def launchApplication(filename=None):
global top
root = Tkinter.Tk()
root.withdraw()
top = ApplicationPopup(root)
project = None
if filename:
file = normalisePath(filename)
askdir = lambda title, prompt, initial_value, default_dir: askDir(
title,
prompt,
initial_value,
parent=top,
extra_dismiss_text='Skip',
default_dir=default_dir)
askfile = lambda title, prompt, initial_value: askFile(
title,
prompt,
initial_value,
parent=top,
extra_dismiss_text='Skip')
try:
project = loadProject(path=file,
showWarning=showWarning,
askDir=askdir,
askFile=askfile)
except ApiError, e:
showError('Reading project', e.error_msg)
def setPeakSize(self, *extra):
axisType = self.getAxisType()
try:
axisType.peakSize = self.peakSizeEntry.get()
except Implementation.ApiError, e:
showError('Setting peak size', e.error_msg, parent=self)
def setDecimal(self, *extra):
axisType = self.getAxisType()
try:
axisType.numDecimals = self.decimalEntry.get()
except Implementation.ApiError, e:
showError('Setting number of decimals', e.error_msg, parent=self)
def setRegion(self, *extra):
axisType = self.getAxisType()
try:
axisType.region = self.regionEntry.get()
except Implementation.ApiError, e:
showError('Setting region', e.error_msg, parent=self)
def setContourLevels(self):
spectrum = self.spectrum
if not spectrum or spectrum.isDeleted is True:
return
try:
analysisSpectrum = spectrum.analysisSpectrum
baseLevel = analysisSpectrum.autoBaseLevel
numberLevels = analysisSpectrum.autoNumLevels
levelChanger = analysisSpectrum.autoLevelChanger
changeMode = analysisSpectrum.autoLevelMode
posLevels = []
if self.which_buttons.isIndexSelected(0):
posLevels.extend(
calcContourLevels(baseLevel, numberLevels, levelChanger,
changeMode))
negLevels = []
if self.which_buttons.isIndexSelected(1):
if changeMode == 'add':
levelChanger = -levelChanger
negLevels.extend(
calcContourLevels(-baseLevel, numberLevels, levelChanger,
changeMode))
self.posLevelsEntry.set(posLevels)
self.negLevelsEntry.set(negLevels)
analysisSpectrum.posLevels = posLevels
analysisSpectrum.negLevels = negLevels
except Implementation.ApiError, e:
showError('Contour levels error', e.error_msg, parent=self)
def setFiles(self, fileNames):
if not self.fileList.multiSelect:
self.setFile(fileNames[0])
return
dirA = None
files = []
for fileName in fileNames:
dirB, file = splitPath(fileName)
if dirA is None:
dirA = dirB
elif dirA != dirB:
msg = 'Cannot select files from different directories'
showError('Set files failure', msg, parent=self)
return
if file in self.fileList.objectList:
files.append(file)
if dirA:
self.setDirectory(dirA)
self.fileList.selectObjects(files)
def apply(self):
columnInfoLong = []
for colIndex in range(0, self.columnLen):
columnInfoLongName = self.columnInfoWidgets[colIndex].getSelected()
if columnInfoLongName != 'None' and columnInfoLongName in columnInfoLong:
showError(
"Unique names",
"Each column needs a unique content - %s repeated twice." %
columnInfoLongName)
return False
columnInfoLong.append(columnInfoLongName)
if columnInfoLong.count('None') == len(columnInfoLong):
showError("Need identifiers",
"Need content for at least one column.")
return False
self.columnConvert = []
for i in range(self.columnLen):
for (longName, attrName, function) in self.columnContents:
if longName == columnInfoLong[i]:
if attrName:
self.columnConvert.append((attrName, function))
else:
self.columnConvert.append(None)
break
return True
def apply(self):
# protect against repeated double-clicking
if (self.project):
return False
path = self.file_select.getDirectory()
if not doesRepositoryContainProject(
path) and not getPossibleProjectFiles(path):
self.file_select.changeDir(path)
return False
self.disableOk()
self.project = None
if not path:
showError('No path', 'Need to select path', self)
self.enableOk()
return False
try:
self.project = self.load_project(path)
except ApiError, e:
showError('Loading project', e.error_msg, self)
self.enableOk()
return False
def apply(self):
shiftListLabel = self.shiftListSelect.getSelected()
shiftList = self.shiftListDict[shiftListLabel]
try:
chainLabel = self.chainListSelect.getSelected()
chain = self.chainDict[chainLabel]
except:
showError(
"No chains",
"No chains were present or selected. Try running linkResonances first."
)
return False
fileName = self.fileButton.__getitem__('text')
if fileName == self.defaultText:
return False
fileCreated = writeBmrbChemShiftDeposition(self.guiParent, chain,
shiftList, fileName)
if fileCreated:
showInfo("Success",
"Succesfully wrote chemical shift deposition file")
else:
showError("Not written",
"Error writing file %s. File not written" % fileName)
return False
return True
def apply(self, *extra):
params = {}
params['scale'] = self.scale_entry.get()
params['buffer'] = self.buffer_entry.get()
params['thickness'] = self.thickness_entry.get()
params['drop'] = self.drop_entry.get()
params['volumeMethod'] = self.method_menu.getText()
n = self.adjacent_buttons.getIndex()
if (n == 0):
nonadjacent = False
else:
nonadjacent = True
params['nonadjacent'] = nonadjacent
n = self.extrema_buttons.getIndex()
if (n == 0):
have_high = True
have_low = True
elif (n == 1):
have_high = True
have_low = False
elif (n == 2):
have_high = False
have_low = True
params['haveHigh'] = have_high
params['haveLow'] = have_low
project = self.project
try:
PeakFindParams.setPeakFindParams(project, params)
except Implementation.ApiError, e:
showError('Parameter error', e.error_msg, parent=self)
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 apply(self):
if not 0:
showError("No root spectrum","Can't continue: need a root spectrum...")
return False
return True
def launchApplication(projectDir=None):
global top
root = Tkinter.Tk()
root.withdraw()
top = EntryCompletionGui(root)
project = None
if projectDir:
projectDir = normalisePath(projectDir)
askdir = lambda title, prompt, initial_value, default_dir: askDir(title, prompt,
initial_value, parent=top, extra_dismiss_text='Skip')
askfile = lambda title, prompt, initial_value: askFile(title, prompt,
initial_value, parent=top, extra_dismiss_text='Skip')
try:
project = loadProject(path=projectDir, showWarning=showWarning, askDir=askdir, askFile=askfile)
userRepos = project.findFirstRepository(name='userData')
chemCompPackLoc = project.findFirstPackageLocator(targetName='ccp.molecule.ChemComp')
if userRepos not in chemCompPackLoc.repositories:
chemCompPackLoc.addRepository(userRepos)
except ApiError, e:
showError('Reading project', e.error_msg, parent=top)
def printStructure(self):
w = self.winfo_width()
h = self.winfo_height()
popup = PrintPopup(self,
width=w,
height=h,
title='Print Structure',
modal=True,
project=self.project,
getOption=self.getPrintOption,
setOption=self.setPrintOption)
outputHandler = popup.outputHandler
popup.destroy()
if (not outputHandler):
return
(x0, y0, x1, y1) = self.handler.getRegion()
try:
printHandler = PrintHandler.PrintHandler(outputHandler,
xRegion=(x0, x1),
yRegion=(y0, y1))
self.drawStructure(handler=printHandler)
file_name = outputHandler.file_name
printHandler.close(
) # clears file_name, hence first need to save, as above
showInfo('Wrote file',
'Successfully wrote file "%s"' % file_name,
parent=self)
except IOError, e:
showError('IO Error', str(e), parent=self)
def readGLE(self, gleFile):
if not os.path.isfile(gleFile):
msg = 'No scorogram Res_%d.pgm\nin directory %s.' % (
resNum, self.dangleDir)
showError('File Reading Error', msg, parent=self)
return None
fopen = open(gleFile, 'r')
lines = fopen.readlines()
dims = lines[2].split()
lines = lines[4:]
fopen.close()
# only read the top left corner of a 10X10 square bin
# all readings in the same bin are identical
binSize = 10
matrix = []
for j in range(36):
x = j * binSize * binSize * 36
for i in range(36):
y = i * binSize
v = int(lines[x + y].strip())
matrix.append(v)
maxVal = float(max(matrix))
for i in range(len(matrix)):
matrix[i] = matrix[i] / maxVal
return matrix
def setSelectedFile(self, *event):
file = self.file_entry.getEntry()
try:
self.fileList.selectObject(file)
except:
showError('Some err', 'some err')
def save(self):
projName = self.proj_name_entry.get()
directory = self.proj_dir_select.getDirectory()
directory = joinPath(directory, projName)
if self.isProjectDirectory(directory):
if not showOkCancel('Overwrite directory',
'Overwrite existing project directory?',
parent=self):
return
self.updateInfo()
self.did_save = False
changeDataLocations = self.dataCheckButton.isSelected()
done = False
try:
done = Io.saveProject(self.project,
newPath=directory,
newProjectName=projName,
createFallback=True,
showYesNo=showYesNo,
changeDataLocations=changeDataLocations,
showWarning=showWarning)
if done:
showInfo('Project saved', 'Project saved successfully')
self.did_save = True
if self.callback:
self.callback(self.project)
elif self.modal:
return # give another chance
except Implementation.ApiError, e:
showError('Save project', e.error_msg)
def entryDir(self, *event):
dirName = self.directory_entry.getEntry()
try:
self.changeDir(dirName)
except:
showError('Not a directory', '"' + dirName + '" is not a directory.')
def changeMolName(self, molName):
newMolName = askString('Enter molecule name', 'New name for molecule',
molName, self)
if newMolName and newMolName != molName:
if newMolName in self.molNames:
showError("Molecule name present",
"This molecule name is already present!")
elif self.project.findFirstMolecule(name=newMolName):
# TODO TODO: allow user to select an existing molecule?!?!
showError(
"Molecule exists",
"A molecule with this name already exists in the data model."
)
else:
moleculeInfo = self.localCreateMoleculeDict[molName]
self.localCreateMoleculeDict[newMolName] = moleculeInfo
del self.localCreateMoleculeDict[molName]
#
# Clean out text...
#
for molName in self.molNames:
self.warningCode[molName].set("")
self.resetInfo()
self.setupWidgets()
def doExport(self):
if self.exportFileName:
chain = self.chainDict[self.chainSelect.getSelected()]
returnValue = self.autoAssignFormat.writeProject(
self.exportFileName, chain=chain, setTag=self.dateTimeFlag)
if not returnValue:
showError(
"No export file written",
"There were problems while exporting the %s project file."
% self.format)
else:
showInfo("File written", "File written successfully")
cdtsTag = "%s-%s" % (self.chainSelect.getSelected(),
self.dateTimeFlag)
if not cdtsTag in self.chainDateTimeSelect.entries:
if "<None>" in self.chainDateTimeSelect.entries:
self.chainDateTimeSelect.entries.pop(
self.chainDateTimeSelect.entries.index("<None>"))
self.chainDateTimeSelect.replace(
[cdtsTag] + self.chainDateTimeSelect.entries)
self.chainDateTimeStampDict[cdtsTag] = chain
else:
showError(
"No export file defined",
"Please define a name for the %s project file to export to." %
self.format)
def launchApplication(projectDir=None):
global top
root = Tkinter.Tk()
root.withdraw(
) # get rid of the root window Tkinter would otherwise put up
top = ApplicationPopup(
root) # creates our controlled window (this class in fact)
project = None
if projectDir:
projectDir = normalisePath(projectDir)
askdir = lambda title, prompt, initial_value, default_dir: askDir(
title,
prompt,
initial_value,
parent=top,
extra_dismiss_text='Skip')
askfile = lambda title, prompt, initial_value: askFile(
title,
prompt,
initial_value,
parent=top,
extra_dismiss_text='Skip')
try:
project = loadProject(path=projectDir,
showWarning=showWarning,
askDir=askdir,
askFile=askfile)
except ApiError, e:
showError('Reading project', e.error_msg, parent=top)
def apply(self):
try:
self.outputHandler = self.printFrame.getOutputHandler(
self.width, self.height)
except IOError, e:
showError('IO Error', str(e), parent=self)
return False
def unsetLink(self, role):
if (self.editMode):
try:
func = getattr(self.object,
'set%s' % upperFirst(role.baseName))
func(None)
except Implementation.ApiError, e:
showError('Unsetting link', e.error_msg, parent=self)
def pickAdaptive(self):
if self.spectrum:
segLevel, threshold, maxPeaks = self.getEntryData()
try:
findAuremolPeaksAdaptive(spectrum=self.spectrum, mode=self.peakMode,
number=maxPeaks, seglevel=segLevel)
except Exception, e:
showError('pickAdaptive', str(e), parent=self)
def fetchValues(self):
directory = self.directoryEntry.get()
template = self.templateEntry.get()
try:
values = getSampledValues(directory, template)
except ApiError, e:
showError('Fetch Values', e.error_msg, parent=self)
return
def pickThreshold(self):
if self.spectrum:
segLevel, threshold, maxPeaks = self.getEntryData()
try:
findAuremolPeaksThreshold(spectrum=self.spectrum, mode=self.peakMode,
useAutoThreshold=0, threshold=threshold, seglevel=segLevel)
except Exception, e:
showError('pickThreshold', str(e), parent=self)
def apply(self):
selected = self.table.currentObject
if (not selected):
showError('No selection', "No object selected", parent=self)
return False
self.selected = selected
return True
def apply(self):
self.result = ''
file = self.file_select.getFile()
if (self.selected_file_must_exist and not os.path.exists(file)):
showError('No file', 'File does not exist', self)
return False
self.result = file
return True
def updateParams(self):
params = self.params
if self.pseudoButton.get() == self.pseudoEntries[0]:
npts = self.nptsEntry.get()
params.npts[self.dim] = npts
values = self.valueEntry.get()
try:
params.setSampledDim(self.dim, values)
except ApiError, e:
showError('Set Sampled Dim', e.error_msg, parent=self)
return
def saveFile(self):
if not self.project:
return False
try:
saveProject(self.project, createFallback=True)
print 'successfully saved project'
return True
except IOError, e:
showError('Saving file', str(e), parent=self)
return False
