def _GetCDR3SHMs(self, src_id, dst_id):
cdr3_src = self.full_length_lineage.Dataset().GetCDR3BySeqName(src_id)
cdr3_dst = self.full_length_lineage.Dataset().GetCDR3BySeqName(dst_id)
cdr3_shms = []
for i in range(len(cdr3_src)):
if cdr3_src[i] != cdr3_dst[i]:
cdr3_shms.append(dataset.SHM(i, -1, cdr3_src[i], cdr3_dst[i]))
return cdr3_shms
def _InitSHMs(self):
self.shms = TreeSHMs(self.clonal_tree.FullLengthLineage(),
self.aa_dict)
for e in self.aa_edges:
src_aa = self.aa_dict.GetAAByIndex(e[0])
dst_aa = self.aa_dict.GetAAByIndex(e[1])
for i in range(len(src_aa)):
if src_aa[i] == dst_aa[i]:
continue
shm = dataset.SHM(i, -1, src_aa[i], dst_aa[i])
self.shms.AddSHM(e, shm)
def GetReverseSHM(self, shm):
return dataset.SHM(shm.pos, -1, shm.dst_n, shm.src_n)
def SHMHasReverse(self, shm):
reverse_shm = dataset.SHM(shm.pos, -1, shm.dst_n, shm.src_n)
return self.ContainsSHM(reverse_shm)
def SHMIsNeutral(self, shm):
reverse_shm = dataset.SHM(shm.pos, -1, shm.dst_n, shm.src_n)
return reverse_shm in self.shm_edge_map