def __init__(self, model_part, parent):
super(OutlineNucleicAcidPartItem, self).__init__(model_part, parent)
self._controller = NucleicAcidPartItemController(self, model_part)
self._model_part = model_part
self.setExpanded(True)
# properties
temp_color = model_part.getColor()
# outlinerview takes responsibility of overriding default part color
if temp_color == "#000000":
index = len(model_part.document().children()) - 1
new_color = styles.PARTCOLORS[index % len(styles.PARTCOLORS)]
model_part.setProperty('color', new_color)
# item groups
self._root_items = {}
self._root_items['VHelixList'] = self.createRootPartItem(
'Virtual Helices', self)
self._root_items['OligoList'] = self.createRootPartItem('Oligos', self)
fs = model_part.document().filter_set
if OutlineVirtualHelixItem.FILTER_NAME in fs:
self._root_items['OligoList'].setFlags(DISABLE_FLAGS)
else:
self._root_items['VHelixList'].setFlags(DISABLE_FLAGS)
# self._root_items['Modifications'] = self._createRootItem('Modifications', self)
if model_part.is_active:
print("should be active")
self.activate()
def __init__(self, model_part_instance, viewroot, parent):
"""parent should always be pathrootitem
Args:
model_part_instance (TYPE): Description
viewroot (TYPE): Description
parent (TYPE): Description
"""
super(PathNucleicAcidPartItem, self).__init__(model_part_instance,
viewroot, parent)
self.setAcceptHoverEvents(True)
self._getActiveTool = viewroot.manager.activeToolGetter
self.active_virtual_helix_item = None
m_p = self._model_part
self._controller = NucleicAcidPartItemController(self, m_p)
self.prexover_manager = PreXoverManager(self)
self._virtual_helix_item_list = []
self._initModifierRect()
self._proxy_parent = ProxyParentItem(self)
self._proxy_parent.setFlag(QGraphicsItem.ItemHasNoContents)
self._scale_2_model = m_p.baseWidth() / _BASE_WIDTH
self._scale_2_Qt = _BASE_WIDTH / m_p.baseWidth()
# self._rect = QRectF()
self._vh_rect = QRectF()
# self.setPen(getPenObj(styles.ORANGE_STROKE, 0))
self.setPen(getNoPen())
# self.setRect(self._rect)
self.outline = outline = PathRectItem(self)
outline.setFlag(QGraphicsItem.ItemStacksBehindParent)
self.setZValue(styles.ZPART)
self._proxy_parent.setZValue(styles.ZPART)
outline.setZValue(styles.ZDESELECTOR)
self.outline.setPen(getPenObj(m_p.getColor(), _DEFAULT_WIDTH))
o_rect = self._configureOutline(outline)
model_color = m_p.getColor()
self.resize_handle_group = ResizeHandleGroup(
o_rect,
_HANDLE_SIZE,
model_color,
True,
# HandleType.LEFT |
HandleType.RIGHT,
self)
self.model_bounds_hint = m_b_h = QGraphicsRectItem(self)
m_b_h.setBrush(getBrushObj(styles.BLUE_FILL, alpha=32))
m_b_h.setPen(getNoPen())
m_b_h.hide()
self.workplane = PathWorkplaneItem(m_p, self)
self.hide() # show on adding first vh
def __init__(self, model_part_instance, viewroot, parent=None):
"""Summary
Args:
model_part_instance (TYPE): Description
viewroot (TYPE): Description
parent (None, optional): Description
"""
super(GridNucleicAcidPartItem, self).__init__(model_part_instance, viewroot, parent)
self._getActiveTool = viewroot.manager.activeToolGetter
m_p = self._model_part
self._controller = NucleicAcidPartItemController(self, m_p)
self.scale_factor = self._RADIUS / m_p.radius()
self.active_virtual_helix_item = None
self.prexover_manager = PreXoverManager(self)
self.hide() # hide while until after attemptResize() to avoid flicker
self._rect = QRectF(0., 0., 1000., 1000.) # set this to a token value
self.boundRectToModel()
self.setPen(getNoPen())
self.setRect(self._rect)
self.setAcceptHoverEvents(True)
# Cache of VHs that were active as of last call to 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)
self.outline = outline = QGraphicsRectItem(self)
o_rect = self._configureOutline(outline)
outline.setFlag(QGraphicsItem.ItemStacksBehindParent)
outline.setZValue(styles.ZDESELECTOR)
model_color = m_p.getColor()
self.outline.setPen(getPenObj(model_color, _DEFAULT_WIDTH))
GC_SIZE = 10
self.grab_cornerTL = GrabCornerItem(GC_SIZE, model_color, True, self)
self.grab_cornerTL.setTopLeft(o_rect.topLeft())
self.grab_cornerBR = GrabCornerItem(GC_SIZE, model_color, True, self)
self.grab_cornerBR.setBottomRight(o_rect.bottomRight())
self.griditem = GridItem(self, self._model_props['grid_type'])
self.griditem.setZValue(1)
self.grab_cornerTL.setZValue(2)
self.grab_cornerBR.setZValue(2)
# 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, **kwargs):
"""Summary
Args:
model_part (Part): The model part
parent (PropertyEditorWidget): The property editor
key (None, optional): Description
"""
super().__init__(**kwargs)
if self._key == "name":
for model_part in self.cnModelList():
self._controller_list.append(NucleicAcidPartItemController(self, model_part))
def __init__(self, model_part_instance, viewroot, parent=None):
"""Summary
Args:
model_part_instance (TYPE): Description
viewroot (TYPE): Description
parent (None, optional): Description
"""
super(SliceNucleicAcidPartItem, self).__init__(model_part_instance,
viewroot, parent)
self.shortest_path_start = None
self.neighbor_map = dict()
self.coordinates_to_vhid = dict()
self.coordinates_to_xy = dict()
self._last_hovered_item = None
self._highlighted_path = []
self.spa_start_vhi = None
self.last_mouse_position = None
self._translated_x = 0.0
self._translated_y = 0.0
self._getActiveTool = viewroot.manager.activeToolGetter
m_p = self._model_part
self._controller = NucleicAcidPartItemController(self, m_p)
self.scale_factor = self._RADIUS / m_p.radius()
self.inverse_scale_factor = m_p.radius() / self._RADIUS
self.active_virtual_helix_item = None
self.prexover_manager = PreXoverManager(self)
self.hide() # hide while until after attemptResize() to avoid flicker
self._rect = QRectF(0., 0., 1000., 1000.) # set this to a token value
self.boundRectToModel()
self.setPen(getNoPen())
self.setRect(self._rect)
self.setAcceptHoverEvents(True)
self.shortest_path_add_mode = False
# Cache of VHs that were active as of last call to activeSliceChanged
# If None, all slices will be redrawn and the cache will be filled.
# Connect destructor. This is for removing a part from scenes.
# initialize the NucleicAcidPartItem with an empty set of old coords
self.setZValue(styles.ZPARTITEM)
self.outline = outline = QGraphicsRectItem(self)
o_rect = self._configureOutline(outline)
outline.setFlag(QGraphicsItem.ItemStacksBehindParent)
outline.setZValue(styles.ZDESELECTOR)
model_color = m_p.getColor()
self.outline.setPen(getPenObj(model_color, _DEFAULT_WIDTH))
self.model_bounds_hint = QGraphicsRectItem(self)
self.model_bounds_hint.setBrush(getBrushObj(model_color, alpha=12))
self.model_bounds_hint.setPen(getNoPen())
self.resize_handle_group = ResizeHandleGroup(
o_rect,
_HANDLE_SIZE,
model_color,
True,
HandleType.TOP | HandleType.BOTTOM | HandleType.LEFT
| HandleType.RIGHT | HandleType.TOP_LEFT | HandleType.TOP_RIGHT
| HandleType.BOTTOM_LEFT | HandleType.BOTTOM_RIGHT,
self,
show_coords=True)
self.griditem = GridItem(self, self._model_props['grid_type'])
self.griditem.setZValue(1)
self.resize_handle_group.setZValue(2)
self.x_axis_line = QGraphicsLineItem(0, 0, self._RADIUS, 0, self)
self.x_axis_line.setPen(getPenObj('#cc0000', _DEFAULT_WIDTH))
self.x_axis_line.setZValue(styles.ZAXIS)
self.y_axis_line = QGraphicsLineItem(0, 0, 0, -self._RADIUS, self)
self.y_axis_line.setPen(getPenObj('#007200', _DEFAULT_WIDTH))
self.y_axis_line.setZValue(styles.ZAXIS)
# select upon creation
for part in m_p.document().children():
if part is m_p:
part.setSelected(True)
else:
part.setSelected(False)
self.show()
class SliceNucleicAcidPartItem(QAbstractPartItem):
"""Parent should be either a SliceRootItem, or an AssemblyItem.
Invariant: keys in _empty_helix_hash = range(_nrows) x range(_ncols)
where x is the cartesian product.
Attributes:
active_virtual_helix_item (cadnano.views.sliceview.virtualhelixitem.SliceVirtualHelixItem): Description
resize_handle_group (ResizeHandleGroup): handles for dragging and resizing
griditem (GridItem): Description
outline (QGraphicsRectItem): Description
prexover_manager (PreXoverManager): Description
scale_factor (float): Description
"""
_RADIUS = styles.SLICE_HELIX_RADIUS
_BOUNDING_RECT_PADDING = 80
def __init__(self, model_part_instance, viewroot, parent=None):
"""Summary
Args:
model_part_instance (TYPE): Description
viewroot (TYPE): Description
parent (None, optional): Description
"""
super(SliceNucleicAcidPartItem, self).__init__(model_part_instance,
viewroot, parent)
self.shortest_path_start = None
self.neighbor_map = dict()
self.coordinates_to_vhid = dict()
self.coordinates_to_xy = dict()
self._last_hovered_item = None
self._highlighted_path = []
self.spa_start_vhi = None
self.last_mouse_position = None
self._translated_x = 0.0
self._translated_y = 0.0
self._getActiveTool = viewroot.manager.activeToolGetter
m_p = self._model_part
self._controller = NucleicAcidPartItemController(self, m_p)
self.scale_factor = self._RADIUS / m_p.radius()
self.inverse_scale_factor = m_p.radius() / self._RADIUS
self.active_virtual_helix_item = None
self.prexover_manager = PreXoverManager(self)
self.hide() # hide while until after attemptResize() to avoid flicker
self._rect = QRectF(0., 0., 1000., 1000.) # set this to a token value
self.boundRectToModel()
self.setPen(getNoPen())
self.setRect(self._rect)
self.setAcceptHoverEvents(True)
self.shortest_path_add_mode = False
# Cache of VHs that were active as of last call to activeSliceChanged
# If None, all slices will be redrawn and the cache will be filled.
# Connect destructor. This is for removing a part from scenes.
# initialize the NucleicAcidPartItem with an empty set of old coords
self.setZValue(styles.ZPARTITEM)
self.outline = outline = QGraphicsRectItem(self)
o_rect = self._configureOutline(outline)
outline.setFlag(QGraphicsItem.ItemStacksBehindParent)
outline.setZValue(styles.ZDESELECTOR)
model_color = m_p.getColor()
self.outline.setPen(getPenObj(model_color, _DEFAULT_WIDTH))
self.model_bounds_hint = QGraphicsRectItem(self)
self.model_bounds_hint.setBrush(getBrushObj(model_color, alpha=12))
self.model_bounds_hint.setPen(getNoPen())
self.resize_handle_group = ResizeHandleGroup(
o_rect,
_HANDLE_SIZE,
model_color,
True,
HandleType.TOP | HandleType.BOTTOM | HandleType.LEFT
| HandleType.RIGHT | HandleType.TOP_LEFT | HandleType.TOP_RIGHT
| HandleType.BOTTOM_LEFT | HandleType.BOTTOM_RIGHT,
self,
show_coords=True)
self.griditem = GridItem(self, self._model_props['grid_type'])
self.griditem.setZValue(1)
self.resize_handle_group.setZValue(2)
self.x_axis_line = QGraphicsLineItem(0, 0, self._RADIUS, 0, self)
self.x_axis_line.setPen(getPenObj('#cc0000', _DEFAULT_WIDTH))
self.x_axis_line.setZValue(styles.ZAXIS)
self.y_axis_line = QGraphicsLineItem(0, 0, 0, -self._RADIUS, self)
self.y_axis_line.setPen(getPenObj('#007200', _DEFAULT_WIDTH))
self.y_axis_line.setZValue(styles.ZAXIS)
# select upon creation
for part in m_p.document().children():
if part is m_p:
part.setSelected(True)
else:
part.setSelected(False)
self.show()
# end def
### SIGNALS ###
### SLOTS ###
def partActiveVirtualHelixChangedSlot(self, part, id_num):
"""Summary
Args:
part (NucleicAcidPart): Description
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
"""
vhi = self._virtual_helix_item_hash.get(id_num)
self.setActiveVirtualHelixItem(vhi)
self.setPreXoverItemsVisible(vhi)
# end def
def partActiveBaseInfoSlot(self, part, info):
"""Summary
Args:
part (TYPE): Description
info (TYPE): Description
Args:
TYPE: Description
"""
pxom = self.prexover_manager
pxom.deactivateNeighbors()
if info and info is not None:
id_num, is_fwd, idx, _ = info
pxom.activateNeighbors(id_num, is_fwd, idx)
# end def
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)
# end def
def partRemovedSlot(self, sender):
"""docstring for partRemovedSlot
Args:
sender (obj): Model object that emitted the signal.
"""
self.parentItem().removePartItem(self)
scene = self.scene()
scene.removeItem(self)
self._model_part = None
self._mod_circ = None
self._controller.disconnectSignals()
self._controller = None
self.resize_handle_group.removeHandles()
self.griditem = None
# end def
def partVirtualHelicesTranslatedSlot(self, sender, vh_set, left_overs,
do_deselect):
"""
left_overs are neighbors that need updating due to changes
Args:
sender (obj): Model object that emitted the signal.
vh_set (TYPE): Description
left_overs (TYPE): Description
do_deselect (TYPE): Description
"""
if do_deselect:
tool = self._getActiveTool()
if tool.methodPrefix() == "selectTool":
if tool.isSelectionActive():
# tool.deselectItems()
tool.modelClear()
# 1. move everything that moved
for id_num in vh_set:
vhi = self._virtual_helix_item_hash[id_num]
vhi.updatePosition()
# 2. now redraw what makes sense to be redrawn
for id_num in vh_set:
vhi = self._virtual_helix_item_hash[id_num]
self._refreshVirtualHelixItemGizmos(id_num, vhi)
for id_num in left_overs:
vhi = self._virtual_helix_item_hash[id_num]
self._refreshVirtualHelixItemGizmos(id_num, vhi)
# 0. clear PreXovers:
# self.prexover_manager.hideGroups()
# if self.active_virtual_helix_item is not None:
# self.active_virtual_helix_item.deactivate()
# self.active_virtual_helix_item = None
avhi = self.active_virtual_helix_item
self.setPreXoverItemsVisible(avhi)
self.enlargeRectToFit()
# end def
def _refreshVirtualHelixItemGizmos(self, id_num, vhi):
"""Update props and appearance of self & recent neighbors. Ultimately
triggered by a partVirtualHelicesTranslatedSignal.
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
vhi (cadnano.views.sliceview.virtualhelixitem.SliceVirtualHelixItem): the item associated with id_num
"""
neighbors = vhi.cnModel().getProperty('neighbors')
neighbors = literal_eval(neighbors)
vhi.beginAddWedgeGizmos()
for nvh in neighbors:
nvhi = self._virtual_helix_item_hash.get(nvh, False)
if nvhi:
vhi.setWedgeGizmo(nvh, nvhi)
# end for
vhi.endAddWedgeGizmos()
# end def
def partVirtualHelixPropertyChangedSlot(self, sender, id_num,
virtual_helix, keys, values):
"""Summary
Args:
sender (obj): Model object that emitted the signal.
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
keys (tuple): keys that changed
values (tuple): new values for each key that changed
Args:
TYPE: Description
"""
if self._model_part == sender:
vh_i = self._virtual_helix_item_hash[id_num]
vh_i.virtualHelixPropertyChangedSlot(keys, values)
# end def
def partVirtualHelixAddedSlot(self, sender, id_num, virtual_helix,
neighbors):
"""Summary
Args:
sender (obj): Model object that emitted the signal.
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
neighbors (TYPE): Description
Args:
TYPE: Description
"""
vhi = SliceVirtualHelixItem(virtual_helix, self)
self._virtual_helix_item_hash[id_num] = vhi
self._refreshVirtualHelixItemGizmos(id_num, vhi)
for neighbor_id in neighbors:
nvhi = self._virtual_helix_item_hash.get(neighbor_id, False)
if nvhi:
self._refreshVirtualHelixItemGizmos(neighbor_id, nvhi)
self.enlargeRectToFit()
position = sender.locationQt(id_num=id_num,
scale_factor=self.scale_factor)
coordinates = ShortestPathHelper.findClosestPoint(
position=position, point_map=self.coordinates_to_xy)
assert id_num not in self.coordinates_to_vhid.values()
self.coordinates_to_vhid[coordinates] = id_num
assert len(self.coordinates_to_vhid.keys()) == len(
set(self.coordinates_to_vhid.keys()))
assert len(self.coordinates_to_vhid.values()) == len(
set(self.coordinates_to_vhid.values()))
# end def
def partVirtualHelixRemovingSlot(self, sender, id_num, virtual_helix,
neighbors):
"""Summary
Args:
sender (obj): Model object that emitted the signal.
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
neighbors (TYPE): Description
Args:
TYPE: Description
"""
tm = self._viewroot.manager
tm.resetTools()
self.removeVirtualHelixItem(id_num)
for neighbor_id in neighbors:
nvhi = self._virtual_helix_item_hash[neighbor_id]
self._refreshVirtualHelixItemGizmos(neighbor_id, nvhi)
for coordinates, current_id in self.coordinates_to_vhid.items():
if current_id == id_num:
del self.coordinates_to_vhid[coordinates]
break
assert id_num not in self.coordinates_to_vhid.values()
assert len(self.coordinates_to_vhid.keys()) == len(
set(self.coordinates_to_vhid.keys()))
assert len(self.coordinates_to_vhid.values()) == len(
set(self.coordinates_to_vhid.values()))
# end def
def partSelectedChangedSlot(self, model_part, is_selected):
"""Set this Z to front, and return other Zs to default.
Args:
model_part (Part): The model part
is_selected (TYPE): Description
"""
if is_selected:
# self._drag_handle.resetAppearance(_SELECTED_COLOR, _SELECTED_WIDTH, _SELECTED_ALPHA)
self.setZValue(styles.ZPARTITEM + 1)
else:
# self._drag_handle.resetAppearance(self.modelColor(), _DEFAULT_WIDTH, _DEFAULT_ALPHA)
self.setZValue(styles.ZPARTITEM)
# end def
def partVirtualHelicesSelectedSlot(self, sender, vh_set, is_adding):
"""is_adding (bool): adding (True) virtual helices to a selection
or removing (False)
Args:
sender (obj): Model object that emitted the signal.
vh_set (TYPE): Description
is_adding (TYPE): Description
"""
select_tool = self._viewroot.select_tool
if is_adding:
select_tool.selection_set.update(vh_set)
select_tool.setPartItem(self)
select_tool.getSelectionBoundingRect()
else:
select_tool.deselectSet(vh_set)
# end def
def partDocumentSettingChangedSlot(self, part, key, value):
"""Summary
Args:
part (TYPE): Description
key (TYPE): Description
value (TYPE): Description
Args:
TYPE: Description
Raises:
ValueError: Description
"""
if key == 'grid':
if value == 'lines and points':
self.griditem.setDrawlines(True)
elif value == 'points':
self.griditem.setDrawlines(False)
elif value == 'circles':
pass # self.griditem.setGridAppearance(False)
else:
raise ValueError("unknown grid styling")
### ACCESSORS ###
def boundingRect(self):
"""Summary
Args:
TYPE: Description
"""
return self._rect
# end def
def modelColor(self):
"""Summary
Args:
TYPE: Description
"""
return self._model_props['color']
# end def
def window(self):
"""Summary
Args:
TYPE: Description
"""
return self.parentItem().window()
# end def
def setActiveVirtualHelixItem(self, new_active_vhi):
"""Summary
Args:
new_active_vhi (TYPE): Description
"""
current_vhi = self.active_virtual_helix_item
if new_active_vhi != current_vhi:
if current_vhi is not None:
current_vhi.deactivate()
if new_active_vhi is not None:
new_active_vhi.activate()
self.active_virtual_helix_item = new_active_vhi
# end def
def setPreXoverItemsVisible(self, virtual_helix_item):
"""
self._pre_xover_items list references prexovers parented to other
PathHelices such that only the activeHelix maintains the list of
visible prexovers
Args:
virtual_helix_item (cadnano.views.sliceview.virtualhelixitem.SliceVirtualHelixItem): Description
"""
vhi = virtual_helix_item
pxom = self.prexover_manager
if vhi is None:
pxom.hideGroups()
return
part = self.part()
info = part.active_base_info
if info:
id_num, is_fwd, idx, to_vh_id_num = info
per_neighbor_hits, pairs = part.potentialCrossoverMap(id_num, idx)
pxom.activateVirtualHelix(virtual_helix_item, idx,
per_neighbor_hits, pairs)
# end def
def removeVirtualHelixItem(self, id_num):
"""Summary
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
Args:
TYPE: Description
"""
vhi = self._virtual_helix_item_hash[id_num]
if vhi == self.active_virtual_helix_item:
self.active_virtual_helix_item = None
vhi.virtualHelixRemovedSlot()
del self._virtual_helix_item_hash[id_num]
# When any VH is removed, turn SPA mode off
self.shortest_path_add_mode = False
self.shortest_path_start = None
# end def
def reconfigureRect(self,
top_left,
bottom_right,
finish=False,
padding=80):
"""Reconfigures the rectangle that is the document.
Args:
top_left (tuple): A tuple corresponding to the x-y coordinates of
top left corner of the document
bottom_right (tuple): A tuple corresponding to the x-y coordinates
of the bottom left corner of the document
Returns:
tuple: tuple of point tuples representing the top_left and
bottom_right as reconfigured with padding
"""
rect = self._rect
ptTL = QPointF(
*self.padTL(padding, *top_left)) if top_left else rect.topLeft()
ptBR = QPointF(*self.padBR(
padding, *bottom_right)) if bottom_right else rect.bottomRight()
self._rect = QRectF(ptTL, ptBR)
self.setRect(self._rect)
self._configureOutline(self.outline)
self.griditem.updateGrid()
return self.outline.rect()
# end def
def padTL(self, padding, xTL, yTL):
return xTL + padding, yTL + padding
# end def
def padBR(self, padding, xBR, yBR):
return xBR - padding, yBR - padding
# end def
def enlargeRectToFit(self):
"""Enlarges Part Rectangle to fit the model bounds.
This should be called when adding a SliceVirtualHelixItem. This
method enlarges the rectangle to ensure that it fits the design.
This method needs to check the model size to do this, but also takes
into account any expansions the user has made to the rectangle as to
not shrink the rectangle after the user has expanded it.
:rtype: None
"""
padding = self._BOUNDING_RECT_PADDING
model_left, model_top, model_right, model_bottom = self.getModelMinBounds(
)
rect_left, rect_right, rect_bottom, rect_top = self.bounds()
xTL = min(rect_left, model_left) - padding
xBR = max(rect_right, model_right) + padding
yTL = min(rect_top, model_top) - padding
yBR = max(rect_bottom, model_bottom) + padding
new_outline_rect = self.reconfigureRect(top_left=(xTL, yTL),
bottom_right=(xBR, yBR))
self.resize_handle_group.alignHandles(new_outline_rect)
# self.grab_cornerTL.alignPos(*top_left)
# self.grab_cornerBR.alignPos(*bottom_right)
### PRIVATE SUPPORT METHODS ###
def _configureOutline(self, outline):
"""Adjusts `outline` size with default padding.
Args:
outline (TYPE): Description
Returns:
o_rect (QRect): `outline` rect adjusted by _BOUNDING_RECT_PADDING
"""
_p = self._BOUNDING_RECT_PADDING
o_rect = self.rect().adjusted(-_p, -_p, _p, _p)
outline.setRect(o_rect)
return o_rect
# end def
def boundRectToModel(self):
"""Update the size of the rectangle corresponding to the grid to
the size of the model or a minimum size (whichever is greater).
:rtype: None
"""
xTL, yTL, xBR, yBR = self.getModelMinBounds()
self._rect = QRectF(QPointF(xTL, yTL), QPointF(xBR, yBR))
# end def
def getModelMinBounds(self, handle_type=None):
"""Bounds in form of Qt scaled from model
Args:
Tuple (top_left, bottom_right)
:rtype: Tuple where
"""
xLL, yLL, xUR, yUR = self.part().boundDimensions(self.scale_factor)
# return xLL, -yUR, xUR, -yLL
r = self._RADIUS
return xLL - r, -yUR - r, xUR + r, -yLL + r
# end def
def bounds(self):
"""x_low, x_high, y_low, y_high
"""
rect = self._rect
return (rect.left(), rect.right(), rect.bottom(), rect.top())
### PUBLIC SUPPORT METHODS ###
def setLastHoveredItem(self, gridpoint_item):
"""Stores the last self-reported griditem to be hovered.
Args:
griditem (GridItem): the hoveree
"""
self._last_hovered_item = gridpoint_item
def setModifyState(self, bool_val):
"""Hides the mod_rect when modify state disabled.
Args:
bool_val (boolean): what the modifystate should be set to.
"""
self._can_show_mod_circ = bool_val
if bool_val is False:
self._mod_circ.hide()
# end def
def showModelMinBoundsHint(self, handle_type, show=True):
"""Shows QGraphicsRectItem reflecting current model bounds.
ResizeHandleGroup should toggle this when resizing.
Args:
status_str (str): Description to display in status bar.
"""
m_b_h = self.model_bounds_hint
if show:
xTL, yTL, xBR, yBR = self.getModelMinBounds()
m_b_h.setRect(QRectF(QPointF(xTL, yTL), QPointF(xBR, yBR)))
m_b_h.show()
else:
m_b_h.hide()
def updateStatusBar(self, status_str):
"""Shows status_str in the MainWindow's status bar.
Args:
status_str (str): Description to display in status bar.
"""
pass # disabled for now.
# self.window().statusBar().showMessage(status_str, timeout)
# end def
def zoomToFit(self):
"""Ask the view to zoom to fit.
"""
thescene = self.scene()
theview = thescene.views()[0]
theview.zoomToFit()
# end def
### EVENT HANDLERS ###
def mousePressEvent(self, event):
"""Handler for user mouse press.
Args:
event (QGraphicsSceneMouseEvent): Contains item, scene, and screen
coordinates of the the event, and previous event.
Args:
event (QMouseEvent): contains parameters that describe a mouse event.
"""
if event.button() == Qt.RightButton:
return
part = self._model_part
part.setSelected(True)
if self.isMovable():
return QGraphicsItem.mousePressEvent(self, event)
tool = self._getActiveTool()
if tool.FILTER_NAME not in part.document().filter_set:
return
tool_method_name = tool.methodPrefix() + "MousePress"
if tool_method_name == 'createToolMousePress':
return
elif hasattr(self, tool_method_name):
getattr(self, tool_method_name)(tool, event)
else:
event.setaccepted(False)
QGraphicsItem.mousePressEvent(self, event)
# end def
def hoverMoveEvent(self, event):
self.last_mouse_position = self.translateEventCoordinates(event)
tool = self._getActiveTool()
tool_method_name = tool.methodPrefix() + "HoverMove"
if hasattr(self, tool_method_name):
getattr(self, tool_method_name)(tool, event)
else:
event.setAccepted(False)
QGraphicsItem.hoverMoveEvent(self, event)
# def hoverLeaveEvent(self, event):
# pass
# tool = self._getActiveTool()
# tool.hideLineItem()
def getModelPos(self, pos):
"""Y-axis is inverted in Qt +y === DOWN
Args:
pos (TYPE): Description
"""
sf = self.scale_factor
x, y = pos.x() / sf, -1.0 * pos.y() / sf
return x, y
# end def
def getVirtualHelixItem(self, id_num):
"""Summary
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
Returns:
TYPE: Description
"""
return self._virtual_helix_item_hash.get(id_num)
# end def
def keyPressEvent(self, event):
is_alt = bool(event.modifiers() & Qt.AltModifier)
if event.key() == Qt.Key_Escape:
self._setShortestPathStart(None)
self.removeAllCreateHints()
if self._inPointItem(self.last_mouse_position,
self.getLastHoveredCoordinates()):
self.highlightOneGridPoint(self.getLastHoveredCoordinates())
elif is_alt and self.shortest_path_add_mode is True:
if self._inPointItem(self.last_mouse_position,
self.getLastHoveredCoordinates()):
x, y = self.coordinates_to_xy.get(
self.getLastHoveredCoordinates())
self._preview_spa((x, y))
elif is_alt:
if self._inPointItem(self.last_mouse_position,
self.getLastHoveredCoordinates()):
self.highlightOneGridPoint(self.getLastHoveredCoordinates(),
styles.SPA_START_HINT_COLOR)
# end def
def keyReleaseEvent(self, event):
is_alt = bool(event.modifiers() & Qt.AltModifier)
if not is_alt:
self.removeAllCreateHints()
if self._inPointItem(self.last_mouse_position,
self.getLastHoveredCoordinates()):
self.highlightOneGridPoint(self.getLastHoveredCoordinates())
# end def
def createToolMousePress(self, tool, event, alt_event=None):
"""Creates individual or groups of VHs in Part on user input.
Shift modifier enables multi-helix addition.
Args:
event (TYPE): Description
alt_event (None, optional): Description
"""
# Abort if a VH already exists here
position = self.translateEventCoordinates(event)
# 1. get point in model coordinates:
part = self._model_part
if alt_event is None:
pt = tool.eventToPosition(self, event)
else:
pt = alt_event.pos()
if pt is None:
tool.deactivate()
return QGraphicsItem.mousePressEvent(self, event)
part_pt_tuple = self.getModelPos(pt)
modifiers = event.modifiers()
is_spa_mode = modifiers == Qt.AltModifier
last_added_spa_vhi_id = self._handleShortestPathMousePress(
tool=tool, position=position, is_spa_mode=is_spa_mode)
if last_added_spa_vhi_id is not None:
return
row, column = self.getLastHoveredCoordinates()
parity = self._getCoordinateParity(row, column)
part.createVirtualHelix(x=part_pt_tuple[0],
y=part_pt_tuple[1],
parity=parity)
id_num = part.getVirtualHelixAtPoint(part_pt_tuple)
vhi = self._virtual_helix_item_hash[id_num]
tool.setVirtualHelixItem(vhi)
tool.startCreation()
if is_spa_mode:
self._highlightSpaVH(id_num)
# end def
def _getCoordinateParity(self, row, column):
if self.griditem.grid_type is GridType.HONEYCOMB:
return 0 if HoneycombDnaPart.isOddParity(row=row,
column=column) else 1
elif self.griditem.grid_type is GridType.SQUARE:
return 0 if SquareDnaPart.isEvenParity(row=row,
column=column) else 1
else:
return None
def _handleShortestPathMousePress(self, tool, position, is_spa_mode):
"""
Handles logic for determining if SPA mode should be activated or
continued.
Args:
tool ():
position (tuple): the xy coordinates of the mouse press
is_spa_mode (bool): whether or not this event is a SPA event
Returns:
True if nothing needs to be done by the caller (i.e. this method
and its callees added VHs as necessary, False otherwise
"""
if is_spa_mode:
# Complete the path
if self.shortest_path_start is not None:
last_vhi_id = self.createToolShortestPath(
tool=tool, start=self.shortest_path_start, end=position)
if last_vhi_id is not None:
self._setShortestPathStart(position)
self._highlightSpaVH(last_vhi_id)
return last_vhi_id
# Initialize SPA
else:
self._setShortestPathStart(position)
else:
self._setShortestPathStart(None)
def _setShortestPathStart(self, position):
# TODO[NF]: Docstring
if position is not None:
self.shortest_path_add_mode = True
self.shortest_path_start = position
else:
self.shortest_path_add_mode = False
self.shortest_path_start = None
self._highlightSpaVH(None)
def _highlightSpaVH(self, vh_id):
# TODO[NF]: Docstring
if self.spa_start_vhi:
self.spa_start_vhi.setBrush(getNoBrush())
if vh_id is None:
self.spa_start_vhi = None
else:
self.spa_start_vhi = self._virtual_helix_item_hash[vh_id]
self.spa_start_vhi.setBrush(
getBrushObj(styles.SPA_START_HINT_COLOR, alpha=32))
# end def
def createToolShortestPath(self, tool, start, end):
"""
Handle the creation of VHIs for SPA mode.
Args:
tool ():
start (tuple): the x-y coordinates of the start point
end (tuple): the x-y coordinates of the end point
Returns:
The ID of the last VHI created
"""
path = ShortestPathHelper.shortestPathXY(
start=start,
end=end,
neighbor_map=self.neighbor_map,
vh_set=self.coordinates_to_vhid.keys(),
point_map=self.coordinates_to_xy,
grid_type=self.griditem.grid_type,
scale_factor=self.inverse_scale_factor,
radius=self._RADIUS)
# Abort and exit SPA if there is no path from start to end
if path == []:
self.shortest_path_start = None
self.shortest_path_add_mode = False
return None
else:
x_list, y_list, parity_list = zip(*path)
id_numbers = self._model_part.batchCreateVirtualHelices(
x_list=x_list, y_list=y_list, parity=parity_list)
for id_number in id_numbers:
vhi = self._virtual_helix_item_hash[id_number]
tool.setVirtualHelixItem(vhi)
tool.startCreation()
return id_number
# end def
def createToolHoverMove(self, tool, event):
"""Summary
Args:
tool (TYPE): Description
event (TYPE): Description
Returns:
TYPE: Description
"""
event_xy = self.translateEventCoordinates(event)
event_coord = ShortestPathHelper.findClosestPoint(
event_xy, self.coordinates_to_xy)
is_alt = True if event.modifiers() & Qt.AltModifier else False
self.last_mouse_position = event_xy
# Un-highlight GridItems if necessary by calling createToolHoverLeave
if len(self._highlighted_path) > 1 or (
self._highlighted_path
and self._highlighted_path[0] != event_coord):
self.createToolHoverLeave(tool=tool, event=event)
# Highlight GridItems if alt is being held down
if is_alt and self.shortest_path_add_mode and self._inPointItem(
event_xy, event_coord):
self._preview_spa(event_xy)
else:
point_item = self.coordinates_to_xy.get(event_coord)
if point_item is not None and self._inPointItem(
event_xy, event_coord) and is_alt:
self.highlightOneGridPoint(self.getLastHoveredCoordinates(),
styles.SPA_START_HINT_COLOR)
elif point_item is not None and self._inPointItem(
event_xy, event_coord) and not is_alt:
part = self._model_part
next_idnums = (part._getNewIdNum(0), part._getNewIdNum(1))
self.griditem.showCreateHint(event_coord,
next_idnums=next_idnums)
self._highlighted_path.append(event_coord)
tool.hoverMoveEvent(self, event)
return QGraphicsItem.hoverMoveEvent(self, event)
# end def
def _inPointItem(self, event_xy, event_coord):
"""
Determine if x-y coordinates are inside the given GridPoint.
Args:
event_xy (tuple): the x-y coordinates corresponding to the
position of the mouse
event_coord (tuple): the i-j coordinates corresponding to the
location of the GridPoint
Returns:
True if the mouse is in the given GridPoint, False otherwise
"""
if event_xy is None or event_coord is None:
return False
point_x, point_y = self.coordinates_to_xy.get(event_coord)
event_x, event_y = event_xy
return (point_x - event_x)**2 + (point_y -
event_y)**2 <= self._RADIUS**2
# end def
def _preview_spa(self, event_xy):
"""
Highlight and add VH ID numbers to the GridPoints that the SPA would
use.
Args:
event_xy (tuple): the x-y coordinates corresponding to the
position of the mouse
Returns:
None
"""
part = self._model_part
start_coord = self.shortest_path_start
end_coord = event_xy
self._highlighted_path = ShortestPathHelper.shortestPathAStar(
start=start_coord,
end=end_coord,
neighbor_map=self.neighbor_map,
vh_set=self.coordinates_to_vhid.keys(),
point_map=self.coordinates_to_xy)
even_id = part._getNewIdNum(0)
odd_id = part._getNewIdNum(1)
for coord in self._highlighted_path:
is_odd = self.griditem.showCreateHint(coord,
next_idnums=(even_id,
odd_id))
if is_odd is True:
odd_id += 2
elif is_odd is False:
even_id += 2
# end def
def createToolHoverLeave(self, tool, event):
self.removeAllCreateHints()
def selectToolMousePress(self, tool, event):
"""
Args:
tool (TYPE): Description
event (TYPE): Description
"""
tool.setPartItem(self)
pt = tool.eventToPosition(self, event)
part_pt_tuple = self.getModelPos(pt)
part = self._model_part
if part.isVirtualHelixNearPoint(part_pt_tuple):
id_num = part.getVirtualHelixAtPoint(part_pt_tuple)
if id_num is not None:
pass
# loc = part.getCoordinate(id_num, 0)
# print("VirtualHelix #{} at ({:.3f}, {:.3f})".format(id_num, loc[0], loc[1]))
else:
# tool.deselectItems()
tool.modelClear()
else:
# tool.deselectItems()
tool.modelClear()
return QGraphicsItem.mousePressEvent(self, event)
# end def
def setNeighborMap(self, neighbor_map):
"""
Update the internal mapping of coordinates to their neighbors.
Args:
neighbor_map (dict): the new mapping of coordinates to their
neighbors
Returns:
None
"""
assert isinstance(neighbor_map, dict)
self.neighbor_map = neighbor_map
# end def
def setPointMap(self, point_map):
"""
Update the internal mapping of coordinates to x-y positions.
Args:
point_map (dict): the new mapping of coordinates to their x-y
position
Returns:
None
"""
assert isinstance(point_map, dict)
self.coordinates_to_xy = point_map
# end def
def updateTranslatedOffsets(self, delta_x, delta_y):
"""
Update the values used to calculate translational offsets.
Args:
delta_x (float): the new value for which we've translated in the x
direction
delta_y (float): the new value for which we've translated in the y
direction
Returns:
None
"""
assert isinstance(delta_x, float)
assert isinstance(delta_y, float)
self._translated_x = delta_x
self._translated_y = delta_y
# end def
def translateEventCoordinates(self, event):
"""
Given an event, return the x-y coordinates of the event accounting for
any translations that may have happened
Args:
event (MousePressEvent): the event for which x-y coordinates should
be returned
Returns:
A tuple of x-y coordinates of the event
"""
assert isinstance(event, QGraphicsSceneEvent)
return event.scenePos().x() - self._translated_x, event.scenePos().y(
) - self._translated_y
# end def
def removeAllCreateHints(self):
"""
Remove the create hints from each currently hinted GridItem.
Iterates over all coordinates in self._highlighted_path.
Returns:
None
"""
for coord in self._highlighted_path:
self.griditem.showCreateHint(coord, show_hint=False)
self._highlighted_path = []
# end def
def highlightOneGridPoint(self, coordinates, color=None):
"""
Add a hint to one GridPoint.
Args:
coordinates (tuple): the row-column coordinates of the gridPoint to
be highlighted
color (): the color that the gridPoint should be changed to
Returns:
None
"""
if coordinates is None:
return
assert isinstance(coordinates, tuple) and len(coordinates) is 2
assert isinstance(coordinates[0], int) and isinstance(
coordinates[1], int)
if self.coordinates_to_xy.get(coordinates) is not None:
part = self._model_part
next_idnums = (part._getNewIdNum(0), part._getNewIdNum(1))
self.griditem.showCreateHint(coordinates,
next_idnums=next_idnums,
color=color)
self._highlighted_path.append(coordinates)
# end def
def getLastHoveredCoordinates(self):
"""
Get the row and column corresponding to the GridPoint that was most
recently hovered over.
This accounts for the fact that the rows are inverted (i.e. the result
returned by this method will match the coordinate system stored in this
class' internal records of coordinates)
Returns:
A tuple corresponding to the row and column of the most recently
hovered GridPoint.
"""
if self._last_hovered_item:
row, column = self._last_hovered_item.coord()
return -row, column
class OutlineNucleicAcidPartItem(CNOutlinerItem, AbstractPartItem):
FILTER_NAME = "part"
def __init__(self, model_part, parent):
super(OutlineNucleicAcidPartItem, self).__init__(model_part, parent)
self._controller = NucleicAcidPartItemController(self, model_part)
self._model_part = model_part
self.setExpanded(True)
# properties
temp_color = model_part.getColor()
# outlinerview takes responsibility of overriding default part color
if temp_color == "#000000":
index = len(model_part.document().children()) - 1
new_color = styles.PARTCOLORS[index % len(styles.PARTCOLORS)]
model_part.setProperty('color', new_color)
# item groups
self._root_items = {}
self._root_items['VHelixList'] = self.createRootPartItem(
'Virtual Helices', self)
self._root_items['OligoList'] = self.createRootPartItem('Oligos', self)
fs = model_part.document().filter_set
if OutlineVirtualHelixItem.FILTER_NAME in fs:
self._root_items['OligoList'].setFlags(DISABLE_FLAGS)
else:
self._root_items['VHelixList'].setFlags(DISABLE_FLAGS)
# self._root_items['Modifications'] = self._createRootItem('Modifications', self)
if model_part.is_active:
print("should be active")
self.activate()
# end def
### PRIVATE SUPPORT METHODS ###
def __repr__(self):
return "OutlineNucleicAcidPartItem %s" % self._cn_model.getProperty(
'name')
### PUBLIC SUPPORT METHODS ###
def rootItems(self):
return self._root_items
# end def
def part(self):
return self._cn_model
# end def
def itemType(self):
return ItemType.NUCLEICACID
# end def
def isModelSelected(self, document):
"""Make sure the item is selected in the model
TODO implement Part selection
Args:
document (Document): reference the the model :class:`Document`
"""
return False
# end def
### SLOTS ###
def partRemovedSlot(self, sender):
self._controller.disconnectSignals()
self._cn_model = None
self._controller = None
# end def
def partOligoAddedSlot(self, model_part, model_oligo):
m_o = model_oligo
m_o.oligoRemovedSignal.connect(self.partOligoRemovedSlot)
o_i = OutlineOligoItem(m_o, self._root_items['OligoList'])
self._oligo_item_hash[m_o] = o_i
# end def
def partOligoRemovedSlot(self, model_part, model_oligo):
m_o = model_oligo
m_o.oligoRemovedSignal.disconnect(self.partOligoRemovedSlot)
o_i = self._oligo_item_hash[m_o]
o_i.parent().removeChild(o_i)
del self._oligo_item_hash[m_o]
# end def
def partVirtualHelixAddedSlot(self, model_part, id_num, virtual_helix,
neighbors):
tw = self.treeWidget()
tw.is_child_adding += 1
vh_i = OutlineVirtualHelixItem(virtual_helix,
self._root_items['VHelixList'])
self._virtual_helix_item_hash[id_num] = vh_i
tw.is_child_adding -= 1
def partVirtualHelixRemovingSlot(self, model_part, id_num, virtual_helix,
neigbors):
vh_i = self._virtual_helix_item_hash.get(id_num)
# in case a OutlineVirtualHelixItem Object is cleaned up before this happends
if vh_i is not None:
del self._virtual_helix_item_hash[id_num]
vh_i.parent().removeChild(vh_i)
# end def
def partPropertyChangedSlot(self, model_part, property_key, new_value):
if self._cn_model == model_part:
self.setValue(property_key, new_value)
if property_key == 'virtual_helix_order':
vhi_dict = self._virtual_helix_item_hash
self.treeWidget().document()
new_list = [vhi_dict[id_num] for id_num in new_value]
# 0. record what was selected
selected_list = [(x, x.isSelected()) for x in new_list]
root_vhi = self._root_items['VHelixList']
# 1. move the items
root_vhi.takeChildren()
for vhi in new_list:
root_vhi.addChild(vhi)
# 2. now reselect the previously selected.
# could also query the model
for vhi, was_selected in selected_list:
if was_selected:
vhi.setSelected(True)
# end def
def partSelectedChangedSlot(self, model_part, is_selected):
# print("part", is_selected)
self.setSelected(is_selected)
# end def
def partVirtualHelixPropertyChangedSlot(self, sender, id_num,
virtual_helix, keys, values):
if self._cn_model == sender:
vh_i = self._virtual_helix_item_hash[id_num]
for key, val in zip(keys, values):
if key in CNOutlinerItem.PROPERTIES:
vh_i.setValue(key, val)
# end def
def partVirtualHelicesSelectedSlot(self, sender, vh_set, is_adding):
""" is_adding (bool): adding (True) virtual helices to a selection
or removing (False)
"""
vhi_hash = self._virtual_helix_item_hash
tw = self.treeWidget()
model = tw.model()
selection_model = tw.selectionModel()
top_idx = tw.indexOfTopLevelItem(self)
top_midx = model.index(top_idx, 0)
vh_list = self._root_items['VHelixList']
root_midx = model.index(self.indexOfChild(vh_list), 0, top_midx)
tw.selection_filter_disabled = True
if is_adding:
flag = QItemSelectionModel.Select
for id_num in vh_set:
vhi = vhi_hash.get(id_num)
# selecting a selected item will deselect it, so check
idx = vh_list.indexOfChild(vhi)
qmodel_idx = model.index(idx, 0, root_midx)
if not vhi.isSelected() and not selection_model.isSelected(
qmodel_idx):
# print("++++++slot Sselect outlinerview", vh_set)
selection_model.select(qmodel_idx, flag)
else:
flag = QItemSelectionModel.Deselect
for id_num in vh_set:
vhi = vhi_hash.get(id_num)
# deselecting a deselected item will select it, so check
idx = vh_list.indexOfChild(vhi)
qmodel_idx = model.index(idx, 0, root_midx)
if vhi.isSelected() and selection_model.isSelected(qmodel_idx):
# print("-----slot deselect outlinerview", vh_set)
selection_model.select(qmodel_idx, flag)
tw.selection_filter_disabled = False
# end def
def partActiveVirtualHelixChangedSlot(self, part, id_num):
vhi = self._virtual_helix_item_hash.get(id_num, None)
# if vhi is not None:
self.setActiveVirtualHelixItem(vhi)
# end def
def partActiveChangedSlot(self, part, is_active):
if part == self._cn_model:
self.activate() if is_active else self.deactivate()
# end def
def setActiveVirtualHelixItem(self, new_active_vhi):
current_vhi = self.active_virtual_helix_item
if new_active_vhi != current_vhi:
if current_vhi is not None:
current_vhi.deactivate()
if new_active_vhi is not None:
new_active_vhi.activate()
self.active_virtual_helix_item = new_active_vhi
class GridNucleicAcidPartItem(QAbstractPartItem):
"""Parent should be either a GridRootItem, or an AssemblyItem.
Invariant: keys in _empty_helix_hash = range(_nrows) x range(_ncols)
where x is the cartesian product.
Attributes:
active_virtual_helix_item (cadnano.views.gridview.virtualhelixitem.GridVirtualHelixItem): Description
grab_cornerBR (TYPE): bottom right bounding box handle
grab_cornerTL (TYPE): top left bounding box handle
griditem (TYPE): Description
outline (TYPE): Description
prexover_manager (TYPE): Description
scale_factor (TYPE): Description
"""
_RADIUS = styles.GRID_HELIX_RADIUS
_BOUNDING_RECT_PADDING = 80
def __init__(self, model_part_instance, viewroot, parent=None):
"""Summary
Args:
model_part_instance (TYPE): Description
viewroot (TYPE): Description
parent (None, optional): Description
"""
super(GridNucleicAcidPartItem, self).__init__(model_part_instance, viewroot, parent)
self._getActiveTool = viewroot.manager.activeToolGetter
m_p = self._model_part
self._controller = NucleicAcidPartItemController(self, m_p)
self.scale_factor = self._RADIUS / m_p.radius()
self.active_virtual_helix_item = None
self.prexover_manager = PreXoverManager(self)
self.hide() # hide while until after attemptResize() to avoid flicker
self._rect = QRectF(0., 0., 1000., 1000.) # set this to a token value
self.boundRectToModel()
self.setPen(getNoPen())
self.setRect(self._rect)
self.setAcceptHoverEvents(True)
# Cache of VHs that were active as of last call to 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)
self.outline = outline = QGraphicsRectItem(self)
o_rect = self._configureOutline(outline)
outline.setFlag(QGraphicsItem.ItemStacksBehindParent)
outline.setZValue(styles.ZDESELECTOR)
model_color = m_p.getColor()
self.outline.setPen(getPenObj(model_color, _DEFAULT_WIDTH))
GC_SIZE = 10
self.grab_cornerTL = GrabCornerItem(GC_SIZE, model_color, True, self)
self.grab_cornerTL.setTopLeft(o_rect.topLeft())
self.grab_cornerBR = GrabCornerItem(GC_SIZE, model_color, True, self)
self.grab_cornerBR.setBottomRight(o_rect.bottomRight())
self.griditem = GridItem(self, self._model_props['grid_type'])
self.griditem.setZValue(1)
self.grab_cornerTL.setZValue(2)
self.grab_cornerBR.setZValue(2)
# select upon creation
for part in m_p.document().children():
if part is m_p:
part.setSelected(True)
else:
part.setSelected(False)
self.show()
# end def
### SIGNALS ###
### SLOTS ###
def partActiveVirtualHelixChangedSlot(self, part, id_num):
"""Summary
Args:
part (TYPE): Description
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
Args:
TYPE: Description
"""
vhi = self._virtual_helix_item_hash.get(id_num, None)
self.setActiveVirtualHelixItem(vhi)
self.setPreXoverItemsVisible(vhi)
# end def
def partActiveBaseInfoSlot(self, part, info):
"""Summary
Args:
part (TYPE): Description
info (TYPE): Description
Args:
TYPE: Description
"""
pxom = self.prexover_manager
pxom.deactivateNeighbors()
if info and info is not None:
id_num, is_fwd, idx, _ = info
pxom.activateNeighbors(id_num, is_fwd, idx)
# end def
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.grab_cornerTL.setPen(getPenObj(new_value, 0))
self.grab_cornerBR.setPen(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)
# end def
def partRemovedSlot(self, sender):
"""docstring for partRemovedSlot
Args:
sender (obj): Model object that emitted the signal.
"""
self.parentItem().removePartItem(self)
scene = self.scene()
scene.removeItem(self)
self._model_part = None
self._mod_circ = None
self._controller.disconnectSignals()
self._controller = None
self.grab_cornerTL = None
self.grab_cornerBR = None
self.griditem = None
# end def
def partVirtualHelicesTranslatedSlot(self, sender,
vh_set, left_overs,
do_deselect):
"""
left_overs are neighbors that need updating due to changes
Args:
sender (obj): Model object that emitted the signal.
vh_set (TYPE): Description
left_overs (TYPE): Description
do_deselect (TYPE): Description
"""
if do_deselect:
tool = self._getActiveTool()
if tool.methodPrefix() == "selectTool":
if tool.isSelectionActive():
# tool.deselectItems()
tool.modelClear()
# 1. move everything that moved
for id_num in vh_set:
vhi = self._virtual_helix_item_hash[id_num]
vhi.updatePosition()
# 2. now redraw what makes sense to be redrawn
for id_num in vh_set:
vhi = self._virtual_helix_item_hash[id_num]
self._refreshVirtualHelixItemGizmos(id_num, vhi)
for id_num in left_overs:
vhi = self._virtual_helix_item_hash[id_num]
self._refreshVirtualHelixItemGizmos(id_num, vhi)
# 0. clear PreXovers:
# self.prexover_manager.hideGroups()
# if self.active_virtual_helix_item is not None:
# self.active_virtual_helix_item.deactivate()
# self.active_virtual_helix_item = None
avhi = self.active_virtual_helix_item
self.setPreXoverItemsVisible(avhi)
self.enlargeRectToFit()
# end def
def _refreshVirtualHelixItemGizmos(self, id_num, vhi):
"""Update props and appearance of self & recent neighbors. Ultimately
triggered by a partVirtualHelicesTranslatedSignal.
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
vhi (cadnano.views.gridview.virtualhelixitem.GridVirtualHelixItem): the item associated with id_num
"""
neighbors = vhi.cnModel().getProperty('neighbors')
neighbors = literal_eval(neighbors)
vhi.beginAddWedgeGizmos()
for nvh in neighbors:
nvhi = self._virtual_helix_item_hash.get(nvh, False)
if nvhi:
vhi.setWedgeGizmo(nvh, nvhi)
# end for
vhi.endAddWedgeGizmos()
# end def
def partVirtualHelixPropertyChangedSlot(self, sender, id_num, virtual_helix, keys, values):
"""Summary
Args:
sender (obj): Model object that emitted the signal.
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
keys (tuple): keys that changed
values (tuple): new values for each key that changed
Args:
TYPE: Description
"""
if self._model_part == sender:
vh_i = self._virtual_helix_item_hash[id_num]
vh_i.virtualHelixPropertyChangedSlot(keys, values)
# end def
def partVirtualHelixAddedSlot(self, sender, id_num, virtual_helix, neighbors):
"""Summary
Args:
sender (obj): Model object that emitted the signal.
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
neighbors (TYPE): Description
Args:
TYPE: Description
"""
vhi = GridVirtualHelixItem(virtual_helix, self)
self._virtual_helix_item_hash[id_num] = vhi
self._refreshVirtualHelixItemGizmos(id_num, vhi)
for neighbor_id in neighbors:
nvhi = self._virtual_helix_item_hash.get(neighbor_id, False)
if nvhi:
self._refreshVirtualHelixItemGizmos(neighbor_id, nvhi)
self.enlargeRectToFit()
# end def
def partVirtualHelixRemovingSlot(self, sender, id_num, virtual_helix, neighbors):
"""Summary
Args:
sender (obj): Model object that emitted the signal.
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
neighbors (TYPE): Description
Args:
TYPE: Description
"""
tm = self._viewroot.manager
tm.resetTools()
self.removeVirtualHelixItem(id_num)
for neighbor_id in neighbors:
nvhi = self._virtual_helix_item_hash[neighbor_id]
self._refreshVirtualHelixItemGizmos(neighbor_id, nvhi)
# end def
def partSelectedChangedSlot(self, model_part, is_selected):
"""Set this Z to front, and return other Zs to default.
Args:
model_part (Part): The model part
is_selected (TYPE): Description
"""
if is_selected:
# self._drag_handle.resetAppearance(_SELECTED_COLOR, _SELECTED_WIDTH, _SELECTED_ALPHA)
self.setZValue(styles.ZPARTITEM + 1)
else:
# self._drag_handle.resetAppearance(self.modelColor(), _DEFAULT_WIDTH, _DEFAULT_ALPHA)
self.setZValue(styles.ZPARTITEM)
# end def
def partVirtualHelicesSelectedSlot(self, sender, vh_set, is_adding):
"""is_adding (bool): adding (True) virtual helices to a selection
or removing (False)
Args:
sender (obj): Model object that emitted the signal.
vh_set (TYPE): Description
is_adding (TYPE): Description
"""
select_tool = self._viewroot.select_tool
if is_adding:
# print("got the adding slot in path")
select_tool.selection_set.update(vh_set)
select_tool.setPartItem(self)
select_tool.getSelectionBoundingRect()
else:
select_tool.deselectSet(vh_set)
# end def
def partDocumentSettingChangedSlot(self, part, key, value):
"""Summary
Args:
part (TYPE): Description
key (TYPE): Description
value (TYPE): Description
Args:
TYPE: Description
Raises:
ValueError: Description
"""
if key == 'grid':
print("grid change", value)
if value == 'lines and points':
self.griditem.setGridAppearance(True)
elif value == 'points':
self.griditem.setGridAppearance(False)
elif value == 'circles':
pass # self.griditem.setGridAppearance(False)
else:
raise ValueError("unknown grid styling")
# end def
### ACCESSORS ###
def boundingRect(self):
"""Summary
Args:
TYPE: Description
"""
return self._rect
# end def
def modelColor(self):
"""Summary
Args:
TYPE: Description
"""
return self._model_props['color']
# end def
def window(self):
"""Summary
Args:
TYPE: Description
"""
return self.parentItem().window()
# end def
def setActiveVirtualHelixItem(self, new_active_vhi):
"""Summary
Args:
new_active_vhi (TYPE): Description
"""
current_vhi = self.active_virtual_helix_item
# print(current_vhi, new_active_vhi)
if new_active_vhi != current_vhi:
if current_vhi is not None:
current_vhi.deactivate()
if new_active_vhi is not None:
new_active_vhi.activate()
self.active_virtual_helix_item = new_active_vhi
# end def
def setPreXoverItemsVisible(self, virtual_helix_item):
"""
self._pre_xover_items list references prexovers parented to other
PathHelices such that only the activeHelix maintains the list of
visible prexovers
Args:
virtual_helix_item (cadnano.views.gridview.virtualhelixitem.GridVirtualHelixItem): Description
"""
vhi = virtual_helix_item
pxom = self.prexover_manager
if vhi is None:
pxom.hideGroups()
return
# print("grid.setPreXoverItemsVisible", virtual_helix_item.idNum())
part = self.part()
info = part.active_base_info
if info:
id_num, is_fwd, idx, to_vh_id_num = info
per_neighbor_hits, pairs = part.potentialCrossoverMap(id_num, idx)
pxom.activateVirtualHelix(virtual_helix_item, idx,
per_neighbor_hits, pairs)
# end def
def removeVirtualHelixItem(self, id_num):
"""Summary
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
Args:
TYPE: Description
"""
vhi = self._virtual_helix_item_hash[id_num]
if vhi == self.active_virtual_helix_item:
self.active_virtual_helix_item = None
vhi.virtualHelixRemovedSlot()
del self._virtual_helix_item_hash[id_num]
# end def
def reconfigureRect(self, top_left, bottom_right, finish=False, padding=80):
"""Summary
Args:
top_left (TYPE): Description
bottom_right (TYPE): Description
Returns:
tuple: tuple of point tuples representing the top_left and
bottom_right as reconfigured with padding
"""
rect = self._rect
ptTL = QPointF(*self.padTL(padding, *top_left)) if top_left else rect.topLeft()
ptBR = QPointF(*self.padBR(padding, *bottom_right)) if bottom_right else rect.bottomRight()
self._rect = new_rect = QRectF(ptTL, ptBR)
self.setRect(new_rect)
self._configureOutline(self.outline)
self.griditem.updateGrid()
return (ptTL.x(), ptTL.y()), (ptBR.x(), ptBR.y())
# end def
def padTL(self, padding, xTL, yTL):
return xTL + padding, yTL + padding
# end def
def padBR(self, padding, xBR, yBR):
return xBR - padding, yBR - padding
# end def
def enlargeRectToFit(self):
"""Enlarges Part Rectangle to fit the model bounds. Call this
when adding a GridVirtualHelixItem.
"""
p = self._BOUNDING_RECT_PADDING
xTL, yTL, xBR, yBR = self.getModelMinBounds()
xTL = xTL - p
yTL = yTL - p
xBR = xBR + p
yBR = yBR + p
tl, br = self.reconfigureRect((xTL, yTL), (xBR, yBR))
self.grab_cornerTL.alignPos(*tl)
self.grab_cornerBR.alignPos(*br)
# end def
### PRIVATE SUPPORT METHODS ###
def _configureOutline(self, outline):
"""Adjusts `outline` size with default padding.
Args:
outline (TYPE): Description
Returns:
o_rect (QRect): `outline` rect adjusted by _BOUNDING_RECT_PADDING
"""
_p = self._BOUNDING_RECT_PADDING
o_rect = self.rect().adjusted(-_p, -_p, _p, _p)
outline.setRect(o_rect)
return o_rect
# end def
def boundRectToModel(self):
"""update the boundaries to what's in the model with a minimum
size
"""
xTL, yTL, xBR, yBR = self.getModelMinBounds()
self._rect = QRectF(QPointF(xTL, yTL), QPointF(xBR, yBR))
# end def
def getModelMinBounds(self, handle_type=None):
"""Bounds in form of Qt scaled from model
Args:
Tuple (top_left, bottom_right)
"""
xLL, yLL, xUR, yUR = self.part().boundDimensions(self.scale_factor)
return xLL, -yUR, xUR, -yLL
# end def
def bounds(self):
"""x_low, x_high, y_low, y_high
"""
rect = self._rect
return (rect.left(), rect.right(), rect.bottom(), rect.top())
### PUBLIC SUPPORT METHODS ###
def setModifyState(self, bool_val):
"""Hides the mod_rect when modify state disabled.
Args:
bool_val (TYPE): what the modifystate should be set to.
"""
self._can_show_mod_circ = bool_val
if bool_val is False:
self._mod_circ.hide()
# end def
def updateStatusBar(self, status_str):
"""Shows status_str in the MainWindow's status bar.
Args:
status_str (TYPE): Description
"""
pass # disabled for now.
# self.window().statusBar().showMessage(status_str, timeout)
# end def
def zoomToFit(self):
"""Summary
Args:
TYPE: Description
"""
thescene = self.scene()
theview = thescene.views()[0]
theview.zoomToFit()
# end def
### EVENT HANDLERS ###
def mousePressEvent(self, event):
"""Handler for user mouse press.
Args:
event (QGraphicsSceneMouseEvent): Contains item, scene, and screen
coordinates of the the event, and previous event.
Args:
TYPE: Description
"""
if event.button() == Qt.RightButton:
return
part = self._model_part
part.setSelected(True)
if self.isMovable():
return QGraphicsItem.mousePressEvent(self, event)
tool = self._getActiveTool()
if tool.FILTER_NAME not in part.document().filter_set:
return
tool_method_name = tool.methodPrefix() + "MousePress"
if hasattr(self, tool_method_name):
getattr(self, tool_method_name)(tool, event)
else:
event.setAccepted(False)
QGraphicsItem.mousePressEvent(self, event)
# end def
def hoverMoveEvent(self, event):
"""Summary
Args:
event (TYPE): Description
Args:
TYPE: Description
"""
tool = self._getActiveTool()
tool_method_name = tool.methodPrefix() + "HoverMove"
if hasattr(self, tool_method_name):
getattr(self, tool_method_name)(tool, event)
else:
event.setAccepted(False)
QGraphicsItem.hoverMoveEvent(self, event)
# end def
def hoverLeaveEvent(self, event):
tool = self._getActiveTool()
tool.hideLineItem()
def getModelPos(self, pos):
"""Y-axis is inverted in Qt +y === DOWN
Args:
pos (TYPE): Description
"""
sf = self.scale_factor
x, y = pos.x()/sf, -1.0*pos.y()/sf
return x, y
# end def
def getVirtualHelixItem(self, id_num):
"""Summary
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
Returns:
TYPE: Description
"""
return self._virtual_helix_item_hash.get(id_num)
# end def
def createToolMousePress(self, tool, event, alt_event=None):
"""Summary
Args:
tool (TYPE): Description
event (TYPE): Description
alt_event (None, optional): Description
Returns:
TYPE: Description
"""
# 1. get point in model coordinates:
part = self._model_part
if alt_event is None:
# print()
pt = tool.eventToPosition(self, event)
# print("reg_event", pt)
else:
# pt = alt_event.scenePos()
# pt = self.mapFromScene(pt)
pt = alt_event.pos()
# print("alt_event", pt)
if pt is None:
tool.deactivate()
return QGraphicsItem.mousePressEvent(self, event)
part_pt_tuple = self.getModelPos(pt)
mod = Qt.MetaModifier
if not (event.modifiers() & mod):
pass
# don't create a new VirtualHelix if the click overlaps with existing
# VirtualHelix
current_id_num = tool.idNum()
check = part.isVirtualHelixNearPoint(part_pt_tuple, current_id_num)
# print("current_id_num", current_id_num, check)
# print(part_pt_tuple)
tool.setPartItem(self)
if check:
id_num = part.getVirtualHelixAtPoint(part_pt_tuple)
# print("got a check", id_num)
if id_num is not None:
# print("restart", id_num)
vhi = self._virtual_helix_item_hash[id_num]
tool.setVirtualHelixItem(vhi)
tool.startCreation()
else:
# print("creating", part_pt_tuple)
part.createVirtualHelix(*part_pt_tuple)
id_num = part.getVirtualHelixAtPoint(part_pt_tuple)
vhi = self._virtual_helix_item_hash[id_num]
tool.setVirtualHelixItem(vhi)
tool.startCreation()
# end def
def createToolHoverMove(self, tool, event):
"""Summary
Args:
tool (TYPE): Description
event (TYPE): Description
Returns:
TYPE: Description
"""
tool.hoverMoveEvent(self, event)
return QGraphicsItem.hoverMoveEvent(self, event)
# end def
def selectToolMousePress(self, tool, event):
"""
Args:
tool (TYPE): Description
event (TYPE): Description
"""
tool.setPartItem(self)
pt = tool.eventToPosition(self, event)
part_pt_tuple = self.getModelPos(pt)
part = self._model_part
if part.isVirtualHelixNearPoint(part_pt_tuple):
id_num = part.getVirtualHelixAtPoint(part_pt_tuple)
if id_num is not None:
print(id_num)
loc = part.getCoordinate(id_num, 0)
print("VirtualHelix #{} at ({:.3f}, {:.3f})".format(id_num, loc[0], loc[1]))
else:
# tool.deselectItems()
tool.modelClear()
else:
# tool.deselectItems()
tool.modelClear()
return QGraphicsItem.mousePressEvent(self, event)
class PathNucleicAcidPartItem(QAbstractPartItem):
"""Summary
Attributes:
active_virtual_helix_item (cadnano.views.pathview.virtualhelixitem.VirtualHelixItem): Description
findChild (TYPE): Description
grab_corner (TYPE): Description
prexover_manager (TYPE): Description
"""
findChild = util.findChild # for debug
_BOUNDING_RECT_PADDING = 20
_GC_SIZE = 10
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
# end def
def proxy(self):
"""Summary
Returns:
TYPE: Description
"""
return self._proxy_parent
# end def
def modelColor(self):
"""Summary
Returns:
TYPE: Description
"""
return self._model_part.getProperty('color')
# end def
def convertToModelZ(self, z):
"""scale Z-axis coordinate to the model
Args:
z (TYPE): Description
"""
return z * self._scale_2_model
# end def
def convertToQtZ(self, z):
"""Summary
Args:
z (TYPE): Description
Returns:
TYPE: Description
"""
return z * self._scale_2_Qt
# end def
def _initModifierRect(self):
"""docstring for _initModifierRect
"""
self._can_show_mod_rect = False
self._mod_rect = m_r = QGraphicsRectItem(_DEFAULT_RECT, self)
m_r.setPen(_MOD_PEN)
m_r.hide()
# end def
def vhItemForIdNum(self, id_num):
"""Returns the pathview VirtualHelixItem corresponding to id_num
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
"""
return self._virtual_helix_item_hash.get(id_num)
### SIGNALS ###
### SLOTS ###
def partActiveVirtualHelixChangedSlot(self, part, id_num):
"""Summary
Args:
part (TYPE): Description
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
Returns:
TYPE: Description
"""
vhi = self._virtual_helix_item_hash.get(id_num, None)
self.setActiveVirtualHelixItem(vhi)
self.setPreXoverItemsVisible(vhi)
# end def
def partActiveBaseInfoSlot(self, part, info):
"""Summary
Args:
part (TYPE): Description
info (TYPE): Description
Returns:
TYPE: Description
"""
pxi_m = self.prexover_manager
pxi_m.deactivateNeighbors()
if info and info is not None:
id_num, is_fwd, idx, to_vh_id_num = info
pxi_m.activateNeighbors(id_num, is_fwd, idx)
# end def
def partZDimensionsChangedSlot(self,
model_part,
min_id_num,
max_id_num,
ztf=False):
"""Summary
Args:
model_part (Part): The model part
min_id_num (TYPE): Description
max_id_num (TYPE): Description
ztf (bool, optional): Description
Returns:
TYPE: Description
"""
if len(self._virtual_helix_item_list) > 0:
vhi_hash = self._virtual_helix_item_hash
vhi_max = vhi_hash[max_id_num]
vhi_rect_max = vhi_max.boundingRect()
self._vh_rect.setRight(vhi_rect_max.right() + vhi_max.x())
vhi_min = vhi_hash[min_id_num]
vhi_h_rect = vhi_min.handle().boundingRect()
self._vh_rect.setLeft(
(vhi_h_rect.left() - styles.VH_XOFFSET + vhi_min.x()))
if ztf:
self.scene().views()[0].zoomToFit()
TLx, TLy, BRx, BRy = self._getVHRectCorners()
self.reconfigureRect((TLx, TLy), (BRx, BRy))
# end def
def partSelectedChangedSlot(self, model_part, is_selected):
"""Summary
Args:
model_part (Part): The model part
is_selected (TYPE): Description
Returns:
TYPE: Description
"""
# print("partSelectedChangedSlot", is_selected)
if is_selected:
self.resetPen(styles.SELECTED_COLOR, styles.SELECTED_PEN_WIDTH)
self.resetBrush(styles.SELECTED_BRUSH_COLOR, styles.SELECTED_ALPHA)
else:
self.resetPen(self.modelColor())
self.resetBrush(styles.DEFAULT_BRUSH_COLOR, styles.DEFAULT_ALPHA)
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.workplane.outline.setPen(getPenObj(new_value, 0))
TLx, TLy, BRx, BRy = self._getVHRectCorners()
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)
# end def
def partVirtualHelicesTranslatedSlot(self, sender, vh_set, left_overs,
do_deselect):
"""Summary
Args:
sender (obj): Model object that emitted the signal.
vh_set (TYPE): Description
left_overs (TYPE): Description
do_deselect (TYPE): Description
Returns:
TYPE: Description
"""
# self.prexover_manager.clearPreXoverItems()
# if self.active_virtual_helix_item is not None:
# self.active_virtual_helix_item.deactivate()
# self.active_virtual_helix_item = None
# if self.active_virtual_helix_item is not None:
# self.setPreXoverItemsVisible(self.active_virtual_helix_item)
pass
# end def
def partRemovedSlot(self, sender):
"""docstring for partRemovedSlot
Args:
sender (obj): Model object that emitted the signal.
"""
self.parentItem().removePartItem(self)
scene = self.scene()
scene.removeItem(self)
self._model_part = None
self._virtual_helix_item_hash = None
self._virtual_helix_item_list = None
self._controller.disconnectSignals()
self._controller = None
# self.grab_corner = None
# end def
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()
# end def
def partVirtualHelixResizedSlot(self, sender, id_num, virtual_helix):
"""Notifies the virtualhelix at coord to resize.
Args:
sender (obj): Model object that emitted the signal.
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
"""
vhi = self._virtual_helix_item_hash[id_num]
# print("resize:", id_num, virtual_helix.getSize())
vhi.resize()
# end def
def partVirtualHelixRemovingSlot(self, sender, id_num, virtual_helix,
neighbors):
"""Summary
Args:
sender (obj): Model object that emitted the signal.
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
Returns:
TYPE: Description
"""
self.removeVirtualHelixItem(id_num)
# end def
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)
if len(self._virtual_helix_item_list) == 0:
self.hide()
self.reconfigureRect((), ())
# end def
def partVirtualHelixPropertyChangedSlot(self, sender, id_num,
virtual_helix, keys, values):
"""Summary
Args:
sender (obj): Model object that emitted the signal.
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
keys (TYPE): Description
values (TYPE): Description
Returns:
TYPE: Description
"""
if self._model_part == sender:
vh_i = self._virtual_helix_item_hash[id_num]
vh_i.virtualHelixPropertyChangedSlot(keys, values)
# end def
def partVirtualHelicesSelectedSlot(self, sender, vh_set, is_adding):
"""is_adding (bool): adding (True) virtual helices to a selection
or removing (False)
Args:
sender (obj): Model object that emitted the signal.
vh_set (TYPE): Description
is_adding (TYPE): Description
"""
vhhi_group = self._viewroot.vhiHandleSelectionGroup()
vh_hash = self._virtual_helix_item_hash
doc = self._viewroot.document()
if is_adding:
# print("got the adding slot in path")
for id_num in vh_set:
vhi = vh_hash[id_num]
vhhi = vhi.handle()
vhhi.modelSelect(doc)
# end for
vhhi_group.processPendingToAddList()
else:
# print("got the removing slot in path")
for id_num in vh_set:
vhi = vh_hash[id_num]
vhhi = vhi.handle()
vhhi.modelDeselect(doc)
# end for
vhhi_group.processPendingToAddList()
# end def
### ACCESSORS ###
def removeVirtualHelixItem(self, id_num):
"""Summary
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
Returns:
TYPE: Description
"""
self.setActiveVirtualHelixItem(None)
vhi = self._virtual_helix_item_hash[id_num]
vhi.virtualHelixRemovedSlot()
self._virtual_helix_item_list.remove(vhi)
del self._virtual_helix_item_hash[id_num]
# end def
def window(self):
"""Summary
Returns:
TYPE: Description
"""
return self.parentItem().window()
# end def
### PRIVATE METHODS ###
def _configureOutline(self, outline):
"""Adjusts `outline` size with default padding.
Args:
outline (TYPE): Description
Returns:
o_rect (QRect): `outline` rect adjusted by _BOUNDING_RECT_PADDING
"""
_p = self._BOUNDING_RECT_PADDING
o_rect = self.rect().adjusted(-_p, -_p, _p, _p)
outline.setRect(o_rect)
return o_rect
# end def
def _getVHRectCorners(self):
vhTL = self._vh_rect.topLeft()
vhBR = self._vh_rect.bottomRight()
# vhTLx, vhTLy = vhTL.x(), vhTL.y()
# vhBRx, vhBRy = vhBR.x(), vhBR.y()
return vhTL.x(), vhTL.y(), vhBR.x(), vhBR.y()
# end def
def _setVirtualHelixItemList(self, new_list, zoom_to_fit=True):
"""
Give me a list of VirtualHelixItems and I'll parent them to myself if
necessary, position them in a column, adopt their handles, and
position them as well.
Args:
new_list (TYPE): Description
zoom_to_fit (bool, optional): Description
"""
y = 0 # How far down from the top the next PH should be
vhi_rect = None
vhi_h_rect = None
vhi_h_selection_group = self._viewroot.vhiHandleSelectionGroup()
for vhi in new_list:
_, _, _z = vhi.cnModel().getAxisPoint(0)
_z *= self._scale_2_Qt
vhi.setPos(_z, y)
if vhi_rect is None:
vhi_rect = vhi.boundingRect()
step = vhi_rect.height() + styles.PATH_HELIX_PADDING
# end if
# get the VirtualHelixHandleItem
vhi_h = vhi.handle()
do_reselect = False
if vhi_h.parentItem() == vhi_h_selection_group:
do_reselect = True
vhi_h.tempReparent() # so positioning works
if vhi_h_rect is None:
vhi_h_rect = vhi_h.boundingRect()
vhi_h_x = _z - _VH_XOFFSET
vhi_h_y = y + (vhi_rect.height() - vhi_h_rect.height()) / 2
vhi_h.setPos(vhi_h_x, vhi_h_y)
y += step
self.updateXoverItems(vhi)
if do_reselect:
vhi_h_selection_group.addToGroup(vhi_h)
# end for
# this need only adjust top and bottom edges of the bounding rectangle
# self._vh_rect.setTop()
self._vh_rect.setBottom(y)
self._virtual_helix_item_list = new_list
# now update Z dimension (X in Qt space in the Path view)
part = self.part()
self.partZDimensionsChangedSlot(part,
*part.zBoundsIds(),
ztf=zoom_to_fit)
# end def
def resetPen(self, color, width=0):
"""Summary
Args:
color (TYPE): Description
width (int, optional): Description
Returns:
TYPE: Description
"""
pen = getPenObj(color, width)
self.outline.setPen(pen)
# self.setPen(pen)
# end def
def resetBrush(self, color, alpha):
"""Summary
Args:
color (TYPE): Description
alpha (TYPE): Description
Returns:
TYPE: Description
"""
brush = getBrushObj(color, alpha=alpha)
self.setBrush(brush)
# end def
def reconfigureRect(self,
top_left,
bottom_right,
finish=False,
padding=80):
"""
Updates the bounding rect to the size of the childrenBoundingRect.
Refreshes the outline and grab_corner locations.
Called by partZDimensionsChangedSlot and partPropertyChangedSlot.
"""
outline = self.outline
hasTL = True if top_left else False
hasBR = True if bottom_right else False
if hasTL ^ hasBR: # called via resizeHandle mouseMove?
ptTL = QPointF(*top_left) if top_left else outline.rect().topLeft()
ptBR = QPointF(*bottom_right) if bottom_right else outline.rect(
).bottomRight()
o_rect = QRectF(ptTL, ptBR)
pad_xoffset = self._BOUNDING_RECT_PADDING * 2
new_size = int(
(o_rect.width() - _VH_XOFFSET - pad_xoffset) / _BASE_WIDTH)
substep = self._model_part.subStepSize()
snap_size = new_size - new_size % substep
snap_offset = -(new_size % substep) * _BASE_WIDTH
self.resize_handle_group.updateText(HandleType.RIGHT, snap_size)
if finish:
self._model_part.setAllVirtualHelixSizes(snap_size)
o_rect = o_rect.adjusted(0, 0, snap_offset, 0)
# print("finish", vh_size, new_size, substep, snap_size)
self.outline.setRect(o_rect)
else:
# 1. Temporarily remove children that shouldn't affect size
outline.setParentItem(None)
self.workplane.setParentItem(None)
self.model_bounds_hint.setParentItem(None)
self.resize_handle_group.setParentItemAll(None)
self.prexover_manager.setParentItem(None)
# 2. Get the tight bounding rect
self.setRect(self.childrenBoundingRect()) # vh_items only
# 3. Restore children like nothing happened
outline.setParentItem(self)
self.workplane.setParentItem(self)
self.model_bounds_hint.setParentItem(self)
self.resize_handle_group.setParentItemAll(self)
self.prexover_manager.setParentItem(self)
self._configureOutline(outline)
self.resetPen(self.modelColor(), 0) # cosmetic
self.resetBrush(styles.DEFAULT_BRUSH_COLOR, styles.DEFAULT_ALPHA)
self.workplane.reconfigureRect((), ())
self.resize_handle_group.alignHandles(outline.rect())
return outline.rect()
# end def
### PUBLIC METHODS ###
def getModelMinBounds(self, handle_type=None):
"""Bounds in form of Qt scaled from model
Absolute min should be 2*stepsize.
Round up from indexOfRightmostNonemptyBase to nearest substep.
Returns:
Tuple (xTL, yTL, xBR, yBR)
"""
_p = self._BOUNDING_RECT_PADDING
default_idx = self._model_part.stepSize() * 2
nonempty_idx = self._model_part.indexOfRightmostNonemptyBase()
right_bound_idx = max(default_idx, nonempty_idx)
substep = self._model_part.subStepSize()
snap_idx = (right_bound_idx / substep) * substep
xTL = 0
xBR = snap_idx * _BASE_WIDTH + _p
min_rect = self.rect().adjusted(-_p, -_p, _p, _p)
yTL = min_rect.top()
yBR = min_rect.bottom()
return xTL, yTL, xBR, yBR
# end def
def showModelMinBoundsHint(self, handle_type, show=True):
"""Shows QGraphicsRectItem reflecting current model bounds.
ResizeHandleGroup should toggle this when resizing.
Args:
status_str (str): Description to display in status bar.
"""
m_b_h = self.model_bounds_hint
if show:
xTL, yTL, xBR, yBR = self.getModelMinBounds()
m_b_h.setRect(QRectF(QPointF(xTL, yTL), QPointF(xBR, yBR)))
m_b_h.show()
else:
m_b_h.hide()
# end def
def setModifyState(self, bool):
"""Hides the modRect when modify state disabled.
Args:
bool (TYPE): Description
"""
self._can_show_mod_rect = bool
if bool is False:
self._mod_rect.hide()
def getOrderedVirtualHelixList(self):
"""Used for encoding.
"""
ret = []
for vhi in self._virtual_helix_item_list:
ret.append(vhi.coord())
return ret
# end def
def reorderHelices(self, id_nums, index_delta):
"""
Reorder helices by moving helices _pathHelixList[first:last]
by a distance delta in the list. Notify each PathHelix and
PathHelixHandle of its new location.
Args:
first (TYPE): Description
last (TYPE): Description
index_delta (TYPE): Description
"""
vhi_list = self._virtual_helix_item_list
helix_numbers = [vhi.idNum() for vhi in vhi_list]
first_index = helix_numbers.index(id_nums[0])
last_index = helix_numbers.index(id_nums[-1]) + 1
for id_num in id_nums:
helix_numbers.remove(id_num)
if index_delta < 0: # move group earlier in the list
new_index = max(0, index_delta + first_index) - len(id_nums)
else: # move group later in list
new_index = min(len(vhi_list),
index_delta + last_index) - len(id_nums)
new_list = helix_numbers[:new_index] + id_nums + helix_numbers[
new_index:]
# call the method to move the items and store the list
self._model_part.setImportedVHelixOrder(new_list, check_batch=False)
# end def
def setActiveVirtualHelixItem(self, new_active_vhi):
"""Summary
Args:
new_active_vhi (TYPE): Description
Returns:
TYPE: Description
"""
current_vhi = self.active_virtual_helix_item
if new_active_vhi != current_vhi:
if current_vhi is not None:
current_vhi.deactivate()
if new_active_vhi is not None:
new_active_vhi.activate()
self.active_virtual_helix_item = new_active_vhi
# end def
def unsetActiveVirtualHelixItem(self):
if self.active_virtual_helix_item is not None:
self.active_virtual_helix_item.deactivate()
self.active_virtual_helix_item = None
self.prexover_manager.reset()
def setPreXoverItemsVisible(self, virtual_helix_item):
"""
self._pre_xover_items list references prexovers parented to other
PathHelices such that only the activeHelix maintains the list of
visible prexovers
Args:
virtual_helix_item (cadnano.views.pathview.virtualhelixitem.VirtualHelixItem): Description
"""
vhi = virtual_helix_item
if vhi is None:
return
# print("path.setPreXoverItemsVisible", virtual_helix_item.idNum())
part = self.part()
info = part.active_base_info
if info and virtual_helix_item is not None:
id_num, is_fwd, idx, to_vh_id_num = info
per_neighbor_hits, pairs = part.potentialCrossoverMap(id_num, idx)
self.prexover_manager.activateVirtualHelix(virtual_helix_item, idx,
per_neighbor_hits)
else:
self.prexover_manager.reset()
# end def
def updateXoverItems(self, virtual_helix_item):
"""Summary
Args:
virtual_helix_item (cadnano.views.pathview.virtualhelixitem.VirtualHelixItem): Description
Returns:
TYPE: Description
"""
for item in virtual_helix_item.childItems():
if isinstance(item, XoverNode3):
item.refreshXover()
# end def
def updateStatusBar(self, status_string):
"""Shows status_string in the MainWindow's status bar.
Args:
status_string (str): The text to be displayed.
"""
self.window().statusBar().showMessage(status_string)
### COORDINATE METHODS ###
def keyPanDeltaX(self):
"""How far a single press of the left or right arrow key should move
the scene (in scene space)
"""
vhs = self._virtual_helix_item_list
return vhs[0].keyPanDeltaX() if vhs else 5
# end def
def keyPanDeltaY(self):
"""How far an an arrow key should move the scene (in scene space)
for a single press
"""
vhs = self._virtual_helix_item_list
if not len(vhs) > 1:
return 5
dy = vhs[0].pos().y() - vhs[1].pos().y()
dummyRect = QRectF(0, 0, 1, dy)
return self.mapToScene(dummyRect).boundingRect().height()
# end def
### TOOL METHODS ###
def mousePressEvent(self, event):
"""Handler for user mouse press.
Args:
event (:obj:`QGraphicsSceneMouseEvent`): Contains item, scene, and screen
coordinates of the the event, and previous event.
"""
self._viewroot.clearSelectionsIfActiveTool()
self.unsetActiveVirtualHelixItem()
return QGraphicsItem.mousePressEvent(self, event)
def hoverMoveEvent(self, event):
"""
Parses a mouseMoveEvent to extract strandSet and base index,
forwarding them to approproate tool method as necessary.
Args:
event (TYPE): Description
"""
active_tool = self._getActiveTool()
tool_method_name = active_tool.methodPrefix() + "HoverMove"
if hasattr(self, tool_method_name):
getattr(self, tool_method_name)(event.pos())
# end def
def createToolHoverMove(self, pt):
"""Create the strand is possible.
Args:
pt (QPointF): mouse cursor location of create tool hover.
"""
active_tool = self._getActiveTool()
if not active_tool.isFloatingXoverBegin():
temp_xover = active_tool.floatingXover()
temp_xover.updateFloatingFromPartItem(self, pt)