def initializePacketInfo(self, paraInfo):
#for split runs
if paraInfo == ['splitRun', 'splitRun']:
self._splitRunFlag = True
paraInfo = [None, None] # now treat paraInfo as if there was nothing...
#for normal runs
if paraInfo != [None, None]:
paraInfo[0] = int(paraInfo[0])
paraInfo[1] = int(paraInfo[1])
self._packetInfo = cgFile.getPacketInfo(self._dataFileName, paraInfo[1])[paraInfo[0] - 1]
def load(self, attNames, paraInfo=[None, None]):
'''paraInfo is [runNumber, numberOfRuns]'''
#t = bioLibCG.cgTimer()
#stage_cumTime = dict( (x, 0.0) for x in (''))
#t.start()
if paraInfo == ['splitRun', 'splitRun']:
self._splitRunFlag = True
paraInfo = [None,
None] # now treat paraInfo as if there was nothing...
if paraInfo != [None, None]:
paraInfo[0] = int(paraInfo[0])
paraInfo[1] = int(paraInfo[1])
self._packetInfo = cgFile.getPacketInfo(
self._dataFileName, paraInfo[1])[paraInfo[0] - 1]
#if running parallel or specific range, mark range info
self._selectedAttNames = attNames
#get casting and column info
self.loadTranscriptionInfo(attNames)
#init master dictionaries
self.initializeMasterDict()
#get number of slots
numSlots = self.getNumberOfSlots()
#open file and binary skip to correct line if packet
dataFile = cgFile.cgFile(self._dataFileName)
if self._packetInfo:
dataFile.seekToLineStart(self._packetInfo[0])
#print 'before loop', t.split()
#transcribe values
currentID = 0
for line in dataFile.file:
ls = line.strip().split('\t')
#get ID
if self.hasIDs:
id = int(ls[0]) #id is always first slot
else:
id = currentID
currentID += 1
#stop if at end of range
if self._packetInfo:
if id == self._packetInfo[1]:
break
#transcribe
#Note lots of copying is SLOW (10x)
#only copy if list?
for attName in attNames:
colPosition = self._attName_columnPosition[attName]
if colPosition < numSlots:
if ls[colPosition] != '.':
self._attName_id_value[attName][
id] = self._attName_casteFromFxn[attName](
ls[colPosition])
else:
self._attName_id_value[attName][id] = copy(
self._attName_defaultValue[attName])
else:
self._attName_id_value[attName][id] = copy(
self._attName_defaultValue[attName])
#print 'after loop', t.split()
dataFile.file.close()
#bind attribute names to dictionaries
self.bindAttributes(attNames)
#bind id attribute to first attribute, they all have the same ids...
self.linkIDsToColumn()
def load(self, attNames, paraInfo = [None, None]):
'''paraInfo is [runNumber, numberOfRuns]'''
#t = bioLibCG.cgTimer()
#stage_cumTime = dict( (x, 0.0) for x in (''))
#t.start()
if paraInfo == ['splitRun', 'splitRun']:
self._splitRunFlag = True
paraInfo = [None, None] # now treat paraInfo as if there was nothing...
if paraInfo != [None, None]:
paraInfo[0] = int(paraInfo[0])
paraInfo[1] = int(paraInfo[1])
self._packetInfo = cgFile.getPacketInfo(self._dataFileName, paraInfo[1])[paraInfo[0] - 1]
#if running parallel or specific range, mark range info
self._selectedAttNames = attNames
#get casting and column info
self.loadTranscriptionInfo(attNames)
#init master dictionaries
self.initializeMasterDict()
#get number of slots
numSlots = self.getNumberOfSlots()
#open file and binary skip to correct line if packet
dataFile = cgFile.cgFile(self._dataFileName)
if self._packetInfo:
dataFile.seekToLineStart(self._packetInfo[0])
#print 'before loop', t.split()
#transcribe values
currentID = 0
for line in dataFile.file:
ls = line.strip().split('\t')
#get ID
if self.hasIDs:
id = int(ls[0]) #id is always first slot
else:
id = currentID
currentID += 1
#stop if at end of range
if self._packetInfo:
if id == self._packetInfo[1]:
break
#transcribe
#Note lots of copying is SLOW (10x)
#only copy if list?
for attName in attNames:
colPosition = self._attName_columnPosition[attName]
if colPosition < numSlots:
if ls[colPosition] != '.':
self._attName_id_value[attName][id] = self._attName_casteFromFxn[attName](ls[colPosition])
else:
self._attName_id_value[attName][id] = copy(self._attName_defaultValue[attName])
else:
self._attName_id_value[attName][id] = copy(self._attName_defaultValue[attName])
#print 'after loop', t.split()
dataFile.file.close()
#bind attribute names to dictionaries
self.bindAttributes(attNames)
#bind id attribute to first attribute, they all have the same ids...
self.linkIDsToColumn()
