resultsResidueNumberEntry.set(self.resultsResidueNumber)
else:
self.resultsResidueNumberEntry.set(self.resultsResidueNumber)
self.updateLink()
self.updateButtons()
self.updateButtons()
self.updateResultsTable()
self.updateResidueLabels()
@lockUntillResults
def solutionUpdateAfterEntry(self, event=None):
'''
Update for entry of residue number in strip plots
'''
Nsolutions = len(self.dataModel.chain.residues[0].solutions)
value = self.resultsSolutionNumberEntry.get()
if value == self.selectedSolution:
return
else:
self.selectedSolution = value
if value < 1:
self.resultsSolutionNumberEntry.set(1)
self.selectedSolution = 1
elif value > Nsolutions:
self.selectedSolution = Nsolutions
self.resultsSolutionNumberEntry.set(self.selectedSolution)
else:
self.resultsSolutionNumberEntry.set(self.selectedSolution)
self.updateLink()
self.updateButtons()
def update(self):
self.updateLink()
self.updateResidueLabels()
self.updateResultsTable()
self.updateButtons()
self.updateButtons()
self.updateEnergy()
def updateResultsTable(self):
resNumber = self.resultsResidueNumber
dataModel = self.dataModel
chain = dataModel.chain
residues = chain.residues
resA = residues[resNumber - 3]
resB = residues[resNumber - 2]
resC = residues[resNumber - 1]
resD = residues[resNumber]
resE = residues[resNumber + 1]
resList = [resA, resB, resC, resD, resE]
tableList = self.displayResultsTables
for res, table in zip(resList, tableList):
ccpCode = res.ccpCode
spinSystemsWithThisCcpCode = dataModel.getSpinSystems()[ccpCode]
data = []
colorMatrix = []
objectList = []
jokers = []
realSpinSystems = []
for spinSys in spinSystemsWithThisCcpCode:
if spinSys.getIsJoker():
jokers.append(spinSys)
else:
realSpinSystems.append(spinSys)
for spinsys in realSpinSystems:
oneRow = []
oneRowColor = []
# self.getStringDescriptionOfSpinSystem(spinsys)
spinSystemInfo = spinsys.getDescription()
oneRow.append(spinSystemInfo)
assignmentPercentage = int(
float(res.solutions.count(spinsys)) / len(res.solutions) *
100.0)
oneRow.append(assignmentPercentage)
objectList.append(spinsys)
color = pick_color_by_percentage(assignmentPercentage)
oneRowColor = [color, color]
data.append(oneRow)
colorMatrix.append(oneRowColor)
if jokers:
oneRow = ['Joker']
NumberOfAssignmentsToJoker = 0
for spinSys in jokers:
NumberOfAssignmentsToJoker += res.solutions.count(spinSys)
assignmentPercentage = int(
float(NumberOfAssignmentsToJoker) / len(res.solutions) *
100.0)
oneRow.append(assignmentPercentage)
color = pick_color_by_percentage(assignmentPercentage)
oneRowColor = [color, color]
data.append(oneRow)
colorMatrix.append(oneRowColor)
objectList.append(jokers[0])
percentages = [datapoint[1] for datapoint in data]
tableData = sorted(zip(percentages, data, objectList, colorMatrix),
reverse=True)
percentage, data, objectList, colorMatrix = zip(*tableData)
table.update(objectList=objectList,
textMatrix=data,
colorMatrix=colorMatrix)
def updateResidueLabels(self):
resList = self.getCurrentlyDisplayedResidues()
labels = self.residueLabels
for residue, label in zip(resList, labels):
text = str(residue.getSeqCode()) + ' ' + residue.getCcpCode()
label.set(text)
def updateButtons(self):
self.updateButtonHighLights()
self.updateResultsTopRowButtons()
self.updateResultsBottomRowButtons()
def updateResultsTopRowButtons(self):
resList = self.getCurrentlyDisplayedResidues()
buttons = self.sequenceButtons.buttons[::2]
for button, res in zip(buttons, resList):
spinsys = res.solutions[self.selectedSolution - 1]
# str(res.getSeqCode()) + ' ' + res.getCcpCode() + ': ' +
# spinsys.getDescription()
# self.getStringDescriptionOfSpinSystem(spinsys)
text = spinsys.getDescription(noSerialWhenSeqCodeIsPresent=False)
button.config(text=text)
def updateResultsBottomRowButtons(self):
resList = self.getCurrentlyDisplayedResidues()
buttons = self.sequenceButtonsB.buttons[::2]
for button, res in zip(buttons, resList):
if res.userDefinedSolution:
selectedSpinSystem = res.userDefinedSolution
text = selectedSpinSystem.getDescription(
noSerialWhenSeqCodeIsPresent=False)
if len(selectedSpinSystem.userDefinedSolutions) > 1:
# The red color signals that the spinssystem is used in
# more than 1 place in the sequence
button.config(text=text, bg=highLightRed)
else:
button.config(text=text)
else:
# str(res.getSeqCode()) + ' ' + res.getCcpCode() + ': -'
text = '-'
button.config(text=text)
def updateButtonHighLights(self):
self.setAllButtonsToGrey()
if self.selectedResidueA:
buttons = [
self.sequenceButtons.buttons[0],
self.sequenceButtons.buttons[2],
self.sequenceButtons.buttons[4],
self.sequenceButtons.buttons[6],
self.sequenceButtons.buttons[8]
]
buttons[self.selectedResidueA - 1].config(bg=highLightYellow)
elif self.selectedResidueB:
buttons = [
self.sequenceButtonsB.buttons[0],
self.sequenceButtonsB.buttons[2],
self.sequenceButtonsB.buttons[4],
self.sequenceButtonsB.buttons[6],
self.sequenceButtonsB.buttons[8]
]
buttons[self.selectedResidueB - 1].config(bg=highLightYellow)
elif self.selectedLinkA:
buttons = [
self.sequenceButtons.buttons[1],
self.sequenceButtons.buttons[3],
self.sequenceButtons.buttons[5],
self.sequenceButtons.buttons[7]
]
buttons[self.selectedLinkA - 1].config(bg=highLightYellow)
elif self.selectedLinkB:
buttons = [
self.sequenceButtonsB.buttons[1],
self.sequenceButtonsB.buttons[3],
self.sequenceButtonsB.buttons[5],
self.sequenceButtonsB.buttons[7]
]
buttons[self.selectedLinkB - 1].config(bg=highLightYellow)
def updateEnergy(self):
text = 'energy: %s' % int(
self.dataModel.getEnergy(self.selectedSolution - 1) + 0.5)
self.energyLabel.set(text)
self.energyLabel.update()
def setAllButtonsToGrey(self):
for button in self.sequenceButtons.buttons + self.sequenceButtonsB.buttons:
button.config(bg='grey83')
def setAllRedButtonsToGrey(self):
for button in self.sequenceButtons.buttons + self.sequenceButtonsB.buttons:
if button.enableFg == highLightRed:
button.config(bg='grey83')
def getCurrentlyDisplayedResidues(self):
resNumber = self.resultsResidueNumber
residues = self.dataModel.chain.residues[resNumber - 3:resNumber + 2]
return residues
def toggleTab(self, index):
pass
class FilterFrame(LabelFrame):
def __init__(self,
guiParent,
basePopup,
borderRelief='raised',
text=' ',
justify='left',
width=None,
font=None,
height=None,
*args,
**kw):
# Base popup required to handle notification of data model changes
# e.g. new peak lists, so that the GUI can update to the latest
# state
self.basePopup = basePopup
self.guiParent = guiParent
self.borderRelief = borderRelief
self.text = text
self.justify = justify
self.width = width
self.font = font
self.height = height
# get a port proxy instance
# this should probably belong to the repository directly
loc = SharedBeanServiceLocator()
self.port = loc.getSharedBean()
self.registerNotify = basePopup.registerNotify
self.unregisterNotify = basePopup.unregisterNotify
LabelFrame.__init__(self, guiParent, borderRelief, text, justify,
width, font, height, *args, **kw)
# set up the grid
self.grid_columnconfigure(0, weight=0, minsize=20)
self.grid_rowconfigure(0, weight=0, minsize=5)
self.grid_rowconfigure(1, weight=0, minsize=10)
self.grid_rowconfigure(2, weight=0, minsize=10)
self.grid_rowconfigure(3, weight=0, minsize=10)
# build up the body.
self.nameLabel = Label(self, text='Name:')
self.nameLabel.grid(row=1, column=0, padx=2, sticky='nw')
self.nameText = Text(self, width=20, height=1)
self.nameText.grid(row=1, column=1, sticky='nw')
self.dateLabel = Label(self, text='Date:')
self.dateLabel.grid(row=2, column=0, padx=2, sticky='nw')
self.dateText = Text(self, width=20, height=1)
self.dateText.grid(row=2, column=1, sticky='nw')
self.userLabel = Label(self, text='User:'******'nw')
self.userText = Text(self, width=20, height=1)
self.userText.grid(row=3, column=1, sticky='nw')
self.clearButton = Button(self,
text='Clear',
command=self.clear_filter,
width=10,
height=1)
self.clearButton.grid(row=4, column=0, columnspan=2, sticky='nw')
self.filterButton = Button(self,
text='Go',
command=self.tmpCall,
width=10,
height=1)
self.filterButton.grid(row=4, column=1, columnspan=2, sticky='ne')
def clear_filter(self):
self.nameText.xlear()
self.dateText.clear()
self.userText.clear()
def tmpCall(self, event=None):
pass
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.Experiment', func)
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.DataSource', func)
def updateAllAfter(self, obj):
self.after_idle(self.updateAll)
def updateAll(self, project=None):
return
def quit(self):
self.guiParent.parent.destroy()
def destroy(self):
self.administerNotifiers(self.basePopup.unregisterNotify)
Frame.destroy(self)
return self.var.get()
def set(self, text = ''):
self.var.set(text)
if (__name__ == '__main__'):
from memops.gui.Button import Button
msg = 'hello world'
count = 0
def func():
global count
count = count + 1
label.set(msg + ' ' + str(count))
print label.get()
root = Tkinter.Tk()
label = Label(root, text='hello world')
label.grid()
button = Button(root, text='hit me', command=func)
button.grid()
root.mainloop()
class RepositoryPropertiesFrame(Frame):
def __init__(self, guiParent, basePopup):
# Base popup required to handle notification of data model changes
# e.g. new peak lists, so that the GUI can update to the latest
# state
self.basePopup = basePopup
self.guiParent = guiParent
self.registerNotify = basePopup.registerNotify
self.unregisterNotify = basePopup.unregisterNotify
Frame.__init__(self, guiParent)
# set up the grid
self.grid_columnconfigure(0, weight=1, minsize=10)
self.grid_columnconfigure(1, weight=0, minsize=10)
self.grid_columnconfigure(2, weight=0, minsize=20)
self.grid_columnconfigure(3, weight=1, minsize=10)
self.grid_rowconfigure(0, weight=1, minsize=5)
self.grid_rowconfigure(1, weight=0, minsize=10)
self.grid_rowconfigure(2, weight=0, minsize=10)
self.grid_rowconfigure(3, weight=0, minsize=10)
self.grid_rowconfigure(4, weight=0, minsize=10)
self.grid_rowconfigure(5, weight=0, minsize=10)
self.grid_rowconfigure(6, weight=1, minsize=5)
# build up the body.
# Column headers
self.name_label = Label(self, text='Repository Name:')
self.name_label.grid(row=1, column=1, padx=5, pady=5, sticky='w')
self.name_value = Text(self, width=20, height=1, text="")
self.name_value.grid(row=1, column=2, padx=5, pady=5, sticky='w')
self.rep_label = Label(self, text='Repository Url:')
self.rep_label.grid(row=2, column=1, padx=5, pady=5, sticky='w')
self.rep_value = Text(self, width=20, height=1, text="")
self.rep_value.grid(row=2, column=2, padx=5, pady=5, sticky='w')
self.user_label = Label(self, text='Username:'******'w')
self.user_value = Text(self, width=20, height=1, text="")
self.user_value.grid(row=3, column=2, padx=5, pady=5, sticky='w')
self.pswd_label = Label(self, text='Password:'******'w')
self.pswd_value = Text(self, width=20, height=1, text="")
self.pswd_value.grid(row=4, column=2, padx=5, pady=5, sticky='w')
self.cancel_button = Button(self,
width=10,
height=1,
text="Cancel",
command=self.quit)
self.cancel_button.grid(row=5, column=1, padx=5, pady=5, sticky='e')
self.login_botton = Button(self,
width=10,
height=1,
text="Connect",
command=self.connectRepository)
self.login_botton.grid(row=5, column=2, padx=5, pady=5, sticky='w')
def connectRepository(self):
# need to check that all values are input
# trim off the end
name = self.name_value.getText()[:-1]
connect = self.rep_value.getText()[:-1]
username = self.user_value.getText()[:-1]
passwd = self.pswd_value.getText()[:-1]
# need to test the connection and store the set of connections
# locally (in rep?)
self.basePopup.parent.repList.newRepository(name, connect, username)
# there must be a better way of finding this!
for ff in self.basePopup.parent.tabbedFrame.frames[0].children.values(
):
ff.draw()
self.basePopup.destroy()
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.Experiment', func)
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.DataSource', func)
def updateAllAfter(self, obj):
self.after_idle(self.updateAll)
def updateAll(self, project=None):
return
def quit(self):
self.guiParent.parent.destroy()
def destroy(self):
self.administerNotifiers(self.basePopup.unregisterNotify)
Frame.destroy(self)
class MultiWidget(Frame):
def __init__(self,
parent,
widgetClass,
options=None,
values=None,
callback=None,
minRows=3,
maxRows=None,
useImages=True,
*args,
**kw):
Frame.__init__(self, parent, **kw)
if not values:
values = []
if not options:
options = []
# Widget types currently: Entries, Pulldown, Checkbutton
if useImages:
gfxDir = path.join(getTopDirectory(), 'python', 'memops', 'gui',
'graphics')
self.crossImage = Tkinter.PhotoImage(
file=path.join(gfxDir, 'cross.gif'))
self.tickImage = Tkinter.PhotoImage(
file=path.join(gfxDir, 'tick.gif'))
self.plusImage = Tkinter.PhotoImage(
file=path.join(gfxDir, 'plus.gif'))
self.minusImage = Tkinter.PhotoImage(
file=path.join(gfxDir, 'minus.gif'))
else:
self.crossImage = None
self.tickImage = None
self.plusImage = None
self.minusImage = None
module = widgetClass.__module__
self.widgetType = module.split('.')[-1]
self.widgetClass = widgetClass
self.callback = callback
self.numRows = 0
self.values = values
self.options = options
self.minRows = minRows
self.maxRows = maxRows
self.widgets = []
self.labels = []
self.grid_columnconfigure(1, weight=1)
self.topFrame = Frame(self)
self.topFrame.grid(row=0, column=0, columnspan=4, sticky=Tkinter.NSEW)
self.topFrame.grid_columnconfigure(1, weight=1)
self.topFrame.grid_rowconfigure(0, weight=1)
self.addButton = None
self.removeButton = None
self.commitButton = None
self.cancelButton = None
self.set(self.values, self.options)
self.updateButtons()
self.bind('<KeyPress-Return>', self.commit)
self.bind('<KeyPress-Escape>', self.cancel)
def get(self):
values = []
if self.widgetType == 'PulldownMenu':
for i in range(self.numRows):
value = self.widgets[i].getSelected()
if value is not None:
values.append(value)
elif self.widgetType == 'PulldownList':
for i in range(self.numRows):
value = self.widgets[i].getObject()
if value is not None:
values.append(value)
else:
for i in range(self.numRows):
value = self.widgets[i].get()
if (value is not None) and (value != ''):
values.append(value)
return values
def set(self, values=None, options=None):
if values is not None:
self.values = values
if options is not None:
self.options = options
N = max(len(self.values), self.minRows)
if self.maxRows is not None:
N = min(N, self.maxRows)
#N = max( min(len(self.values), self.maxRows), self.minRows)
#N = len(self.values)
if self.numRows < N:
for i in range(self.numRows, N):
self.addRow()
elif self.numRows > N:
for i in range(N, self.numRows):
self.removeRow(doClear=1)
for i in range(self.numRows):
if i < len(self.values):
value = self.values[i]
else:
value = None
if i < len(self.options):
option = self.options[i]
else:
option = None
self.updateWidget(i, value, option)
def setOptions(self, options):
self.set(self.values, options)
def setValues(self, values):
self.set(values, self.options)
def updateWidget(self, row, value, option):
if self.labels:
font = self.labels[0].cget('font')
else:
font = None
widget = self.widgets[row]
if self.widgetType in ('Entry', 'IntEntry', 'FloatEntry'):
widget.set(value)
label = self.labels[row]
label.set(option or '')
if font:
label.config(font=font)
elif self.widgetType == 'PulldownMenu':
index = -1
if value in self.options:
index = self.options.index(value or self.options[0])
widget.setup(self.options, index)
elif self.widgetType == 'PulldownList':
index = 0
if value in self.options:
index = self.options.index(value or self.options[0])
widget.setup(self.options, self.options, index)
elif self.widgetType == 'CheckButton':
widget.set(value)
label = self.labels[row]
label.set(option or '')
if font:
label.config(font=font)
else:
raise 'Widget type %s not supported in MultiWidget' % self.widgetType
def updateButtons(self):
row = 1
col = 0
if self.widgetType != 'CheckButton':
if (self.maxRows is None) or (self.numRows < self.maxRows):
if not self.addButton:
if self.plusImage:
self.addButton = Button(self,
image=self.plusImage,
command=self.addRow,
borderwidth=1)
else:
self.addButton = Button(self,
text='+',
command=self.addRow,
borderwidth=1,
bg=blueColor)
self.addButton.grid(row=row, column=col, sticky=Tkinter.EW)
col += 1
elif self.addButton:
self.addButton.grid_forget()
if self.numRows > self.minRows:
if not self.removeButton:
if self.minusImage:
self.removeButton = Button(self,
image=self.minusImage,
command=self.removeRow,
borderwidth=1)
else:
self.removeButton = Button(self,
text='-',
command=self.removeRow,
borderwidth=1,
bg=blueColor)
self.removeButton.grid(row=row, column=col, sticky=Tkinter.EW)
col += 1
elif self.removeButton:
self.removeButton.grid_forget()
if self.callback:
if not self.commitButton:
if self.tickImage:
self.commitButton = Button(self,
image=self.tickImage,
command=self.commit,
borderwidth=1)
else:
self.commitButton = Button(self,
text='OK',
command=self.commit,
borderwidth=1,
bg=blueColor)
self.commitButton.grid(row=row, column=col, sticky=Tkinter.EW)
self.grid_columnconfigure(col, weight=1)
col += 1
if not self.cancelButton:
if self.crossImage:
self.cancelButton = Button(self,
image=self.crossImage,
command=self.cancel,
borderwidth=1)
else:
self.cancelButton = Button(self,
text='Cancel',
command=self.cancel,
borderwidth=1,
bg=blueColor)
self.cancelButton.grid(row=row, column=col, sticky=Tkinter.EW)
self.grid_columnconfigure(col, weight=1)
def addWidget(self, row, value=None):
if self.widgetType in ('Entry', 'IntEntry', 'FloatEntry'):
option = ''
if row < len(self.options):
option = self.options[row]
label = Label(self.topFrame, text=option or '', anchor='w')
label.grid(row=row, column=0, sticky=Tkinter.E)
self.labels.append(label)
widget = self.widgetClass(self.topFrame, text=value, width=12)
widget.grid(row=row, column=1, sticky=Tkinter.EW)
widget.bind('<KeyPress-Return>', self.commit)
widget.bind('<KeyPress-Escape>', self.cancel)
elif self.widgetType == 'PulldownList':
index = -1
if value in self.options:
index = self.options.index(value or self.options[0])
widget = self.widgetClass(self.topFrame)
widget.setup(self.options, self.options, index)
widget.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
elif self.widgetType == 'PulldownMenu':
index = -1
if value in self.options:
index = self.options.index(value or self.options[0])
widget = self.widgetClass(self.topFrame)
widget.setup(self.options, index)
widget.grid(row=row, column=0, columnspan=2, sticky=Tkinter.W)
elif self.widgetType == 'CheckButton':
widget = self.widgetClass(self.topFrame)
widget.set(value)
widget.grid(row=row, column=0, sticky=Tkinter.W)
option = ''
if row < len(self.options):
option = self.options[row]
label = Label(self.topFrame, text=option or '', anchor='w')
label.grid(row=row, column=1, sticky=Tkinter.W)
self.labels.append(label)
else:
raise 'Widget type %s not supported in MultiWidget' % self.widgetType
return widget
def commit(self, event=None):
values = self.get()
if self.callback:
self.callback(values)
def cancel(self, event=None):
if self.callback:
self.callback(None)
def addRow(self):
if (self.maxRows is None) or (self.numRows < self.maxRows):
row = self.numRows
self.numRows += 1
if self.numRows > len(self.widgets):
widget = self.addWidget(row)
self.widgets.append(widget)
else:
widget = self.widgets[row]
if self.widgetType in ('Entry', 'IntEntry', 'FloatEntry'):
label = self.labels[row]
label.grid(row=row, column=0, sticky=Tkinter.E)
widget.grid(row=row, column=1, sticky=Tkinter.EW)
elif self.widgetType == 'CheckButton':
widget.grid(row=row, column=0, sticky=Tkinter.W)
label = self.labels[row]
label.grid(row=row, column=1, sticky=Tkinter.W)
else:
widget.grid(row=row,
column=0,
columnspan=2,
sticky=Tkinter.W)
if row == 0:
self.topFrame.grid(row=0,
column=0,
columnspan=4,
sticky=Tkinter.NSEW)
self.updateButtons()
def removeRow(self, doClear=0):
if self.numRows > self.minRows:
self.numRows -= 1
row = self.numRows
widget = self.widgets[row]
widget.grid_forget()
if self.widgetType == 'CheckButton':
label = self.labels[row]
label.grid_forget()
elif self.widgetType in ('Entry', 'IntEntry', 'FloatEntry'):
label = self.labels[row]
label.grid_forget()
if doClear:
self.updateWidget(row, None, '')
if self.numRows == 0:
self.topFrame.grid_forget()
self.updateButtons()
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
class TaskFilterFrame(LabelFrame):
def __init__(self, guiParent, basePopup, borderRelief='raised', text=' ', justify='left',
width=None, font=None, height=None, *args, **kw):
# Base popup required to handle notification of data model changes
# e.g. new peak lists, so that the GUI can update to the latest
# state
self.basePopup = basePopup
self.guiParent = guiParent
self.borderRelief = borderRelief
self.text = text
self.justify = justify
self.width = width
self.font = font
self.height = height
self.registerNotify=basePopup.registerNotify
self.unregisterNotify=basePopup.unregisterNotify
LabelFrame.__init__(self, guiParent, borderRelief, text, justify,
width, font, height, *args, **kw)
# set up the grid
self.grid_columnconfigure(0, weight=0, minsize=20)
self.grid_rowconfigure(0, weight=0, minsize=5)
self.grid_rowconfigure(1, weight=0, minsize=10)
self.grid_rowconfigure(2, weight=0, minsize=10)
self.grid_rowconfigure(3, weight=0, minsize=10)
# FIXME
# should be an enumerated list
self.statusLabel = Label(self,text='Type:')
self.statusText = Text(self, width=20, height=1)
# FIXME
# should be an enumerated list
self.typeLabel = Label(self,text='Type:')
self.typeText = Text(self, width=20, height=1)
# FIXME
# should be an enumerated list
self.projLabel = Label(self,text='Project:')
self.projText = Text(self, width=20, height=1)
# FIXME
# should be an enumerated list
self.userLabel = Label(self,text='User:'******'Clear', command=self.clear_filter, width=10, height=1)
self.filterButton = Button(self, text='Go', command=self.refresh_filter, width=10, height=1)
self.statusLabel.grid(row=2, column=0, padx=2, sticky='nw')
self.statusText.grid(row=2, column=1, sticky='nw')
self.typeLabel.grid(row=3, column=0, padx=2, sticky='nw')
self.typeText.grid(row=3, column=1, sticky='nw')
self.projLabel.grid(row=4, column=0, padx=2, sticky='nw')
self.projText.grid(row=4, column=1, sticky='nw')
self.userLabel.grid(row=5, column=0, padx=2, sticky='nw')
self.userText.grid(row=5, column=1, sticky='nw')
self.clearButton.grid(row=6, column=0, columnspan=2, sticky='nw')
self.filterButton.grid(row=6, column=1, columnspan=2, sticky='ne')
def clear_filter(self):
self.statusText.clear()
self.typeText.clear()
self.projText.clear()
self.userText.clear()
def refresh_filter(self):
status = self.statusText.getText()[:-1]
type = self.typeText.getText()[:-1]
proj = self.projText.getText()[:-1]
user = self.userText.getText()[:-1]
print 'status ',status,'.'
print 'type ', type,'.'
print 'proj ', proj,'.'
print 'user ', user,'.'
select = {}
if status not in ["", None]:
select['status'] = status.__str__()
# this is going to be a little harder to work in to the Bean
# if type not in ["", None]:
# select['type'] = type
# really we need to be able to put in text here that allows more
# than one project etc to be included. But what should the syntax be?
if proj not in ["", None]:
select['proj'] = proj
if user not in ["", None]:
select['user'] = user.__str__()
print 'set select hash ', select
self.guiParent.select = select
self.guiParent.drawFrame()
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
class ProjectFrame(Frame):
def __init__(self, guiParent, basePopup):
self.basePopup = basePopup
self.guiParent = guiParent
self.basePopup.frameShortcuts['Project'] = self
#self.registerNotify=basePopup.registerNotify
#self.unregisterNotify=basePopup.unregisterNotify
Frame.__init__(self, guiParent)
# set up the grid
self.grid_columnconfigure(0, weight=0, minsize=10)
self.grid_columnconfigure(1, weight=0, minsize=50)
self.grid_columnconfigure(2, weight=1, minsize=20)
self.grid_columnconfigure(3, weight=0, minsize=40)
self.grid_rowconfigure(0, weight=0, minsize=5)
self.grid_rowconfigure(1, weight=0, minsize=10)
self.grid_rowconfigure(2, weight=0, minsize=10)
self.grid_rowconfigure(3, weight=0, minsize=10)
# we could in theory choose to store the last visited
# project in the user config file and load this on log in
# if we then decide that login is mandatory then this
# would give as a project from the start
self.repository = None
self.projectName = None
self.versionTag = None
# we define as much as possible once on startup and use the
# grid manager to control the display thereafter
# when no data
self.noData_widgets = []
self.null_proj_label = Label(self, text='No Project selected')
self.noData_widgets.append(self.null_proj_label)
# when data
self.data_widgets = []
self.proj_rep_title = Label(self, text='Project:', font='Helvetica16')
self.data_widgets.append(self.proj_rep_title)
self.proj_rep_label = Label(self, text='Repository:')
self.data_widgets.append(self.proj_rep_label)
self.proj_rep_value = Label(self, text='')
self.data_widgets.append(self.proj_rep_value)
# This is more complex than it seems. We need to have some
# user information accoisated with this too (who has the lock)
self.proj_status_label = Label(self, text = 'Status:')
self.data_widgets.append(self.proj_status_label)
self.proj_status_value = Label(self, text='')
self.data_widgets.append(self.proj_status_value)
self.proj_details_label = Label(self, text='Description:')
self.proj_details = Text(self, width=75, height=6, text='')
self.data_widgets.append(self.proj_details)
info_modes = ['versions','tasks','raw data']
self.info_mode_select = PulldownList(self, self.tmpCall, info_modes)
self.data_widgets.append(self.info_mode_select)
initial_cols = ['Project','Version','Created by Task', 'Created from Project version']
self.proj_history_matrix = ScrolledMatrix(self, headingList=initial_cols, initialRows=7,
doubleCallback=self.history_callback)
self.data_widgets.append(self.proj_history_matrix)
initial_cols = ['ID','Task','User','Status', 'Date']
self.proj_tasks_matrix = ScrolledMatrix(self, headingList=initial_cols, initialRows=7,
doubleCallback=self.history_callback)
self.data_widgets.append(self.proj_tasks_matrix)
initial_cols = ['name','type','size','details']
self.proj_files_matrix = ScrolledMatrix(self, headingList=initial_cols, initialRows=7,
doubleCallback=self.history_callback)
self.data_widgets.append(self.proj_files_matrix)
self.proj_export_button = Button(self,
height=1, width=14,text='Export',
command=self.export_project)
self.data_widgets.append(self.proj_export_button)
self.proj_import_button = Button(self,
height=1, width=14,text='Import',
command=self.export_project)
self.data_widgets.append(self.proj_import_button)
self.run_testtask1_button = Button(self,
height=1, width=14,text='Run TestTask1',
command=self.goto_task1_tab)
self.data_widgets.append(self.run_testtask1_button)
# FIXME JMCI
# insert this inside this Frame directly: not worth abstracting out
self.filter_frame = FilterFrame(self, self.basePopup, text='Filter')
self.data_widgets.append(self.filter_frame)
self.drawFrame()
# Refreshing of the Frame is meaningless without setting the full
# connection parameters
def drawFrame(self):
if self.basePopup.repList:
self.repository = self.basePopup.repList.currentRepository
if self.repository:
self.projectName = self.repository.currentProjectName
self.versionTag = self.repository.currentVersionTag
print 'in drawFrame ', self.repository, self.projectName, self.versionTag
if self.projectName == None:
for widget in self.data_widgets:
widget.grid_remove()
self.null_proj_label.grid(row=1, column=1, columnspan=4, sticky='nswe')
else:
# build up the body.
for widget in self.noData_widgets:
widget.grid_remove()
# OK, so we need to determine the project that we are showing
# in this frame. To uniquely describe a project we need to
# know the repository, the project name, and the project version
# so all these need to be set somehow. Maybe the best approach is
# so have a public method that takes these arguments and to force
# every refresh to operate through this. Then the drawFrame() method
# would be private.
loc = SharedBeanServiceLocator()
port = loc.getSharedBean()
# need two calls, one for the Project and one for the version
hm1 = {'name': self.projectName }
wsstr_in1 = WSString(hm1)
request1 = getFields();
request1._arg0 = 'org.pimslims.applet.server.ProjectBean';
request1._arg1 = 'getFields';
request1._arg2 = wsstr_in1.str
response1 = port.getFields(request1)
wsstr_out1 = WSString(response1._return)
hm_proj = wsstr_out1.getStructHM()
# now the version
hm2 = {'project' : { 'name': self.projectName },
'versionTag': self.versionTag }
wsstr_in2 = WSString(hm2)
request2 = getFields();
request2._arg0 = 'org.pimslims.applet.server.ProjectVersionBean';
request2._arg1 = 'getFields';
request2._arg2 = wsstr_in2.str
response2 = port.getFields(request2)
wsstr_out2 = WSString(response2._return)
hm_pv = wsstr_out2.getStructHM()
self.proj_rep_title.set('Project: ' + self.projectName + ' v ' + self.versionTag)
self.proj_rep_title.grid(row=1, column=1, sticky='w')
self.proj_rep_label.grid(row=2, column=1, sticky='w')
self.proj_rep_value.set(self.repository.name)
self.proj_rep_value.grid(row=2, column=2, sticky='w')
status = 'N/A'
if hm_pv['status'] != 'valIsNullPointer':
status = hm_pv['status']
self.proj_status_label.grid(row=3, column=1, sticky='w')
self.proj_status_value.set(status)
self.proj_status_value.grid(row=3, column=2, sticky='w')
# also want to know:
# * how this file was created
# * what external file (e.g. spectrum files) it uses
# * the log history
# * what processes it has been used in
# * if locked, what process, user is responsible for this
details = 'N/A'
if hm_proj['details'] != 'valIsNullPointer':
details = hm_proj['details']
self.proj_details_label.grid(row=4, column=1, columnspan=2, sticky='nw')
self.proj_details.setText(details)
self.proj_details.grid(row=4, column=2, pady=10, sticky='nw')
self.info_mode_select.grid(row=5, column=1, sticky='w')
# this needs to go into a separate subroutine
# get al the version
hm3 = {'project' : { 'name': self.projectName }}
wsstr_in3 = WSString(hm3)
request3 = getList()
request3._arg0 = 'org.pimslims.applet.server.ProjectVersionBean';
request3._arg1 = 'getListWithFields';
request3._arg2 = wsstr_in3.str
response3 = port.getList(request3)
wsstr_out3 = WSString(response3._return)
vers = wsstr_out3.getStruct()
matrix = [];
objs = [];
print 'PROJECT: ', vers
for ver in vers:
taskSerial = 'unknown'
if (ver.has_key('createdByTask')):
task = ver['createdByTask']
taskSerial = task['serial']
# FIXME JMCI
# Really should get this from the task, of it exists
parentVersionTag = 'unknown'
if (ver.has_key('sourceVersion')):
pv = ver['sourceVersion']
pvp = pv['project']
parentName = pvp['name']
parentVersionTag = pvp['name'] + ' ' + pv['versionTag']
new_row = (self.projectName, ver['versionTag'], taskSerial, parentVersionTag )
matrix.append(new_row)
objs.append(ver)
self.proj_history_matrix.update(objectList=objs, textMatrix=matrix)
self.proj_history_matrix.grid(row=6, column=1, columnspan=2, pady=10, sticky='nsew')
self.filter_frame.grid(row=6, column=3, pady=10, sticky='n')
# have a button to export. It should now be clear which version
# of which project in which repository should be exported
self.proj_import_button.grid(row=1, column=3, padx=3,pady=3, sticky='ew')
self.proj_export_button.grid(row=2, column=3, padx=3,pady=3, sticky='ew')
self.run_testtask1_button.grid(row=4, column=3, padx=3,pady=3, sticky='ew')
# It is not clear precisely how methods should be triggered from
# the project frame, as there may be >1 input to a given task with
# a specific role. It maybe that we need to parse out a metadescription
# of the task and use this to produce the correct buttons (maybe
# even depending on the contents of the file ?)
#self.task_button_texts=['Test1Task','Test2Task']
#self.task_button_cmds=[self.runTest1Task, self.runTest2Task]
#self.task_button_list = ButtonList(self, self.task_button_texts, self.task_button_cmds,
# None, 1, 1, True, None, Tkinter.VERTICAL)
#
#self.task_button_list.grid(row=1, rowspan=3, column=4, padx=3, sticky='w')
def history_callback (self, obj, row, col):
if (col == 1):
pv = obj['versionTag']
print 'PROJECT -> PROJECT (DIRECT) ', pv
self.repository.currentVersionTag = pv.__str__()
self.drawFrame()
elif (col == 2):
task = obj['createdByTask']
taskSerial = task['serial']
print 'PROJECT -> TASK ', taskSerial
self.basePopup.currentTask = taskSerial.__str__()
# FIXME
# This is more complex. Need to navigate to the correct
# panel within the Task submenu
if self.basePopup.frameShortcuts.has_key('Task'):
taskFrame = self.basePopup.frameShortcuts['Task']
# really need to check on the type of task
if taskFrame.frameShortcuts.has_key('Test1'):
taskFrame.frameShortcuts['Test1'].drawFrame()
# also need to select the current tabbed frame
self.basePopup.tabbedFrame.select(2)
# FIXME JMCI
# need to look into this. Really we need both the project and
# the version for this (in theory this could be based on a different
# project although it is highly unlikely!)
elif (col == 3):
pv = obj['sourceVersion']
parentVersion = pv['versionTag']
pvp = pv['project']
parentName = pvp['name']
print 'PROJECT -> PROJECT (SOURCE) ', parentVersion
self.repository.currentVersionTag = parentVersion.__str__()
self.repository.currentProjectName = parentName.__str__()
self.drawFrame()
# create a new task with this project as an input
# it is not clear how we should do this:- construct data locally
# and then save, or save a first cut and then ammend. On the basis
# that the serial has to be generated by the DB, we will go for the
# former for now
# it would be better to pass this to a processor layer that
# determines parameters and then builds the stub.
def goto_task1_tab(self):
# create a new task (provisional status)
loc = SharedBeanServiceLocator()
port = loc.getSharedBean()
#hm0 = { 'project': { 'name': self.projectName},
# 'versionTag' : self.versionTag,
# '_handle' : 'findOrFail' }
# FIXME
# We have an error here (it seems to be a problem between the CCPN
# and hibernate layers that is not picking objects as the same for
# some reason. Therefore do not set the inputVersion for now
hm0 = { 'project': { 'name': self.projectName},
'versionTag' : self.versionTag}
hm2 = { 'inputVersion' : hm0,
'status' : 'PROVISIONAL' }
#hm2 = { 'status' : 'PROVISIONAL' }
wsstr_in1 = WSString(hm2)
req1 = recordAndLoad();
req1._arg0 = 'org.pimslims.applet.server.TaskBean';
req1._arg1 = 'recordTest1';
req1._arg2 = wsstr_in1.str
resp1 = port.recordAndLoad(req1)
wsstr_out1 = WSString(resp1._return)
v = wsstr_out1.getStructHM()
self.basePopup.currentTask = v['serial'].__str__()
# FIXME
# This is more complex. Need to navigate to the correct
# panel within the Task submenu
if self.basePopup.frameShortcuts.has_key('Task'):
taskFrame = self.basePopup.frameShortcuts['Task']
# really need to check on the type of task
if taskFrame.frameShortcuts.has_key('Test1'):
taskFrame.frameShortcuts['Test1'].drawFrame()
# also need to select the current tabbed frame
self.basePopup.tabbedFrame.select(2)
# method for exporting repository directory to local file
# system. This is a very basic approach, essentially first
# listing all the files required for transfer and then
# copying them over one by one. Note that due to limitations
# in ZSI we cannot do much better than base64 encoding each
# file. We could consider storing a tgz on the server and
# exporting that. It might be a considerable improvement as
# the compression leads to a file < 10% of the original size
# which would cut down on traffic enormously
def export_project(self):
versionTag = self.versionTag
name = self.projectName
# need to preserve the current status. Take a default from the
# Wms layer
rootDir = self.basePopup.repList.current_export_dir
# This should be obtained from a query box. Hard code for now
fileSelectPopup = FileSelectPopup(self, None, rootDir)
exp_project_dir = fileSelectPopup.getDirectory()
self.basePopup.repList.current_export_dir = exp_project_dir
# These should come from the repository object
loc = SharedBeanServiceLocator()
port = loc.getSharedBean()
req1 = getList()
hm1 = {'projectName': name,
'versionTag': versionTag,
'segment': 'jionides' }
wsstr1 = WSString(hm1)
# these are actually static
req1._arg0 = 'org.pimslims.applet.server.CcpnFileBean';
req1._arg1 = 'getList';
req1._arg2 = wsstr1.str
# get the response
resp1 = port.getList(req1)
# this is a hack at present. It needs to be written properly
wsstr = WSString(resp1._return)
ss = wsstr.getStruct()
print 'got array ', ss
for strg in ss:
print 'trying to handle file ', strg
hm2 = {'projectName': name,
'versionTag': versionTag,
'segment': 'jionides',
'fileName' : '/' + strg.__str__(),
'random' : 'test',
'raw' : False}
print 'trying to handle file 2 ', strg
print 'trying to handle file 2 ', hm2
req2 = getDocWithParams()
wsstr2 = WSString(hm2)
# these are actually static
req2._arg0 = 'org.pimslims.applet.server.CcpnFileBean';
req2._arg1 = wsstr2.str
# get the response
resp2 = port.getDocWithParams(req2)
local_file_path = exp_project_dir + '/' + name + '/' + strg
idx = local_file_path.rfind('/')
local_dir = local_file_path[:idx]
print 'trying to create ', local_dir
os.makedirs(local_dir)
print 'writing to local area; ', local_file_path
f = open(local_file_path, 'w')
f.write(resp2._return)
# it is likely that these methods are going to have to be highly specialised
# as some tasks are going to have many input files and we need to know which
# role the project we are in takes in the task.
def runTest1Task(self):
pass
def runTest2Task(self):
pass
def view_project(self, project):
self.project = project
self.drawFrame()
def tmpCall(self):
return
def administerNotifiers(self, notifyFunc):
for func in ('__init__','delete','setName'):
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.Experiment', func)
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.DataSource', func)
def updateAllAfter(self, obj):
self.after_idle(self.updateAll)
def updateAll(self, project=None):
return
def quit(self):
self.guiParent.parent.destroy()
def destroy(self):
self.administerNotifiers(self.basePopup.unregisterNotify)
Frame.destroy(self)
def __init__(self, parent, getOption = None, setOption = None,
haveTicks = False, doOutlineBox = True, *args, **kw):
self.getOption = getOption
self.setOption = setOption
self.haveTicks = haveTicks
self.doOutlineBox = doOutlineBox
Frame.__init__(self, parent=parent, *args, **kw)
self.file_select_popup = None
self.getOptionValues()
try:
size_index = paper_types.index(self.paper_type)
except:
size_index = 0
try:
other_unit_index = paper_units.index(self.other_unit)
except:
other_unit_index = 0
try:
orientation_index = paper_orientations.index(self.paper_orientation)
except:
orientation_index = 0
try:
style_index = style_choices.index(self.output_style)
except:
style_index = 0
try:
format_index = format_choices.index(self.output_format)
except:
format_index = 0
if haveTicks:
try:
tick_location_index = tick_locations.index(self.tick_location)
except:
tick_location_index = 0
self.grid_columnconfigure(1, weight=1)
row = 0
button = Button(self, text='File:', command=self.findFile,
tipText='Select location to save print file')
button.grid(row=row, column=0, sticky='e')
self.file_entry = Entry(self, width=40, text=self.file_name,
tipText='Location where file is saved on disk')
self.file_entry.grid(row=row, column=1, sticky='ew')
row += 1
label = Label(self, text='Title:')
label.grid(row=row, column=0, sticky='e')
self.title_entry = Entry(self, width=40, text=self.title,
tipText='Title of the printout, displayed at top')
self.title_entry.grid(row=row, column=1, sticky='ew')
row += 1
label = Label(self, text='X axis label:')
label.grid(row=row, column=0, sticky='e')
self.x_axis_entry = Entry(self, width=40, text=self.x_axis_label,
tipText='X axis label for the printout')
self.x_axis_entry.grid(row=row, column=1, sticky='ew')
row += 1
label = Label(self, text='Y axis label:')
label.grid(row=row, column=0, sticky='e')
self.y_axis_entry = Entry(self, width=40, text=self.y_axis_label,
tipText='Y axis label for the printout')
self.y_axis_entry.grid(row=row, column=1, sticky='ew')
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=2, sticky='ew')
frame.grid_columnconfigure(4, weight=1)
label = Label(frame, text='Paper size:')
label.grid(row=0, column=0, sticky='e')
entries = []
for t in paper_types:
if t == Output.other_paper_type:
entry = t
else:
(w, h, u) = paper_sizes[t]
entry = t + ' (%2.1f %s x %2.1f %s)' % (w, u, h, u)
entries.append(entry)
self.size_menu = PulldownList(frame, callback=self.changedSize,
texts=entries, index=size_index,
tipText='The paper size for the printout')
self.size_menu.grid(row=0, column=1, sticky='w')
self.other_frame = Frame(frame)
self.other_frame.grid_columnconfigure(0, weight=1)
self.other_entry = FloatEntry(self.other_frame, text=self.other_size,
isArray=True,
tipText='The size of the Other paper in both dimensions; this requires two values, space or comma separated')
self.other_entry.grid(row=0, column=0, sticky='ew')
self.other_unit_menu= PulldownList(self.other_frame, texts=paper_units,
index=other_unit_index,
tipText='The unit for the Other paper size')
self.other_unit_menu.grid(row=0, column=1, sticky='ew')
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='ew')
frame.grid_columnconfigure(1, weight=1)
frame.grid_columnconfigure(3, weight=1)
frame.grid_columnconfigure(5, weight=1)
label = Label(frame, text='Orientation:')
label.grid(row=0, column=0, sticky='e')
self.orientation_menu = PulldownList(frame, texts=paper_orientations,
index=orientation_index,
tipText='Whether the paper should be set in Portrait or Landscape mode')
self.orientation_menu.grid(row=0, column=1, sticky='w')
label = Label(frame, text=' Style:')
label.grid(row=0, column=2, sticky='e')
self.style_menu = PulldownList(frame, texts=style_choices,
index=style_index,
tipText='Whether the printout should be in colour or black and white')
self.style_menu.grid(row=0, column=3, sticky='w')
label = Label(frame, text=' Format:')
label.grid(row=0, column=4, sticky='e')
self.format_menu = PulldownList(frame, callback=self.changedFormat,
texts=format_choices, index=format_index,
tipText='Whether to save as PS, EPS or PDF')
self.format_menu.grid(row=0, column=5, sticky='w')
if haveTicks:
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='ew')
frame.grid_columnconfigure(1, weight=1)
frame.grid_columnconfigure(3, weight=1)
label = Label(frame, text='Tick Location:')
label.grid(row=0, column=0, sticky='e')
self.tick_menu = PulldownList(frame, texts=tick_locations,
index=tick_location_index,
tipText='Whether the tick marks appear on the inside or outside of the frame')
self.tick_menu.grid(row=0, column=1, sticky='w')
label = Label(frame, text=' Tick Placement:')
label.grid(row=0, column=2, sticky='e')
if self.tick_placement is None:
selected = None
else:
selected = [(x in self.tick_placement) for x in tick_placements]
self.tick_buttons = CheckButtons(frame, entries=tick_placements,
selected=selected,
tipTexts=('Whether the tick marks appear on the top and/or bottom and/or left and/or right',))
self.tick_buttons.grid(row=0, column=3, sticky='w')
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='ew')
frame.grid_columnconfigure(1, weight=1)
frame.grid_columnconfigure(3, weight=1)
label = Label(frame, text='Tick Font:')
label.grid(row=0, column=0, sticky='e')
self.tick_font_list = FontList(frame, mode='Print',
selected=self.tick_font,
extraTexts=[PrintTicks.no_tick_text],
tipText='The font used for the tick mark labels')
self.tick_font_list.grid(row=0, column=1, sticky='w')
label = Label(frame, text='Tick Spacing:')
label.grid(row=0, column=2, sticky='e')
# TBD: put preferred choice in data model
self.spacing_menu = PulldownList(frame, texts=spacing_choices, index=0,
callback=self.changedSpacing,
tipText='Whether the program should automatically calculate the major/minor tick spacings and how many decimal places are used for the ticks, or whether the these are specified manually')
self.spacing_menu.grid(row=0, column=3, sticky='w')
ff = self.spacing_frame = Frame(frame)
ff.grid_columnconfigure(1, weight=1)
ff.grid_columnconfigure(2, weight=1)
label = Label(ff, text='Tick Spacing')
label.grid(row=0, column=0, sticky='w')
label = Label(ff, text='Major')
label.grid(row=0, column=1, sticky='ew')
label = Label(ff, text='Minor')
label.grid(row=0, column=2, sticky='ew')
label = Label(ff, text='Decimals')
label.grid(row=0, column=3, sticky='ew')
label = Label(ff, text='X:')
label.grid(row=1, column=0, sticky='w')
self.x_major_entry = FloatEntry(ff, tipText='The spacing in display units of the major tick marks in the X dimension')
self.x_major_entry.grid(row=1, column=1, sticky='ew')
self.x_minor_entry = FloatEntry(ff, tipText='The spacing in display units of the minor tick marks in the X dimension (not printed if left blank)')
self.x_minor_entry.grid(row=1, column=2, sticky='ew')
self.x_decimal_entry = IntEntry(ff, tipText='The number of decimal places for the tick numbers in the X dimension')
self.x_decimal_entry.grid(row=1, column=3, sticky='ew')
label = Label(ff, text='Y:')
label.grid(row=2, column=0, sticky='w')
self.y_major_entry = FloatEntry(ff, tipText='The spacing in display units of the major tick marks in the Y dimension')
self.y_major_entry.grid(row=2, column=1, sticky='ew')
self.y_minor_entry = FloatEntry(ff, tipText='The spacing in display units of the minor tick marks in the Y dimension (not printed if left blank)')
self.y_minor_entry.grid(row=2, column=2, sticky='ew')
self.y_decimal_entry = IntEntry(ff, tipText='The number of decimal places for the tick numbers in the Y dimension')
self.y_decimal_entry.grid(row=2, column=3, sticky='ew')
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='ew')
frame.grid_columnconfigure(1, weight=1)
label = Label(frame, text='Tick Length:')
label.grid(row=0, column=0, sticky='e')
# TBD: put preferred choice in data model
self.tick_length_menu = PulldownList(frame, texts=tick_length_choices, index=0,
callback=self.changedLength,
tipText='Whether the program should automatically calculate the major/minor tick lengths, or whether the these are specified manually')
self.tick_length_menu.grid(row=0, column=1, sticky='w')
ff = self.length_frame = Frame(frame)
ff.grid_columnconfigure(1, weight=1)
label = Label(ff, text=' Major length:')
label.grid(row=0, column=0, sticky='w')
self.length_major_entry = FloatEntry(ff, tipText='The length in points of the major tick marks')
self.length_major_entry.grid(row=0, column=1, sticky='w')
label = Label(ff, text='Minor length:')
label.grid(row=0, column=2, sticky='w')
self.length_minor_entry = FloatEntry(ff, tipText='The length in points of the minor tick marks')
self.length_minor_entry.grid(row=0, column=3, sticky='w')
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='ew')
frame.grid_columnconfigure(3, weight=1)
frame.grid_columnconfigure(4, weight=1)
label = Label(frame, text='Scaling:')
label.grid(row=0, column=0, sticky='e')
# TBD: put preferred choice in data model
self.scaling_menu = PulldownList(frame, texts=scaling_choices, index=0,
callback=self.changedScaling,
tipText='Whether the plot should be scaled as a percentage of the maximum size that would fit on the paper, or instead should be specified by the number of cms or inches per unit')
self.scaling_menu.grid(row=0, column=1, sticky='ew')
self.scaling_scale = Scale(frame, orient=Tkinter.HORIZONTAL, value=self.scaling, tipText='The percentage of the maximum size that would fit on the paper that the plot is scaled by')
self.scaling_scale.grid(row=0, column=2, columnspan=3, sticky='ew')
self.x_scaling_label = Label(frame, text='X:')
self.x_scaling_entry = FloatEntry(frame, tipText='The scaling that should be used in the X dimension as cms or inches per unit')
self.y_scaling_label = Label(frame, text='Y:')
self.y_scaling_entry = FloatEntry(frame, tipText='The scaling that should be used in the Y dimension as cms or inches per unit')
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='w')
frame.grid_columnconfigure(2, weight=1)
label = Label(frame, text='Include:')
label.grid(row=0, column=0, sticky='e')
tipTexts = ('Whether the time and date should be included in the printout',
'Whether the file name should be included in the printout')
if self.border_decoration is None:
selected = None
else:
selected = [(x in self.border_decoration) for x in border_decorations]
self.border_buttons = CheckButtons(frame, entries=border_decorations,
selected=selected,
tipTexts=tipTexts)
self.border_buttons.grid(row=0, column=1, sticky='w')
label = Label(frame, text=' Using Font:')
label.grid(row=0, column=2, sticky='e')
self.border_font_list = FontList(frame, mode='Print',
selected=self.border_font,
tipText='The font used for the border texts')
self.border_font_list.grid(row=0, column=3, sticky='w')
row += 1
label = Label(self, text='Line width:')
label.grid(row=row, column=0, sticky='w')
self.linewidth_entry = FloatEntry(self, width=10,
text=self.linewidth,
tipText='Line width for drawing')
self.linewidth_entry.grid(row=row, column=1, sticky='w')
class AnnealingSettingsTab(object):
'''This class describes the tab in the GUI where the user
can change setting that govern the monte carlo / annleaing
procedure. This also includes which information from the ccpn
analysis project is used and which information is
ignored. This includes:
* present sequential assignments
* tentative assignments
* amino acid type information
* whether to include untyped spin systems
* assignments to peak dimensions
ALso the chain can be selected here.
Furthermore the user can set the temperature
regime of the annealing, the amount of times the procedure
is repeated to obtain statistics. The fraction of peaks
that is left out in each run to diversify the results,
the treshhold score for amino acid typing and the treshhold
collabelling for a peak to be expected.
'''
def __init__(self, parent, frame):
'''Init. args: parent: the guiElement that this
tab is part of.
frame: the frame this part of the
GUI lives in.
'''
self.guiParent = parent
self.frame = frame
self.project = parent.project
self.nmrProject = parent.nmrProject
self.minIsoFrac = 0.1
self.leavePeaksOutFraction = 0.0
self.minTypeScore = 1.0
self.chain = None
self.amountOfRepeats = 10
self.amountOfSteps = 10000
self.acceptanceConstantList = [0.0, 0.01, 0.015, 0.022,
0.033, 0.050, 0.075, 0.113,
0.170, 0.256, 0.384, 0.576,
0.864, 1.297, 1.946, 2.919,
4.378, 6.568, 9.852, 14.77,
22.16, 33.25]
self.energyDataSets = [[]]
self.residues = []
self.body()
def body(self):
'''describes the body of this tab. It bascically consists
of some field to fill out for the user at the top and
a ScrolledGraph that shows the progess of the annealing
procedure a the bottom.
'''
frame = self.frame
# frame.expandGrid(13,0)
frame.expandGrid(15, 1)
row = 0
text = 'Calculate Assignment Suggestions'
command = self.runCalculations
self.startButton = Button(frame, command=command, text=text)
self.startButton.grid(row=row, column=0, sticky='nsew', columnspan=2)
row += 1
Label(frame, text='Amount of runs: ', grid=(row, 0))
tipText = 'The amount of times the whole optimization procedure is performed, each result is safed'
self.repeatEntry = IntEntry(frame, grid=(row, 1), width=7, text=10,
returnCallback=self.updateRepeatEntry,
tipText=tipText, sticky='nsew')
self.repeatEntry.bind('<Leave>', self.updateRepeatEntry, '+')
row += 1
Label(frame, text='Temperature regime: ', grid=(row, 0))
tipText = 'This list of numbers govern the temperature steps during the annealing, every number represents 1/(kb*t), where kb is the Boltzmann constant and t the temperature of one step.'
self.tempEntry = Entry(frame, text=map(str, self.acceptanceConstantList), width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateAcceptanceConstantList,
tipText=tipText, sticky='nsew')
row += 1
Label(frame, text='Amount of attempts per temperature:', grid=(row, 0))
tipText = 'The amount of attempts to switch the position of two spinsystems in the sequence are performed for each temperature point'
self.NAStepEntry = IntEntry(frame, grid=(row, 1), width=7, text=10000,
returnCallback=self.updateStepEntry,
tipText=tipText, sticky='nsew')
self.NAStepEntry.bind('<Leave>', self.updateStepEntry, '+')
row += 1
Label(frame, text='Fraction of peaks to leave out:', grid=(row, 0))
tipText = 'In each run a fraction of the peaks can be left out of the optimization, thereby increasing the variability in the outcome and reducing false negatives. In each run this will be different randomly chosen sub-set of all peaks. 0.1 (10%) can be a good value.'
self.leaveOutPeaksEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.0,
returnCallback=self.updateLeavePeaksOutEntry,
tipText=tipText, sticky='nsew')
self.leaveOutPeaksEntry.bind(
'<Leave>', self.updateLeavePeaksOutEntry, '+')
row += 1
Label(frame, text='Minmal amino acid typing score:', grid=(row, 0))
tipText = 'If automatic amino acid typing is selected, a cut-off value has to set. Every amino acid type that scores higher than the cut-off is taken as a possible type. This is the same score as can be found under resonance --> spin systems --> predict type. Value should be between 0 and 100'
self.minTypeScoreEntry = FloatEntry(frame, grid=(row, 1), width=7, text=1.0,
returnCallback=self.updateMinTypeScoreEntry,
tipText=tipText, sticky='nsew')
self.minTypeScoreEntry.bind(
'<Leave>', self.updateMinTypeScoreEntry, '+')
row += 1
Label(frame, text='Minimal colabelling fraction:', grid=(row, 0))
tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.'
self.minLabelEntry = FloatEntry(frame, grid=(row, 1), width=7, text=0.1,
returnCallback=self.updateMinLabelEntry,
tipText=tipText, sticky='nsew')
self.minLabelEntry.bind('<Leave>', self.updateMinLabelEntry, '+')
row += 1
Label(frame, text='Use sequential assignments:', grid=(row, 0))
tipText = 'When this option is select the present sequential assignments will be kept in place'
self.useAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use tentative assignments:', grid=(row, 0))
tipText = 'If a spin system has tentative assignments this can be used to narrow down the amount of possible sequential assignments.'
self.useTentativeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use amino acid types:', grid=(row, 0))
tipText = 'Use amino acid types of the spin systems. If this option is not checked the spin systems are re-typed, only resonance names and frequencies are used'
self.useTypeCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Include untyped spin systems:', grid=(row, 0))
tipText = 'Also include spin system that have no type information. Amino acid typing will be done on the fly.'
self.useAlsoUntypedSpinSystemsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Use dimensional assignments:', grid=(row, 0))
tipText = 'If one or more dimensions of a peak is already assigned, assume that this assignment is the only option. If not the check the program will consider all possibilities for the assignment of the dimension.'
self.useDimensionalAssignmentsCheck = CheckButton(
frame, selected=True, tipText=tipText, grid=(row, 1))
row += 1
Label(frame, text='Chain:', grid=(row, 0))
self.molPulldown = PulldownList(
frame, callback=self.changeMolecule, grid=(row, 1))
self.updateChains()
row += 1
Label(frame, text='Residue ranges: ', grid=(row, 0))
tipText = 'Which residues should be included. Example: "10-35, 62-100, 130".'
self.residueRangeEntry = Entry(frame, text=None, width=64,
grid=(row, 1), isArray=True, returnCallback=self.updateResidueRanges,
tipText=tipText, sticky='nsew')
self.updateResidueRanges(fromChain=True)
row += 1
self.energyPlot = ScrolledGraph(frame, symbolSize=2, width=600,
height=200, title='Annealing',
xLabel='temperature step', yLabel='energy')
self.energyPlot.grid(row=row, column=0, columnspan=2, sticky='nsew')
def runCalculations(self):
'''Run all calculations. Also triggers the disabling of
some buttons and fields.
'''
self.startButton.disable()
self.disableIllegalButtonsAfterPrecalculations()
self.guiParent.connector.runAllCalculations()
self.startButton.configure(text='More runs')
self.startButton.enable()
def disableIllegalButtonsAfterPrecalculations(self):
'''Disable buttons and field the user can not alter
any longer after the model is set up and the
'pre-calculations' have finished.
This is done because this part of the calculation
should only be run once. All settings that would
be changed after this point will not have any influence.
'''
illegalButtons = [self.minTypeScoreEntry, self.minLabelEntry,
self.useAlsoUntypedSpinSystemsCheck, self.useAssignmentsCheck,
self.useTypeCheck, self.useDimensionalAssignmentsCheck,
self.useTentativeCheck]
for illegalButton in illegalButtons:
illegalButton.configure(state='disabled')
self.molPulldown.disable()
def getChainName(self, chain):
'''Get the name for a chain.
args: chain: ccpn analysis
chain object
returns: chain name
'''
return '%s:%s (%s)' % (chain.molSystem.code, chain.code, chain.molecule.molType)
def getChains(self):
'''Get all chains present in the project.
returns: list of ccpn analysis chain objects
'''
chains = []
if self.project:
for molSystem in self.project.sortedMolSystems():
for chain in molSystem.sortedChains():
if chain.residues:
chains.append(chain)
return chains
def updateChains(self, *opt):
'''Updates the list of chains if a new one is added
to or deleted from the project. Updates the
pull down list where a chain can be selected.
'''
index = 0
texts = []
chains = self.getChains()
chain = self.chain
if chains:
if chain not in chains:
chain = chains[0]
texts = [self.getChainName(c) for c in chains]
index = chains.index(chain)
else:
chain = None
self.molPulldown.setup(texts, chains, index)
if chain is not self.chain:
self.chain = chain
def changeMolecule(self, chain):
'''Select a molecular chain.'''
if chain is not self.chain:
self.chain = chain
self.updateResidueRanges(fromChain=True)
def updateStepEntry(self, event=None):
'''Update the value and entry that sets the amount of
steps per temperature point.
'''
value = self.NAStepEntry.get()
if value == self.amountOfSteps:
return
if value < 1:
self.NAStepEntry.set(1)
self.amountOfSteps = 1
else:
self.amountOfSteps = value
self.NAStepEntry.set(value)
def updateRepeatEntry(self, event=None):
'''Update the value and entry of that sets
the amount of times the whole annealing
procedure is repeated in order
to obtain statistics.
'''
value = self.repeatEntry.get()
if value == self.amountOfRepeats:
return
if value < 1:
self.repeatEntry.set(1)
self.amountOfRepeats = 1
else:
self.amountOfRepeats = value
self.repeatEntry.set(value)
def updateMinTypeScoreEntry(self, event=None):
'''Updates the value and the entry for the
treshhold value for amino acid typing.
'''
value = self.minTypeScoreEntry.get()
if value == self.minTypeScore:
return
if value < 0:
self.minTypeScoreEntry.set(0.0)
self.minTypeScore = 0.0
elif value > 100:
self.minTypeScoreEntry.set(100.0)
self.minTypeScore = 100.0
else:
self.minTypeScoreEntry.set(value)
self.minTypeScore = value
def updateMinLabelEntry(self, event=None):
'''Updates the minimum colabelling fraction
for which a peak is expected to be present
in the spectra.
'''
value = self.minLabelEntry.get()
if value == self.minIsoFrac:
return
if value < 0:
self.minIsoFrac = 0.0
self.minLabelEntry.set(0.0)
elif value > 1:
self.minIsoFrac = 1.0
self.minLabelEntry.set(1.0)
else:
self.minIsoFrac = value
self.minLabelEntry.set(value)
def updateLeavePeaksOutEntry(self, event=None):
'''Updates the value and entry of the fraction
of peaks that should be left out in each
run in order to diversify the results.
'''
value = self.leaveOutPeaksEntry.get()
if value == self.leavePeaksOutFraction:
return
if value < 0:
self.leavePeaksOutFraction = 0.0
self.leaveOutPeaksEntry.set(0.0)
elif value > 1:
self.leavePeaksOutFraction = 1.0
self.leaveOutPeaksEntry.set(1.0)
else:
self.leavePeaksOutFraction = value
self.leaveOutPeaksEntry.set(value)
def updateAcceptanceConstantList(self, event=None):
'''Updates the list with constants that are used
during the monte carlo procedure to decide whether
a changed is accepted or not.
'''
acList = self.tempEntry.get()
newList = []
for constant in acList:
try:
number = float(constant)
newList.append(number)
except ValueError:
string = constant + \
' in temperature constants is not a number.'
showWarning('Not A Number', string, parent=self.guiParent)
return False
self.acceptanceConstantList = newList
return True
def updateResidueRanges(self, event=None, fromChain=False):
self.residues = set()
subRanges = self.residueRangeEntry.get()
if not subRanges or fromChain:
self.residues = set(self.chain.residues)
residues = self.chain.sortedResidues()
text = '{}-{}'.format(residues[0].seqCode, residues[-1].seqCode)
self.residueRangeEntry.set(text=text)
return
for subRange in subRanges:
indeces = subRange.split('-')
start = int(indeces[0])
stop = int(indeces[-1]) + 1
for seqCode in range(start, stop):
residue = self.chain.findFirstResidue(seqCode=seqCode)
if not residue:
showWarning('Residue out of range.',
'There is no residue at position {}'.format(seqCode),
parent=self.guiParent)
self.residues = set()
return
self.residues.add(residue)
def addEnergyPoint(self, energy, time):
'''Adds a point to the graph that shows the progress
of the annealling procedure.
args: energy: the y-value
time: the x-value
'''
point = (time, energy * -1)
# This means one run has finished
if len(self.energyDataSets[-1]) / (len(self.acceptanceConstantList) + 1):
self.energyDataSets.append([point])
else:
self.energyDataSets[-1].append(point)
colors = colorSeries
Ncolors = len(colors)
NdataSets = len(self.energyDataSets)
colorList = (NdataSets / Ncolors) * colors + \
colors[:NdataSets % Ncolors]
self.energyPlot.update(dataSets=self.energyDataSets,
dataColors=colorList)
# Forcing the graph to draw, eventhough calculations
# are still running. Only do this with high numbers of
# steps, otherwise drawing takes longer than annealling.
if self.amountOfSteps >= 100000:
self.energyPlot.draw()
def __init__(self,
parent,
getOption=None,
setOption=None,
text='Print Options',
haveTicks=False,
doOutlineBox=True,
*args,
**kw):
self.getOption = getOption
self.setOption = setOption
self.haveTicks = haveTicks
self.doOutlineBox = doOutlineBox
LabelFrame.__init__(self, parent=parent, text=text, *args, **kw)
self.file_select_popup = None
self.getOptionValues()
try:
size_index = self.paper_types.index(self.paper_type)
except:
size_index = 0
try:
other_unit_index = self.paper_units.index(self.other_unit)
except:
other_unit_index = 0
try:
orientation_index = self.paper_orientations.index(self.orientation)
except:
orientation_index = 0
try:
style_index = self.style_choices.index(self.output_style)
except:
style_index = 0
try:
format_index = self.format_choices.index(self.output_format)
except:
format_index = 0
if haveTicks:
try:
tick_location_index = self.tick_locations.index(
self.tick_location)
except:
tick_location_index = 0
self.grid_columnconfigure(2, weight=1)
row = 0
label = Label(self, text='File:')
label.grid(row=row, column=0, sticky='e')
self.file_entry = Entry(self, width=40, text=self.file_name)
self.file_entry.grid(row=row, column=1, columnspan=2, sticky='ew')
button = Button(self, text='Choose File', command=self.findFile)
button.grid(row=row, column=3, rowspan=2, sticky='nsew')
row += 1
label = Label(self, text='Title:')
label.grid(row=row, column=0, sticky='e')
self.title_entry = Entry(self, width=40, text=self.title)
self.title_entry.grid(row=row, column=1, columnspan=2, sticky='ew')
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='ew')
frame.grid_columnconfigure(4, weight=1)
label = Label(frame, text='Paper size:')
label.grid(row=0, column=0, sticky='e')
entries = []
for t in paper_types:
if t == Output.other_paper_type:
entry = t
else:
(w, h, u) = paper_sizes[t]
entry = t + ' (%2.1f %s x %2.1f %s)' % (w, u, h, u)
entries.append(entry)
self.size_menu = PulldownList(frame,
callback=self.changedSize,
texts=entries,
index=size_index)
self.size_menu.grid(row=0, column=1, sticky='w')
self.other_frame = Frame(frame)
self.other_frame.grid_columnconfigure(0, weight=1)
self.other_entry = FloatEntry(self.other_frame,
text=self.other_size,
isArray=True)
self.other_entry.grid(row=0, column=0, sticky='ew')
self.other_unit_menu = PulldownList(self.other_frame,
texts=paper_units,
index=other_unit_index)
self.other_unit_menu.grid(row=0, column=1, sticky='ew')
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='ew')
frame.grid_columnconfigure(1, weight=1)
frame.grid_columnconfigure(3, weight=1)
frame.grid_columnconfigure(5, weight=1)
label = Label(frame, text='Orientation:')
label.grid(row=0, column=0, sticky='e')
self.orientation_menu = PulldownList(frame,
texts=paper_orientations,
index=orientation_index)
self.orientation_menu.grid(row=0, column=1, sticky='w')
label = Label(frame, text=' Style:')
label.grid(row=0, column=2, sticky='e')
self.style_menu = PulldownList(frame,
texts=style_choices,
index=style_index)
self.style_menu.grid(row=0, column=3, sticky='w')
label = Label(frame, text=' Format:')
label.grid(row=0, column=4, sticky='e')
self.format_menu = PulldownList(frame,
callback=self.changedFormat,
texts=format_choices,
index=format_index)
self.format_menu.grid(row=0, column=5, sticky='w')
if haveTicks:
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='ew')
frame.grid_columnconfigure(1, weight=1)
frame.grid_columnconfigure(3, weight=1)
label = Label(frame, text='Tick Location:')
label.grid(row=0, column=0, sticky='e')
self.tick_menu = PulldownList(frame,
texts=tick_locations,
index=tick_location_index)
self.tick_menu.grid(row=0, column=1, sticky='w')
label = Label(frame, text=' Tick Placement:')
label.grid(row=0, column=2, sticky='e')
self.tick_buttons = CheckButtons(frame,
entries=tick_placements,
selected=self.tick_placement)
self.tick_buttons.grid(row=0, column=3, sticky='w')
row += 1
frame = Frame(self)
frame.grid(row=row, column=0, columnspan=4, sticky='ew')
frame.grid_columnconfigure(3, weight=1)
label = Label(frame, text='Include:')
label.grid(row=0, column=0, sticky='e')
self.border_buttons = CheckButtons(frame,
entries=border_decorations,
selected=self.border_decoration)
self.border_buttons.grid(row=0, column=1, sticky='w')
label = Label(frame, text=' Scaling:')
label.grid(row=0, column=2, sticky='e')
self.scaling_scale = Scale(frame,
orient=Tkinter.HORIZONTAL,
value=self.scaling)
self.scaling_scale.grid(row=0, column=3, sticky='ew')
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)
def body(self, master):
fileName = self.fileName
directory = os.path.dirname(fileName)
if not directory:
directory = os.getcwd()
fileName = os.path.basename(fileName)
m = template_re.match(fileName)
if m:
n = len(m.groups(2))
ss = '%%0%dd' % n
template = re.sub(template_re, r'\1%s\3' % ss, fileName)
else:
template = fileName
master.rowconfigure(0, weight=1)
master.rowconfigure(1, weight=1)
master.columnconfigure(1, weight=1)
tipTexts = [
'The experiment is pseudo-N dimensional, with a sampled axis',
'The experiment is the regular kind with only NMR frequency axes'
]
self.pseudoButton = RadioButtons(
master,
entries=self.pseudoEntries,
select_callback=self.changedPseudoMode,
grid=(0, 0),
sticky='nw',
tipTexts=tipTexts)
frame = self.pseudoFrame = Frame(master)
self.pseudoFrame.grid(row=1, column=0, sticky='nsew')
row = 0
npts = self.params.npts[self.dim]
tipText = 'Number of data points (planes) along sampled axis'
label = Label(frame, text='Number of points: ')
label.grid(row=row, column=0, sticky='e')
self.nptsEntry = IntEntry(frame,
text=npts,
tipText=tipText,
width=8,
grid=(row, 1))
tipText = 'Load the values for the sampled axis from a text file containing a list of numeric values'
Button(frame,
text='Load values from text file',
command=self.loadValues,
tipText=tipText,
grid=(row, 2),
sticky='ew')
row = row + 1
tipText = 'The values (e.g. T1, T2) corresponding to each data point (plane) along sampled axis'
label = Label(frame, text='Point values: ')
label.grid(row=row, column=0, sticky='e')
self.valueEntry = FloatEntry(frame, isArray=True, tipText=tipText)
self.valueEntry.grid(row=row, column=1, columnspan=2, sticky='ew')
row = row + 1
tipText = 'Fetch the Point values from the files given by the NMRPipe template'
button = Button(
frame,
text='Fetch values from file(s) specified by template below',
command=self.fetchValues,
tipText=tipText)
button.grid(row=row, column=1, columnspan=2, sticky='w')
row = row + 1
tipText = 'The directory where the data files reside'
button = Button(frame,
text='Data directory: ',
command=self.chooseDirectory)
button.grid(row=row, column=0, sticky='e')
self.directoryEntry = Entry(frame,
text=directory,
width=40,
tipText=tipText)
self.directoryEntry.grid(row=row, column=1, columnspan=2, sticky='ew')
row = row + 1
tipText = 'The NMRPipe template for the data files, if you want to use these to fetch the point values from'
button = Button(frame,
text='NMRPipe template: ',
command=self.chooseFile)
button.grid(row=row, column=0, sticky='e')
self.templateEntry = Entry(frame, text=template, tipText=tipText)
self.templateEntry.grid(row=row, column=1, columnspan=2, sticky='ew')
for n in range(row):
frame.rowconfigure(n, weight=1)
frame.columnconfigure(1, weight=1)
buttons = UtilityButtonList(master,
closeText='Ok',
doClone=False,
closeCmd=self.updateParams,
helpUrl=self.help_url)
buttons.grid(row=2, column=0, sticky='ew')
import sys
import Tkinter
from memops.gui.Button import Button
popup_select = None
def callback(text):
global popup_select
if (popup_select):
print 'callback: selected =', popup_select.getSelected()
def toggle():
global popup_select
if (popup_select.getSelected()):
popup_select.setSelected(False)
else:
popup_select.setSelected(True)
root = Tkinter.Tk()
popup_select = BooleanPulldownMenu(root, callback=callback, selected=False)
popup_select.grid(row=0, column=0, columnspan=2)
button = Button(root, text='toggle extra state', command=toggle)
button.grid(row=1, column=0)
button = Button(root, text='quit', command=sys.exit)
button.grid(row=1, column=1)
root.mainloop()
def drawFrame(self):
# build up the body.
# what are the rules governing when this tab should show something and
# when it should not? In fact, there is the whole question of how the
# two different sections (file management and task management) should
# interract sensibly.
# This needs to be composed. We know the task type (from the tab) so what
# we need to know is how to handle ids. should we generate a placeholder
# id, or would it be better not to assign an id to begin with or else
# just use id(new)
self.task_id = self.basePopup.currentTask
print 'trying to render task with serial ', self.task_id
if self.task_id == None:
for widget in self.data_widgets:
widget.grid_remove()
self.null_task_label.grid(row=1,
column=1,
columnspan=4,
sticky='nswe')
else:
for widget in self.noData_widgets:
widget.grid_remove()
loc = SharedBeanServiceLocator()
port = loc.getSharedBean()
# need two calls, one for the Project and one for the version
hm1 = {'serial': int(self.task_id)}
wsstr_in1 = WSString(hm1)
request1 = getFieldsWithMethod()
request1._arg0 = 'org.pimslims.applet.server.TaskBean'
request1._arg1 = 'getTest1Fields'
request1._arg2 = wsstr_in1.str
response1 = port.getFieldsWithMethod(request1)
wsstr_out1 = WSString(response1._return)
hm_tv = wsstr_out1.getStructHM()
print 'RESULT ', hm_tv
self.task_rep_title.set('Task: ' + self.task_id)
self.task_rep_title.grid(row=1, column=1, columnspan=2, sticky='w')
self.repository = self.basePopup.repList.currentRepository
self.task_rep_label.grid(row=2, column=1, sticky='w')
self.task_rep_value.set(self.repository.user + '@' +
self.repository.name + ' ( ' +
self.repository.connect + ' )')
self.task_rep_value.grid(row=2, column=2, columnspan=2, sticky='w')
# FIXME JMCI
# This actually needs to be editable
self.task_status_label.grid(row=3,
column=1,
columnspan=2,
sticky='w')
self.task_status_value.set(hm_tv['status'])
#self.task_status_value.set('PENDING')
self.task_status_value.grid(row=3,
column=2,
columnspan=2,
sticky='w')
par1 = 'N/A'
if hm_tv['par1'] != 'valIsNullPointer':
par1 = hm_tv['par1']
self.task_par1_label.grid(row=4,
column=1,
columnspan=2,
sticky='w')
self.task_par1_value.set(par1)
self.task_par1_value.grid(row=4,
column=2,
columnspan=2,
sticky='w')
par2 = 'N/A'
if hm_tv['par1'] != 'valIsNullPointer':
par2 = hm_tv['par2']
self.task_par2_label.grid(row=5,
column=1,
columnspan=2,
sticky='w')
self.task_par2_value.set(par2)
self.task_par2_value.grid(row=5,
column=2,
columnspan=2,
sticky='w')
# this will depend on the status
#self.task_date_label.grid(row=4, column=1, columnspan=2, sticky='w')
#self.task_date_value.set('11 FEB 2009:11:36')
#self.task_date_value.grid(row=4, column=2, columnspan=2, sticky='w')
# FIXME JMCI
# This is not in the current model
#self.task_details_label.grid(row=4, column=1, columnspan=2, sticky='w')
#self.task_details_value.set(hm_pv['details'])
#self.task_details_value.grid(row=4, column=2, columnspan=2, sticky='w')
inputProject = 'N/A'
# This needs to be populated from the fields hash
# It is also going to be dependent on the precise task
if hm_tv.has_key('inputVersion'):
inputProjectName = hm_tv['inputVersion']['project']['name']
inputVersionTag = hm_tv['inputVersion']['versionTag']
inputProject = inputProjectName + '::' + inputVersionTag
self.task_input_label.grid(row=6, column=1, sticky='w')
self.task_input_value.set(inputProject)
self.task_input_value.grid(row=6, column=2, sticky='w')
self.button_file_in_browse.grid(row=6, column=3, sticky='e')
outputProject = 'N/A'
# This needs to be populated from the fields hash
# It is also going to be dependent on the precise task
if hm_tv.has_key('generatedVersion'):
outputProjectName = hm_tv['generatedVersion']['project'][
'name']
outputVersionTag = hm_tv['generatedVersion']['versionTag']
outputProject = outputProjectName + '::' + outputVersionTag
self.task_output_label.grid(row=7, column=1, sticky='w')
self.task_output_value.set(outputProject)
self.task_output_value.grid(row=7, column=2, sticky='w')
# it not clear when we would want to allow the project to be
# set, but allow it anyway for now
self.button_file_out_browse.grid(row=7, column=3, sticky='e')
# FIXME JMCI
# again, this really depends on what the status is. Need to decide
# the transitions
button_submit = Button(self, text='Submit', command=self.submit)
button_submit.grid(row=8, column=2, sticky='w')
def body(self, mainFrame):
mainFrame.grid_columnconfigure(1, weight=1, minsize=100)
mainFrame.config(borderwidth=5, relief='solid')
row = 0
label = Label(mainFrame, text="Frame (with sub-widgets):")
label.grid(row=row, column=0, sticky=Tkinter.E)
frame = Frame(mainFrame, relief='raised', border=2, background='#8080D0')
# Frame expands East-West
frame.grid(row=row, column=1, sticky=Tkinter.EW)
# Last column expands => Widgets pusted to the West
frame.grid_columnconfigure(3, weight=1)
# Label is within the sub frame
label = Label(frame, text='label ')
label.grid(row=0, column=0, sticky=Tkinter.W)
entry = Entry(frame, text='Entry', returnCallback=self.showWarning)
entry.grid(row=0, column=1, sticky=Tkinter.W)
self.check = CheckButton(frame, text='Checkbutton', selected=True, callback=self.updateObjects)
self.check.grid(row=0, column=2, sticky=Tkinter.W)
# stick a button to the East wall
button = Button(frame, text='Button', command=self.pressButton)
button.grid(row=0, column=3, sticky=Tkinter.E)
row += 1
label = Label(mainFrame, text="Text:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.textWindow = Text(mainFrame, text='Initial Text\n', width=60, height=5)
self.textWindow.grid(row=row, column=1, sticky=Tkinter.NSEW)
row += 1
label = Label(mainFrame, text="CheckButtons:")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Alpha','Beta','Gamma','Delta']
selected = entries[2:]
self.checkButtons = CheckButtons(mainFrame, entries, selected=selected,select_callback=self.changedCheckButtons)
self.checkButtons.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="PartitionedSelector:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labels = ['Bool','Int','Float','String']
objects = [type(0),type(1),type(1.0),type('a')]
selected = [type('a')]
self.partitionedSelector= PartitionedSelector(mainFrame, labels=labels,
objects=objects,
colors = ['red','yellow','green','#000080'],
callback=self.toggleSelector,selected=selected)
self.partitionedSelector.grid(row=row, column=1, sticky=Tkinter.EW)
row += 1
label = Label(mainFrame, text="PulldownMenu")
label.grid(row=row, column=0, sticky=Tkinter.E)
entries = ['Frodo','Pipin','Merry','Sam','Bill','Gandalf','Strider','Gimli','Legolas']
self.pulldownMenu = PulldownMenu(mainFrame, callback=self.selectPulldown,
entries=entries, selected_index=2,
do_initial_callback=False)
self.pulldownMenu.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="RadioButtons in a\nScrolledFrame.frame:")
label.grid(row=row, column=0, sticky=Tkinter.EW)
frame = ScrolledFrame(mainFrame, yscroll = False, doExtraConfig = True, width=100)
frame.grid(row=row, column=1, sticky=Tkinter.EW)
frame.grid_columnconfigure(0, weight=1)
self.radioButtons = RadioButtons(frame.frame, entries=entries,
select_callback=self.checkRadioButtons,
selected_index=1, relief='groove')
self.radioButtons.grid(row=0, column=0, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="LabelFrame with\nToggleLabels inside:")
label.grid(row=row, column=0, sticky=Tkinter.E)
labelFrame = LabelFrame(mainFrame, text='Frame Title')
labelFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
labelFrame.grid_rowconfigure(0, weight=1)
labelFrame.grid_columnconfigure(3, weight=1)
self.toggleLabel1 = ToggleLabel(labelFrame, text='ScrolledMatrix', callback=self.toggleFrame1)
self.toggleLabel1.grid(row=0, column=0, sticky=Tkinter.W)
self.toggleLabel1.arrowOn()
self.toggleLabel2 = ToggleLabel(labelFrame, text='ScrolledGraph', callback=self.toggleFrame2)
self.toggleLabel2.grid(row=0, column=1, sticky=Tkinter.W)
self.toggleLabel3 = ToggleLabel(labelFrame, text='ScrolledCanvas', callback=self.toggleFrame3)
self.toggleLabel3.grid(row=0, column=2, sticky=Tkinter.W)
row += 1
mainFrame.grid_rowconfigure(row, weight=1)
label = Label(mainFrame, text="changing/shrinking frames:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.toggleRow = row
self.toggleFrame = Frame(mainFrame)
self.toggleFrame.grid(row=row, column=1, sticky=Tkinter.NSEW)
self.toggleFrame.grid_rowconfigure(0, weight=1)
self.toggleFrame.grid_columnconfigure(0, weight=1)
# option 1
self.intEntry = IntEntry(self, returnCallback = self.setNumber, width=8)
self.multiWidget = MultiWidget(self, Entry, options=None,
values=None, callback=self.setKeywords,
minRows=3, maxRows=5)
editWidgets = [None, None, self.intEntry, self.multiWidget]
editGetCallbacks = [None, None, self.getNumber, self.getKeywords]
editSetCallbacks = [None, None, self.setNumber, self.setKeywords]
headingList = ['Name','Color','Number','Keywords']
self.scrolledMatrix = ScrolledMatrix(self.toggleFrame, headingList=headingList,
editSetCallbacks=editSetCallbacks,
editGetCallbacks=editGetCallbacks,
editWidgets=editWidgets,
callback=self.selectObject,
multiSelect=False)
self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW)
# option 2
self.scrolledGraph = ScrolledGraph(self.toggleFrame, width=400,
height=300, symbolSize=5,
symbols=['square','circle'],
dataColors=['#000080','#800000'],
lineWidths=[0,1] )
self.scrolledGraph.setZoom(1.3)
dataSet1 = [[0,0],[1,1],[2,4],[3,9],[4,16],[5,25]]
dataSet2 = [[0,0],[1,3],[2,6],[3,9],[4,12],[5,15]]
self.scrolledGraph.update(dataSets=[dataSet1,dataSet2],
xLabel = 'X axis label',
yLabel = 'Y axis label',
title = 'Main Title')
self.scrolledGraph.draw()
# option 3
self.scrolledCanvas = ScrolledCanvas(self.toggleFrame,relief = 'groove', borderwidth = 2, resizeCallback=None)
canvas = self.scrolledCanvas.canvas
font = 'Helvetica 10'
box = canvas.create_rectangle(10,10,150,200, outline='grey', fill='grey90')
line = canvas.create_line(0,0,200,200,fill='#800000', width=2)
text = canvas.create_text(120,50, text='Text', font=font, fill='black')
circle = canvas.create_oval(30,30,50,50,outline='#008000',fill='#404040',width=3)
row += 1
label = Label(mainFrame, text="FloatEntry:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.floatEntry = FloatEntry(mainFrame, text=3.14159265, returnCallback=self.floatEntryReturn)
self.floatEntry.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Scale:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.scale = Scale(mainFrame, from_=10, to=90, value=50, orient=Tkinter.HORIZONTAL)
self.scale.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="Value Ramp:")
label.grid(row=row, column=0, sticky=Tkinter.E)
self.valueRamp = ValueRamp(mainFrame, self.valueRampCallback, speed = 1.5, delay = 50)
self.valueRamp.grid(row=row, column=1, sticky=Tkinter.W)
row += 1
label = Label(mainFrame, text="ButtonList:")
label.grid(row=row, column=0, sticky=Tkinter.E)
texts = ['Select File','Close','Quit']
commands = [self.selectFile, self.close, self.quit]
bottomButtons = ButtonList(mainFrame, texts=texts, commands=commands, expands=True)
bottomButtons.grid(row=row, column=1, sticky=Tkinter.EW)
self.protocol('WM_DELETE_WINDOW', self.quit)
class Test1Frame(Frame):
def __init__(self, guiParent, basePopup):
self.guiParent = guiParent
self.basePopup = basePopup
#self.registerNotify=basePopup.registerNotify
#self.unregisterNotify=basePopup.unregisterNotify
self.task_id = None
# should be set in parent initMethod() call now
#self.basePopup.frameShortcuts['Task'].frameShortcuts['Test1'] = self
# NOTE: JMCI
# We can reasonably set the repository from the current repository. It is
# harder to know how project/projectVersion and task interract
# TODO
# decide whether we really need this
self.repository = self.basePopup.repList.currentRepository
Frame.__init__(self, guiParent)
# set up the grid
self.grid_columnconfigure(0, weight=0, minsize=20)
self.grid_columnconfigure(1, weight=0, minsize=30)
self.grid_columnconfigure(2, weight=1, minsize=20)
self.grid_columnconfigure(3, weight=0, minsize=20)
self.grid_columnconfigure(4, weight=1, minsize=20)
self.grid_rowconfigure(0, weight=0, minsize=20)
self.grid_rowconfigure(1, weight=0, minsize=10)
self.grid_rowconfigure(2, weight=0, minsize=10)
self.grid_rowconfigure(3, weight=0, minsize=10)
self.grid_rowconfigure(4, weight=0, minsize=20)
# we define as much as possible once on startup and use the
# grid manager to control the display thereafter
# when no data
self.noData_widgets = []
self.null_task_label = Label(self, text='No Task selected')
self.noData_widgets.append(self.null_task_label)
# when data
self.data_widgets = []
self.task_rep_title = Label(self, text='Task:', font='Helvetica16')
self.data_widgets.append(self.task_rep_title)
self.task_rep_label = Label(self, text='Repository:')
self.data_widgets.append(self.task_rep_label)
self.task_rep_value = Label(self, text='')
self.data_widgets.append(self.task_rep_value)
self.task_status_label = Label(self, text='Status:')
self.data_widgets.append(self.task_status_label)
self.task_status_value = Label(self, text='')
self.data_widgets.append(self.task_status_value)
self.task_details_label = Label(self, text='Details:')
self.data_widgets.append(self.task_details_label)
self.task_details_value = Label(self, text='')
self.data_widgets.append(self.task_details_value)
self.task_date_label = Label(self, text='Date:')
self.data_widgets.append(self.task_date_label)
self.task_date_value = Label(self, text='')
self.data_widgets.append(self.task_date_value)
self.task_par1_label = Label(self, text='Par1:')
self.data_widgets.append(self.task_par1_label)
self.task_par1_value = Label(self, text='')
self.data_widgets.append(self.task_par1_value)
self.task_par2_label = Label(self, text='Par2:')
self.data_widgets.append(self.task_par2_label)
self.task_par2_value = Label(self, text='')
self.data_widgets.append(self.task_par2_value)
self.task_input_label = Label(self, text='Input Data:')
self.data_widgets.append(self.task_input_label)
self.task_input_value = Label(self, text='')
self.data_widgets.append(self.task_input_value)
self.button_file_in_browse = Button(self,
text='Browse',
command=self.tmpCall)
self.data_widgets.append(self.button_file_in_browse)
self.button_file_out_browse = Button(self,
text='Browse',
command=self.tmpCall)
self.data_widgets.append(self.button_file_out_browse)
self.task_output_label = Label(self, text='Output Data:')
self.data_widgets.append(self.task_output_label)
self.task_output_value = Label(self, text='')
self.data_widgets.append(self.task_output_value)
self.drawFrame()
def drawFrame(self):
# build up the body.
# what are the rules governing when this tab should show something and
# when it should not? In fact, there is the whole question of how the
# two different sections (file management and task management) should
# interract sensibly.
# This needs to be composed. We know the task type (from the tab) so what
# we need to know is how to handle ids. should we generate a placeholder
# id, or would it be better not to assign an id to begin with or else
# just use id(new)
self.task_id = self.basePopup.currentTask
print 'trying to render task with serial ', self.task_id
if self.task_id == None:
for widget in self.data_widgets:
widget.grid_remove()
self.null_task_label.grid(row=1,
column=1,
columnspan=4,
sticky='nswe')
else:
for widget in self.noData_widgets:
widget.grid_remove()
loc = SharedBeanServiceLocator()
port = loc.getSharedBean()
# need two calls, one for the Project and one for the version
hm1 = {'serial': int(self.task_id)}
wsstr_in1 = WSString(hm1)
request1 = getFieldsWithMethod()
request1._arg0 = 'org.pimslims.applet.server.TaskBean'
request1._arg1 = 'getTest1Fields'
request1._arg2 = wsstr_in1.str
response1 = port.getFieldsWithMethod(request1)
wsstr_out1 = WSString(response1._return)
hm_tv = wsstr_out1.getStructHM()
print 'RESULT ', hm_tv
self.task_rep_title.set('Task: ' + self.task_id)
self.task_rep_title.grid(row=1, column=1, columnspan=2, sticky='w')
self.repository = self.basePopup.repList.currentRepository
self.task_rep_label.grid(row=2, column=1, sticky='w')
self.task_rep_value.set(self.repository.user + '@' +
self.repository.name + ' ( ' +
self.repository.connect + ' )')
self.task_rep_value.grid(row=2, column=2, columnspan=2, sticky='w')
# FIXME JMCI
# This actually needs to be editable
self.task_status_label.grid(row=3,
column=1,
columnspan=2,
sticky='w')
self.task_status_value.set(hm_tv['status'])
#self.task_status_value.set('PENDING')
self.task_status_value.grid(row=3,
column=2,
columnspan=2,
sticky='w')
par1 = 'N/A'
if hm_tv['par1'] != 'valIsNullPointer':
par1 = hm_tv['par1']
self.task_par1_label.grid(row=4,
column=1,
columnspan=2,
sticky='w')
self.task_par1_value.set(par1)
self.task_par1_value.grid(row=4,
column=2,
columnspan=2,
sticky='w')
par2 = 'N/A'
if hm_tv['par1'] != 'valIsNullPointer':
par2 = hm_tv['par2']
self.task_par2_label.grid(row=5,
column=1,
columnspan=2,
sticky='w')
self.task_par2_value.set(par2)
self.task_par2_value.grid(row=5,
column=2,
columnspan=2,
sticky='w')
# this will depend on the status
#self.task_date_label.grid(row=4, column=1, columnspan=2, sticky='w')
#self.task_date_value.set('11 FEB 2009:11:36')
#self.task_date_value.grid(row=4, column=2, columnspan=2, sticky='w')
# FIXME JMCI
# This is not in the current model
#self.task_details_label.grid(row=4, column=1, columnspan=2, sticky='w')
#self.task_details_value.set(hm_pv['details'])
#self.task_details_value.grid(row=4, column=2, columnspan=2, sticky='w')
inputProject = 'N/A'
# This needs to be populated from the fields hash
# It is also going to be dependent on the precise task
if hm_tv.has_key('inputVersion'):
inputProjectName = hm_tv['inputVersion']['project']['name']
inputVersionTag = hm_tv['inputVersion']['versionTag']
inputProject = inputProjectName + '::' + inputVersionTag
self.task_input_label.grid(row=6, column=1, sticky='w')
self.task_input_value.set(inputProject)
self.task_input_value.grid(row=6, column=2, sticky='w')
self.button_file_in_browse.grid(row=6, column=3, sticky='e')
outputProject = 'N/A'
# This needs to be populated from the fields hash
# It is also going to be dependent on the precise task
if hm_tv.has_key('generatedVersion'):
outputProjectName = hm_tv['generatedVersion']['project'][
'name']
outputVersionTag = hm_tv['generatedVersion']['versionTag']
outputProject = outputProjectName + '::' + outputVersionTag
self.task_output_label.grid(row=7, column=1, sticky='w')
self.task_output_value.set(outputProject)
self.task_output_value.grid(row=7, column=2, sticky='w')
# it not clear when we would want to allow the project to be
# set, but allow it anyway for now
self.button_file_out_browse.grid(row=7, column=3, sticky='e')
# FIXME JMCI
# again, this really depends on what the status is. Need to decide
# the transitions
button_submit = Button(self, text='Submit', command=self.submit)
button_submit.grid(row=8, column=2, sticky='w')
def submit(self):
print 'submitting a process (set status to pending)'
# get a port proxy instance
# this should probably belong to the repository directly
h2 = {'serial': int(self.task_id), 'status': 'PENDING'}
loc = SharedBeanServiceLocator()
self.port = loc.getSharedBean()
request2 = record()
request2._arg0 = 'org.pimslims.applet.server.TaskBean'
request2._arg1 = 'updateStatus'
wsstr_in = WSString(h2)
print 'trying to update status with ', h2, ', ', wsstr_in.str
request2._arg2 = wsstr_in.str
response2 = self.port.record(request2)
# now need to redraw task-related frames
self.drawFrame()
if self.basePopup.frameShortcuts.has_key('Tasks'):
self.basePopup.frameShortcuts['Tasks'].drawFrame()
def tmpCall(self):
pass
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete', 'setName'):
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.Experiment', func)
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.DataSource', func)
def updateAllAfter(self, obj):
self.after_idle(self.updateAll)
def updateAll(self, project=None):
return
def quit(self):
self.guiParent.parent.destroy()
def destroy(self):
#self.administerNotifiers(self.basePopup.unregisterNotify)
Frame.destroy(self)
else:
self.var.set(0)
def toggle(self):
self.setSelected(not self.getSelected())
if __name__ == '__main__':
from memops.gui.Button import Button
def get_me():
print 'get_me:', c.getSelected()
def toggle_me():
c.toggle()
def my_callback(selected):
print 'my_callback:', selected
root = Tkinter.Tk()
c = CheckButton(root, 'check button', callback=my_callback)
c.grid()
b = Button(root, text='get me', command=get_me)
b.grid()
b = Button(root, text='toggle me', command=toggle_me)
b.grid()
root.mainloop()
class BacusPopup(BasePopup):
def __init__(self, parent, *args, **kw):
self.project = parent.project
self.hNoesy = None
self.nNoesy = None
self.cNoesy = None
self.shiftList = None
BasePopup.__init__(self, parent, title="BACUS control module", **kw)
def body(self, guiParent):
guiParent.grid_columnconfigure(0, weight=1)
row = 0
guiParent.grid_rowconfigure(row, weight=1)
inputFrame = LabelFrame(guiParent, text='Inputs:')
inputFrame.grid(row=row, column=0, sticky=Tkinter.NSEW)
label = Label(inputFrame, text='NOESY:')
label.grid(row=0, column=0, sticky=Tkinter.NW)
self.hNoesyPulldown = PulldownMenu(inputFrame,callback=self.setHNoesy)
self.hNoesyPulldown.grid(row=0, column=1, sticky=Tkinter.NW)
label = Label(inputFrame, text='15N NOESY:')
label.grid(row=1, column=0, sticky=Tkinter.NW)
self.nNoesyPulldown = PulldownMenu(inputFrame,callback=self.setNNoesy)
self.nNoesyPulldown.grid(row=1, column=1, sticky=Tkinter.NW)
label = Label(inputFrame, text='13C NOESY:')
label.grid(row=2, column=0, sticky=Tkinter.NW)
self.cNoesyPulldown = PulldownMenu(inputFrame,callback=self.setCNoesy)
self.cNoesyPulldown.grid(row=2, column=1, sticky=Tkinter.NW)
label = Label(inputFrame, text='Shift List:')
label.grid(row=3, column=0, sticky=Tkinter.NW)
self.shiftListPulldown = PulldownMenu(inputFrame,callback=self.setShiftList)
self.shiftListPulldown.grid(row=3, column=1, sticky=Tkinter.NW)
label = Label(inputFrame, text='2d BACUS executable:')
label.grid(row=4, column=0, sticky=Tkinter.NW)
self.executableEntry = Entry(inputFrame, text='/home/tjs23/clouds/justin/SpiBacusMidge/bacus/bacus_tjs.exe')
self.executableEntry.grid(row=4, column=1, sticky=Tkinter.NW)
self.executableButton = Button(inputFrame, text='Choose file', command=self.chooseExecutable)
self.executableButton.grid(row=5, column=1, sticky=Tkinter.EW)
row += 1
outputFrame = LabelFrame(guiParent, text='Output:')
outputFrame.grid(row=row, column=0, sticky=Tkinter.NSEW)
row += 1
texts = ['Run BACUS 2d','Run BACUS 3d']
commands = [self.runBacus,self.runBacus3d]
self.bottomButtons = createDismissHelpButtonList(guiParent,texts=texts,commands=commands,expands=0,help_url=None)
self.bottomButtons.grid(row=row, column=0, sticky=Tkinter.EW)
self.update()
def chooseExecutable(self):
fileTypes = [FileType('Table', ['*.exe']), FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(self, file_types = fileTypes,
title = 'Choose 2d BACUS executable', dismiss_text = 'Cancel',
selected_file_must_exist = False)
fileName = fileSelectPopup.getFile()
if fileName:
self.executableEntry.set(fileName)
def update(self):
# set defaults via pulldown callbacks
names = [self.getPeakListlabel(x) for x in self.gethNoesys()]
if names:
self.hNoesyPulldown.setup(names,0)
else:
self.hNoesyPulldown.setup([],-1)
names = [self.getPeakListlabel(x) for x in self.getNNoesys()]
if names:
self.nNoesyPulldown.setup(names,0)
else:
self.nNoesyPulldown.setup([],-1)
names = [self.getPeakListlabel(x) for x in self.getCNoesys()]
if names:
self.cNoesyPulldown.setup(names,0)
else:
self.cNoesyPulldown.setup([],-1)
names = ['Shift List %d' % x.serial for x in self.getShiftLists()]
if names:
self.shiftListPulldown.setup(names,0)
else:
self.shiftListPulldown.setup([],-1)
self.updateButtons()
def updateButtons(self):
if ( self.cNoesy or self.nNoesy ) and self.shiftList:
self.bottomButtons.buttons[1].enable()
else:
self.bottomButtons.buttons[1].disable()
if self.hNoesy and self.executableEntry.get() and self.shiftList:
self.bottomButtons.buttons[0].enable()
else:
self.bottomButtons.buttons[0].disable()
def runBacus3d(self, fileRoot='CCPN1'):
if ( self.cNoesy or self.nNoesy ) and self.shiftList:
run3dBacus(fileRoot,self.shiftList,self.cNoesy,self.nNoesy)
def runBacus(self, fileRoot='CCPN1'):
executable = self.executableEntry.get()
if self.hNoesy and self.shiftList and executable:
run2dBacus(fileRoot, executable, self.hNoesy, self.shiftList)
def getPeakListlabel(self, peakList):
return '%s:%s:%d' % (peakList.dataSource.experiment.name, peakList.dataSource.name, peakList.serial)
def getShiftLists(self):
shiftLists = []
if self.project:
nmrProject = self.project.currentNmrProject
shiftLists = nmrProject.findAllMeasurementLists(className='ShiftList')
return list(shiftLists)
def setShiftList(self, index, name=None):
shiftLists = self.getShiftLists()
if shiftLists:
self.shiftList = shiftLists[index]
else:
self.shiftList = None
def gethNoesys(self):
peakLists = []
if self.project:
for experiment in self.project.currentNmrProject.experiments:
for spectrum in experiment.dataSources:
isotopes = getSpectrumIsotopes(spectrum)
if isotopes == ['1H', '1H']:
for peakList in spectrum.peakLists:
#if 'NOE' in experiment.name.upper():
# peakLists.insert(0, peakList)
#else:
peakLists.append(peakList)
return peakLists
def getNNoesys(self):
peakLists = []
if self.project:
for experiment in self.project.currentNmrProject.experiments:
for spectrum in experiment.dataSources:
isotopes = getSpectrumIsotopes(spectrum)
isotopes.sort()
if isotopes == ['15N', '1H', '1H']:
for peakList in spectrum.peakLists:
#if 'NOE' in experiment.name.upper():
# peakLists.insert(0, peakList)
#else:
peakLists.append(peakList)
return peakLists
def getCNoesys(self):
peakLists = []
if self.project:
for experiment in self.project.currentNmrProject.experiments:
for spectrum in experiment.dataSources:
isotopes = getSpectrumIsotopes(spectrum)
isotopes.sort()
if isotopes == ['13C', '1H', '1H']:
for peakList in spectrum.peakLists:
if 'NOE' in experiment.name.upper():
peakLists.insert(0, peakList)
else:
peakLists.append(peakList)
return peakLists
def setHNoesy(self, index, name=None):
peakLists = self.gethNoesys()
if peakLists:
self.hNoesy = peakLists[index]
else:
self.hNoesy = None
def setNNoesy(self, index, name=None):
peakLists = self.getNNoesys()
if peakLists:
self.nNoesy = peakLists[index]
else:
self.nNoesy = None
def setCNoesy(self, index, name=None):
peakLists = self.getCNoesys()
if peakLists:
self.cNoesy = peakLists[index]
else:
self.cNoesy = None
def destroy(self):
BasePopup.destroy(self)
'#000040', '#000080', '#0000A0', '#0000FF', '#0040FF', '#0080FF',
'#00A0FF', '#00C0FF', '#00E0FF', '#00FFFF', '#40FFFF', '#80FFFF',
'#A0FFFF', '#D0FFFF', '#FFFFFF'
], None
]
selected_index = 2
popup_select = PulldownMenu(root,
callback=callback,
entries=entries,
colors=colors,
selected_index=selected_index)
popup_select.grid(row=0, column=0, columnspan=3)
button = Button(root, text='add', command=add)
button.grid(row=1, column=0)
button = Button(root, text='remove', command=remove)
button.grid(row=1, column=1)
button = Button(root, text='getSelected', command=getSelected)
button.grid(row=1, column=2)
button = Button(root, text='getSelectedInd', command=getSelectedInd)
button.grid(row=1, column=3)
button = Button(root, text='quit', command=sys.exit)
button.grid(row=1, column=4)
root.mainloop()
class FileBrowserFrame(Frame):
def __init__(self, guiParent, basePopup, callback=None):
# Base popup required to handle notification of data model changes
# e.g. new peak lists, so that the GUI can update to the latest
# state
self.basePopup = basePopup
self.guiParent = guiParent
# we need to be able to define a callback before exit
self.callback = callback
Frame.__init__(self, guiParent)
# Basic principle is that we want to supply a root directory
# and we will get a tree that will allow us to browse anything
# below the directory. We will also have a button for going
# up a directory.
self.rootDir = '/home/jionides/work/CCPN/test_WMS_archive'
self.icon_dict = {
'none': 'text-x-generic-template',
'text': 'text-x-generic',
'text/plain': 'text-x-generic',
'text/html': 'text-html',
'text/script': 'text-x-script',
'text/x-python': 'text-x-script',
'text/x-perl': 'text-x-script',
'image': 'image-x-generic',
'application': 'applications-other',
'video': 'video-x-generic',
'message': 'internet-mail',
'audio': 'audio-x-generic',
'chemical': 'applications-internet',
'application/x-tar': 'package-x-generic',
'application/msword': 'x-office-document',
'application/postscript': 'x-office-drawing',
'application/pdf': 'x-office-drawing',
'application/xml': 'text-x-script',
'application/x-python-code': 'application-x-executable',
}
self.grid_rowconfigure(1, weight=1)
self.grid_columnconfigure(1, weight=1)
self.fileTree = Tree(self)
self.fileTree.grid(row=1, column=1, padx=10, pady=10, sticky='nsew')
self.ok_button = Button(self, width=10, text='OK', command=self.isOk)
#self.ok_button = Button(self, text='OK', command=self.isOk)
self.ok_button.grid(row=2, column=1, padx=10, pady=10, sticky='e')
self.cancel_button = Button(self,
width=10,
text='Cancel',
command=self.isCancel)
#self.cancel_button = Button(self,text='Cancel', command=self.isCancel)
self.cancel_button.grid(row=2, column=1, padx=10, pady=10, sticky='w')
files = listdir(self.rootDir)
parents = [None] * len(files)
icons = []
objects = []
texts = []
callbacks = []
for file in files:
file = path.join(self.rootDir, file)
text, icon, isDir = self.getData(file)
icons.append(icon)
texts.append(text)
objects.append(file)
if isDir:
callbacks.append(self.openDir)
else:
callbacks.append(None)
print 'updating', texts
self.fileTree.update(parents, objects, texts, icons, callbacks)
def getData(self, file):
dirr, text = path.split(file)
readable = access(file, R_OK)
isDir = False
if path.isdir(file):
if not readable:
icon = 'emblem-unreadable'
elif path.islink(file):
isDir = True
icon = 'folder-remote'
else:
isDir = True
icon = 'folder'
text += '/'
elif path.isfile(file):
if not readable:
icon = 'emblem-unreadable'
#elif path.islink(file):
# icon = 'text-html'
else:
mimeType = mimetypes.guess_type(file)[0]
if mimeType:
if not self.icon_dict.get(mimeType):
print mimeType
icon = self.icon_dict.get(mimeType) \
or self.icon_dict.get(mimeType.split('/')[0]) \
or self.icon_dict['none']
else:
icon = self.icon_dict['none']
elif not readable:
icon = 'emblem-unreadable'
else:
icon = 'emblem-system'
return text, icon, isDir
def openDir(self, node):
tree = node.tree
filePath = node.object
files = listdir(filePath)
for file in files:
file = path.join(filePath, file)
text, icon, isDir = self.getData(file)
parent, null = path.split(file)
if isDir and access(file, R_OK):
callback = self.openDir
else:
callback = None
tree.add(node, file, text, icon, callback)
def isCancel(self):
print 'should be exiting'
self.quit()
def isOk(self):
print 'setting selected ', self.fileTree.getSelected()
def destroy(self):
print 'in main destroy method'
Frame.destroy(self)
def quit(self):
print 'in main quit method'
self.guiParent.parent.destroy()
def __init__(self,
parent,
texts,
commands,
images=None,
buttonBorderwidth=1,
spacers=1,
expands=True,
font=None,
direction=HORIZONTAL,
sticky='ew',
*args,
**kw):
assert direction in (HORIZONTAL,
VERTICAL), 'direction = %s' % direction
if (type(commands) is types.DictType):
have_dict = True
for key in commands.keys():
assert key in texts, 'key = %s' % key
else:
have_dict = False
assert len(texts) == len(
commands), 'len(texts) = %s, len(commands) = %s' % (
len(texts), len(commands))
if not kw.has_key('bg'):
kw['bg'] = 'grey82'
Frame.__init__(self, parent, sticky=sticky, *args, **kw)
if (direction == Tkinter.HORIZONTAL):
self.grid_rowconfigure(0, weight=1)
else:
self.grid_columnconfigure(0, weight=1)
if images is None:
images = [None] * len(texts)
self.font = font
self.spacers = spacers
r = 0
c = 0
if expands:
self.spacers = spacers = 0
for i in range(len(texts)):
if texts[i]:
if (direction == Tkinter.HORIZONTAL):
self.grid_columnconfigure(i, weight=1)
else:
self.grid_rowconfigure(i, weight=1)
else:
if spacers and (direction == Tkinter.HORIZONTAL):
self.grid_columnconfigure(c, weight=1)
self.grid_columnconfigure(len(texts) + 1, weight=1)
spacer1 = Spacer(self)
spacer2 = Spacer(self)
spacer1.grid(row=r, column=c, sticky=Tkinter.NSEW)
spacer2.grid(row=r, column=len(texts) + 1, sticky=Tkinter.NSEW)
c += 1
self.buttons = []
bg = kw['bg']
for n, text in enumerate(texts):
if n < len(images):
image = images[n]
else:
image = None
if type(text) not in (STRING_TYPE, UNICODE_TYPE):
text = str(text)
if (have_dict):
try:
command = commands[text]
except:
command = lambda x=text: notYetImplemented(x)
else:
command = commands[n]
if not command:
command = lambda x=text: notYetImplemented(x)
button = Button(self,
text=text,
command=command,
bg=bg,
image=image,
borderwidth=buttonBorderwidth,
font=self.font)
button.grid(row=r, column=c, sticky=Tkinter.NSEW)
self.buttons.append(button)
if direction == Tkinter.HORIZONTAL:
c = c + 1
else:
r = r + 1
class LoginFrame(Frame):
def __init__(self, guiParent, basePopup):
# Base popup required to handle notification of data model changes
# e.g. new peak lists, so that the GUI can update to the latest
# state
self.basePopup = basePopup
self.guiParent = guiParent
self.registerNotify=basePopup.registerNotify
self.unregisterNotify=basePopup.unregisterNotify
Frame.__init__(self, guiParent)
# set up the grid
self.grid_columnconfigure(0, weight=1, minsize=10)
self.grid_columnconfigure(1, weight=0, minsize=10)
self.grid_columnconfigure(2, weight=0, minsize=20)
self.grid_columnconfigure(3, weight=1, minsize=10)
self.grid_rowconfigure(0, weight=1, minsize=5)
self.grid_rowconfigure(1, weight=0, minsize=10)
self.grid_rowconfigure(2, weight=0, minsize=10)
self.grid_rowconfigure(3, weight=0, minsize=10)
self.grid_rowconfigure(4, weight=1, minsize=5)
# build up the body.
# Column headers
self.user_label = Label(self,text='Username:'******'w')
self.user_value = Text(self, width=20, height=1, text="")
self.user_value.grid(row=1, column=2, padx=5, pady=5, sticky='w')
self.pswd_label = Label(self,text='Password:'******'w')
self.pswd_value = Text(self, width=20, height=1, text="")
self.pswd_value.grid(row=2, column=2, padx=5, pady=5, sticky='w')
self.cancel_button = Button(self, width=10, height=1,
text="Cancel",
command=self.quit )
self.cancel_button.grid(row=3, column=1, padx=5, pady=5, sticky='e')
self.login_botton = Button(self, width=10, height=1,
text="Login",
command=self.login )
self.login_botton.grid(row=3, column=2, padx=5, pady=5, sticky='w')
def login(self):
username = self.user_value.getText()
# obviously need an authentication check here!
self.basePopup.parent.setUsername(username)
self.basePopup.parent.readConfig(username)
self.basePopup.destroy()
def administerNotifiers(self, notifyFunc):
for func in ('__init__','delete','setName'):
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.Experiment', func)
notifyFunc(self.updateAllAfter, 'ccp.nmr.Nmr.DataSource', func)
def updateAllAfter(self, obj):
self.after_idle(self.updateAll)
def updateAll(self, project=None):
return
def quit(self):
self.guiParent.parent.destroy()
def destroy(self):
self.administerNotifiers(self.basePopup.unregisterNotify)
Frame.destroy(self)
