def __init__(self, strand_low: Strand, strand_high: Strand,
priority_strand: Strand):
super(MergeCommand, self).__init__("merge strands")
# Store strands
self._strand_low = strand_low
self._strand_high = strand_high
self._s_set = s_set = priority_strand.strandSet()
# Store oligos
self._new_oligo = priority_strand.oligo().shallowCopy()
self._s_low_oligo = s_low_olg = strand_low.oligo()
self._s_high_oligo = s_high_olg = strand_high.oligo()
# self._s_set_idx = low_strandset_idx
# update the new oligo length if it's not a loop
if s_low_olg != s_high_olg:
self._new_oligo._setLength(s_low_olg.length() +
s_high_olg.length(),
emit_signals=True)
# Create the new_strand by copying the priority strand to
# preserve its properties
new_idxs = strand_low.lowIdx(), strand_high.highIdx()
new_strand = strand_low.shallowCopy()
new_strand.setIdxs(new_idxs)
new_strand.setConnectionHigh(strand_high.connectionHigh())
self._new_strand = new_strand
# Update the oligo for things like its 5prime end and isCircular
self._new_oligo._strandMergeUpdate(strand_low, strand_high, new_strand)
# set the new sequence by concatenating the sequence properly
if strand_low._sequence or strand_high._sequence:
tL = strand_low.totalLength()
tH = strand_high.totalLength()
seqL = strand_low._sequence if strand_low._sequence else "".join(
[" " for i in range(tL)])
seqH = strand_high._sequence if strand_high._sequence else "".join(
[" " for i in range(tH)])
if new_strand.isForward():
new_strand._sequence = seqL + seqH
else:
new_strand._sequence = seqH + seqL
class CreateStrandCommand(UndoCommand):
"""
Create a new Strand based with bounds (base_idx_low, base_idx_high),
and insert it into the strandset at position strandset_idx. Also,
create a new Oligo, add it to the Part, and point the new Strand
at the oligo.
"""
def __init__(self, strandset, base_idx_low, base_idx_high, strandset_idx):
super(CreateStrandCommand, self).__init__("create strand")
self._strandset = strandset
self._s_set_idx = strandset_idx
doc = strandset.document()
self._strand = Strand(strandset, base_idx_low, base_idx_high)
colorList = prefs.STAP_COLORS if strandset.isStaple() else prefs.SCAF_COLORS
color = random.choice(colorList).name()
self._new_oligo = Oligo(None, color) # redo will set part
self._new_oligo.setLength(self._strand.totalLength())
# end def
def redo(self):
# Add the new strand to the StrandSet strand_list
strand = self._strand
strandset = self._strandset
strandset._strand_list.insert(self._s_set_idx, strand)
# Set up the new oligo
oligo = self._new_oligo
oligo.setStrand5p(strand)
oligo.addToPart(strandset.part())
strand.setOligo(oligo)
if strandset.isStaple():
strand.reapplySequence()
# Emit a signal to notify on completion
strandset.strandsetStrandAddedSignal.emit(strandset, strand)
# for updating the Slice View displayed helices
strandset.part().partStrandChangedSignal.emit(strandset.part(), strandset.virtualHelix())
# end def
def undo(self):
# Remove the strand from StrandSet strand_list and selectionList
strand = self._strand
strandset = self._strandset
strandset._doc.removeStrandFromSelection(strand)
strandset._strand_list.pop(self._s_set_idx)
# Get rid of the new oligo
oligo = self._new_oligo
oligo.setStrand5p(None)
oligo.removeFromPart()
# Emit a signal to notify on completion
strand.strandRemovedSignal.emit(strand)
strand.setOligo(None)
# for updating the Slice View displayed helices
strandset.part().partStrandChangedSignal.emit(strandset.part(), strandset.virtualHelix())
# end def
# end class
def __init__(self, strand_low: Strand,
strand_high: Strand,
priority_strand: Strand):
super(MergeCommand, self).__init__("merge strands")
# Store strands
self._strand_low = strand_low
self._strand_high = strand_high
self._s_set = s_set = priority_strand.strandSet()
# Store oligos
self._new_oligo = priority_strand.oligo().shallowCopy()
self._s_low_oligo = s_low_olg = strand_low.oligo()
self._s_high_oligo = s_high_olg = strand_high.oligo()
# self._s_set_idx = low_strandset_idx
# update the new oligo length if it's not a loop
if s_low_olg != s_high_olg:
self._new_oligo._setLength(s_low_olg.length() + s_high_olg.length(),
emit_signals=True)
# Create the new_strand by copying the priority strand to
# preserve its properties
new_idxs = strand_low.lowIdx(), strand_high.highIdx()
new_strand = strand_low.shallowCopy()
new_strand.setIdxs(new_idxs)
new_strand.setConnectionHigh(strand_high.connectionHigh())
self._new_strand = new_strand
# Update the oligo for things like its 5prime end and isCircular
self._new_oligo._strandMergeUpdate(strand_low, strand_high, new_strand)
# set the new sequence by concatenating the sequence properly
if strand_low._sequence or strand_high._sequence:
tL = strand_low.totalLength()
tH = strand_high.totalLength()
seqL = strand_low._sequence if strand_low._sequence else "".join([" " for i in range(tL)])
seqH = strand_high._sequence if strand_high._sequence else "".join([" " for i in range(tH)])
if new_strand.isForward():
new_strand._sequence = seqL + seqH
else:
new_strand._sequence = seqH + seqL
class CreateStrandCommand(UndoCommand):
"""Create a new `Strand` based with bounds (base_idx_low, base_idx_high),
and insert it into the strandset at position strandset_idx. Also,
create a new Oligo, add it to the Part, and point the new Strand
at the oligo.
`Strand` explicitly do not create `Oligo` as do to the 1 to many nature of
Oligos
"""
def __init__(self,
strandset,
base_idx_low,
base_idx_high,
color,
update_segments=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
# end def
def strand(self):
return self._strand
# end def
def redo(self):
# Add the new strand to the StrandSet strand_list
strand = self._strand
strandset = self._strandset
strandset._addToStrandList(strand, self.update_segments)
# Set up the new oligo
oligo = self._new_oligo
oligo.setStrand5p(strand)
strand.setOligo(oligo)
oligo.addToPart(strandset.part(), emit_signals=True)
# strand.reapplySequence()
# Emit a signal to notify on completion
strandset.strandsetStrandAddedSignal.emit(strandset, strand)
# for updating the Slice View displayed helices
strandset.part().partStrandChangedSignal.emit(strandset.part(),
strandset.idNum())
# end def
def undo(self):
# Remove the strand from StrandSet strand_list and selectionList
strand = self._strand
strandset = self._strandset
strandset._document.removeStrandFromSelection(strand)
strandset._removeFromStrandList(strand, self.update_segments)
# Get rid of the new oligo
oligo = self._new_oligo
oligo.setStrand5p(None)
oligo.removeFromPart(emit_signals=True)
# Emit a signal to notify on completion
strand.strandRemovedSignal.emit(strand)
strand.setOligo(None)
# for updating the Slice View displayed helices
strandset.part().partStrandChangedSignal.emit(strandset.part(),
strandset.idNum())
def __init__(self, strand: Strand, base_idx: int, update_sequence: bool = True):
super(SplitCommand, self).__init__("split strand")
# Store inputs
self._old_strand = strand
# TODO possibly implement selection preserving
# doc = strand.document()
# self.was_selected = was_selected = doc.isModelStrandSelected(strand)
# if was_selected:
# self.select_values = doc.getSelectedStrandValue(strand)
# else:
# self.select_values = (None, None)
old_sequence = strand._sequence
is5to3 = strand.isForward()
self._s_set = strand.strandSet()
self._old_oligo = oligo = strand.oligo()
# Create copies
self.strand_low = strand_low = strand.shallowCopy()
self.strand_high = strand_high = strand.shallowCopy()
if oligo.isCircular():
self._l_oligo = self._h_oligo = l_oligo = h_oligo = oligo.shallowCopy()
else:
self._l_oligo = l_oligo = oligo.shallowCopy()
self._h_oligo = h_oligo = oligo.shallowCopy()
color_list = pathstyles.STAP_COLORS
# Determine oligo retention based on strand priority
if is5to3: # strand_low has priority
i_new_low = base_idx
color_low = oligo.getColor()
color_high = random.choice(color_list)
olg5p, olg3p = l_oligo, h_oligo
std5p, std3p = strand_low, strand_high
else: # strand_high has priority
i_new_low = base_idx - 1
color_low = random.choice(color_list)
color_high = oligo.getColor()
olg5p, olg3p = h_oligo, l_oligo
std5p, std3p = strand_high, strand_low
# this is for updating a connected xover view object
# there is only ever one xover a strand is in charge of
self._strand3p = std3p
self._strand5p = std5p
# Update strand connectivity
strand_low.setConnectionHigh(None)
strand_high.setConnectionLow(None)
# Resize strands and update decorators
strand_low.setIdxs((strand.lowIdx(), i_new_low))
strand_high.setIdxs((i_new_low + 1, strand.highIdx()))
# Update the oligo for things like its 5prime end and isCircular
olg5p._strandSplitUpdate(std5p, std3p, olg3p, strand)
if not oligo.isCircular():
# Update the oligo color if necessary
l_oligo._setColor(color_low)
h_oligo._setColor(color_high)
# settle the oligo length
length = 0
for strand in std3p.generator3pStrand():
length += strand.totalLength()
# end for
olg5p._setLength(olg5p.length() - length, emit_signals=True)
olg3p._setLength(length, emit_signals=True)
# end if
if update_sequence and old_sequence:
if is5to3: # strand_low has priority
tL = strand_low.totalLength()
strand_low._sequence = old_sequence[0:tL]
strand_high._sequence = old_sequence[tL:]
else:
tH = strand_high.totalLength()
strand_high._sequence = old_sequence[0:tH]
strand_low._sequence = old_sequence[tH:]
class CreateStrandCommand(UndoCommand):
"""
Create a new Strand based with bounds (base_idx_low, base_idx_high),
and insert it into the strandset at position strandset_idx. Also,
create a new Oligo, add it to the Part, and point the new Strand
at the oligo.
"""
def __init__(self, strandset, base_idx_low, base_idx_high, strandset_idx):
super(CreateStrandCommand, self).__init__("create strand")
self._strandset = strandset
self._s_set_idx = strandset_idx
doc = strandset.document()
self._strand = Strand(strandset, base_idx_low, base_idx_high)
colorList = prefs.STAP_COLORS if strandset.isStaple(
) else prefs.SCAF_COLORS
color = random.choice(colorList).name()
self._new_oligo = Oligo(None, color) # redo will set part
self._new_oligo.setLength(self._strand.totalLength())
# end def
def redo(self):
# Add the new strand to the StrandSet strand_list
strand = self._strand
strandset = self._strandset
strandset._strand_list.insert(self._s_set_idx, strand)
# Set up the new oligo
oligo = self._new_oligo
oligo.setStrand5p(strand)
oligo.addToPart(strandset.part())
strand.setOligo(oligo)
if strandset.isStaple():
strand.reapplySequence()
# Emit a signal to notify on completion
strandset.strandsetStrandAddedSignal.emit(strandset, strand)
# for updating the Slice View displayed helices
strandset.part().partStrandChangedSignal.emit(strandset.part(),
strandset.virtualHelix())
# end def
def undo(self):
# Remove the strand from StrandSet strand_list and selectionList
strand = self._strand
strandset = self._strandset
strandset._doc.removeStrandFromSelection(strand)
strandset._strand_list.pop(self._s_set_idx)
# Get rid of the new oligo
oligo = self._new_oligo
oligo.setStrand5p(None)
oligo.removeFromPart()
# Emit a signal to notify on completion
strand.strandRemovedSignal.emit(strand)
strand.setOligo(None)
# for updating the Slice View displayed helices
strandset.part().partStrandChangedSignal.emit(strandset.part(),
strandset.virtualHelix())
# end def
# end class
class CreateStrandCommand(UndoCommand):
"""Create a new `Strand` based with bounds (base_idx_low, base_idx_high),
and insert it into the strandset at position strandset_idx. Also,
create a new Oligo, add it to the Part, and point the new Strand
at the oligo.
`Strand` explicitly do not create `Oligo` as do to the 1 to many nature of
Oligos
"""
def __init__(self, strandset,
base_idx_low, base_idx_high,
color,
update_segments=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
doc = 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
# end def
def strand(self):
return self._strand
# end def
def redo(self):
# Add the new strand to the StrandSet strand_list
strand = self._strand
strandset = self._strandset
strandset._addToStrandList(strand, self.update_segments)
# Set up the new oligo
oligo = self._new_oligo
oligo.setStrand5p(strand)
strand.setOligo(oligo)
oligo.addToPart(strandset.part(), emit_signals=True)
# strand.reapplySequence()
# Emit a signal to notify on completion
strandset.strandsetStrandAddedSignal.emit(strandset, strand)
# for updating the Slice View displayed helices
strandset.part().partStrandChangedSignal.emit( strandset.part(),
strandset.idNum())
# end def
def undo(self):
# Remove the strand from StrandSet strand_list and selectionList
strand = self._strand
strandset = self._strandset
strandset._document.removeStrandFromSelection(strand)
strandset._removeFromStrandList(strand, self.update_segments)
# Get rid of the new oligo
oligo = self._new_oligo
oligo.setStrand5p(None)
oligo.removeFromPart(emit_signals=True)
# Emit a signal to notify on completion
strand.strandRemovedSignal.emit(strand)
strand.setOligo(None)
# for updating the Slice View displayed helices
strandset.part().partStrandChangedSignal.emit( strandset.part(),
strandset.idNum())