def __init__(self, part, row, col, idnum=0):
self._doc = part.document()
super(VirtualHelix, self).__init__(part)
self._coord = (row, col) # col, row
self._part = part
self._scaf_strandset = StrandSet(StrandType.SCAFFOLD, self)
self._stap_strandset = StrandSet(StrandType.STAPLE, self)
# If self._part exists, it owns self._number
# in that only it may modify it through the
# private interface. The public interface for
# setNumber just routes the call to the parent
# dnapart if one is present. If self._part == None
# the virtualhelix owns self._number and may modify it.
self._number = None
self.setNumber(idnum)
def __init__(self, part, row, col, idnum=0):
self._doc = part.document()
super(VirtualHelix, self).__init__(part)
self._coord = (row, col) # col, row
self._part = part
self._scaf_strandset = StrandSet(StrandType.SCAFFOLD, self)
self._stap_strandset = StrandSet(StrandType.STAPLE, self)
# If self._part exists, it owns self._number
# in that only it may modify it through the
# private interface. The public interface for
# setNumber just routes the call to the parent
# dnapart if one is present. If self._part == None
# the virtualhelix owns self._number and may modify it.
self._number = None
self.setNumber(idnum)
class VirtualHelix(ProxyObject):
"""
VirtualHelix is a container class for two StrandSet objects (one scaffold
and one staple). The Strands all share the same helix axis. It is called
"virtual" because many different Strands (i.e. sub-oligos) combine to
form the "helix", just as many fibers may be braided together to
form a length of rope.
"""
def __init__(self, part, row, col, idnum=0):
self._doc = part.document()
super(VirtualHelix, self).__init__(part)
self._coord = (row, col) # col, row
self._part = part
self._scaf_strandset = StrandSet(StrandType.SCAFFOLD, self)
self._stap_strandset = StrandSet(StrandType.STAPLE, self)
# If self._part exists, it owns self._number
# in that only it may modify it through the
# private interface. The public interface for
# setNumber just routes the call to the parent
# dnapart if one is present. If self._part == None
# the virtualhelix owns self._number and may modify it.
self._number = None
self.setNumber(idnum)
# end def
def __repr__(self):
return "<%s(%d)>" % (self.__class__.__name__, self._number)
### SIGNALS ###
virtualHelixRemovedSignal = ProxySignal(ProxyObject, name='virtualHelixRemovedSignal') #pyqtSignal(QObject) # self
virtualHelixNumberChangedSignal = ProxySignal(ProxyObject, int, name='virtualHelixNumberChangedSignal') #pyqtSignal(QObject, int) # self, num
### SLOTS ###
### ACCESSORS ###
def scaf(self, idx):
""" Returns the strand at idx in self's scaffold, if any """
return self._scaf_strandset.getStrand(idx)
def stap(self, idx):
""" Returns the strand at idx in self's scaffold, if any """
return self._stap_strandset.getStrand(idx)
def coord(self):
return self._coord
# end def
def number(self):
return self._number
# end def
def part(self):
return self._part
# end def
def document(self):
return self._doc
# end def
def setNumber(self, number):
if self._number != number:
num_to_vh_dict = self._part._number_to_virtual_helix
# if self._number is not None:
num_to_vh_dict[self._number] = None
self._number = number
self.virtualHelixNumberChangedSignal.emit(self, number)
num_to_vh_dict[number] = self
# end def
def setPart(self, new_part):
self._part = new_part
self.setParent(new_part)
# end def
def scaffoldStrandSet(self):
return self._scaf_strandset
# end def
def stapleStrandSet(self):
return self._stap_strandset
# end def
def undoStack(self):
return self._part.undoStack()
# end def
### METHODS FOR QUERYING THE MODEL ###
def scaffoldIsOnTop(self):
return self.isEvenParity()
def getStrandSetByIdx(self, idx):
"""
This is a path-view-specific accessor
idx == 0 means top strand
idx == 1 means bottom strand
"""
if idx == 0:
if self.isEvenParity():
return self._scaf_strandset
else:
return self._stap_strandset
else:
if self.isEvenParity():
return self._stap_strandset
else:
return self._scaf_strandset
# end def
def getStrandSetByType(self, strand_type):
if strand_type == StrandType.SCAFFOLD:
return self._scaf_strandset
else:
return self._stap_strandset
# end def
def getStrandSets(self):
"""Return a tuple of the scaffold and staple StrandSets."""
return self._scaf_strandset, self._stap_strandset
# end def
def hasStrandAtIdx(self, idx):
"""Return a tuple for (Scaffold, Staple). True if
a strand is present at idx, False otherwise."""
return (self._scaf_strandset.hasStrandAt(idx, idx),\
self._stap_strandset.hasStrandAt(idx, idx))
# end def
def indexOfRightmostNonemptyBase(self):
"""Returns the rightmost nonempty base in either scaf of stap."""
return max(self._scaf_strandset.indexOfRightmostNonemptyBase(),\
self._stap_strandset.indexOfRightmostNonemptyBase())
# end def
def isDrawn5to3(self, strandset):
is_scaf = strandset == self._scaf_strandset
is_even = self.isEvenParity()
return is_even == is_scaf
# end def
def isEvenParity(self):
return self._part.isEvenParity(*self._coord)
# end def
def strandSetBounds(self, idx_helix, idx_type):
"""
forwards the query to the strandset
"""
return self.strandSet(idx_helix, idx_type).bounds()
# end def
### METHODS FOR EDITING THE MODEL ###
def destroy(self):
# QObject also emits a destroyed() Signal
self.setParent(None)
self.deleteLater()
# end def
def remove(self, use_undostack=True):
"""
Removes a VirtualHelix from the model. Accepts a reference to the
VirtualHelix, or a (row,col) lattice coordinate to perform a lookup.
"""
if use_undostack:
self.undoStack().beginMacro("Delete VirtualHelix")
self._scaf_strandset.remove(use_undostack)
self._stap_strandset.remove(use_undostack)
c = RemoveVirtualHelixCommand(self.part(), self)
if use_undostack:
self.undoStack().push(c)
self.undoStack().endMacro()
else:
c.redo()
# end def
### PUBLIC SUPPORT METHODS ###
def deepCopy(self, part):
"""
This only copies as deep as the VirtualHelix
strands get copied at the oligo and added to the Virtual Helix
"""
vh = VirtualHelix(part, self._number)
vh._coords = (self._coord[0], self._coord[1])
# If self._part exists, it owns self._number
# in that only it may modify it through the
# private interface. The public interface for
# setNumber just routes the call to the parent
# dnapart if one is present. If self._part == None
# the virtualhelix owns self._number and may modify it.
self._number = idnum
# end def
def getLegacyStrandSetArray(self, strand_type):
"""Called by legacyencoder."""
if strand_type == StrandType.SCAFFOLD:
return self._scaf_strandset.getLegacyArray()
else:
return self._stap_strandset.getLegacyArray()
def shallowCopy(self):
pass
# end def
# def translateCoords(self, deltaCoords):
# """
# for expanding a helix
# """
# deltaRow, deltaCol = deltaCoords
# row, col = self._coord
# self._coord = row + deltaRow, col + deltaCol
# # end def
# end class
class VirtualHelix(ProxyObject):
"""
VirtualHelix is a container class for two StrandSet objects (one scaffold
and one staple). The Strands all share the same helix axis. It is called
"virtual" because many different Strands (i.e. sub-oligos) combine to
form the "helix", just as many fibers may be braided together to
form a length of rope.
"""
def __init__(self, part, row, col, idnum=0):
self._doc = part.document()
super(VirtualHelix, self).__init__(part)
self._coord = (row, col) # col, row
self._part = part
self._scaf_strandset = StrandSet(StrandType.SCAFFOLD, self)
self._stap_strandset = StrandSet(StrandType.STAPLE, self)
# If self._part exists, it owns self._number
# in that only it may modify it through the
# private interface. The public interface for
# setNumber just routes the call to the parent
# dnapart if one is present. If self._part == None
# the virtualhelix owns self._number and may modify it.
self._number = None
self.setNumber(idnum)
# end def
def __repr__(self):
return "<%s(%d)>" % (self.__class__.__name__, self._number)
### SIGNALS ###
virtualHelixRemovedSignal = ProxySignal(
ProxyObject,
name='virtualHelixRemovedSignal') #pyqtSignal(QObject) # self
virtualHelixNumberChangedSignal = ProxySignal(
ProxyObject, int, name='virtualHelixNumberChangedSignal'
) #pyqtSignal(QObject, int) # self, num
### SLOTS ###
### ACCESSORS ###
def scaf(self, idx):
""" Returns the strand at idx in self's scaffold, if any """
return self._scaf_strandset.getStrand(idx)
def stap(self, idx):
""" Returns the strand at idx in self's scaffold, if any """
return self._stap_strandset.getStrand(idx)
def coord(self):
return self._coord
# end def
def number(self):
return self._number
# end def
def part(self):
return self._part
# end def
def document(self):
return self._doc
# end def
def setNumber(self, number):
if self._number != number:
num_to_vh_dict = self._part._number_to_virtual_helix
# if self._number is not None:
num_to_vh_dict[self._number] = None
self._number = number
self.virtualHelixNumberChangedSignal.emit(self, number)
num_to_vh_dict[number] = self
# end def
def setPart(self, new_part):
self._part = new_part
self.setParent(new_part)
# end def
def scaffoldStrandSet(self):
return self._scaf_strandset
# end def
def stapleStrandSet(self):
return self._stap_strandset
# end def
def undoStack(self):
return self._part.undoStack()
# end def
### METHODS FOR QUERYING THE MODEL ###
def scaffoldIsOnTop(self):
return self.isEvenParity()
def getStrandSetByIdx(self, idx):
"""
This is a path-view-specific accessor
idx == 0 means top strand
idx == 1 means bottom strand
"""
if idx == 0:
if self.isEvenParity():
return self._scaf_strandset
else:
return self._stap_strandset
else:
if self.isEvenParity():
return self._stap_strandset
else:
return self._scaf_strandset
# end def
def getStrandSetByType(self, strand_type):
if strand_type == StrandType.SCAFFOLD:
return self._scaf_strandset
else:
return self._stap_strandset
# end def
def getStrandSets(self):
"""Return a tuple of the scaffold and staple StrandSets."""
return self._scaf_strandset, self._stap_strandset
# end def
def hasStrandAtIdx(self, idx):
"""Return a tuple for (Scaffold, Staple). True if
a strand is present at idx, False otherwise."""
return (self._scaf_strandset.hasStrandAt(idx, idx),\
self._stap_strandset.hasStrandAt(idx, idx))
# end def
def indexOfRightmostNonemptyBase(self):
"""Returns the rightmost nonempty base in either scaf of stap."""
return max(self._scaf_strandset.indexOfRightmostNonemptyBase(),\
self._stap_strandset.indexOfRightmostNonemptyBase())
# end def
def isDrawn5to3(self, strandset):
is_scaf = strandset == self._scaf_strandset
is_even = self.isEvenParity()
return is_even == is_scaf
# end def
def isEvenParity(self):
return self._part.isEvenParity(*self._coord)
# end def
def strandSetBounds(self, idx_helix, idx_type):
"""
forwards the query to the strandset
"""
return self.strandSet(idx_helix, idx_type).bounds()
# end def
### METHODS FOR EDITING THE MODEL ###
def destroy(self):
# QObject also emits a destroyed() Signal
self.setParent(None)
self.deleteLater()
# end def
def remove(self, use_undostack=True):
"""
Removes a VirtualHelix from the model. Accepts a reference to the
VirtualHelix, or a (row,col) lattice coordinate to perform a lookup.
"""
if use_undostack:
self.undoStack().beginMacro("Delete VirtualHelix")
self._scaf_strandset.remove(use_undostack)
self._stap_strandset.remove(use_undostack)
c = RemoveVirtualHelixCommand(self.part(), self)
if use_undostack:
self.undoStack().push(c)
self.undoStack().endMacro()
else:
c.redo()
# end def
### PUBLIC SUPPORT METHODS ###
def deepCopy(self, part):
"""
This only copies as deep as the VirtualHelix
strands get copied at the oligo and added to the Virtual Helix
"""
vh = VirtualHelix(part, self._number)
vh._coords = (self._coord[0], self._coord[1])
# If self._part exists, it owns self._number
# in that only it may modify it through the
# private interface. The public interface for
# setNumber just routes the call to the parent
# dnapart if one is present. If self._part == None
# the virtualhelix owns self._number and may modify it.
self._number = idnum
# end def
def getLegacyStrandSetArray(self, strand_type):
"""Called by legacyencoder."""
if strand_type == StrandType.SCAFFOLD:
return self._scaf_strandset.getLegacyArray()
else:
return self._stap_strandset.getLegacyArray()
def shallowCopy(self):
pass
# end def
# def translateCoords(self, deltaCoords):
# """
# for expanding a helix
# """
# deltaRow, deltaCol = deltaCoords
# row, col = self._coord
# self._coord = row + deltaRow, col + deltaCol
# # end def
# end class
def determineStrandSetBounds(self, selected_strand_list: List[Tuple[
Strand, EndsSelected]], strandset: StrandSet) -> Tuple[int, int]:
"""Determine the bounds of a :class:`StrandSet` ``strandset`` among a
a list of selected strands in that same ``strandset``
Args:
selected_strand_list: list of ``( Strands, (is_low, is_high) )`` items
strandset: of interest
Returns:
tuple: min low bound and min high bound index
"""
length = strandset.length()
min_high_delta = min_low_delta = max_ss_idx = length - 1 # init the return values
ss_dict = self._selection_dict[strandset]
for strand, value in selected_strand_list:
idx_low, idx_high = strand.idxs()
low_neighbor, high_neighbor = strandset.getNeighbors(strand)
# print(low_neighbor, high_neighbor)
if value[0]: # the end is selected
if low_neighbor is None:
temp = idx_low - 0
else:
if low_neighbor in ss_dict:
value_N = ss_dict[low_neighbor]
# we only care if the low neighbor is not selected
temp = min_low_delta if value_N[
1] else idx_low - low_neighbor.highIdx() - 1
# end if
else: # not selected
temp = idx_low - low_neighbor.highIdx() - 1
# end else
if temp < min_low_delta:
min_low_delta = temp
# end if
# check the other end of the strand
if not value[1]:
temp = idx_high - idx_low - 1
if temp < min_high_delta:
min_high_delta = temp
# end if
if value[1]:
if high_neighbor is None:
temp = max_ss_idx - idx_high
else:
if high_neighbor in ss_dict:
value_N = ss_dict[high_neighbor]
# we only care if the low neighbor is not selected
temp = min_high_delta if value_N[
0] else high_neighbor.lowIdx() - idx_high - 1
# end if
else: # not selected
temp = high_neighbor.lowIdx() - idx_high - 1
# end else
# end else
if temp < min_high_delta:
min_high_delta = temp
# end if
# check the other end of the strand
if not value[0]:
temp = idx_high - idx_low - 1
if temp < min_low_delta:
min_low_delta = temp
# end if
# end for
return (min_low_delta, min_high_delta)
#Determine position for oligo strands (first oligo: from 1 --> length/2 second oligo: next (length/2)+1 --> length )
oligo_pos.append([1,int(int(i[2])/2),int(int(i[2])/2)+1,int(i[2])])
# Max length of the Strand Set
MAX_LENGTH = 64
offset_idx = 0
# Make the container for the StrandSets
ss_fwd = [None]*vhCounter
ss_rev = [None]*vhCounter
# Create the StrandsSets and fill them with Strands
# The assumption here is that Scaffold is forward strand and that the reverse strands is Staple Strands
try:
for i in range(vhCounter):
ss_fwd[i] = StrandSet(is_fwd=True, id_num=i, part=part, initial_size=MAX_LENGTH)
ss_rev[i] = StrandSet(is_fwd=False, id_num=i, part=part, initial_size=MAX_LENGTH)
ss_fwd[i].createStrand(base_idx_low=offset_idx, base_idx_high=offset_idx+oligo_pos[i][3], color='#0066cc')
ss_rev[i].createStrand(base_idx_low=offset_idx, base_idx_high=offset_idx+oligo_pos[i][1], color='#f44242')
ss_rev[i].createStrand(base_idx_low=offset_idx+oligo_pos[i][2], base_idx_high=offset_idx+oligo_pos[i][3], color='#007200')
part.fwd_strandsets[i] = ss_fwd[i]
part.rev_strandsets[i] = ss_rev[i]
except Exception:
print('Failed to create StrandSet/Strands')
"""
print('\t', fwd_ss, '\t', [s.idxs() for s in fwd_ss.strands()], '\n\t\t\t\t',
[s.getColor() for s in fwd_ss.strands()])
print('\t', rev_ss, '\t', [s.idxs() for s in rev_ss.strands()], '\n\t\t\t\t',
[s.getColor() for s in rev_ss.strands()])
def determineStrandSetBounds(self, selected_strand_list: List[Tuple[Strand, EndsSelected]],
strandset: StrandSet) -> Tuple[int, int]:
"""Determine the bounds of a :class:`StrandSet` ``strandset`` among a
a list of selected strands in that same ``strandset``
Args:
selected_strand_list: list of ``( Strands, (is_low, is_high) )`` items
strandset: of interest
Returns:
tuple: min low bound and min high bound index
"""
length = strandset.length()
min_high_delta = min_low_delta = max_ss_idx = length - 1 # init the return values
ss_dict = self._selection_dict[strandset]
for strand, value in selected_strand_list:
idx_low, idx_high = strand.idxs()
low_neighbor, high_neighbor = strandset.getNeighbors(strand)
# print(low_neighbor, high_neighbor)
if value[0]: # the end is selected
if low_neighbor is None:
temp = idx_low - 0
else:
if low_neighbor in ss_dict:
value_N = ss_dict[low_neighbor]
# we only care if the low neighbor is not selected
temp = min_low_delta if value_N[1] else idx_low - low_neighbor.highIdx() - 1
# end if
else: # not selected
temp = idx_low - low_neighbor.highIdx() - 1
# end else
if temp < min_low_delta:
min_low_delta = temp
# end if
# check the other end of the strand
if not value[1]:
temp = idx_high - idx_low - 1
if temp < min_high_delta:
min_high_delta = temp
# end if
if value[1]:
if high_neighbor is None:
temp = max_ss_idx - idx_high
else:
if high_neighbor in ss_dict:
value_N = ss_dict[high_neighbor]
# we only care if the low neighbor is not selected
temp = min_high_delta if value_N[0] else high_neighbor.lowIdx() - idx_high - 1
# end if
else: # not selected
temp = high_neighbor.lowIdx() - idx_high - 1
# end else
# end else
if temp < min_high_delta:
min_high_delta = temp
# end if
# check the other end of the strand
if not value[0]:
temp = idx_high - idx_low - 1
if temp < min_low_delta:
min_low_delta = temp
# end if
# end for
return (min_low_delta, min_high_delta)