def __init__(self, model_strand: StrandT,
virtual_helix_item: PathVirtualHelixItemT):
"""The parent should be a VirtualHelixItem.
Args:
model_strand:
virtual_helix_item:
"""
super(StrandItem, self).__init__(virtual_helix_item)
self._model_strand = model_strand
self._virtual_helix_item = virtual_helix_item
self._viewroot: PathRootItemT = virtual_helix_item._viewroot
self._getActiveTool = self._viewroot.manager.activeToolGetter
self._controller = StrandItemController(self, model_strand)
is_forward = model_strand.strandSet().isForward()
self._strand_filter = model_strand.strandFilter()
self._insertion_items = {}
# caps
self._low_cap = EndpointItem(self, 'low', is_forward)
self._high_cap = EndpointItem(self, 'high', is_forward)
self._dual_cap = EndpointItem(self, 'dual', is_forward)
# orientation
self.is_forward = is_forward
self._seq_label = QGraphicsSimpleTextItem(self)
self.refreshInsertionItems(model_strand)
if not getBatch():
self._updateSequenceText()
# create a larger click area rect to capture mouse events
self._click_area = c_a = QGraphicsRectItem(_DEFAULT_RECT, self)
c_a.mousePressEvent = self.mousePressEvent
c_a.setPen(_NO_PEN)
self.setAcceptHoverEvents(True)
c_a.setAcceptHoverEvents(True)
c_a.hoverMoveEvent = self.hoverMoveEvent
self.setZValue(styles.ZSTRANDITEM)
# xover comming from the 3p end
self.xover_3p_end = XoverItem(self, virtual_helix_item)
if not getBatch():
# initial refresh
self._updateColor(model_strand)
self._updateAppearance(model_strand)
self.setZValue(styles.ZSTRANDITEM)
self.setFlag(QGraphicsItem.ItemIsSelectable)
def __init__(self, model_strand, virtual_helix_item, viewroot):
"""The parent should be a VirtualHelixItem.
Args:
model_strand (:obj:`cadnano.strand.Strand`):
virtual_helix_item (:obj:`cadnano.views.pathview.virtualhelixitem.VirtualHelixItem`):
viewroot (:obj:`cadnano.views.pathview.pathrootitem.PathRootItem`):
"""
super(StrandItem, self).__init__(virtual_helix_item)
self._model_strand = model_strand
self._virtual_helix_item = virtual_helix_item
self._viewroot = viewroot
self._getActiveTool = viewroot.manager.activeToolGetter
self._controller = StrandItemController(model_strand, self)
is_forward = model_strand.strandSet().isForward()
self._strand_filter = model_strand.strandFilter()
self._insertion_items = {}
# caps
self._low_cap = EndpointItem(self, 'low', is_forward)
self._high_cap = EndpointItem(self, 'high', is_forward)
self._dual_cap = EndpointItem(self, 'dual', is_forward)
# orientation
self.is_forward = is_forward
self._seq_label = QGraphicsSimpleTextItem(self)
self.refreshInsertionItems(model_strand)
if not getBatch():
self._updateSequenceText()
# create a larger click area rect to capture mouse events
self._click_area = c_a = QGraphicsRectItem(_DEFAULT_RECT, self)
c_a.mousePressEvent = self.mousePressEvent
c_a.setPen(_NO_PEN)
self.setAcceptHoverEvents(True)
c_a.setAcceptHoverEvents(True)
c_a.hoverMoveEvent = self.hoverMoveEvent
self.setZValue(styles.ZSTRANDITEM)
# xover comming from the 3p end
self.xover_3p_end = XoverItem(self, virtual_helix_item)
if not getBatch():
# initial refresh
self._updateColor(model_strand)
self._updateAppearance(model_strand)
self.setZValue(styles.ZSTRANDITEM)
self.setFlag(QGraphicsItem.ItemIsSelectable)
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
self._virtual_helix_item = virtual_helix_item
self._viewroot = viewroot
self._getActiveTool = virtual_helix_item._getActiveTool
self._controller = StrandItemController(self, model_strand)
is_drawn_5to3 = model_strand.strandSet().isDrawn5to3()
self._strand_filter = model_strand.strandFilter()
self._insertion_items = {}
# caps
self._low_cap = EndpointItem(self, 'low', is_drawn_5to3)
self._high_cap = EndpointItem(self, 'high', is_drawn_5to3)
# self._high_cap = None
self._dual_cap = EndpointItem(self, 'dual', is_drawn_5to3)
# orientation
self._is_drawn_5to3 = is_drawn_5to3
# self._isOnTop = virtual_helix_item.isStrandOnTop(model_strand)
# label
self._seq_label = QGraphicsSimpleTextItem(self)
self.refreshInsertionItems(model_strand)
if not getBatch():
self._updateSequenceText()
# create a larger click area rect to capture mouse events
self._click_area = c_a = QGraphicsRectItem(_DEFAULT_RECT, self)
c_a.mousePressEvent = self.mousePressEvent
c_a.setPen(_NO_PEN)
self.setAcceptHoverEvents(True)
c_a.setAcceptHoverEvents(True)
c_a.hoverMoveEvent = self.hoverMoveEvent
self.setZValue(styles.ZSTRANDITEM)
# xover comming from the 3p end
self._xover3pEnd = XoverItem(self, virtual_helix_item)
if not getBatch():
# initial refresh
self._updateColor(model_strand)
self._updateAppearance(model_strand)
self.setZValue(styles.ZSTRANDITEM)
self.setFlag(QGraphicsItem.ItemIsSelectable)
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
self._virtual_helix_item = virtual_helix_item
self._viewroot = viewroot
self._getActiveTool = virtual_helix_item._getActiveTool
self._controller = StrandItemController(self, model_strand)
is_drawn_5to3 = model_strand.strandSet().isDrawn5to3()
self._strand_filter = model_strand.strandFilter()
self._insertion_items = {}
# caps
self._low_cap = EndpointItem(self, 'low', is_drawn_5to3)
self._high_cap = EndpointItem(self, 'high', is_drawn_5to3)
# self._high_cap = None
self._dual_cap = EndpointItem(self, 'dual', is_drawn_5to3)
# orientation
self._is_drawn_5to3 = is_drawn_5to3
# self._isOnTop = virtual_helix_item.isStrandOnTop(model_strand)
# label
self._seq_label = QGraphicsSimpleTextItem(self)
self.refreshInsertionItems(model_strand)
if not getBatch():
self._updateSequenceText()
# create a larger click area rect to capture mouse events
self._click_area = c_a = QGraphicsRectItem(_DEFAULT_RECT, self)
c_a.mousePressEvent = self.mousePressEvent
c_a.setPen(_NO_PEN)
self.setAcceptHoverEvents(True)
c_a.setAcceptHoverEvents(True)
c_a.hoverMoveEvent = self.hoverMoveEvent
self.setZValue(styles.ZSTRANDITEM)
# xover comming from the 3p end
self._xover3pEnd = XoverItem(self, virtual_helix_item)
if not getBatch():
# initial refresh
self._updateColor(model_strand)
self._updateAppearance(model_strand)
self.setZValue(styles.ZSTRANDITEM)
self.setFlag(QGraphicsItem.ItemIsSelectable)
def partVirtualHelixAddedSlot(self, model_part, id_num, virtual_helix,
neighbors):
"""
When a virtual helix is added to the model, this slot handles
the instantiation of a virtualhelix item.
Args:
model_part (Part): The model part
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
"""
# print("NucleicAcidPartItem.partVirtualHelixAddedSlot")
vhi = PathVirtualHelixItem(virtual_helix, self, self._viewroot)
self._virtual_helix_item_hash[id_num] = vhi
vhi_list = self._virtual_helix_item_list
# reposition when first VH is added
if len(vhi_list) == 0:
view = self.window().path_graphics_view
p = view.scene_root_item.childrenBoundingRect().bottomLeft()
_p = _BOUNDING_RECT_PADDING
self.setPos(p.x() + _p * 6 + styles.VIRTUALHELIXHANDLEITEM_RADIUS,
p.y() + _p * 3)
# self.setPos(p.x() + _VH_XOFFSET, p.y() + _p*3)
vhi_list.append(vhi)
ztf = not getBatch()
self._setVirtualHelixItemList(vhi_list, zoom_to_fit=ztf)
def removeVirtualHelixItem(self, virtual_helix_item):
vh = virtual_helix_item.virtualHelix()
self._virtual_helix_item_list.remove(virtual_helix_item)
del self._virtual_helix_hash[vh.coord()]
ztf = not getBatch()
self._setVirtualHelixItemList(self._virtual_helix_item_list,
zoom_to_fit=ztf)
self._updateBoundingRect()
def partVirtualHelixRemovedSlot(self, sender: NucleicAcidPartT, id_num: int):
"""Step 2 of removing a VHI
"""
ztf = not getBatch()
self._setVirtualHelixItemList(self._virtual_helix_item_list, zoom_to_fit=ztf)
if len(self._virtual_helix_item_list) == 0:
self.hide()
self.reconfigureRect((), ())
def removeVirtualHelixItem(self, virtual_helix_item):
vh = virtual_helix_item.virtualHelix()
self._virtual_helix_item_list.remove(virtual_helix_item)
del self._virtual_helix_hash[vh.coord()]
ztf = not getBatch()
self._setVirtualHelixItemList(self._virtual_helix_item_list,
zoom_to_fit=ztf)
self._updateBoundingRect()
def partVirtualHelicesReorderedSlot(self, sender, ordered_coord_list):
"""docstring for partVirtualHelicesReorderedSlot"""
new_list = self._virtual_helix_item_list
decorated = [(ordered_coord_list.index(vhi.coord()), vhi)\
for vhi in self._virtual_helix_item_list]
decorated.sort()
new_list = [vhi for idx, vhi in decorated]
ztf = not getBatch()
self._setVirtualHelixItemList(new_list, zoom_to_fit=ztf)
def partVirtualHelicesReorderedSlot(self, sender, ordered_coord_list):
"""docstring for partVirtualHelicesReorderedSlot"""
new_list = self._virtual_helix_item_list
decorated = [(ordered_coord_list.index(vhi.coord()), vhi)\
for vhi in self._virtual_helix_item_list]
decorated.sort()
new_list = [vhi for idx, vhi in decorated]
ztf = not getBatch()
self._setVirtualHelixItemList(new_list, zoom_to_fit=ztf)
def partVirtualHelixAddedSlot(self, sender, model_virtual_helix):
"""
When a virtual helix is added to the model, this slot handles
the instantiation of a virtualhelix item.
"""
# print("PartItem.partVirtualHelixAddedSlot")
vh = model_virtual_helix
vhi = VirtualHelixItem(self, model_virtual_helix, self._viewroot)
self._virtual_helix_hash[vh.coord()] = vhi
self._virtual_helix_item_list.append(vhi)
ztf = not getBatch()
self._setVirtualHelixItemList(self._virtual_helix_item_list, zoom_to_fit=ztf)
self._updateBoundingRect()
def partVirtualHelixAddedSlot(self, sender, model_virtual_helix):
"""
When a virtual helix is added to the model, this slot handles
the instantiation of a virtualhelix item.
"""
# print("PartItem.partVirtualHelixAddedSlot")
vh = model_virtual_helix
vhi = VirtualHelixItem(self, model_virtual_helix, self._viewroot)
self._virtual_helix_hash[vh.coord()] = vhi
self._virtual_helix_item_list.append(vhi)
ztf = not getBatch()
self._setVirtualHelixItemList(self._virtual_helix_item_list, zoom_to_fit=ztf)
self._updateBoundingRect()
def partVirtualHelixAddedSlot(self, model_part, id_num, virtual_helix,
neighbors):
"""
When a virtual helix is added to the model, this slot handles
the instantiation of a virtualhelix item.
Args:
model_part (Part): The model part
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
"""
# print("NucleicAcidPartItem.partVirtualHelixAddedSlot")
vhi = PathVirtualHelixItem(virtual_helix, self, self._viewroot)
self._virtual_helix_item_hash[id_num] = vhi
vhi_list = self._virtual_helix_item_list
vhi_list.append(vhi)
ztf = not getBatch()
self._setVirtualHelixItemList(vhi_list, zoom_to_fit=ztf)
if not self.isVisible():
self.show()
def partVirtualHelixAddedSlot(self, sender: NucleicAcidPartT, id_num: int,
virtual_helix: VirtualHelixT,
neighbors: List[int]):
"""When a virtual helix is added to the model, this slot handles
the instantiation of a virtualhelix item.
Args:
sender: Model object that emitted the signal.
id_num: VirtualHelix ID number. See ``NucleicAcidPart`` for
description and related methods.
virtual_helix:
neighbors: Description
"""
# print("NucleicAcidPartItem.partVirtualHelixAddedSlot")
if self._viewroot.are_signals_on:
vhi = PathVirtualHelixItem(id_num, self)
self._virtual_helix_item_hash[id_num] = vhi
vhi_list = self._virtual_helix_item_list
vhi_list.append(vhi)
ztf = not getBatch()
self._setVirtualHelixItemList(vhi_list, zoom_to_fit=ztf)
if not self.isVisible():
self.show()
def partVirtualHelixAddedSlot(self, sender: NucleicAcidPartT,
id_num: int,
virtual_helix: VirtualHelixT,
neighbors: List[int]):
"""When a virtual helix is added to the model, this slot handles
the instantiation of a virtualhelix item.
Args:
sender: Model object that emitted the signal.
id_num: VirtualHelix ID number. See ``NucleicAcidPart`` for
description and related methods.
virtual_helix:
neighbors: Description
"""
# print("NucleicAcidPartItem.partVirtualHelixAddedSlot")
if self._viewroot.are_signals_on:
vhi = PathVirtualHelixItem(id_num, self)
self._virtual_helix_item_hash[id_num] = vhi
vhi_list = self._virtual_helix_item_list
vhi_list.append(vhi)
ztf = not getBatch()
self._setVirtualHelixItemList(vhi_list, zoom_to_fit=ztf)
if not self.isVisible():
self.show()
def partVirtualHelixRemovedSlot(self, sender, id_num):
""" Step 2 of removing a VHI
"""
ztf = not getBatch()
self._setVirtualHelixItemList(self._virtual_helix_item_list,
zoom_to_fit=ztf)
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
self._virtual_helix_item = virtual_helix_item
self._viewroot = viewroot
self._selected = model_strand.oligo()._selected
if self._selected:
self.strandSelectedSlot()
else:
self.strandRemovedFromSelectionSlot()
self._controller = StrandItemController(self, model_strand)
is_drawn_5to3 = model_strand.strandSet().isDrawn5to3()
self._strand_filter = model_strand.strandFilter()
self._insertion_items = {}
# end point squares and arrows
self._low_cap = EndpointItem(self, 'low', is_drawn_5to3)
self._high_cap = EndpointItem(self, 'high', is_drawn_5to3)
# tick mark for connection btw two adjacent domains on the same helix
self._tick = EndpointItem(self,'tick',is_drawn_5to3)
# self._high_cap = None
self._dual_cap = EndpointItem(self, 'dual', is_drawn_5to3)
# orientation
self._is_drawn_5to3 = is_drawn_5to3
# self._isOnTop = virtual_helix_item.isStrandOnTop(model_strand)
# label
self._is_on_top = self._virtual_helix_item.isStrandOnTop(self._model_strand)
self._seq_label = QGraphicsSimpleTextItem(self)
self.refreshInsertionItems(model_strand)
if not getBatch():
self._updateSequenceText()
# create a larger click area rect to capture mouse events
self._click_area = c_a = QGraphicsRectItem(_DEFAULT_RECT, self)
c_a.mousePressEvent = self.mousePressEvent
c_a.setPen(_NO_PEN)
self.setAcceptHoverEvents(True)
c_a.setAcceptHoverEvents(True)
c_a.hoverMoveEvent = self.hoverMoveEvent
self.setZValue(styles.ZSTRANDITEM)
self._toehold_item_3p = None
self._toehold_item_5p = None
self._toehold_cap_3p = None
self._toehold_cap_5p = None
if self._is_drawn_5to3:
self._toehold_cap_3p = EndpointItem(self,'low',not self._is_drawn_5to3)
self._toehold_cap_5p = EndpointItem(self,'low',self._is_drawn_5to3)
self.toeholdCapHigh = self.toeholdCap3p
self.toeholdCapLow = self.toeholdCap5p
else:
self._toehold_cap_3p = EndpointItem(self,'high',not self._is_drawn_5to3)
self._toehold_cap_5p = EndpointItem(self,'high',self._is_drawn_5to3)
self.toeholdCapHigh = self.toeholdCap5p
self.toeholdCapLow = self.toeholdCap3p
# xover comming from the 3p end
self._xover3pEnd = XoverItem(self, virtual_helix_item)
if not getBatch():
# initial refresh
self._updateColor(model_strand)
self._updateAppearance(model_strand)
self.setZValue(styles.ZSTRANDITEM)
self.setFlag(QGraphicsItem.ItemIsSelectable)
self.shown_attributes=[]
self.refresh_toehold()
