def openAfterMaybeSaveCallback(self, selected):
"""
Receives file selection info from the dialog created by
openAfterMaybeSave, following user input.
Extracts the file name and passes it to the decode method, which
returns a new document doc, which is then set as the open document
by newDocument. Calls finalizeImport and disconnects dialog signaling.
"""
if isinstance(selected, QStringList) or isinstance(selected, list):
fname = selected[0]
else:
fname = selected
if not fname or os.path.isdir(fname):
return False
fname = str(fname)
self._writeFileOpenPath(os.path.dirname(fname))
self.newDocument(fname=fname)
decode(self._document, file(fname).read())
if hasattr(self, "filesavedialog"): # user did save
if self.fileopendialog != None:
self.fileopendialog.filesSelected.disconnect(\
self.openAfterMaybeSaveCallback)
# manual garbage collection to prevent hang (in osx)
del self.fileopendialog
self.fileopendialog = None
def openAfterMaybeSaveCallback(self, selected):
"""
Receives file selection info from the dialog created by
openAfterMaybeSave, following user input.
Extracts the file name and passes it to the decode method, which
returns a new document doc, which is then set as the open document
by newDocument. Calls finalizeImport and disconnects dialog signaling.
"""
if isinstance(selected, QStringList) or isinstance(selected, list):
fname = selected[0]
else:
fname = selected
if not fname or os.path.isdir(fname):
return False
fname = str(fname)
self._writeFileOpenPath(os.path.dirname(fname))
self.newDocument(fname=fname)
with open(fname) as fd:
decode(self._document, fd.read())
if hasattr(self, "filesavedialog"): # user did save
if self.fileopendialog != None:
self.fileopendialog.filesSelected.disconnect(\
self.openAfterMaybeSaveCallback)
# manual garbage collection to prevent hang (in osx)
del self.fileopendialog
self.fileopendialog = None
def openAfterMaybeSaveCallback(self, selected):
"""
Receives file selection info from the dialog created by
openAfterMaybeSave, following user input.
Extracts the file name and passes it to the decode method, which
returns a new document doc, which is then set as the open document
by newDocument. Calls finalizeImport and disconnects dialog signaling.
"""
if isinstance(selected, (list, tuple)):
fname = selected[0]
else:
fname = selected
if fname is None or fname == '' or os.path.isdir(fname):
return False
if not os.path.exists(fname):
return False
self._writeFileOpenPath(os.path.dirname(fname))
self.newDocument(fname=fname)
with io.open(fname, 'r', encoding='utf-8') as fd:
decode(self._document, fd.read())
if hasattr(self, "filesavedialog"): # user did save
if self.fileopendialog is not None:
self.fileopendialog.filesSelected.disconnect(
self.openAfterMaybeSaveCallback)
# manual garbage collection to prevent hang (in osx)
del self.fileopendialog
self.fileopendialog = None
def newDocument(self, isFirstNewDoc=False, fp=None):
"""
Creates a new document, ensuring that a document controller is also instantiated if required.
If isFirstNewDoc is True, a new documentController is always instantiated.
A new documentController will create a new document during __init__().
This method is called by finishInit() to ensure a document is created on application init.
"""
from controllers.documentcontroller import DocumentController
defaultFile = fp or os.environ.get('CADNANO_DEFAULT_DOCUMENT', None)
if defaultFile and isFirstNewDoc:
defaultFile = path.expanduser(defaultFile)
defaultFile = path.expandvars(defaultFile)
dc = DocumentController()
doc = dc.document()
from model.io.decoder import decode
decode(doc, file(defaultFile).read())
print "Loaded default document: %s" % doc
else:
dc = next(iter(self.documentControllers), None)
# cadnano currently only supports ONE documentcontroller per app instance, controlling exactly ONE document.
if dc: # if a documentcontroller already exists
dc.newDocument() # currently, this just empties the existing document object.
else: # first dc
# A DocumentController creates a new doc during init and adds itself to app.documentControllers:
dc = DocumentController()
return dc.document()
def application_openFile_(self, app, f):
if f == "main.py": # ignore
return
extension = os.path.splitext(f)[1].lower()
if extension not in ('.nno', '.json', '.cadnano'):
print("Could not open file %s (bad extension %s)" % (f, extension))
return
dc = list(sharedCadnanoObj().documentControllers)[0]
decode(dc.document(), file(str(f)).read())
return None
def application_openFile_(self, app, f):
if f == "main.py": # ignore
return
extension = os.path.splitext(f)[1].lower()
if extension not in ('.nno', '.json', '.cadnano'):
print "Could not open file %s (bad extension %s)"%(f, extension)
return
dc = list(sharedCadnanoObj().documentControllers)[0]
decode(dc.document(), file(str(f)).read())
return None
def __init__(self, fileName):
self._fN=fileName
self._doc=Document()
self._numStaples=0
self._scaffoldLength=0
decode(self._doc,file(self._fN).read())
self.getModelInfo()
self.printModelInfo()
self.vhLoop()
self.numberScaffold()
def newDocument(self, isFirstNewDoc=False):
from controllers.documentcontroller import DocumentController
defaultFile = os.environ.get('CADNANO_DEFAULT_DOCUMENT', None)
if defaultFile and isFirstNewDoc:
defaultFile = path.expanduser(defaultFile)
defaultFile = path.expandvars(defaultFile)
dc = DocumentController()
doc = dc.document()
from model.io.decoder import decode
decode(doc, file(defaultFile).read())
print "Loaded default document: %s" % doc
else:
docCtrlrCount = len(self.documentControllers)
if docCtrlrCount == 0: # first dc
# dc adds itself to app.documentControllers
dc = DocumentController()
elif docCtrlrCount == 1: # dc already exists
dc = list(self.documentControllers)[0]
dc.newDocument() # tell it to make a new doucment
return dc.document()
def newDocument(self, isFirstNewDoc=False):
from controllers.documentcontroller import DocumentController
defaultFile = os.environ.get('CADNANO_DEFAULT_DOCUMENT', None)
if defaultFile and isFirstNewDoc:
defaultFile = path.expanduser(defaultFile)
defaultFile = path.expandvars(defaultFile)
dc = DocumentController()
doc = dc.document()
from model.io.decoder import decode
decode(doc, file(defaultFile).read())
print "Loaded default document: %s" % doc
else:
docCtrlrCount = len(self.documentControllers)
if docCtrlrCount == 0: # first dc
# dc adds itself to app.documentControllers
dc = DocumentController()
elif docCtrlrCount == 1: # dc already exists
dc = list(self.documentControllers)[0]
dc.newDocument() # tell it to make a new doucment
return dc.document()
def getTestSequences(self, designname, sequencesToApply):
"""
Called by a sequence-verification functional test to read in a file
(designname), apply scaffold sequence(s) to that design, and return
the set of staple sequences."""
# set up the document
from model.io.decoder import decode
inputfile = "tests/functionaltestinputs/%s" % designname
document = self.documentController.document()
with file(inputfile) as f:
decode(document, f.read())
self.setWidget(self.documentController.win, False, None)
part = document.selectedPart()
# apply one or more sequences to the design
for sequenceName, startVhNum, startIdx in sequencesToApply:
sequence = sequences.get(sequenceName, None)
for vh in part.getVirtualHelices():
if vh.number() == startVhNum:
strand = vh.scaffoldStrandSet().getStrand(startIdx)
strand.oligo().applySequence(sequence)
generatedSequences = part.getStapleSequences()
return set(generatedSequences.splitlines())
def getTestSequences(self, designname, sequencesToApply):
"""
Called by a sequence-verification functional test to read in a file
(designname), apply scaffold sequence(s) to that design, and return
the set of staple sequences."""
# set up the document
from model.io.decoder import decode
inputfile = "tests/functionaltestinputs/%s" % designname
document = self.documentController.document()
with file(inputfile) as f:
decode(document, f.read())
self.setWidget(self.documentController.win, False, None)
part = document.selectedPart()
# apply one or more sequences to the design
for sequenceName, startVhNum, startIdx in sequencesToApply:
sequence = sequences.get(sequenceName, None)
for vh in part.getVirtualHelices():
if vh.number() == startVhNum:
strand = vh.scaffoldStrandSet().getStrand(startIdx)
strand.oligo().applySequence(sequence)
generatedSequences = part.getStapleSequences()
return set(generatedSequences.splitlines())
