def __init__(self, is_fwd, pre_xover_item):
"""
Args:
is_fwd (bool): True if forward strand base, False if reverse.
pre_xover_item (TYPE): Description
"""
super(Triangle, self).__init__(pre_xover_item)
color = pre_xover_item.color
self.adapter = PropertyWrapperObject(self)
self.setAcceptHoverEvents(True)
self.setFiltersChildEvents(True)
self._click_area = click_area = QGraphicsRectItem(PXI_RECT, self)
click_area.setAcceptHoverEvents(True)
click_area.setPen(getNoPen())
click_area.hoverMoveEvent = self.hoverMoveEvent
if is_fwd:
# grad = QLinearGradient(0., 0., 0., 1.)
# grad.setColorAt(0, getColorObj(color))
# grad.setColorAt(1, Qt.black)
# self.setBrush(grad)
self.setBrush(getBrushObj(color, alpha=128))
self.setPath(FWDPXI_PP)
self.setPen(getNoPen())
self._click_area.setPos(-0.5 * IW, -0.75 * IW)
else:
self.setPath(REVPXI_PP)
self.setPen(getPenObj(color, 0.25, alpha=128))
# grad = QLinearGradient(0., 0., 0., -1.)
# grad.setColorAt(1, getColorObj(color))
# grad.setColorAt(0, Qt.black)
# self.setPen(getNoPen())
# self.setBrush(grad)
self._click_area.setPos(-0.5 * IW, -0.25 * IW)
def __init__(self, is_fwd, pre_xover_item):
"""
Args:
is_fwd (bool): True if forward strand base, False if reverse.
pre_xover_item (TYPE): Description
"""
super(Triangle, self).__init__(pre_xover_item)
color = pre_xover_item.color
self.adapter = PropertyWrapperObject(self)
self.setAcceptHoverEvents(True)
self.setFiltersChildEvents(True)
self._click_area = click_area = QGraphicsRectItem(PXI_RECT, self)
click_area.setAcceptHoverEvents(True)
click_area.setPen(getNoPen())
click_area.hoverMoveEvent = self.hoverMoveEvent
if is_fwd:
# grad = QLinearGradient(0., 0., 0., 1.)
# grad.setColorAt(0, getColorObj(color))
# grad.setColorAt(1, Qt.black)
# self.setBrush(grad)
self.setBrush(getBrushObj(color, alpha=128))
self.setPath(FWDPXI_PP)
self.setPen(getNoPen())
self._click_area.setPos(-0.5*IW, -0.75*IW)
else:
self.setPath(REVPXI_PP)
self.setPen(getPenObj(color, 0.25, alpha=128))
# grad = QLinearGradient(0., 0., 0., -1.)
# grad.setColorAt(1, getColorObj(color))
# grad.setColorAt(0, Qt.black)
# self.setPen(getNoPen())
# self.setBrush(grad)
self._click_area.setPos(-0.5*IW, -0.25*IW)
def __init__(self, rect, parent=None):
super(QGraphicsEllipseItem, self).__init__(rect, parent)
self._parent = parent
self.setPen(getNoPen())
iw = _ITEM_WIDTH = 3
x = _RECT.width() - 2*rect_gain - 2*styles.SLICE_HELIX_STROKE_WIDTH - 1
y = _RECT.center().y()
prexo_items = {}
fwd_angles = [0, 240, 120]
fwd_colors = ['#cc0000', '#00cc00', '#0000cc']
for i in range(len(fwd_angles)):
item = QGraphicsEllipseItem(x, y, iw, iw, self)
item.setPen(getNoPen())
item.setBrush(getBrushObj(fwd_colors[i]))
item.setTransformOriginPoint(_RECT.center())
item.setRotation(fwd_angles[i])
prexo_items[i] = item
rev_angles = [150, 30, 270]
rev_colors = ['#800000cc', '#80cc0000', '#8000cc00']
# rev_colors = ['#ff00ff', '#3399ff', '#ff6600']
for i in range(len(fwd_angles)):
item = QGraphicsEllipseItem(x, y, iw, iw, self)
item.setPen(getPenObj(rev_colors[i],0.5))
item.setBrush(getNoBrush())
item.setTransformOriginPoint(_RECT.center())
item.setRotation(rev_angles[i])
prexo_items[i] = item
def __init__(self, model_part, part_item):
super(QGraphicsRectItem, self).__init__(BASE_RECT, part_item)
# self.setAcceptHoverEvents(True)
# self.setBrush(getNoBrush())
self.setBrush(getBrushObj(styles.BLUE_FILL, alpha=12))
self.setPen(getNoPen())
self.setZValue(styles.ZWORKPLANE)
self._model_part = model_part
self._part_item = part_item
self._idx_low, self._idx_high = model_part.getProperty('workplane_idxs')
self._low_drag_bound = 0 # idx, not pos
self._high_drag_bound = model_part.getProperty('max_vhelix_length') # idx, not pos
self.outline = PathWorkplaneOutline(self)
self.resize_handle_group = ResizeHandleGroup(self.rect(),
self._HANDLE_SIZE,
styles.BLUE_STROKE,
True,
HandleType.LEFT | HandleType.RIGHT,
self,
translates_in=Axis.X)
# Minimum size hint (darker internal rect, visible during resizing)
self.model_bounds_hint = m_b_h = QGraphicsRectItem(self)
m_b_h.setBrush(getBrushObj(styles.BLUE_FILL, alpha=64))
m_b_h.setPen(getNoPen())
m_b_h.hide()
# Low and high idx labels
self.resize_handle_group.updateText(HandleType.LEFT, self._idx_low)
self.resize_handle_group.updateText(HandleType.RIGHT, self._idx_high)
def __init__(self, model_part_instance, viewroot, parent):
"""parent should always be pathrootitem
Args:
model_part_instance (TYPE): Description
viewroot (TYPE): Description
parent (TYPE): Description
"""
super(PathNucleicAcidPartItem, self).__init__(model_part_instance,
viewroot, parent)
self.setAcceptHoverEvents(True)
self._getActiveTool = viewroot.manager.activeToolGetter
self.active_virtual_helix_item = None
m_p = self._model_part
self._controller = NucleicAcidPartItemController(self, m_p)
self.prexover_manager = PreXoverManager(self)
self._virtual_helix_item_list = []
self._initModifierRect()
self._proxy_parent = ProxyParentItem(self)
self._proxy_parent.setFlag(QGraphicsItem.ItemHasNoContents)
self._scale_2_model = m_p.baseWidth() / _BASE_WIDTH
self._scale_2_Qt = _BASE_WIDTH / m_p.baseWidth()
# self._rect = QRectF()
self._vh_rect = QRectF()
# self.setPen(getPenObj(styles.ORANGE_STROKE, 0))
self.setPen(getNoPen())
# self.setRect(self._rect)
self.outline = outline = PathRectItem(self)
outline.setFlag(QGraphicsItem.ItemStacksBehindParent)
self.setZValue(styles.ZPART)
self._proxy_parent.setZValue(styles.ZPART)
outline.setZValue(styles.ZDESELECTOR)
self.outline.setPen(getPenObj(m_p.getColor(), _DEFAULT_WIDTH))
o_rect = self._configureOutline(outline)
model_color = m_p.getColor()
self.resize_handle_group = ResizeHandleGroup(
o_rect,
_HANDLE_SIZE,
model_color,
True,
# HandleType.LEFT |
HandleType.RIGHT,
self)
self.model_bounds_hint = m_b_h = QGraphicsRectItem(self)
m_b_h.setBrush(getBrushObj(styles.BLUE_FILL, alpha=32))
m_b_h.setPen(getNoPen())
m_b_h.hide()
self.workplane = PathWorkplaneItem(m_p, self)
self.hide() # show on adding first vh
def __init__(self, part_instance: ObjectInstance, viewroot: PathRootItemT):
"""parent should always be ``PathRootItem``
Args:
part_instance: ``ObjectInstance`` of the ``Part``
viewroot: ``PathRootItem`` and parent object
"""
super(PathNucleicAcidPartItem, self).__init__(part_instance, viewroot)
self.setAcceptHoverEvents(True)
self._getActiveTool = viewroot.manager.activeToolGetter
self.active_virtual_helix_item: PathVirtualHelixItem = None
m_p = self._model_part
self._controller = NucleicAcidPartItemController(self, m_p)
self.prexover_manager: PreXoverManager = PreXoverManager(self)
self._virtual_helix_item_list = []
self._initModifierRect()
self._proxy_parent = ProxyParentItem(self)
self._proxy_parent.setFlag(QGraphicsItem.ItemHasNoContents)
self._scale_2_model: float = m_p.baseWidth() / _BASE_WIDTH
self._scale_2_Qt: float = _BASE_WIDTH / m_p.baseWidth()
self._vh_rect: QRectF = QRectF()
self.setPen(getNoPen())
self.outline: PathRectItem = PathRectItem(self)
outline = self.outline
outline.setFlag(QGraphicsItem.ItemStacksBehindParent)
self.setZValue(styles.ZPART)
self._proxy_parent.setZValue(styles.ZPART)
outline.setZValue(styles.ZDESELECTOR)
self.outline.setPen(getPenObj(m_p.getColor(), _DEFAULT_WIDTH))
o_rect = self._configureOutline(outline)
model_color = m_p.getColor()
self.resize_handle_group: ResizeHandleGroup = ResizeHandleGroup(
o_rect,
_HANDLE_SIZE,
model_color,
True,
# HandleEnum.LEFT |
HandleEnum.RIGHT,
self)
self.model_bounds_hint = m_b_h = QGraphicsRectItem(self)
m_b_h.setBrush(getBrushObj(styles.BLUE_FILL, alpha=32))
m_b_h.setPen(getNoPen())
m_b_h.hide()
self.hide() # show on adding first vh
def __init__(self, part_instance: ObjectInstance,
viewroot: PathRootItemT):
"""parent should always be ``PathRootItem``
Args:
part_instance: ``ObjectInstance`` of the ``Part``
viewroot: ``PathRootItem`` and parent object
"""
super(PathNucleicAcidPartItem, self).__init__(part_instance, viewroot)
self.setAcceptHoverEvents(True)
self._getActiveTool = viewroot.manager.activeToolGetter
self.active_virtual_helix_item: PathVirtualHelixItem = None
m_p = self._model_part
self._controller = NucleicAcidPartItemController(self, m_p)
self.prexover_manager: PreXoverManager = PreXoverManager(self)
self._virtual_helix_item_list = []
self._initModifierRect()
self._proxy_parent = ProxyParentItem(self)
self._proxy_parent.setFlag(QGraphicsItem.ItemHasNoContents)
self._scale_2_model: float = m_p.baseWidth()/_BASE_WIDTH
self._scale_2_Qt: float = _BASE_WIDTH / m_p.baseWidth()
self._vh_rect: QRectF = QRectF()
self.setPen(getNoPen())
self.outline: PathRectItem = PathRectItem(self)
outline = self.outline
outline.setFlag(QGraphicsItem.ItemStacksBehindParent)
self.setZValue(styles.ZPART)
self._proxy_parent.setZValue(styles.ZPART)
outline.setZValue(styles.ZDESELECTOR)
self.outline.setPen(getPenObj(m_p.getColor(), _DEFAULT_WIDTH))
o_rect = self._configureOutline(outline)
model_color = m_p.getColor()
self.resize_handle_group: ResizeHandleGroup = ResizeHandleGroup(
o_rect, _HANDLE_SIZE,
model_color, True,
# HandleEnum.LEFT |
HandleEnum.RIGHT,
self)
self.model_bounds_hint = m_b_h = QGraphicsRectItem(self)
m_b_h.setBrush(getBrushObj(styles.BLUE_FILL, alpha=32))
m_b_h.setPen(getNoPen())
m_b_h.hide()
self.hide() # show on adding first vh
def __init__(self, from_virtual_helix_item: PathVirtualHelixItemT,
is_fwd: bool,
from_index: int,
nearby_idxs: List[int],
to_vh_id_num: int,
prexoveritem_manager: PreXoverManagerT):
"""Summary
Args:
from_virtual_helix_item: Description
is_fwd: is this a forward strand?
from_index: index of the Virtual Helix this xover is coming from
nearby_idxs:
to_vh_id_num: Virtual Helix number this Xover point might connect to
prexoveritem_manager: Manager of the PreXoverItems
"""
super(QGraphicsRectItem, self).__init__(BASE_RECT, from_virtual_helix_item)
self.adapter = PropertyWrapperObject(self)
self._tick_marks = QGraphicsPathItem(self)
self._tick_marks.setAcceptHoverEvents(True)
self._bond_item = QGraphicsPathItem(self)
self._bond_item.hide()
self._label = PreXoverLabel(is_fwd, self)
self._path = QGraphicsPathItem()
self.setZValue(styles.ZPREXOVERITEM)
self.setPen(getNoPen())
self.resetItem(from_virtual_helix_item, is_fwd, from_index, nearby_idxs, to_vh_id_num, prexoveritem_manager)
self._getActiveTool = from_virtual_helix_item.viewroot().manager.activeToolGetter
def __init__(self, from_virtual_helix_item: PathVirtualHelixItemT,
is_fwd: bool, from_index: int, nearby_idxs: List[int],
to_vh_id_num: int, prexoveritem_manager: PreXoverManagerT):
"""Summary
Args:
from_virtual_helix_item: Description
is_fwd: is this a forward strand?
from_index: index of the Virtual Helix this xover is coming from
nearby_idxs:
to_vh_id_num: Virtual Helix number this Xover point might connect to
prexoveritem_manager: Manager of the PreXoverItems
"""
super(QGraphicsRectItem, self).__init__(BASE_RECT,
from_virtual_helix_item)
self.adapter = PropertyWrapperObject(self)
self._tick_marks = QGraphicsPathItem(self)
self._tick_marks.setAcceptHoverEvents(True)
self._bond_item = QGraphicsPathItem(self)
self._bond_item.hide()
self._label = PreXoverLabel(is_fwd, self)
self._path = QGraphicsPathItem()
self.setZValue(styles.ZPREXOVERITEM)
self.setPen(getNoPen())
self.resetItem(from_virtual_helix_item, is_fwd, from_index,
nearby_idxs, to_vh_id_num, prexoveritem_manager)
self._getActiveTool = from_virtual_helix_item.viewroot(
).manager.activeToolGetter
def __init__(self, step_idx, twist_per_base, bases_per_repeat,
color, pre_xover_item_group, is_fwd=True):
"""Summary
Args:
step_idx (int): the base index within the virtual helix
twist_per_base (float): (turns per repeat)*360/(base per repeat)
bases_per_repeat (int): number of bases that will be displayed
color (str): hexadecimal color code in the form: `#RRGGBB`
pre_xover_item_group (TYPE): Description
is_fwd (bool, optional): Description
"""
super(PreXoverItem, self).__init__(pre_xover_item_group)
self.step_idx = step_idx
self.color = color
self.is_fwd = is_fwd
self.pre_xover_item_group = pre_xover_item_group
self.phos_item = Triangle(is_fwd, self)
self.phos_item.setScale((bases_per_repeat - step_idx)/(2*bases_per_repeat) + 0.5)
self.theta0 = rot = twist_per_base/2 if is_fwd else -twist_per_base/2
self.phos_item.setRotation(rot)
self.is_active5p = self.is_active3p = False
self.item_5p = None
self.item_3p = None
self._default_bond_3p = QLineF()
self._default_p2_3p = QPointF(0, 0)
self.bond_3p = PhosBond(is_fwd, self)
self.setAcceptHoverEvents(True)
self.setFiltersChildEvents(True)
self.setRect(self.phos_item.boundingRect())
self.setPen(getNoPen())
def __init__(self, diameter, parent):
nd = 2*self._RADIUS
offset = -0.5*nd + diameter/2
super(ClickArea, self).__init__(offset, offset, nd, nd, parent=parent)
self.parent_obj = parent
self.setAcceptHoverEvents(True)
self.setPen(getNoPen())
def __init__(self, step_idx, twist_per_base, bases_per_repeat,
color, pre_xover_item_group, is_fwd=True):
"""Summary
Args:
step_idx (int): the base index within the virtual helix
twist_per_base (float): (turns per repeat)*360/(base per repeat)
bases_per_repeat (int): number of bases that will be displayed
color (str): hexadecimal color code in the form: `#RRGGBB`
pre_xover_item_group (TYPE): Description
is_fwd (bool, optional): Description
"""
super(PreXoverItem, self).__init__(pre_xover_item_group)
self.step_idx = step_idx
self.color = color
self.is_fwd = is_fwd
self.pre_xover_item_group = pre_xover_item_group
self.phos_item = Triangle(is_fwd, self)
self.phos_item.setScale((bases_per_repeat - step_idx)/(2*bases_per_repeat) + 0.5)
self.theta0 = rot = twist_per_base/2 if is_fwd else -twist_per_base/2
self.phos_item.setRotation(rot)
self.is_active5p = self.is_active3p = False
self.item_5p = None
self.item_3p = None
self._default_bond_3p = QLineF()
self._default_p2_3p = QPointF(0, 0)
self.bond_3p = PhosBond(is_fwd, self)
self.setAcceptHoverEvents(True)
self.setFiltersChildEvents(True)
self.setRect(self.phos_item.boundingRect())
self.setPen(getNoPen())
def __init__(self, diameter, parent):
nd = 2 * self._RADIUS
offset = -0.5 * nd + diameter / 2
super(ClickArea, self).__init__(offset, offset, nd, nd, parent=parent)
self.parent_obj = parent
self.setAcceptHoverEvents(True)
self.setPen(getNoPen())
def __init__(self, strand_item, virtual_helix_item):
"""
strand_item is a the model representation of the 5prime most strand
of a Xover
Args:
strand_item (TYPE): Description
virtual_helix_item (cadnano.views.pathview.virtualhelixitem.VirtualHelixItem): Description
"""
super(XoverItem, self).__init__(virtual_helix_item.partItem())
self._strand_item = strand_item
self._virtual_helix_item = virtual_helix_item
self._strand5p = None
self._node5 = None
self._node3 = None
self.hide()
# for easier mouseclick
self._click_area = c_a = QGraphicsRectItem(self)
# self._click_area.setAcceptHoverEvents(True)
# c_a.hoverMoveEvent = self.hoverMoveEvent
c_a.mousePressEvent = self.mousePressEvent
c_a.mouseMoveEvent = self.mouseMoveEvent
c_a.setPen(getNoPen())
self._getActiveTool = strand_item._getActiveTool
def __init__(self, part_instance: ObjectInstance, viewroot: GridRootItemT):
"""Summary
Args:
part_instance: ``ObjectInstance`` of the ``Part``
viewroot: ``GridRootItem``
parent: Default is ``None``
"""
super(GridNucleicAcidPartItem, self).__init__(part_instance, viewroot)
self._getActiveTool = viewroot.manager.activeToolGetter
m_p = self._model_part
self._controller = NucleicAcidPartItemController(self, m_p)
self.scale_factor: float = self._RADIUS / m_p.radius()
self.active_virtual_helix_item: GridVirtualHelixItem = None
self.prexover_manager = PreXoverManager(self)
self.hide() # hide while until after attemptResize() to avoid flicker
# set this to a token value
self._rect: QRectF = QRectF(0., 0., 1000., 1000.)
self.boundRectToModel()
self.setPen(getNoPen())
self.setRect(self._rect)
self.setAcceptHoverEvents(True)
# Cache of VHs that were active as of last call to activeGridChanged
# If None, all grids will be redrawn and the cache will be filled.
# Connect destructor. This is for removing a part from scenes.
# initialize the NucleicAcidPartItem with an empty set of old coords
self.setZValue(styles.ZPARTITEM)
outline = QGraphicsRectItem(self)
self.outline: QGraphicsRectItem = outline
o_rect = self._configureOutline(outline)
outline.setFlag(QGraphicsItem.ItemStacksBehindParent)
outline.setZValue(styles.ZDESELECTOR)
model_color = m_p.getColor()
outline.setPen(getPenObj(model_color, _DEFAULT_WIDTH))
GC_SIZE = 10
self.grab_cornerTL: GrabCornerItem = GrabCornerItem(
GC_SIZE, model_color, True, self)
self.grab_cornerTL.setTopLeft(o_rect.topLeft())
self.grab_cornerBR: GrabCornerItem = GrabCornerItem(
GC_SIZE, model_color, True, self)
self.grab_cornerBR.setBottomRight(o_rect.bottomRight())
self.griditem: GridItem = GridItem(self,
self._model_props['grid_type'])
self.griditem.setZValue(1)
self.grab_cornerTL.setZValue(2)
self.grab_cornerBR.setZValue(2)
# select upon creation
for part in m_p.document().children():
if part is m_p:
part.setSelected(True)
else:
part.setSelected(False)
self.show()
def resetItem(self, from_virtual_helix_item, is_fwd, from_index,
to_vh_id_num, prexoveritemgroup, color):
"""Summary
Args:
from_virtual_helix_item (cadnano.gui.views.pathview.virtualhelixitem.VirtualHelixItem): Description
is_fwd (TYPE): Description
from_index (TYPE): Description
to_vh_id_num (TYPE): Description
prexoveritemgroup (TYPE): Description
color (TYPE): Description
Returns:
TYPE: Description
"""
self.setParentItem(from_virtual_helix_item)
self.resetTransform()
self._id_num = from_virtual_helix_item.idNum()
self.idx = from_index
self.is_fwd = is_fwd
self.to_vh_id_num = to_vh_id_num
self._color = color
self.prexoveritemgroup = prexoveritemgroup
self._bond_item.hide()
self._label_txt = lbt = None if to_vh_id_num is None else str(
to_vh_id_num)
self.setLabel(text=lbt)
self._label.resetItem(is_fwd, color)
phos = self._phos_item
bonditem = self._bond_item
if is_fwd:
phos.setPath(FWDPHOS_PP)
phos.setTransformOriginPoint(0, phos.boundingRect().center().y())
phos.setPos(0.5 * BASE_WIDTH, BASE_WIDTH)
phos.setPen(getNoPen())
phos.setBrush(getBrushObj(color))
bonditem.setPen(getPenObj(color, styles.PREXOVER_STROKE_WIDTH))
self.setPos(from_index * BASE_WIDTH, -BASE_WIDTH)
else:
phos.setPath(REVPHOS_PP)
phos.setTransformOriginPoint(0, phos.boundingRect().center().y())
phos.setPos(0.5 * BASE_WIDTH, 0)
phos.setPen(getPenObj(color, 0.25))
phos.setBrush(getNoBrush())
bonditem.setPen(
getPenObj(color,
styles.PREXOVER_STROKE_WIDTH,
penstyle=Qt.DotLine,
capstyle=Qt.RoundCap))
self.setPos(from_index * BASE_WIDTH, 2 * BASE_WIDTH)
if to_vh_id_num is not None:
inactive_alpha = PROX_ALPHA
self.setBrush(getBrushObj(color, alpha=inactive_alpha))
else:
self.setBrush(getBrushObj(color, alpha=0))
self.show()
def __init__(self, parent: QGraphicsItem = None):
"""
Args:
parent: default is ``None``
"""
super(PathWorkplaneOutline, self).__init__(parent)
self.setPen(getNoPen())
self._path = QGraphicsPathItem(self)
self._path.setBrush(getNoBrush())
self._path.setPen(newPenObj(styles.BLUE_STROKE, 0))
def __init__(self, parent: QGraphicsItem = None):
"""
Args:
parent: default is ``None``
"""
super(PathWorkplaneOutline, self).__init__(parent)
self.setPen(getNoPen())
self._path = QGraphicsPathItem(self)
self._path.setBrush(getNoBrush())
self._path.setPen(newPenObj(styles.BLUE_STROKE, 0))
def resetItem(self, from_virtual_helix_item, is_fwd, from_index,
to_vh_id_num, prexoveritemgroup, color):
"""Summary
Args:
from_virtual_helix_item (cadnano.gui.views.pathview.virtualhelixitem.VirtualHelixItem): Description
is_fwd (TYPE): Description
from_index (TYPE): Description
to_vh_id_num (TYPE): Description
prexoveritemgroup (TYPE): Description
color (TYPE): Description
Returns:
TYPE: Description
"""
self.setParentItem(from_virtual_helix_item)
self.resetTransform()
self._id_num = from_virtual_helix_item.idNum()
self.idx = from_index
self.is_fwd = is_fwd
self.to_vh_id_num = to_vh_id_num
self._color = color
self.prexoveritemgroup = prexoveritemgroup
self._bond_item.hide()
self._label_txt = lbt = None if to_vh_id_num is None else str(to_vh_id_num)
self.setLabel(text=lbt)
self._label.resetItem(is_fwd, color)
phos = self._phos_item
bonditem = self._bond_item
if is_fwd:
phos.setPath(FWDPHOS_PP)
phos.setTransformOriginPoint(0, phos.boundingRect().center().y())
phos.setPos(0.5*BASE_WIDTH, BASE_WIDTH)
phos.setPen(getNoPen())
phos.setBrush(getBrushObj(color))
bonditem.setPen(getPenObj(color, styles.PREXOVER_STROKE_WIDTH))
self.setPos(from_index*BASE_WIDTH, -BASE_WIDTH)
else:
phos.setPath(REVPHOS_PP)
phos.setTransformOriginPoint(0, phos.boundingRect().center().y())
phos.setPos(0.5*BASE_WIDTH, 0)
phos.setPen(getPenObj(color, 0.25))
phos.setBrush(getNoBrush())
bonditem.setPen(getPenObj(color, styles.PREXOVER_STROKE_WIDTH,
penstyle=Qt.DotLine, capstyle=Qt.RoundCap))
self.setPos(from_index*BASE_WIDTH, 2*BASE_WIDTH)
if to_vh_id_num is not None:
inactive_alpha = PROX_ALPHA
self.setBrush(getBrushObj(color, alpha=inactive_alpha))
else:
self.setBrush(getBrushObj(color, alpha=0))
self.show()
def __init__(self, diameter: float, parent: GridPoint):
"""
Args:
diameter: defines the size of the clickarea.
parent: the item.
"""
nd = 2 * self._RADIUS
offset = -0.5 * nd + diameter / 2
super(ClickArea, self).__init__(offset, offset, nd, nd, parent=parent)
self.parent_obj = parent
self.setAcceptHoverEvents(True)
self.setPen(getNoPen())
def __init__(self, diameter: float, parent: GridPoint):
"""
Args:
diameter: defines the size of the clickarea.
parent: the item.
"""
nd = 2*self._RADIUS
offset = -0.5*nd + diameter/2
super(ClickArea, self).__init__(offset, offset, nd, nd, parent=parent)
self.parent_obj = parent
self.setAcceptHoverEvents(True)
self.setPen(getNoPen())
def __init__(self, model_part: NucleicAcidPartT,
part_item: PathNucleicAcidPartItemT):
"""
Args:
model_part:
part_item:
"""
super(QGraphicsRectItem, self).__init__(BASE_RECT, part_item.proxy())
self.setAcceptHoverEvents(True)
self.setBrush(getBrushObj(styles.BLUE_FILL, alpha=12))
self.setPen(getNoPen())
self.setZValue(styles.ZWORKPLANE)
self._model_part = model_part
self._part_item = part_item
self._low_drag_bound = 0 # idx, not pos
self._high_drag_bound = model_part.getProperty('max_vhelix_length') # idx, not pos
self._moving_via_handle = False
self.outline = PathWorkplaneOutline(self)
self.resize_handle_group = ResizeHandleGroup(self.rect(),
self._HANDLE_SIZE,
styles.BLUE_STROKE,
True,
HandleEnum.LEFT | HandleEnum.RIGHT,
self,
translates_in=AxisEnum.X)
# Minimum size hint (darker internal rect, visible during resizing)
self.model_bounds_hint = m_b_h = QGraphicsRectItem(self)
m_b_h.setBrush(getBrushObj(styles.BLUE_FILL, alpha=64))
m_b_h.setPen(getNoPen())
m_b_h.hide()
# Low and high idx labels
self.resize_handle_group.updateText(HandleEnum.LEFT, self._idx_low)
self.resize_handle_group.updateText(HandleEnum.RIGHT, self._idx_high)
def __init__(self, radius, rect, pre_xover_item_group):
"""parent could be a PreXoverItemGroup or a VirtualHelixItem
Args:
radius (TYPE): Description
rect (TYPE): Description
pre_xover_item_group (TYPE): Description
"""
super(WedgeGizmo, self).__init__(pre_xover_item_group)
self._radius = radius
self._rect = rect
self.pre_xover_item_group = pre_xover_item_group
self.setPen(getNoPen())
self.setZValue(styles.ZWEDGEGIZMO - 10)
self._last_params = None
def __init__(self, radius, rect, pre_xover_item_group):
"""parent could be a PreXoverItemGroup or a VirtualHelixItem
Args:
radius (TYPE): Description
rect (TYPE): Description
pre_xover_item_group (TYPE): Description
"""
super(WedgeGizmo, self).__init__(pre_xover_item_group)
self._radius = radius
self._rect = rect
self.pre_xover_item_group = pre_xover_item_group
self.setPen(getNoPen())
self.setZValue(styles.ZWEDGEGIZMO - 10)
self._last_params = None
def paint(self, painter: QPainter,
option: QStyleOptionGraphicsItem,
widget: QWidget = None):
"""
Args:
painter: Description
option: Description
widget: Default is ``None``
"""
AbstractPathTool.paint(self, painter, option, widget)
painter.setPen(getNoPen())
painter.setBrush(_BRUSH)
if self._is_top_strand:
painter.drawPath(_FWD_A)
else:
painter.drawPath(_REV_A)
def __init__(self, radius, rect, virtual_helix_item, is_active):
"""Summary
Args:
radius (TYPE): Description
rect (TYPE): Description
virtual_helix_item (VirtualHelixItem): Description
is_active (TYPE): Description
"""
super(PreXoverItemGroup, self).__init__(rect, virtual_helix_item)
self._radius = radius
self._rect = rect
self.virtual_helix_item = virtual_helix_item
self.model_part = virtual_helix_item.part()
self.id_num = virtual_helix_item.idNum()
self.is_active = is_active
self.active_wedge_gizmo = WedgeGizmo(radius, rect, self)
self.fwd_prexover_items = fwd_pxis = {}
self.rev_prexover_items = rev_pxis = {}
self._colors = self._getColors()
self.addItems()
self.setPen(getNoPen())
z = styles.ZPXIGROUP + 10 if is_active else styles.ZPXIGROUP
self.setZValue(z)
self.setTransformOriginPoint(rect.center())
bpr, tpr, eulerZ = virtual_helix_item.getProperty(['bases_per_repeat',
'turns_per_repeat',
'eulerZ'])
self.setRotation(-eulerZ) # add 180
# for baseNearestPoint
fwd_pos, rev_pos = [], []
step_size = self.virtual_helix_item.getProperty('bases_per_repeat')
for i in range(int(step_size)):
fwd_pos.append((fwd_pxis[i].scenePos().x(),
fwd_pxis[i].scenePos().y()))
rev_pos.append((rev_pxis[i].scenePos().x(),
rev_pxis[i].scenePos().y()))
self.fwd_pos_array = np.asarray(fwd_pos)
self.rev_pos_array = np.asarray(rev_pos)
self.baseNearLine = QGraphicsLineItem(self)
self.baseNearLine.setPen(getPenObj("#000000", 0.25, capstyle=Qt.RoundCap))
def __init__(self, radius, rect, virtual_helix_item, is_active):
"""Summary
Args:
radius (TYPE): Description
rect (TYPE): Description
virtual_helix_item (VirtualHelixItem): Description
is_active (TYPE): Description
"""
super(PreXoverItemGroup, self).__init__(rect, virtual_helix_item)
self._radius = radius
self._rect = rect
self.virtual_helix_item = virtual_helix_item
self.model_part = virtual_helix_item.part()
self.id_num = virtual_helix_item.idNum()
self.is_active = is_active
self.active_wedge_gizmo = WedgeGizmo(radius, rect, self)
self.fwd_prexover_items = fwd_pxis = {}
self.rev_prexover_items = rev_pxis = {}
self._colors = self._getColors()
self.addItems()
self.setPen(getNoPen())
z = styles.ZPXIGROUP + 10 if is_active else styles.ZPXIGROUP
self.setZValue(z)
self.setTransformOriginPoint(rect.center())
bpr, tpr, eulerZ = virtual_helix_item.getProperty(
['bases_per_repeat', 'turns_per_repeat', 'eulerZ'])
self.setRotation(-eulerZ) # add 180
# for baseNearestPoint
fwd_pos, rev_pos = [], []
step_size = self.virtual_helix_item.getProperty('bases_per_repeat')
for i in range(int(step_size)):
fwd_pos.append(
(fwd_pxis[i].scenePos().x(), fwd_pxis[i].scenePos().y()))
rev_pos.append(
(rev_pxis[i].scenePos().x(), rev_pxis[i].scenePos().y()))
self.fwd_pos_array = np.asarray(fwd_pos)
self.rev_pos_array = np.asarray(rev_pos)
self.baseNearLine = QGraphicsLineItem(self)
self.baseNearLine.setPen(
getPenObj("#000000", 0.25, capstyle=Qt.RoundCap))
def paint(self, painter, option, widget=None):
"""Summary
Args:
painter (TYPE): Description
option (TYPE): Description
widget (None, optional): Description
Returns:
TYPE: Description
"""
AbstractPathTool.paint(self, painter, option, widget)
painter.setPen(getNoPen())
painter.setBrush(_BRUSH)
if self._is_top_strand:
painter.drawPath(_FWD_A)
else:
painter.drawPath(_REV_A)
def __init__(self, from_virtual_helix_item, is_fwd, from_index,
to_vh_id_num, prexoveritemgroup, color):
"""Summary
Args:
from_virtual_helix_item (cadnano.gui.views.pathview.virtualhelixitem.VirtualHelixItem): Description
is_fwd (TYPE): Description
from_index (TYPE): Description
to_vh_id_num (TYPE): Description
prexoveritemgroup (TYPE): Description
color (TYPE): Description
"""
super(QGraphicsRectItem, self).__init__(BASE_RECT, from_virtual_helix_item)
self.adapter = PropertyWrapperObject(self)
self._bond_item = QGraphicsPathItem(self)
self._bond_item.hide()
self._label = PreXoverLabel(is_fwd, color, self)
self._phos_item = Triangle(FWDPHOS_PP, self)
self.setPen(getNoPen())
self.resetItem(from_virtual_helix_item, is_fwd, from_index,
to_vh_id_num, prexoveritemgroup, color)
def __init__(self, part_item: PathNucleicAcidPartItemT):
"""
Args:
part_item: Description
"""
super(QGraphicsRectItem, self).__init__(part_item)
self.part_item = part_item
self.virtual_helix_item = None
self.setPen(getNoPen())
self._colors = []
# dictionary of tuple of a (PreXoverItem, List[PreXoverItem])
# for activating on hover events
self.prexover_item_map = {}
self.neighbor_prexover_items = {} # just a dictionary of neighbors
self.hovered_items = []
self._key_press_dict = {}
# for reuse of PreXoverItem objects
self.pxi_pool = deque()
self.active_pxis = {}
def __init__(self, from_virtual_helix_item, is_fwd, from_index, nearby_idxs,
to_vh_id_num, prexoveritem_manager):
"""Summary
Args:
from_virtual_helix_item (cadnano.views.pathview.virtualhelixitem.VirtualHelixItem): Description
is_fwd (TYPE): Description
from_index (TYPE): Description
to_vh_id_num (TYPE): Description
prexoveritem_manager (TYPE): Description
"""
super(QGraphicsRectItem, self).__init__(BASE_RECT, from_virtual_helix_item)
self.adapter = PropertyWrapperObject(self)
self._tick_marks = QGraphicsPathItem(self)
self._tick_marks.setAcceptHoverEvents(True)
self._bond_item = QGraphicsPathItem(self)
self._bond_item.hide()
self._label = PreXoverLabel(is_fwd, self)
self._path = QGraphicsPathItem()
self.setZValue(styles.ZPREXOVERITEM)
self.setPen(getNoPen())
self.resetItem(from_virtual_helix_item, is_fwd, from_index, nearby_idxs, to_vh_id_num, prexoveritem_manager)
def __init__(self, from_virtual_helix_item, is_fwd, from_index,
to_vh_id_num, prexoveritemgroup, color):
"""Summary
Args:
from_virtual_helix_item (cadnano.gui.views.pathview.virtualhelixitem.VirtualHelixItem): Description
is_fwd (TYPE): Description
from_index (TYPE): Description
to_vh_id_num (TYPE): Description
prexoveritemgroup (TYPE): Description
color (TYPE): Description
"""
super(QGraphicsRectItem, self).__init__(BASE_RECT,
from_virtual_helix_item)
self.adapter = PropertyWrapperObject(self)
self._bond_item = QGraphicsPathItem(self)
self._bond_item.hide()
self._label = PreXoverLabel(is_fwd, color, self)
self._phos_item = Triangle(FWDPHOS_PP, self)
self.setPen(getNoPen())
self.resetItem(from_virtual_helix_item, is_fwd, from_index,
to_vh_id_num, prexoveritemgroup, color)
def __init__(self, part_item: PathNucleicAcidPartItemT):
"""
Args:
part_item: Description
"""
super(QGraphicsRectItem, self).__init__(part_item)
self.part_item = part_item
self.virtual_helix_item = None
self.setPen(getNoPen())
self._colors = []
# dictionary of tuple of a (PreXoverItem, List[PreXoverItem])
# for activating on hover events
self.prexover_item_map = {}
self.neighbor_prexover_items = {} # just a dictionary of neighbors
self.hovered_items = []
self._key_press_dict = {}
# for reuse of PreXoverItem objects
self.pxi_pool = deque()
self.active_pxis = {}
def __init__(self, virtual_helix_item, xover_item, strand3p, idx):
"""Summary
Args:
virtual_helix_item (VirtualHelixItem): Description
xover_item (TYPE): Description
strand3p (Strand): reference to the 3' strand
idx (int): the base index within the virtual helix
"""
super(XoverNode3, self).__init__(virtual_helix_item)
self._vhi = virtual_helix_item
self._xover_item = xover_item
self._idx = idx
self.is_forward = strand3p.strandSet().isForward()
self.setPartnerVirtualHelix(strand3p)
self.setPen(getNoPen())
self._label = None
self.setBrush(_NO_BRUSH)
self.setRect(_RECT)
self.setZValue(styles.ZXOVERITEM)
def __init__(self, part_instance: ObjectInstance,
viewroot: GridRootItemT):
"""Summary
Args:
part_instance: ``ObjectInstance`` of the ``Part``
viewroot: ``GridRootItem``
parent: Default is ``None``
"""
super(GridNucleicAcidPartItem, self).__init__( part_instance,
viewroot)
self._getActiveTool = viewroot.manager.activeToolGetter
m_p = self._model_part
self._controller = NucleicAcidPartItemController(self, m_p)
self.scale_factor: float = self._RADIUS / m_p.radius()
self.active_virtual_helix_item: GridVirtualHelixItem = None
self.prexover_manager = PreXoverManager(self)
self.hide() # hide while until after attemptResize() to avoid flicker
# set this to a token value
self._rect: QRectF = QRectF(0., 0., 1000., 1000.)
self.boundRectToModel()
self.setPen(getNoPen())
self.setRect(self._rect)
self.setAcceptHoverEvents(True)
# Cache of VHs that were active as of last call to activeGridChanged
# If None, all grids will be redrawn and the cache will be filled.
# Connect destructor. This is for removing a part from scenes.
# initialize the NucleicAcidPartItem with an empty set of old coords
self.setZValue(styles.ZPARTITEM)
outline = QGraphicsRectItem(self)
self.outline: QGraphicsRectItem = outline
o_rect = self._configureOutline(outline)
outline.setFlag(QGraphicsItem.ItemStacksBehindParent)
outline.setZValue(styles.ZDESELECTOR)
model_color = m_p.getColor()
outline.setPen(getPenObj(model_color, _DEFAULT_WIDTH))
GC_SIZE = 10
self.grab_cornerTL: GrabCornerItem = GrabCornerItem(GC_SIZE,
model_color,
True,
self)
self.grab_cornerTL.setTopLeft(o_rect.topLeft())
self.grab_cornerBR: GrabCornerItem = GrabCornerItem(GC_SIZE,
model_color,
True,
self)
self.grab_cornerBR.setBottomRight(o_rect.bottomRight())
self.griditem: GridItem = GridItem(self, self._model_props['grid_type'])
self.griditem.setZValue(1)
self.grab_cornerTL.setZValue(2)
self.grab_cornerBR.setZValue(2)
# select upon creation
for part in m_p.document().children():
if part is m_p:
part.setSelected(True)
else:
part.setSelected(False)
self.show()
from cadnano.gui.palette import getPenObj, getBrushObj, getNoPen
from PyQt5.QtCore import QRectF, Qt, QPointF, QEvent
from PyQt5.QtGui import QBrush, QPen, QFont, QColor, QFontMetricsF, QPainterPath
from PyQt5.QtGui import QTransform, QTextCursor
from PyQt5.QtWidgets import QGraphicsItem, QGraphicsPathItem, QGraphicsRectItem
from PyQt5.QtWidgets import QGraphicsTextItem, QLabel
_BASE_WIDTH = _BW = styles.PATH_BASE_WIDTH
_HALF_BASE_WIDTH = _HBW = _BASE_WIDTH / 2
_OFFSET1 = _BASE_WIDTH / 4
_DEFAULT_RECT = QRectF(0, 0, _BW, _BW)
_B_PEN = getPenObj(styles.BLUE_STROKE, styles.INSERTWIDTH)
_R_PEN = getPenObj(styles.RED_STROKE, styles.SKIPWIDTH)
_NO_PEN = getNoPen()
def _insertGen(path, start, c1, p1, c2):
path.moveTo(start)
path.quadTo(c1, p1)
path.quadTo(c2, start)
# end def
_PATH_START = QPointF(_HBW, _HBW)
_PATH_MID_UP = QPointF(_HBW, -_BW)
_PATH_UP_UP_CTRL_PT = QPointF(-_HBW, -_BW)
_PATH_UP_DOWN_CTRL_PT = QPointF(1.5 * _BW, -_BW)
_PATH_MID_DOWN = QPointF(_HBW, 2 * _BW)
_PATH_DOWN_DOWN_CTRL_PT = QPointF(-_HBW, 2 * _BW)
_PATH_DOWN_UP_CTRL_PT = QPointF(1.5 * _BW, 2 * _BW)
def __init__(self, diameter: float, parent: GridPoint):
nd = 2 * self._RADIUS
offset = -0.5 * nd + diameter / 2
super(ClickArea, self).__init__(offset, offset, nd, nd, parent=parent)
self.parent_obj = parent
self.setPen(getNoPen())
def __init__(self, model_part_instance, viewroot, parent=None):
"""Summary
Args:
model_part_instance (TYPE): Description
viewroot (TYPE): Description
parent (None, optional): Description
"""
super(SliceNucleicAcidPartItem, self).__init__(model_part_instance, viewroot, parent)
self._getActiveTool = viewroot.manager.activeToolGetter
m_p = self._model_part
self._controller = NucleicAcidPartItemController(self, m_p)
self.scale_factor = self._RADIUS / m_p.radius()
self.active_virtual_helix_item = None
self.prexover_manager = PreXoverManager(self)
self.hide() # hide while until after attemptResize() to avoid flicker
self._rect = QRectF(0., 0., 1000., 1000.) # set this to a token value
self.boundRectToModel()
self.setPen(getNoPen())
self.setRect(self._rect)
self.setAcceptHoverEvents(True)
# Cache of VHs that were active as of last call to activeSliceChanged
# If None, all slices will be redrawn and the cache will be filled.
# Connect destructor. This is for removing a part from scenes.
# initialize the NucleicAcidPartItem with an empty set of old coords
self.setZValue(styles.ZPARTITEM)
self.outline = outline = QGraphicsRectItem(self)
o_rect = self.configureOutline(outline)
outline.setFlag(QGraphicsItem.ItemStacksBehindParent)
outline.setZValue(styles.ZDESELECTOR)
model_color = m_p.getColor()
self.outline.setPen(getPenObj(model_color, _DEFAULT_WIDTH))
GC_SIZE = 20
self.grab_cornerTL = GrabCornerItem(GC_SIZE, model_color, True, self)
self.grab_cornerTL.setTopLeft(o_rect.topLeft())
self.grab_cornerBR = GrabCornerItem(GC_SIZE, model_color, True, self)
self.grab_cornerBR.setBottomRight(o_rect.bottomRight())
self.griditem = GridItem(self, self._model_props['grid_type'])
self.griditem.setZValue(1)
self.grab_cornerTL.setZValue(2)
self.grab_cornerBR.setZValue(2)
self.vhi_hint_item = QGraphicsEllipseItem(_DEFAULT_RECT, self)
self.vhi_hint_item.setPen(_MOD_PEN)
self.vhi_hint_item.setZValue(styles.ZPARTITEM)
# select upon creation
for part in m_p.document().children():
if part is m_p:
part.setSelected(True)
else:
part.setSelected(False)
self.show()
def __init__(self, parent=None):
super(PathWorkplaneOutline, self).__init__(parent)
self.setPen(getNoPen())
self._path = QGraphicsPathItem(self)
self._path.setBrush(getNoBrush())
self._path.setPen(newPenObj(styles.BLUE_STROKE, 0))
def __init__(self, model_part_instance, viewroot, parent=None):
"""Summary
Args:
model_part_instance (TYPE): Description
viewroot (TYPE): Description
parent (None, optional): Description
"""
super(SliceNucleicAcidPartItem, self).__init__(model_part_instance,
viewroot, parent)
self.shortest_path_start = None
self.neighbor_map = dict()
self.coordinates_to_vhid = dict()
self.coordinates_to_xy = dict()
self._last_hovered_item = None
self._highlighted_path = []
self.spa_start_vhi = None
self.last_mouse_position = None
self._translated_x = 0.0
self._translated_y = 0.0
self._getActiveTool = viewroot.manager.activeToolGetter
m_p = self._model_part
self._controller = NucleicAcidPartItemController(self, m_p)
self.scale_factor = self._RADIUS / m_p.radius()
self.inverse_scale_factor = m_p.radius() / self._RADIUS
self.active_virtual_helix_item = None
self.prexover_manager = PreXoverManager(self)
self.hide() # hide while until after attemptResize() to avoid flicker
self._rect = QRectF(0., 0., 1000., 1000.) # set this to a token value
self.boundRectToModel()
self.setPen(getNoPen())
self.setRect(self._rect)
self.setAcceptHoverEvents(True)
self.shortest_path_add_mode = False
# Cache of VHs that were active as of last call to activeSliceChanged
# If None, all slices will be redrawn and the cache will be filled.
# Connect destructor. This is for removing a part from scenes.
# initialize the NucleicAcidPartItem with an empty set of old coords
self.setZValue(styles.ZPARTITEM)
self.outline = outline = QGraphicsRectItem(self)
o_rect = self._configureOutline(outline)
outline.setFlag(QGraphicsItem.ItemStacksBehindParent)
outline.setZValue(styles.ZDESELECTOR)
model_color = m_p.getColor()
self.outline.setPen(getPenObj(model_color, _DEFAULT_WIDTH))
self.model_bounds_hint = QGraphicsRectItem(self)
self.model_bounds_hint.setBrush(getBrushObj(model_color, alpha=12))
self.model_bounds_hint.setPen(getNoPen())
self.resize_handle_group = ResizeHandleGroup(
o_rect,
_HANDLE_SIZE,
model_color,
True,
HandleType.TOP | HandleType.BOTTOM | HandleType.LEFT
| HandleType.RIGHT | HandleType.TOP_LEFT | HandleType.TOP_RIGHT
| HandleType.BOTTOM_LEFT | HandleType.BOTTOM_RIGHT,
self,
show_coords=True)
self.griditem = GridItem(self, self._model_props['grid_type'])
self.griditem.setZValue(1)
self.resize_handle_group.setZValue(2)
self.x_axis_line = QGraphicsLineItem(0, 0, self._RADIUS, 0, self)
self.x_axis_line.setPen(getPenObj('#cc0000', _DEFAULT_WIDTH))
self.x_axis_line.setZValue(styles.ZAXIS)
self.y_axis_line = QGraphicsLineItem(0, 0, 0, -self._RADIUS, self)
self.y_axis_line.setPen(getPenObj('#007200', _DEFAULT_WIDTH))
self.y_axis_line.setZValue(styles.ZAXIS)
# select upon creation
for part in m_p.document().children():
if part is m_p:
part.setSelected(True)
else:
part.setSelected(False)
self.show()
from PyQt5.QtWidgets import QGraphicsLineItem, QGraphicsSimpleTextItem
from cadnano import getBatch
from cadnano.controllers.stranditemcontroller import StrandItemController
from cadnano.gui.palette import getColorObj, getPenObj, getBrushObj, getNoPen
from cadnano.views.pathview import pathstyles as styles
from .decorators.insertionitem import InsertionItem
from .endpointitem import EndpointItem
from .xoveritem import XoverItem
# import logging
# logger = logging.getLogger(__name__)
_BASE_WIDTH = styles.PATH_BASE_WIDTH
_DEFAULT_RECT = QRectF(0, 0, _BASE_WIDTH, _BASE_WIDTH)
_NO_PEN = getNoPen()
SELECT_COLOR = "#ff3333"
class StrandItem(QGraphicsLineItem):
FILTER_NAME = "strand"
__slots__ = ('_model_strand', '_virtual_helix_item', '_viewroot',
'_getActiveTool', '_controller', 'is_forward',
'_strand_filter', '_insertion_items', '_low_cap', '_high_cap',
'_dual_cap', '_seq_label', '_click_area', 'xover_3p_end')
def __init__(self, model_strand, virtual_helix_item, viewroot):
"""The parent should be a VirtualHelixItem."""
super(StrandItem, self).__init__(virtual_helix_item)
self._model_strand = model_strand
def __init__(self, diameter: float, parent: GridPoint):
nd = 2*self._RADIUS
offset = -0.5*nd + diameter/2
super(ClickArea, self).__init__(offset, offset, nd, nd, parent=parent)
self.parent_obj = parent
self.setPen(getNoPen())
