def partPropertyChangedSlot(self, model_part, property_key, new_value):
"""Summary
Args:
model_part (Part): The model part
property_key (TYPE): Description
new_value (TYPE): Description
Args:
TYPE: Description
"""
if self._model_part == model_part:
self._model_props[property_key] = new_value
if property_key == 'color':
self.outline.setPen(getPenObj(new_value, _DEFAULT_WIDTH))
for vhi in self._virtual_helix_item_hash.values():
vhi.updateAppearance()
self.resize_handle_group.setPens(getPenObj(new_value, 0))
elif property_key == 'is_visible':
if new_value:
self.show()
else:
self.hide()
elif property_key == 'grid_type':
self.griditem.setGridType(new_value)
def updateAppearance(self):
"""Check item's current visibility, color and active state, and sets
pen, brush, text according to style defaults.
"""
is_visible, color = self._model_part.getVirtualHelixProperties(self._id_num, ['is_visible', 'color'])
if is_visible:
self.show()
else:
self.hide()
return
pwidth = styles.GRID_HELIX_STROKE_WIDTH if self.old_pen is None else SNAP_WIDTH
if self.is_active:
self._USE_PEN = getPenObj(styles.ACTIVE_STROKE, pwidth)
else:
self._USE_PEN = getPenObj(color, pwidth)
self._TEXT_BRUSH = getBrushObj(styles.GRID_TEXT_COLOR)
self._BRUSH = _BRUSH_DEFAULT
self._USE_BRUSH = getBrushObj(color, alpha=150)
self._label.setBrush(self._TEXT_BRUSH)
self.setBrush(self._BRUSH)
self.setPen(self._USE_PEN)
self.setRect(_RECT)
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 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, handle_type, width, color, handle_group, parent):
''' parent is a :class:`QGraphicsItem` such as a :class:`NucleicAcidPartItem`
'''
super(HandleItem, self).__init__(parent)
self.setAcceptHoverEvents(True)
self._handle_type = handle_type
self._group = handle_group
self.width = w = width
self.half_width = w/2
self.align_offset = parent._BOUNDING_RECT_PADDING
self.model_bounds = ()
self.can_move_x = handle_group.translates_in & AxisEnum.X
self.can_move_y = handle_group.translates_in & AxisEnum.Y
self.setBrush(getBrushObj(styles.RESIZEHANDLE_FILL_COLOR))
self.setPen(getPenObj(color, 0))
self.setRect(QRectF(0, 0, w, w))
self.label = HandleItemLabel(self)
self.event_start_position = QPointF(0, 0)
self.event_scene_start_position = QPointF(0, 0)
if handle_type & (HandleEnum.LEFT | HandleEnum.RIGHT):
self._resize_cursor = Qt.SizeHorCursor
elif handle_type & (HandleEnum.TOP | HandleEnum.BOTTOM):
self._resize_cursor = Qt.SizeVerCursor
elif handle_type & (HandleEnum.TOP_LEFT | HandleEnum.BOTTOM_RIGHT):
self._resize_cursor = Qt.SizeFDiagCursor
elif handle_type & (HandleEnum.TOP_RIGHT | HandleEnum.BOTTOM_LEFT):
self._resize_cursor = Qt.SizeBDiagCursor
else:
self._resize_cursor = Qt.ClosedHandCursor
def hoverLeaveEvent(self, event: QGraphicsSceneHoverEvent):
"""
Args:
event: Description
"""
self.setBrush(getBrushObj(styles.DEFAULT_GRID_DOT_COLOR))
self.setPen(getPenObj(styles.DEFAULT_GRID_DOT_COLOR, 1.0))
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 hoverLeaveEvent(self, event: QGraphicsSceneHoverEvent):
"""
Args:
event: Description
"""
self.setBrush(getBrushObj(styles.DEFAULT_GRID_DOT_COLOR))
self.setPen(getPenObj(styles.DEFAULT_GRID_DOT_COLOR, 1.0))
def partPropertyChangedSlot(self, model_part, property_key, new_value):
"""Summary
Args:
model_part (Part): The model part
property_key (TYPE): Description
new_value (TYPE): Description
Returns:
TYPE: Description
"""
if self._model_part == model_part:
self._model_props[property_key] = new_value
if property_key == 'color':
for vhi in self._virtual_helix_item_list:
vhi.handle().refreshColor()
# self.grab_corner.setPen(getPenObj(new_value, 0))
self.workplane.outline.setPen(getPenObj(new_value, 0))
TLx, TLy, BRx, BRy = self._getVHRectasPoints()
self.reconfigureRect((TLx, TLy), (BRx, BRy))
elif property_key == 'is_visible':
if new_value:
self.show()
else:
self.hide()
elif property_key == 'virtual_helix_order':
vhi_dict = self._virtual_helix_item_hash
new_list = [vhi_dict[id_num] for id_num in new_value]
ztf = False
self._setVirtualHelixItemList(new_list, zoom_to_fit=ztf)
elif property_key == 'workplane_idxs':
if hasattr(self, 'workplane'):
self.workplane.setIdxs(new_idxs=new_value)
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, 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 __init__(self, part_item: SliceNucleicAcidPartItemT,
grid_type: EnumType):
"""previous_grid_bounds (tuple): a tuple corresponding to the bounds of
the grid.
Args:
part_item: Description
grid_type: Description
"""
super(GridItem, self).__init__(parent=part_item)
self.setFlag(QGraphicsItem.ItemClipsChildrenToShape)
self._path = None
self.part_item = part_item
self._path = QGraphicsPathItem(self)
self.dots = (styles.DOT_SIZE, styles.DOT_SIZE / 2)
# self.allow_snap = part_item.window().action_vhelix_snap.isChecked()
self._draw_gridpoint_coordinates = False
self.draw_lines = False
self.points = []
self.points_dict = dict()
self.previous_grid_bounds = None
self.bounds = None
self.grid_type = None
self.setPen(getPenObj(styles.GRAY_STROKE, styles.EMPTY_HELIX_STROKE_WIDTH))
self.setGridType(grid_type)
self.previous_grid_type = grid_type
def __init__(self, part_item, grid_type):
"""Summary
previous_grid_bounds (tuple): a tuple corresponding to the bounds of
the grid.
Args:
part_item (TYPE): Description
grid_type (TYPE): Description
"""
super(GridItem, self).__init__(parent=part_item)
self.setFlag(QGraphicsItem.ItemClipsChildrenToShape)
self._path = None
self.part_item = part_item
self._path = QGraphicsPathItem(self)
self.dots = (styles.DOT_SIZE, styles.DOT_SIZE / 2)
# self.allow_snap = part_item.window().action_vhelix_snap.isChecked()
self._draw_gridpoint_coordinates = False
self.draw_lines = False
self.points = []
self.points_dict = dict()
self.previous_grid_bounds = None
self.bounds = None
self.grid_type = None
self.setPen(
getPenObj(styles.GRAY_STROKE, styles.EMPTY_HELIX_STROKE_WIDTH))
self.setGridType(grid_type)
self.previous_grid_type = grid_type
def doHoneycomb(self, part_item, radius, bounds):
"""Summary
Args:
part_item (TYPE): Description
radius (TYPE): Description
bounds (TYPE): Description
Returns:
TYPE: Description
"""
doLattice = HoneycombDnaPart.latticeCoordToPositionXY
doPosition = HoneycombDnaPart.positionToLatticeCoordRound
isEven = HoneycombDnaPart.isEvenParity
x_l, x_h, y_l, y_h = bounds
dot_size, half_dot_size = self.dots
sf = part_item.scale_factor
points = self.points
row_l, col_l = doPosition(radius, x_l, -y_l, False, False, scale_factor=sf)
row_h, col_h = doPosition(radius, x_h, -y_h, True, True, scale_factor=sf)
# print(row_l, row_h, col_l, col_h)
path = QPainterPath()
is_pen_down = False
draw_lines = self.draw_lines
for i in range(row_l, row_h):
for j in range(col_l, col_h+1):
x, y = doLattice(radius, i, j, scale_factor=sf)
if draw_lines:
if is_pen_down:
path.lineTo(x, -y)
else:
is_pen_down = True
path.moveTo(x, -y)
""" +x is Left and +y is down
origin of ellipse is Top Left corner so we subtract half in X
and subtract in y
"""
pt = GridPoint(x - half_dot_size,
-y - half_dot_size,
dot_size, self)
pt.setPen(getPenObj(Qt.blue, 1.0))
points.append(pt)
is_pen_down = False
# end for i
# DO VERTICAL LINES
if draw_lines:
for j in range(col_l, col_h+1):
# print("newcol")
for i in range(row_l, row_h):
x, y = doLattice(radius, i, j, scale_factor=sf)
if is_pen_down and isEven(i, j):
path.lineTo(x, -y)
is_pen_down = False
else:
is_pen_down = True
path.moveTo(x, -y)
is_pen_down = False
# end for j
self.setPath(path)
def __init__(self, handle_type, width, color, handle_group, parent):
''' parent is a :class:`QGraphicsItem` such as a :class:`NucleicAcidPartItem`
'''
super(HandleItem, self).__init__(parent)
self.setAcceptHoverEvents(True)
self._handle_type = handle_type
self._group = handle_group
self.width = w = width
self.half_width = w / 2
self.align_offset = parent._BOUNDING_RECT_PADDING
self.model_bounds = ()
self.can_move_x = handle_group.translates_in & AxisEnum.X
self.can_move_y = handle_group.translates_in & AxisEnum.Y
self.setBrush(getBrushObj(styles.RESIZEHANDLE_FILL_COLOR))
self.setPen(getPenObj(color, 0))
self.setRect(QRectF(0, 0, w, w))
self.label = HandleItemLabel(self)
self.event_start_position = QPointF(0, 0)
self.event_scene_start_position = QPointF(0, 0)
if handle_type & (HandleEnum.LEFT | HandleEnum.RIGHT):
self._resize_cursor = Qt.SizeHorCursor
elif handle_type & (HandleEnum.TOP | HandleEnum.BOTTOM):
self._resize_cursor = Qt.SizeVerCursor
elif handle_type & (HandleEnum.TOP_LEFT | HandleEnum.BOTTOM_RIGHT):
self._resize_cursor = Qt.SizeFDiagCursor
elif handle_type & (HandleEnum.TOP_RIGHT | HandleEnum.BOTTOM_LEFT):
self._resize_cursor = Qt.SizeBDiagCursor
else:
self._resize_cursor = Qt.ClosedHandCursor
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 resetPen(self, color: str, width: int = 0):
"""
Args:
color: color string
width: Default is 0
"""
pen = getPenObj(color, width)
self.outline.setPen(pen)
def __init__(self, is_fwd, parent=None):
"""Summary
Args:
is_fwd (TYPE): Description
parent (None, optional): Description
"""
super(PhosBond, self).__init__(parent)
self.adapter = PropertyWrapperObject(self)
color = parent.color
if is_fwd: # lighter solid
self.setPen(getPenObj(color, 0.25, alpha=42, capstyle=Qt.RoundCap))
else: # darker, dotted
self.setPen(getPenObj(color, 0.25,
alpha=64,
penstyle=Qt.DotLine,
capstyle=Qt.RoundCap))
def __init__(self, is_fwd, parent=None):
"""Summary
Args:
is_fwd (TYPE): Description
parent (None, optional): Description
"""
super(PhosBond, self).__init__(parent)
self.adapter = PropertyWrapperObject(self)
color = parent.color
if is_fwd: # lighter solid
self.setPen(getPenObj(color, 0.25, alpha=42, capstyle=Qt.RoundCap))
else: # darker, dotted
self.setPen(getPenObj(color, 0.25,
alpha=64,
penstyle=Qt.DotLine,
capstyle=Qt.RoundCap))
def refreshColor(self):
"""
"""
part_color = self._model_part.getProperty('color')
self._USE_PEN = getPenObj(part_color, styles.VIRTUALHELIXHANDLEITEM_STROKE_WIDTH)
self._USE_BRUSH = getBrushObj(styles.DEFAULT_BRUSH_COLOR)
self.setPen(self._USE_PEN)
self.setBrush(self._USE_BRUSH)
self.update(self.boundingRect())
def resetItem(self, from_virtual_helix_item: PathVirtualHelixItemT,
is_fwd: bool, from_index: int, nearby_idxs: List[int],
to_vh_id_num: int, prexoveritem_manager: PreXoverManagerT):
"""Update this pooled PreXoverItem with current info.
Called by PreXoverManager.
Args:
from_virtual_helix_item: the associated vh_item
is_fwd: True if associated with fwd strand, False if rev strand
from_index: idx of associated vh
nearby_idxs:
to_vh_id_num: id_num of the other vh
prexoveritem_manager: the manager
"""
# to_vh_item = from_virtual_helix_item.partItem().idToVirtualHelixItem(to_vh_id_num)
self.setParentItem(from_virtual_helix_item)
# self.setParentItem(to_vh_item)
self.resetTransform()
self._id_num = from_virtual_helix_item.idNum()
self._model_part = from_virtual_helix_item.part()
self.idx = from_index
self.is_low = False
self.is_high = False
self.nearby_idxs = nearby_idxs
self.is_fwd = is_fwd
self.color = None
self.is3p = None
self.enter_pos = None
self.exit_pos = None
self.to_vh_id_num = to_vh_id_num
self._label_txt = None
self.prexoveritem_manager = prexoveritem_manager
# todo: check here if xover present and disable
result = self.setPathAppearance(from_virtual_helix_item)
if result:
self.setBrush(getNoBrush())
if is_fwd:
self.setPos(from_index * BASE_WIDTH,
-BASE_WIDTH - 0.1 * BASE_WIDTH)
else:
self.setPos(from_index * BASE_WIDTH, 2 * BASE_WIDTH)
self.show()
# label
self._label_txt = lbt = None if to_vh_id_num is None else str(
to_vh_id_num)
self._label.resetItem(is_fwd, self.color)
self.setLabel(text=lbt)
# bond line
bonditem = self._bond_item
bonditem.setPen(
getPenObj(self.color,
styles.PREXOVER_STROKE_WIDTH,
penstyle=Qt.DotLine))
bonditem.hide()
def resetItem(self, from_virtual_helix_item: PathVirtualHelixItemT,
is_fwd: bool,
from_index: int,
nearby_idxs: List[int],
to_vh_id_num: int,
prexoveritem_manager: PreXoverManagerT):
"""Update this pooled PreXoverItem with current info.
Called by PreXoverManager.
Args:
from_virtual_helix_item: the associated vh_item
is_fwd: True if associated with fwd strand, False if rev strand
from_index: idx of associated vh
nearby_idxs:
to_vh_id_num: id_num of the other vh
prexoveritem_manager: the manager
"""
# to_vh_item = from_virtual_helix_item.partItem().idToVirtualHelixItem(to_vh_id_num)
self.setParentItem(from_virtual_helix_item)
# self.setParentItem(to_vh_item)
self.resetTransform()
self._id_num = from_virtual_helix_item.idNum()
self._model_part = from_virtual_helix_item.part()
self.idx = from_index
self.is_low = False
self.is_high = False
self.nearby_idxs = nearby_idxs
self.is_fwd = is_fwd
self.color = None
self.is3p = None
self.enter_pos = None
self.exit_pos = None
self.to_vh_id_num = to_vh_id_num
self._label_txt = None
self.prexoveritem_manager = prexoveritem_manager
# todo: check here if xover present and disable
result = self.setPathAppearance(from_virtual_helix_item)
if result:
self.setBrush(getNoBrush())
if is_fwd:
self.setPos(from_index*BASE_WIDTH, -BASE_WIDTH - 0.1*BASE_WIDTH)
else:
self.setPos(from_index*BASE_WIDTH, 2*BASE_WIDTH)
self.show()
# label
self._label_txt = lbt = None if to_vh_id_num is None else str(to_vh_id_num)
self._label.resetItem(is_fwd, self.color)
self.setLabel(text=lbt)
# bond line
bonditem = self._bond_item
bonditem.setPen(getPenObj( self.color,
styles.PREXOVER_STROKE_WIDTH,
penstyle=Qt.DotLine))
bonditem.hide()
def setPathAppearance(
self, from_virtual_helix_item: PathVirtualHelixItemT) -> bool:
"""Sets the PainterPath according to the index (low = Left, high = Right)
and strand position (top = Up, bottom = Down).
Args:
from_virtual_helix_item:
"""
part = self._model_part
idx = self.idx
is_fwd = self.is_fwd
id_num = self._id_num
strand_type = StrandEnum.FWD if is_fwd else StrandEnum.REV
# relative position info
bpr = from_virtual_helix_item.getProperty('bases_per_repeat')
self.is_low = is_low = idx + 1 in self.nearby_idxs or (
idx + 1) % bpr in self.nearby_idxs
self.is_high = is_high = idx - 1 in self.nearby_idxs or (
idx - 1) % bpr in self.nearby_idxs
# check strand for xover and color
if part.hasStrandAtIdx(id_num, idx)[strand_type]:
strand = part.getStrand(self.is_fwd, id_num, idx)
if strand.hasXoverAt(idx):
return False
self.color = strand.getColor() if strand is not None else EMPTY_COL
else:
self.color = EMPTY_COL
if is_low and is_high:
path = (_FWD_DUAL_PATH, _REV_DUAL_PATH)[strand_type]
raise NotImplementedError("Dual xovers not yet supported")
elif is_low:
path = (_FWD_LO_PATH, _REV_LO_PATH)[strand_type]
self.is3p = True if is_fwd else False
self.enter_pos = _FWD_LO_PTS[0][-1] if is_fwd else _REV_LO_PTS[0][
-1]
self.exit_pos = _FWD_LO_PTS[0][-1] if is_fwd else _REV_LO_PTS[0][-1]
elif is_high:
path = (_FWD_HI_PATH, _REV_HI_PATH)[strand_type]
self.is3p = False if is_fwd else True
self.enter_pos = _FWD_HI_PTS[0][-1] if is_fwd else _REV_HI_PTS[0][
-1]
self.exit_pos = _FWD_HI_PTS[0][-1] if is_fwd else _REV_HI_PTS[0][-1]
else:
# print("unpaired PreXoverItem at {}[{}]".format(self._id_num, self.idx), self.nearby_idxs)
return False
self._tick_marks.setPen(
getPenObj(self.color,
styles.PREXOVER_STROKE_WIDTH,
capstyle=Qt.FlatCap,
joinstyle=Qt.RoundJoin))
self._tick_marks.setPath(path)
self._tick_marks.show()
return True
def _updateFloatPen(self):
"""Summary
Returns:
TYPE: Description
"""
pen_width = styles.PATH_STRAND_STROKE_WIDTH
pen = getPenObj(_PENCIL_COLOR, pen_width)
pen.setCapStyle(Qt.FlatCap)
self.setPen(pen)
def hoverEnterEvent(self, event: QGraphicsSceneHoverEvent):
"""Summary
Args:
event: Description
"""
self.setBrush(getBrushObj(styles.ACTIVE_GRID_DOT_COLOR))
self.setPen(getPenObj(styles.ACTIVE_GRID_DOT_COLOR, 1.0))
part_item = self.grid.part_item
part_item._getActiveTool()
def hoverEnterEvent(self, event):
"""Summary
Args:
event (QGraphicsSceneHoverEvent): Description
"""
self.setBrush(getBrushObj(styles.ACTIVE_GRID_DOT_COLOR))
self.setPen(getPenObj(styles.ACTIVE_GRID_DOT_COLOR, 1.0))
part_item = self.grid.part_item
part_item._getActiveTool()
def _updateFloatPen(self):
"""Summary
Returns:
TYPE: Description
"""
pen_width = styles.PATH_STRAND_STROKE_WIDTH
pen = getPenObj(_PENCIL_COLOR, pen_width)
pen.setCapStyle(Qt.FlatCap)
self.setPen(pen)
def hoverEnterEvent(self, event):
"""Summary
Args:
event (QGraphicsSceneHoverEvent): Description
"""
self.setBrush(getBrushObj(styles.ACTIVE_GRID_DOT_COLOR))
self.setPen(getPenObj(styles.ACTIVE_GRID_DOT_COLOR, 1.0))
self.grid.part_item.vhi_hint_item.setPos(
self.scenePos() - QPointF(_RADIUS - DELTA, _RADIUS - DELTA))
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 doSquare(self, part_item, radius, bounds):
"""Summary
Args:
part_item (TYPE): Description
radius (TYPE): Description
bounds (TYPE): Description
Returns:
TYPE: Description
"""
doLattice = SquareDnaPart.latticeCoordToPositionXY
doPosition = SquareDnaPart.positionToLatticeCoordRound
x_l, x_h, y_l, y_h = bounds
dot_size, half_dot_size = self.dots
sf = part_item.scale_factor
points = self.points
row_l, col_l = doPosition(radius, x_l, -y_l, scale_factor=sf)
row_h, col_h = doPosition(radius, x_h, -y_h, scale_factor=sf)
# print(row_l, row_h, col_l, col_h)
path = QPainterPath()
is_pen_down = False
draw_lines = self.draw_lines
for i in range(row_l, row_h + 1):
for j in range(col_l, col_h + 1):
x, y = doLattice(radius, i, j, scale_factor=sf)
if draw_lines:
if is_pen_down:
path.lineTo(x, -y)
else:
is_pen_down = True
path.moveTo(x, -y)
""" +x is Left and +y is down
origin of ellipse is Top Left corner so we subtract half in X
and subtract in y
"""
pt = GridPoint(x - half_dot_size, -y - half_dot_size, dot_size,
self)
pt.setPen(getPenObj(Qt.blue, 1.0))
points.append(pt)
is_pen_down = False # pen up
# DO VERTICAL LINES
if draw_lines:
for j in range(col_l, col_h + 1):
for i in range(row_l, row_h + 1):
x, y = doLattice(radius, i, j, scale_factor=sf)
if is_pen_down:
path.lineTo(x, -y)
else:
is_pen_down = True
path.moveTo(x, -y)
is_pen_down = False # pen up
self.setPath(path)
def doSquare(self, part_item: GridNucleicAcidPartItemT,
radius: float,
bounds: RectT):
"""
Args:
part_item: Description
radius: Description
bounds: Description
"""
doLattice = SquareDnaPart.latticeCoordToModelXY
doPosition = SquareDnaPart.positionToLatticeCoordRound
x_l, x_h, y_l, y_h = bounds
dot_size, half_dot_size = self.dots
sf = part_item.scale_factor
points = self.points
row_l, col_l = doPosition(radius, x_l, -y_l, scale_factor=sf)
row_h, col_h = doPosition(radius, x_h, -y_h, scale_factor=sf)
# print(row_l, row_h, col_l, col_h)
path = QPainterPath()
is_pen_down = False
draw_lines = self.draw_lines
for i in range(row_l, row_h + 1):
for j in range(col_l, col_h + 1):
x, y = doLattice(radius, i, j, scale_factor=sf)
if draw_lines:
if is_pen_down:
path.lineTo(x, -y)
else:
is_pen_down = True
path.moveTo(x, -y)
"""+x is Left and +y is down
origin of ellipse is Top Left corner so we subtract half in X
and subtract in y
"""
pt = GridPoint(x - half_dot_size,
-y - half_dot_size,
dot_size, self)
pt.setPen(getPenObj(Qt.blue, 1.0))
points.append(pt)
is_pen_down = False # pen up
# DO VERTICAL LINES
if draw_lines:
for j in range(col_l, col_h + 1):
for i in range(row_l, row_h + 1):
x, y = doLattice(radius, i, j, scale_factor=sf)
if is_pen_down:
path.lineTo(x, -y)
else:
is_pen_down = True
path.moveTo(x, -y)
is_pen_down = False # pen up
self.setPath(path)
def resetPen(self, color, width=0):
"""Summary
Args:
color (TYPE): Description
width (int, optional): Description
Returns:
TYPE: Description
"""
pen = getPenObj(color, width)
self.setPen(pen)
def __init__(self, boxtype: QGraphicsItem,
constraint: str,
viewroot: PathRootItemT):
"""
Args:
boxtype: :class:`EndpointHandleSelectionBox` or
:class:`VirtualHelixHandleSelectionBox` instance
constraint: ``x`` or ``y``. Default to ``y`` (up and down)
viewroot: view root item and object parent
"""
super(SelectionItemGroup, self).__init__(viewroot)
self.viewroot: PathRootItemT = viewroot
self.setFiltersChildEvents(True)
# LOOK at Qt Source for deprecated code to replace this behavior
# self.setHandlesChildEvents(True) # commented out NC
self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setFlag(QGraphicsItem.ItemIsFocusable) # for keyPressEvents
self.setFlag(QGraphicsItem.ItemHasNoContents)
self._rect = QRectF()
self._PEN = getPenObj(styles.BLUE_STROKE,
styles.PATH_SELECTBOX_STROKE_WIDTH)
self.selectionbox = boxtype(self)
self._drag_enable = False
self._dragged = False
self._r0 = 0 # save original mousedown
self._r = 0 # latest position for moving
# self._lastKid = 0
# this keeps track of mousePressEvents within the class
# to aid in intellignetly removing items from the group
self._added_to_press_list = False
self._pending_to_add_dict = {}
if constraint == 'y':
self.getR = self.selectionbox.getY
self.translateR = self.selectionbox.translateY
else:
self.getR = self.selectionbox.getX
self.translateR = self.selectionbox.translateX
self._normal_select = True
self.setZValue(styles.ZPATHSELECTION)
def updateProperty(self):
part_color = self.part().getProperty('color')
self._USE_PEN = getPenObj(part_color, styles.SLICE_HELIX_STROKE_WIDTH)
self._OUT_OF_SLICE_PEN = getPenObj(part_color, styles.SLICE_HELIX_STROKE_WIDTH)
self._USE_BRUSH = getBrushObj(part_color, alpha=128)
self._OUT_OF_SLICE_BRUSH = getBrushObj(part_color, alpha=64)
if self.part().crossSectionType() == LatticeType.HONEYCOMB:
self._USE_PEN = getPenObj(styles.BLUE_STROKE, styles.SLICE_HELIX_STROKE_WIDTH)
self._OUT_OF_SLICE_PEN = getPenObj(styles.BLUE_STROKE,\
styles.SLICE_HELIX_STROKE_WIDTH)
if self.part().partType() == PartType.NUCLEICACIDPART:
self._OUT_OF_SLICE_BRUSH = self._OUT_OF_SLICE_BRUSH_DEFAULT
# self._USE_BRUSH = getBrushObj(part_color, lighter=180)
self._USE_BRUSH = getBrushObj(part_color, alpha=150)
self._label.setBrush(self._OUT_OF_SLICE_TEXT_BRUSH)
self.setBrush(self._OUT_OF_SLICE_BRUSH)
self.setPen(self._OUT_OF_SLICE_PEN)
self.setRect(self._RECT)
def __init__(self, boxtype: QGraphicsItem, constraint: str,
viewroot: PathRootItemT):
"""
Args:
boxtype: :class:`EndpointHandleSelectionBox` or
:class:`VirtualHelixHandleSelectionBox` instance
constraint: ``x`` or ``y``. Default to ``y`` (up and down)
viewroot: view root item and object parent
"""
super(SelectionItemGroup, self).__init__(viewroot)
self.viewroot: PathRootItemT = viewroot
self.setFiltersChildEvents(True)
# LOOK at Qt Source for deprecated code to replace this behavior
# self.setHandlesChildEvents(True) # commented out NC
self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setFlag(QGraphicsItem.ItemIsFocusable) # for keyPressEvents
self.setFlag(QGraphicsItem.ItemHasNoContents)
self._rect = QRectF()
self._PEN = getPenObj(styles.BLUE_STROKE,
styles.PATH_SELECTBOX_STROKE_WIDTH)
self.selectionbox = boxtype(self)
self._drag_enable = False
self._dragged = False
self._r0 = 0 # save original mousedown
self._r = 0 # latest position for moving
# self._lastKid = 0
# this keeps track of mousePressEvents within the class
# to aid in intellignetly removing items from the group
self._added_to_press_list = False
self._pending_to_add_dict = {}
if constraint == 'y':
self.getR = self.selectionbox.getY
self.translateR = self.selectionbox.translateY
else:
self.getR = self.selectionbox.getX
self.translateR = self.selectionbox.translateX
self._normal_select = True
self.setZValue(styles.ZPATHSELECTION)
def setPathAppearance(self, from_virtual_helix_item: PathVirtualHelixItemT) -> bool:
"""Sets the PainterPath according to the index (low = Left, high = Right)
and strand position (top = Up, bottom = Down).
Args:
from_virtual_helix_item:
"""
part = self._model_part
idx = self.idx
is_fwd = self.is_fwd
id_num = self._id_num
strand_type = StrandEnum.FWD if is_fwd else StrandEnum.REV
# relative position info
bpr = from_virtual_helix_item.getProperty('bases_per_repeat')
self.is_low = is_low = idx+1 in self.nearby_idxs or (idx+1) % bpr in self.nearby_idxs
self.is_high = is_high = idx-1 in self.nearby_idxs or (idx-1) % bpr in self.nearby_idxs
# check strand for xover and color
if part.hasStrandAtIdx(id_num, idx)[strand_type]:
strand = part.getStrand(self.is_fwd, id_num, idx)
if strand.hasXoverAt(idx):
return False
self.color = strand.getColor() if strand is not None else EMPTY_COL
else:
self.color = EMPTY_COL
if is_low and is_high:
path = (_FWD_DUAL_PATH, _REV_DUAL_PATH)[strand_type]
raise NotImplementedError("Dual xovers not yet supported")
elif is_low:
path = (_FWD_LO_PATH, _REV_LO_PATH)[strand_type]
self.is3p = True if is_fwd else False
self.enter_pos = _FWD_LO_PTS[0][-1] if is_fwd else _REV_LO_PTS[0][-1]
self.exit_pos = _FWD_LO_PTS[0][-1] if is_fwd else _REV_LO_PTS[0][-1]
elif is_high:
path = (_FWD_HI_PATH, _REV_HI_PATH)[strand_type]
self.is3p = False if is_fwd else True
self.enter_pos = _FWD_HI_PTS[0][-1] if is_fwd else _REV_HI_PTS[0][-1]
self.exit_pos = _FWD_HI_PTS[0][-1] if is_fwd else _REV_HI_PTS[0][-1]
else:
# print("unpaired PreXoverItem at {}[{}]".format(self._id_num, self.idx), self.nearby_idxs)
return False
self._tick_marks.setPen(getPenObj( self.color,
styles.PREXOVER_STROKE_WIDTH,
capstyle=Qt.FlatCap,
joinstyle=Qt.RoundJoin))
self._tick_marks.setPath(path)
self._tick_marks.show()
return True
def setSnapOrigin(self, is_snap: bool):
"""Used to toggle an item as the snap origin. See :class:`SelectGridTool`.
Args:
is_snap (bool): True if this should be the snap origin, False otherwise.
"""
if is_snap:
op = self.pen()
if self.old_pen is None:
self.old_pen = op
self.setPen(getPenObj(op.color().name(), SNAP_WIDTH))
else:
self.setPen(self.old_pen)
self.old_pen = None
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 partPropertyChangedSlot(self, part: NucleicAcidPartT, key: str, new_value):
"""Slot
Args:
part: The model part
key: Description
new_value: Description
"""
if self._model_part == part:
self._model_props[key] = new_value
if key == 'color':
self.outline.setPen(getPenObj(new_value, _DEFAULT_WIDTH))
for vhi in self._virtual_helix_item_hash.values():
vhi.updateAppearance()
self.grab_cornerTL.setPen(getPenObj(new_value, 0))
self.grab_cornerBR.setPen(getPenObj(new_value, 0))
elif key == 'is_visible':
if new_value:
self.show()
else:
self.hide()
elif key == 'grid_type':
self.griditem.setGridType(new_value)
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, boxtype, constraint='y', parent=None):
"""Summary
Args:
boxtype (TYPE): Description
constraint (str, optional): Description
parent (None, optional): Description
"""
super(SelectionItemGroup, self).__init__(parent)
self.viewroot = parent
self.setFiltersChildEvents(True)
# LOOK at Qt Source for deprecated code to replace this behavior
# self.setHandlesChildEvents(True) # commented out NC
self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setFlag(QGraphicsItem.ItemIsFocusable) # for keyPressEvents
self.setFlag(QGraphicsItem.ItemHasNoContents)
self._rect = QRectF()
self._PEN = getPenObj(styles.BLUE_STROKE,
styles.PATH_SELECTBOX_STROKE_WIDTH)
self.selectionbox = boxtype(self)
self._drag_enable = False
self._dragged = False
self._r0 = 0 # save original mousedown
self._r = 0 # latest position for moving
# self._lastKid = 0
# this keeps track of mousePressEvents within the class
# to aid in intellignetly removing items from the group
self._added_to_press_list = False
self._pending_to_add_dict = {}
if constraint == 'y':
self.getR = self.selectionbox.getY
self.translateR = self.selectionbox.translateY
else:
self.getR = self.selectionbox.getX
self.translateR = self.selectionbox.translateX
self._normal_select = True
self.setZValue(styles.ZPATHSELECTION)
def __init__(self, boxtype, constraint='y', parent=None):
"""Summary
Args:
boxtype (TYPE): Description
constraint (str, optional): Description
parent (None, optional): Description
"""
super(SelectionItemGroup, self).__init__(parent)
self.viewroot = parent
self.setFiltersChildEvents(True)
# LOOK at Qt Source for deprecated code to replace this behavior
# self.setHandlesChildEvents(True) # commented out NC
self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setFlag(QGraphicsItem.ItemIsFocusable) # for keyPressEvents
self.setFlag(QGraphicsItem.ItemHasNoContents)
self._rect = QRectF()
self._PEN = getPenObj(styles.BLUE_STROKE,
styles.PATH_SELECTBOX_STROKE_WIDTH)
self.selectionbox = boxtype(self)
self._drag_enable = False
self._dragged = False
self._r0 = 0 # save original mousedown
self._r = 0 # latest position for moving
# self._lastKid = 0
# this keeps track of mousePressEvents within the class
# to aid in intellignetly removing items from the group
self._added_to_press_list = False
self._pending_to_add_dict = {}
if constraint == 'y':
self.getR = self.selectionbox.getY
self.translateR = self.selectionbox.translateY
else:
self.getR = self.selectionbox.getX
self.translateR = self.selectionbox.translateX
self._normal_select = True
self.setZValue(styles.ZPATHSELECTION)
def _updateBoundingRect(self):
"""
Updates the bounding rect to the size of the childrenBoundingRect,
and refreshes the addBases and removeBases buttons accordingly.
Called by partZDimensionsChangedSlot and partPropertyChangedSlot
"""
self.setPen(getPenObj(self.modelColor(), 0))
self.resetBrush(styles.DEFAULT_BRUSH_COLOR, styles.DEFAULT_ALPHA)
# self.setRect(self.childrenBoundingRect())
_p = _BOUNDING_RECT_PADDING
temp_rect = self._vh_rect.adjusted(-_p/2, -_p, _p, -_p/2)
self.grab_corner.setTopLeft(temp_rect.topLeft())
self.setRect(temp_rect)
def __init__(self, width, color, is_resizable, parent):
super(GrabCornerItem, self).__init__(parent)
self.setRect(QRectF(0, 0, width, width))
self.width = width
self.half_width = width/2
self.offset = QPointF(width, width)
self.offset_x = QPointF(width, 0)
self.offset_y = QPointF(0, width)
self.align_offset = self.parentItem()._BOUNDING_RECT_PADDING
self.is_grabbing = False
self.setBrush(getBrushObj(FILL_COLOR))
self.setPen(getPenObj(color, 0))
self.is_resizable = is_resizable
self.model_bounds = ()
self.corner_type = TOP_LEFT
def _updateColor(self, strand):
oligo = strand.oligo()
color = SELECT_COLOR if self.isSelected() else oligo.getColor()
if oligo.shouldHighlight():
alpha = 128
pen_width = styles.PATH_STRAND_HIGHLIGHT_STROKE_WIDTH
else:
pen_width = styles.PATH_STRAND_STROKE_WIDTH
alpha = None
self.xover_3p_end._updateColor(strand)
pen = getPenObj(color, pen_width, alpha=alpha, capstyle=Qt.FlatCap)
brush = getBrushObj(color, alpha=alpha)
self.setPen(pen)
self._low_cap.updateHighlight(brush)
self._high_cap.updateHighlight(brush)
self._dual_cap.updateHighlight(brush)
def _updateColor(self, strand):
oligo = strand.oligo()
color = SELECT_COLOR if self.isSelected() else oligo.getColor()
if oligo.shouldHighlight():
alpha = 128
pen_width = styles.PATH_STRAND_HIGHLIGHT_STROKE_WIDTH
else:
pen_width = styles.PATH_STRAND_STROKE_WIDTH
alpha = None
self.xover_3p_end._updateColor(strand)
pen = getPenObj(color, pen_width, alpha=alpha, capstyle=Qt.FlatCap)
brush = getBrushObj(color, alpha=alpha)
self.setPen(pen)
self._low_cap.updateHighlight(brush)
self._high_cap.updateHighlight(brush)
self._dual_cap.updateHighlight(brush)
def __init__(self, width, color, is_resizable, parent):
super(GrabCornerItem, self).__init__(parent)
self.setRect(QRectF(0, 0, width, width))
self.width = width
self.half_width = width / 2
self.offset = QPointF(width, width)
self.offset_x = QPointF(width, 0)
self.offset_y = QPointF(0, width)
self.align_offset = self.parentItem()._BOUNDING_RECT_PADDING
self.is_grabbing = False
self.setBrush(getBrushObj(FILL_COLOR))
self.setPen(getPenObj(color, 0))
self.is_resizable = is_resizable
self.model_bounds = ()
self.corner_type = TOP_LEFT
def resetItem(self, from_virtual_helix_item, is_fwd, from_index, nearby_idxs,
to_vh_id_num, prexoveritem_manager):
"""Update this pooled PreXoverItem with current info.
Called by PreXoverManager.
Args:
from_virtual_helix_item (cadnano.views.pathview.virtualhelixitem.VirtualHelixItem): the associated vh_item
is_fwd (bool): True if associated with fwd strand, False if rev strand
from_index (int): idx of associated vh
to_vh_id_num (int): id_num of the other vh
prexoveritem_manager (cadnano.views.pathview.prexoermanager.PreXoverManager): the manager
"""
self.setParentItem(from_virtual_helix_item)
self.resetTransform()
self._id_num = from_virtual_helix_item.idNum()
self._model_vh = from_virtual_helix_item.cnModel()
self.idx = from_index
self.is_low = False
self.is_high = False
self.nearby_idxs = nearby_idxs
self.is_fwd = is_fwd
self.color = None
self.is3p = None
self.enter_pos = None
self.exit_pos = None
self.to_vh_id_num = to_vh_id_num
self.prexoveritem_manager = prexoveritem_manager
# todo: check here if xover present and disable
result = self.setPathAppearance(from_virtual_helix_item)
if result:
self.setBrush(getNoBrush())
if is_fwd:
self.setPos(from_index*BASE_WIDTH, -BASE_WIDTH)
else:
self.setPos(from_index*BASE_WIDTH, 2*BASE_WIDTH)
self.show()
# label
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, self.color)
# bond line
bonditem = self._bond_item
bonditem.setPen(getPenObj(self.color, styles.PREXOVER_STROKE_WIDTH))
bonditem.hide()
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 __init__(self, tool: SelectGridTool,
parent: GridNucleicAcidPartItemT = None):
"""
Args:
tool: the selection tool
parent: default is ``None``. a :class:`GridNucleicAcidPartItem`
"""
super(GridSelectionGroup, self).__init__(parent)
self.tool = tool
self.setFiltersChildEvents(True)
self.setFlag(QGraphicsItem.ItemIsFocusable) # for keyPressEvents
self.setFlag(QGraphicsItem.ItemIsMovable)
self.bounding_rect_item = bri = QGraphicsRectItem(tool)
bri.hide()
bri.setPen(getPenObj(_SELECT_COLOR, _SELECT_PEN_WIDTH))
self.setZValue(styles.ZSELECTION)
self.drag_start_position = QPointF()
self.drag_last_position = QPointF()
def __init__(self, tool, parent=None):
"""Summary
Args:
tool (TYPE): Description
parent (None, optional): Description
"""
super(SliceSelectionGroup, self).__init__(parent)
self.tool = tool
self.setFiltersChildEvents(True)
self.setFlag(QGraphicsItem.ItemIsFocusable) # for keyPressEvents
self.setFlag(QGraphicsItem.ItemIsMovable)
self.bounding_rect_item = bri = QGraphicsRectItem(tool)
bri.hide()
bri.setPen(getPenObj(_SELECT_COLOR, _SELECT_PEN_WIDTH))
self.setZValue(styles.ZSELECTION)
self.drag_start_position = QPointF()
self.drag_last_position = QPointF()
def setTextAndStyle(self, text, outline=False):
"""Summary
Args:
text (TYPE): Description
outline (bool, optional): Description
Returns:
TYPE: Description
"""
str_txt = str(text)
self._tbr = tBR = self._FM.tightBoundingRect(str_txt)
half_label_H = tBR.height() / 2.0
half_label_W = tBR.width() / 2.0
labelX = BASE_WIDTH/2.0 - half_label_W
if str_txt == '1': # adjust for the number one
labelX -= tBR.width()
labelY = half_label_H if self.is_fwd else (BASE_WIDTH - tBR.height())/2
self.setPos(labelX, labelY)
self.setText(str_txt)
if outline:
self.setFont(self._XO_BOLD)
self.setBrush(getBrushObj('#ff0000'))
else:
self.setFont(self._XO_FONT)
self.setBrush(getBrushObj('#666666'))
if outline:
r = QRectF(self._tbr).adjusted(-half_label_W, 0,
half_label_W, half_label_H)
self._outline.setRect(r)
self._outline.setPen(getPenObj('#ff0000', 0.25))
self._outline.setY(2*half_label_H)
self._outline.show()
else:
self._outline.hide()
def showWedge(self, angle, color,
extended=False, rev_gradient=False, outline_only=False):
"""Summary
Args:
angle (TYPE): Description
color (TYPE): Description
extended (bool, optional): Description
rev_gradient (bool, optional): Description
outline_only (bool, optional): Description
"""
# Hack to keep wedge in front
# self.setRotation(self.pre_xover_item_group.rotation())
self._last_params = (angle, color, extended, rev_gradient, outline_only)
radius = self._radius
span = self.pre_xover_item_group.partCrossoverSpanAngle() / 2
radius_adjusted = radius + (_WEDGE_RECT_GAIN / 2)
tip = QPointF(radius_adjusted, radius_adjusted)
EXT = 1.35 if extended else 1.0
# print("wtf", tip, pos)
base_p2 = QPointF(1, 1)
line0 = QLineF(tip, QPointF(base_p2))
line1 = QLineF(tip, QPointF(base_p2))
line2 = QLineF(tip, QPointF(base_p2))
quad_scale = 1 + (.22*(span - 5) / 55) # lo+(hi-lo)*(val-min)/(max-min)
line0.setLength(radius_adjusted * EXT*quad_scale) # for quadTo control point
line1.setLength(radius_adjusted * EXT)
line2.setLength(radius_adjusted * EXT)
line0.setAngle(angle)
line1.setAngle(angle - span)
line2.setAngle(angle + span)
path = QPainterPath()
if outline_only:
self.setPen(getPenObj(color, 0.5, alpha=128, capstyle=Qt.RoundCap))
path.moveTo(line1.p2())
path.quadTo(line0.p2(), line2.p2())
else:
gradient = QRadialGradient(tip, radius_adjusted * EXT)
color1 = getColorObj(color, alpha=80)
color2 = getColorObj(color, alpha=0)
if rev_gradient:
color1, color2 = color2, color1
if extended:
gradient.setColorAt(0, color1)
gradient.setColorAt(radius_adjusted / (radius_adjusted * EXT), color1)
gradient.setColorAt(radius_adjusted / (radius_adjusted * EXT) + 0.01, color2)
gradient.setColorAt(1, color2)
else:
gradient.setColorAt(0, getColorObj(color, alpha=50))
brush = QBrush(gradient)
self.setBrush(brush)
path.moveTo(line1.p1())
path.lineTo(line1.p2())
path.quadTo(line0.p2(), line2.p2())
path.lineTo(line2.p1())
self.setPath(path)
self.show()
GridVirtualHelixItemT
)
from cadnano.cntypes import (
KeyT,
ValueT
)
# set up default, hover, and active drawing styles
_RADIUS = styles.GRID_HELIX_RADIUS
_RECT = QRectF(0, 0, 2 * _RADIUS, 2 * _RADIUS)
_FONT = styles.GRID_NUM_FONT
_ZVALUE = styles.ZGRIDHELIX
_BRUSH_DEFAULT = getBrushObj(styles.GRID_FILL)
_USE_TEXT_BRUSH = getBrushObj(styles.USE_TEXT_COLOR)
_HOVER_PEN = getPenObj('#ffffff', 128)
_HOVER_BRUSH = getBrushObj('#ffffff', alpha=5)
SNAP_WIDTH = 3
class GridVirtualHelixItem(AbstractVirtualHelixItem, QGraphicsEllipseItem):
"""The VirtualHelixItem is an individual circle that gets drawn in the GridView
as a child of the NucleicAcidPartItem. Taken as a group, many GridHelix
instances make up the crossection of the NucleicAcidPart. Clicking on a GridHelix
adds a VirtualHelix to the PlasmidPart. The GridHelix then changes appearence
and paints its corresponding VirtualHelix number.
Attributes:
FILTER_NAME (str): Belongs to the filter class 'virtual_helix'.
is_active (bool): Does the item have focus.