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
self._domain = Domain(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._domain.totalLength())
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
self._domain = Domain(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._domain.totalLength())
# end def
def redo(self):
# Add the new strand to the StrandSet strand_list
domain = self._domain
strandset = self._strandset
strandset._addToStrandList(domain,self._s_set_idx)
# Set up the new oligo
oligo = self._new_oligo
oligo.setStrand5p(domain)
oligo.addToPart(strandset.part())
domain.setOligo(oligo)
# Emit signal to virtual helix item upon completion
strandset.strandsetStrandAddedSignal.emit(strandset, domain) #vhitem strandAddedSlot
# 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._domain
strandset = self._domainset
strandset._doc.removeStrandFromSelection(strand)
strandset.removeDomainFromStrandList.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 redo(self):
'''
domains connected by connection3p or connection5p will have the same oligo;
connection3p and connection5p are pointers to domains crossover-ed to, added
when installing xover.
'''
visited = {}
doc = self._part.document()
for vh in self._part.getVirtualHelices():
stap_ss = vh.stapleStrandSet()
list = stap_ss.getStrandList()
for strand in stap_ss:
visited[strand] = False
if self.include_scaffold:
scap_ss = vh.scaffoldStrandSet()
for strand in scap_ss:
visited[strand] = False
colors = self.colors
for strand in visited.keys():
if visited[strand]:
continue
visited[strand] = True
start_oligo = strand.oligo()
if colors is not None:
if strand.isStaple():
start_oligo.setColor(colors[1])
else:
start_oligo.setColor(colors[0])
strand5gen = strand.generator5pStrand()
# this gets the oligo and burns a strand in the generator
strand5 = next(strand5gen)
for strand5 in strand5gen:
oligo5 = strand5.oligo()
if oligo5 != start_oligo:
oligo5.removeFromPart()
Domain.setOligo(strand5, start_oligo) # emits strandHasNewOligoSignal
visited[strand5] = True
# end for
start_oligo.setStrand5p(strand5)
# is it a loop?
if strand.connection3p() == strand5:
start_oligo.setLoop(True)
else:
strand3gen = strand.generator3pStrand()
strand3 = next(strand3gen) # burn one
for strand3 in strand3gen:
oligo3 = strand3.oligo()
if oligo3 != start_oligo:
oligo3.removeFromPart()
Domain.setOligo(strand3, start_oligo) # emits strandHasNewOligoSignal
visited[strand3] = True
# end for
start_oligo.refreshLength()
# end for
for strand in visited.keys():
strand.strandUpdateSignal.emit(strand)
