def _getSortedBoundingRegionsAndGenomeElements(geSource):
geSource = GEDependentAttributesHolder(geSource)
doubleElList = [[
brTuple, geList
] for brTuple, geList in iterateOverBRTuplesWithContainedGEs(geSource)]
noBoundingRegions = doubleElList[0][0] is None
if not noBoundingRegions:
doubleElList.sort(key=lambda x: x[0].region)
for x in doubleElList:
if len(x[1]) >= 2:
if x[1][0].reprIsDense():
break
x[1].sort()
return doubleElList, geSource
def __init__(self, geSource, genome=None):
from gtrackcore.input.wrappers.GEDependentAttributesHolder import GEDependentAttributesHolder
geSource = GEDependentAttributesHolder(geSource)
GESourceWrapper.__init__(self, geSource)
GenomeElementSource.__init__(self, '', genome=genome)
def _decorateGESource(self, geSource):
return GEDependentAttributesHolder(geSource)
