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 _createColumnSpec(self, cols, addAnyExtraFixedCols=True):
GtrackGenomeElementSource._createColumnSpec(self, cols,
addAnyExtraFixedCols)
self._headerDict[
'track type'] = GtrackGenomeElementSource.getTrackTypeFromColumnSpec(
self._columnSpec)
def getOptionsBoxTrackType(prevChoices):
if prevChoices.columnSelection == 'Base columns on existing GTrack file' and not prevChoices.colSpecFile:
return
if prevChoices.history or prevChoices.input:
trackType = GtrackGenomeElementSource.getTrackTypeFromColumnSpec(TabularToGtrackTool._getHeaders(prevChoices))
if trackType is not None:
words = [x.capitalize() for x in trackType.split()]
abbrv = ''.join([x[0] for x in words])
fullTrackType = ' '.join(words) + ' (%s)' % abbrv
return (fullTrackType, 1, True)
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 getOptionsBoxTrackType(prevChoices):
if prevChoices.columnSelection == 'Base columns on existing GTrack file' and not prevChoices.colSpecFile:
return
if prevChoices.history or prevChoices.input:
headers = set(TabularToGtrackTool._getHeaders(prevChoices))
if prevChoices.createDense == 'Yes' and 'start' in headers:
headers.remove('start')
if not 'edges' in headers and TabularToGtrackTool._create3dData(prevChoices):
headers.add('edges')
trackType = GtrackGenomeElementSource.getTrackTypeFromColumnSpec(headers)
if trackType is not None:
words = [x.capitalize() for x in trackType.split()]
abbrv = ''.join([x[0] for x in words])
fullTrackType = ' '.join(words) + ' (%s)' % abbrv
return (fullTrackType, 1, True)
def _createColumnSpec(self, cols, addAnyExtraFixedCols=True):
GtrackGenomeElementSource._createColumnSpec(self, cols, addAnyExtraFixedCols)
self._headerDict['track type'] = GtrackGenomeElementSource.getTrackTypeFromColumnSpec(self._columnSpec)