def importFastaSeq(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('Fasta', ['*.fsa']),
FileType('All', ['*']) ]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import Fasta sequence file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
name = os.path.split(fileName)[1]
if '.' in name:
name = name.split('.')[0]
fastaObj = FastaFormat(self.project, self, verbose=True)
fastaObj.readSequence(fileName, minimalPrompts=True)
self.eciFrame.updateAll()
return fastaObj
def importPdb(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('PDB', ['*.pdb']),
FileType('PDB Entry', ['*.ent']),
FileType('All', ['*']) ]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import PDB 3.20 file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
name = os.path.split(fileName)[1]
if '.' in name:
name = name.split('.')[0]
pdbObj = ReadPdb(fileName, self.project, 'PDB_'+ name, self)
self.eciFrame.updateAll()
return pdbObj
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()
def importPdbCoords(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('PDB', ['*.pdb']),
FileType('PDB Entry', ['*.ent']),
FileType('All', ['*']) ]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import PDB coordinates file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
name = os.path.split(fileName)[1]
if '.' in name:
name = name.split('.')[0]
pdbObj = PseudoPdbFormat(self.project, self, verbose=True)
pdbObj.readCoordinates(fileName, minimalPrompts=True)
self.eciFrame.updateAll()
return pdbObj
def importNmrStar31(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('STAR', ['*.str']),
FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import NMR-STAR 3.1 file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
nmrStarObj = NmrStarFormat(self.project, self, verbose=True)
nmrStarObj.readProject(fileName, minimalPrompts=True, version='3.1')
self.eciFrame.updateAll()
return nmrStarObj
def import_project(self):
# FIXME JMCI
# need to preserve the current status. Take default from the
# Wms layer
rootDir = self.basePopup.repList.current_import_dir
fileSelectPopup = FileSelectPopup(self, None, rootDir)
new_project_dir = fileSelectPopup.getDirectory()
self.basePopup.repList.current_import_dir = new_project_dir
print 'in import project with directory', new_project_dir
idx = new_project_dir.rfind('/')
new_project_name = new_project_dir[idx + 1:]
print 'in import project with project', new_project_name
# FIXME
# need to set the project version number somewhere. For now set to none
# and this gets picked up and set to a default 1.1 later
self.repository.import_project(new_project_name, None, new_project_dir)
self.drawFrame()
def 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()
def exportText(self, *event):
from memops.gui.FileSelect import FileType
from memops.gui.FileSelectPopup import FileSelectPopup
if self.textOut:
fileTypes = [
FileType('Text', ['*.txt']),
FileType('CSV', ['*.csv']),
FileType('All', ['*'])
]
fileSelectPopup = FileSelectPopup(self,
file_types=fileTypes,
title='Save table as text',
dismiss_text='Cancel',
selected_file_must_exist=False)
fileName = fileSelectPopup.getFile()
if fileName:
file = open(fileName, 'w')
if fileName.endswith('.csv'):
for textRow in self.textMatrix:
file.write(','.join(textRow) + '\n')
else:
file.write(self.textOut)
def selectFile(self):
fileSelectPopup = FileSelectPopup(self, title = 'Choose file', dismiss_text = 'Cancel',
selected_file_must_exist = True)
fileName = fileSelectPopup.getFile()
self.textWindow.setText('File Selected: %s\n' % fileName)
def selectDir(self):
popup = FileSelectPopup(self, show_file=False)
dir = popup.getDirectory()
popup.destroy()
if (dir):
self.dir_entry.set(dir)
self.setDir()
def chooseExecutable(self):
fileTypes = [FileType('Table', ['*.exe']), FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(self, file_types = fileTypes,
title = 'Choose 2d BACUS executable', dismiss_text = 'Cancel',
selected_file_must_exist = False)
fileName = fileSelectPopup.getFile()
if fileName:
self.executableEntry.set(fileName)
def getDirectory(self, widget, obj, attrName):
"""Is called by updateGeneral. No widget because table placement is irrelevent and setting process not interruptable"""
value = getattr(obj, attrName)
if not os.path.exists(value): value = None
popup = FileSelectPopup(self, directory=value, show_file=False)
value = popup.getDirectory()
if value:
setattr(obj, attrName, value)
def selectWorkingDir(self):
popup = FileSelectPopup(self, show_file=False)
directory = popup.getDirectory()
if directory:
self.workingDirEntry.set(directory)
popup.destroy()
self.updateAfter()
def selectTempDir(self):
popup = FileSelectPopup(self, show_file=False)
directory = popup.getDirectory()
if directory:
self.tempDirEntry.set( directory )
popup.destroy()
self.updateEntryParams()
def selectExecutable(self):
""" Choose the MODULE executable appropriate for your system. """
popup = FileSelectPopup(self, show_file=True)
executable = popup.getFile()
if executable:
self.moduleExeEntry.set(executable)
popup.destroy()
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()
def chooseDirectory(self):
directory = os.path.dirname(self.fileName)
if not directory:
directory = os.getcwd()
popup = FileSelectPopup(self, directory=directory, show_file=False)
directory = popup.getDirectory()
popup.destroy()
if directory:
self.directoryEntry.set(directory)
def chooseValidScript(self):
# Prepend default Cyana file extension below
fileTypes = [ FileType('Python', ['*.py']), ]
popup = FileSelectPopup(self, file_types = fileTypes,
title='Python file', dismiss_text='Cancel',
selected_file_must_exist = True)
fileName = popup.getFile()
self.validScriptEntry.set(fileName)
popup.destroy()
def chooseZipFile(self):
fileTypes = [ FileType('Zip', ['*.zip']), ]
popup = FileSelectPopup(self, file_types=fileTypes, file=self.resultFileEntry.get(),
title='Results zip file location', dismiss_text='Cancel',
selected_file_must_exist=False)
fileName = popup.getFile()
if fileName:
self.resultFileEntry.set(fileName)
popup.destroy()
def selectFile(self):
spectrum = self.spectrum
if spectrum:
directory = spectrum.analysisSpectrum.contourDir.dataLocation
else:
directory = os.getcwd()
popup = FileSelectPopup(self, directory=directory)
fileName = popup.getFile()
popup.destroy()
if fileName:
self.file_entry.set(fileName)
def chooseFile(self):
directory = self.directoryEntry.get()
if not directory:
directory = os.getcwd()
popup = FileSelectPopup(self, directory=directory)
file = popup.getFile()
popup.destroy()
if file:
template = os.path.basename(file)
self.templateEntry.set(template)
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()
def findFile(self):
if self.file_select_popup:
self.file_select_popup.open()
else:
file_types = [ FileType('All', ['*']),
FileType('PostScript', ['*.ps', '*.eps']),
FileType('PDF', ['*.pdf', '*.ai']) ]
self.file_select_popup = FileSelectPopup(self, file_types=file_types)
file = self.file_select_popup.getFile()
if file:
self.file_entry.set(file)
def selectCnsExe(self):
fileTypes = [ FileType("All", ["*"]), FileType("EXE", ["*.exe"]) ]
popup = FileSelectPopup(self, fileTypes)
file = popup.getFile()
if file:
self.cnsExeEntry.set( file )
popup.destroy()
self.updateEntryParams()
def askFile(title, prompt, initial_value = '', parent = None,
dismiss_text='Cancel', extra_dismiss_text = ''):
if (parent):
popup = FileSelectPopup(parent, title=title, prompt=prompt, show_file=True,
dismiss_text=dismiss_text,
extra_dismiss_text=extra_dismiss_text,
file=initial_value)
file = popup.getFile()
popup.destroy()
return file
else:
return askString(title, prompt, initial_value)
def askDir(title, prompt, initial_value = '', parent = None,
dismiss_text='Cancel', extra_dismiss_text = '', default_dir = None):
if (parent):
popup = FileSelectPopup(parent, title=title, prompt=prompt, show_file=False,
dismiss_text=dismiss_text,
extra_dismiss_text=extra_dismiss_text,
file=initial_value, default_dir = default_dir)
dir = popup.getDirectory()
popup.destroy()
return dir
else:
return askString(title, prompt, initial_value)
def readPCSFileChange(self):
fileTypes = [FileType('PCS', ['*.npc']), FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(
self,
file=os.path.basename(self.calPCSEntry.get()),
directory=os.path.dirname(self.calPCSEntry.get()),
file_types=fileTypes,
title='Save PCS values to file',
dismiss_text='Cancel',
selected_file_must_exist=False,
multiSelect=False,
)
self.calPCSEntry.set(fileSelectPopup.getFile())
def writeScriptFileChange(self):
fileTypes = [FileType('python', ['*.py']), FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(
self,
file=os.path.basename(self.scriptEntry.get()),
directory=os.path.dirname(self.scriptEntry.get()),
file_types=fileTypes,
title='Paramagpy script',
dismiss_text='Cancel',
selected_file_must_exist=False,
multiSelect=False,
)
self.scriptEntry.set(fileSelectPopup.getFile())
def printCanvas(self, *event):
fileTypes = [ FileType('PostScript', ['*.ps']), FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(self, file_types = fileTypes,
title = 'Print canvas to file', dismiss_text = 'Cancel',
selected_file_must_exist = False)
fileName = fileSelectPopup.getFile()
self.bbox = bbox = self.canvas.bbox('all')
w = bbox[2] - bbox[0]
h = bbox[3] - bbox[1]
self.canvas.postscript(colormode='color',file=fileName,
x=bbox[0], y=bbox[1], width=w+2,
pagewidth='21.c', height=h+2, fontmap='fontmap')
def printCanvas(self, *event):
from memops.gui.FileSelect import FileType
from memops.gui.FileSelectPopup import FileSelectPopup
fileTypes = [FileType('PostScript', ['*.ps']), FileType('All', ['*'])]
fileSelectPopup = FileSelectPopup(self,
file_types=fileTypes,
title='Print canvas to file',
dismiss_text='Cancel',
selected_file_must_exist=False)
fileName = fileSelectPopup.getFile()
self.postscript(colormode='color', file=fileName)
def getDataUrl(self, *extra):
if self.dataStore:
dataStore = self.dataStore
oldPath = dataStore.dataUrl.url.dataLocation
if os.path.exists(oldPath):
directory = oldPath
elif os.path.exists(os.path.dirname(oldPath)):
directory = os.path.dirname(oldPath)
else:
directory = None
popup = FileSelectPopup(self, directory=directory, show_file=False)
newPath = popup.getDirectory()
popup.destroy()
if newPath and oldPath != newPath:
changeDataStoreUrl(dataStore, newPath)
def findFile(self):
format = self.format_menu.getSelected()
if (format == tabFormat):
file_types = [FileType('All', ['*']), FileType('Text', ['*.txt'])]
else:
file_types = [FileType('All', ['*']), FileType('CSV', ['*.csv'])]
popup = FileSelectPopup(self, file_types=file_types)
file = popup.getFile()
if (file):
self.file_entry.set(file)
popup.destroy()
def loadValues(self):
directory = self.parent.fileSelect.getDirectory()
fileSelectPopup = FileSelectPopup(self,
title='Select Sampled Data File',
dismiss_text='Cancel',
selected_file_must_exist=True,
multiSelect=False,
directory=directory)
fileName = fileSelectPopup.file_select.getFile()
if not fileName:
return
fileObj = open(fileName, 'rU')
data = ''
line = fileObj.readline()
while line:
data += line
line = fileObj.readline()
fileObj.close()
data = re.sub(',\s+', ',', data)
data = re.sub('\s+', ',', data)
data = re.sub(',,', ',', data)
data = re.sub('[^0-9,.\-+eE]', '', data)
self.valueEntry.set(data)
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()
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()