from .BaseClass import *
from .Track import *
[docs]def get_panel_int(panel):
if panel.lower().startswith("d"):
return 1
elif panel.lower().startswith("f"):
return 2
else:
raise ValueError('Panel can only be "Data" or "Feature"')
[docs]class Session(Element):
def __init__(
self,
genome="mm10",
hasGeneTrack="false",
hasSequenceTrack="true",
locus="chr1:19000000-19100000",
version="8",
refseq_track=True,
):
_tag = "Session"
_attrib = {
"genome": genome,
"hasGeneTrack": hasGeneTrack,
"hasSequenceTrack": hasSequenceTrack,
"locus": locus,
"version": version,
}
super().__init__(_tag, attrib=_attrib)
# add children
self.__add_resources()
self.__add_data_panel()
self.__add_feature_panel()
self.__add_other_routine()
# add grandchildren
self.__add_sequence_track()
if refseq_track:
self.__add_refseq_gene()
return
[docs] def __add_resources(self):
self.append(Resources())
[docs] def __add_data_panel(self):
self.append(Panel(height="2080", name="DataPanel", width="1903"))
[docs] def __add_feature_panel(self):
self.append(Panel(height="95", name="FeaturePanel", width="1903"))
[docs] def __add_other_routine(self):
self.append(PanelLayout())
self.append(HiddenAttributes())
[docs] def __add_resource(self, path):
# self[0] is Resources
self[0].append(Resource(path))
[docs] def __add_sequence_track(self):
# self[2] is FeaturePanel
self[2].append(
Track(
clazz="org.broad.igv.track.SequenceTrack",
fontSize="10",
id="Reference sequence",
name="Reference sequence",
visible="true",
)
)
[docs] def __add_refseq_gene(self):
self[2].append(
Track(
altColor="0,0,178",
clazz="org.broad.igv.track.FeatureTrack",
color="0,0,178",
colorScale="ContinuousColorScale;0.0;185.0;255,255,255;0,0,178",
fontSize="10",
height="35",
id="mm10_genes",
name="Refseq genes",
visible="true",
)
)
[docs] def add_data_track(self, track_kws, data_range_kws, panel="Data"):
_panel = get_panel_int(panel)
track = DataTrack(**track_kws)
track.add_data_range(**data_range_kws)
self[_panel].append(track)
# id is track path, checked key existence in Track.__init__
self.__add_resource(track_kws["id"])
pass
[docs] def add_feature_track(self, track_kws, panel="Feature"):
_panel = get_panel_int(panel)
track = FeatureTrack(**track_kws)
self[_panel].append(track)
self.__add_resource(track_kws["id"])
pass
