def setProcessList( self, processList ):
'''
set and detect a pathway
processList: (list) a list of process full ID
'''
# check the existence of processes,
# and create relatedVariableList
self.__processList = []
self.__variableList = []
for processFullID in processList:
# if not self.theEmlSupport.isEntityExist( processFullID ):
# continue
self.__processList.append( processFullID )
try:
aVariableReferenceList = self.theEmlSupport.getEntityProperty( processFullID + ':VariableReferenceList' )
except AttributeError, e:
continue
for aVariableReference in aVariableReferenceList:
fullID = createVariableReferenceFullID( aVariableReference[ 1 ], processFullID )
fullIDString = ecell.ecssupport.createFullIDString( fullID )
if self.__variableList.count( fullIDString ) == 0:
self.__variableList.append( fullIDString )
def addVariable( self, variableFullID ):
'''
recover a removed variable to the pathway
variableFullID: (str) a variable full ID
'''
if not self.__variableList.count( variableFullID ) == 0:
return 1
# elif not ecell.eml.Eml.isEntityExist( variableFullID ):
# return 0
for processFullID in self.__processList:
try:
aVariableReferenceList = self.theEmlSupport.getEntityProperty( processFullID + ':VariableReferenceList' )
except AttributeError, e:
continue
for aVariableReference in aVariableReferenceList:
fullID = createVariableReferenceFullID( aVariableReference[ 1 ], processFullID )
fullIDString = fullID[ 1 ] + ':' + fullID[ 2 ]
if fullIDString == variableFullID:
self.__variableList.append( variableFullID )
self.__variableList.sort()
return 1
def getStoichiometryMatrix( self ):
'''
create the stoichiometry matrix (array)
return stoichiometryMatrix
'''
stoichiometryMatrix = numpy.zeros( ( len( self.__variableList ), len( self.__processList ) ), float )
for j in range( len( self.__processList ) ):
processFullID = self.__processList[ j ]
try:
aVariableReferenceList = self.theEmlSupport.getEntityProperty( processFullID + ':VariableReferenceList' )
except AttributeError, e:
continue
for aVariableReference in aVariableReferenceList:
fullID = createVariableReferenceFullID( aVariableReference[ 1 ], processFullID )
fullIDString = ecell.ecssupport.createFullIDString( fullID )
try:
i = self.__variableList.index( fullIDString )
except ValueError:
# should some warning message be showed?
continue
if len( aVariableReference ) > 2:
coeff = int( aVariableReference[ 2 ] )
if coeff != 0:
stoichiometryMatrix[ i ][ j ] += coeff
def setProcessList( self, processList ):
'''
set and detect a pathway
processList: (list) a list of process full ID
'''
# check the existence of processes,
# and create relatedVariableList
self.__processList = []
self.__variableList = []
for processFullID in processList:
# if not self.theEmlSupport.isEntityExist( processFullID ):
# continue
self.__processList.append( processFullID )
try:
aVariableReferenceList = self.theEmlSupport.getEntityProperty( processFullID + ':VariableReferenceList' )
except AttributeError, e:
continue
for aVariableReference in aVariableReferenceList:
fullID = createVariableReferenceFullID( aVariableReference[ 1 ], processFullID )
fullIDString = ecell.ecssupport.createFullIDString( fullID )
if self.__variableList.count( fullIDString ) == 0:
self.__variableList.append( fullIDString )
def removeProcess( self, processIndexList ):
'''
remove processes from the pathway
processIndexList: (list) a list of indices of processes
'''
indexList = copy.copy( processIndexList )
indexList.sort()
indexList.reverse()
removedProcessList = []
for i in indexList:
if len( self.__processList ) > i:
removedProcessList.append( self.__processList.pop( i ) )
removedVariableList = []
for processFullID in removedProcessList:
# if not ecell.eml.Eml.isEntityExist( self.theEmlSupport, processFullID ):
# continue
try:
aVariableReferenceList = self.theEmlSupport.getEntityProperty( processFullID + ':VariableReferenceList' )
except AttributeError, e:
continue
for aVariableReference in aVariableReferenceList:
fullID = createVariableReferenceFullID( aVariableReference[ 1 ], processFullID )
fullIDString = ecell.ecssupport.createFullIDString( fullID )
if removedVariableList.count( fullIDString ) == 0:
removedVariableList.append( fullIDString )
def getStoichiometryMatrix( self ):
'''
create the stoichiometry matrix (array)
return stoichiometryMatrix
'''
stoichiometryMatrix = numpy.zeros( ( len( self.__variableList ), len( self.__processList ) ), float )
for j in range( len( self.__processList ) ):
processFullID = self.__processList[ j ]
try:
aVariableReferenceList = self.theEmlSupport.getEntityProperty( processFullID + ':VariableReferenceList' )
except AttributeError, e:
continue
for aVariableReference in aVariableReferenceList:
fullID = createVariableReferenceFullID( aVariableReference[ 1 ], processFullID )
fullIDString = ecell.ecssupport.createFullIDString( fullID )
try:
i = self.__variableList.index( fullIDString )
except ValueError:
# should some warning message be showed?
continue
if len( aVariableReference ) > 2:
coeff = int( aVariableReference[ 2 ] )
if coeff != 0:
stoichiometryMatrix[ i ][ j ] += coeff
def addVariable( self, variableFullID ):
'''
recover a removed variable to the pathway
variableFullID: (str) a variable full ID
'''
if not self.__variableList.count( variableFullID ) == 0:
return 1
# elif not ecell.eml.Eml.isEntityExist( variableFullID ):
# return 0
for processFullID in self.__processList:
try:
aVariableReferenceList = self.theEmlSupport.getEntityProperty( processFullID + ':VariableReferenceList' )
except AttributeError, e:
continue
for aVariableReference in aVariableReferenceList:
fullID = createVariableReferenceFullID( aVariableReference[ 1 ], processFullID )
fullIDString = fullID[ 1 ] + ':' + fullID[ 2 ]
if fullIDString == variableFullID:
self.__variableList.append( variableFullID )
self.__variableList.sort()
return 1
def removeProcess( self, processIndexList ):
'''
remove processes from the pathway
processIndexList: (list) a list of indices of processes
'''
indexList = copy.copy( processIndexList )
indexList.sort()
indexList.reverse()
removedProcessList = []
for i in indexList:
if len( self.__processList ) > i:
removedProcessList.append( self.__processList.pop( i ) )
removedVariableList = []
for processFullID in removedProcessList:
# if not ecell.eml.Eml.isEntityExist( self.theEmlSupport, processFullID ):
# continue
try:
aVariableReferenceList = self.theEmlSupport.getEntityProperty( processFullID + ':VariableReferenceList' )
except AttributeError, e:
continue
for aVariableReference in aVariableReferenceList:
fullID = createVariableReferenceFullID( aVariableReference[ 1 ], processFullID )
fullIDString = ecell.ecssupport.createFullIDString( fullID )
if removedVariableList.count( fullIDString ) == 0:
removedVariableList.append( fullIDString )
def getIncidentMatrix(self, mode=0):
'''
create the incident matrix (array)
mode: (0 or 1) 0 means that only the \'write\' variables are checked. 0 is set as default.
return incidentMatrix
'''
incidentMatrix = numpy.zeros(
(len(self.__variableList), len(self.__processList)))
for j in range(len(self.__processList)):
processFullID = self.__processList[j]
try:
aVariableReferenceList = self.theEmlSupport.getEntityProperty(
processFullID + ':VariableReferenceList')
except AttributeError, e:
continue
for aVariableReference in aVariableReferenceList:
fullID = createVariableReferenceFullID(aVariableReference[1],
processFullID)
fullIDString = ecell.ecssupport.createFullIDString(fullID)
try:
i = self.__variableList.index(fullIDString)
except ValueError:
# should some warning message be showed?
continue
if mode:
if len(aVariableReference) > 2:
coeff = int(aVariableReference[2])
if coeff != 0:
incidentMatrix[i][j] = 1
else:
incidentMatrix[i][j] = 1
def getIncidentMatrix( self, mode=0 ):
'''
create the incident matrix (array)
mode: (0 or 1) 0 means that only the \'write\' variables are checked. 0 is set as default.
return incidentMatrix
'''
incidentMatrix = numpy.zeros( ( len( self.__variableList ), len( self.__processList ) ) )
for j in range( len( self.__processList ) ):
processFullID = self.__processList[ j ]
try:
aVariableReferenceList = self.theEmlSupport.getEntityProperty( processFullID + ':VariableReferenceList' )
except AttributeError, e:
continue
for aVariableReference in aVariableReferenceList:
fullID = createVariableReferenceFullID( aVariableReference[ 1 ], processFullID )
fullIDString = ecell.ecssupport.createFullIDString( fullID )
try:
i = self.__variableList.index( fullIDString )
except ValueError:
# should some warning message be showed?
continue
if mode:
if len( aVariableReference ) > 2:
coeff = int( aVariableReference[ 2 ] )
if coeff != 0:
incidentMatrix[ i ][ j ] = 1
else:
incidentMatrix[ i ][ j ] = 1
# elif not ecell.eml.Eml.isEntityExist( processFullID ):
# return
# add process
self.__processList.append( processFullID )
self.__processList.sort()
# update the related variable list
try:
aVariableReferenceList = self.theEmlSupport.getEntityProperty( processFullID + ':VariableReferenceList' )
except AttributeError, e:
return
for aVariableReference in aVariableReferenceList:
fullID = createVariableReferenceFullID( aVariableReference[ 1 ], processFullID )
fullIDString = ecell.ecssupport.createFullIDString( fullID )
if self.__variableList.count( fullIDString ) == 0:
self.__variableList.append( fullIDString )
self.__variableList.sort()
# end of addProcess
def removeProcess( self, processIndexList ):
'''
remove processes from the pathway
processIndexList: (list) a list of indices of processes
'''
# elif not ecell.eml.Eml.isEntityExist( processFullID ):
# return
# add process
self.__processList.append( processFullID )
self.__processList.sort()
# update the related variable list
try:
aVariableReferenceList = self.theEmlSupport.getEntityProperty( processFullID + ':VariableReferenceList' )
except AttributeError, e:
return
for aVariableReference in aVariableReferenceList:
fullID = createVariableReferenceFullID( aVariableReference[ 1 ], processFullID )
fullIDString = ecell.ecssupport.createFullIDString( fullID )
if self.__variableList.count( fullIDString ) == 0:
self.__variableList.append( fullIDString )
self.__variableList.sort()
# end of addProcess
def removeProcess( self, processIndexList ):
'''
remove processes from the pathway
processIndexList: (list) a list of indices of processes
'''