def strandCanBeSplit(self, strand: StrandT, base_idx: int) -> bool:
"""Make sure the base index is within the strand
Don't split right next to a 3Prime end
Don't split on endpoint (AKA a crossover)
Args:
strand: the :class:`Strand`
base_idx: the index to split at
Returns:
``True`` if can be split, ``False`` otherwise
"""
# no endpoints
lo, hi = strand.idxs()
if base_idx == lo or base_idx == hi:
return False
# make sure the base index within the strand
elif lo > base_idx or base_idx > hi:
return False
elif self._is_fwd:
if base_idx - lo > 0 and hi - base_idx > 1:
return True
else:
return False
elif base_idx - lo > 1 and hi - base_idx > 0: # reverse
return True
else:
return False
def strandCanBeSplit(self, strand: StrandT, base_idx: int) -> bool:
"""Make sure the base index is within the strand
Don't split right next to a 3Prime end
Don't split on endpoint (AKA a crossover)
Args:
strand: the :class:`Strand`
base_idx: the index to split at
Returns:
``True`` if can be split, ``False`` otherwise
"""
# no endpoints
lo, hi = strand.idxs()
if base_idx == lo or base_idx == hi:
return False
# make sure the base index within the strand
elif lo > base_idx or base_idx > hi:
return False
elif self._is_fwd:
if base_idx - lo > 0 and hi - base_idx > 1:
return True
else:
return False
elif base_idx - lo > 1 and hi - base_idx > 0: # reverse
return True
else:
return False
def _addToStrandList(self, strand: StrandT, update_segments: bool = True):
"""Inserts strand into the strand_array at idx
Args:
strand: the strand to add
update_segments (optional): whether to signal default=``True``
"""
idx_low, idx_high = strand.idxs()
for i in range(idx_low, idx_high + 1):
self.strand_array[i] = strand
insort_left(self.strand_heap, strand)
if update_segments:
self._part.refreshSegments(self._id_num)
def _addToStrandList(self, strand: StrandT, update_segments: bool = True):
"""Inserts strand into the strand_array at idx
Args:
strand: the strand to add
update_segments (optional): whether to signal default=``True``
"""
idx_low, idx_high = strand.idxs()
for i in range(idx_low, idx_high+1):
self.strand_array[i] = strand
insort_left(self.strand_heap, strand)
if update_segments:
self._part.refreshSegments(self._id_num)
def _removeFromStrandList(self, strand: StrandT, update_segments: bool = True):
"""Remove strand from strand_array.
Args:
strand: the strand
update_segments (optional): whether to signal default=``True``
"""
self._document.removeStrandFromSelection(strand) # make sure the strand is no longer selected
idx_low, idx_high = strand.idxs()
for i in range(idx_low, idx_high + 1):
self.strand_array[i] = None
i = bisect_left(self.strand_heap, strand)
self.strand_heap.pop(i)
if update_segments:
self._part.refreshSegments(self._id_num)
def _removeFromStrandList(self, strand: StrandT, update_segments: bool = True):
"""Remove strand from strand_array.
Args:
strand: the strand
update_segments (optional): whether to signal default=``True``
"""
self._document.removeStrandFromSelection(strand) # make sure the strand is no longer selected
idx_low, idx_high = strand.idxs()
for i in range(idx_low, idx_high + 1):
self.strand_array[i] = None
i = bisect_left(self.strand_heap, strand)
self.strand_heap.pop(i)
if update_segments:
self._part.refreshSegments(self._id_num)
def strandModsRemovedSlot(self, strand: StrandT, document: DocT,
mod_id: str, idx: int):
"""Slot for removing a modification on the Strand
Args:
strand:
document:
mod_id:
idx:
"""
idx_l, idx_h = strand.idxs()
# color = document.getModProperties(mod_id)['color']
if idx == idx_h:
self._high_cap.destroyMod()
else:
self._low_cap.destroyMod()
def strandModsChangedSlot(self, strand: StrandT, document: DocT,
mod_id: str, idx: int):
"""Slot for changing a modification on the Strand
Args:
strand:
document:
mod_id:
idx:
"""
idx_l, idx_h = strand.idxs()
color = document.getModProperties(mod_id)['color']
if idx == idx_h:
self._high_cap.changeMod(mod_id, color)
else:
self._low_cap.changeMod(mod_id, color)
def strandModsAddedSlot(self, strand: StrandT, document: DocT, mod_id: str,
idx: int):
"""Slot for adding a modification on the Strand
Args:
strand:
document:
mod_id:
idx:
"""
if self._viewroot.are_signals_on:
idx_l, idx_h = strand.idxs()
color = document.getModProperties(mod_id)['color']
if idx == idx_h:
self._high_cap.showMod(mod_id, color)
else:
self._low_cap.showMod(mod_id, color)
def strandModsRemovedSlot(self, strand: StrandT,
document: DocT,
mod_id: str,
idx: int):
"""Slot for removing a modification on the Strand
Args:
strand:
document:
mod_id:
idx:
"""
idx_l, idx_h = strand.idxs()
# color = document.getModProperties(mod_id)['color']
if idx == idx_h:
self._high_cap.destroyMod()
else:
self._low_cap.destroyMod()
def strandModsChangedSlot(self, strand: StrandT,
document: DocT,
mod_id: str,
idx: int):
"""Slot for changing a modification on the Strand
Args:
strand:
document:
mod_id:
idx:
"""
idx_l, idx_h = strand.idxs()
color = document.getModProperties(mod_id)['color']
if idx == idx_h:
self._high_cap.changeMod(mod_id, color)
else:
self._low_cap.changeMod(mod_id, color)
def strandModsAddedSlot(self, strand: StrandT,
document: DocT,
mod_id: str,
idx: int):
"""Slot for adding a modification on the Strand
Args:
strand:
document:
mod_id:
idx:
"""
if self._viewroot.are_signals_on:
idx_l, idx_h = strand.idxs()
color = document.getModProperties(mod_id)['color']
if idx == idx_h:
self._high_cap.showMod(mod_id, color)
else:
self._low_cap.showMod(mod_id, color)
def __init__(self, strand: StrandT,
new_idxs: SegmentT,
update_segments: bool = True):
super(ResizeCommand, self).__init__("resize strand")
self.strand = strand
self.old_indices = o_i = strand.idxs()
self.new_idxs = new_idxs
# an increase in length leads to positive delta
self.delta = (new_idxs[1] - new_idxs[0]) - (o_i[1] - o_i[0])
# now handle insertion deltas
oldInsertions = strand.insertionsOnStrand(*o_i)
newInsertions = strand.insertionsOnStrand(*new_idxs)
o_l = 0
for i in oldInsertions:
o_l += i.length()
n_l = 0
for i in newInsertions:
n_l += i.length()
self.delta += (n_l - o_l)
self.update_segments = update_segments
def __init__(self,
strand: StrandT,
new_idxs: SegmentT,
update_segments: bool = True):
super(ResizeCommand, self).__init__("resize strand")
self.strand = strand
self.old_indices = o_i = strand.idxs()
self.new_idxs = new_idxs
# an increase in length leads to positive delta
self.delta = (new_idxs[1] - new_idxs[0]) - (o_i[1] - o_i[0])
# now handle insertion deltas
oldInsertions = strand.insertionsOnStrand(*o_i)
newInsertions = strand.insertionsOnStrand(*new_idxs)
o_l = 0
for i in oldInsertions:
o_l += i.length()
n_l = 0
for i in newInsertions:
n_l += i.length()
self.delta += (n_l - o_l)
self.update_segments = update_segments
def setComplementSequence(self, sequence: str, strand: StrandT) -> str:
"""This version takes anothers strand and only sets the indices that
align with the given complimentary strand.
As it depends which direction this is going, and strings are stored in
memory left to right, we need to test for is_forward to map the
reverse compliment appropriately, as we traverse overlapping strands.
We reverse the sequence ahead of time if we are applying it 5' to 3',
otherwise we reverse the sequence post parsing if it's 3' to 5'
Again, sequences are stored as strings in memory 5' to 3' so we need
to jump through these hoops to iterate 5' to 3' through them correctly
Perhaps it's wiser to merely store them left to right and reverse them
at draw time, or export time
Args:
sequence (str):
strand (Strand):
Returns:
str: the used portion of the sequence
"""
s_low_idx, s_high_idx = self._base_idx_low, self._base_idx_high
c_low_idx, c_high_idx = strand.idxs()
is_forward = self._is_forward
self_seq = self._sequence
# get the ovelap
low_idx, high_idx = util.overlap(s_low_idx, s_high_idx, c_low_idx, c_high_idx)
# only get the characters we're using, while we're at it, make it the
# reverse compliment
total_length = self.totalLength()
# see if we are applying
if sequence is None:
# clear out string for in case of not total overlap
use_seq = ''.join([' ' for x in range(total_length)])
else: # use the string as is
use_seq = sequence[::-1] if is_forward else sequence
temp = array(ARRAY_TYPE, sixb(use_seq))
if self_seq is None:
temp_self = array(ARRAY_TYPE, sixb(''.join([' ' for x in range(total_length)])))
else:
temp_self = array(ARRAY_TYPE, sixb(self_seq) if is_forward else sixb(self_seq[::-1]))
# generate the index into the compliment string
a = self.insertionLengthBetweenIdxs(s_low_idx, low_idx - 1)
b = self.insertionLengthBetweenIdxs(low_idx, high_idx)
c = strand.insertionLengthBetweenIdxs(c_low_idx, low_idx - 1)
start = low_idx - c_low_idx + c
end = start + b + high_idx - low_idx + 1
temp_self[low_idx - s_low_idx + a:high_idx - s_low_idx + 1 + a + b] = temp[start:end]
# print("old sequence", self_seq)
self._sequence = tostring(temp_self)
# if we need to reverse it do it now
if not is_forward:
self._sequence = self._sequence[::-1]
# test to see if the string is empty(), annoyingly expensive
# if len(self._sequence.strip()) == 0:
if not self._sequence:
self._sequence = None
# print("new sequence", self._sequence)
return self._sequence