def _calcStatisticsInExtraPass(self):
if not self._hasCalculatedStats:
prevPrintWarnings = self._geSource.getPrintWarnings()
self._geSource.setPrintWarnings(False)
for el in self._geSource:
chr = el.chr
self._numElements[chr] += 1
if el.isBlankElement:
continue
if self._areValsCategorical:
self._valCategories.add(el.val)
if self._areEdgeWeightsCategorical:
self._edgeWeightCategories |= set(el.weights)
for prefix in self._maxStrLens[chr]:
content = getattr(el, prefix, None)
if content is not None:
self._maxStrLens[chr][prefix] = \
max( self._maxStrLens[chr][prefix], \
max(1, len(content)) if isinstance(content, basestring) else \
max([1] + [len(x) for x in flatten(content)]) )
if prefix == 'edges':
self._maxNumEdges[chr] = max(self._maxNumEdges[chr], len(el.edges))
self._geSource.setPrintWarnings(prevPrintWarnings)
self._hasCalculatedStats = True
def _calcStatisticsInExtraPass(self):
if not self._hasCalculatedStats:
prevPrintWarnings = self._geSource.getPrintWarnings()
self._geSource.setPrintWarnings(False)
if self._geSource.isSliceSource():
if len(self._getMaxStrLensKeys()):
raise NotImplementedError('Dimension calculation not yet implemented for slice-based GenomeElementSources.')
prefixList = self._geSource.getPrefixList()
for el in self._geSource:
chr = el.chr
self._numElements[chr] += len(getattr(el, prefixList[0]))
else:
for el in self._geSource:
chr = el.chr
self._numElements[chr] += 1
if el.isBlankElement:
continue
if self._areValsCategorical:
self._valCategories.add(el.val)
if self._areEdgeWeightsCategorical:
self._edgeWeightCategories |= set(el.weights)
for prefix in self._maxStrLens[chr]:
content = getattr(el, prefix, None)
if content is not None:
self._maxStrLens[chr][prefix] = \
max( self._maxStrLens[chr][prefix], \
max(1, len(content)) if isinstance(content, basestring) else \
max([1] + [len(x) for x in flatten(content)]) )
if prefix == 'edges':
self._maxNumEdges[chr] = max(self._maxNumEdges[chr], len(el.edges))
self._geSource.setPrintWarnings(prevPrintWarnings)
self._hasCalculatedStats = True
