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
