def __init__(self,
parent,
serverLocation=UPDATE_SERVER_LOCATION,
serverDirectory=UPDATE_DIRECTORY,
dataFile=UPDATE_DATABASE_FILE,
exitOnClose=False,
helpUrl=None):
self.exitOnClose = exitOnClose
self.helpUrl = helpUrl
UpdateAgent.__init__(self,
serverLocation,
serverDirectory,
dataFile,
isStandAlone=exitOnClose)
self.fileUpdate = None
if exitOnClose:
quitFunc = sys.exit
else:
quitFunc = None
BasePopup.__init__(self,
parent=parent,
title='CcpNmr Software Updates',
quitFunc=quitFunc)
def startBasePopup(self, parent, title, modal, True):
BasePopup.__init__(self,
parent=parent,
title=title,
modal=modal,
transient=True)
def __init__(self, parent, project):
self.project = project
self.guiParent = parent
self.selectedFormats = []
self.defaultText = 'Select file'
self.chainDict = {}
self.chainList = []
self.shiftListDict = {}
self.shiftLists = []
for shiftList in self.project.currentNmrProject.findAllMeasurementLists(
className='ShiftList'):
if shiftList.measurements != ():
label = str(shiftList.serial) + ':' + str(shiftList.name)
self.shiftListDict[label] = shiftList
self.shiftLists.append(label)
if not self.shiftLists:
showError('Error', 'No shift lists available!')
return
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Write BMRB chemical shift deposition file',
modal=False,
transient=True)
def __init__(self, parent, project, molName, createMoleculeDict,
localCreateMoleculeDict):
self.molName = molName
self.project = project
self.createMoleculeDict = createMoleculeDict
self.localCreateMoleculeDict = localCreateMoleculeDict
self.hasChanged = False
self.molecule = self.localCreateMoleculeDict[self.molName][0]
self.deleteText = 'Delete'
self.okText = 'OK'
self.startText = 'Insert at start'
self.endText = 'Append to end'
self.newMoleculeList = []
for molName in self.localCreateMoleculeDict.keys():
if molName != self.molName and not self.localCreateMoleculeDict[
molName][0]:
self.newMoleculeList.append(molName)
# modal = true means that it won't continue unless this one returns value
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Set chemComps for sequence',
modal=True,
transient=True)
def __init__(self, parent, project):
self.project = project
self.guiParent = parent
self.autoAssignFormat = AutoAssignFormat(project, guiParent=parent)
self.format = 'autoAssign'
self.chainStampSep = '-'
self.dateTimeFlag = time.strftime("%Y%m%d.%H:%M")
self.getPreviousDateTimeStamps()
self.getChainsAndChainStamps()
self.importFileName = self.exportFileName = None
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'AutoAssign export/import cycle.',
modal=True,
transient=True)
def __init__(self,
parent,
headings,
entries,
title='',
file='',
*args,
**kw):
headings = [heading.replace('\n', ' ') for heading in headings]
if (headings[0].lower() == 'number'):
self.addNumber = False
else:
self.addNumber = True
headings.insert(0, 'Number')
if (not title):
title = 'Export data'
self.exportSelection = parent.tableExportSelection
self.headings = headings
self.entries = entries
self.file = file
kw['title'] = title
kw['transient'] = True
kw['modal'] = True
BasePopup.__init__(self, parent=parent, *args, **kw)
def __init__(self,
parent,
message,
nmrRes,
optionList,
title,
urlFile=None):
# Constructor doesn't do much except call body
# The parent is self.parent (parent of the popup)
self.singleResonanceStatus = None
self.message = message
self.optionList = optionList
self.nmrRes = nmrRes
if urlFile:
self.help_url = joinPath(getHelpUrlDir(), urlFile + '.html')
else:
self.help_url = None
# modal = true means that it won't continue unless this one returns value
BasePopup.__init__(self,
parent=parent,
title=title,
modal=True,
transient=True)
def __init__(self, guiParent, run, protocolInterface, *args, **kw):
self.run = run
self.protocolInterface = protocolInterface
self.widgetDict = {} # maps interfaceParameter --> widget
BasePopup.__init__(self, guiParent, *args, **kw)
def __init__(self, parent, peakList, *args, **kw):
self.peakList = peakList
self.colours = ['red', 'green']
self.dataSets = []
BasePopup.__init__(self, parent=parent, title='Test Popup', **kw)
def __init__(self, parent, project, autoAssignProjectFile):
self.project = project
self.guiParent = parent
self.autoAssignProjectFile = autoAssignProjectFile
self.validSelection = False
self.peakLists = []
for nmrExp in self.project.currentNmrProject.sortedExperiments():
for ds in nmrExp.sortedDataSources():
for pl in ds.sortedPeakLists():
self.peakLists.append(pl)
if not self.peakLists:
raise ('No peak lists available!')
(self.peakNameList,
self.peakNameDict) = createSelection(self.peakLists)
self.peakNameList.insert(0, 'None')
self.peakNameDict['None'] = None
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Write AutoAssign project file',
modal=True,
transient=True)
def __init__(self,
parent,
resonanceList,
resonanceDict,
code3Letter,
resName,
helpText,
multi,
title='Select resonances'):
# Constructor doesn't do much except call body
# The parent is self.parent (parent of the popup)
self.selectedResonances = None
self.resonanceList = resonanceList
self.resonanceDict = resonanceDict
self.code3Letter = code3Letter
self.resName = resName
self.helpText = helpText
if multi:
self.selectmode = Tkinter.MULTIPLE
else:
self.selectmode = Tkinter.SINGLE
# modal = true means that it won't continue unless this one returns value
BasePopup.__init__(self,
parent=parent,
title=title,
modal=True,
transient=True)
def __init__(self,
parent,
file_types=None,
directory=None,
multiSelect=False,
title='Browse files',
prompt=None,
show_file=True,
file='',
dismiss_text='Close',
extra_dismiss_text='',
selected_file_must_exist=False,
default_dir=None,
*args,
**kw):
self.file_types = file_types
self.directory = directory
self.prompt = prompt
self.show_file = show_file
self.dismiss_text = dismiss_text
self.extra_dismiss_text = extra_dismiss_text
self.initial_file = file
self.selected_file_must_exist = selected_file_must_exist
self.default_dir = default_dir
self.multiSelect = multiSelect
kw['title'] = title
kw['transient'] = True
kw['modal'] = True
BasePopup.__init__(self, parent=parent, *args, **kw)
def __init__(self, parent, title='Text output'):
BasePopup.__init__(self,
parent=parent,
title=title,
modal=False,
transient=False)
def __init__(self, parent, project):
self.project = project
self.selectedFormats = []
self.defaultText = 'Select file'
self.formats = allFormatsDict.keys()
self.formats.sort()
BasePopup.__init__(self, parent=parent, title= "Project '%s': " % project.name + 'Write ccpNmr mapping file', modal=False, transient=True)
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 __init__(self, parent, project):
#
# Info for writing file...
#
self.groupText = {}
#
# Set up molSystem information
#
self.project = project
self.molSysList = list(project.sortedMolSystems())
self.molSystems = None
self.molSysLabelList = []
self.molSysLabelDict = {}
self.molSysRelationDict = {}
molSysLabel = 'All molSystems'
if self.setChainLabels(molSysLabel, self.molSysList):
self.molSysLabelList.append(molSysLabel)
self.molSysLabelDict[molSysLabel] = self.molSysList
for molSys in self.molSysList:
molSysLabel = '%s' % molSys.code
if self.setChainLabels(molSysLabel, [molSys]):
self.molSysLabelList.append(molSysLabel)
self.molSysLabelDict[molSysLabel] = [molSys]
if not self.molSysLabelList:
showWarning('Warning',
'No chemical shift lists available! Exiting...')
return
#
# Some initializing...
#
self.chains = None
self.shiftList = None
self.shiftListLabel = None
self.results = None
# modal = true means that it won't continue unless this one returns value
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Group chemical shift values',
modal=False,
transient=True)
def __init__(self, parent, project):
self.project = project
self.peakLists = []
BasePopup.__init__(self,
parent=parent,
title="Project '%s': " % project.name +
'Create shift list from peak lists',
modal=False,
transient=True)
def __init__(self, parent, text = '', progress = 0, total = 100, title=None,
width = 200, height = 15, transient = True, *args, **kw):
self.progress = float(progress)
self.cWidth = width
self.cHeight = height
self.total = float(total) or 1.0
self.text = text
BasePopup.__init__(self, parent=parent, title=title or 'Progress Bar',
transient=transient, *args, **kw)
def __init__(self, parent, objects, key=None, labels=None, objectName=None,
refClassName=None, **kw):
self.parent = parent
self.resetObjectType(objects, key, labels, objectName, refClassName)
self.doRegisters()
BasePopup.__init__(self, parent, title= "Object Selection",
borderwidth=5, **kw)
def __init__(self,
parent,
file=None,
files=None,
component=None,
selectionText='Select',
title=None,
format=None,
multiSelect=False):
#
# Also get format (from self?)
#
self.file = None # Use this to return single file info, for backward compat
if not multiSelect and file:
self.files = [file]
elif files:
self.files = files
else:
self.files = []
if self.files:
for i in range(len(self.files)):
self.files[i] = normalisePath(self.files[i])
self.component = component
self.fileSelected = False
self.selectionText = selectionText
self.format = format
self.multiSelect = multiSelect
if not title:
title = 'Select %s file' % component
BasePopup.__init__(self,
parent=parent,
title=title,
modal=True,
transient=True)
def __init__(self,
parent,
resonanceNameList,
resonanceLineDict,
ccpCode,
title='Group resonances'):
self.resNameGroups = None
self.resonanceNameList = resonanceNameList
self.resonanceLineDict = resonanceLineDict
self.checkButtons = []
self.ccpCode = ccpCode
BasePopup.__init__(self,
parent=parent,
title=title,
modal=True,
transient=True)
def __init__(self,
parent,
entries,
label='',
message='',
select_text='Select',
*args,
**kw):
self.entries = entries
self.label = label
self.message = message
self.select_text = select_text
self.item = None
kw['title'] = 'Select item'
kw['transient'] = True
kw['modal'] = True
BasePopup.__init__(self, parent=parent, *args, **kw)
def __init__(self,
parent,
serverLocation=UPDATE_SERVER_LOCATION,
serverDirectory=UPDATE_DIRECTORY,
dataFile=UPDATE_DATABASE_FILE):
UpdateAgent.__init__(self,
serverLocation,
serverDirectory,
dataFile,
admin=1)
self.fileTypes = [
FileType('Python', ['*.py']),
FileType('C', ['*.c']),
FileType('All', ['*'])
]
self.fileUpdate = None
BasePopup.__init__(self,
parent=parent,
title='CcpNmr Update Administrator',
quitFunc=self.quit)
def __init__(self, parent, acqProcPars, format):
self.rawData = acqProcPars.experiment.rawData
self.freqData = acqProcPars.freqDataDims[format][0].dataSource
self.expDimRefs = acqProcPars.expDimRefs
self.format = format
self.updateAcqProcPars = acqProcPars.parameterUpdate
self.updateAcqProcParsWidget = acqProcPars.updateFromWidget
self.getDataDimRefs = acqProcPars.getDataDimRefs
self.formatObjectDict = parent.formatObjectDict
self.guiParent = parent
self.project = self.rawData.root
#
# Dict for setup
#
# TODO: really need two datasources for nmrPipe... one fid, one processed!?!?
#
for writeFormatName in acqProcPars.writeFormats:
setattr(self,writeFormatName,writeFormatName)
value = 0
self.fileSetup = {}
self.writeSetup = {}
#
# nmrPipe definitions
#
self.fileSetup[self.nmrPipe] = [
['Conversion script file\n (outputs to...)',
lambda: self.rawData.findFirstApplicationData(application = self.nmrPipe,keyword = 'conversion script'),
lambda x = value: self.setApplData(self.rawData,self.nmrPipe,'conversion script',x),
['autoconv.com'],
'conversion script'],
[' nmrPipe FIDs\n(inputs to...)',
lambda: self.rawData.findFirstApplicationData(application = self.nmrPipe,keyword = 'FID'),
lambda x = value: self.setApplData(self.rawData,self.nmrPipe,'FID',x),
['auto.fid','auto%03d.fid'],
'FID'],
['Processing script file\n (outputs to...)',
lambda: self.freqData.findFirstApplicationData(application = self.nmrPipe,keyword = 'processing script'),
lambda x = value: self.setApplData(self.freqData,self.nmrPipe,'processing script',x),
['autoproc.com'],
'processing script'],
['Processed data',
lambda: self.getDataSourceFileName(self.freqData),
lambda x = value: self.doDataStoreFileName(self.freqData,x),
['auto.ft','auto%03d.ft'],
'processed data']
]
# TODO: can add execute nmrPipe program buttons... see dataNavigator
self.writeSetup[self.nmrPipe] = [
['Write conversion file',
lambda : self.writeFile(self.nmrPipe,['conversion'])],
['Write processing file',
lambda : self.writeFile(self.nmrPipe,['processing'])],
['Write all',
lambda : self.writeFile(self.nmrPipe,['conversion','processing'])]
]
#
# azara definitions
#
self.fileSetup[self.azara] = [
['Processing parameters file\n (inputs to...)',
lambda: self.rawData.findFirstApplicationData(application = self.azara,keyword = 'processing parameters'),
lambda x = value: self.setApplData(self.rawData,self.azara,'processing parameters',x),
['autoproc.par'],
'processing parameters'],
['Processing script file\n (outputs to both...)',
lambda: self.freqData.findFirstApplicationData(application = self.azara,keyword = 'processing script'),
lambda x = value: self.setApplData(self.freqData,self.azara,'processing script',x),
['autoproc.scr'],
'processing script'],
['Processed data',
lambda: self.getDataSourceFileName(self.freqData),
lambda x = value: self.doDataStoreFileName(self.freqData,x),
['spectrum.ft'],
'spectrum'],
['Processed data parameter file\n',
lambda: self.freqData.findFirstApplicationData(application = self.azara,keyword = 'spectrum parameters'),
lambda x = value: self.setApplData(self.freqData,self.azara,'spectrum parameters',x),
['spectrum.par'],
'spectrum parameters']
]
# TODO: can add execute process program buttons... see dataNavigator
self.writeSetup[self.azara] = [
['Write processing parameters file',
lambda : self.writeFile(self.azara,['processingPars'])],
['Write processing script file',
lambda : self.writeFile(self.azara,['processingScript'])],
['Write all',
lambda : self.writeFile(self.azara,['processingPars','processingScript'])]
]
BasePopup.__init__(self,parent = parent, title = "Project '%s': " % self.project.name + '%s processing write' % format, modal = False, transient=False)
def __init__(self, parent, format, dim, getValue):
#
# General setup
#
self.maxArgs = 4
self.nmrPipe = 'nmrPipe'
self.azara = 'azara'
self.format = format
self.freqDataDim = parent.freqDataDims[format][dim]
self.expDimRef = parent.expDimRefs[dim]
#
# Window function settings (different per program)
#
self.windowFunctions = {}
specWidth = self.freqDataDim.spectralWidthOrig
# TODO: these for azara still have to change a bit...
self.windowFunctions[self.azara] = [
['sine', 'sinebell', [['Angle (deg)', 0, 'deg']]],
['sine^2', 'sinebell2', [['Angle (deg)', 0, 'deg']]],
['exponential (fixed)', 'decay', [['End value', 0.5, 'end']]],
[
'exponential', 'decay_sw',
[['Line broadening (Hz)', 10, 'lb'],
['Spectral width (Hz)', specWidth, 'sw']]
],
[
'gaussian (fixed)', 'gaussian',
[['Total points fraction for max', 0.25, 'frac'],
['End value', 1, 'end']]
],
[
'gaussian', 'gaussian_sw',
[['Line broadening (Hz)', 10, 'lb'],
['Sharpening factor', 0.7, 'shrp'],
['Spectral width (Hz)', specWidth, 'sw']]
],
[
'inverse cosine', 'inv_cosine',
[['Frequency (Hz)', 0, 'freq'],
['Spectral width (Hz)', specWidth, 'sw']]
]
]
self.windowFunctions[self.nmrPipe] = [
[
'sine', 'SP',
[['Start sine at (pi)', 0, 'off'],
['End sine at (pi)', 1, 'end'], ['Sine to power', 1, 'pow']]
], ['exponential', 'EM', [['Line broadening (Hz)', 10, 'lb']]],
[
'lorentz-gauss', 'GM',
[['Inverse exp width (Hz)', 0, 'g1'],
['Gaussian width (Hz)', 0, 'g2'], ['Center (0-1)', 0, 'g3']]
],
[
'gaussian', 'GMB',
[['Exponential term', 0, 'lb'], ['Gaussian term', 0, 'gb']]
],
[
'trapezoid', 'TM',
[['Ramp length left', 0, 't1'], ['Ramp length right', 0, 't2']]
],
[
'triangle', 'TRI',
[['Point loc of apex', 0,
'loc'], ['Left edge height', 0, 'lHi'],
['Right edge height', 0, 'rHi']]
]
]
#
# Make list of names for pulldown menu
#
self.windowFuncList = []
for (winFunc, winFuncAppl,
winFuncArgs) in self.windowFunctions[format]:
self.windowFuncList.append(winFunc)
#
# Get the right window function from appldata (if there)
#
self.windowFunctionKeyword = 'windowFunction'
self.winFuncIndex = self.getWindowFunctionIndex()
#
# Set defaults depending on nucleus type if no window function set
#
if self.winFuncIndex == -1:
if format == self.nmrPipe:
self.winFuncIndex = 0
if self.expDimRef.isotopeCodes[0] == '1H':
# use SP '-off 0.3333 -pow 2.0'
self.windowFunctions[self.nmrPipe][
self.winFuncIndex][2][0][1] = 0.3333
self.windowFunctions[self.nmrPipe][
self.winFuncIndex][2][2][1] = 2.0
else:
# for non-H, use SP '-off 0.5 -pow 2.0'
self.windowFunctions[self.nmrPipe][
self.winFuncIndex][2][0][1] = 0.5
self.windowFunctions[self.nmrPipe][
self.winFuncIndex][2][2][1] = 2.0
elif format == self.azara:
self.winFuncIndex = 1
if self.expDimRef.isotopeCodes[0] == '1H':
# use sinebell2 60
self.windowFunctions[self.azara][
self.winFuncIndex][2][0][1] = 60
else:
# for non-H, use sinebell2 90
self.windowFunctions[self.azara][
self.winFuncIndex][2][0][1] = 90
# Get actual values for arguments from appldata if they exists!
self.updateWindowFunctions()
# Also using this to return the current window function 'string value'
if not getValue:
# modal = true means that it won't continue unless this one returns value
BasePopup.__init__(
self,
parent=parent,
title='Select window function',
modal=False,
transient=True,
)
def __init__(self, parent, format, component = None, threading = True):
self.project = parent.project
self.guiParent = parent
self.format = format
self.formatObjectDict = parent.formatObjectDict
self.component = component
self.threading = threading
self.setImportExportFlag()
self.files = {}
self.function = {}
self.components = []
self.widgetSetup = {}
self.toggleInfoIndex = {}
#
# Do the import of the relevant format class and the IOkeywords dictionary
#
self.formatLabel = allFormatsDict[self.format]
self.formatModule = __import__('ccpnmr.format.converters.%sFormat' % self.formatLabel,{},{},['%sFormat' % self.formatLabel,'IOkeywords'])
#
# Definitions for import/export windows, files and functions (come from IoDefinitions)
#
self.exportFunc = {}
self.importFunc = {}
self.IOkeywords = {}
for (component,readFunc,writeFunc,fileDict,importSetup,exportSetup,exportFunc,importFunc) in IoSetupList:
#
# If component passed in, only do that one.
#
if self.component and self.component != component:
continue
#
# Set import or export info
#
self.toggleInfoIndex[component] = 0
if self.importExportFlag == 'import':
self.widgetSetup[component] = importSetup[:]
self.function[component] = readFunc
componentAction = 'read'
#
# For multiple file import, don't bother with project files
#
if not self.component and component == 'project':
continue
else:
self.widgetSetup[component] = exportSetup[:]
self.function[component] = writeFunc
componentAction = 'write'
#
# Set some variables and functions...
#
componentKeyWord = writeFunc[5:] # This is also OK for import...
self.exportFunc[component] = exportFunc
self.importFunc[component] = importFunc
#
# Now set format specific information
#
if fileDict.has_key(format):
(fileName,importFlag,exportFlag,addImport,addExport) = fileDict[format]
if self.importExportFlag == 'import':
validFlag = importFlag
addInfo = addImport
else:
validFlag = exportFlag
addInfo = addExport
if validFlag:
self.files[component] = fileName
self.components.append(component)
self.IOkeywords[component] = {}
#
# Normal import/export flag
#
if validFlag == 1:
#
# Set fileName(s) info if available (is not in IOkeywords from Format files!!)
#
for widgetInfo in self.widgetSetup[component]:
if widgetInfo[1] == 'fileName':
self.IOkeywords[component]['fileName'] = (None,True,'The file name to be %sed.' % self.importExportFlag)
break
elif widgetInfo[1] == 'fileNames':
self.IOkeywords[component]['fileNames'] = (None,True,'The file names to be %sed.' % self.importExportFlag)
break
#
# Get IOkeywords info from Format files...
#
if self.formatModule.IOkeywords.has_key(self.function[component]):
self.IOkeywords[component].update(self.formatModule.IOkeywords[self.function[component]])
for superClass in self.formatModule.IOkeywords['subClasses']:
if componentKeyWord in self.formatModule.IOkeywords['subClasses'][superClass]:
superClassFunc = componentAction + superClass
self.IOkeywords[component].update(self.formatModule.IOkeywords[superClassFunc])
else:
print " Warning: no IOkeywords information for %s!" % self.function[component]
self.IOkeywords[component] = {}
#
# Also add to self.toggleInfoIndex[component] if required keywords...
#
for IoKeyword in self.IOkeywords[component].keys():
if self.IOkeywords[component][IoKeyword][1]:
for widgetInfo in self.widgetSetup[component]:
if widgetInfo[1] == IoKeyword:
self.toggleInfoIndex[component] += 1
#
# Display text for import that refers to other mechanism...
#
else:
self.IOkeywords[component]['showText'] = "Please use %s to %s %s." % (validFlag,self.importExportFlag,component)
addInfo = None
if addInfo:
#
# Now add format specific widget info and make sure it's all valid...
#
for addItem in addInfo:
inputKeyWord = addItem[1]
if inputKeyWord not in self.IOkeywords[component]:
print " Error: invalid %s keyword '%s' for %s!" % (self.importExportFlag,inputKeyWord,component)
continue
# Check whether keyword already exists! If so, replace...
for widgetIndex in range(0,len(self.widgetSetup[component])):
widgetInfo = self.widgetSetup[component][widgetIndex]
if inputKeyWord == widgetInfo[1]:
self.widgetSetup[component][widgetIndex] = addItem
inputKeyWord = None
# If the keyword wasn't found, then append to the full list.
if inputKeyWord:
self.widgetSetup[component].insert(self.toggleInfoIndex[component],addItem)
self.toggleInfoIndex[component] += 1
# TODO: use labels here instead of name
BasePopup.__init__(self,parent = parent, title = self.titleText, modal = False, transient=False)