class PreXoverItem(QGraphicsRectItem):
"""A PreXoverItem exists between a single 'from' VirtualHelixItem index
and zero or more 'to' VirtualHelixItem Indices
Attributes:
adapter (:obj:`PropertyWrapperObject`): Description
idx (int): the base index within the virtual helix
is_fwd (bool): is this a forward strand?
prexoveritem_manager (:obj:`PreXoverManager`): Manager of the PreXoverItems
to_vh_id_num (int): Virtual Helix number this Xover point might connect to
"""
FILTER_NAME = "xover"
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
# end def
def shutdown(self):
"""Summary
"""
self.setBrush(getNoBrush())
self.to_vh_id_num = None
self.adapter.resetAnimations()
self.setAcceptHoverEvents(False)
self.hide()
# end def
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()
# end def
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
# end def
### ACCESSORS ###
def color(self) -> str:
"""The PreXoverItem's color, derived from the associated strand's oligo.
Returns:
str: color in hex code
"""
return self.color
def getInfo(self) -> ABInfoT:
"""
Returns:
Tuple: (from_id_num, is_fwd, from_index, to_vh_id_num)
"""
return (self._id_num, self.is_fwd, self.idx, self.to_vh_id_num)
def destroyItem(self):
"""Removes animation adapter, label, bond_item, and this item from scene.
"""
scene = self.scene()
self.adapter.destroyItem()
if scene:
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._bond_item)
self._bond_item = None
self.adapter.resetAnimations()
self.adapter = None
scene.removeItem(self)
# end defS
### EVENT HANDLERS ###
def hoverEnterEvent(self, event: QGraphicsSceneHoverEvent):
"""Only ``if enableActive(True)`` is called hover and key events disabled
by default
Args:
event: the hover event
"""
if self._getActiveTool().methodPrefix() != "selectTool":
return
self.setFocus(Qt.MouseFocusReason)
self.prexoveritem_manager.updateModelActiveBaseInfo(self.getInfo())
self.setActiveHovered(True)
status_string = "%d[%d]" % (self._id_num, self.idx)
self.parentItem().window().statusBar().showMessage(status_string)
return QGraphicsItem.hoverEnterEvent(self, event)
# end def
def hoverLeaveEvent(self, event: QGraphicsSceneHoverEvent):
"""Summary
Args:
event (QGraphicsSceneHoverEvent): the hover event
"""
self.prexoveritem_manager.updateModelActiveBaseInfo(None)
self.setActiveHovered(False)
self.clearFocus()
self.parentItem().window().statusBar().showMessage("")
return QGraphicsItem.hoverLeaveEvent(self, event)
# end def
def mousePressEvent(self, event: QGraphicsSceneMouseEvent):
"""TODO: NEED TO ADD FILTER FOR A CLICK ON THE 3' MOST END OF THE XOVER
TO DISALLOW OR HANDLE DIFFERENTLY
"""
viewroot = self.parentItem().viewroot()
current_filter_set = viewroot.selectionFilterSet()
if (self._getActiveTool().methodPrefix() != "selectTool"
or (self.FILTER_NAME not in current_filter_set)):
return
part = self._model_part
is_fwd = self.is_fwd
if self.is3p:
strand5p = part.getStrand(is_fwd, self._id_num, self.idx)
strand3p = part.getStrand(not is_fwd, self.to_vh_id_num, self.idx)
else:
strand5p = part.getStrand(not is_fwd, self.to_vh_id_num, self.idx)
strand3p = part.getStrand(is_fwd, self._id_num, self.idx)
if strand5p is None or strand3p is None:
return
# print(strand3p, strand5p)
part.createXover(strand5p, self.idx, strand3p, self.idx)
nkey = (self.to_vh_id_num, not is_fwd, self.idx)
npxi = self.prexoveritem_manager.neighbor_prexover_items.get(
nkey, None)
if npxi:
npxi.shutdown()
self.shutdown()
part.setActiveVirtualHelix(self._id_num, is_fwd, self.idx)
# self.prexoveritem_manager.handlePreXoverClick(self)
def keyPressEvent(self, event: QKeyEvent):
"""
Args:
event: Description
"""
self.prexoveritem_manager.handlePreXoverKeyPress(event.key())
# end def
### PUBLIC SUPPORT METHODS ###
def setLabel(self, text: str = None, outline: bool = False):
"""Summary
Args:
text: Default is ``None``
outline: Default is ``False``
"""
if text:
self._label.setTextAndStyle(text=text, outline=outline)
self._label.show()
else:
self._label.hide()
# end def
def animate(self, item: QGraphicsItem, property_name: str, duration: int,
start_value, end_value):
"""
Args:
item: Description
property_name: Description
duration: Description
start_value (QVariant): Description
end_value (QVariant): Description
"""
b_name = property_name.encode('ascii')
anim = item.adapter.getRef(property_name)
if anim is None:
anim = QPropertyAnimation(item.adapter, b_name)
item.adapter.saveRef(property_name, anim)
anim.setDuration(duration)
anim.setStartValue(start_value)
anim.setEndValue(end_value)
anim.start()
# end def
def setActiveHovered(self, is_active: bool):
"""Rotate phosphate Triangle if `self.to_vh_id_num` is not `None`
Args:
is_active: whether or not the PreXoverItem is parented to the
active VirtualHelixItem
"""
pass
# end def
def enableActive(self, is_active: bool, to_vh_id_num: int = None):
"""Call on PreXoverItems created on the active VirtualHelixItem
Args:
is_active: Description
to_vh_id_num: Default is ``None``
"""
if is_active:
self.to_vh_id_num = to_vh_id_num
self.setAcceptHoverEvents(True)
if to_vh_id_num is None:
self.setLabel(text=None)
else:
self.setLabel(text=str(to_vh_id_num))
else:
self.setBrush(getNoBrush())
self.setAcceptHoverEvents(False)
def activateNeighbor(self,
active_prexoveritem: 'PreXoverItem',
shortcut: str = None):
"""Draws a quad line starting from the item5p to the item3p.
To be called with whatever the active_prexoveritem is for the parts
`active_base`.
Args:
active_prexoveritem: Description
shortcut: Default is None
"""
if self._getActiveTool().methodPrefix() != "selectTool":
return
if self.is3p and not active_prexoveritem.is3p:
item5p = active_prexoveritem
item3p = self
elif not self.is3p and active_prexoveritem.is3p:
item5p = self
item3p = active_prexoveritem
else:
return
same_parity = self.is_fwd == active_prexoveritem.is_fwd
p1 = item5p._tick_marks.scenePos() + item5p.exit_pos
p2 = item3p._tick_marks.scenePos() + item3p.exit_pos
c1 = QPointF()
# case 1: same parity
if same_parity:
dy = abs(p2.y() - p1.y())
c1.setX(p1.x() + _X_SCALE * dy)
c1.setY(0.5 * (p1.y() + p2.y()))
# case 2: different parity
else:
if item3p.is_fwd:
c1.setX(p1.x() - _X_SCALE * abs(p2.y() - p1.y()))
else:
c1.setX(p1.x() + _X_SCALE * abs(p2.y() - p1.y()))
c1.setY(0.5 * (p1.y() + p2.y()))
pp = QPainterPath()
pp.moveTo(self._tick_marks.mapFromScene(p1))
pp.quadTo(self._tick_marks.mapFromScene(c1),
self._tick_marks.mapFromScene(p2))
# pp.cubicTo(c1, c2, self._tick_marks.mapFromScene(p2))
self._bond_item.setPath(pp)
self._bond_item.show()
# end def
def deactivateNeighbor(self):
"""Summary
"""
if self.isVisible():
self._bond_item.hide()
self.setLabel(text=self._label_txt)
class PreXoverItem(QGraphicsRectItem):
"""A PreXoverItem exists between a single 'from' VirtualHelixItem index
and zero or more 'to' VirtualHelixItem Indices
Attributes:
adapter (:obj:`PropertyWrapperObject`): Description
idx (int): the base index within the virtual helix
is_fwd (bool): is this a forward strand?
prexoveritem_manager (:obj:`PreXoverManager`): Manager of the PreXoverItems
to_vh_id_num (int): Virtual Helix number this Xover point might connect to
"""
FILTER_NAME = "xover"
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
# end def
def shutdown(self):
"""Summary
"""
self.setBrush(getNoBrush())
self.to_vh_id_num = None
self.adapter.resetAnimations()
self.setAcceptHoverEvents(False)
self.hide()
# end def
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()
# end def
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
# end def
### ACCESSORS ###
def color(self) -> str:
"""The PreXoverItem's color, derived from the associated strand's oligo.
Returns:
str: color in hex code
"""
return self.color
def getInfo(self) -> ABInfoT:
"""
Returns:
Tuple: (from_id_num, is_fwd, from_index, to_vh_id_num)
"""
return (self._id_num, self.is_fwd, self.idx, self.to_vh_id_num)
def destroyItem(self):
"""Removes animation adapter, label, bond_item, and this item from scene.
"""
scene = self.scene()
self.adapter.destroyItem()
if scene:
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._bond_item)
self._bond_item = None
self.adapter.resetAnimations()
self.adapter = None
scene.removeItem(self)
# end defS
### EVENT HANDLERS ###
def hoverEnterEvent(self, event: QGraphicsSceneHoverEvent):
"""Only ``if enableActive(True)`` is called hover and key events disabled
by default
Args:
event: the hover event
"""
if self._getActiveTool().methodPrefix() != "selectTool":
return
self.setFocus(Qt.MouseFocusReason)
self.prexoveritem_manager.updateModelActiveBaseInfo(self.getInfo())
self.setActiveHovered(True)
status_string = "%d[%d]" % (self._id_num, self.idx)
self.parentItem().window().statusBar().showMessage(status_string)
return QGraphicsItem.hoverEnterEvent(self, event)
# end def
def hoverLeaveEvent(self, event: QGraphicsSceneHoverEvent):
"""Summary
Args:
event (QGraphicsSceneHoverEvent): the hover event
"""
self.prexoveritem_manager.updateModelActiveBaseInfo(None)
self.setActiveHovered(False)
self.clearFocus()
self.parentItem().window().statusBar().showMessage("")
return QGraphicsItem.hoverLeaveEvent(self, event)
# end def
def mousePressEvent(self, event: QGraphicsSceneMouseEvent):
"""TODO: NEED TO ADD FILTER FOR A CLICK ON THE 3' MOST END OF THE XOVER
TO DISALLOW OR HANDLE DIFFERENTLY
"""
viewroot = self.parentItem().viewroot()
current_filter_set = viewroot.selectionFilterSet()
if (self._getActiveTool().methodPrefix() != "selectTool" or
(self.FILTER_NAME not in current_filter_set) ):
return
part = self._model_part
is_fwd = self.is_fwd
if self.is3p:
strand5p = part.getStrand(is_fwd, self._id_num, self.idx)
strand3p = part.getStrand(not is_fwd, self.to_vh_id_num, self.idx)
else:
strand5p = part.getStrand(not is_fwd, self.to_vh_id_num, self.idx)
strand3p = part.getStrand(is_fwd, self._id_num, self.idx)
if strand5p is None or strand3p is None:
return
# print(strand3p, strand5p)
part.createXover(strand5p, self.idx, strand3p, self.idx)
nkey = (self.to_vh_id_num, not is_fwd, self.idx)
npxi = self.prexoveritem_manager.neighbor_prexover_items.get(nkey, None)
if npxi:
npxi.shutdown()
self.shutdown()
part.setActiveVirtualHelix(self._id_num, is_fwd, self.idx)
# self.prexoveritem_manager.handlePreXoverClick(self)
def keyPressEvent(self, event: QKeyEvent):
"""
Args:
event: Description
"""
self.prexoveritem_manager.handlePreXoverKeyPress(event.key())
# end def
### PUBLIC SUPPORT METHODS ###
def setLabel(self, text: str = None, outline: bool = False):
"""Summary
Args:
text: Default is ``None``
outline: Default is ``False``
"""
if text:
self._label.setTextAndStyle(text=text, outline=outline)
self._label.show()
else:
self._label.hide()
# end def
def animate(self, item: QGraphicsItem,
property_name: str, duration: int,
start_value, end_value):
"""
Args:
item: Description
property_name: Description
duration: Description
start_value (QVariant): Description
end_value (QVariant): Description
"""
b_name = property_name.encode('ascii')
anim = item.adapter.getRef(property_name)
if anim is None:
anim = QPropertyAnimation(item.adapter, b_name)
item.adapter.saveRef(property_name, anim)
anim.setDuration(duration)
anim.setStartValue(start_value)
anim.setEndValue(end_value)
anim.start()
# end def
def setActiveHovered(self, is_active: bool):
"""Rotate phosphate Triangle if `self.to_vh_id_num` is not `None`
Args:
is_active: whether or not the PreXoverItem is parented to the
active VirtualHelixItem
"""
pass
# end def
def enableActive(self, is_active: bool, to_vh_id_num: int = None):
"""Call on PreXoverItems created on the active VirtualHelixItem
Args:
is_active: Description
to_vh_id_num: Default is ``None``
"""
if is_active:
self.to_vh_id_num = to_vh_id_num
self.setAcceptHoverEvents(True)
if to_vh_id_num is None:
self.setLabel(text=None)
else:
self.setLabel(text=str(to_vh_id_num))
else:
self.setBrush(getNoBrush())
self.setAcceptHoverEvents(False)
def activateNeighbor(self, active_prexoveritem: 'PreXoverItem',
shortcut: str = None):
"""Draws a quad line starting from the item5p to the item3p.
To be called with whatever the active_prexoveritem is for the parts
`active_base`.
Args:
active_prexoveritem: Description
shortcut: Default is None
"""
if self._getActiveTool().methodPrefix() != "selectTool":
return
if self.is3p and not active_prexoveritem.is3p:
item5p = active_prexoveritem
item3p = self
elif not self.is3p and active_prexoveritem.is3p:
item5p = self
item3p = active_prexoveritem
else:
return
same_parity = self.is_fwd == active_prexoveritem.is_fwd
p1 = item5p._tick_marks.scenePos() + item5p.exit_pos
p2 = item3p._tick_marks.scenePos() + item3p.exit_pos
c1 = QPointF()
# case 1: same parity
if same_parity:
dy = abs(p2.y() - p1.y())
c1.setX(p1.x() + _X_SCALE * dy)
c1.setY(0.5 * (p1.y() + p2.y()))
# case 2: different parity
else:
if item3p.is_fwd:
c1.setX(p1.x() - _X_SCALE * abs(p2.y() - p1.y()))
else:
c1.setX(p1.x() + _X_SCALE * abs(p2.y() - p1.y()))
c1.setY(0.5 * (p1.y() + p2.y()))
pp = QPainterPath()
pp.moveTo(self._tick_marks.mapFromScene(p1))
pp.quadTo(self._tick_marks.mapFromScene(c1),
self._tick_marks.mapFromScene(p2))
# pp.cubicTo(c1, c2, self._tick_marks.mapFromScene(p2))
self._bond_item.setPath(pp)
self._bond_item.show()
# end def
def deactivateNeighbor(self):
"""Summary
"""
if self.isVisible():
self._bond_item.hide()
self.setLabel(text=self._label_txt)
class PreXoverItem(QGraphicsRectItem):
"""A PreXoverItem exists between a single 'from' VirtualHelixItem index
and zero or more 'to' VirtualHelixItem Indices
Attributes:
adapter (TYPE): Description
idx (int): the base index within the virtual helix
is_fwd (TYPE): Description
prexoveritem_manager (TYPE): Description
to_vh_id_num (TYPE): Description
"""
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)
# end def
def shutdown(self):
"""Summary
Returns:
TYPE: Description
"""
self.setBrush(getNoBrush())
self.to_vh_id_num = None
self.adapter.resetAnimations()
self.setAcceptHoverEvents(False)
self.hide()
# end def
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()
# end def
def setPathAppearance(self, from_virtual_helix_item):
"""
Sets the PainterPath according to the index (low = Left, high = Right)
and strand position (top = Up, bottom = Down).
"""
part = self._model_vh.part()
idx = self.idx
is_fwd = self.is_fwd
id_num = self._id_num
strand_type = StrandType.FWD if is_fwd else StrandType.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:
print("dual xover")
path = (_FWD_DUAL_PATH, _REV_DUAL_PATH)[strand_type]
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
# end def
### ACCESSORS ###
def color(self):
"""The PreXoverItem's color, derived from the associated strand's oligo.
Returns:
str: color in hex code
"""
return self.color
def getInfo(self):
"""
Returns:
Tuple: (from_id_num, is_fwd, from_index, to_vh_id_num)
"""
return (self._id_num, self.is_fwd, self.idx, self.to_vh_id_num)
def remove(self):
"""Removes animation adapter, label, bond_item, and this item from scene.
"""
scene = self.scene()
self.adapter.destroy()
if scene:
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._bond_item)
self._bond_item = None
self.adapter.resetAnimations()
self.adapter = None
scene.removeItem(self)
# end defS
### EVENT HANDLERS ###
def hoverEnterEvent(self, event):
"""Only if enableActive(True) is called hover and key events disabled by default
Args:
event (QGraphicsSceneHoverEvent): the hover event
"""
self.setFocus(Qt.MouseFocusReason)
self.prexoveritem_manager.updateModelActiveBaseInfo(self.getInfo())
self.setActiveHovered(True)
status_string = "%d[%d]" % (self._id_num, self.idx)
self.parentItem().window().statusBar().showMessage(status_string)
# end def
def hoverLeaveEvent(self, event):
"""Summary
Args:
event (QGraphicsSceneHoverEvent): the hover event
Returns:
TYPE: Description
"""
self.prexoveritem_manager.updateModelActiveBaseInfo(None)
self.setActiveHovered(False)
self.clearFocus()
self.parentItem().window().statusBar().showMessage("")
# end def
def mousePressEvent(self, event):
part = self._model_vh.part()
is_fwd = self.is_fwd
if self.is3p:
strand5p = part.getStrand(is_fwd, self._id_num, self.idx)
strand3p = part.getStrand(not is_fwd, self.to_vh_id_num, self.idx)
else:
strand5p = part.getStrand(not is_fwd, self.to_vh_id_num, self.idx)
strand3p = part.getStrand(is_fwd, self._id_num, self.idx)
if strand5p is None or strand3p is None:
return
part.createXover(strand5p, self.idx, strand3p, self.idx)
nkey = (self.to_vh_id_num, not is_fwd, self.idx)
npxi = self.prexoveritem_manager.neighbor_prexover_items.get(nkey, None)
if npxi:
npxi.shutdown()
self.shutdown()
part.setActiveVirtualHelix(self._id_num, is_fwd, self.idx)
# self.prexoveritem_manager.handlePreXoverClick(self)
def keyPressEvent(self, event):
"""Summary
Args:
event (TYPE): Description
Returns:
TYPE: Description
"""
self.prexoveritem_manager.handlePreXoverKeyPress(event.key())
# end def
### PUBLIC SUPPORT METHODS ###
def setLabel(self, text=None, outline=False):
"""Summary
Args:
text (None, optional): Description
outline (bool, optional): Description
Returns:
TYPE: Description
"""
if text:
self._label.setTextAndStyle(text=text, outline=outline)
self._label.show()
else:
self._label.hide()
# end def
def animate(self, item, property_name, duration, start_value, end_value):
"""Summary
Args:
item (TYPE): Description
property_name (TYPE): Description
duration (TYPE): Description
start_value (TYPE): Description
end_value (TYPE): Description
Returns:
TYPE: Description
"""
b_name = property_name.encode('ascii')
anim = item.adapter.getRef(property_name)
if anim is None:
anim = QPropertyAnimation(item.adapter, b_name)
item.adapter.saveRef(property_name, anim)
anim.setDuration(duration)
anim.setStartValue(start_value)
anim.setEndValue(end_value)
anim.start()
# end def
def setActiveHovered(self, is_active):
"""Rotate phosphate Triangle if `self.to_vh_id_num` is not `None`
Args:
is_active (bool): whether or not the PreXoverItem is parented to the
active VirtualHelixItem
"""
pass
# end def
def enableActive(self, is_active, to_vh_id_num=None):
"""Call on PreXoverItems created on the active VirtualHelixItem
Args:
is_active (TYPE): Description
to_vh_id_num (None, optional): Description
"""
if is_active:
self.to_vh_id_num = to_vh_id_num
self.setAcceptHoverEvents(True)
if to_vh_id_num is None:
self.setLabel(text=None)
else:
self.setLabel(text=str(to_vh_id_num))
else:
self.setBrush(getNoBrush())
self.setAcceptHoverEvents(False)
def activateNeighbor(self, active_prexoveritem, shortcut=None):
"""
Draws a quad line starting from the item5p to the item3p.
To be called with whatever the active_prexoveritem is for the parts `active_base`.
Args:
active_prexoveritem (TYPE): Description
shortcut (None, optional): Description
"""
if self.is3p and not active_prexoveritem.is3p:
item5p = active_prexoveritem
item3p = self
elif not self.is3p and active_prexoveritem.is3p:
item5p = self
item3p = active_prexoveritem
else:
return
same_parity = self.is_fwd == active_prexoveritem.is_fwd
p1 = item5p._tick_marks.scenePos() + item5p.exit_pos
p2 = item3p._tick_marks.scenePos() + item3p.exit_pos
c1 = QPointF()
# case 1: same parity
if same_parity:
dy = abs(p2.y() - p1.y())
c1.setX(p1.x() + _X_SCALE * dy)
c1.setY(0.5 * (p1.y() + p2.y()))
# case 2: different parity
else:
if item3p.is_fwd:
c1.setX(p1.x() - _X_SCALE * abs(p2.y() - p1.y()))
else:
c1.setX(p1.x() + _X_SCALE * abs(p2.y() - p1.y()))
c1.setY(0.5 * (p1.y() + p2.y()))
pp = QPainterPath()
pp.moveTo(self._tick_marks.mapFromScene(p1))
pp.quadTo(self._tick_marks.mapFromScene(c1),
self._tick_marks.mapFromScene(p2))
# pp.cubicTo(c1, c2, self._tick_marks.mapFromScene(p2))
self._bond_item.setPath(pp)
self._bond_item.show()
# end def
def deactivateNeighbor(self):
"""Summary
Returns:
TYPE: Description
"""
if self.isVisible():
self._bond_item.hide()
self.setLabel(text=self._label_txt)
