def standardSequenceChangedSlot(self, optionChosen):
"""
Connected to signalMapper to receive a signal whenever user selects
a different sequence in the standard tab.
"""
sequenceName = str(self.buttons[optionChosen].text())
self.validatedSequenceToApply = sequences.get(sequenceName, None)
self.chosenStandardSequence = optionChosen
self.applyButton.setEnabled(True)
def standardSequenceChangedSlot(self, optionChosen):
"""
Connected to signalMapper to receive a signal whenever user selects
a different sequence in the standard tab.
"""
sequenceName = str(self.buttons[optionChosen].text())
self.validatedSequenceToApply = sequences.get(sequenceName, None)
self.chosenStandardSequence = optionChosen
self.applyButton.setEnabled(True)
def userChoseSeq(self, optionChosen):
optionChosen = str(optionChosen)
seqToUse = ""
knownSeqNamedByChosenOption = sequences.get(optionChosen, None)
sequenceAfterExtractionOfBasePairChars = util.strToDna(optionChosen)
if knownSeqNamedByChosenOption:
seqToUse = knownSeqNamedByChosenOption
elif len(sequenceAfterExtractionOfBasePairChars)==len(optionChosen):
seqToUse = sequenceAfterExtractionOfBasePairChars
vh, strandType, idx = self.vh, self.strandType, self.idx
vh.applySequenceAt(strandType, idx, seqToUse)
def tabWidgetChangedSlot(self, index):
applyEnabled = False
if index == 1: # Custom Sequence
self.validateCustomSequence()
if self.customSequenceIsValid:
applyEnabled = True
else: # Standard Sequence
self.useCustomSequence = False
if self.chosenStandardSequence != None:
# Overwrite sequence in case custom has been applied
activeButton = self.buttons[self.chosenStandardSequence]
sequenceName = str(activeButton.text())
self.validatedSequenceToApply = sequences.get(sequenceName, None)
applyEnabled = True
self.applyButton.setEnabled(applyEnabled)
def tabWidgetChangedSlot(self, index):
applyEnabled = False
if index == 1: # Custom Sequence
self.validateCustomSequence()
if self.customSequenceIsValid:
applyEnabled = True
else: # Standard Sequence
self.useCustomSequence = False
if self.chosenStandardSequence != None:
# Overwrite sequence in case custom has been applied
activeButton = self.buttons[self.chosenStandardSequence]
sequenceName = str(activeButton.text())
self.validatedSequenceToApply = sequences.get(
sequenceName, None)
applyEnabled = True
self.applyButton.setEnabled(applyEnabled)
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())