class Track(object):
IS_MEMOIZABLE = True
def __new__(cls, trackName):
if trackName == [] or trackName is None:
return None
else:
if ExternalTrackManager.isVirtualTrack(trackName):
return VirtualMinimalTrack.__new__(VirtualMinimalTrack)
else:
return object.__new__(cls)
def __init__(self, trackName):
self.trackName = trackName
self._trackSource = TrackSource()
self._trackViewLoader = TrackViewLoader()
self._trackFormatReq = NeutralTrackFormatReq()
self.formatConverters = None
self._trackId = None
def _getRawTrackView(self, region, borderHandling, allowOverlaps):
trackData = self._trackSource.getTrackData(self.trackName,
region.genome, region.chr,
allowOverlaps)
return self._trackViewLoader.loadTrackView(trackData, region,
borderHandling,
allowOverlaps,
self.trackName)
def getTrackView(self, region):
allowOverlaps = self._trackFormatReq.allowOverlaps()
borderHandling = self._trackFormatReq.borderHandling()
assert (allowOverlaps is not None)
assert (borderHandling is not None)
origTrackView = self._getRawTrackView(region, borderHandling,
allowOverlaps)
if self.formatConverters is None:
self.formatConverters = getFormatConverters(
origTrackView.trackFormat, self._trackFormatReq)
if self.formatConverters == []:
raise IncompatibleTracksError(prettyPrintTrackName(self.trackName) + ' with format: '\
+ str(origTrackView.trackFormat) +
('(' + origTrackView.trackFormat._val + ')' if origTrackView.trackFormat._val else '') + \
' does not satisfy ' + str(self._trackFormatReq))
if not self.formatConverters[0].canHandle(origTrackView.trackFormat,
self._trackFormatReq):
raise IncompatibleTracksError(getClassName(self.formatConverters[0]) +\
' does not support conversion from ' + str(origTrackView.trackFormat) + \
' to ' + str(self._trackFormatReq))
return self.formatConverters[0].convert(origTrackView)
def addFormatReq(self, requestedTrackFormat):
prevFormatReq = self._trackFormatReq
self._trackFormatReq = TrackFormatReq.merge(self._trackFormatReq,
requestedTrackFormat)
if self._trackFormatReq is None:
raise IncompatibleTracksError(str(prevFormatReq ) + \
' is incompatible with additional ' + str(requestedTrackFormat))
def setFormatConverter(self, converterClassName):
assert (self.formatConverters is None)
if converterClassName is not None:
self.formatConverters = [
getFormatConverterByName(converterClassName)
]
def getUniqueKey(self, genome):
assert self.formatConverters is not None and len(
self.formatConverters) == 1, 'FC: ' + str(self.formatConverters)
assert( not None in [self._trackFormatReq.allowOverlaps(), \
self._trackFormatReq.borderHandling()] )
if not self._trackId:
self._trackId = TrackInfo(genome, self.trackName).id
return hash((tuple(self.trackName), self._trackId, getClassName(self.formatConverters[0]), \
self.formatConverters[0].VERSION, self._trackFormatReq.allowOverlaps(), \
self._trackFormatReq.borderHandling()))
class Track(object):
IS_MEMOIZABLE = True
def __new__(cls, trackName):
if trackName == [] or trackName is None:
return None
else:
if ExternalTrackManager.isVirtualTrack(trackName):
return VirtualMinimalTrack.__new__(VirtualMinimalTrack)
else:
return object.__new__(cls)
def __init__(self, trackName):
self.trackName = trackName
self._trackSource = TrackSource()
self._trackViewLoader = TrackViewLoader()
self._trackFormatReq = NeutralTrackFormatReq()
self.formatConverters = None
self._trackId = None
def _getRawTrackView(self, region, borderHandling, allowOverlaps):
trackData = self._trackSource.getTrackData(self.trackName, region.genome, region.chr, allowOverlaps)
return self._trackViewLoader.loadTrackView(trackData, region, borderHandling, allowOverlaps, self.trackName)
def getTrackView(self, region):
allowOverlaps = self._trackFormatReq.allowOverlaps()
borderHandling = self._trackFormatReq.borderHandling()
assert(allowOverlaps is not None)
assert(borderHandling is not None)
origTrackView = self._getRawTrackView(region, borderHandling, allowOverlaps)
if self.formatConverters is None:
self.formatConverters = getFormatConverters(origTrackView.trackFormat, self._trackFormatReq)
if self.formatConverters == []:
raise IncompatibleTracksError(prettyPrintTrackName(self.trackName) + ' with format: '\
+ str(origTrackView.trackFormat) +
('(' + origTrackView.trackFormat._val + ')' if origTrackView.trackFormat._val else '') + \
' does not satisfy ' + str(self._trackFormatReq))
if not self.formatConverters[0].canHandle(origTrackView.trackFormat, self._trackFormatReq):
raise IncompatibleTracksError(getClassName(self.formatConverters[0]) +\
' does not support conversion from ' + str(origTrackView.trackFormat) + \
' to ' + str(self._trackFormatReq))
return self.formatConverters[0].convert(origTrackView)
def addFormatReq(self, requestedTrackFormat):
prevFormatReq = self._trackFormatReq
self._trackFormatReq = TrackFormatReq.merge(self._trackFormatReq, requestedTrackFormat)
if self._trackFormatReq is None:
raise IncompatibleTracksError(str(prevFormatReq ) + \
' is incompatible with additional ' + str(requestedTrackFormat))
def setFormatConverter(self, converterClassName):
assert( self.formatConverters is None )
if converterClassName is not None:
self.formatConverters = [getFormatConverterByName(converterClassName)]
def getUniqueKey(self, genome):
assert self.formatConverters is not None and len(self.formatConverters) == 1, 'FC: '+str(self.formatConverters)
assert( not None in [self._trackFormatReq.allowOverlaps(), \
self._trackFormatReq.borderHandling()] )
if not self._trackId:
self._trackId = TrackInfo(genome, self.trackName).id
return hash((tuple(self.trackName), self._trackId, getClassName(self.formatConverters[0]), \
self.formatConverters[0].VERSION, self._trackFormatReq.allowOverlaps(), \
self._trackFormatReq.borderHandling()))
