def standardSequenceChangedSlot(self, optionChosen):
"""
Connected to signal_mapper to receive a signal whenever user selects
a different sequence in the standard tab.
"""
sequence_name = self.buttons[optionChosen].text()
self.validated_sequence_to_apply = sequences.get(sequence_name, None)
self.chosen_standard_sequence = optionChosen
self.apply_button.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 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):
apply_enabled = False
if index == 1: # Custom Sequence
self.validateCustomSequence()
if self.custom_sequence_is_valid:
apply_enabled = True
else: # Standard Sequence
self.use_custom_sequence = False
if self.chosen_standard_sequence != None:
# Overwrite sequence in case custom has been applied
active_button = self.buttons[self.chosen_standard_sequence]
sequence_name = active_button.text()
self.validated_sequence_to_apply = sequences.get(sequence_name, None)
apply_enabled = True
self.apply_button.setEnabled(apply_enabled)
def tabWidgetChangedSlot(self, index):
apply_enabled = False
if index == 1: # Custom Sequence
self.validateCustomSequence()
if self.custom_sequence_is_valid:
apply_enabled = True
else: # Standard Sequence
self.use_custom_sequence = False
if self.chosen_standard_sequence != None:
# Overwrite sequence in case custom has been applied
active_button = self.buttons[self.chosen_standard_sequence]
sequence_name = active_button.text()
self.validated_sequence_to_apply = sequences.get(
sequence_name, None)
apply_enabled = True
self.apply_button.setEnabled(apply_enabled)
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 sequenceOptionChangedSlot(self, option_chosen):
"""
Connects to signal_mapper to receive a signal whenever user selects
a sequence option.
Args:
option_chosen (TYPE): Description
"""
option_name = self.buttons[option_chosen].text()
if option_name == 'Abstract':
self.use_abstract_sequence = True
elif option_name == 'Custom':
self.use_abstract_sequence = False
else:
self.use_abstract_sequence = False
user_sequence = sequences.get(option_name, None)
if self.seq_box.toPlainText() != user_sequence:
self.seq_box.setText(user_sequence)
def sequenceOptionChangedSlot(self, option_chosen):
"""
Connects to signal_mapper to receive a signal whenever user selects
a sequence option.
Args:
option_chosen (TYPE): Description
"""
option_name = self.buttons[option_chosen].text()
if option_name == 'Abstract':
self.use_abstract_sequence = True
elif option_name == 'Custom':
self.use_abstract_sequence = False
else:
self.use_abstract_sequence = False
user_sequence = sequences.get(option_name, None)
if self.seq_box.toPlainText() != user_sequence:
self.seq_box.setText(user_sequence)
def getTestSequences(self, designname, sequences_to_apply):
"""
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
inputfile = pjoin(TEST_PATH, "data", designname)
document = self.document
document.readFile(inputfile)
part = document.activePart()
# apply one or more sequences to the design
for sequence_name, start_id_num, start_idx in sequences_to_apply:
sequence = sequences.get(sequence_name, None)
for id_num in part.getIdNums():
fwd_ss, rev_ss = part.getStrandSets(id_num)
if id_num == start_id_num:
strand = fwd_ss.getStrand(start_idx)
strand.oligo().applySequence(sequence)
generated_sequences = part.getSequences()
return set(generated_sequences.splitlines())
def getTestSequences(self, designname, sequences_to_apply):
"""
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
inputfile = pjoin(TEST_PATH,
"data", designname)
document = self.document
document.readFile(inputfile)
part = document.activePart()
# apply one or more sequences to the design
for sequence_name, start_id_num, start_idx in sequences_to_apply:
sequence = sequences.get(sequence_name, None)
for id_num in part.getIdNums():
fwd_ss, rev_ss = part.getStrandSets(id_num)
if id_num == start_id_num:
strand = fwd_ss.getStrand(start_idx)
strand.oligo().applySequence(sequence)
generated_sequences = part.getSequences()
return set(generated_sequences.splitlines())
