def execute( self, notification ) : proxy = self.facade.retrieveProxy( RunningStateProxy.NAME ) settings = proxy.getData()[ PairwiseSelectorVO.VONAME ] data = proxy.getData()[ DataSelectorVO.VONAME ] matrix = proxy.getData()[ MatrixFileVO.VONAME ].matrix if settings.analysisBoxValue == 'Affine': try : openGap = int( settings.openGapValue ) except ValueError : openGap = StaticStateProxy.DEFAULT_OPEN_PENALTY try : extendGap = int( settings.extendedGapValue ) except ValueError : extendGap = StaticStateProxy.DEFAULT_EXT_PENALTY result = Sequencing.affineSequence( 1, openGap, extendGap, matrix, data.sequenceOne, data.sequenceTwo ) else : try : gapPenalty = int( settings.gapPenaltyValue ) except ValueError : gapPenalty = StaticStateProxy.DEFAULT_GAP_PENALTY if settings.analysisBoxValue == 'Global': useGlobal = 1 else : useGlobal = 0 result = Sequencing.linearSequence( useGlobal, gapPenalty, matrix, data.sequenceOne, data.sequenceTwo ) self.sendNotification( Messages.SHOW_RESULTS, result ) self.sendNotification( Messages.UPDATE_STATUS_TEXT, 'Sequences successfully aligned.' )
def execute( self, notification ) : proxy = self.facade.retrieveProxy( RunningStateProxy.NAME ) state = proxy.getData()[PairwiseSelectorVO.VONAME] matrix = MatrixFileVO() if notification.getName() == Messages.GET_CUSTOM_SUB_MATRIX : matrixFile = state.matrixFileValue else : fileName = self.facade.retrieveProxy( StaticStateProxy.NAME ) matrixFile = fileName.getData()[state.matrixBoxValue] if matrixFile is not None : try : matrix.matrix = Sequencing.loadSubstitutionMatrix( matrixFile ) # TODO determine what other kinds of errors could be thrown by the matrix file creation. except IOError: if matrixFile != None : message = "Unable to open the file: " + matrixFile + " please try another." else : message = "Unable to open a null file." title = 'Data Not Set Error' self.sendNotification( Messages.SHOW_INFO, ( title, message ) ) else : #TODO determine if there is clean up code required to be handled. pass proxy.setData( matrix )
def execute(self, notification): proxy = self.facade.retrieveProxy(RunningStateProxy.NAME) state = proxy.getData()[PairwiseSelectorVO.VONAME] matrix = MatrixFileVO() if notification.getName() == Messages.GET_CUSTOM_SUB_MATRIX: matrixFile = state.matrixFileValue else: fileName = self.facade.retrieveProxy(StaticStateProxy.NAME) matrixFile = fileName.getData()[state.matrixBoxValue] if matrixFile is not None: try: matrix.matrix = Sequencing.loadSubstitutionMatrix(matrixFile) # TODO determine what other kinds of errors could be thrown by the matrix file creation. except IOError: if matrixFile != None: message = "Unable to open the file: " + matrixFile + " please try another." else: message = "Unable to open a null file." title = 'Data Not Set Error' self.sendNotification(Messages.SHOW_INFO, (title, message)) else: #TODO determine if there is clean up code required to be handled. pass proxy.setData(matrix)
def execute( self, notification ) : proxy = self.facade.retrieveProxy( RunningStateProxy.NAME ) scoreMatrix = proxy.getData()[ ScoreMatrixResultVO.VONAME ] settings = proxy.getData()[ PairwiseSelectorVO.VONAME ] scores = scoreMatrix.result names = scoreMatrix.names result = Sequencing.constructNewickTree( scores, names ) self.sendNotification( Messages.SHOW_RESULTS, result ) if settings.useForester : self.sendNotification( Messages.SHOW_TREE_GRAPHICALLY, result )
def execute(self, notification): proxy = self.facade.retrieveProxy(RunningStateProxy.NAME) scoreMatrix = proxy.getData()[ScoreMatrixResultVO.VONAME] settings = proxy.getData()[PairwiseSelectorVO.VONAME] scores = scoreMatrix.result names = scoreMatrix.names result = Sequencing.constructNewickTree(scores, names) self.sendNotification(Messages.SHOW_RESULTS, result) if settings.useForester: self.sendNotification(Messages.SHOW_TREE_GRAPHICALLY, result)
def execute(self, notification): proxy = self.facade.retrieveProxy(RunningStateProxy.NAME) settings = proxy.getData()[PairwiseSelectorVO.VONAME] data = proxy.getData()[DataSelectorVO.VONAME] matrix = proxy.getData()[MatrixFileVO.VONAME].matrix if settings.analysisBoxValue == 'Affine': try: openGap = int(settings.openGapValue) except ValueError: openGap = StaticStateProxy.DEFAULT_OPEN_PENALTY try: extendGap = int(settings.extendedGapValue) except ValueError: extendGap = StaticStateProxy.DEFAULT_EXT_PENALTY result = Sequencing.affineSequence(1, openGap, extendGap, matrix, data.sequenceOne, data.sequenceTwo) else: try: gapPenalty = int(settings.gapPenaltyValue) except ValueError: gapPenalty = StaticStateProxy.DEFAULT_GAP_PENALTY if settings.analysisBoxValue == 'Global': useGlobal = 1 else: useGlobal = 0 result = Sequencing.linearSequence(useGlobal, gapPenalty, matrix, data.sequenceOne, data.sequenceTwo) self.sendNotification(Messages.SHOW_RESULTS, result) self.sendNotification(Messages.UPDATE_STATUS_TEXT, 'Sequences successfully aligned.')
def doAffinePairwise(openGap, extendGap, matrix, sequenceOne, sequenceTwo): # elements 0 and 1 of the return value of the affine sequence are the strings ith gaps inserted. score = Sequencing.affineSequence(1, openGap, extendGap, matrix, sequenceOne, sequenceTwo)[2] return score
def doLinearPairwise(useGlobal, gapPenalty, matrix, sequenceOne, sequenceTwo): # elements 0 and 1 of the return value of the linear sequence are the strings ith gaps inserted. score = Sequencing.linearSequence(useGlobal, gapPenalty, matrix, sequenceOne, sequenceTwo)[2] return score
def doAffinePairwise( openGap, extendGap, matrix, sequenceOne, sequenceTwo ) : # elements 0 and 1 of the return value of the affine sequence are the strings ith gaps inserted. score = Sequencing.affineSequence( 1, openGap, extendGap, matrix, sequenceOne, sequenceTwo )[ 2 ] return score
def doLinearPairwise( useGlobal, gapPenalty, matrix, sequenceOne, sequenceTwo ) : # elements 0 and 1 of the return value of the linear sequence are the strings ith gaps inserted. score = Sequencing.linearSequence( useGlobal, gapPenalty, matrix, sequenceOne, sequenceTwo )[ 2 ] return score