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,
color: str,
update_segments: bool = True):
""" TODO: Now that parts have a UUID this could be instantiated via
a document, uuid, id_num, is_fwd, base_idx_low, ... instead of an object
to be independent of parts keeping strandsets live
"""
super(CreateStrandCommand, self).__init__("create strand")
self._strandset = strandset
strandset.document()
self._strand = Strand(strandset, base_idx_low, base_idx_high)
self._new_oligo = Oligo(None, color, length=self._strand.totalLength()) # redo will set part
self.update_segments = update_segments
def initStrandItemFromVHI(self, virtual_helix_item: PathVirtualHelixItemT,
strand_set: StrandSetT,
idx: int):
"""Called from VHI createToolMousePress. Stores the starting point
of the strand to be created.
Args:
virtual_helix_item: reference to the VHI
strand_set (StrandSet): reference to the clicked strand_set
idx (int): index where clicked
"""
s_i = self._temp_strand_item
self._start_idx = idx
self._start_strand_set = strand_set
s_i.resetStrandItem(virtual_helix_item, strand_set.isForward())
self._low_drag_bound, self._high_drag_bound = strand_set.getBoundsOfEmptyRegionContaining(idx)
def initStrandItemFromVHI(self, virtual_helix_item: PathVirtualHelixItemT,
strand_set: StrandSetT, idx: int):
"""Called from VHI createToolMousePress. Stores the starting point
of the strand to be created.
Args:
virtual_helix_item: reference to the VHI
strand_set (StrandSet): reference to the clicked strand_set
idx (int): index where clicked
"""
s_i = self._temp_strand_item
self._start_idx = idx
self._start_strand_set = strand_set
s_i.resetStrandItem(virtual_helix_item, strand_set.isForward())
self._low_drag_bound, self._high_drag_bound = strand_set.getBoundsOfEmptyRegionContaining(
idx)
def createToolMousePress(self, strand_set: StrandSetT, idx: int, modifiers):
""":meth:`Strand.getDragBounds`
Args:
strand_set: Description
idx: the base index within the virtual helix
"""
# print("%s: %s[%s]" % (util.methodName(), strand_set, idx))
if modifiers & Qt.ShiftModifier:
bounds = strand_set.getBoundsOfEmptyRegionContaining(idx)
ret = strand_set.createStrand(*bounds)
print("creating strand {} was successful: {}".format(bounds, ret))
return
active_tool = self._getActiveTool()
if not active_tool.isDrawingStrand():
active_tool.initStrandItemFromVHI(self, strand_set, idx)
active_tool.setIsDrawingStrand(True)
def createToolMousePress(self, strand_set: StrandSetT, idx: int,
modifiers):
""":meth:`Strand.getDragBounds`
Args:
strand_set: Description
idx: the base index within the virtual helix
"""
# print("%s: %s[%s]" % (util.methodName(), strand_set, idx))
if modifiers & Qt.ShiftModifier:
bounds = strand_set.getBoundsOfEmptyRegionContaining(idx)
ret = strand_set.createStrand(*bounds)
print("creating strand {} was successful: {}".format(bounds, ret))
return
active_tool = self._getActiveTool()
if not active_tool.isDrawingStrand():
active_tool.initStrandItemFromVHI(self, strand_set, idx)
active_tool.setIsDrawingStrand(True)
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