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, 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())
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())
def deselectOligo(self, oligo: Oligo):
"""Deselect given ``Oligo``
Args:
oligo: ``Oligo`` object
"""
strand5p = oligo.strand5p()
for strand in strand5p.generator3pStrand():
self.removeStrandFromSelection(strand)
self.updateStrandSelection()
def deselectOligo(self, oligo: Oligo):
"""Deselect given ``Oligo``
Args:
oligo: ``Oligo`` object
"""
strand5p = oligo.strand5p()
for strand in strand5p.generator3pStrand():
self.removeStrandFromSelection(strand)
self.updateStrandSelection()
def selectOligo(self, oligo: Oligo):
"""Select given ``Oligo``
Args:
oligo: ``Oligo`` object
"""
strand5p = oligo.strand5p()
both_ends = (True, True)
for strand in strand5p.generator3pStrand():
self.addStrandToSelection(strand, both_ends)
self.updateStrandSelection()
def selectOligo(self, oligo: Oligo):
"""Select given ``Oligo``
Args:
oligo: ``Oligo`` object
"""
strand5p = oligo.strand5p()
both_ends = (True, True)
for strand in strand5p.generator3pStrand():
self.addStrandToSelection(strand, both_ends)
self.updateStrandSelection()
def isOligoSelected(self, oligo: Oligo) -> bool:
"""Determine if given ``Oligo`` is selected
Args:
oligo: ``Oligo`` object
Returns:
``True`` if ``oligo`` is selected otherwise ``False``
"""
strand5p = oligo.strand5p()
for strand in strand5p.generator3pStrand():
if self.isModelStrandSelected(strand):
return True
return False
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
def isOligoSelected(self, oligo: Oligo) -> bool:
"""Determine if given ``Oligo`` is selected
Args:
oligo: ``Oligo`` object
Returns:
``True`` if ``oligo`` is selected otherwise ``False``
"""
strand5p = oligo.strand5p()
for strand in strand5p.generator3pStrand():
if self.isModelStrandSelected(strand):
return True
return False
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