class TasksFrame(Frame):
def __init__(self, guiParent, basePopup):
self.guiParent = guiParent
self.basePopup = basePopup
# selection hash. This needs to be stored so that we can
# refresh with the same criteria
self.select = None
# should the screen autorefresh
self.autoRefresh = False
# add this to shortcuts to ease navigation
self.basePopup.frameShortcuts['Tasks'] = self
#self.registerNotify=basePopup.registerNotify
#self.unregisterNotify=basePopup.unregisterNotify
#self.frames = []
# FIXME JMCI
# This frame is specific for a single repository so we need a
# method for identifying one from the whole set (or could have
# subtabs)
Frame.__init__(self, guiParent)
# set up the grid
self.grid_columnconfigure(0, weight=0, minsize=20)
self.grid_columnconfigure(1, weight=1, minsize=30)
self.grid_columnconfigure(2, weight=0, minsize=40)
self.grid_rowconfigure(0, weight=0, minsize=20)
self.grid_rowconfigure(1, weight=0, minsize=10)
self.grid_rowconfigure(2, weight=0, minsize=0)
self.grid_rowconfigure(3, weight=0, minsize=0)
self.grid_rowconfigure(4, weight=0, minsize=0)
self.grid_rowconfigure(5, weight=1, minsize=0)
self.grid_rowconfigure(6, weight=0, minsize=10)
self.grid_rowconfigure(7, weight=0, minsize=10)
initial_cols = ['ID','Task','User','Status']
self.task_matrix = ScrolledMatrix(self, headingList=initial_cols, initialRows=15,
doubleCallback=self.goto_task_tab)
# Filters for narrowing down tasks. should probably code this
# specifically inside this package
#self.filter = FilterFrame(self, self.basePopup, text='Filter')
self.filter = TaskFilterFrame(self, self.basePopup, text='Filter')
# Frame for controlling the main client side daemon
# seems to be a problem. add a simple button for now
opts = ['Client','Server']
self.daemonFrame = TabbedFrame(self, options=opts,
toggleOff=False, selected=0)
self.daemonSwitchLabel = Label(self, text= 'Task Daemon')
self.daemonSwitch = RadioButtons(self, ['on', 'off'], select_callback=self.set_daemon, selected_index = 1)
sel = 1
if self.autoRefresh:
sel = 0
self.autoRefreshSwitchLabel = Label(self, text= 'Auto Refresh')
self.autoRefreshSwitch = RadioButtons(self, ['on', 'off'], select_callback=self.set_refresh, selected_index = sel)
self.label_rep = Label(self, text='', font='Helvetica16')
# set up a loop
self.refresh()
def drawFrame(self):
# build up the body.
# This is a very simple mock up. In reality we need to be
# able to select a number of different input files that
# depend on the task type
# we need to have the current repository in context
self.repository = self.basePopup.repList.currentRepository
if self.repository == None:
self.label_rep.grid_remove()
self.task_matrix.grid_remove()
self.filter.grid_remove()
self.daemonSwitchLabel.grid_remove()
self.daemonSwitch.grid_remove()
else:
strg = self.repository.user + '@' + self.repository.name + ' (' + self.repository.connect + ')'
self.label_rep.set('TaskManager: Repository ' + strg)
self.label_rep.grid(row=1, column=1, columnspan=2, sticky='w')
self.task_matrix.grid(row=2, column=1, rowspan=4, sticky='nsew')
loc = SharedBeanServiceLocator()
port = loc.getSharedBean()
request1 = getList();
request1._arg0 = 'org.pimslims.applet.server.TaskBean';
request1._arg1 = 'getListWithFields';
if self.select==None:
request1._arg2 = ''
else:
wsstr_in = WSString(self.select)
request1._arg2 = wsstr_in.str
response1 = port.getList(request1)
wsstr1 = WSString(response1._return)
ss1 = wsstr1.getStruct()
matrix = [];
objs = [];
for el in ss1:
new_row = (el['serial'], 'TestTask1', 'jionides', el['status'])
matrix.append(new_row)
objs.append(el)
self.task_matrix.update(objectList=objs, textMatrix=matrix)
self.filter.grid(row=2, column=2, sticky='n')
# FIXME JMCI
# The tabbed frame seems to cause the GUI to hang over expansion.
# use a simple radio button for now
# self.daemonFrame.grid(row=3, column=2, padx=10, sticky='nsew')
self.daemonSwitchLabel.grid(row=3, column=2, padx=10, sticky='n')
self.daemonSwitch.grid(row=4, column=2, padx=10, sticky='n')
self.autoRefreshSwitchLabel.grid(row=6, column=1, padx=10, sticky='w')
self.autoRefreshSwitch.grid(row=6, column=1, padx=10, sticky='e')
def selectTask(self):
row = self.task_matrix.currentCell
print 'in select task ', row
def set_daemon(self, text):
print 'setting daemon ', text
if text == 'on':
self.basePopup.taskDaemon.active = True
else:
self.basePopup.taskDaemon.active = False
def set_refresh(self, text):
print 'setting refresh ', text
if text == 'on':
self.autoRefresh = True
else:
self.autoRefresh = False
def refresh(self):
if self.autoRefresh:
print 'refreshing frame ', time.time()
self.drawFrame()
self.after(5000, self.refresh)
def goto_task_tab(self, obj, row, col):
print obj
self.basePopup.currentTask = obj['serial'].__str__()
# This is really awkward because we actually have to go to the
# correct tab. We have some horrible hacks here. Need a dictionary
# that can take us straight to the correct frame based on a
# keyword
self.basePopup.tabbedFrame.select(2)
#for ff in self.basePopup.tabbedFrame.frames[2].children.values():
# ff.tabbedFrame.select(0)
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)
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 PopupTemplate(BasePopup):
def __init__(self, parent, project=None, *args, **kw):
self.project = project
self.parent = parent
self.objects = self.getObjects()
self.object = None
BasePopup.__init__(self, parent=parent, title='Popup Template', **kw)
self.updateObjects()
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)
def floatEntryReturn(self, event):
value = self.floatEntry.get()
self.textWindow.setText('%s\n' % value)
def selectObject(self, object, row, col):
self.object = object
def getKeywords(self, object):
if object :
values = object.keywords
self.multiWidget.set(values)
def setKeywords(self, event):
values = self.multiWidget.get()
self.object.keywords = values
self.updateObjects()
def getNumber(self, object):
if object :
self.intEntry.set(object.quantity)
def setNumber(self, event):
value = self.intEntry.get()
self.object.quantity = value
self.updateObjects()
def toggleFrame1(self, isHidden):
if isHidden:
self.scrolledMatrix.grid_forget()
self.toggleFrame.grid_forget()
else:
self.scrolledGraph.grid_forget()
self.scrolledCanvas.grid_forget()
self.scrolledMatrix.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW)
self.toggleLabel2.arrowOff()
self.toggleLabel3.arrowOff()
def toggleFrame2(self, isHidden):
if isHidden:
self.scrolledGraph.grid_forget()
self.toggleFrame.grid_forget()
else:
self.scrolledMatrix.grid_forget()
self.scrolledCanvas.grid_forget()
self.scrolledGraph.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW)
self.toggleLabel1.arrowOff()
self.toggleLabel3.arrowOff()
def toggleFrame3(self, isHidden):
if isHidden:
self.scrolledCanvas.grid_forget()
self.toggleFrame.grid_forget()
else:
self.scrolledMatrix.grid_forget()
self.scrolledGraph.grid_forget()
self.scrolledCanvas.grid(row=0, column=0, sticky=Tkinter.NSEW)
self.toggleFrame.grid(row=self.toggleRow, column=1,sticky=Tkinter.NSEW)
self.toggleLabel1.arrowOff()
self.toggleLabel2.arrowOff()
def valueRampCallback(self, value):
self.textWindow.setText('%s\n' % value)
def checkRadioButtons(self, value):
self.textWindow.setText('%s\n' % value)
def selectPulldown(self, index, name):
self.textWindow.setText('%d, %s\n' % (index, name))
def toggleSelector(self, value):
self.textWindow.setText('%s\n' % value)
def changedCheckButtons(self, values):
self.textWindow.setText(','.join(values) + '\n')
def getObjects(self):
objects = []
objects.append( Fruit('Lemon', '#FFFF00',1,keywords=['Bitter','Tangy'] ) )
objects.append( Fruit('Orange', '#FF8000',4 ) )
objects.append( Fruit('Banana', '#FFF000',5 ) )
objects.append( Fruit('Pinapple','#FFD000',9 ) )
objects.append( Fruit('Kiwi', '#008000',12) )
objects.append( Fruit('Lime', '#00FF00',2 ) )
objects.append( Fruit('Apple', '#800000',5,keywords=['Crunchy'] ) )
objects.append( Fruit('Pear', '#408000',6 ) )
objects.append( Fruit('Peach', '#FFE0C0',2,keywords=['Sweet','Furry'] ) )
objects.append( Fruit('Plumb', '#800080',7 ) )
return objects
def updateObjects(self, event=None):
textMatrix = []
objectList = []
colorMatrix = []
for object in self.objects:
datum = []
datum.append( object.name )
datum.append( None )
datum.append( object.quantity )
datum.append( ','.join(object.keywords) )
colors = [None, object.color, None, None]
textMatrix.append(datum)
objectList.append(object)
colorMatrix.append(colors)
if self.check.get():
self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList)
else:
self.scrolledMatrix.update(textMatrix=textMatrix, objectList=objectList, colorMatrix=colorMatrix)
def selectFile(self):
fileSelectPopup = FileSelectPopup(self, title = 'Choose file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = fileSelectPopup.getFile()
self.textWindow.setText('File Selected: %s\n' % fileName)
def showWarning(self, eventObject):
self.textWindow.setText('Text Entry Return Pressed\n')
showWarning('Warning Title','Warning Message')
return
def pressButton(self):
self.textWindow.setText('Button Pressed\n')
if showYesNo('Title','Prompt: Clear text window?'):
self.textWindow.clear()
return
def quit(self):
BasePopup.destroy(self)
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 PeakSeparatorGui(BasePopup):
"""
**Separate Merged Peaks Using Peak Models**
The Peak Separator code uses a Markov Chain Monte Carlo search which, using
idealised peak shapes, attempts to deconvolve overlapped peak regions into
their separate constituent peaks.
This routine is also suitable for accurately fitting model shapes to single
peaks in order to calculate precise intensities.
**Options Peak Separator Parameters**
*Min. Number of peaks* is by default set to one, it is not possible to set
this to a value less than one.
*Max. Number of peaks* is by default set to one, increasing this value allows
the search routine to fit more models. The best fit may be found with fewer than
the maximum number models. Higher numbers slow the routine, and setting this
value to 0 allows the routine to (effectively) fit unlimited peaks.
*Only pick positive peaks*. If you are not interested in negative peaks, removing
the possibility of fitting negative peaks can reduce search time.
*Peak Model* fits the spectra with either a Gaussian peak model or a Lorentzian
peak model.
**Options Region**
*Peak List* choose which peak list newly picked peaks should be added to. Peaks
picked using this method will have their details appended with 'PeakSepartor'
so you know where they came from.
*Region Table* shows which area of the current spectrum is about to be searched.
*Add Region*. Once an area of spectra has been highlighted clicking this button
will pass it's details on to the Peak Separator.
*Reset All* will reset all search parameters.
*Separate Peaks* will run the Peak Separator code with your current settings. This
may take a few minutes to run, depending on the size of the spectral region being
searched, the number of peaks being fitted and the speed of your machine. Please
wait while this completes.
After a successful Peak Separation run, the found peaks will be added to the
selected peak list. These peaks intensties (volume) have been found using the
peak model selected.
**Advanced Settings Tab**
*Rate* affects the speed of the Markov Chain Monte Carlo routine. A smaller value
results in longer execution, but possibly higher quality results. The default
setting is deemed sensible for the majority of runs.
*Line Width* offers a finer degree of control over maximum and minimum peak widths
for each dimension. The default values are *very* stupid and could do with
re-checking for each experiment.
*Re-Pick Entire Peak List* if you would like to use the Peak Separator to repick
*every* peak in your peak list, try this option - but note that this may take
a very long time!
"""
def __init__(self, parent, programName='Peak Separator', **kw):
self.parent = parent
self.programName = programName
self.versionInfo = 'Version 0.2'
self.help_url = 'http://www.ccpn.ac.uk/'
self.window = None
self.waiting = False
self.rootWindow = None
# just used for display - PeakSeparator will not see this
self._minSigmaHz = None
self._maxSigmaHz = None
self.customSigma = False
self.rePickPeakList = False
self._sampleStartPpm = None
self._sampleEndPpm = None
try:
self.project = parent.project
except:
pass
self.params = PeakSeparatorParams()
BasePopup.__init__(self,
parent=parent,
title=programName,
location='+100+100',
**kw)
if not self.analysisProject:
print '&&& init: No analysis project found ...'
try:
if parent.argumentServer:
self.argServer = parent.argumentServer
else:
print '&&& init: No argument server found...'
except:
print '&&& init: Test'
###########################################################################
def body(self, guiFrame):
self.geometry('450x500')
guiFrame.grid_rowconfigure(0, weight=1)
guiFrame.grid_columnconfigure(0, weight=1)
options = ['Peak Separator', 'Advanced Settings']
tabbedFrame = TabbedFrame(guiFrame, options=options)
tabbedFrame.grid(row=0, column=0, sticky='nsew')
buttons = UtilityButtonList(tabbedFrame.sideFrame,
helpUrl=self.help_url)
buttons.grid(row=0, column=0, sticky='e')
self.tabbedFrame = tabbedFrame
frameA, frameB = tabbedFrame.frames
#
# FrameA : Main Settings
#
frameA.grid_columnconfigure(1, weight=1)
row = 0 # Label row
row += 1
div = LabelDivider(frameA, text='Peak Separator Parameters')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameA, text='Min. number of peaks:')
label.grid(row=row, column=0, sticky='w')
self.minPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \
tipText='Minimum number of peaks to find (must be > 0)')
self.minPeaksEntry.grid(row=row, column=1, sticky='n')
self.minPeaksEntry.bind('<Leave>', self.applyChange, '+')
row += 1
label = Label(frameA, text='Max. number of peaks:')
label.grid(row=row, column=0, sticky='w')
self.maxPeaksEntry = IntEntry(frameA, returnCallback=self.applyChange, width=10, \
tipText='Maximum number of peaks to find (0 is unlimited - not recommended)')
self.maxPeaksEntry.grid(row=row, column=1, sticky='n')
self.maxPeaksEntry.bind('<Leave>', self.applyChange, '+')
row += 1
label = Label(frameA, text='Only pick positive peaks:')
label.grid(row=row, column=0, sticky='w')
entries = ['False', 'True']
self.posPeaksButtons = RadioButtons(
frameA,
entries=entries,
select_callback=self.applyChange,
direction='horizontal',
tipTexts=[
'Search for both positive and negative intensity peaks',
'Limit search to only positive peaks'
])
self.posPeaksButtons.grid(row=row, column=1, sticky='n')
row += 1
label = Label(frameA, text='Peak Model:')
label.grid(row=row, column=0, sticky='w')
### G/L Mixture works, but volume calculation involves Gamma function
# entries = ['Gaussian', 'Lorentzian', 'G/L Mixture']
entries = ['Gaussian', 'Lorentzian']
self.shapeButtons = RadioButtons(
frameA,
entries=entries,
select_callback=self.applyChange,
direction='horizontal',
tipTexts=[
'Choose a Gaussian model peak shape to fit to peaks',
'Choose a Lorentzian model peak shape to fit to peaks'
])
self.shapeButtons.grid(row=row, column=1, sticky='n')
row += 1
div = LabelDivider(frameA,
text='Region',
tipText='Region that search will limit itself to')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameA, text='Peak List:')
label.grid(row=row, column=0, sticky='nw')
self.peakListPulldown = PulldownList(
frameA,
callback=self.setManuallyPickPeakList,
tipText='Select which peak list new peaks are to be added to')
self.peakListPulldown.grid(row=row, column=1, sticky='nw')
# tricky scrolled matrix
row += 1
self.regionTable = None
frameA.grid_rowconfigure(row, weight=1)
headings = ('dim.', 'start (ppm)', 'end (ppm)', 'actual size')
self.editDimEntry = IntEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Dimension number')
self.editStartEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Search area lower bound')
self.editEndEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Search area upper bound')
editWidgets = [
self.editDimEntry, self.editStartEntry, self.editEndEntry, None
]
editGetCallbacks = [None, None, None, None]
editSetCallbacks = [None, None, None, None]
self.regionTable = ScrolledMatrix(frameA,
headingList=headings,
multiSelect=False,
editWidgets=editWidgets,
editGetCallbacks=editGetCallbacks,
editSetCallbacks=editSetCallbacks,
initialRows=5)
self.regionTable.grid(row=row, column=0, columnspan=2, sticky='nsew')
# Run Button
row += 1
texts = ['Add Region']
commands = [self.updateFromRegion]
self.addResetButtons = ButtonList(
frameA,
texts=texts,
commands=commands,
tipTexts=['Add selected specrtral region'])
self.addResetButtons.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
texts = ['Separate Peaks']
commands = [self.runPeakSeparator]
self.runButton = ButtonList(frameA,
texts=texts,
commands=commands,
expands=True,
tipTexts=['Run peak search now'])
self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew')
#
# FrameB : Further Settings
#
frameB.grid_columnconfigure(0, weight=1)
row = 0
div = LabelDivider(frameB, text='Rate:')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameB, text='Rate of MCMC step size change')
label.grid(row=row, column=0, columnspan=1, sticky='w')
self.rateEntry = FloatEntry(frameB, returnCallback=self.applyChange, width=10, \
tipText='Rate effects speed of run, smaller values take longer but may produce better results')
self.rateEntry.grid(row=row, column=1, sticky='n')
self.rateEntry.bind('<Leave>', self.applyChange, '+')
self.rateEntry.set(self.params.rate)
# tricky scrolled matrix for line width
row += 2
div = LabelDivider(frameB, text='Line Width (Hz):')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
label = Label(frameB, text="Descr.")
label.grid(row=row, rowspan=2, column=0, sticky='w')
row += 1
self.lineWidthTable = None
frameB.grid_rowconfigure(row, weight=1)
lineWidthHeadings = ('dim.', 'min. σ (Hz)', 'max. σ (Hz)')
self.editMinSigmaEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Minimum line width (Hz)')
self.editMaxSigmaEntry = FloatEntry(self,
returnCallback=self.applyChange,
width=5,
tipText='Maximum line width (Hz)')
# self.editDimEntry is also from regionTable
initialWidthRows = 4
editLineWidthWidgets = [
None, self.editMinSigmaEntry, self.editMaxSigmaEntry
]
editLineWidthGetCallbacks = [None, self.getSigmaMin, self.getSigmaMax]
editLineWidthSetCallbacks = [None, self.setSigmaMin, self.setSigmaMax]
self.lineWidthTable = ScrolledMatrix(
frameB,
headingList=lineWidthHeadings,
multiSelect=False,
editWidgets=editLineWidthWidgets,
editGetCallbacks=editLineWidthGetCallbacks,
editSetCallbacks=editLineWidthSetCallbacks,
initialRows=initialWidthRows)
self.lineWidthTable.grid(row=row,
column=0,
columnspan=2,
sticky='nsew')
# option to 'repick' exisiting peak list
row += initialWidthRows
div = LabelDivider(frameB, text='(optional - repick entire peak list)')
div.grid(row=row, column=0, columnspan=2, sticky='ew')
row += 1
self.repickListPulldown = PulldownList(
frameB,
callback=self.setRePickPeakList,
tipText=
'Select which peak list to repick (new peaks will be put into a new peak list)'
)
self.repickListPulldown.grid(row=row, column=0, sticky='nw')
texts = ['Repick Peak List']
commands = [self.runRepickPeaks]
self.runButton = ButtonList(
frameB,
texts=texts,
commands=commands,
expands=True,
tipTexts=['Repick selected peak list into a new peak list.'])
self.runButton.grid(row=row, column=1, columnspan=1, sticky='nsew')
row += 1
div = LabelDivider(frameB)
row += 1
texts = ['Separate Peaks']
commands = [self.runPeakSeparator]
self.runButton = ButtonList(frameB,
texts=texts,
commands=commands,
expands=True,
tipTexts=['Run peak search now'])
self.runButton.grid(row=row, column=0, columnspan=2, sticky='nsew')
self.setWidgetEntries()
self.administerNotifiers(self.registerNotify)
def administerNotifiers(self, notifyFunc):
for func in ('__init__', 'delete'):
notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.PeakList', func)
notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.Experiment', 'setName')
notifyFunc(self.updateAfter, 'ccp.nmr.Nmr.DataSource', 'setName')
def destroy(self):
self.administerNotifiers(self.unregisterNotify)
BasePopup.destroy(self)
###########################################################################
# update parameters from PS Region
def updateFromRegion(self):
if not self.params.peakList:
print '&&& update from region: Need a peak list'
return
if (self.argServer.parent.currentRegion) == None:
showError('No Region',
'Please select a peak region to be separated')
return
self.rePickPeakList = False
getRegionParams(self.params, argServer=self.argServer)
if not self.customSigma: self.initSigmaParams()
self.setWidgetEntries()
###########################################################################
# update parameters from PS PeakList
def updateFromPeakList(self):
if not self.params.peakList:
print '&&& update from peakList: Need a peak list'
return
getPeakListParams(self.params)
if not self.customSigma: self.initSigmaParams()
self.setWidgetEntries()
###########################################################################
# Run the C library!
def runPeakSeparator(self):
""" run the peak separator """
# hack for Macs - focus isn't always lost on mouse move
# so bind event not always called. Shouldn't affect other OS.
self.applyChange()
if not self.params.peakList:
print '&&& Peak list not yet set'
else:
# SeparatePeakRoutine(self.params, self.params.peakList, routine='pymc' )
SeparatePeakRoutine(self.params,
self.params.peakList,
routine='bayesys')
def runRepickPeaks(self):
""" Run the Peak Separator on entire chosen peak list """
# hack for Macs - focus isn't always lost on mouse move
# so bind event not always called. Shouldn't affect other OS.
self.applyChange()
if not self.params.peakList:
print '&&& Peak list not yet set'
else:
SeparatePeaksInPeakList(self.params)
###########################################################################
def setWidgetEntries(self):
### Page One widgets
self.minPeaksEntry.set(self.params.minAtoms)
self.maxPeaksEntry.set(self.params.maxAtoms)
if self.params.positivePeaks == 1:
self.posPeaksButtons.set('True') # only pick pos peaks
else:
self.posPeaksButtons.set('False')
# do something fancy if different shapes for each dim!
n = self.params.peakShape - 3 # shape is only 3, 4, (5)
self.shapeButtons.setIndex(n)
if self.project is not None:
self.updatePeakListList()
self.updateSpectrumWindow()
if self.params.sampleStart and self.params.peakList:
if not self.rePickPeakList:
objectList = []
textMatrix = []
if len(self.params.samplePpmStart) != self.params.Ndim: return
for i in range(self.params.Ndim):
dim_entry = []
dim_entry.append('%2d' % (i + 1))
dim_entry.append('%7.3f' % self.params.samplePpmStart[i])
dim_entry.append('%7.3f' % self.params.samplePpmEnd[i])
dim_entry.append('%3d' % self.params.sampleSize[i])
textMatrix.append(dim_entry)
self.regionTable.update(textMatrix=textMatrix,
objectList=objectList)
### Page Two widgets
self.rateEntry.set(self.params.rate)
if self.params.peakList and self.params.Ndim:
textMatrix = []
objectList = []
for i in range(self.params.Ndim):
if self.params.isFreqDim[i]:
dim_entry = []
objectList.append(i)
dim_entry.append('%2d' % (i + 1))
dim_entry.append('%7.3f' % self._minSigmaHz[i])
dim_entry.append('%7.3f' % self._maxSigmaHz[i])
textMatrix.append(dim_entry)
self.lineWidthTable.update(textMatrix=textMatrix,
objectList=objectList)
def applyChange(self, *event):
""" Upon change, add settings to params """
# Page One apply changes
self.params.minAtoms = self.minPeaksEntry.get()
self.params.maxAtoms = self.maxPeaksEntry.get()
if self.posPeaksButtons.get() == 'True': # asked only pick pos peaks
self.params.positivePeaks = 1
else:
self.params.positivePeaks = 0
# do something fancy if different shapes for each dim!
n = self.shapeButtons.getIndex() # shape is only 3, 4, (5)
self.params.peakShape = n + 3
# Page Two apply changes
self.params.rate = float(self.rateEntry.get())
self.updateSigmaParams()
###########################################################################
# Peak list functions provide PeakSeparator some inherited params
def getPeakListList(self):
""" given a spectrum, get list of peak lists """
project = self.project
peakLists = []
for experiment in self.nmrProject.experiments:
for spectrum in experiment.dataSources:
for peakList in spectrum.peakLists:
peakLists.append([
'%s:%s:%d' %
(experiment.name, spectrum.name, peakList.serial),
peakList
])
peakLists.sort()
return peakLists
def updatePeakListList(self):
""" set the peaklist list in the pulldown menu """
peakListData = self.getPeakListList()
index = -1
names = []
peakList = self.params.peakList
if peakListData:
names = [x[0] for x in peakListData]
peakLists = [x[1] for x in peakListData]
if peakList not in peakLists:
peakList = peakLists[0]
index = peakLists.index(peakList)
else:
peakList = None
peakLists = []
if peakList is not self.params.peakList:
self.params.peakList = peakList
self.peakListPulldown.setup(names, peakLists, index)
self.repickListPulldown.setup(names, peakLists, index)
def setRePickPeakList(self, peakList):
""" Set the peak list to be repicked (and hit a Flag) """
self.rePickPeakList = True
self.setPeakList(peakList)
def setManuallyPickPeakList(self, peakList):
""" Set the peak list to add new peaks to (and hit a Flag) """
self.rePickPeakList = False
self.setPeakList(peakList)
def setPeakList(self, peakList):
""" Sets the Peak List """
if peakList is not self.params.peakList:
self.params.peakList = peakList
# # interrogate the peak list and get all the usefull parameters out
self.updateFromPeakList()
self.updateSpectrumWindow()
self.setWidgetEntries()
###########################################################################
# TBD I suspect this is for matching region with peak list, but may be obsolete now
def getSpectrumWindowList(self):
""" get list of windows which spectrum could be in """
windows = {}
if self.params.peakList:
views = getSpectrumViews(self.params.peakList.dataSource)
for view in views:
windows[view.spectrumWindowPane.spectrumWindow] = None
return [[w.name, w] for w in windows.keys()]
def updateSpectrumWindow(self):
""" update the spectrum window """
windowData = self.getSpectrumWindowList()
index = -1
names = []
window = self.rootWindow
if windowData:
names = [x[0] for x in windowData]
windows = [x[1] for x in windowData]
if window not in windows:
window = windows[0]
index = windows.index(window)
else:
window = None
windows = []
if window is not self.rootWindow:
self.rootWindow = window
###########################################################################
# get and set sigma stuff
def setSigmaMin(self, dim):
value = self.editMinSigmaEntry.get()
self._minSigmaHz[dim] = value
# dont go and re-write users settings
self.customSigma = True
# make sure changes are in params object
self.updateSigmaParams(dim)
self.setWidgetEntries()
def getSigmaMin(self, dim):
if dim is not None:
self.editMinSigmaEntry.set(self._minSigmaHz[dim])
def setSigmaMax(self, dim):
value = self.editMaxSigmaEntry.get()
self._maxSigmaHz[dim] = value
# dont go and re-write users settings
self.customSigma = True
# make sure changes are in params object
self.updateSigmaParams(dim)
self.setWidgetEntries()
def getSigmaMax(self, dim):
if dim is not None:
self.editMaxSigmaEntry.set(self._maxSigmaHz[dim])
def updateSigmaParams(self, dim=None):
""" updateSigmaParams Just updates the parameters (params obj) for sigma values.
If dim is None, do this for each dim
"""
dataDimRefs = self.params.dataDimRefs
if not dataDimRefs: return
if not self.params.minSigma or len(
self.params.minSigma) != self.params.Ndim:
self.params.minSigma = [0.] * self.params.Ndim
if not self.params.maxSigma or len(
self.params.maxSigma) != self.params.Ndim:
self.params.maxSigma = [0.] * self.params.Ndim
def updateSigmaParam(dim, dataDimRefs):
""" Convert and update sigma for dim """
if self.params.isFreqDim[dim]:
# note factor of two!
self.params.minSigma[dim] = self.rHz2pnt(
self._minSigmaHz[dim], dataDimRefs[dim]) / 2.
self.params.maxSigma[dim] = self.rHz2pnt(
self._maxSigmaHz[dim], dataDimRefs[dim]) / 2.
else:
self.params.minSigma[dim] = 1.0
self.params.maxSigma[dim] = 1.0
if dim:
updateSigmaParam(dim, dataDimRefs)
else:
for dim in range(self.params.Ndim):
updateSigmaParam(dim, dataDimRefs)
# utility functions for sigma values
def pnt2rHz(self, point, dataDimRef):
""" Point to relative Hz frequency relative to frequency at Zeroeth point
Necessary when (for example) looking for width of peak in Hz
"""
assert point, dataDimRef
sigmaBase = pnt2hz(0, dataDimRef)
sigmaHz = pnt2hz(point, dataDimRef)
return abs(sigmaHz - sigmaBase)
def rHz2pnt(self, freq, dataDimRef):
""" Relative Hz to point frequency relative to frequency at Zeroeth point
Necessary when (for example) looking for width of peak in Hz
"""
assert freq, dataDimRef
sigmaBase = hz2pnt(0, dataDimRef)
sigmaPoint = hz2pnt(freq, dataDimRef)
return abs(sigmaPoint - sigmaBase)
def initSigmaParams(self):
""" Set some initial default values for sigma """
self._minSigmaHz = []
self._maxSigmaHz = []
if self.params.Ndim:
for dim in range(self.params.Ndim):
self._minSigmaHz.append(6.)
self._maxSigmaHz.append(28.)
###########################################################################
def updateAll(self):
self.updateSpectrumWindow()
self.updatePeakListList()
self.waiting = False
def updateAfter(self, obj=None):
if self.waiting:
return
else:
self.waiting = True
self.after_idle(self.updateAll)
class RepositoryFrame(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
# should the screen autorefresh
self.autoRefresh = False
# add this to shortcuts to ease navigation
self.basePopup.frameShortcuts['Repository'] = self
# get a port proxy instance
# this should probably belong to the repository directly
# or else should belong in a dictionary in the main gui
# layer when it can be picked up easily
# FIXME JMCI
# need to work out how to get a number of these!
loc = SharedBeanServiceLocator()
self.port = loc.getSharedBean()
self.registerNotify = basePopup.registerNotify
self.unregisterNotify = basePopup.unregisterNotify
Frame.__init__(self, guiParent)
# set up the grid
self.grid_columnconfigure(0, weight=0, minsize=20)
self.grid_columnconfigure(1, weight=1, minsize=10)
self.grid_columnconfigure(2, weight=0, minsize=20)
self.grid_rowconfigure(0, weight=0, minsize=5)
self.grid_rowconfigure(1, weight=0, minsize=0)
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=1, minsize=10)
self.grid_rowconfigure(6, weight=0, minsize=10)
self.grid_rowconfigure(7, weight=0, minsize=10)
# widgets for view when no data
self.noDataWidgets = []
self.noRepLabel = Label(self, text='No repository currently selected.')
self.noDataWidgets.append(self.noRepLabel)
# widgets for view when current repository set
self.dataWidgets = []
self.repTitle = Label(self, text='Repository:', font='Helvetica16')
self.dataWidgets.append(self.repTitle)
#self.repLabel = Label(self,text='All Projects in Repository')
#self.dataWidgets.append(self.repLabel)
self.repTree = Tree(self, doubleCallback=self.goto_project_tab)
self.dataWidgets.append(self.repTree)
sel = 1
if self.autoRefresh:
sel = 0
self.autoRefreshSwitchLabel = Label(self, text='Auto Refresh')
self.autoRefreshSwitch = RadioButtons(self, ['on', 'off'],
select_callback=self.set_refresh,
selected_index=sel)
# need to decide whether this is static or not
r_button_texts = [
'Add to Basket', ' Import ', ' Export ', ' Refresh ',
'Properties'
]
r_button_cmds = [
self.tmpCall, self.import_project, self.export_project,
self.drawFrame, self.goto_project_tab
]
self.rep_button_list = ButtonList(self, r_button_texts, r_button_cmds)
self.dataWidgets.append(self.rep_button_list)
self.filterFrame = FilterFrame(self, self.basePopup, text='Filter')
self.dataWidgets.append(self.filterFrame)
baskets = ('basket1', 'basket2', 'basket3')
self.basketSelect = PulldownList(self, self.tmpCall, baskets)
self.dataWidgets.append(self.basketSelect)
basketElements = ('1ay3', '1ay7')
self.basketList = ScrolledListbox(self, basketElements, 25, 18)
self.dataWidgets.append(self.basketList)
b_button_texts = ['Remove from Basket', 'New Basket']
b_button_cmds = [self.tmpCall, self.tmpCall]
self.b_button_list = ButtonList(self, b_button_texts, b_button_cmds)
self.dataWidgets.append(self.b_button_list)
# draw if not automatically refreshing
if sel == 1:
self.drawFrame()
# set up a loop
self.refresh()
def drawFrame(self):
if self.basePopup.repList.currentRepository == None:
for widget in self.dataWidgets:
widget.grid_remove()
self.noRepLabel.grid(row=1, column=1, sticky='n')
else:
self.repository = self.basePopup.repList.currentRepository
for widget in self.noDataWidgets:
widget.grid_remove()
# Column headers
# want to have a general admin panel; current repository, button to change, info
# about login and so on
self.repTitle.set('Repository: ' + self.repository.user + '@' +
self.repository.name + ' ( ' +
self.repository.connect + ' )')
self.repTitle.grid(row=1, column=1, sticky='w')
# self.repLabel.grid(row=2, column=1, sticky='w')
# Repository block
#grid and update
self.repTree.grid(row=3, column=1, rowspan=3, sticky='nsew')
self.updateRepTree()
self.autoRefreshSwitchLabel.grid(row=6,
column=1,
padx=10,
sticky='w')
self.autoRefreshSwitch.grid(row=6, column=1, padx=10, sticky='e')
# the buttons for functionality in repository area
self.rep_button_list.grid(row=7, column=1, padx=3, sticky='ew')
# filter frame
self.filterFrame.grid(row=3, column=2, stick='nsew')
# list of baskest. Will callback to change current basket
self.basketSelect.grid(row=4, column=2, padx=10, stick='w')
# lists projects per basket
self.basketList.grid(row=5,
rowspan=2,
column=2,
padx=10,
stick='nsew')
self.b_button_list.grid(row=7, column=2, padx=5, stick='ew')
def openLink(self, node):
tree = node.tree
par = node.object
# this should be associated with the repository object
request = getList()
# FIXME JMCI
# 1. Potentially need to traverse up the node tree
# 2. Currently there is bug in expansion/contraction
# 3. Search needs to work off proxy method (not off
# generated stubs
# pass the parent name for now. may need other criteria later
h1 = {'name': par.__str__()}
h2 = {'project': h1}
wsstr_in = WSString(h2)
request._arg0 = 'org.pimslims.applet.server.ProjectVersionBean'
request._arg1 = 'getListWithFields'
request._arg2 = wsstr_in.str
# get the response
response = self.port.getList(request)
# currently we just get a list of numbers. May want to send
# all the fields for every object too to cut down on db calls
wsstr_out = WSString(response._return)
ss = wsstr_out.getStruct()
for hm in ss:
print 'handling ', hm, ', ', hm['status'].__str__()
#if hm['status'].__str__() == 'AVAILABLE':
icon = 'text-x-generic'
#else:
# icon='emblem-readonly'
pv = par.__str__() + '::' + hm['versionTag'].__str__()
obj = pv
text = hm['versionTag'].__str__()
callback = None
tree.add(node, obj, text, icon, callback)
def set_refresh(self, text):
print 'setting refresh ', text
if text == 'on':
self.autoRefresh = True
else:
self.autoRefresh = False
def refresh(self):
if self.autoRefresh:
print 'refreshing frame ', time.time()
self.drawFrame()
self.after(5000, self.refresh)
# FIME JMCI
# it would probably be a good idea to have a method that allowed
# a user to unlock a given project version. Would need to check
# permissions very carefully, though
def unlock_project_version(self):
pass
def goto_project_tab(self, node=None):
if node is None:
# get the selected node
selected_nodes = self.repTree.getSelectedNodes()
# restrict the choice to one
node = selected_nodes[0]
# we really need to traverse the tree a lot more carefully
pv = node.object.__str__()
print 'GOTO PROJECT ', pv, ', ', node, ', ', node.object
pat = re.compile('::')
matcher = pat.search(pv, 0)
name = pv[0:matcher.start()]
versionTag = pv[matcher.end():]
print 'GOTO PROJECT ', name, ', ', versionTag
#versionTag = node.object.__str__()
#name = node.parent.object.__str__()
#print node.__dict__
#print node.parent.__dict__
self.basePopup.repList.currentRepository.currentProjectName = name
self.basePopup.repList.currentRepository.currentVersionTag = versionTag
# this is going to have to be keyed on a natural key that then
# gets set into the criteria of a ws query
# hack for now. build in later. Essentially, we have to handle two
# cases; that of a specific projectVersion request and that of a
# request on a project alone. Probably the best behaviour would be
# for the project-only request to default to the latest trunk
# version of the project and the most elegent way of triggering
# this would probably be to have this as a property of the project
# returned in the main hash from Project.getFields().
self.basePopup.tabbedFrame.select(1)
if self.basePopup.frameShortcuts.has_key('Project'):
self.basePopup.frameShortcuts['Project'].drawFrame()
def import_project(self):
# FIXME JMCI
# need to preserve the current status. Take default from the
# Wms layer
rootDir = self.basePopup.repList.current_import_dir
fileSelectPopup = FileSelectPopup(self, None, rootDir)
new_project_dir = fileSelectPopup.getDirectory()
self.basePopup.repList.current_import_dir = new_project_dir
print 'in import project with directory', new_project_dir
idx = new_project_dir.rfind('/')
new_project_name = new_project_dir[idx + 1:]
print 'in import project with project', new_project_name
# FIXME
# need to set the project version number somewhere. For now set to none
# and this gets picked up and set to a default 1.1 later
self.repository.import_project(new_project_name, None, new_project_dir)
self.drawFrame()
def export_project(self):
# get the selected node
selected_nodes = self.repTree.getSelectedNodes()
# restrict the choice to one
node = selected_nodes[0]
# we really need to traverse the tree a lot more carefully
name = node.parent.object.__str__()
versionTag = node.object.__str__()[len(name) + 2:]
# 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
self.repository.export_project(name, versionTag, exp_project_dir)
def disconnectRepository(self):
# do we need to formally break a connection and destroy the session?
# yes we probably should.
# need an "are you sure" dialog box
# need to protect
self.repository.repList.repositories.remove(self.repository)
self.grid_remove()
for ff in self.guiParent.guiParent.parent.frames[0].children.values():
ff.drawFrame()
def tmpCall(self):
return
# This will need a separate call to the WS with an additional
# criterion (picking up the checkout version)
def updateRepTree(self):
texts = []
icons = []
parents = []
callbacks = []
objects = []
# OK, this would be a good point to access the list
# this should be associated with the repository object
loc = SharedBeanServiceLocator()
port = loc.getSharedBean()
request = getList()
# these are actually static
request._arg0 = 'org.pimslims.applet.server.ProjectBean'
request._arg1 = 'getList'
request._arg2 = ''
# get the response
response = port.getList(request)
# this is a hack at present. It needs to be written properly
wsstr = WSString(response._return)
ss = wsstr.getStruct()
for strg in ss:
texts.append(strg)
icons.append('folder')
parents.append(None)
objects.append(strg)
callbacks.append(self.openLink)
print 'UPDATE ', ss
print 'UPDATE ', len(ss)
if len(ss) > 0:
print 'UPDATE: updating '
self.repTree.update(parents, objects, texts, icons, callbacks)
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 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 WidgetCountPopup(BasePopup):
on_off_entries = ['on', 'off']
def __init__(self, parent, help_msg='', help_url='', *args, **kw):
self.help_msg = help_msg
self.help_url = help_url
BasePopup.__init__(self,
parent=parent,
title='Widget Count',
*args,
**kw)
def body(self, master):
self.alarm_id = None
self.root_widget = getRoot(self)
row = 0
label = Label(master, text='Widget count:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.count_label = Label(master,
text='',
tipText='Number of Tkinter widget objects')
self.count_label.grid(row=row, column=1, sticky=Tkinter.W)
row = row + 1
ind = 1
label = Label(master, text='Auto count:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.on_off_buttons = RadioButtons(master,
entries=self.on_off_entries,
select_callback=self.applyAuto,
selected_index=ind)
self.on_off_buttons.grid(row=row, column=1, sticky=Tkinter.EW)
row = row + 1
label = Label(master, text='Auto frequency:')
label.grid(row=row, column=0, sticky=Tkinter.W)
self.freq_entry = IntEntry(master,
text=60,
returnCallback=self.applyAuto)
self.freq_entry.grid(row=row, column=1, sticky=Tkinter.EW)
label = Label(master, text='seconds')
label.grid(row=row, column=2, sticky=Tkinter.W)
row = row + 1
texts = ['Do Immediate Count']
commands = [self.applyManual]
buttons = createDismissHelpButtonList(master,
texts=texts,
commands=commands,
help_msg=self.help_msg,
help_url=self.help_url)
buttons.grid(row=row, column=0, columnspan=3, sticky=Tkinter.EW)
self.doCount()
def applyAuto(self, *event):
on_off = self.on_off_buttons.get()
if on_off == 'on':
self.setCountOn()
else:
self.setCountOff()
def applyManual(self):
self.doCount()
def setCountOn(self):
self.setCountOff()
freq = self.freq_entry.get()
if freq is not None and freq > 0:
freq *= 1000 # convert from sec to msec
self.alarm_id = self.after(freq, self.doCountAuto)
def setCountOff(self):
if self.alarm_id:
self.after_cancel(self.alarm_id)
self.alarm_id = None
def doCountAuto(self):
if self.on_off_buttons.get() == 'on':
self.doCount()
freq = self.freq_entry.get()
if freq is not None and freq > 0:
freq *= 1000 # convert from sec to msec
self.alarm_id = self.after(freq, self.doCountAuto)
def doCount(self):
count = getWidgetCount(self.root_widget)
self.count_label.set('%d' % count)
