def __init__(self, model_virtual_helix, part_item):
"""
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
part_item (cadnano.gui.views.sliceview.nucleicacidpartitem.NucleicAcidPartItem): the part item
"""
AbstractVirtualHelixItem.__init__(self, model_virtual_helix, part_item)
QGraphicsEllipseItem.__init__(self, parent=part_item)
self._controller = VirtualHelixItemController(self, self._model_part, False, True)
self.hide()
model_part = self._model_part
x, y = model_part.locationQt(self._id_num, part_item.scaleFactor())
# set position to offset for radius
# self.setTransformOriginPoint(_RADIUS, _RADIUS)
self.setCenterPos(x, y)
self.wedge_gizmos = {}
self._added_wedge_gizmos = set()
# self._prexo_gizmos = []
self.setAcceptHoverEvents(True)
self.setZValue(_ZVALUE)
# handle the label specific stuff
self._label = self.createLabel()
self.setNumber()
self.old_pen = None
self.is_active = False
self.updateAppearance()
self.show()
self._right_mouse_move = False
def __init__(self, model_virtual_helix, empty_helix_item):
"""
empty_helix_item is a EmptyHelixItem that will act as a QGraphicsItem parent
"""
super(VirtualHelixItem, self).__init__(parent=empty_helix_item)
self._virtual_helix = model_virtual_helix
self._empty_helix_item = empty_helix_item
self.hide()
# drawing related
self.isHovered = False
self.setAcceptHoverEvents(True)
# self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setZValue(self._ZVALUE)
self.lastMousePressAddedBases = False
self.setBrush(self._OUT_OF_SLICE_BRUSH)
self.setPen(self._OUT_OF_SLICE_PEN)
self.setRect(self._RECT)
# handle the label specific stuff
self._label = self.createLabel()
self.setNumber()
self.createArrow()
self._controller = VirtualHelixItemController(self, model_virtual_helix)
self.show()
def __init__(self, part_item, model_virtual_helix, viewroot):
super(VirtualHelixItem, self).__init__(part_item.proxy())
self._part_item = part_item
self._model_virtual_helix = model_virtual_helix
self._viewroot = viewroot
self._getActiveTool = part_item._getActiveTool
self._controller = VirtualHelixItemController(self, model_virtual_helix)
self._handle = VirtualHelixHandleItem(model_virtual_helix, part_item, viewroot)
self._last_strand_set = None
self._last_idx = None
self._scaffoldBackground = None
self.setFlag(QGraphicsItem.ItemUsesExtendedStyleOption)
self.setCacheMode(QGraphicsItem.DeviceCoordinateCache)
self.setBrush(QBrush(Qt.NoBrush))
view = viewroot.scene().views()[0]
view.levelOfDetailChangedSignal.connect(self.levelOfDetailChangedSlot)
shouldShowDetails = view.shouldShowDetails()
pen = QPen(styles.MINOR_GRID_STROKE, styles.MINOR_GRID_STROKE_WIDTH)
pen.setCosmetic(shouldShowDetails)
self.setPen(pen)
self.refreshPath()
self.setAcceptHoverEvents(True) # for pathtools
self.setZValue(styles.ZPATHHELIX)
def __init__(self, model_virtual_helix, empty_helix_item):
"""
empty_helix_item is a EmptyHelixItem that will act as a QGraphicsItem parent
"""
super(VirtualHelixItem, self).__init__(parent=empty_helix_item)
self._virtual_helix = model_virtual_helix
self._empty_helix_item = empty_helix_item
self.hide()
# drawing related
self.isHovered = False
self.setAcceptHoverEvents(True)
# self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setZValue(self._ZVALUE)
self.lastMousePressAddedBases = False
self.setBrush(self._OUT_OF_SLICE_BRUSH)
self.setPen(self._OUT_OF_SLICE_PEN)
self.setRect(self._RECT)
# handle the label specific stuff
self._label = self.createLabel()
self.setNumber()
self._pen1, self._pen2 = (QPen(), QPen())
self.createArrows()
self._controller = VirtualHelixItemController(self, model_virtual_helix)
self.show()
def __init__(self, model_virtual_helix, empty_helix_item):
"""
empty_helix_item is a EmptyHelixItem that will act as a QGraphicsItem parent
"""
super(VirtualHelixItem, self).__init__(parent=empty_helix_item)
self._virtual_helix = model_virtual_helix
self._empty_helix_item = empty_helix_item
self._controller = VirtualHelixItemController(self, model_virtual_helix)
self.hide()
# drawing related
self.setAcceptHoverEvents(True)
# self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setZValue(self._ZVALUE)
self.lastMousePressAddedBases = False
# handle the label specific stuff
self._label = self.createLabel()
self.setNumber()
self._pen1, self._pen2 = (QPen(), QPen())
self.createArrows()
self.updateProperty()
self._rect = QRectF()
self._hover_rect = QRectF()
self._outer_line = RotateLine(self._rect, self)
# self._inner_line = RotateLine(self._rect, self)
self._hover_region = RotateHoverRegion(self._hover_rect, self)
self.updateRects()
self.show()
def __init__(self, model_virtual_helix, empty_helix_item):
"""
empty_helix_item is a EmptyHelixItem that will act as a QGraphicsItem parent
"""
super(VirtualHelixItem, self).__init__(parent=empty_helix_item)
self._virtual_helix = model_virtual_helix
self._empty_helix_item = ehi = empty_helix_item
self._controller = VirtualHelixItemController(self, model_virtual_helix)
self.hide()
self.setAcceptHoverEvents(True)
# self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setZValue(_ZVALUE)
self.lastMousePressAddedBases = False
# handle the label specific stuff
self._label = self.createLabel()
self.setNumber()
self._pen1, self._pen2 = (QPen(), QPen())
self.createArrows()
self.updateAppearance()
self._prexoveritemgroup = _pxig = PreXoverItemGroup(_RECT, self)
_pxig.setTransformOriginPoint(_RECT.center())
# self._rect = QRectF(_RECT)
# self._hover_rect = QRectF(_RECT)
# self._outer_line = RotaryDialLine(self._rect, self)
# self._hover_region = RotaryDialHoverRegion(self._hover_rect, self)
self.show()
# self._virtual_helix.setProperty('ehiX', ehi.mapToScene(0,0).x())
# self._virtual_helix.setProperty('ehiY', ehi.mapToScene(0,0).y())
self.getNeighbors()
def __init__(self, model_virtual_helix, part_item, viewroot):
"""Summary
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
part_item (TYPE): Description
viewroot (TYPE): Description
"""
AbstractVirtualHelixItem.__init__(self, model_virtual_helix, part_item)
QGraphicsPathItem.__init__(self, parent=part_item.proxy())
self._viewroot = viewroot
self._getActiveTool = part_item._getActiveTool
self._controller = VirtualHelixItemController(self, self._model_part,
False, True)
self._handle = VirtualHelixHandleItem(self, part_item, viewroot)
self._last_strand_set = None
self._last_idx = None
self.setFlag(QGraphicsItem.ItemUsesExtendedStyleOption)
self.setCacheMode(QGraphicsItem.DeviceCoordinateCache)
self.setBrush(getNoBrush())
view = self.view()
view.levelOfDetailChangedSignal.connect(self.levelOfDetailChangedSlot)
should_show_details = view.shouldShowDetails()
pen = newPenObj(styles.MINOR_GRID_STROKE,
styles.MINOR_GRID_STROKE_WIDTH)
pen.setCosmetic(should_show_details)
self.setPen(pen)
self.is_active = False
self.refreshPath()
self.setAcceptHoverEvents(True) # for pathtools
self.setZValue(styles.ZPATHHELIX)
self._right_mouse_move = False
self.drag_last_position = self.handle_start = self.pos()
def __init__(self, **kwargs):
"""Summary
Args:
model_part (Part): The model part
parent (TYPE): Description
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
key (None, optional): Description
"""
super().__init__(**kwargs)
if self._key == "name":
for vh in self.cnModelList():
self._controller_list.append(
VirtualHelixItemController(self, vh.part(), True, False))
def __init__(self, model_virtual_helix, part_item, viewroot):
"""Summary
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
part_item (TYPE): Description
viewroot (TYPE): Description
"""
AbstractVirtualHelixItem.__init__(self, model_virtual_helix, part_item)
QGraphicsPathItem.__init__(self, parent=part_item.proxy())
self._viewroot = viewroot
self._getActiveTool = part_item._getActiveTool
self._controller = VirtualHelixItemController(self, self._model_part, False, True)
self._handle = VirtualHelixHandleItem(self, part_item, viewroot)
self._last_strand_set = None
self._last_idx = None
self.setFlag(QGraphicsItem.ItemUsesExtendedStyleOption)
self.setCacheMode(QGraphicsItem.DeviceCoordinateCache)
self.setBrush(getNoBrush())
view = self.view()
view.levelOfDetailChangedSignal.connect(self.levelOfDetailChangedSlot)
should_show_details = view.shouldShowDetails()
pen = newPenObj(styles.MINOR_GRID_STROKE, styles.MINOR_GRID_STROKE_WIDTH)
pen.setCosmetic(should_show_details)
self.setPen(pen)
self.is_active = False
self.refreshPath()
self.setAcceptHoverEvents(True) # for pathtools
self.setZValue(styles.ZPATHHELIX)
self._right_mouse_move = False
self.drag_last_position = self.handle_start = self.pos()
class VirtualHelixItem(QGraphicsPathItem):
"""VirtualHelixItem for PathView"""
findChild = util.findChild # for debug
def __init__(self, part_item, model_virtual_helix, viewroot):
super(VirtualHelixItem, self).__init__(part_item.proxy())
self._part_item = part_item
self._model_virtual_helix = model_virtual_helix
self._viewroot = viewroot
self._getActiveTool = part_item._getActiveTool
self._controller = VirtualHelixItemController(self, model_virtual_helix)
self._handle = VirtualHelixHandleItem(model_virtual_helix, part_item, viewroot)
self._last_strand_set = None
self._last_idx = None
self._scaffoldBackground = None
self.setFlag(QGraphicsItem.ItemUsesExtendedStyleOption)
self.setCacheMode(QGraphicsItem.DeviceCoordinateCache)
self.setBrush(QBrush(Qt.NoBrush))
view = viewroot.scene().views()[0]
view.levelOfDetailChangedSignal.connect(self.levelOfDetailChangedSlot)
shouldShowDetails = view.shouldShowDetails()
pen = QPen(styles.MINOR_GRID_STROKE, styles.MINOR_GRID_STROKE_WIDTH)
pen.setCosmetic(shouldShowDetails)
self.setPen(pen)
self.refreshPath()
self.setAcceptHoverEvents(True) # for pathtools
self.setZValue(styles.ZPATHHELIX)
# end def
### SIGNALS ###
### SLOTS ###
def levelOfDetailChangedSlot(self, boolval):
"""Not connected to the model, only the QGraphicsView"""
pen = self.pen()
pen.setCosmetic(boolval)
self.setPen(pen)
# end def
def strandAddedSlot(self, sender, strand):
"""
Instantiates a StrandItem upon notification that the model has a
new Strand. The StrandItem is responsible for creating its own
controller for communication with the model, and for adding itself to
its parent (which is *this* VirtualHelixItem, i.e. 'self').
"""
StrandItem(strand, self, self._viewroot)
# end def
def decoratorAddedSlot(self, decorator):
"""
Instantiates a DecoratorItem upon notification that the model has a
new Decorator. The Decorator is responsible for creating its own
controller for communication with the model, and for adding itself to
its parent (which is *this* VirtualHelixItem, i.e. 'self').
"""
pass
def virtualHelixNumberChangedSlot(self, virtualHelix, number):
self._handle.setNumber()
# end def
def virtualHelixRemovedSlot(self, virtualHelix):
self._controller.disconnectSignals()
self._controller = None
scene = self.scene()
self._handle.remove()
scene.removeItem(self)
self._part_item.removeVirtualHelixItem(self)
self._part_item = None
self._model_virtual_helix = None
self._getActiveTool = None
self._handle = None
# end def
### ACCESSORS ###
def coord(self):
return self._model_virtual_helix.coord()
# end def
def viewroot(self):
return self._viewroot
# end def
def handle(self):
return self._handle
# end def
def part(self):
return self._part_item.part()
# end def
def partItem(self):
return self._part_item
# end def
def number(self):
return self._model_virtual_helix.number()
# end def
def virtualHelix(self):
return self._model_virtual_helix
# end def
def window(self):
return self._part_item.window()
# end def
### DRAWING METHODS ###
def isStrandOnTop(self, strand):
sS = strand.strandSet()
isEvenParity = self._model_virtual_helix.isEvenParity()
return isEvenParity and sS.isScaffold() or\
not isEvenParity and sS.isStaple()
# end def
def isStrandTypeOnTop(self, strand_type):
isEvenParity = self._model_virtual_helix.isEvenParity()
return isEvenParity and strand_type == StrandType.SCAFFOLD or \
not isEvenParity and strand_type == StrandType.STAPLE
# end def
def upperLeftCornerOfBase(self, idx, strand):
x = idx * _BASE_WIDTH
y = 0 if self.isStrandOnTop(strand) else _BASE_WIDTH
return x, y
# end def
def upperLeftCornerOfBaseType(self, idx, strand_type):
x = idx * _BASE_WIDTH
y = 0 if self.isStrandTypeOnTop(strand_type) else _BASE_WIDTH
return x, y
# end def
def refreshPath(self):
"""
Returns a QPainterPath object for the minor grid lines.
The path also includes a border outline and a midline for
dividing scaffold and staple bases.
"""
bw = _BASE_WIDTH
bw2 = 2 * bw
part = self.part()
path = QPainterPath()
sub_step_size = part.subStepSize()
canvas_size = part.maxBaseIdx() + 1
# border
path.addRect(0, 0, bw * canvas_size, 2 * bw)
# minor tick marks
for i in range(canvas_size):
x = round(bw * i) + .5
if i % sub_step_size == 0:
path.moveTo(x - .5, 0)
path.lineTo(x - .5, bw2)
path.lineTo(x - .25, bw2)
path.lineTo(x - .25, 0)
path.lineTo(x, 0)
path.lineTo(x, bw2)
path.lineTo(x + .25, bw2)
path.lineTo(x + .25, 0)
path.lineTo(x + .5, 0)
path.lineTo(x + .5, bw2)
# path.moveTo(x-.5, 0)
# path.lineTo(x-.5, 2 * bw)
# path.lineTo(x+.5, 2 * bw)
# path.lineTo(x+.5, 0)
else:
path.moveTo(x, 0)
path.lineTo(x, 2 * bw)
# staple-scaffold divider
path.moveTo(0, bw)
path.lineTo(bw * canvas_size, bw)
self.setPath(path)
if self._model_virtual_helix.scaffoldIsOnTop():
scaffoldY = 0
else:
scaffoldY = bw
# if self._scaffoldBackground == None:
# highlightr = QGraphicsRectItem(0, scaffoldY, bw * canvas_size, bw, self)
# highlightr.setBrush(QBrush(styles.scaffold_bkg_fill))
# highlightr.setPen(QPen(Qt.NoPen))
# highlightr.setFlag(QGraphicsItem.ItemStacksBehindParent)
# self._scaffoldBackground = highlightr
# else:
# self._scaffoldBackground.setRect(0, scaffoldY, bw * canvas_size, bw)
# end def
def resize(self):
"""Called by part on resize."""
self.refreshPath()
### PUBLIC SUPPORT METHODS ###
def setActive(self, idx):
"""Makes active the virtual helix associated with this item."""
self.part().setActiveVirtualHelix(self._model_virtual_helix, idx)
# end def
### EVENT HANDLERS ###
def mousePressEvent(self, event):
"""
Parses a mousePressEvent to extract strand_set and base index,
forwarding them to approproate tool method as necessary.
"""
self.scene().views()[0].addToPressList(self)
strand_set, idx = self.baseAtPoint(event.pos())
self.setActive(idx)
tool_method_name = self._getActiveTool().methodPrefix() + "MousePress"
### uncomment for debugging modifier selection
# strand_set, idx = self.baseAtPoint(event.pos())
# row, col = strand_set.virtualHelix().coord()
# self._part_item.part().selectPreDecorator([(row,col,idx)])
if hasattr(self, tool_method_name):
self._last_strand_set, self._last_idx = strand_set, idx
getattr(self, tool_method_name)(strand_set, idx)
else:
event.setAccepted(False)
# end def
def mouseMoveEvent(self, event):
"""
Parses a mouseMoveEvent to extract strand_set and base index,
forwarding them to approproate tool method as necessary.
"""
tool_method_name = self._getActiveTool().methodPrefix() + "MouseMove"
if hasattr(self, tool_method_name):
strand_set, idx = self.baseAtPoint(event.pos())
if self._last_strand_set != strand_set or self._last_idx != idx:
self._last_strand_set, self._last_idx = strand_set, idx
getattr(self, tool_method_name)(strand_set, idx)
else:
event.setAccepted(False)
# end def
def customMouseRelease(self, event):
"""
Parses a mouseReleaseEvent to extract strand_set and base index,
forwarding them to approproate tool method as necessary.
"""
tool_method_name = self._getActiveTool().methodPrefix() + "MouseRelease"
if hasattr(self, tool_method_name):
getattr(self, tool_method_name)(self._last_strand_set, self._last_idx)
else:
event.setAccepted(False)
# end def
### COORDINATE UTILITIES ###
def baseAtPoint(self, pos):
"""
Returns the (strand_type, index) under the location x,y or None.
It shouldn't be possible to click outside a pathhelix and still call
this function. However, this sometimes happens if you click exactly
on the top or bottom edge, resulting in a negative y value.
"""
x, y = pos.x(), pos.y()
mVH = self._model_virtual_helix
base_idx = int(floor(x / _BASE_WIDTH))
min_base, max_base = 0, mVH.part().maxBaseIdx()
if base_idx < min_base or base_idx >= max_base:
base_idx = util.clamp(base_idx, min_base, max_base)
if y < 0:
y = 0 # HACK: zero out y due to erroneous click
strandIdx = floor(y * 1. / _BASE_WIDTH)
if strandIdx < 0 or strandIdx > 1:
strandIdx = int(util.clamp(strandIdx, 0, 1))
strand_set = mVH.getStrandSetByIdx(strandIdx)
return (strand_set, base_idx)
# end def
def keyPanDeltaX(self):
"""How far a single press of the left or right arrow key should move
the scene (in scene space)"""
dx = self._part_item.part().stepSize() * _BASE_WIDTH
return self.mapToScene(QRectF(0, 0, dx, 1)).boundingRect().width()
# end def
def hoverLeaveEvent(self, event):
self._part_item.updateStatusBar("")
# end def
def hoverMoveEvent(self, event):
"""
Parses a mouseMoveEvent to extract strand_set and base index,
forwarding them to approproate tool method as necessary.
"""
base_idx = int(floor(event.pos().x() / _BASE_WIDTH))
loc = "%d[%d]" % (self.number(), base_idx)
self._part_item.updateStatusBar(loc)
active_tool = self._getActiveTool()
tool_method_name = self._getActiveTool().methodPrefix() + "HoverMove"
if hasattr(self, tool_method_name):
strand_type, idx_x, idx_y = active_tool.baseAtPoint(self, event.pos())
getattr(self, tool_method_name)(strand_type, idx_x, idx_y)
# end def
### TOOL METHODS ###
def pencilToolMousePress(self, strand_set, idx):
"""strand.getDragBounds"""
# print "%s: %s[%s]" % (util.methodName(), strand_set, idx)
active_tool = self._getActiveTool()
if not active_tool.isDrawingStrand():
active_tool.initStrandItemFromVHI(self, strand_set, idx)
active_tool.setIsDrawingStrand(True)
# end def
def pencilToolMouseMove(self, strand_set, idx):
"""strand.getDragBounds"""
# print "%s: %s[%s]" % (util.methodName(), strand_set, idx)
active_tool = self._getActiveTool()
if active_tool.isDrawingStrand():
active_tool.updateStrandItemFromVHI(self, strand_set, idx)
# end def
def pencilToolMouseRelease(self, strand_set, idx):
"""strand.getDragBounds"""
# print "%s: %s[%s]" % (util.methodName(), strand_set, idx)
active_tool = self._getActiveTool()
if active_tool.isDrawingStrand():
active_tool.setIsDrawingStrand(False)
active_tool.attemptToCreateStrand(self, strand_set, idx)
# end def
def pencilToolHoverMove(self, strand_type, idx_x, idx_y):
"""Pencil the strand is possible."""
part_item = self.partItem()
active_tool = self._getActiveTool()
if not active_tool.isFloatingXoverBegin():
temp_xover = active_tool.floatingXover()
temp_xover.updateFloatingFromVHI(self, strand_type, idx_x, idx_y)
class VirtualHelixItem(QGraphicsEllipseItem):
"""
The VirtualHelixItem is an individual circle that gets drawn in the SliceView
as a child of the PartItem. Taken as a group, many SliceHelix
instances make up the crossection of the DNAPart. Clicking on a SliceHelix
adds a VirtualHelix to the DNAPart. The SliceHelix then changes appearence
and paints its corresponding VirtualHelix number.
"""
# set up default, hover, and active drawing styles
_USE_BRUSH = QBrush(styles.ORANGE_FILL)
_USE_PEN = QPen(styles.ORANGE_STROKE, styles.SLICE_HELIX_STROKE_WIDTH)
_RADIUS = styles.SLICE_HELIX_RADIUS
_OUT_OF_SLICE_PEN = QPen(styles.LIGHT_ORANGE_STROKE,\
styles.SLICE_HELIX_STROKE_WIDTH)
_OUT_OF_SLICE_BRUSH = QBrush(styles.LIGHT_ORANGE_FILL)
_RECT = QRectF(0, 0, 2 * _RADIUS, 2 * _RADIUS)
_FONT = styles.SLICE_NUM_FONT
_ZVALUE = styles.ZSLICEHELIX+3
def __init__(self, model_virtual_helix, empty_helix_item):
"""
empty_helix_item is a EmptyHelixItem that will act as a QGraphicsItem parent
"""
super(VirtualHelixItem, self).__init__(parent=empty_helix_item)
self._virtual_helix = model_virtual_helix
self._empty_helix_item = empty_helix_item
self.hide()
# drawing related
self.isHovered = False
self.setAcceptHoverEvents(True)
# self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setZValue(self._ZVALUE)
self.lastMousePressAddedBases = False
self.setBrush(self._OUT_OF_SLICE_BRUSH)
self.setPen(self._OUT_OF_SLICE_PEN)
self.setRect(self._RECT)
# handle the label specific stuff
self._label = self.createLabel()
self.setNumber()
self.createArrow()
self._controller = VirtualHelixItemController(self, model_virtual_helix)
self.show()
# end def
### SIGNALS ###
### SLOTS ###
def virtualHelixNumberChangedSlot(self, virtualHelix):
"""
receives a signal containing a virtualHelix and the oldNumber
as a safety check
"""
self.setNumber()
# end def
def virtualHelixRemovedSlot(self, virtualHelix):
self._controller.disconnectSignals()
self._controller = None
self._empty_helix_item.setNotHovered()
self._virtual_helix = None
self._empty_helix_item = None
self.scene().removeItem(self._label)
self._label = None
self.scene().removeItem(self)
# end def
def strandAddedSlot(self, sender, strand):
pass
# end def
###
def createLabel(self):
label = QGraphicsSimpleTextItem("%d" % self._virtual_helix.number())
label.setFont(self._FONT)
label.setZValue(self._ZVALUE)
label.setParentItem(self)
return label
# end def
def createArrow(self):
rad = self._RADIUS
pen = QPen()
pen.setWidth(3)
color = QColor(Qt.blue)
color.setAlphaF(0.25)
pen.setBrush(color)
if self._virtual_helix.isEvenParity():
arrow = QGraphicsLineItem(rad, rad, 2*rad, rad, self)
else:
arrow = QGraphicsLineItem(0, rad, rad, rad, self)
arrow.setTransformOriginPoint(rad, rad)
arrow.setZValue(400)
arrow.setPen(pen)
self.arrow = arrow
self.arrow.hide()
# end def
def updateArrow(self, idx):
part = self.part()
tpb = part._TWIST_PER_BASE
angle = idx*tpb
# for some reason rotation is CW and not CCW with increasing angle
self.arrow.setRotation(angle + part._TWIST_OFFSET)
# end def
def setNumber(self):
"""docstring for setNumber"""
vh = self._virtual_helix
num = vh.number()
label = self._label
radius = self._RADIUS
if num != None:
label.setText("%d" % num)
else:
return
y_val = radius / 3
if num < 10:
label.setPos(radius / 1.5, y_val)
elif num < 100:
label.setPos(radius / 3, y_val)
else: # _number >= 100
label.setPos(0, y_val)
b_rect = label.boundingRect()
posx = b_rect.width()/2
posy = b_rect.height()/2
label.setPos(radius-posx, radius-posy)
# end def
def part(self):
return self._empty_helix_item.part()
def virtualHelix(self):
return self._virtual_helix
# end def
def number(self):
return self.virtualHelix().number()
def setActiveSliceView(self, is_active_now, idx):
if is_active_now:
self.setPen(self._USE_PEN)
self.setBrush(self._USE_BRUSH)
self.updateArrow(idx)
self.arrow.show()
else:
self.setPen(self._OUT_OF_SLICE_PEN)
self.setBrush(self._OUT_OF_SLICE_BRUSH)
self.arrow.hide()
# end def
############################ User Interaction ############################
def sceneEvent(self, event):
"""Included for unit testing in order to grab events that are sent
via QGraphicsScene.sendEvent()."""
# if self._parent.sliceController.testRecorder:
# coord = (self._row, self._col)
# self._parent.sliceController.testRecorder.sliceSceneEvent(event, coord)
if event.type() == QEvent.MouseButtonPress:
self.mousePressEvent(event)
return True
elif event.type() == QEvent.MouseButtonRelease:
self.mouseReleaseEvent(event)
return True
elif event.type() == QEvent.MouseMove:
self.mouseMoveEvent(event)
return True
QGraphicsItem.sceneEvent(self, event)
return False
def hoverEnterEvent(self, event):
"""
If the selection is configured to always select
everything, we don't draw a focus ring around everything,
instead we only draw a focus ring around the hovered obj.
"""
# if self.selectAllBehavior():
# self.setSelected(True)
# forward the event to the empty_helix_item as well
self._empty_helix_item.hoverEnterEvent(event)
# end def
def hoverLeaveEvent(self, event):
# if self.selectAllBehavior():
# self.setSelected(False)
self._empty_helix_item.hoverEnterEvent(event)
class VirtualHelixItem(QGraphicsEllipseItem, AbstractVirtualHelixItem):
"""
The VirtualHelixItem is an individual circle that gets drawn in the SliceView
as a child of the OrigamiPartItem. Taken as a group, many SliceHelix
instances make up the crossection of the PlasmidPart. Clicking on a SliceHelix
adds a VirtualHelix to the PlasmidPart. The SliceHelix then changes appearence
and paints its corresponding VirtualHelix number.
"""
def __init__(self, model_virtual_helix, empty_helix_item):
"""
empty_helix_item is a EmptyHelixItem that will act as a QGraphicsItem parent
"""
super(VirtualHelixItem, self).__init__(parent=empty_helix_item)
self._virtual_helix = model_virtual_helix
self._empty_helix_item = ehi = empty_helix_item
self._controller = VirtualHelixItemController(self, model_virtual_helix)
self.hide()
self.setAcceptHoverEvents(True)
# self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setZValue(_ZVALUE)
self.lastMousePressAddedBases = False
# handle the label specific stuff
self._label = self.createLabel()
self.setNumber()
self._pen1, self._pen2 = (QPen(), QPen())
self.createArrows()
self.updateAppearance()
self._prexoveritemgroup = _pxig = PreXoverItemGroup(_RECT, self)
_pxig.setTransformOriginPoint(_RECT.center())
# self._rect = QRectF(_RECT)
# self._hover_rect = QRectF(_RECT)
# self._outer_line = RotaryDialLine(self._rect, self)
# self._hover_region = RotaryDialHoverRegion(self._hover_rect, self)
self.show()
# self._virtual_helix.setProperty('ehiX', ehi.mapToScene(0,0).x())
# self._virtual_helix.setProperty('ehiY', ehi.mapToScene(0,0).y())
self.getNeighbors()
# end def
def getNeighbors(self):
items = filter(lambda x: type(x) is VirtualHelixItem, self.collidingItems())
name = self._virtual_helix.getName()
pos = self.scenePos()
print("\n%s (%d, %d)" % (name, pos.x(), pos.y()))
for nvhi in items:
npos = nvhi.scenePos()
line = QLineF(pos, npos)
print("\t%s (%d, %d) %d" % (nvhi.virtualHelix().getName(), npos.x(), npos.y(), line.length()))
def modelColor(self):
return self.part().getProperty('color')
# end def
def updateAppearance(self):
part_color = self.part().getProperty('color')
self._USE_PEN = getPenObj(part_color, styles.SLICE_HELIX_STROKE_WIDTH)
self._OUT_OF_SLICE_PEN = getPenObj(part_color, styles.SLICE_HELIX_STROKE_WIDTH)
self._USE_BRUSH = getBrushObj(part_color, alpha=128)
self._OUT_OF_SLICE_BRUSH = getBrushObj(part_color, alpha=64)
self._OUT_OF_SLICE_TEXT_BRUSH = getBrushObj(styles.OUT_OF_SLICE_TEXT_COLOR)
if self.part().crossSectionType() == LatticeType.HONEYCOMB:
self._USE_PEN = getPenObj(styles.BLUE_STROKE, styles.SLICE_HELIX_STROKE_WIDTH)
self._OUT_OF_SLICE_PEN = getPenObj(styles.BLUE_STROKE,\
styles.SLICE_HELIX_STROKE_WIDTH)
if self.part().partType() == PartType.NUCLEICACIDPART:
self._OUT_OF_SLICE_BRUSH = _OUT_OF_SLICE_BRUSH_DEFAULT
# self._USE_BRUSH = getBrushObj(part_color, lighter=180)
self._USE_BRUSH = getBrushObj(part_color, alpha=150)
self._label.setBrush(self._OUT_OF_SLICE_TEXT_BRUSH)
self.setBrush(self._OUT_OF_SLICE_BRUSH)
self.setPen(self._OUT_OF_SLICE_PEN)
self.setRect(_RECT)
# end def
### SIGNALS ###
### SLOTS ###
def virtualHelixNumberChangedSlot(self, virtual_helix):
"""
receives a signal containing a virtual_helix and the oldNumber
as a safety check
"""
self.setNumber()
# end def
def virtualHelixPropertyChangedSlot(self, virtual_helix, property_key, new_value):
if property_key == 'eulerZ':
self._prexoveritemgroup.setRotation(new_value)
scamZ = self._virtual_helix.getProperty('scamZ')
if scamZ != new_value:
self._virtual_helix.setProperty('scamZ', new_value)
elif property_key == 'scamZ':
eulerZ = self._virtual_helix.getProperty('eulerZ')
if eulerZ != new_value:
self._virtual_helix.setProperty('eulerZ', new_value)
elif property_key == 'ehiX':
ehi_pos = self._empty_helix_item.scenePos()
self._empty_helix_item.setPos(new_value, ehi_pos.y())
pass
elif property_key == 'ehiY':
ehi_pos = self._empty_helix_item.scenePos()
self._empty_helix_item.setPos(ehi_pos.x(),new_value)
# end def
def virtualHelixRemovedSlot(self, virtual_helix):
self._controller.disconnectSignals()
self._controller = None
self._empty_helix_item.setNotHovered()
self._virtual_helix = None
self._empty_helix_item = None
self.scene().removeItem(self._label)
self._label = None
self.scene().removeItem(self)
# end def
def createLabel(self):
label = QGraphicsSimpleTextItem("%d" % self._virtual_helix.number())
label.setFont(_FONT)
label.setZValue(_ZVALUE)
label.setParentItem(self)
return label
# end def
def createArrows(self):
rad = _RADIUS
pen1 = self._pen1
pen2 = self._pen2
pen1.setWidth(3)
pen2.setWidth(3)
pen1.setBrush(Qt.gray)
pen2.setBrush(Qt.lightGray)
if self._virtual_helix.isEvenParity():
arrow1 = QGraphicsLineItem(rad, rad, 2*rad, rad, self)
arrow2 = QGraphicsLineItem(0, rad, rad, rad, self)
else:
arrow1 = QGraphicsLineItem(0, rad, rad, rad, self)
arrow2 = QGraphicsLineItem(rad, rad, 2*rad, rad, self)
arrow1.setTransformOriginPoint(rad, rad)
arrow2.setTransformOriginPoint(rad, rad)
arrow1.setZValue(400)
arrow2.setZValue(400)
arrow1.setPen(pen1)
arrow2.setPen(pen2)
self.arrow1 = arrow1
self.arrow2 = arrow2
self.arrow1.hide()
self.arrow2.hide()
# end def
def updateScafArrow(self, idx):
scaf_strand = self._virtual_helix.scaf(idx)
if scaf_strand:
scaf_strand_color = scaf_strand.oligo().getColor()
scaf_alpha = 230 if scaf_strand.hasXoverAt(idx) else 128
else:
scaf_strand_color = '#a0a0a4' #Qt.gray
scaf_alpha = 26
scaf_strand_color_obj = getColorObj(scaf_strand_color, alpha=scaf_alpha)
self._pen1.setBrush(scaf_strand_color_obj)
self.arrow1.setPen(self._pen1)
part = self.part()
tpb = part._TWIST_PER_BASE
angle = idx*tpb
# for some reason rotation is CW and not CCW with increasing angle
self.arrow1.setRotation(angle + part._TWIST_OFFSET)
def updateStapArrow(self, idx):
stap_strand = self._virtual_helix.stap(idx)
if stap_strand:
stap_strand_color = stap_strand.oligo().getColor()
stap_alpha = 230 if stap_strand.hasXoverAt(idx) else 128
else:
stap_strand_color = '#c0c0c0' # Qt.lightGray
stap_alpha = 26
stap_strand_color_obj = getColorObj(stap_strand_color, alpha=stap_alpha)
self._pen2.setBrush(stap_strand_color_obj)
self.arrow2.setPen(self._pen2)
part = self.part()
tpb = part._TWIST_PER_BASE
angle = idx*tpb
self.arrow2.setRotation(angle + part._TWIST_OFFSET)
# end def
def setNumber(self):
"""docstring for setNumber"""
vh = self._virtual_helix
num = vh.number()
label = self._label
if num is not None:
label.setText("%d" % num)
else:
return
y_val = _RADIUS / 3
if num < 10:
label.setPos(_RADIUS / 1.5, y_val)
elif num < 100:
label.setPos(_RADIUS / 3, y_val)
else: # _number >= 100
label.setPos(0, y_val)
b_rect = label.boundingRect()
posx = b_rect.width()/2
posy = b_rect.height()/2
label.setPos(_RADIUS-posx, _RADIUS-posy)
# end def
def part(self):
return self._empty_helix_item.part()
def virtualHelix(self):
return self._virtual_helix
# end def
def number(self):
return self.virtualHelix().number()
def setActiveSliceView(self, idx, has_scaf, has_stap):
if has_scaf:
self.setPen(self._USE_PEN)
self.setBrush(self._USE_BRUSH)
self._label.setBrush(_USE_TEXT_BRUSH)
self.updateScafArrow(idx)
self.arrow1.show()
else:
self.setPen(self._OUT_OF_SLICE_PEN)
self.setBrush(self._OUT_OF_SLICE_BRUSH)
self._label.setBrush(self._OUT_OF_SLICE_TEXT_BRUSH)
self.arrow1.hide()
if has_stap:
self.updateStapArrow(idx)
self.arrow2.show()
else:
self.arrow2.hide()
# end def
############################ User Interaction ############################
def sceneEvent(self, event):
"""Included for unit testing in order to grab events that are sent
via QGraphicsScene.sendEvent()."""
# if self._parent.sliceController.testRecorder:
# coord = (self._row, self._col)
# self._parent.sliceController.testRecorder.sliceSceneEvent(event, coord)
if event.type() == QEvent.MouseButtonPress:
self.mousePressEvent(event)
return True
elif event.type() == QEvent.MouseButtonRelease:
self.mouseReleaseEvent(event)
return True
elif event.type() == QEvent.MouseMove:
self.mouseMoveEvent(event)
return True
QGraphicsItem.sceneEvent(self, event)
return False
def hoverEnterEvent(self, event):
"""
If the selection is configured to always select
everything, we don't draw a focus ring around everything,
instead we only draw a focus ring around the hovered obj.
"""
# if self.selectAllBehavior():
# self.setSelected(True)
# forward the event to the empty_helix_item as well
self._empty_helix_item.hoverEnterEvent(event)
# end def
def hoverLeaveEvent(self, event):
# if self.selectAllBehavior():
# self.setSelected(False)
self._empty_helix_item.hoverEnterEvent(event)
class VirtualHelixItem(QGraphicsEllipseItem, AbstractVirtualHelixItem):
"""
The VirtualHelixItem is an individual circle that gets drawn in the SliceView
as a child of the OrigamiPartItem. Taken as a group, many SliceHelix
instances make up the crossection of the PlasmidPart. Clicking on a SliceHelix
adds a VirtualHelix to the PlasmidPart. The SliceHelix then changes appearence
and paints its corresponding VirtualHelix number.
"""
# set up default, hover, and active drawing styles
_RADIUS = styles.SLICE_HELIX_RADIUS
_RECT = QRectF(0, 0, 2 * _RADIUS, 2 * _RADIUS)
rect_gain = 0.25
_RECT = _RECT.adjusted(rect_gain, rect_gain, rect_gain, rect_gain)
_FONT = styles.SLICE_NUM_FONT
_ZVALUE = styles.ZSLICEHELIX+3
_OUT_OF_SLICE_BRUSH_DEFAULT = getBrushObj(styles.OUT_OF_SLICE_FILL) # QBrush(QColor(250, 250, 250))
_USE_TEXT_BRUSH = getBrushObj(styles.USE_TEXT_COLOR)
_OUT_OF_SLICE_TEXT_BRUSH = getBrushObj(styles.OUT_OF_SLICE_TEXT_COLOR)
def __init__(self, model_virtual_helix, empty_helix_item):
"""
empty_helix_item is a EmptyHelixItem that will act as a QGraphicsItem parent
"""
super(VirtualHelixItem, self).__init__(parent=empty_helix_item)
self._virtual_helix = model_virtual_helix
self._empty_helix_item = empty_helix_item
self._controller = VirtualHelixItemController(self, model_virtual_helix)
self.hide()
# drawing related
self.setAcceptHoverEvents(True)
# self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setZValue(self._ZVALUE)
self.lastMousePressAddedBases = False
# handle the label specific stuff
self._label = self.createLabel()
self.setNumber()
self._pen1, self._pen2 = (QPen(), QPen())
self.createArrows()
self.updateProperty()
self._rect = QRectF()
self._hover_rect = QRectF()
self._outer_line = RotateLine(self._rect, self)
# self._inner_line = RotateLine(self._rect, self)
self._hover_region = RotateHoverRegion(self._hover_rect, self)
self.updateRects()
self.show()
# end def
def radius(self):
return self._radius
# end def
def modelColor(self):
return self.part().getProperty('color')
# end def
def updateRects(self):
diameter = self.boundingRect().width()/2 # round(dna_length * pi / 100,2)
self._radius = self._RADIUS
diameter = self._RADIUS * 2
self._rect = QRectF(0, 0, diameter, diameter)
self._outer_line.updateRect(QRectF(-GAP/2, -GAP/2, diameter+GAP, diameter+GAP))
# self._inner_line.updateRect(QRectF(GAP/2, GAP/2, diameter-GAP, diameter-GAP))
# self._hover_rect = self._rect.adjusted(-H_W, -H_W, H_W, H_W)
self._hover_region.updateRect(self._rect)
# end def
def updateProperty(self):
part_color = self.part().getProperty('color')
self._USE_PEN = getPenObj(part_color, styles.SLICE_HELIX_STROKE_WIDTH)
self._OUT_OF_SLICE_PEN = getPenObj(part_color, styles.SLICE_HELIX_STROKE_WIDTH)
self._USE_BRUSH = getBrushObj(part_color, alpha=128)
self._OUT_OF_SLICE_BRUSH = getBrushObj(part_color, alpha=64)
if self.part().crossSectionType() == LatticeType.HONEYCOMB:
self._USE_PEN = getPenObj(styles.BLUE_STROKE, styles.SLICE_HELIX_STROKE_WIDTH)
self._OUT_OF_SLICE_PEN = getPenObj(styles.BLUE_STROKE,\
styles.SLICE_HELIX_STROKE_WIDTH)
if self.part().partType() == PartType.NUCLEICACIDPART:
self._OUT_OF_SLICE_BRUSH = self._OUT_OF_SLICE_BRUSH_DEFAULT
# self._USE_BRUSH = getBrushObj(part_color, lighter=180)
self._USE_BRUSH = getBrushObj(part_color, alpha=150)
self._label.setBrush(self._OUT_OF_SLICE_TEXT_BRUSH)
self.setBrush(self._OUT_OF_SLICE_BRUSH)
self.setPen(self._OUT_OF_SLICE_PEN)
self.setRect(self._RECT)
# end def
### SIGNALS ###
### SLOTS ###
def virtualHelixNumberChangedSlot(self, virtual_helix):
"""
receives a signal containing a virtual_helix and the oldNumber
as a safety check
"""
self.setNumber()
# end def
def virtualHelixPropertyChangedSlot(self, virtual_helix, property_key, new_value):
if property_key == 'eulerZ':
self.setTransformOriginPoint(self.boundingRect().center())
self.setRotation(new_value)
self.setTransformOriginPoint(QPointF(0,0))
# end def
def virtualHelixRemovedSlot(self, virtual_helix):
self._controller.disconnectSignals()
self._controller = None
self._empty_helix_item.setNotHovered()
self._virtual_helix = None
self._empty_helix_item = None
self.scene().removeItem(self._label)
self._label = None
self.scene().removeItem(self)
# end def
def createLabel(self):
label = QGraphicsSimpleTextItem("%d" % self._virtual_helix.number())
label.setFont(self._FONT)
label.setZValue(self._ZVALUE)
label.setParentItem(self)
return label
# end def
def createArrows(self):
rad = self._RADIUS
pen1 = self._pen1
pen2 = self._pen2
pen1.setWidth(3)
pen2.setWidth(3)
pen1.setBrush(Qt.gray)
pen2.setBrush(Qt.lightGray)
if self._virtual_helix.isEvenParity():
arrow1 = QGraphicsLineItem(rad, rad, 2*rad, rad, self)
arrow2 = QGraphicsLineItem(0, rad, rad, rad, self)
else:
arrow1 = QGraphicsLineItem(0, rad, rad, rad, self)
arrow2 = QGraphicsLineItem(rad, rad, 2*rad, rad, self)
arrow1.setTransformOriginPoint(rad, rad)
arrow2.setTransformOriginPoint(rad, rad)
arrow1.setZValue(400)
arrow2.setZValue(400)
arrow1.setPen(pen1)
arrow2.setPen(pen2)
self.arrow1 = arrow1
self.arrow2 = arrow2
self.arrow1.hide()
self.arrow2.hide()
# end def
def updateScafArrow(self, idx):
scaf_strand = self._virtual_helix.scaf(idx)
if scaf_strand:
scaf_strand_color = scaf_strand.oligo().color()
scaf_alpha = 230 if scaf_strand.hasXoverAt(idx) else 128
else:
scaf_strand_color = '#a0a0a4' #Qt.gray
scaf_alpha = 26
scaf_strand_color_obj = getColorObj(scaf_strand_color, alpha=scaf_alpha)
self._pen1.setBrush(scaf_strand_color_obj)
self.arrow1.setPen(self._pen1)
part = self.part()
tpb = part._TWIST_PER_BASE
angle = idx*tpb
# for some reason rotation is CW and not CCW with increasing angle
self.arrow1.setRotation(angle + part._TWIST_OFFSET)
def updateStapArrow(self, idx):
stap_strand = self._virtual_helix.stap(idx)
if stap_strand:
stap_strand_color = stap_strand.oligo().color()
stap_alpha = 230 if stap_strand.hasXoverAt(idx) else 128
else:
stap_strand_color = '#c0c0c0' # Qt.lightGray
stap_alpha = 26
stap_strand_color_obj = getColorObj(stap_strand_color, alpha=stap_alpha)
self._pen2.setBrush(stap_strand_color_obj)
self.arrow2.setPen(self._pen2)
part = self.part()
tpb = part._TWIST_PER_BASE
angle = idx*tpb
self.arrow2.setRotation(angle + part._TWIST_OFFSET)
# end def
def setNumber(self):
"""docstring for setNumber"""
vh = self._virtual_helix
num = vh.number()
label = self._label
radius = self._RADIUS
if num is not None:
label.setText("%d" % num)
else:
return
y_val = radius / 3
if num < 10:
label.setPos(radius / 1.5, y_val)
elif num < 100:
label.setPos(radius / 3, y_val)
else: # _number >= 100
label.setPos(0, y_val)
b_rect = label.boundingRect()
posx = b_rect.width()/2
posy = b_rect.height()/2
label.setPos(radius-posx, radius-posy)
# end def
def part(self):
return self._empty_helix_item.part()
def virtualHelix(self):
return self._virtual_helix
# end def
def number(self):
return self.virtualHelix().number()
def setActiveSliceView(self, idx, has_scaf, has_stap):
if has_scaf:
self.setPen(self._USE_PEN)
self.setBrush(self._USE_BRUSH)
self._label.setBrush(self._USE_TEXT_BRUSH)
self.updateScafArrow(idx)
self.arrow1.show()
else:
self.setPen(self._OUT_OF_SLICE_PEN)
self.setBrush(self._OUT_OF_SLICE_BRUSH)
self._label.setBrush(self._OUT_OF_SLICE_TEXT_BRUSH)
self.arrow1.hide()
if has_stap:
self.updateStapArrow(idx)
self.arrow2.show()
else:
self.arrow2.hide()
# end def
############################ User Interaction ############################
def sceneEvent(self, event):
"""Included for unit testing in order to grab events that are sent
via QGraphicsScene.sendEvent()."""
# if self._parent.sliceController.testRecorder:
# coord = (self._row, self._col)
# self._parent.sliceController.testRecorder.sliceSceneEvent(event, coord)
if event.type() == QEvent.MouseButtonPress:
self.mousePressEvent(event)
return True
elif event.type() == QEvent.MouseButtonRelease:
self.mouseReleaseEvent(event)
return True
elif event.type() == QEvent.MouseMove:
self.mouseMoveEvent(event)
return True
QGraphicsItem.sceneEvent(self, event)
return False
def hoverEnterEvent(self, event):
"""
If the selection is configured to always select
everything, we don't draw a focus ring around everything,
instead we only draw a focus ring around the hovered obj.
"""
# if self.selectAllBehavior():
# self.setSelected(True)
# forward the event to the empty_helix_item as well
self._empty_helix_item.hoverEnterEvent(event)
# end def
def hoverLeaveEvent(self, event):
# if self.selectAllBehavior():
# self.setSelected(False)
self._empty_helix_item.hoverEnterEvent(event)
class SliceVirtualHelixItem(AbstractVirtualHelixItem, QGraphicsEllipseItem):
"""The VirtualHelixItem is an individual circle that gets drawn in the SliceView
as a child of the NucleicAcidPartItem. Taken as a group, many SliceHelix
instances make up the crossection of the NucleicAcidPart. Clicking on a SliceHelix
adds a VirtualHelix to the PlasmidPart. The SliceHelix then changes appearence
and paints its corresponding VirtualHelix number.
Attributes:
FILTER_NAME (str): Belongs to the filter class 'virtual_helix'.
is_active (bool): Does the item have focus.
old_pen (QPen): temp storage for pen for easy restoration on appearance change.
wedge_gizmos (dict): dictionary of `WedgeGizmo` objects.
"""
FILTER_NAME = 'virtual_helix'
def __init__(self, model_virtual_helix, part_item):
"""
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
part_item (cadnano.gui.views.sliceview.nucleicacidpartitem.NucleicAcidPartItem): the part item
"""
AbstractVirtualHelixItem.__init__(self, model_virtual_helix, part_item)
QGraphicsEllipseItem.__init__(self, parent=part_item)
self._controller = VirtualHelixItemController(self, self._model_part, False, True)
self.hide()
model_part = self._model_part
x, y = model_part.locationQt(self._id_num, part_item.scaleFactor())
# set position to offset for radius
# self.setTransformOriginPoint(_RADIUS, _RADIUS)
self.setCenterPos(x, y)
self.wedge_gizmos = {}
self._added_wedge_gizmos = set()
# self._prexo_gizmos = []
self.setAcceptHoverEvents(True)
self.setZValue(_ZVALUE)
# handle the label specific stuff
self._label = self.createLabel()
self.setNumber()
self.old_pen = None
self.is_active = False
self.updateAppearance()
self.show()
self._right_mouse_move = False
# end def
### ACCESSORS ###
def part(self):
"""Reference to the model part associated with the parent part item.
Returns:
NucleicAcidPart: the model part
"""
return self._part_item.part()
# end def
def setSnapOrigin(self, is_snap):
"""Used to toggle an item as the snap origin. See `SelectSliceTool`.
Args:
is_snap (bool): True if this should be the snap origin, False otherwise.
"""
if is_snap:
op = self.pen()
if self.old_pen is None:
self.old_pen = op
self.setPen(getPenObj(op.color().name(), SNAP_WIDTH))
else:
self.setPen(self.old_pen)
self.old_pen = None
def partItem(self):
"""Reference to the parent part item.
Returns:
NucleicAcidPartItem: the part item
"""
return self._part_item
# end def
def idNum(self):
"""Virual helix ID number.
Returns:
int: the id_num of the virtual helix object.
"""
return self._id_num
# end def
def activate(self):
"""Sets the VirtualHelixItem object as active (i.e. having focus due
to user input) and calls updateAppearance.
"""
self.is_active = True
self.updateAppearance()
def deactivate(self):
"""Sets the VirtualHelixItem object as not active (i.e. does not have
focus) and calls updateAppearance.
"""
self.is_active = False
self.updateAppearance()
def setCenterPos(self, x, y):
"""Moves this item a new position such that its center is located at
(x,y).
Args:
x (float): new x coordinate
y (float): new y coordinate
"""
# invert the y axis
part_item = self._part_item
parent_item = self.parentItem()
pos = QPointF(x - _RADIUS, y - _RADIUS)
if parent_item != part_item:
pos = parent_item.mapFromItem(part_item, pos)
self.setPos(pos)
# end def
def getCenterScenePos(self):
"""
Returns:
QPointF: the scenePos of the virtualhelixitem center
"""
return self.scenePos() + QPointF(_RADIUS, _RADIUS)
# end def
def modelColor(self):
"""The color associated with this item's `Part`.
Returns:
str: hex representation of Color, e.g. `#0066cc`.
"""
return self._model_part.getProperty('color')
# end def
def partCrossoverSpanAngle(self):
"""The angle span, centered at each base, within which crossovers
will be allowed by the interface. The span is drawn by the WedgeGizmo.
Returns:
int: The span angle (default is set in NucleicAcidPart init)
"""
return float(self._model_part.getProperty('crossover_span_angle'))
# end def
### SIGNALS ###
### SLOTS ###
def mousePressEvent(self, event):
"""Event handler for when the mouse button is pressed inside
this item. If a tool-specific mouse press method is defined, it will be
called for the currently active tool. Otherwise, the default
QGraphicsItem.mousePressEvent will be called.
Note:
Only applies the event if the clicked item is in the part
item's active filter set.
Args:
event (QMouseEvent): contains parameters that describe the mouse event.
"""
if self.FILTER_NAME not in self._part_item.getFilterSet():
return
if event.button() == Qt.RightButton:
return
part_item = self._part_item
tool = part_item._getActiveTool()
tool_method_name = tool.methodPrefix() + "MousePress"
if hasattr(self, tool_method_name):
getattr(self, tool_method_name)(tool, part_item, event)
else:
QGraphicsItem.mousePressEvent(self, event)
# end def
def selectToolMousePress(self, tool, part_item, event):
"""The event handler for when the mouse button is pressed inside this
item with the SelectTool active.
Args:
tool (SelectSliceTool): reference to call tool-specific methods
part_item (cadnano.gui.views.sliceview.nucleicacidpartitem.NucleicAcidPartItem): reference to the part item
event (QMouseEvent): contains parameters that describe the mouse event
"""
part = self._model_part
part.setSelected(True)
tool.selectOrSnap(part_item, self, event)
# return QGraphicsItem.mousePressEvent(self, event)
# end def
def pencilToolMousePress(self, tool, part_item, event):
"""Summary
Args:
tool (SelectSliceTool): reference to call tool-specific methods
part_item (cadnano.gui.views.sliceview.nucleicacidpartitem.NucleicAcidPartItem): reference to the part item
event (QMouseEvent): contains parameters that describe the mouse event
"""
part = self._model_part
print("pencilToolMousePress", part)
# tool.attemptToCreateStrand
def virtualHelixPropertyChangedSlot(self, keys, values):
"""The event handler for when the a model virtual helix propety has
changed. See partVirtualHelixPropertyChangedSignal.
Calls updateAppearance(), which will refresh styles if needed.
Args:
keys (tuple): names of properties that changed
values (tuple): new values of properties that change
"""
# for key, val in zip(keys, values):
# pass
self.updateAppearance()
# end def
def virtualHelixRemovedSlot(self):
"""The event handler for when a virtual helix is removed from the model.
Disconnects signals, and sets internal references to label, part_item,
and model_part to None, and finally removes the item from the scene.
"""
self._controller.disconnectSignals()
self._controller = None
part_item = self._part_item
tool = part_item._getActiveTool()
if tool.methodPrefix() == "selectTool":
tool.hideLineItem()
self.scene().removeItem(self._label)
self._label = None
self._part_item = None
self._model_part = None
self.scene().removeItem(self)
# end def
def updateAppearance(self):
"""Check item's current visibility, color and active state, and sets
pen, brush, text according to style defaults.
"""
is_visible, color = self._model_vh.getProperty(['is_visible', 'color'])
if is_visible:
self.show()
else:
self.hide()
return
pwidth = styles.SLICE_HELIX_STROKE_WIDTH if self.old_pen is None else SNAP_WIDTH
if self.is_active:
self._USE_PEN = getPenObj(styles.ACTIVE_STROKE, pwidth)
else:
self._USE_PEN = getPenObj(color, pwidth)
self._TEXT_BRUSH = getBrushObj(styles.SLICE_TEXT_COLOR)
self._BRUSH = _BRUSH_DEFAULT
self._USE_BRUSH = getBrushObj(color, alpha=150)
self._label.setBrush(self._TEXT_BRUSH)
self.setBrush(self._BRUSH)
self.setPen(self._USE_PEN)
self.setRect(_RECT)
# end def
def updatePosition(self):
"""Queries the model virtual helix for latest x,y coodinates, and sets
them in the scene if necessary.
Note:
coordinates in the model are always in the part
"""
part_item = self._part_item
# sf = part_item.scaleFactor()
x, y = self._model_part.locationQt(self._id_num, part_item.scaleFactor())
new_pos = QPointF(x - _RADIUS, y - _RADIUS) # top left
tl_pos = part_item.mapFromScene(self.scenePos()) # top left
"""
better to compare QPointF's since it handles difference
tolerances for you with !=
"""
if new_pos != tl_pos:
parent_item = self.parentItem()
if parent_item != part_item:
new_pos = parent_item.mapFromItem(part_item, new_pos)
self.setPos(new_pos)
# end def
def createLabel(self):
"""Creates a text label to display the ID number. Font and Z are set
in slicestyles.
Returns:
QGraphicsSimpleTextItem: the label
"""
label = QGraphicsSimpleTextItem("%d" % self.idNum())
label.setFont(_FONT)
label.setZValue(_ZVALUE)
label.setParentItem(self)
return label
# end def
def beginAddWedgeGizmos(self):
"""Resets the list of WedgeGizmos that will be processed by
endAddWedgeGizmos.
Called by NucleicAcidPartItem _refreshVirtualHelixItemGizmos, before
setWedgeGizmo and endAddWedgeGizmos.
"""
self._added_wedge_gizmos.clear()
# end def
def endAddWedgeGizmos(self):
"""Removes beginAddWedgeGizmos that no longer point at a neighbor virtual helix.
Called by NucleicAcidPartItem _refreshVirtualHelixItemGizmos in,
after beginAddWedgeGizmos and setWedgeGizmo.
"""
remove_list = []
scene = self.scene()
wg_dict = self.wedge_gizmos
recently_added = self._added_wedge_gizmos
for neighbor_virtual_helix in wg_dict.keys():
if neighbor_virtual_helix not in recently_added:
remove_list.append(neighbor_virtual_helix)
for nvh in remove_list:
wg = wg_dict.get(nvh)
del wg_dict[nvh]
scene.removeItem(wg)
# end def
def setWedgeGizmo(self, neighbor_virtual_helix, neighbor_virtual_helix_item):
"""Adds a WedgeGizmo to oriented toward the specified neighbor vhi.
Called by NucleicAcidPartItem _refreshVirtualHelixItemGizmos, in between
with beginAddWedgeGizmos and endAddWedgeGizmos.
Args:
neighbor_virtual_helix (int): the id_num of neighboring virtual helix
neighbor_virtual_helix_item (cadnano.gui.views.sliceview.virtualhelixitem.VirtualHelixItem):
the neighboring virtual helix item
"""
wg_dict = self.wedge_gizmos
nvhi = neighbor_virtual_helix_item
nvhi_name = nvhi.cnModel().getProperty('name')
pos = self.scenePos()
line = QLineF(pos, nvhi.scenePos())
line.translate(_RADIUS, _RADIUS)
if line.length() > (_RADIUS*1.99):
color = '#5a8bff'
else:
color = '#cc0000'
nvhi_name = nvhi_name + '*' # mark as invalid
line.setLength(_RADIUS)
if neighbor_virtual_helix in wg_dict:
wedge_item = wg_dict[neighbor_virtual_helix]
else:
wedge_item = WedgeGizmo(_RADIUS, WEDGE_RECT, self)
wg_dict[neighbor_virtual_helix] = wedge_item
wedge_item.showWedge(line.angle(), color, outline_only=False)
self._added_wedge_gizmos.add(neighbor_virtual_helix)
# end def
def setNumber(self):
"""Updates the associated QGraphicsSimpleTextItem label text to match
the id_num. Adjusts the label position so it is centered regardless
of number of digits in the label.
"""
num = self.idNum()
label = self._label
if num is not None:
label.setText("%d" % num)
else:
return
y_val = _RADIUS / 3
if num < 10:
label.setPos(_RADIUS / 1.5, y_val)
elif num < 100:
label.setPos(_RADIUS / 3, y_val)
else: # _number >= 100
label.setPos(0, y_val)
b_rect = label.boundingRect()
posx = b_rect.width()/2
posy = b_rect.height()/2
label.setPos(_RADIUS-posx, _RADIUS-posy)
def __init__(self, model_virtual_helix, part_item):
AbstractVirtualHelixItem.__init__(self, model_virtual_helix, part_item)
CNOutlinerItem.__init__(self, model_virtual_helix, parent=part_item)
self.setFlags(LEAF_FLAGS)
self._controller = VirtualHelixItemController(self, model_virtual_helix.part(), False, False)
class PathVirtualHelixItem(AbstractVirtualHelixItem, QGraphicsPathItem):
"""VirtualHelixItem for PathView
Attributes:
drag_last_position (TYPE): Description
FILTER_NAME (str): Description
findChild (TYPE): Description
handle_start (TYPE): Description
is_active (bool): Description
"""
findChild = util.findChild # for debug
FILTER_NAME = "virtual_helix"
def __init__(self, model_virtual_helix, part_item, viewroot):
"""Summary
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
part_item (TYPE): Description
viewroot (TYPE): Description
"""
AbstractVirtualHelixItem.__init__(self, model_virtual_helix, part_item)
QGraphicsPathItem.__init__(self, parent=part_item.proxy())
self._viewroot = viewroot
self._getActiveTool = part_item._getActiveTool
self._controller = VirtualHelixItemController(self, self._model_part,
False, True)
self._handle = VirtualHelixHandleItem(self, part_item, viewroot)
self._last_strand_set = None
self._last_idx = None
self.setFlag(QGraphicsItem.ItemUsesExtendedStyleOption)
self.setCacheMode(QGraphicsItem.DeviceCoordinateCache)
self.setBrush(getNoBrush())
view = self.view()
view.levelOfDetailChangedSignal.connect(self.levelOfDetailChangedSlot)
should_show_details = view.shouldShowDetails()
pen = newPenObj(styles.MINOR_GRID_STROKE,
styles.MINOR_GRID_STROKE_WIDTH)
pen.setCosmetic(should_show_details)
self.setPen(pen)
self.is_active = False
self.refreshPath()
self.setAcceptHoverEvents(True) # for pathtools
self.setZValue(styles.ZPATHHELIX)
self._right_mouse_move = False
self.drag_last_position = self.handle_start = self.pos()
# end def
### SIGNALS ###
### SLOTS indirectly called from the part ###
def levelOfDetailChangedSlot(self, boolval):
"""Not connected to the model, only the QGraphicsView
Args:
boolval (TYPE): Description
"""
pen = self.pen()
pen.setCosmetic(boolval)
# print("levelOfDetailChangedSlot", boolval, pen.width())
# if boolval:
# pass
# else:
# pass
self.setPen(pen)
# end def
def strandAddedSlot(self, sender, strand):
"""
Instantiates a StrandItem upon notification that the model has a
new Strand. The StrandItem is responsible for creating its own
controller for communication with the model, and for adding itself to
its parent (which is *this* VirtualHelixItem, i.e. 'self').
Args:
sender (obj): Model object that emitted the signal.
strand (TYPE): Description
"""
StrandItem(strand, self, self._viewroot)
# end def
def virtualHelixRemovedSlot(self):
"""Summary
Returns:
TYPE: Description
"""
self.view().levelOfDetailChangedSignal.disconnect(
self.levelOfDetailChangedSlot)
self._controller.disconnectSignals()
self._controller = None
scene = self.scene()
self._handle.remove()
scene.removeItem(self)
self._part_item = None
self._model_part = None
self._getActiveTool = None
self._handle = None
# end def
def virtualHelixPropertyChangedSlot(self, keys, values):
"""Summary
Args:
keys (TYPE): Description
values (TYPE): Description
Returns:
TYPE: Description
"""
for key, val in zip(keys, values):
if key == 'is_visible':
if val:
self.show()
self._handle.show()
self.showXoverItems()
else:
self.hideXoverItems()
self.hide()
self._handle.hide()
return
if key == 'z':
part_item = self._part_item
z = part_item.convertToQtZ(val)
if self.x() != z:
self.setX(z)
""" The handle is selected, so deselect to
accurately position then reselect
"""
vhi_h = self._handle
vhi_h.tempReparent()
vhi_h.setX(z - _VH_XOFFSET)
# if self.isSelected():
# print("ImZ", self.idNum())
part_item.updateXoverItems(self)
vhi_h_selection_group = self._viewroot.vhiHandleSelectionGroup(
)
vhi_h_selection_group.addToGroup(vhi_h)
elif key == 'eulerZ':
self._handle.rotateWithCenterOrigin(val)
# self._prexoveritemgroup.updatePositionsAfterRotation(value)
### GEOMETRY PROPERTIES ###
elif key == 'repeat_hint':
pass
# self.updateRepeats(int(val))
elif key == 'bases_per_repeat':
pass
# self.updateBasesPerRepeat(int(val))
elif key == 'turns_per_repeat':
# self.updateTurnsPerRepeat(int(val))
pass
### RUNTIME PROPERTIES ###
elif key == 'neighbors':
# this means a virtual helix in the slice view has moved
# so we need to clear and redraw the PreXoverItems just in case
if self.isActive():
self._part_item.setPreXoverItemsVisible(self)
self.refreshPath()
# end def
def showXoverItems(self):
"""Summary
Returns:
TYPE: Description
"""
for item in self.childItems():
if isinstance(item, XoverNode3):
item.showXover()
# end def
def hideXoverItems(self):
"""Summary
Returns:
TYPE: Description
"""
for item in self.childItems():
if isinstance(item, XoverNode3):
item.hideXover()
# end def
### ACCESSORS ###
def viewroot(self):
"""Summary
Returns:
TYPE: Description
"""
return self._viewroot
# end def
def handle(self):
"""Summary
Returns:
TYPE: Description
"""
return self._handle
# end def
def window(self):
"""Summary
Returns:
TYPE: Description
"""
return self._part_item.window()
# end def
def view(self):
return self._viewroot.scene().views()[0]
# end def
### DRAWING METHODS ###
def upperLeftCornerOfBase(self, idx, strand):
"""Summary
Args:
idx (int): the base index within the virtual helix
strand (TYPE): Description
Returns:
TYPE: Description
"""
x = idx * _BASE_WIDTH
y = 0 if strand.isForward() else _BASE_WIDTH
return x, y
# end def
def upperLeftCornerOfBaseType(self, idx, is_fwd):
"""Summary
Args:
idx (int): the base index within the virtual helix
is_fwd (TYPE): Description
Returns:
TYPE: Description
"""
x = idx * _BASE_WIDTH
y = 0 if is_fwd else _BASE_WIDTH
return x, y
# end def
def refreshPath(self):
"""
Returns a QPainterPath object for the minor grid lines.
The path also includes a border outline and a midline for
dividing scaffold and staple bases.
"""
bw = _BASE_WIDTH
bw2 = 2 * bw
part = self.part()
path = QPainterPath()
sub_step_size = part.subStepSize()
canvas_size = self._model_vh.getSize()
# border
path.addRect(0, 0, bw * canvas_size, 2 * bw)
# minor tick marks
for i in range(canvas_size):
x = round(bw * i) + .5
if i % sub_step_size == 0:
path.moveTo(x - .5, 0)
path.lineTo(x - .5, bw2)
path.lineTo(x - .25, bw2)
path.lineTo(x - .25, 0)
path.lineTo(x, 0)
path.lineTo(x, bw2)
path.lineTo(x + .25, bw2)
path.lineTo(x + .25, 0)
path.lineTo(x + .5, 0)
path.lineTo(x + .5, bw2)
# path.moveTo(x-.5, 0)
# path.lineTo(x-.5, 2 * bw)
# path.lineTo(x+.5, 2 * bw)
# path.lineTo(x+.5, 0)
else:
path.moveTo(x, 0)
path.lineTo(x, 2 * bw)
# staple-scaffold divider
path.moveTo(0, bw)
path.lineTo(bw * canvas_size, bw)
self.setPath(path)
# end def
def resize(self):
"""Called by part on resize.
"""
self.refreshPath()
# end def
### PUBLIC SUPPORT METHODS ###
def activate(self):
"""Summary
Returns:
TYPE: Description
"""
pen = self.pen()
pen.setColor(getColorObj(styles.MINOR_GRID_STROKE_ACTIVE))
self.setPen(pen)
self.is_active = True
# end def
def deactivate(self):
"""Summary
Returns:
TYPE: Description
"""
pen = self.pen()
pen.setColor(getColorObj(styles.MINOR_GRID_STROKE))
self.setPen(pen)
self.is_active = False
# end def
### EVENT HANDLERS ###
def mousePressEvent(self, event):
"""
Parses a mousePressEvent to extract strand_set and base index,
forwarding them to approproate tool method as necessary.
Args:
event (TYPE): Description
"""
# 1. Check if we are doing a Z translation
if event.button() == Qt.RightButton:
viewroot = self._viewroot
current_filter_set = viewroot.selectionFilterSet()
if self.FILTER_NAME in current_filter_set and self.part(
).isZEditable():
self._right_mouse_move = True
self.drag_last_position = event.scenePos()
self.handle_start = self.pos()
return
self.scene().views()[0].addToPressList(self)
strand_set, idx = self.baseAtPoint(event.pos())
self._model_vh.setActive(strand_set.isForward(), idx)
tool = self._getActiveTool()
tool_method_name = tool.methodPrefix() + "MousePress"
if hasattr(self, tool_method_name):
self._last_strand_set, self._last_idx = strand_set, idx
getattr(self, tool_method_name)(strand_set, idx, event.modifiers())
else:
event.setAccepted(False)
# end def
def mouseMoveEvent(self, event):
"""
Parses a mouseMoveEvent to extract strand_set and base index,
forwarding them to approproate tool method as necessary.
Args:
event (TYPE): Description
"""
# 1. Check if we are doing a Z translation
if self._right_mouse_move:
MOVE_THRESHOLD = 0.01 # ignore small moves
new_pos = event.scenePos()
delta = new_pos - self.drag_last_position
dx = int(floor(delta.x() / _BASE_WIDTH)) * _BASE_WIDTH
x = self.handle_start.x() + dx
if abs(dx) > MOVE_THRESHOLD or dx == 0.0:
old_x = self.x()
self.setX(x)
vhi_h = self._handle
vhi_h.tempReparent()
vhi_h.setX(x - _VH_XOFFSET)
self._part_item.updateXoverItems(self)
dz = self._part_item.convertToModelZ(x - old_x)
self._model_part.translateVirtualHelices([self.idNum()],
0,
0,
dz,
False,
use_undostack=False)
return
# 2. Forward event to tool
tool = self._getActiveTool()
tool_method_name = tool.methodPrefix() + "MouseMove"
if hasattr(self, tool_method_name):
strand_set, idx = self.baseAtPoint(event.pos())
if self._last_strand_set != strand_set or self._last_idx != idx:
self._last_strand_set, self._last_idx = strand_set, idx
getattr(self, tool_method_name)(strand_set, idx)
else:
event.setAccepted(False)
# end def
def mouseReleaseEvent(self, event):
"""Called in the event of doing a Z translation drag
Args:
event (TYPE): Description
"""
if self._right_mouse_move and event.button() == Qt.RightButton:
MOVE_THRESHOLD = 0.01 # ignore small moves
self._right_mouse_move = False
delta = self.pos() - self.handle_start
dz = delta.x()
if abs(dz) > MOVE_THRESHOLD:
dz = self._part_item.convertToModelZ(dz)
self._model_part.translateVirtualHelices([self.idNum()],
0,
0,
dz,
True,
use_undostack=True)
# end def
def customMouseRelease(self, event):
"""
Parses a mouseReleaseEvent to extract strand_set and base index,
forwarding them to approproate tool method as necessary.
Args:
event (TYPE): Description
"""
tool = self._getActiveTool()
tool_method_name = tool.methodPrefix() + "MouseRelease"
if hasattr(self, tool_method_name):
getattr(self, tool_method_name)(self._last_strand_set,
self._last_idx)
else:
event.setAccepted(False)
# end def
### COORDINATE UTILITIES ###
def baseAtPoint(self, pos):
"""
Returns the (Strandset, index) under the location x, y or None.
It shouldn't be possible to click outside a pathhelix and still call
this function. However, this sometimes happens if you click exactly
on the top or bottom edge, resulting in a negative y value.
Args:
pos (TYPE): Description
"""
x, y = pos.x(), pos.y()
part = self._model_part
id_num = self._id_num
base_idx = int(floor(x / _BASE_WIDTH))
min_base, max_base = 0, part.maxBaseIdx(id_num)
if base_idx < min_base or base_idx >= max_base:
base_idx = util.clamp(base_idx, min_base, max_base)
if y < 0:
y = 0 # HACK: zero out y due to erroneous click
strand_type = floor(y * 1. / _BASE_WIDTH) # 0 for fwd, 1 for rev
strand_type = int(util.clamp(strand_type, 0, 1))
strand_set = part.getStrandSets(id_num)[strand_type]
return (strand_set, base_idx)
# end def
def keyPanDeltaX(self):
"""How far a single press of the left or right arrow key should move
the scene (in scene space)
"""
dx = self._part_item.part().stepSize() * _BASE_WIDTH
return self.mapToScene(QRectF(0, 0, dx, 1)).boundingRect().width()
# end def
def hoverLeaveEvent(self, event):
"""Summary
Args:
event (TYPE): Description
Returns:
TYPE: Description
"""
self._part_item.updateStatusBar("")
# end def
def hoverMoveEvent(self, event):
"""
Parses a mouseMoveEvent to extract strand_set and base index,
forwarding them to approproate tool method as necessary.
Args:
event (TYPE): Description
"""
base_idx = int(floor(event.pos().x() / _BASE_WIDTH))
loc = "%d[%d]" % (self._id_num, base_idx)
self._part_item.updateStatusBar(loc)
active_tool = self._getActiveTool()
tool_method_name = active_tool.methodPrefix() + "HoverMove"
if hasattr(self, tool_method_name):
is_fwd, idx_x, idx_y = active_tool.baseAtPoint(self, event.pos())
getattr(self, tool_method_name)(is_fwd, idx_x, idx_y)
# end def
### TOOL METHODS ###
def pencilToolMousePress(self, strand_set, idx, modifiers):
"""strand.getDragBounds
Args:
strand_set (StrandSet): Description
idx (int): the base index within the virtual helix
"""
# print("%s: %s[%s]" % (util.methodName(), strand_set, idx))
if modifiers & Qt.ShiftModifier:
bounds = strand_set.getBoundsOfEmptyRegionContaining(idx)
ret = strand_set.createStrand(*bounds)
print("creating strand {} was successful: {}".format(bounds, ret))
return
active_tool = self._getActiveTool()
if not active_tool.isDrawingStrand():
active_tool.initStrandItemFromVHI(self, strand_set, idx)
active_tool.setIsDrawingStrand(True)
# end def
def pencilToolMouseMove(self, strand_set, idx):
"""strand.getDragBounds
Args:
strand_set (StrandSet): Description
idx (int): the base index within the virtual helix
"""
# print("%s: %s[%s]" % (util.methodName(), strand_set, idx))
active_tool = self._getActiveTool()
if active_tool.isDrawingStrand():
active_tool.updateStrandItemFromVHI(self, strand_set, idx)
# end def
def pencilToolMouseRelease(self, strand_set, idx):
"""strand.getDragBounds
Args:
strand_set (StrandSet): Description
idx (int): the base index within the virtual helix
"""
# print("%s: %s[%s]" % (util.methodName(), strand_set, idx))
active_tool = self._getActiveTool()
if active_tool.isDrawingStrand():
active_tool.setIsDrawingStrand(False)
active_tool.attemptToCreateStrand(self, strand_set, idx)
# end def
def pencilToolHoverMove(self, is_fwd, idx_x, idx_y):
"""Pencil the strand is possible.
Args:
is_fwd (TYPE): Description
idx_x (TYPE): Description
idx_y (TYPE): Description
"""
active_tool = self._getActiveTool()
if not active_tool.isFloatingXoverBegin():
temp_xover = active_tool.floatingXover()
temp_xover.updateFloatingFromVHI(self, is_fwd, idx_x, idx_y)
class VirtualHelixItem(QGraphicsEllipseItem):
"""
The VirtualHelixItem is an individual circle that gets drawn in the SliceView
as a child of the PartItem. Taken as a group, many SliceHelix
instances make up the crossection of the DNAPart. Clicking on a SliceHelix
adds a VirtualHelix to the DNAPart. The SliceHelix then changes appearence
and paints its corresponding VirtualHelix number.
"""
# set up default, hover, and active drawing styles
_USE_BRUSH = QBrush(styles.ORANGE_FILL)
_USE_PEN = QPen(styles.ORANGE_STROKE, styles.SLICE_HELIX_STROKE_WIDTH)
_RADIUS = styles.SLICE_HELIX_RADIUS
_OUT_OF_SLICE_PEN = QPen(styles.LIGHT_ORANGE_STROKE,\
styles.SLICE_HELIX_STROKE_WIDTH)
_OUT_OF_SLICE_BRUSH = QBrush(styles.LIGHT_ORANGE_FILL)
_RECT = QRectF(0, 0, 2 * _RADIUS, 2 * _RADIUS)
_FONT = styles.SLICE_NUM_FONT
_ZVALUE = styles.ZSLICEHELIX+3
def __init__(self, model_virtual_helix, empty_helix_item):
"""
empty_helix_item is a EmptyHelixItem that will act as a QGraphicsItem parent
"""
super(VirtualHelixItem, self).__init__(parent=empty_helix_item)
self._virtual_helix = model_virtual_helix
self._empty_helix_item = empty_helix_item
self.hide()
# drawing related
self.isHovered = False
self.setAcceptHoverEvents(True)
# self.setFlag(QGraphicsItem.ItemIsSelectable)
self.setZValue(self._ZVALUE)
self.lastMousePressAddedBases = False
self.setBrush(self._OUT_OF_SLICE_BRUSH)
self.setPen(self._OUT_OF_SLICE_PEN)
self.setRect(self._RECT)
# handle the label specific stuff
self._label = self.createLabel()
self.setNumber()
self._pen1, self._pen2 = (QPen(), QPen())
self.createArrows()
self._controller = VirtualHelixItemController(self, model_virtual_helix)
self.show()
# end def
### SIGNALS ###
### SLOTS ###
def virtualHelixNumberChangedSlot(self, virtualHelix):
"""
receives a signal containing a virtualHelix and the oldNumber
as a safety check
"""
self.setNumber()
# end def
def virtualHelixRemovedSlot(self, virtualHelix):
self._controller.disconnectSignals()
self._controller = None
self._empty_helix_item.setNotHovered()
self._virtual_helix = None
self._empty_helix_item = None
self.scene().removeItem(self._label)
self._label = None
self.scene().removeItem(self)
# end def
def strandAddedSlot(self, sender, strand):
pass
# end def
def createLabel(self):
label = QGraphicsSimpleTextItem("%d" % self._virtual_helix.number())
label.setFont(self._FONT)
label.setZValue(self._ZVALUE)
label.setParentItem(self)
return label
# end def
def createArrows(self):
rad = self._RADIUS
pen1 = self._pen1
pen2 = self._pen2
pen1.setWidth(3)
pen2.setWidth(3)
pen1.setBrush(Qt.gray)
pen2.setBrush(Qt.lightGray)
if self._virtual_helix.isEvenParity():
arrow1 = QGraphicsLineItem(rad, rad, 2*rad, rad, self)
arrow2 = QGraphicsLineItem(0, rad, rad, rad, self)
else:
arrow1 = QGraphicsLineItem(0, rad, rad, rad, self)
arrow2 = QGraphicsLineItem(rad, rad, 2*rad, rad, self)
arrow1.setTransformOriginPoint(rad, rad)
arrow2.setTransformOriginPoint(rad, rad)
arrow1.setZValue(400)
arrow2.setZValue(400)
arrow1.setPen(pen1)
arrow2.setPen(pen2)
self.arrow1 = arrow1
self.arrow2 = arrow2
self.arrow1.hide()
self.arrow2.hide()
# end def
def updateScafArrow(self, idx):
scafStrand = self._virtual_helix.scaf(idx)
if scafStrand:
scafStrandColor = QColor(scafStrand.oligo().color())
scafAlpha = 0.9 if scafStrand.hasXoverAt(idx) else 0.3
else:
scafStrandColor = QColor(Qt.gray)
scafAlpha = 0.1
scafStrandColor.setAlphaF(scafAlpha)
self._pen1.setBrush(scafStrandColor)
self.arrow1.setPen(self._pen1)
part = self.part()
tpb = part._TWIST_PER_BASE
angle = idx*tpb
# for some reason rotation is CW and not CCW with increasing angle
self.arrow1.setRotation(angle + part._TWIST_OFFSET)
def updateStapArrow(self, idx):
stapStrand = self._virtual_helix.stap(idx)
if stapStrand:
stapStrandColor = QColor(stapStrand.oligo().color())
stapAlpha = 0.9 if stapStrand.hasXoverAt(idx) else 0.3
else:
stapStrandColor = QColor(Qt.lightGray)
stapAlpha = 0.1
stapStrandColor.setAlphaF(stapAlpha)
self._pen2.setBrush(stapStrandColor)
self.arrow2.setPen(self._pen2)
part = self.part()
tpb = part._TWIST_PER_BASE
angle = idx*tpb
self.arrow2.setRotation(angle + part._TWIST_OFFSET)
# end def
def setNumber(self):
"""docstring for setNumber"""
vh = self._virtual_helix
num = vh.number()
label = self._label
radius = self._RADIUS
if num != None:
label.setText("%d" % num)
else:
return
y_val = radius / 3
if num < 10:
label.setPos(radius / 1.5, y_val)
elif num < 100:
label.setPos(radius / 3, y_val)
else: # _number >= 100
label.setPos(0, y_val)
b_rect = label.boundingRect()
posx = b_rect.width()/2
posy = b_rect.height()/2
label.setPos(radius-posx, radius-posy)
# end def
def part(self):
return self._empty_helix_item.part()
def virtualHelix(self):
return self._virtual_helix
# end def
def number(self):
return self.virtualHelix().number()
def setActiveSliceView(self, idx, has_scaf, has_stap):
if has_scaf:
self.setPen(self._USE_PEN)
self.setBrush(self._USE_BRUSH)
self.updateScafArrow(idx)
self.arrow1.show()
else:
self.setPen(self._OUT_OF_SLICE_PEN)
self.setBrush(self._OUT_OF_SLICE_BRUSH)
self.arrow1.hide()
if has_stap:
self.updateStapArrow(idx)
self.arrow2.show()
else:
self.arrow2.hide()
# end def
############################ User Interaction ############################
def sceneEvent(self, event):
"""Included for unit testing in order to grab events that are sent
via QGraphicsScene.sendEvent()."""
# if self._parent.sliceController.testRecorder:
# coord = (self._row, self._col)
# self._parent.sliceController.testRecorder.sliceSceneEvent(event, coord)
if event.type() == QEvent.MouseButtonPress:
self.mousePressEvent(event)
return True
elif event.type() == QEvent.MouseButtonRelease:
self.mouseReleaseEvent(event)
return True
elif event.type() == QEvent.MouseMove:
self.mouseMoveEvent(event)
return True
QGraphicsItem.sceneEvent(self, event)
return False
def hoverEnterEvent(self, event):
"""
If the selection is configured to always select
everything, we don't draw a focus ring around everything,
instead we only draw a focus ring around the hovered obj.
"""
# if self.selectAllBehavior():
# self.setSelected(True)
# forward the event to the empty_helix_item as well
self._empty_helix_item.hoverEnterEvent(event)
# end def
def hoverLeaveEvent(self, event):
# if self.selectAllBehavior():
# self.setSelected(False)
self._empty_helix_item.hoverEnterEvent(event)
class PathVirtualHelixItem(AbstractVirtualHelixItem, QGraphicsPathItem):
"""VirtualHelixItem for PathView
Attributes:
drag_last_position (TYPE): Description
FILTER_NAME (str): Description
findChild (TYPE): Description
handle_start (TYPE): Description
is_active (bool): Description
"""
findChild = util.findChild # for debug
FILTER_NAME = "virtual_helix"
def __init__(self, model_virtual_helix, part_item, viewroot):
"""Summary
Args:
id_num (int): VirtualHelix ID number. See `NucleicAcidPart` for description and related methods.
part_item (TYPE): Description
viewroot (TYPE): Description
"""
AbstractVirtualHelixItem.__init__(self, model_virtual_helix, part_item)
QGraphicsPathItem.__init__(self, parent=part_item.proxy())
self._viewroot = viewroot
self._getActiveTool = part_item._getActiveTool
self._controller = VirtualHelixItemController(self, self._model_part, False, True)
self._handle = VirtualHelixHandleItem(self, part_item, viewroot)
self._last_strand_set = None
self._last_idx = None
self.setFlag(QGraphicsItem.ItemUsesExtendedStyleOption)
self.setCacheMode(QGraphicsItem.DeviceCoordinateCache)
self.setBrush(getNoBrush())
view = self.view()
view.levelOfDetailChangedSignal.connect(self.levelOfDetailChangedSlot)
should_show_details = view.shouldShowDetails()
pen = newPenObj(styles.MINOR_GRID_STROKE, styles.MINOR_GRID_STROKE_WIDTH)
pen.setCosmetic(should_show_details)
self.setPen(pen)
self.is_active = False
self.refreshPath()
self.setAcceptHoverEvents(True) # for pathtools
self.setZValue(styles.ZPATHHELIX)
self._right_mouse_move = False
self.drag_last_position = self.handle_start = self.pos()
# end def
### SIGNALS ###
### SLOTS indirectly called from the part ###
def levelOfDetailChangedSlot(self, boolval):
"""Not connected to the model, only the QGraphicsView
Args:
boolval (TYPE): Description
"""
pen = self.pen()
pen.setCosmetic(boolval)
# print("levelOfDetailChangedSlot", boolval, pen.width())
# if boolval:
# pass
# else:
# pass
self.setPen(pen)
# end def
def strandAddedSlot(self, sender, strand):
"""
Instantiates a StrandItem upon notification that the model has a
new Strand. The StrandItem is responsible for creating its own
controller for communication with the model, and for adding itself to
its parent (which is *this* VirtualHelixItem, i.e. 'self').
Args:
sender (obj): Model object that emitted the signal.
strand (TYPE): Description
"""
StrandItem(strand, self, self._viewroot)
# end def
def virtualHelixRemovedSlot(self):
"""Summary
Returns:
TYPE: Description
"""
self.view().levelOfDetailChangedSignal.disconnect(self.levelOfDetailChangedSlot)
self._controller.disconnectSignals()
self._controller = None
scene = self.scene()
self._handle.remove()
scene.removeItem(self)
self._part_item = None
self._model_part = None
self._getActiveTool = None
self._handle = None
# end def
def virtualHelixPropertyChangedSlot(self, keys, values):
"""Summary
Args:
keys (TYPE): Description
values (TYPE): Description
Returns:
TYPE: Description
"""
for key, val in zip(keys, values):
if key == 'is_visible':
if val:
self.show()
self._handle.show()
self.showXoverItems()
else:
self.hideXoverItems()
self.hide()
self._handle.hide()
return
if key == 'z':
part_item = self._part_item
z = part_item.convertToQtZ(val)
if self.x() != z:
self.setX(z)
""" The handle is selected, so deselect to
accurately position then reselect
"""
vhi_h = self._handle
vhi_h.tempReparent()
vhi_h.setX(z - _VH_XOFFSET)
# if self.isSelected():
# print("ImZ", self.idNum())
part_item.updateXoverItems(self)
vhi_h_selection_group = self._viewroot.vhiHandleSelectionGroup()
vhi_h_selection_group.addToGroup(vhi_h)
elif key == 'eulerZ':
self._handle.rotateWithCenterOrigin(val)
# self._prexoveritemgroup.updatePositionsAfterRotation(value)
### GEOMETRY PROPERTIES ###
elif key == 'repeat_hint':
pass
# self.updateRepeats(int(val))
elif key == 'bases_per_repeat':
pass
# self.updateBasesPerRepeat(int(val))
elif key == 'turns_per_repeat':
# self.updateTurnsPerRepeat(int(val))
pass
### RUNTIME PROPERTIES ###
elif key == 'neighbors':
# this means a virtual helix in the slice view has moved
# so we need to clear and redraw the PreXoverItems just in case
if self.isActive():
self._part_item.setPreXoverItemsVisible(self)
self.refreshPath()
# end def
def showXoverItems(self):
"""Summary
Returns:
TYPE: Description
"""
for item in self.childItems():
if isinstance(item, XoverNode3):
item.showXover()
# end def
def hideXoverItems(self):
"""Summary
Returns:
TYPE: Description
"""
for item in self.childItems():
if isinstance(item, XoverNode3):
item.hideXover()
# end def
### ACCESSORS ###
def viewroot(self):
"""Summary
Returns:
TYPE: Description
"""
return self._viewroot
# end def
def handle(self):
"""Summary
Returns:
TYPE: Description
"""
return self._handle
# end def
def window(self):
"""Summary
Returns:
TYPE: Description
"""
return self._part_item.window()
# end def
def view(self):
return self._viewroot.scene().views()[0]
# end def
### DRAWING METHODS ###
def upperLeftCornerOfBase(self, idx, strand):
"""Summary
Args:
idx (int): the base index within the virtual helix
strand (TYPE): Description
Returns:
TYPE: Description
"""
x = idx * _BASE_WIDTH
y = 0 if strand.isForward() else _BASE_WIDTH
return x, y
# end def
def upperLeftCornerOfBaseType(self, idx, is_fwd):
"""Summary
Args:
idx (int): the base index within the virtual helix
is_fwd (TYPE): Description
Returns:
TYPE: Description
"""
x = idx * _BASE_WIDTH
y = 0 if is_fwd else _BASE_WIDTH
return x, y
# end def
def refreshPath(self):
"""
Returns a QPainterPath object for the minor grid lines.
The path also includes a border outline and a midline for
dividing scaffold and staple bases.
"""
bw = _BASE_WIDTH
bw2 = 2 * bw
part = self.part()
path = QPainterPath()
sub_step_size = part.subStepSize()
canvas_size = self._model_vh.getSize()
# border
path.addRect(0, 0, bw * canvas_size, 2 * bw)
# minor tick marks
for i in range(canvas_size):
x = round(bw * i) + .5
if i % sub_step_size == 0:
path.moveTo(x - .5, 0)
path.lineTo(x - .5, bw2)
path.lineTo(x - .25, bw2)
path.lineTo(x - .25, 0)
path.lineTo(x, 0)
path.lineTo(x, bw2)
path.lineTo(x + .25, bw2)
path.lineTo(x + .25, 0)
path.lineTo(x + .5, 0)
path.lineTo(x + .5, bw2)
# path.moveTo(x-.5, 0)
# path.lineTo(x-.5, 2 * bw)
# path.lineTo(x+.5, 2 * bw)
# path.lineTo(x+.5, 0)
else:
path.moveTo(x, 0)
path.lineTo(x, 2 * bw)
# staple-scaffold divider
path.moveTo(0, bw)
path.lineTo(bw * canvas_size, bw)
self.setPath(path)
# end def
def resize(self):
"""Called by part on resize.
"""
self.refreshPath()
# end def
### PUBLIC SUPPORT METHODS ###
def activate(self):
"""Summary
Returns:
TYPE: Description
"""
pen = self.pen()
pen.setColor(getColorObj(styles.MINOR_GRID_STROKE_ACTIVE))
self.setPen(pen)
self.is_active = True
# end def
def deactivate(self):
"""Summary
Returns:
TYPE: Description
"""
pen = self.pen()
pen.setColor(getColorObj(styles.MINOR_GRID_STROKE))
self.setPen(pen)
self.is_active = False
# end def
### EVENT HANDLERS ###
def mousePressEvent(self, event):
"""
Parses a mousePressEvent to extract strand_set and base index,
forwarding them to approproate tool method as necessary.
Args:
event (TYPE): Description
"""
# 1. Check if we are doing a Z translation
if event.button() == Qt.RightButton:
viewroot = self._viewroot
current_filter_set = viewroot.selectionFilterSet()
if self.FILTER_NAME in current_filter_set and self.part().isZEditable():
self._right_mouse_move = True
self.drag_last_position = event.scenePos()
self.handle_start = self.pos()
return
self.scene().views()[0].addToPressList(self)
strand_set, idx = self.baseAtPoint(event.pos())
self._model_vh.setActive(strand_set.isForward(), idx)
tool = self._getActiveTool()
tool_method_name = tool.methodPrefix() + "MousePress"
if hasattr(self, tool_method_name):
self._last_strand_set, self._last_idx = strand_set, idx
getattr(self, tool_method_name)(strand_set, idx, event.modifiers())
else:
event.setAccepted(False)
# end def
def mouseMoveEvent(self, event):
"""
Parses a mouseMoveEvent to extract strand_set and base index,
forwarding them to approproate tool method as necessary.
Args:
event (TYPE): Description
"""
# 1. Check if we are doing a Z translation
if self._right_mouse_move:
MOVE_THRESHOLD = 0.01 # ignore small moves
new_pos = event.scenePos()
delta = new_pos - self.drag_last_position
dx = int(floor(delta.x() / _BASE_WIDTH))*_BASE_WIDTH
x = self.handle_start.x() + dx
if abs(dx) > MOVE_THRESHOLD or dx == 0.0:
old_x = self.x()
self.setX(x)
vhi_h = self._handle
vhi_h.tempReparent()
vhi_h.setX(x - _VH_XOFFSET)
self._part_item.updateXoverItems(self)
dz = self._part_item.convertToModelZ(x - old_x)
self._model_part.translateVirtualHelices([self.idNum()],
0, 0, dz, False,
use_undostack=False)
return
# 2. Forward event to tool
tool = self._getActiveTool()
tool_method_name = tool.methodPrefix() + "MouseMove"
if hasattr(self, tool_method_name):
strand_set, idx = self.baseAtPoint(event.pos())
if self._last_strand_set != strand_set or self._last_idx != idx:
self._last_strand_set, self._last_idx = strand_set, idx
getattr(self, tool_method_name)(strand_set, idx)
else:
event.setAccepted(False)
# end def
def mouseReleaseEvent(self, event):
"""Called in the event of doing a Z translation drag
Args:
event (TYPE): Description
"""
if self._right_mouse_move and event.button() == Qt.RightButton:
MOVE_THRESHOLD = 0.01 # ignore small moves
self._right_mouse_move = False
delta = self.pos() - self.handle_start
dz = delta.x()
if abs(dz) > MOVE_THRESHOLD:
dz = self._part_item.convertToModelZ(dz)
self._model_part.translateVirtualHelices([self.idNum()],
0, 0, dz, True,
use_undostack=True)
# end def
def customMouseRelease(self, event):
"""
Parses a mouseReleaseEvent to extract strand_set and base index,
forwarding them to approproate tool method as necessary.
Args:
event (TYPE): Description
"""
tool = self._getActiveTool()
tool_method_name = tool.methodPrefix() + "MouseRelease"
if hasattr(self, tool_method_name):
getattr(self, tool_method_name)(self._last_strand_set, self._last_idx)
else:
event.setAccepted(False)
# end def
### COORDINATE UTILITIES ###
def baseAtPoint(self, pos):
"""
Returns the (Strandset, index) under the location x, y or None.
It shouldn't be possible to click outside a pathhelix and still call
this function. However, this sometimes happens if you click exactly
on the top or bottom edge, resulting in a negative y value.
Args:
pos (TYPE): Description
"""
x, y = pos.x(), pos.y()
part = self._model_part
id_num = self._id_num
base_idx = int(floor(x / _BASE_WIDTH))
min_base, max_base = 0, part.maxBaseIdx(id_num)
if base_idx < min_base or base_idx >= max_base:
base_idx = util.clamp(base_idx, min_base, max_base)
if y < 0:
y = 0 # HACK: zero out y due to erroneous click
strand_type = floor(y * 1. / _BASE_WIDTH) # 0 for fwd, 1 for rev
strand_type = int(util.clamp(strand_type, 0, 1))
strand_set = part.getStrandSets(id_num)[strand_type]
return (strand_set, base_idx)
# end def
def keyPanDeltaX(self):
"""How far a single press of the left or right arrow key should move
the scene (in scene space)
"""
dx = self._part_item.part().stepSize() * _BASE_WIDTH
return self.mapToScene(QRectF(0, 0, dx, 1)).boundingRect().width()
# end def
def hoverLeaveEvent(self, event):
"""Summary
Args:
event (TYPE): Description
Returns:
TYPE: Description
"""
self._part_item.updateStatusBar("")
# end def
def hoverMoveEvent(self, event):
"""
Parses a mouseMoveEvent to extract strand_set and base index,
forwarding them to approproate tool method as necessary.
Args:
event (TYPE): Description
"""
base_idx = int(floor(event.pos().x() / _BASE_WIDTH))
loc = "%d[%d]" % (self._id_num, base_idx)
self._part_item.updateStatusBar(loc)
active_tool = self._getActiveTool()
tool_method_name = active_tool.methodPrefix() + "HoverMove"
if hasattr(self, tool_method_name):
is_fwd, idx_x, idx_y = active_tool.baseAtPoint(self, event.pos())
getattr(self, tool_method_name)(is_fwd, idx_x, idx_y)
# end def
### TOOL METHODS ###
def pencilToolMousePress(self, strand_set, idx, modifiers):
"""strand.getDragBounds
Args:
strand_set (StrandSet): Description
idx (int): the base index within the virtual helix
"""
# print("%s: %s[%s]" % (util.methodName(), strand_set, idx))
if modifiers & Qt.ShiftModifier:
bounds = strand_set.getBoundsOfEmptyRegionContaining(idx)
ret = strand_set.createStrand(*bounds)
print("creating strand {} was successful: {}".format(bounds, ret))
return
active_tool = self._getActiveTool()
if not active_tool.isDrawingStrand():
active_tool.initStrandItemFromVHI(self, strand_set, idx)
active_tool.setIsDrawingStrand(True)
# end def
def pencilToolMouseMove(self, strand_set, idx):
"""strand.getDragBounds
Args:
strand_set (StrandSet): Description
idx (int): the base index within the virtual helix
"""
# print("%s: %s[%s]" % (util.methodName(), strand_set, idx))
active_tool = self._getActiveTool()
if active_tool.isDrawingStrand():
active_tool.updateStrandItemFromVHI(self, strand_set, idx)
# end def
def pencilToolMouseRelease(self, strand_set, idx):
"""strand.getDragBounds
Args:
strand_set (StrandSet): Description
idx (int): the base index within the virtual helix
"""
# print("%s: %s[%s]" % (util.methodName(), strand_set, idx))
active_tool = self._getActiveTool()
if active_tool.isDrawingStrand():
active_tool.setIsDrawingStrand(False)
active_tool.attemptToCreateStrand(self, strand_set, idx)
# end def
def pencilToolHoverMove(self, is_fwd, idx_x, idx_y):
"""Pencil the strand is possible.
Args:
is_fwd (TYPE): Description
idx_x (TYPE): Description
idx_y (TYPE): Description
"""
active_tool = self._getActiveTool()
if not active_tool.isFloatingXoverBegin():
temp_xover = active_tool.floatingXover()
temp_xover.updateFloatingFromVHI(self, is_fwd, idx_x, idx_y)
