def displayVHs(part: NucleicAcidPart,
id_nums: List[int] = [],
radius: float = 1.0,
color: str = 'coral',
width: int = WIDTH,
height: int = HEIGHT,
camera_z: float = CAM_Z,
colors=['coral']):
if len(id_nums) == 0:
id_nums = part.getIdNums()
len_colors = len(colors)
items = []
mid_point_sum = (0, 0, 0)
i = 0
for id_num in id_nums:
color = colors[i]
vh = part.getVirtualHelix(id_num)
pos1 = vh.getAxisPoint(0)
pos2 = vh.getAxisPoint(vh.getSize() - 1)
vhm, mid_point = virtualHelixMesh(pos1,
pos2,
radius=radius,
color=color)
items.append(vhm)
mid_point_sum += mid_point
i += 1
i %= len_colors
mid_point = mid_point_sum / len(id_nums)
renderer, sc, cam = renderScene(items, width, height, camera_z,
mid_point.tolist())
display(renderer)
renderer.render(sc, cam)
def displayVHs( part: NucleicAcidPart,
id_nums: List[int] = [],
radius: float = 1.0,
color: str = 'coral',
width: int = WIDTH,
height: int = HEIGHT,
camera_z: float = CAM_Z,
colors=['coral']):
if len(id_nums) == 0:
id_nums = part.getIdNums()
len_colors = len(colors)
items = []
mid_point_sum = (0, 0, 0)
i = 0
for id_num in id_nums:
color = colors[i]
vh = part.getVirtualHelix(id_num)
pos1 = vh.getAxisPoint(0)
pos2 = vh.getAxisPoint(vh.getSize()-1)
vhm, mid_point = virtualHelixMesh(pos1, pos2, radius=radius, color=color)
items.append(vhm)
mid_point_sum += mid_point
i += 1
i %= len_colors
mid_point = mid_point_sum / len(id_nums)
renderer, sc, cam = renderScene(items, width, height, camera_z, mid_point.tolist())
display(renderer)
renderer.render(sc, cam)
def deleteStrandSelection(self, use_undostack=True):
"""
Delete selected strands. First iterates through all selected strands
and extracts refs to xovers and strands. Next, calls removeXover
on xoverlist as part of its own macroed command for isoluation
purposes. Finally, calls removeStrand on all strands that were
fully selected (low and high), or had at least one non-xover
endpoint selected.
"""
xoList = []
strand_dict = {}
for strandset_dict in self._selection_dict.values():
for strand, selected in strandset_dict.items():
part = strand.part()
idx_low, idx_high = strand.idxs()
strand5p = strand.connection5p()
strand3p = strand.connection3p()
# both ends are selected
strand_dict[strand] = selected[0] and selected[1]
# only look at 3' ends to handle xover deletion
sel3p = selected[0] if idx_low == strand.idx3Prime(
) else selected[1]
if sel3p: # is idx3p selected?
if strand3p: # is there an xover
xoList.append((part, strand, strand3p, use_undostack))
else: # idx3p is a selected endpoint
strand_dict[strand] = True
else:
if not strand5p: # idx5p is a selected endpoint
strand_dict[strand] = True
if use_undostack and xoList:
self.undoStack().beginMacro("Delete xovers")
for part, strand, strand3p, useUndo in xoList:
NucleicAcidPart.removeXover(part, strand, strand3p, useUndo)
self.removeStrandFromSelection(strand)
self.removeStrandFromSelection(strand3p)
self._selection_dict = {}
self.documentClearSelectionsSignal.emit(self)
if use_undostack:
if xoList: # end xover macro if it was started
self.undoStack().endMacro()
if True in strand_dict.values():
self.undoStack().beginMacro("Delete selection")
else:
return # nothing left to do
for strand, delete in strand_dict.items():
if delete:
strand.strandSet().removeStrand(strand)
if use_undostack:
self.undoStack().endMacro()
def deleteStrandSelection(self, use_undostack=True):
"""
Delete selected strands. First iterates through all selected strands
and extracts refs to xovers and strands. Next, calls removeXover
on xoverlist as part of its own macroed command for isoluation
purposes. Finally, calls removeStrand on all strands that were
fully selected (low and high), or had at least one non-xover
endpoint selected.
"""
xoList = []
strand_dict = {}
for strandset_dict in self._selection_dict.values():
for strand, selected in strandset_dict.items():
part = strand.part()
idx_low, idx_high = strand.idxs()
strand5p = strand.connection5p()
strand3p = strand.connection3p()
# both ends are selected
strand_dict[strand] = selected[0] and selected[1]
# only look at 3' ends to handle xover deletion
sel3p = selected[0] if idx_low == strand.idx3Prime() else selected[1]
if sel3p: # is idx3p selected?
if strand3p: # is there an xover
xoList.append((part, strand, strand3p, use_undostack))
else: # idx3p is a selected endpoint
strand_dict[strand] = True
else:
if not strand5p: # idx5p is a selected endpoint
strand_dict[strand] = True
if use_undostack and xoList:
self.undoStack().beginMacro("Delete xovers")
for part, strand, strand3p, useUndo in xoList:
NucleicAcidPart.removeXover(part, strand, strand3p, useUndo)
self.removeStrandFromSelection(strand)
self.removeStrandFromSelection(strand3p)
self._selection_dict = {}
self.documentClearSelectionsSignal.emit(self)
if use_undostack:
if xoList: # end xover macro if it was started
self.undoStack().endMacro()
if True in strand_dict.values():
self.undoStack().beginMacro("Delete selection")
else:
return # nothing left to do
for strand, delete in strand_dict.items():
if delete:
strand.strandSet().removeStrand(strand)
if use_undostack:
self.undoStack().endMacro()
def createNucleicAcidPart(self, use_undostack=True, grid_type=GridType.HONEYCOMB):
""" Create and store a new DnaPart and instance, and return the instance.
Args:
use_undostack (bool): optional, defaults to True
"""
dna_part = NucleicAcidPart(document=self, grid_type=grid_type)
self._addPart(dna_part, use_undostack=use_undostack)
return dna_part
def createNucleicAcidPart(self, use_undostack=True):
""" Create and store a new DnaPart and instance, and return the instance.
Args:
use_undostack (bool): optional, defaults to True
"""
dnapart = NucleicAcidPart(document=self)
self._addPart(dnapart, use_undostack=use_undostack)
return dnapart
def createNucleicAcidPart(
self,
use_undostack: bool = True,
grid_type: EnumType = GridEnum.NONE) -> NucleicAcidPart:
"""Create and store a new DnaPart and instance, and return the instance.
Args:
use_undostack: optional, defaults to True
grid_type: optional default to HoneyComb
Returns
new :obj:`NucleicAcidPart`
"""
dna_part = NucleicAcidPart(document=self, grid_type=grid_type)
self._addPart(dna_part, use_undostack=use_undostack)
return dna_part