def _determineHeaderLines(self, hbColumns, columns):
self._setHeaderDict('track type', Gtrack.getTrackTypeFromColumnSpec(columns))
self._setHeaderDict('value type', self._getGtrackValueType())
self._setHeaderDict('value dimension', Gtrack.getGtrackValueDimension(self._geSource.getValDim()))
self._setHeaderDict('undirected edges', self._geSource.hasUndirectedEdges())
self._setHeaderDict('edge weights', ('weights' in hbColumns))
self._setHeaderDict('edge weight type', self._getGtrackEdgeWeightType())
self._setHeaderDict('edge weight dimension', Gtrack.getGtrackValueDimension(self._geSource.getEdgeWeightDim()))
self._setHeaderDict('uninterrupted data lines', not self._hasMoreThanOneBoundingRegion())
self._setHeaderDict('sorted elements', self._geSource.isSorted())
self._setHeaderDict('no overlapping elements', self._geSource.hasNoOverlappingElements())
self._setHeaderDict('circular elements', self._geSource.hasCircularElements())
compliesToSubtype = False
if self._USE_EXTENDED_GTRACK:
self._setHeaderDict('fixed length', self._geSource.getFixedLength())
self._setHeaderDict('fixed gap size', self._geSource.getFixedGapSize())
self._setHeaderDict('fixed-size data lines', self._determineIfFixedSizeDataLines(columns))
if self._headerDict['fixed-size data lines']:
self._setHeaderDict('data line size', self._geSource.getValDim())
hbColumns, columns = self._adjustColumnsAccordingToHeaderLines(hbColumns, columns)
hbColumns, columns, compliesToSubtype = self._determineIfFileCompliesToSubtypes(hbColumns, columns)
if not compliesToSubtype:
self._setHeaderDict('1-indexed', self._geSource.inputIsOneIndexed())
self._setHeaderDict('end inclusive', self._geSource.inputIsEndInclusive())
for header, val in self._forcedHeaderDict.iteritems():
if header not in self._headerDict:
self._headerDict[header] = val
return hbColumns, columns
def _determineHeaderLines(self, hbColumns, columns):
self._setHeaderDict('track type',
Gtrack.getTrackTypeFromColumnSpec(columns))
self._setHeaderDict('value type', self._getGtrackValueType())
self._setHeaderDict(
'value dimension',
Gtrack.getGtrackValueDimension(self._geSource.getValDim()))
self._setHeaderDict('undirected edges',
self._geSource.hasUndirectedEdges())
self._setHeaderDict('edge weights', ('weights' in hbColumns))
self._setHeaderDict('edge weight type',
self._getGtrackEdgeWeightType())
self._setHeaderDict(
'edge weight dimension',
Gtrack.getGtrackValueDimension(self._geSource.getEdgeWeightDim()))
self._setHeaderDict('uninterrupted data lines',
not self._hasMoreThanOneBoundingRegion())
self._setHeaderDict('sorted elements', self._geSource.isSorted())
self._setHeaderDict('no overlapping elements',
self._geSource.hasNoOverlappingElements())
self._setHeaderDict('circular elements',
self._geSource.hasCircularElements())
compliesToSubtype = False
if self._USE_EXTENDED_GTRACK:
self._setHeaderDict('fixed length',
self._geSource.getFixedLength())
self._setHeaderDict('fixed gap size',
self._geSource.getFixedGapSize())
self._setHeaderDict('fixed-size data lines',
self._determineIfFixedSizeDataLines(columns))
if self._headerDict['fixed-size data lines']:
self._setHeaderDict('data line size',
self._geSource.getValDim())
hbColumns, columns = self._adjustColumnsAccordingToHeaderLines(
hbColumns, columns)
hbColumns, columns, compliesToSubtype = self._determineIfFileCompliesToSubtypes(
hbColumns, columns)
if not compliesToSubtype:
self._setHeaderDict('1-indexed',
self._geSource.inputIsOneIndexed())
self._setHeaderDict('end inclusive',
self._geSource.inputIsEndInclusive())
for header, val in self._forcedHeaderDict.iteritems():
if header not in self._headerDict:
self._headerDict[header] = val
return hbColumns, columns
def _getGtrackValueDim(self, val, valTypeInfo, valueOrEdgeWeight):
valLen = len(val.split(valTypeInfo.delim) if valTypeInfo.delim != '' else val)
if valueOrEdgeWeight in self._valLenDict:
if self._valLenDict[valueOrEdgeWeight] != valLen:
self._valLenDict[valueOrEdgeWeight] = 0
else:
self._valLenDict[valueOrEdgeWeight] = valLen
valDim = GtrackGenomeElementSource.getGtrackValueDimension(self._valLenDict[valueOrEdgeWeight])
return valDim
