def getLegacyStrandSetArray(ss: StrandSetT,
max_base_idx: int) -> List[List[int]]:
"""Given a strandset and max_base_idx, return legacy serialization array format."""
num = ss.idNum()
ret = [[-1, -1, -1, -1] for i in range(max_base_idx)]
if ss.isForward():
for strand in ss.strands():
lo, hi = strand.idxs()
assert strand.idx5Prime() == lo and strand.idx3Prime() == hi
# map the first base (5' xover if necessary)
s5p = strand.connection5p()
if s5p is not None:
ret[lo][0] = s5p.idNum()
ret[lo][1] = s5p.idx3Prime()
ret[lo][2] = num
ret[lo][3] = lo + 1
# map the internal bases
for idx in range(lo + 1, hi):
ret[idx][0] = num
ret[idx][1] = idx - 1
ret[idx][2] = num
ret[idx][3] = idx + 1
# map the last base (3' xover if necessary)
ret[hi][0] = num
ret[hi][1] = hi - 1
s3p = strand.connection3p()
if s3p is not None:
ret[hi][2] = s3p.idNum()
ret[hi][3] = s3p.idx5Prime()
# end if
# end for
# end if
else:
for strand in ss.strands():
lo, hi = strand.idxs()
assert strand.idx3Prime() == lo and strand.idx5Prime() == hi
# map the first base (3' xover if necessary)
ret[lo][0] = num
ret[lo][1] = lo + 1
s3p = strand.connection3p()
if s3p is not None:
ret[lo][2] = s3p.idNum()
ret[lo][3] = s3p.idx5Prime()
# map the internal bases
for idx in range(lo + 1, hi):
ret[idx][0] = num
ret[idx][1] = idx + 1
ret[idx][2] = num
ret[idx][3] = idx - 1
# map the last base (5' xover if necessary)
ret[hi][2] = num
ret[hi][3] = hi - 1
s5p = strand.connection5p()
if s5p is not None:
ret[hi][0] = s5p.idNum()
ret[hi][1] = s5p.idx3Prime()
# end if
# end for
return ret
def getLegacyStrandSetArray(ss: StrandSetT, max_base_idx: int) -> List[List[int]]:
"""Given a strandset and max_base_idx, return legacy serialization array format."""
num = ss.idNum()
ret = [[-1, -1, -1, -1] for i in range(max_base_idx)]
if ss.isForward():
for strand in ss.strands():
lo, hi = strand.idxs()
assert strand.idx5Prime() == lo and strand.idx3Prime() == hi
# map the first base (5' xover if necessary)
s5p = strand.connection5p()
if s5p is not None:
ret[lo][0] = s5p.idNum()
ret[lo][1] = s5p.idx3Prime()
ret[lo][2] = num
ret[lo][3] = lo + 1
# map the internal bases
for idx in range(lo + 1, hi):
ret[idx][0] = num
ret[idx][1] = idx - 1
ret[idx][2] = num
ret[idx][3] = idx + 1
# map the last base (3' xover if necessary)
ret[hi][0] = num
ret[hi][1] = hi - 1
s3p = strand.connection3p()
if s3p is not None:
ret[hi][2] = s3p.idNum()
ret[hi][3] = s3p.idx5Prime()
# end if
# end for
# end if
else:
for strand in ss.strands():
lo, hi = strand.idxs()
assert strand.idx3Prime() == lo and strand.idx5Prime() == hi
# map the first base (3' xover if necessary)
ret[lo][0] = num
ret[lo][1] = lo + 1
s3p = strand.connection3p()
if s3p is not None:
ret[lo][2] = s3p.idNum()
ret[lo][3] = s3p.idx5Prime()
# map the internal bases
for idx in range(lo + 1, hi):
ret[idx][0] = num
ret[idx][1] = idx + 1
ret[idx][2] = num
ret[idx][3] = idx - 1
# map the last base (5' xover if necessary)
ret[hi][2] = num
ret[hi][3] = hi - 1
s5p = strand.connection5p()
if s5p is not None:
ret[hi][0] = s5p.idNum()
ret[hi][1] = s5p.idx3Prime()
# end if
# end for
return ret
def __init__(self,
strandset: StrandSetT,
base_idx_low: int,
base_idx_high: int,
oligo: OligoT = None):
self._document = strandset.document()
super(Strand, self).__init__(strandset)
self._strandset = strandset
self._id_num = strandset.idNum()
"""Keep track of its own segments. Updated on creation and resizing
"""
self._base_idx_low = base_idx_low # base index of the strand's left bound
self._base_idx_high = base_idx_high # base index of the right bound
self._oligo = oligo
self._strand5p = None # 5' connection to another strand
self._strand3p = None # 3' connection to another strand
self._sequence = None
self.segments = []
self.abstract_sequence = []
# dynamic methods for mapping high/low connection /indices
# to corresponding 3Prime 5Prime
is_forward = strandset.isForward()
if is_forward:
self.idx5Prime = self.lowIdx
self.idx3Prime = self.highIdx
self.connectionLow = self.connection5p
self.connectionHigh = self.connection3p
self.setConnectionLow = self.setConnection5p
self.setConnectionHigh = self.setConnection3p
else:
self.idx5Prime = self.highIdx
self.idx3Prime = self.lowIdx
self.connectionLow = self.connection3p
self.connectionHigh = self.connection5p
self.setConnectionLow = self.setConnection3p
self.setConnectionHigh = self.setConnection5p
self._is_forward = is_forward
def __init__(self, strandset: StrandSetT,
base_idx_low: int, base_idx_high: int,
oligo: OligoT = None):
self._document = strandset.document()
super(Strand, self).__init__(strandset)
self._strandset = strandset
self._id_num = strandset.idNum()
"""Keep track of its own segments. Updated on creation and resizing
"""
self._base_idx_low = base_idx_low # base index of the strand's left bound
self._base_idx_high = base_idx_high # base index of the right bound
self._oligo = oligo
self._strand5p = None # 5' connection to another strand
self._strand3p = None # 3' connection to another strand
self._sequence = None
self.segments = []
self.abstract_sequence = []
# dynamic methods for mapping high/low connection /indices
# to corresponding 3Prime 5Prime
is_forward = strandset.isForward()
if is_forward:
self.idx5Prime = self.lowIdx
self.idx3Prime = self.highIdx
self.connectionLow = self.connection5p
self.connectionHigh = self.connection3p
self.setConnectionLow = self.setConnection5p
self.setConnectionHigh = self.setConnection3p
else:
self.idx5Prime = self.highIdx
self.idx3Prime = self.lowIdx
self.connectionLow = self.connection3p
self.connectionHigh = self.connection5p
self.setConnectionLow = self.setConnection3p
self.setConnectionHigh = self.setConnection5p
self._is_forward = is_forward