def encodePart(part: PartT) -> dict:
"""
Args:
part (Part):
Returns:
dict:
"""
# iterate through virtualhelix list
group_props = part.getModelProperties().copy()
if not group_props.get('is_lattice', True):
vh_props, origins, directions = part.helixProperties()
group_props['virtual_helices'] = vh_props
group_props['origins'] = origins
group_props['directions'] = directions
else:
vh_props, origins, directions = part.helixProperties()
group_props['virtual_helices'] = vh_props
group_props['origins'] = origins
group_props['directions'] = directions
# print("ORIGINS")
# print(group_props['origins'])
# print("DIRECTIONS")
# print(group_props['directions'])
xover_list = []
strand_list = []
prop_list = []
vh_list = []
for id_num in part.getidNums():
offset_and_size = part.getOffsetAndSize(id_num)
if offset_and_size is None:
# add a placeholder
strand_list.append(None)
prop_list.append(None)
else:
offset, size = offset_and_size
vh_list.append((id_num, size))
fwd_ss, rev_ss = part.getStrandSets(id_num)
fwd_idxs, fwd_colors = fwd_ss.dump(xover_list)
rev_idxs, rev_colors = rev_ss.dump(xover_list)
strand_list.append((fwd_idxs, rev_idxs))
prop_list.append((fwd_colors, rev_colors))
# end for
group_props['vh_list'] = vh_list
group_props['strands'] = {'indices': strand_list,
'properties': prop_list
}
group_props['insertions'] = list(part.dumpInsertions())
group_props['xovers'] = xover_list
group_props['oligos'] = [o.dump() for o in part.oligos()]
instance_props = list(part.instanceProperties())
group_props['instance_properties'] = instance_props
group_props['uuid'] = part.uuid
return group_props
def __init__(self, part: PartT, part_instance: ObjectInstanceT,
view_name: str, key: str, val: Any):
super(ChangeInstancePropertyCommand,
self).__init__("change instance property")
self.part = part
self.part_instance = part_instance
self.view_name = view_name
self.flat_key = flat_key = '%s:%s' % (view_name, key)
self.keyval = (key, val)
self.old_keyval = (key,
part.getInstanceProperty(part_instance, flat_key))
def encodePart(part: PartT) -> dict:
"""
Args:
part (Part):
Returns:
dict:
"""
# iterate through virtualhelix list
group_props = part.getModelProperties().copy()
if group_props.get('point_type') == PointEnum.ARBITRARY:
# TODO add code to encode Parts with ARBITRARY point configurations
pass
else:
vh_props, origins = part.helixPropertiesAndOrigins()
group_props['virtual_helices'] = vh_props
group_props['origins'] = origins
xover_list = []
strand_list = []
prop_list = []
vh_list = []
for id_num in part.getidNums():
offset_and_size = part.getOffsetAndSize(id_num)
if offset_and_size is None:
# add a placeholder
strand_list.append(None)
prop_list.append(None)
else:
offset, size = offset_and_size
vh_list.append((id_num, size))
fwd_ss, rev_ss = part.getStrandSets(id_num)
fwd_idxs, fwd_colors = fwd_ss.dump(xover_list)
rev_idxs, rev_colors = rev_ss.dump(xover_list)
strand_list.append((fwd_idxs, rev_idxs))
prop_list.append((fwd_colors, rev_colors))
# end for
group_props['vh_list'] = vh_list
group_props['strands'] = {'indices': strand_list,
'properties': prop_list
}
group_props['insertions'] = list(part.dumpInsertions())
group_props['xovers'] = xover_list
group_props['oligos'] = [o.dump() for o in part.oligos()]
instance_props = list(part.instanceProperties())
group_props['instance_properties'] = instance_props
group_props['uuid'] = part.uuid
return group_props
def __init__(self, part: PartT,
part_instance: ObjectInstanceT,
view_name: str,
key: str,
val: Any):
super(ChangeInstancePropertyCommand, self).__init__("change instance property")
self.part = part
self.part_instance = part_instance
self.view_name = view_name
self.flat_key = flat_key = '%s:%s' % (view_name, key)
self.keyval = (key, val)
self.old_keyval = (key, part.getInstanceProperty(part_instance, flat_key))
def reEmitPart(part: PartT):
"""
Args:
part (Part):
"""
# iterate through virtualhelix list
group_props = part.getModelProperties().copy()
if not group_props.get('is_lattice', True):
# TODO add code to encode Parts with ARBITRARY point configurations
pass
else:
vh_props, origins = part.helixPropertiesAndOrigins()
group_props['virtual_helices'] = vh_props
group_props['origins'] = origins
xover_list = []
threshold = 2.1 * part.radius()
for id_num in part.getidNums():
offset_and_size = part.getOffsetAndSize(id_num)
if offset_and_size is not None:
offset, size = offset_and_size
vh = part.getVirtualHelix(id_num)
neighbors = part._getVirtualHelixOriginNeighbors(id_num, threshold)
part.partVirtualHelixAddedSignal.emit(part, id_num, vh, neighbors)
fwd_ss, rev_ss = part.getStrandSets(id_num)
for strand in fwd_ss.strands():
fwd_ss.strandsetStrandAddedSignal.emit(fwd_ss, strand)
for strand in rev_ss.strands():
fwd_ss.strandsetStrandAddedSignal.emit(rev_ss, strand)
part.partStrandChangedSignal.emit(part, id_num)
fwd_idxs, fwd_colors = fwd_ss.dump(xover_list)
rev_idxs, rev_colors = rev_ss.dump(xover_list)
# end for
for from_id, from_is_fwd, from_idx, to_id, to_is_fwd, to_idx in xover_list:
strand5p = from_strand = part.getStrand(from_is_fwd, from_id, from_idx)
strand3p = to_strand = part.getStrand(to_is_fwd, to_id, to_idx)
strand5p.strandConnectionChangedSignal.emit(strand5p)
strand3p.strandConnectionChangedSignal.emit(strand3p)
# end for
for id_num, id_dict in part.insertions().items():
for idx, insertion in id_dict.items():
fwd_strand = part.getStrand(True, id_num, idx)
rev_strand = part.getStrand(False, id_num, idx)
if fwd_strand:
fwd_strand.strandInsertionAddedSignal.emit(
fwd_strand, insertion)
if rev_strand:
rev_strand.strandInsertionAddedSignal.emit(
rev_strand, insertion)
# end for
# instance_props = list(part.instanceProperties())
# emit instance properties
return group_props
def __init__(self, part: PartT):
super(RemovePartCommand, self).__init__("remove part")
self._part = part
self._instances = part.instances().copy()
self._document = part.document()