Example #1
0
 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)
Example #2
0
 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)
Example #3
0
 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)
Example #4
0
 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)
Example #5
0
 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)
Example #6
0
    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())