class AssignMentTransferTab(object):
    '''the tab in the GUI where assignments
       can be transferred in bulk to the ccpn analysis
       project. A difference is made between two types
       of assignments:
           1) spin systems to residues, which also
              implies resonanceSets to atomSets.
           2) resonances to peak dimensions.
       The user is able to configure which assignments
       should be transferred to the project.

      Attributes:

          guiParent: gui object this tab is part of.

          frame: the frame in which this element lives.

          dataModel(src.cython.malandro.DataModel): dataModel
              object describing the assignment proposed by
              the algorithm.

          selectedSolution (int): The index of the solution/run
              that is used asa the template to make the assignments.

          resonanceToDimension (bool): True if resonances should
              be assigned to peak dimensions. False if not.

          spinSystemToResidue (bool): True if spin system to
              residue assignment should be carried out.

          minScore (float): The minimal score of a spin system
              assignment to a residue to be allowed
              to transfer this assignment to the project

          intra (bool): True if intra-residual peaks should be
              assigned.

          sequential (bool): True if sequential peaks should be
              assigned.

          noDiagonal (bool): If True, purely diagonal peaks are
              ignored during the transfer of assignments.

          allSpectra (bool): If True, all spectra will be assigned.
              If False, one specified spectrum will be assigned.

          spectrum (src.cython.malandro.Spectrum): The spectrum
              that should be assigned.
    '''

    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

        # Buttons and fields,
        # will be set in body():
        self.peaksCheckButton = None
        self.residuesCheckButton = None
        self.intraCheckButton = None
        self.sequentialCheckButton = None
        self.noDiagonalCheckButton = None
        self.spinSystemTypeSelect = None
        self.minScoreEntry = None
        self.solutionNumberEntry = None
        self.spectrumSelect = None
        self.spectraPullDown = None
        self.assignedResidueStrategySelect = None
        self.transferButton = None

        # Settings that determine how assignments
        # are transferred to the analysis project:
        self.minScore = 80.0
        self.dataModel = None
        self.spectrum = None
        self.selectedSolution = 1
        self.body()
        self.resonanceToDimension = True
        self.spinSystemToResidue = True
        self.intra = True
        self.sequential = True
        self.noDiagonal = True
        self.allSpectra = True
        self.spinSystemType = 0
        self.strategy = 0


    def body(self):
        '''Describes the body of this tab. It consists
           out of a number of radio buttons, check buttons
           and number entries that allow the user to
           indicate which assignments should be transferred.
        '''

        # self.frame.expandColumn(0)
        self.frame.expandGrid(8, 0)
        self.frame.expandGrid(8, 1)

        typeOfAssignmentFrame = LabelFrame(
            self.frame, text='type of assignment')
        typeOfAssignmentFrame.grid(row=0, column=0, sticky='nesw')
        # typeOfAssignmentFrame.expandGrid(0,5)

        peakSelectionFrame = LabelFrame(
            self.frame, text='which peaks to assign')
        peakSelectionFrame.grid(row=0, column=1, sticky='nesw', rowspan=2)

        spinSystemSelectionFrame = LabelFrame(self.frame,
                                              text='Which spin-systems to use')
        spinSystemSelectionFrame.grid(row=2, column=0, sticky='nesw')

        tipText = 'What to do when a residue has already a spin system assigned to it.'
        assignedResidueFrame = LabelFrame(self.frame,
                                          text='if residue already has spin-system',
                                          tipText=tipText)
        assignedResidueFrame.grid(row=2, column=1, sticky='nesw')

        spectrumSelectionFrame = LabelFrame(self.frame, text='spectra')
        spectrumSelectionFrame.grid(row=1, column=0, sticky='nesw')

        row = 0

        Label(typeOfAssignmentFrame,
              text='Resonances to Peak Dimensions',
              grid=(row, 0))
        self.peaksCheckButton = CheckButton(typeOfAssignmentFrame,
                                            selected=True,
                                            grid=(row, 1))

        row += 1

        Label(typeOfAssignmentFrame,
              text='SpinSystems to Residues',
              grid=(row, 0))
        self.residuesCheckButton = CheckButton(
            typeOfAssignmentFrame, selected=True, grid=(row, 1))

        row = 0

        Label(peakSelectionFrame, text='Intra-Residual', grid=(row, 0))
        self.intraCheckButton = CheckButton(
            peakSelectionFrame, selected=True, grid=(row, 1))

        row += 1

        Label(peakSelectionFrame, text='Sequential', grid=(row, 0))
        self.sequentialCheckButton = CheckButton(
            peakSelectionFrame, selected=True, grid=(row, 1))

        row += 1

        Label(peakSelectionFrame,
              text='Do not assign diagonal peaks',
              grid=(row, 0))
        self.noDiagonalCheckButton = CheckButton(
            peakSelectionFrame, selected=True, grid=(row, 1))

        entries = ['Only assigned spin systems',
                   'All that have a score of at least: ',
                   'User Defined',
                   'Solution number:']
        tipTexts = ['Only assign resonances of spin systems that already have a sequential assignment for the assignment of peak dimensions. Spin system to residue assignment is not relevant in this case.',
                    'Assign all spin systems that have a score of at least a given percentage. 50% or lower is not possible, because than spin systems might have to be assigned to more than 1 residue, which is impossible.',
                    "As defined in the lower row of buttons in the 'results' tab.",
                    'One of the single solutions of the annealing.']
        self.spinSystemTypeSelect = RadioButtons(spinSystemSelectionFrame,
                                                 entries=entries, grid=(0, 0),
                                                 select_callback=None,
                                                 direction=VERTICAL,
                                                 gridSpan=(4, 1),
                                                 tipTexts=tipTexts)

        tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.'
        self.minScoreEntry = FloatEntry(spinSystemSelectionFrame,
                                        grid=(1, 1), width=7,
                                        text=str(self.minScore),
                                        returnCallback=self.changeMinScore,
                                        tipText=tipText)
        self.minScoreEntry.bind('<Leave>', self.changeMinScore, '+')

        self.solutionNumberEntry = IntEntry(spinSystemSelectionFrame,
                                            grid=(3, 1), width=7, text=1,
                                            returnCallback=self.solutionUpdate,
                                            tipText=tipText)
        self.solutionNumberEntry.bind('<Leave>', self.solutionUpdate, '+')

        #self.solutionPullDown = PulldownList(spinSystemSelectionFrame, None, grid=(3,1), sticky='w')

        entries = ['all spectra', 'only:']
        tipTexts = ['Assign peaks in all the spectra that where selected before the annealing ran.',
                    'Only assign peaks in one particular spectrum. You can of course repeat this multiple times for different spectra.']
        self.spectrumSelect = RadioButtons(spectrumSelectionFrame,
                                           entries=entries,
                                           grid=(0, 0),
                                           select_callback=None,
                                           direction=VERTICAL,
                                           gridSpan=(2, 1), tipTexts=tipTexts)

        self.spectraPullDown = PulldownList(spectrumSelectionFrame,
                                            self.changeSpectrum,
                                            grid=(1, 1), sticky='w')

        entries = ['skip this residue',
                   'de-assign old spin system from residue',
                   'assign, but never merge',
                   'warn to merge']
        tipTexts = ["Don't assign the new spin system to the residue. The residue is not skipped when the old spin system does not contain any resonances",
                    "De-assign old spin system from residue, unless the old spin system is a spin system without any resonances.",
                    "Don't merge any spin systems, merging can be performed later if nescesary in the Resonance --> SpinSystems window.",
                    "Ask to merge individually for each spin system, this might result in clicking on a lot of popups."]
        self.assignedResidueStrategySelect = RadioButtons(assignedResidueFrame,
                                                          entries=entries,
                                                          grid=(0, 0),
                                                          select_callback=None,
                                                          direction=VERTICAL,
                                                          gridSpan=(2, 1),
                                                          tipTexts=tipTexts)

        texts = ['Transfer Assignments']
        commands = [self.transferAssignments]
        self.transferButton = ButtonList(
            self.frame, commands=commands, texts=texts)
        self.transferButton.grid(row=5, column=0, sticky='nsew', columnspan=2)

    def update(self):
        '''Update the nescesary elements in the
           tab. Is called when the algorithm
           has produced possible assignments.
           The only thing that has to be updated
           in practice in this tab is the pulldown
           with spectra.
        '''

        self.dataModel = self.guiParent.connector.results
        self.updateSpectra()

    def setDataModel(self, dataModel):
        '''Here the dataModel, which is the dataModel
           containing the suggested assignments body
           the algorithm, can be set.
        '''

        self.dataModel = dataModel
        self.update()

    def updateSpectra(self, *opt):
        '''Updates the spectra shown in the spectra
           pulldown. These are only the spectra that
           were used by the algorithm. All other spectra
           in the project are not relevant since for those
           no simulated peaks have been matched to real
           peaks.
        '''

        if not self.dataModel:

            return

        spectrum = self.spectrum

        spectra = self.dataModel.getSpectra()

        if spectra:

            names = [spectrum.name for spectrum in spectra]
            index = 0

            if self.spectrum not in spectra:

                self.spectrum = spectra[0]

            else:

                index = spectra.index(self.spectrum)

        self.spectraPullDown.setup(names, spectra, index)

    def changeSpectrum(self, spectrum):
        '''Select a spectum to be assigned.'''

        self.spectrum = spectrum

    def solutionUpdate(self, event=None, value=None):
        '''Select a solution. A solution is a
           one to one mapping of spin systems
           to residues produced by one run of
           the algorithm.
               args: event: event object, this is
                            one of the values the number
                            entry calls his callback
                            function with.
                     value: the index of the solution/run.
        '''

        if not self.dataModel:

            return

        Nsolutions = len(self.dataModel.chain.residues[0].solutions)

        if value is None:

            value = self.solutionNumberEntry.get()

        if value == self.selectedSolution:
            return
        else:
            self.selectedSolution = value
        if value < 1:
            self.solutionNumberEntry.set(1)
            self.selectedSolution = 1
        elif value > Nsolutions:
            self.selectedSolution = Nsolutions
            self.solutionNumberEntry.set(self.selectedSolution)
        else:
            self.solutionNumberEntry.set(self.selectedSolution)

    def fetchOptions(self):
        '''Fetches user set options from the gui in
           one go and stores them in their corresponding
           instance variables.
        '''

        self.resonanceToDimension = self.peaksCheckButton.get()
        self.spinSystemToResidue = self.residuesCheckButton.get()
        self.intra = self.intraCheckButton.get()
        self.sequential = self.sequentialCheckButton.get()
        self.noDiagonal = self.noDiagonalCheckButton.get()
        self.spinSystemType = self.spinSystemTypeSelect.getIndex()
        self.strategy = ['skip', 'remove', 'noMerge', None][
            self.assignedResidueStrategySelect.getIndex()]
        self.allSpectra = [True, False][self.spectrumSelect.getIndex()]

    def changeMinScore(self, event=None):
        '''Set the minimal score for which a spin system
           to residue assignment gets transferred to the
           ccpn analysis project.
        '''

        newMinScore = self.minScoreEntry.get()

        if self.minScore != newMinScore:

            if newMinScore <= 50.0:

                self.minScore = 51.0
                self.minScoreEntry.set(51.0)

            elif newMinScore > 100.0:

                self.minScore = 100.0
                self.minScoreEntry.set(100.0)

            else:

                self.minScore = newMinScore

    def transferAssignments(self):
        '''Transfer assignments to project depending
           on the settings from the GUI.
        '''

        self.fetchOptions()

        if not self.dataModel or (not self.resonanceToDimension and not self.spinSystemToResidue):

            return

        strategy = self.strategy

        lookupSpinSystem = [self.getAssignedSpinSystem,
                            self.getBestScoringSpinSystem,
                            self.getUserDefinedSpinSystem,
                            self.getSelectedSolutionSpinSystem][self.spinSystemType]

        residues = self.dataModel.chain.residues

        spinSystemSequence = [lookupSpinSystem(res) for res in residues]

        ccpnSpinSystems = []
        ccpnResidues = []

        # if self.spinSystemType == 0 it means that it for sure already
        # assigned like this
        if self.spinSystemToResidue and not self.spinSystemType == 0:

            for spinSys, res in zip(spinSystemSequence, residues):

                if spinSys and res:

                    ccpnSpinSystems.append(spinSys.getCcpnResonanceGroup())
                    ccpnResidues.append(res.getCcpnResidue())

            assignSpinSystemstoResidues(ccpnSpinSystems,
                                        ccpnResidues,
                                        strategy=strategy,
                                        guiParent=self.guiParent)

        if self.resonanceToDimension:

            allSpectra = self.allSpectra

            if self.intra:

                for residue, spinSystem in zip(residues, spinSystemSequence):

                    if not spinSystem:

                        continue

                    intraLink = residue.getIntraLink(spinSystem)

                    for pl in intraLink.getPeakLinks():

                        peak = pl.getPeak()

                        if not allSpectra and peak.getSpectrum() is not self.spectrum:

                            continue

                        if not peak:

                            continue

                        resonances = pl.getResonances()

                        if self.noDiagonal and len(set(resonances)) < len(resonances):

                            continue

                        for resonance, dimension in zip(resonances, peak.getDimensions()):

                            ccpnResonance = resonance.getCcpnResonance()
                            ccpnDimension = dimension.getCcpnDimension()
                            assignResToDim(ccpnDimension, ccpnResonance)

            if self.sequential:

                for residue, spinSystemA, spinSystemB in zip(residues,
                                                             spinSystemSequence,
                                                             spinSystemSequence[1:]):

                    if not spinSystemA or not spinSystemB:

                        continue

                    link = residue.getLink(spinSystemA, spinSystemB)

                    for pl in link.getPeakLinks():

                        peak = pl.getPeak()

                        if not allSpectra and peak.getSpectrum() is not self.spectrum:

                            continue

                        if not peak:

                            continue

                        resonances = pl.getResonances()

                        if self.noDiagonal and len(set(resonances)) < len(resonances):

                            continue

                        for resonance, dimension in zip(resonances, peak.getDimensions()):

                            ccpnResonance = resonance.getCcpnResonance()
                            ccpnDimension = dimension.getCcpnDimension()

                            assignResToDim(ccpnDimension, ccpnResonance)

        self.guiParent.resultsTab.update()

    def getAssignedSpinSystem(self, residue):
        '''Get the spinSystem that is assigned in the project
           to a residue.
           args:  residue (src.cython.malandro.Residue)
           return: spinSystem (src.cython.malandro.SpinSystem)
        '''

        ccpCode = residue.ccpCode
        seqCode = residue.getSeqCode()
        spinSystems = self.dataModel.getSpinSystems()[ccpCode]

        ccpnResidue = residue.getCcpnResidue()
        if ccpnResidue:
            assignedResonanceGroups = ccpnResidue.getResonanceGroups()
            if len(assignedResonanceGroups) > 1:
                print 'There is more than one spin system assigned to residue %s, did not know which one to use to assign peaks. Therefor this residue is skipped.' % (seqCode)
                return

            assignedResonanceGroup = ccpnResidue.findFirstResonanceGroup()

            if assignedResonanceGroup:

                for spinSystem in spinSystems:

                    if spinSystem.getSerial() == assignedResonanceGroup.serial:
                        # Just checking to make sure, analysis project could
                        # have changed
                        if not self.skipResidue(residue, spinSystem):

                            return spinSystem

    def getBestScoringSpinSystem(self, residue):
        '''Get the spinSystem that scores the highest,
           i.e. is assigned in most of the runs to the
           given residue.
           args:  residue (src.cython.malandro.Residue)
           return: spinSystem (src.cython.malandro.SpinSystem)
        '''

        solutions = residue.solutions
        weigth = 1.0 / len(solutions)
        score, bestSpinSystem = max([(solutions.count(solution) * weigth * 100.0, solution) for solution in solutions])

        if score >= self.minScore and not bestSpinSystem.getIsJoker() and not self.skipResidue(residue, bestSpinSystem):

            return bestSpinSystem

        return None

    def getUserDefinedSpinSystem(self, residue):
        '''Get the spinSystem that is defined by the user
           (probably in the resultsTab) as the correct
           assignment of the given residue.
           args:  residue (src.cython.malandro.Residue)
           return: spinSystem (src.cython.malandro.SpinSystem)
        '''

        userDefinedSpinSystem = residue.userDefinedSolution

        if userDefinedSpinSystem and not userDefinedSpinSystem.getIsJoker() and not self.skipResidue(residue, userDefinedSpinSystem):

            return userDefinedSpinSystem

        return None

    def getSelectedSolutionSpinSystem(self, residue):
        '''I a solution corresponding to one specific run
           of the algorithm is defined, return which spinSystem
           in that run got assigned to the given residue.
           args:  residue (src.cython.malandro.Residue)
           return: spinSystem (src.cython.malandro.SpinSystem)
        '''

        solutions = residue.solutions

        spinSystem = solutions[self.selectedSolution - 1]

        if not spinSystem.getIsJoker() and not self.skipResidue(residue, spinSystem):

            return spinSystem

        return None

    def skipResidue(self, residue, spinSystem):
        '''One strategy is to skip all residues that
           already have a spin system assignment.
           If that is the case determine whether to
           skip the given residue.
           args: residue (src.cython.malandro.Residue)
                 spinSystem (src.cython.malandro.SpinSystem)
           return: boolean, True if residue should be skipped.
        '''

        if self.strategy == 0:

            assignedGroups = residue.getCcpnResidue().getResonanceGroups()
            assignedSerials = set([spinSys.serial for spinSys in assignedGroups])

            if assignedSerials and spinSystem.getSerial() not in assignedSerials:

                return True

        return False
Example #2
0
    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):
        '''Describes the body of this tab. It consists
           out of a number of radio buttons, check buttons
           and number entries that allow the user to
           indicate which assignments should be transferred.
        '''

        # self.frame.expandColumn(0)
        self.frame.expandGrid(8, 0)
        self.frame.expandGrid(8, 1)

        typeOfAssignmentFrame = LabelFrame(
            self.frame, text='type of assignment')
        typeOfAssignmentFrame.grid(row=0, column=0, sticky='nesw')
        # typeOfAssignmentFrame.expandGrid(0,5)

        peakSelectionFrame = LabelFrame(
            self.frame, text='which peaks to assign')
        peakSelectionFrame.grid(row=0, column=1, sticky='nesw', rowspan=2)

        spinSystemSelectionFrame = LabelFrame(self.frame,
                                              text='Which spin-systems to use')
        spinSystemSelectionFrame.grid(row=2, column=0, sticky='nesw')

        tipText = 'What to do when a residue has already a spin system assigned to it.'
        assignedResidueFrame = LabelFrame(self.frame,
                                          text='if residue already has spin-system',
                                          tipText=tipText)
        assignedResidueFrame.grid(row=2, column=1, sticky='nesw')

        spectrumSelectionFrame = LabelFrame(self.frame, text='spectra')
        spectrumSelectionFrame.grid(row=1, column=0, sticky='nesw')

        row = 0

        Label(typeOfAssignmentFrame,
              text='Resonances to Peak Dimensions',
              grid=(row, 0))
        self.peaksCheckButton = CheckButton(typeOfAssignmentFrame,
                                            selected=True,
                                            grid=(row, 1))

        row += 1

        Label(typeOfAssignmentFrame,
              text='SpinSystems to Residues',
              grid=(row, 0))
        self.residuesCheckButton = CheckButton(
            typeOfAssignmentFrame, selected=True, grid=(row, 1))

        row = 0

        Label(peakSelectionFrame, text='Intra-Residual', grid=(row, 0))
        self.intraCheckButton = CheckButton(
            peakSelectionFrame, selected=True, grid=(row, 1))

        row += 1

        Label(peakSelectionFrame, text='Sequential', grid=(row, 0))
        self.sequentialCheckButton = CheckButton(
            peakSelectionFrame, selected=True, grid=(row, 1))

        row += 1

        Label(peakSelectionFrame,
              text='Do not assign diagonal peaks',
              grid=(row, 0))
        self.noDiagonalCheckButton = CheckButton(
            peakSelectionFrame, selected=True, grid=(row, 1))

        entries = ['Only assigned spin systems',
                   'All that have a score of at least: ',
                   'User Defined',
                   'Solution number:']
        tipTexts = ['Only assign resonances of spin systems that already have a sequential assignment for the assignment of peak dimensions. Spin system to residue assignment is not relevant in this case.',
                    'Assign all spin systems that have a score of at least a given percentage. 50% or lower is not possible, because than spin systems might have to be assigned to more than 1 residue, which is impossible.',
                    "As defined in the lower row of buttons in the 'results' tab.",
                    'One of the single solutions of the annealing.']
        self.spinSystemTypeSelect = RadioButtons(spinSystemSelectionFrame,
                                                 entries=entries, grid=(0, 0),
                                                 select_callback=None,
                                                 direction=VERTICAL,
                                                 gridSpan=(4, 1),
                                                 tipTexts=tipTexts)

        tipText = 'The minimal amount of colabelling the different nuclei should have in order to still give rise to a peak.'
        self.minScoreEntry = FloatEntry(spinSystemSelectionFrame,
                                        grid=(1, 1), width=7,
                                        text=str(self.minScore),
                                        returnCallback=self.changeMinScore,
                                        tipText=tipText)
        self.minScoreEntry.bind('<Leave>', self.changeMinScore, '+')

        self.solutionNumberEntry = IntEntry(spinSystemSelectionFrame,
                                            grid=(3, 1), width=7, text=1,
                                            returnCallback=self.solutionUpdate,
                                            tipText=tipText)
        self.solutionNumberEntry.bind('<Leave>', self.solutionUpdate, '+')

        #self.solutionPullDown = PulldownList(spinSystemSelectionFrame, None, grid=(3,1), sticky='w')

        entries = ['all spectra', 'only:']
        tipTexts = ['Assign peaks in all the spectra that where selected before the annealing ran.',
                    'Only assign peaks in one particular spectrum. You can of course repeat this multiple times for different spectra.']
        self.spectrumSelect = RadioButtons(spectrumSelectionFrame,
                                           entries=entries,
                                           grid=(0, 0),
                                           select_callback=None,
                                           direction=VERTICAL,
                                           gridSpan=(2, 1), tipTexts=tipTexts)

        self.spectraPullDown = PulldownList(spectrumSelectionFrame,
                                            self.changeSpectrum,
                                            grid=(1, 1), sticky='w')

        entries = ['skip this residue',
                   'de-assign old spin system from residue',
                   'assign, but never merge',
                   'warn to merge']
        tipTexts = ["Don't assign the new spin system to the residue. The residue is not skipped when the old spin system does not contain any resonances",
                    "De-assign old spin system from residue, unless the old spin system is a spin system without any resonances.",
                    "Don't merge any spin systems, merging can be performed later if nescesary in the Resonance --> SpinSystems window.",
                    "Ask to merge individually for each spin system, this might result in clicking on a lot of popups."]
        self.assignedResidueStrategySelect = RadioButtons(assignedResidueFrame,
                                                          entries=entries,
                                                          grid=(0, 0),
                                                          select_callback=None,
                                                          direction=VERTICAL,
                                                          gridSpan=(2, 1),
                                                          tipTexts=tipTexts)

        texts = ['Transfer Assignments']
        commands = [self.transferAssignments]
        self.transferButton = ButtonList(
            self.frame, commands=commands, texts=texts)
        self.transferButton.grid(row=5, column=0, sticky='nsew', columnspan=2)
Example #4
0
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