def addInsertion(self, idx, length, useUndoStack=True):
"""
Adds an insertion or skip at idx.
length should be
>0 for an insertion
-1 for a skip
"""
cmds = []
idxLow, idxHigh = self.idxs()
if idxLow <= idx <= idxHigh:
if not self.hasInsertionAt(idx):
# make sure length is -1 if a skip
if length < 0:
length = -1
if useUndoStack:
cmds.append(self.oligo().applySequenceCMD(
None, useUndoStack=useUndoStack))
for strand in self.getComplementStrands():
cmds.append(strand.oligo().applySequenceCMD(
None, useUndoStack=useUndoStack))
cmds.append(Strand.AddInsertionCommand(self, idx, length))
util.execCommandList(self,
cmds,
desc="Add Insertion",
useUndoStack=useUndoStack)
def _addPart(self, part, useUndoStack=True):
"""Add part to the document via AddPartCommand."""
c = self.AddPartCommand(self, part)
util.execCommandList(self, [c],
desc="Add part",
useUndoStack=useUndoStack)
return c.part()
def applyColor(self, color, useUndoStack=True):
if color == self._color:
return # oligo already has color
c = Oligo.ApplyColorCommand(self, color)
util.execCommandList(self, [c],
desc="Color Oligo",
useUndoStack=useUndoStack)
def resize(self, newIdxs, useUndoStack=True):
cmds = []
if self.strandSet().isScaffold():
cmds.append(self.oligo().applySequenceCMD(None))
cmds += self.getRemoveInsertionCommands(newIdxs)
cmds.append(Strand.ResizeCommand(self, newIdxs))
util.execCommandList(self,
cmds,
desc="Resize strand",
useUndoStack=useUndoStack)
def mergeStrands(self, priorityStrand, otherStrand, useUndoStack=True):
"""
Merge the priorityStrand and otherStrand into a single new strand.
The oligo of priority should be propagated to the other and all of
its connections.
"""
lowAndHighStrands = self.strandsCanBeMerged(priorityStrand, otherStrand)
if lowAndHighStrands:
strandLow, strandHigh = lowAndHighStrands
isInSet, overlap, lowStrandSetIdx = self._findIndexOfRangeFor(strandLow)
if isInSet:
c = StrandSet.MergeCommand(strandLow, strandHigh, \
lowStrandSetIdx, priorityStrand)
util.execCommandList(self, [c], desc="Merge", useUndoStack=useUndoStack)
def splitStrand(self, strand, baseIdx, updateSequence=True, useUndoStack=True):
"""
Break strand into two strands. Reapply sequence by default (disabled
during autostaple).
"""
if self.strandCanBeSplit(strand, baseIdx):
isInSet, overlap, strandSetIdx = self._findIndexOfRangeFor(strand)
if isInSet:
c = StrandSet.SplitCommand(strand, baseIdx, strandSetIdx, updateSequence)
util.execCommandList(self, [c], desc="Split", useUndoStack=useUndoStack)
return True
else:
return False
else:
return False
def removeInsertion(self, idx, useUndoStack=True):
cmds = []
idxLow, idxHigh = self.idxs()
if idxLow <= idx <= idxHigh:
if self.hasInsertionAt(idx):
cmds.append(self.oligo().applySequenceCMD(
None, useUndoStack=useUndoStack))
for strand in self.getComplementStrands():
cmds.append(strand.oligo().applySequenceCMD(
None, useUndoStack=useUndoStack))
cmds.append(Strand.RemoveInsertionCommand(self, idx))
util.execCommandList(self,
cmds,
desc="Remove Insertion",
useUndoStack=useUndoStack)
def removeStrand(self, strand, strandSetIdx=None, useUndoStack=True, solo=True):
"""
solo is an argument to enable limiting signals emiting from
the command in the case the command is instantiated part of a larger
command
"""
cmds = []
if strandSetIdx == None:
isInSet, overlap, strandSetIdx = self._findIndexOfRangeFor(strand)
if not isInSet:
raise IndexError
if self.isScaffold() and strand.sequence() != None:
cmds.append(strand.oligo().applySequenceCMD(None))
cmds += strand.clearDecoratorCommands()
cmds.append(StrandSet.RemoveStrandCommand(self, strand, strandSetIdx, solo))
util.execCommandList(self, cmds, desc="Remove strand", useUndoStack=useUndoStack)
return strandSetIdx
def createDeserializedStrand(self, baseIdxLow, baseIdxHigh, useUndoStack=False):
"""
Passes a strand to AddStrandCommand that was read in from file input.
Omits the step of checking _couldStrandInsertAtLastIndex, since
we assume that deserialized strands will not cause collisions.
"""
boundsLow, boundsHigh = self.getBoundsOfEmptyRegionContaining(baseIdxLow)
assert(baseIdxLow < baseIdxHigh)
assert(boundsLow <= baseIdxLow)
assert(baseIdxHigh <= boundsHigh)
canInsert, strandSetIdx = self.getIndexToInsert(baseIdxLow, baseIdxHigh)
if canInsert:
c = StrandSet.CreateStrandCommand(self, baseIdxLow, baseIdxHigh, strandSetIdx)
util.execCommandList(self, [c], desc=None, useUndoStack=useUndoStack)
return strandSetIdx
else:
return -1
def createStrand(self, baseIdxLow, baseIdxHigh, useUndoStack=True):
"""
Assumes a strand is being created at a valid set of indices.
"""
boundsLow, boundsHigh = \
self.getBoundsOfEmptyRegionContaining(baseIdxLow)
canInsert, strandSetIdx = \
self.getIndexToInsert(baseIdxLow, baseIdxHigh)
if canInsert:
c = StrandSet.CreateStrandCommand(self,
baseIdxLow, baseIdxHigh, strandSetIdx)
row, col = self._virtualHelix.coord()
# d = "(%d,%d).%d + [%d,%d]" % \
# (row, col, self._strandType, baseIdxLow, baseIdxHigh)
d = "(%d,%d).%d^%d" % (row, col, self._strandType, strandSetIdx)
util.execCommandList(self, [c], desc=d, useUndoStack=useUndoStack)
return strandSetIdx
else:
return -1
def changeInsertion(self, idx, length, useUndoStack=True):
cmds = []
idxLow, idxHigh = self.idxs()
if idxLow <= idx <= idxHigh:
if self.hasInsertionAt(idx):
if length == 0:
self.removeInsertion(idx)
else:
# make sure length is -1 if a skip
if length < 0:
length = -1
cmds.append(self.oligo().applySequenceCMD(
None, useUndoStack=useUndoStack))
for strand in self.getComplementStrands():
cmds.append(strand.oligo().applySequenceCMD(
None, useUndoStack=useUndoStack))
cmds.append(
Strand.ChangeInsertionCommand(self, idx, length))
util.execCommandList(self,
cmds,
desc="Change Insertion",
useUndoStack=useUndoStack)
def applySequence(self, sequence, useUndoStack=True):
c = Oligo.ApplySequenceCommand(self, sequence)
util.execCommandList(self, [c],
desc="Apply Sequence",
useUndoStack=useUndoStack)
def remove(self, useUndoStack=True):
c = Oligo.RemoveOligoCommand(self)
util.execCommandList(self, [c],
desc="Color Oligo",
useUndoStack=useUndoStack)