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)
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 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 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
