class PreXoverItem(QGraphicsRectItem):
"""A PreXoverItem exists between a single 'from' VirtualHelixItem index
and zero or more 'to' VirtualHelixItem Indices
Attributes:
adapter (TYPE): Description
idx (int): the base index within the virtual helix
is_fwd (TYPE): Description
prexoveritemgroup (TYPE): Description
to_vh_id_num (TYPE): Description
"""
def __init__(self, from_virtual_helix_item, is_fwd, from_index,
to_vh_id_num, prexoveritemgroup, color):
"""Summary
Args:
from_virtual_helix_item (cadnano.gui.views.pathview.virtualhelixitem.VirtualHelixItem): Description
is_fwd (TYPE): Description
from_index (TYPE): Description
to_vh_id_num (TYPE): Description
prexoveritemgroup (TYPE): Description
color (TYPE): Description
"""
super(QGraphicsRectItem, self).__init__(BASE_RECT,
from_virtual_helix_item)
self.adapter = PropertyWrapperObject(self)
self._bond_item = QGraphicsPathItem(self)
self._bond_item.hide()
self._label = PreXoverLabel(is_fwd, color, self)
self._phos_item = Triangle(FWDPHOS_PP, self)
self.setPen(getNoPen())
self.resetItem(from_virtual_helix_item, is_fwd, from_index,
to_vh_id_num, prexoveritemgroup, color)
# end def
def shutdown(self):
"""Summary
Returns:
TYPE: Description
"""
self.setBrush(getBrushObj(self._color, alpha=0))
self.to_vh_id_num = None
self.adapter.resetAnimations()
phos = self._phos_item
phos.adapter.resetAnimations()
phos.resetTransform()
phos.setPos(0, 0)
self.setAcceptHoverEvents(False)
self.setFlag(KEYINPUT_ACTIVE_FLAG, False)
self.hide()
# end def
def resetItem(self, from_virtual_helix_item, is_fwd, from_index,
to_vh_id_num, prexoveritemgroup, color):
"""Summary
Args:
from_virtual_helix_item (cadnano.gui.views.pathview.virtualhelixitem.VirtualHelixItem): Description
is_fwd (TYPE): Description
from_index (TYPE): Description
to_vh_id_num (TYPE): Description
prexoveritemgroup (TYPE): Description
color (TYPE): Description
Returns:
TYPE: Description
"""
self.setParentItem(from_virtual_helix_item)
self.resetTransform()
self._id_num = from_virtual_helix_item.idNum()
self.idx = from_index
self.is_fwd = is_fwd
self.to_vh_id_num = to_vh_id_num
self._color = color
self.prexoveritemgroup = prexoveritemgroup
self._bond_item.hide()
self._label_txt = lbt = None if to_vh_id_num is None else str(
to_vh_id_num)
self.setLabel(text=lbt)
self._label.resetItem(is_fwd, color)
phos = self._phos_item
bonditem = self._bond_item
if is_fwd:
phos.setPath(FWDPHOS_PP)
phos.setTransformOriginPoint(0, phos.boundingRect().center().y())
phos.setPos(0.5 * BASE_WIDTH, BASE_WIDTH)
phos.setPen(getNoPen())
phos.setBrush(getBrushObj(color))
bonditem.setPen(getPenObj(color, styles.PREXOVER_STROKE_WIDTH))
self.setPos(from_index * BASE_WIDTH, -BASE_WIDTH)
else:
phos.setPath(REVPHOS_PP)
phos.setTransformOriginPoint(0, phos.boundingRect().center().y())
phos.setPos(0.5 * BASE_WIDTH, 0)
phos.setPen(getPenObj(color, 0.25))
phos.setBrush(getNoBrush())
bonditem.setPen(
getPenObj(color,
styles.PREXOVER_STROKE_WIDTH,
penstyle=Qt.DotLine,
capstyle=Qt.RoundCap))
self.setPos(from_index * BASE_WIDTH, 2 * BASE_WIDTH)
if to_vh_id_num is not None:
inactive_alpha = PROX_ALPHA
self.setBrush(getBrushObj(color, alpha=inactive_alpha))
else:
self.setBrush(getBrushObj(color, alpha=0))
self.show()
# end def
def getInfo(self):
"""
Returns:
Tuple: (from_id_num, is_fwd, from_index, to_vh_id_num)
"""
return (self._id_num, self.is_fwd, self.idx, self.to_vh_id_num)
### ACCESSORS ###
def color(self):
"""Summary
Returns:
TYPE: Description
"""
return self._color
def remove(self):
"""Summary
Returns:
TYPE: Description
"""
scene = self.scene()
self.adapter.destroy()
if scene:
scene.removeItem(self._label)
self._label = None
self._phos_item.adapter.resetAnimations()
self._phos_item.adapter = None
scene.removeItem(self._phos_item)
self._phos_item = None
scene.removeItem(self._bond_item)
self._bond_item = None
self.adapter.resetAnimations()
self.adapter = None
scene.removeItem(self)
# end defS
### EVENT HANDLERS ###
def hoverEnterEvent(self, event):
"""Only if enableActive(True) is called
hover and key events disabled by default
Args:
event (TYPE): Description
"""
self.setFocus(Qt.MouseFocusReason)
self.prexoveritemgroup.updateModelActiveBaseInfo(self.getInfo())
self.setActiveHovered(True)
status_string = "%d[%d]" % (self._id_num, self.idx)
self.parentItem().window().statusBar().showMessage(status_string)
# end def
def hoverLeaveEvent(self, event):
"""Summary
Args:
event (TYPE): Description
Returns:
TYPE: Description
"""
self.prexoveritemgroup.updateModelActiveBaseInfo(None)
self.setActiveHovered(False)
self.clearFocus()
self.parentItem().window().statusBar().showMessage("")
# end def
def keyPressEvent(self, event):
"""Summary
Args:
event (TYPE): Description
Returns:
TYPE: Description
"""
self.prexoveritemgroup.handlePreXoverKeyPress(event.key())
# end def
### PUBLIC SUPPORT METHODS ###
def setLabel(self, text=None, outline=False):
"""Summary
Args:
text (None, optional): Description
outline (bool, optional): Description
Returns:
TYPE: Description
"""
if text:
self._label.setTextAndStyle(text=text, outline=outline)
self._label.show()
else:
self._label.hide()
# end def
def animate(self, item, property_name, duration, start_value, end_value):
"""Summary
Args:
item (TYPE): Description
property_name (TYPE): Description
duration (TYPE): Description
start_value (TYPE): Description
end_value (TYPE): Description
Returns:
TYPE: Description
"""
b_name = property_name.encode('ascii')
anim = item.adapter.getRef(property_name)
if anim is None:
anim = QPropertyAnimation(item.adapter, b_name)
item.adapter.saveRef(property_name, anim)
anim.setDuration(duration)
anim.setStartValue(start_value)
anim.setEndValue(end_value)
anim.start()
# end def
def setActiveHovered(self, is_active):
"""Rotate phosphate Triangle if `self.to_vh_id_num` is not `None`
Args:
is_active (bool): whether or not the PreXoverItem is parented to the
active VirtualHelixItem
"""
if is_active:
self.setBrush(getBrushObj(self._color, alpha=128))
self.animate(self, 'brush_alpha', 1, 0,
128) # overwrite running anim
# if self.to_vh_id_num is not None:
self.animate(self._phos_item, 'rotation', 500, 0, -90)
else:
inactive_alpha = 0 if self.to_vh_id_num is None else PROX_ALPHA
self.setBrush(getBrushObj(self._color, alpha=inactive_alpha))
self.animate(self, 'brush_alpha', 1000, 128, inactive_alpha)
self.animate(self._phos_item, 'rotation', 500, -90, 0)
# end def
def enableActive(self, is_active, to_vh_id_num=None):
"""Call on PreXoverItems created on the active VirtualHelixItem
Args:
is_active (TYPE): Description
to_vh_id_num (None, optional): Description
"""
if is_active:
self.to_vh_id_num = to_vh_id_num
self.setAcceptHoverEvents(True)
if to_vh_id_num is None:
self.setLabel(text=None)
self.setBrush(getBrushObj(self._color, alpha=0))
else:
self.setLabel(text=str(to_vh_id_num))
inactive_alpha = PROX_ALPHA
self.setBrush(getBrushObj(self._color, alpha=inactive_alpha))
self.animate(self, 'brush_alpha', 1000, 128, inactive_alpha)
self.setFlag(KEYINPUT_ACTIVE_FLAG, True)
else:
self.setBrush(getNoBrush())
# self.setLabel(text=None)
self.setAcceptHoverEvents(False)
self.setFlag(KEYINPUT_ACTIVE_FLAG, False)
def activateNeighbor(self, active_prexoveritem, shortcut=None):
"""To be called with whatever the active_prexoveritem
is for the parts `active_base`
Args:
active_prexoveritem (TYPE): Description
shortcut (None, optional): Description
"""
p1 = self._phos_item.scenePos()
p2 = active_prexoveritem._phos_item.scenePos()
scale = 3
delta1 = -BASE_WIDTH * scale if self.is_fwd else BASE_WIDTH * scale
delta2 = BASE_WIDTH * scale if active_prexoveritem.is_fwd else -BASE_WIDTH * scale
c1 = self.mapFromScene(QPointF(p1.x(), p1.y() + delta1))
c2 = self.mapFromScene(QPointF(p2.x(), p2.y() - delta2))
pp = QPainterPath()
pp.moveTo(self._phos_item.pos())
pp.cubicTo(c1, c2, self._bond_item.mapFromScene(p2))
self._bond_item.setPath(pp)
self._bond_item.show()
alpha = 32
idx, active_idx = self.idx, active_prexoveritem.idx
if self.is_fwd != active_prexoveritem.is_fwd:
if idx == active_idx:
alpha = 255
elif idx == active_idx + 1:
alpha = 255
elif idx == active_idx - 1:
alpha = 255
inactive_alpha = PROX_ALPHA if self.to_vh_id_num is not None else 0
self.setBrush(getBrushObj(self._color, alpha=inactive_alpha))
self.animate(self, 'brush_alpha', 500, inactive_alpha, alpha)
self.animate(self._phos_item, 'rotation', 500, 0, -90)
self.setLabel(text=shortcut, outline=True)
# end def
def deactivateNeighbor(self):
"""Summary
Returns:
TYPE: Description
"""
if self.isVisible():
inactive_alpha = PROX_ALPHA if self.to_vh_id_num is not None else 0
self.setBrush(getBrushObj(self._color, alpha=inactive_alpha))
self.animate(self, 'brush_alpha', 1000, 128, inactive_alpha)
self.animate(self._phos_item, 'rotation', 500, -90, 0)
self._bond_item.hide()
self.setLabel(text=self._label_txt)
class ForcedXoverNode3(QGraphicsRectItem):
"""
This is a QGraphicsRectItem to allow actions and also a
QGraphicsSimpleTextItem to allow a label to be drawn
Attributes:
is_forward (TYPE): Description
"""
def __init__(self, virtual_helix_item, xover_item, strand3p, idx):
"""Summary
Args:
virtual_helix_item (cadnano.views.pathview.virtualhelixitem.VirtualHelixItem): from vhi
xover_item (TYPE): Description
strand3p (Strand): reference to the 3' strand
idx (int): the base index within the virtual helix
"""
super(ForcedXoverNode3, self).__init__(virtual_helix_item)
self._vhi = virtual_helix_item
self._xover_item = xover_item
self._idx = idx
self.is_forward = strand3p.strandSet().isForward()
self._is_on_top = self.is_forward
self._partner_virtual_helix = virtual_helix_item
self._blank_thing = QGraphicsRectItem(_blankRect, self)
self._blank_thing.setBrush(QBrush(Qt.white))
self._path_thing = QGraphicsPathItem(self)
self.configurePath()
self._label = None
self.setPen(_NO_PEN)
self.setBrush(_NO_BRUSH)
self.setRect(_rect)
self.setZValue(styles.ZENDPOINTITEM + 1)
# end def
def updateForFloatFromVHI(self, virtual_helix_item, is_forward, idx_x, idx_y):
"""
Args:
virtual_helix_item (cadnano.views.pathview.virtualhelixitem.VirtualHelixItem): Description
is_forward (TYPE): Description
idx_x (TYPE): Description
idx_y (TYPE): Description
"""
self._vhi = virtual_helix_item
self.setParentItem(virtual_helix_item)
self._idx = idx_x
self._is_on_top = self.is_forward = True if is_forward else False
self.updatePositionAndAppearance(is_from_strand=False)
# end def
def updateForFloatFromStrand(self, virtual_helix_item, strand3p, idx):
"""
Args:
virtual_helix_item (cadnano.views.pathview.virtualhelixitem.VirtualHelixItem): Description
strand3p (Strand): reference to the 3' strand
idx (int): the base index within the virtual helix
"""
self._vhi = virtual_helix_item
self._strand = strand3p
self.setParentItem(virtual_helix_item)
self._idx = idx
self._is_on_top = self.is_forward = strand3p.strandSet().isForward()
self.updatePositionAndAppearance()
# end def
def configurePath(self):
"""Summary
Returns:
TYPE: Description
"""
self._path_thing.setBrush(getBrushObj(_PENCIL_COLOR))
path = PPR3 if self.is_forward else PPL3
offset = -_BASE_WIDTH if self.is_forward else _BASE_WIDTH
self._path_thing.setPath(path)
self._path_thing.setPos(offset, 0)
offset = -_BASE_WIDTH if self.is_forward else 0
self._blank_thing.setPos(offset, 0)
self._blank_thing.show()
self._path_thing.show()
# end def
def refreshXover(self):
"""Summary
Returns:
TYPE: Description
"""
self._xover_item.refreshXover()
# end def
def setPartnerVirtualHelix(self, virtual_helix_item):
"""Summary
Args:
virtual_helix_item (cadnano.views.pathview.virtualhelixitem.VirtualHelixItem): Description
Returns:
TYPE: Description
"""
self._partner_virtual_helix = virtual_helix_item
# end def
def idx(self):
"""Summary
Returns:
TYPE: Description
"""
return self._idx
# end def
def virtualHelixItem(self):
"""Summary
Returns:
TYPE: Description
"""
return self._vhi
# end def
def point(self):
"""Summary
Returns:
TYPE: Description
"""
return self._vhi.upperLeftCornerOfBaseType(self._idx, self.is_forward)
# end def
def floatPoint(self):
"""Summary
Returns:
TYPE: Description
"""
pt = self.pos()
return pt.x(), pt.y()
# end def
def isForward(self):
"""Summary
Returns:
TYPE: Description
"""
return self.is_forward
# end def
def updatePositionAndAppearance(self, is_from_strand=True):
"""
Sets position by asking the VirtualHelixItem
Sets appearance by choosing among pre-defined painterpaths (from
normalstrandgraphicsitem) depending on drawing direction.
Args:
is_from_strand (bool, optional): Description
"""
self.setPos(*self.point())
n5 = self._xover_item._node5
if is_from_strand:
from_strand, from_idx = (n5._strand, n5._idx) if n5 != self else (None, None)
if self._strand.canInstallXoverAt(self._idx, from_strand, from_idx):
self.configurePath()
# We can only expose a 5' end. But on which side?
is_left = True if self.is_forward else False
self._updateLabel(is_left)
else:
self.hideItems()
else:
self.hideItems()
# end def
def remove(self):
"""Clean up this joint
"""
scene = self.scene()
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._path_thing)
self._path_thing = None
scene.removeItem(self._blank_thing)
self._blank_thing = None
scene.removeItem(self)
# end def
def _updateLabel(self, is_left):
"""Called by updatePositionAndAppearance during init.
Updates drawing and position of the label.
Args:
is_left (TYPE): Description
"""
lbl = self._label
if self._idx is not None:
bw = _BASE_WIDTH
num = self._partner_virtual_helix.idNum()
tBR = _FM.tightBoundingRect(str(num))
half_label_h = tBR.height()/2.0
half_label_w = tBR.width()/2.0
# determine x and y positions
label_x = bw/2.0 - half_label_w
if self._is_on_top:
label_y = -0.25*half_label_h - 0.5 - 0.5*bw
else:
label_y = 2*half_label_h + 0.5 + 0.5*bw
# adjust x for left vs right
label_x_offset = 0.25*bw if is_left else -0.25*bw
label_x += label_x_offset
# adjust x for numeral 1
if num == 1:
label_x -= half_label_w/2.0
# create text item
if lbl is None:
lbl = QGraphicsSimpleTextItem(str(num), self)
lbl.setPos(label_x, label_y)
lbl.setBrush(_ENAB_BRUSH)
lbl.setFont(_TO_HELIX_NUM_FONT)
self._label = lbl
lbl.setText(str(self._partner_virtual_helix.idNum()))
lbl.show()
# end if
# end def
def hideItems(self):
"""Summary
Returns:
TYPE: Description
"""
if self._label:
self._label.hide()
if self._blank_thing:
self._path_thing.hide()
if self._blank_thing:
self._blank_thing.hide()
class ForcedXoverNode3(QGraphicsRectItem):
"""
This is a QGraphicsRectItem to allow actions and also a
QGraphicsSimpleTextItem to allow a label to be drawn
Attributes:
is_forward (TYPE): Description
"""
def __init__(self, virtual_helix_item, xover_item, strand3p, idx):
"""Summary
Args:
virtual_helix_item (cadnano.gui.views.pathview.virtualhelixitem.VirtualHelixItem): from vhi
xover_item (TYPE): Description
strand3p (Strand): reference to the 3' strand
idx (int): the base index within the virtual helix
"""
super(ForcedXoverNode3, self).__init__(virtual_helix_item)
self._vhi = virtual_helix_item
self._xover_item = xover_item
self._idx = idx
self.is_forward = strand3p.strandSet().isForward()
self._is_on_top = self.is_forward
self._partner_virtual_helix = virtual_helix_item
self._blank_thing = QGraphicsRectItem(_blankRect, self)
self._blank_thing.setBrush(QBrush(Qt.white))
self._path_thing = QGraphicsPathItem(self)
self.configurePath()
self._label = None
self.setPen(_NO_PEN)
self.setBrush(_NO_BRUSH)
self.setRect(_rect)
self.setZValue(styles.ZENDPOINTITEM + 1)
# end def
def updateForFloatFromVHI(self, virtual_helix_item, is_forward, idx_x, idx_y):
"""
Args:
virtual_helix_item (cadnano.gui.views.pathview.virtualhelixitem.VirtualHelixItem): Description
is_forward (TYPE): Description
idx_x (TYPE): Description
idx_y (TYPE): Description
"""
self._vhi = virtual_helix_item
self.setParentItem(virtual_helix_item)
self._idx = idx_x
self._is_on_top = self.is_forward = True if is_forward else False
self.updatePositionAndAppearance(is_from_strand=False)
# end def
def updateForFloatFromStrand(self, virtual_helix_item, strand3p, idx):
"""
Args:
virtual_helix_item (cadnano.gui.views.pathview.virtualhelixitem.VirtualHelixItem): Description
strand3p (Strand): reference to the 3' strand
idx (int): the base index within the virtual helix
"""
self._vhi = virtual_helix_item
self._strand = strand3p
self.setParentItem(virtual_helix_item)
self._idx = idx
self._is_on_top = self.is_forward = strand3p.strandSet().isForward()
self.updatePositionAndAppearance()
# end def
def configurePath(self):
"""Summary
Returns:
TYPE: Description
"""
self._path_thing.setBrush(getBrushObj(_PENCIL_COLOR))
path = PPR3 if self.is_forward else PPL3
offset = -_BASE_WIDTH if self.is_forward else _BASE_WIDTH
self._path_thing.setPath(path)
self._path_thing.setPos(offset, 0)
offset = -_BASE_WIDTH if self.is_forward else 0
self._blank_thing.setPos(offset, 0)
self._blank_thing.show()
self._path_thing.show()
# end def
def refreshXover(self):
"""Summary
Returns:
TYPE: Description
"""
self._xover_item.refreshXover()
# end def
def setPartnerVirtualHelix(self, virtual_helix_item):
"""Summary
Args:
virtual_helix_item (cadnano.gui.views.pathview.virtualhelixitem.VirtualHelixItem): Description
Returns:
TYPE: Description
"""
self._partner_virtual_helix = virtual_helix_item
# end def
def idx(self):
"""Summary
Returns:
TYPE: Description
"""
return self._idx
# end def
def virtualHelixItem(self):
"""Summary
Returns:
TYPE: Description
"""
return self._vhi
# end def
def point(self):
"""Summary
Returns:
TYPE: Description
"""
return self._vhi.upperLeftCornerOfBaseType(self._idx, self.is_forward)
# end def
def floatPoint(self):
"""Summary
Returns:
TYPE: Description
"""
pt = self.pos()
return pt.x(), pt.y()
# end def
def isForward(self):
"""Summary
Returns:
TYPE: Description
"""
return self.is_forward
# end def
def updatePositionAndAppearance(self, is_from_strand=True):
"""
Sets position by asking the VirtualHelixItem
Sets appearance by choosing among pre-defined painterpaths (from
normalstrandgraphicsitem) depending on drawing direction.
Args:
is_from_strand (bool, optional): Description
"""
self.setPos(*self.point())
n5 = self._xover_item._node5
if is_from_strand:
from_strand, from_idx = (n5._strand, n5._idx) if n5 != self else (None, None)
if self._strand.canInstallXoverAt(self._idx, from_strand, from_idx):
self.configurePath()
# We can only expose a 5' end. But on which side?
is_left = True if self.is_forward else False
self._updateLabel(is_left)
else:
self.hideItems()
else:
self.hideItems()
# end def
def remove(self):
"""Clean up this joint
"""
scene = self.scene()
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._path_thing)
self._path_thing = None
scene.removeItem(self._blank_thing)
self._blank_thing = None
scene.removeItem(self)
# end def
def _updateLabel(self, is_left):
"""Called by updatePositionAndAppearance during init.
Updates drawing and position of the label.
Args:
is_left (TYPE): Description
"""
lbl = self._label
if self._idx is not None:
bw = _BASE_WIDTH
num = self._partner_virtual_helix.idNum()
tBR = _FM.tightBoundingRect(str(num))
half_label_h = tBR.height()/2.0
half_label_w = tBR.width()/2.0
# determine x and y positions
label_x = bw/2.0 - half_label_w
if self._is_on_top:
label_y = -0.25*half_label_h - 0.5 - 0.5*bw
else:
label_y = 2*half_label_h + 0.5 + 0.5*bw
# adjust x for left vs right
label_x_offset = 0.25*bw if is_left else -0.25*bw
label_x += label_x_offset
# adjust x for numeral 1
if num == 1:
label_x -= half_label_w/2.0
# create text item
if lbl is None:
lbl = QGraphicsSimpleTextItem(str(num), self)
lbl.setPos(label_x, label_y)
lbl.setBrush(_ENAB_BRUSH)
lbl.setFont(_TO_HELIX_NUM_FONT)
self._label = lbl
lbl.setText(str(self._partner_virtual_helix.idNum()))
lbl.show()
# end if
# end def
def hideItems(self):
"""Summary
Returns:
TYPE: Description
"""
if self._label:
self._label.hide()
if self._blank_thing:
self._path_thing.hide()
if self._blank_thing:
self._blank_thing.hide()
class ForcedXoverNode3(QGraphicsRectItem):
"""
This is a QGraphicsRectItem to allow actions and also a
QGraphicsSimpleTextItem to allow a label to be drawn
"""
def __init__(self, virtual_helix_item, xover_item, strand3p, idx):
super(ForcedXoverNode3, self).__init__(virtual_helix_item)
self._vhi = virtual_helix_item
self._xover_item = xover_item
self._idx = idx
self._is_on_top = virtual_helix_item.isStrandOnTop(strand3p)
self._is_drawn_5_to_3 = strand3p.strandSet().isDrawn5to3()
self._strand_type = strand3p.strandSet().strandType()
self._partner_virtual_helix = virtual_helix_item
self._blank_thing = QGraphicsRectItem(_blankRect, self)
self._blank_thing.setBrush(QBrush(Qt.white))
self._path_thing = QGraphicsPathItem(self)
self.configurePath()
self.setPen(_NO_PEN)
self._label = None
self.setPen(_NO_PEN)
self.setBrush(_NO_BRUSH)
self.setRect(_rect)
self.setZValue(styles.ZENDPOINTITEM + 1)
# end def
def updateForFloatFromVHI(self, virtual_helix_item, strand_type, idx_x, idx_y):
"""
"""
self._vhi = virtual_helix_item
self.setParentItem(virtual_helix_item)
self._strand_type = strand_type
self._idx = idx_x
self._is_on_top = self._is_drawn_5_to_3 = True if idx_y == 0 else False
self.updatePositionAndAppearance(is_from_strand=False)
# end def
def updateForFloatFromStrand(self, virtual_helix_item, strand3p, idx):
"""
"""
self._vhi = virtual_helix_item
self._strand = strand3p
self.setParentItem(virtual_helix_item)
self._idx = idx
self._is_on_top = virtual_helix_item.isStrandOnTop(strand3p)
self._is_drawn_5_to_3 = strand3p.strandSet().isDrawn5to3()
self._strand_type = strand3p.strandSet().strandType()
self.updatePositionAndAppearance()
# end def
def strandType(self):
return self._strand_type
# end def
def configurePath(self):
self._path_thing.setBrush(QBrush(styles.RED_STROKE))
path = PPR3 if self._is_drawn_5_to_3 else PPL3
offset = -_BASE_WIDTH if self._is_drawn_5_to_3 else _BASE_WIDTH
self._path_thing.setPath(path)
self._path_thing.setPos(offset, 0)
offset = -_BASE_WIDTH if self._is_drawn_5_to_3 else 0
self._blank_thing.setPos(offset, 0)
self._blank_thing.show()
self._path_thing.show()
# end def
def refreshXover(self):
self._xover_item.refreshXover()
# end def
def setPartnerVirtualHelix(self, virtual_helix_item):
self._partner_virtual_helix = virtual_helix_item
# end def
def idx(self):
return self._idx
# end def
def virtualHelixItem(self):
return self._vhi
# end def
def point(self):
return self._vhi.upperLeftCornerOfBaseType(self._idx, self._strand_type)
# end def
def floatPoint(self):
pt = self.pos()
return pt.x(), pt.y()
# end def
def isOnTop(self):
return self._is_on_top
# end def
def isDrawn5to3(self):
return self._is_drawn_5_to_3
# end def
def updatePositionAndAppearance(self, is_from_strand=True):
"""
Sets position by asking the VirtualHelixItem
Sets appearance by choosing among pre-defined painterpaths (from
normalstrandgraphicsitem) depending on drawing direction.
"""
self.setPos(*self.point())
n5 = self._xover_item._node5
if is_from_strand:
from_strand, from_idx = (n5._strand, n5._idx) if n5 != self else (None, None)
if self._strand.canInstallXoverAt(self._idx, from_strand, from_idx):
self.configurePath()
# We can only expose a 5' end. But on which side?
is_left = True if self._is_drawn_5_to_3 else False
self._updateLabel(is_left)
else:
self.hideItems()
else:
self.hideItems()
# end def
def updateConnectivity(self):
is_left = True if self._is_drawn_5_to_3 else False
self._updateLabel(is_left)
# end def
def remove(self):
"""
Clean up this joint
"""
scene = self.scene()
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._path_thing)
self._path_thing = None
scene.removeItem(self._blank_thing)
self._blank_thing = None
scene.removeItem(self)
# end def
def _updateLabel(self, is_left):
"""
Called by updatePositionAndAppearance during init, or later by
updateConnectivity. Updates drawing and position of the label.
"""
lbl = self._label
if self._idx != None:
bw = _BASE_WIDTH
num = self._partner_virtual_helix.number()
tBR = _FM.tightBoundingRect(str(num))
half_label_h = tBR.height()/2.0
half_label_w = tBR.width()/2.0
# determine x and y positions
label_x = bw/2.0 - half_label_w
if self._is_on_top:
label_y = -0.25*half_label_h - 0.5 - 0.5*bw
else:
label_y = 2*half_label_h + 0.5 + 0.5*bw
# adjust x for left vs right
label_x_offset = 0.25*bw if is_left else -0.25*bw
label_x += label_x_offset
# adjust x for numeral 1
if num == 1: label_x -= half_label_w/2.0
# create text item
if lbl == None:
lbl = QGraphicsSimpleTextItem(str(num), self)
lbl.setPos(label_x, label_y)
lbl.setBrush(_ENAB_BRUSH)
lbl.setFont(_TO_HELIX_NUM_FONT)
self._label = lbl
lbl.setText( str(self._partner_virtual_helix.number()) )
lbl.show()
# end if
# end def
def hideItems(self):
if self._label:
self._label.hide()
if self._blank_thing:
self._path_thing.hide()
if self._blank_thing:
self._blank_thing.hide()
class InsertionItem(QGraphicsPathItem):
"""
This is just the shape of the Insert item
"""
def __init__(self, virtual_helix_item, strand, insertion):
super(InsertionItem, self).__init__(virtual_helix_item)
self.hide()
self._strand = strand
self._insertion = insertion
self._seq_item = QGraphicsPathItem(parent=self)
self._is_on_top = is_on_top = strand.isForward()
y = 0 if is_on_top else _BW
self.setPos(_BW*insertion.idx(), y)
self.setZValue(styles.ZINSERTHANDLE)
self._initLabel()
self._initClickArea()
self.updateItem()
self.show()
# end def
def _initLabel(self):
"""Display the length of the insertion."""
self._label = InsertionLabel(self)
self._seq_item = QGraphicsPathItem(parent=self)
self._seq_text = None
self.show()
# end def
def _initClickArea(self):
"""docstring for _initClickArea"""
self._clickArea = cA = QGraphicsRectItem(_DEFAULT_RECT, self)
cA.setPen(_NO_PEN)
cA.mousePressEvent = self.mousePressEvent
cA.mouseDoubleClickEvent = self.mouseDoubleClickEvent
# end def
### PUBLIC SUPPORT METHODS ###
def remove(self):
"""
Called from the following stranditem methods:
strandRemovedSlot
strandInsertionRemovedSlot
refreshInsertionItems
"""
scene = self.scene()
self._label.setTextInteractionFlags(Qt.NoTextInteraction)
self._label.clearFocus()
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._seq_item)
self._seq_item = None
scene.removeItem(self)
self._insertion = None
self._strand = None
# end def
def updateItem(self):
self._updatePath()
self._label.updateLabel()
self._updateSequenceText()
self._label.resetPosition()
# end def
### PRIVATE SUPPORT METHODS ###
def _updatePath(self):
strand = self._strand
if strand is None:
self.hide()
return
else:
self.show()
is_on_top = self._is_on_top
if self._insertion.length() > 0:
self.setPen(QPen(QColor(strand.oligo().getColor()), styles.INSERTWIDTH))
self.setBrush(QBrush(Qt.NoBrush))
self.setPath(_insert_path.getInsert(is_on_top))
else: # insertion_size < 0 (a skip)
self.setPen(_skip_path.getPen())
self.setPath(_skip_path.getSkip())
# end def
def setSequence(self, sequence):
self._seq_text = sequence
self._updateSequenceText()
self._seq_item.show()
# end def
def hideSequence(self):
self._seq_item.hide()
# end def
def _updateSequenceText(self):
seq_item = self._seq_item
is_on_top = self._is_on_top
index = self._insertion.idx()
base_text = self._seq_text
font = styles.SEQUENCEFONT
seq_font_h = styles.SEQUENCEFONTH
insert_w = styles.INSERTWIDTH
seq_font_char_w = styles.SEQUENCEFONTCHARWIDTH
# draw sequence on the insert
if base_text: # only draw sequences if they exist i.e. not None!
len_BT = len(base_text)
if is_on_top:
angle_offset = 0
else:
angle_offset = 180
if len_BT > 20:
base_text = base_text[:17] + '...'
len_BT = len(base_text)
fraction_arc_len_per_char = (1.0 - 2.0*_FRACTION_INSERT_TO_PAD) / (len_BT + 1)
seq_item.setPen(QPen(Qt.NoPen))
seq_item.setBrush(QBrush(Qt.black))
seq_path = QPainterPath()
loop_path = self.path()
for i in range(len_BT):
frac = _FRACTION_INSERT_TO_PAD + (i+1)*fraction_arc_len_per_char
pt = loop_path.pointAtPercent(frac)
tang_ang = loop_path.angleAtPercent(frac)
temp_path = QPainterPath()
# 1. draw the text
temp_path.addText(0, 0, font, base_text[i if is_on_top else -i-1])
# 2. center it at the zero point different for top and bottom
# strands
if not is_on_top:
temp_path.translate(0, -seq_font_h - insert_w)
temp_path.translate(QPointF(-seq_font_char_w / 2.,
-2 if is_on_top else seq_font_h))
mat = QTransform()
# 3. rotate it
mat.rotate(-tang_ang + angle_offset)
rotated_path = mat.map(temp_path)
# 4. translate the rotate object to it's position on the part
rotated_path.translate(pt)
seq_path.addPath(rotated_path)
# end for
seq_item.setPath(seq_path)
# end if
# end def
### EVENT HANDLERS ###
def mouseDoubleClickEvent(self, event):
"""Double clicks remove the insertion/skip."""
self._strand.changeInsertion(self._insertion.idx(), 0)
def mousePressEvent(self, event):
"""This needs to be present for mouseDoubleClickEvent to work."""
pass
class InsertionItem(QGraphicsPathItem):
"""This is just the shape of the Insert item
"""
def __init__(self, virtual_helix_item: PathVirtualHelixItemT,
strand: StrandT,
insertion: InsertionT):
super(InsertionItem, self).__init__(virtual_helix_item)
self.hide()
self._strand = strand
self._insertion = insertion
self._seq_item = QGraphicsPathItem(parent=self)
self._is_on_top = is_on_top = strand.isForward()
y = 0 if is_on_top else _BW
self.setPos(_BW*insertion.idx(), y)
self.setZValue(styles.ZINSERTHANDLE)
self._initLabel()
self._initClickArea()
self.updateItem()
self.show()
# end def
def _initLabel(self):
"""Display the length of the insertion."""
self._label = InsertionLabel(self)
self._seq_item = QGraphicsPathItem(parent=self)
self._seq_text = None
self.show()
# end def
def _initClickArea(self):
""""""
self._clickArea = cA = QGraphicsRectItem(_DEFAULT_RECT, self)
cA.setPen(_NO_PEN)
cA.mousePressEvent = self.mousePressEvent
cA.mouseDoubleClickEvent = self.mouseDoubleClickEvent
# end def
### PUBLIC SUPPORT METHODS ###
def destroyItem(self):
"""Called from the following stranditem methods:
strandRemovedSlot
strandInsertionRemovedSlot
refreshInsertionItems
"""
scene = self.scene()
self._label.setTextInteractionFlags(Qt.NoTextInteraction)
self._label.clearFocus()
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._seq_item)
self._seq_item = None
scene.removeItem(self)
self._insertion = None
self._strand = None
# end def
def updateItem(self):
self._updatePath()
self._label.updateLabel()
self._updateSequenceText()
self._label.resetPosition()
# end def
### PRIVATE SUPPORT METHODS ###
def _updatePath(self):
strand = self._strand
if strand is None:
self.hide()
return
else:
self.show()
is_on_top = self._is_on_top
if self._insertion.length() > 0:
self.setPen(QPen(QColor(strand.oligo().getColor()), styles.INSERTWIDTH))
self.setBrush(QBrush(Qt.NoBrush))
self.setPath(_insert_path.getInsert(is_on_top))
else: # insertion_size < 0 (a skip)
self.setPen(_skip_path.getPen())
self.setPath(_skip_path.getSkip())
# end def
def setSequence(self, sequence: str):
self._seq_text = sequence
self._updateSequenceText()
self._seq_item.show()
# end def
def hideSequence(self):
self._seq_item.hide()
# end def
def _updateSequenceText(self):
seq_item = self._seq_item
is_on_top = self._is_on_top
self._insertion.idx()
base_text = self._seq_text
font = styles.SEQUENCEFONT
seq_font_h = styles.SEQUENCEFONTH
insert_w = styles.INSERTWIDTH
seq_font_char_w = styles.SEQUENCEFONTCHARWIDTH
# draw sequence on the insert
if base_text: # only draw sequences if they exist i.e. not None!
len_BT = len(base_text)
if is_on_top:
angle_offset = 0
else:
angle_offset = 180
if len_BT > 20:
base_text = base_text[:17] + '...'
len_BT = len(base_text)
fraction_arc_len_per_char = (1.0 - 2.0*_FRACTION_INSERT_TO_PAD) / (len_BT + 1)
seq_item.setPen(QPen(Qt.NoPen))
seq_item.setBrush(QBrush(Qt.black))
seq_path = QPainterPath()
loop_path = self.path()
for i in range(len_BT):
frac = _FRACTION_INSERT_TO_PAD + (i+1)*fraction_arc_len_per_char
pt = loop_path.pointAtPercent(frac)
tang_ang = loop_path.angleAtPercent(frac)
temp_path = QPainterPath()
# 1. draw the text
temp_path.addText(0, 0, font, base_text[i if is_on_top else -i-1])
# 2. center it at the zero point different for top and bottom
# strands
if not is_on_top:
temp_path.translate(0, -seq_font_h - insert_w)
temp_path.translate(QPointF(-seq_font_char_w / 2.,
-2 if is_on_top else seq_font_h))
mat = QTransform()
# 3. rotate it
mat.rotate(-tang_ang + angle_offset)
rotated_path = mat.map(temp_path)
# 4. translate the rotate object to its position on the part
rotated_path.translate(pt)
seq_path.addPath(rotated_path)
# end for
seq_item.setPath(seq_path)
# end if
# end def
### EVENT HANDLERS ###
def mouseDoubleClickEvent(self, event: QGraphicsSceneMouseEvent):
"""Double clicks remove the insertion/skip."""
self._strand.changeInsertion(self._insertion.idx(), 0)
def mousePressEvent(self, event: QGraphicsSceneMouseEvent):
"""This needs to be present for mouseDoubleClickEvent to work."""
class InsertionItem(QGraphicsPathItem):
"""
This is just the shape of the Insert item
"""
def __init__(self, virtualHelixItem, strand, insertion):
super(InsertionItem, self).__init__(virtualHelixItem)
self.hide()
self._strand = strand
self._insertion = insertion
self._seqItem = QGraphicsPathItem(parent=self)
self._isOnTop = isOnTop = virtualHelixItem.isStrandOnTop(strand)
y = 0 if isOnTop else _bw
self.setPos(_bw*insertion.idx(), y)
self.setZValue(styles.ZINSERTHANDLE)
self._initLabel()
self._initClickArea()
self.updateItem()
self.show()
# end def
def _initLabel(self):
"""Display the length of the insertion."""
self._label = label = QGraphicsTextItem("", parent=self)
label.setFont(_font)
label.setTextInteractionFlags(Qt.TextEditorInteraction)
label.inputMethodEvent = self.inputMethodEventHandler
label.keyPressEvent = self.textkeyPressEvent
label.mousePressEvent = self.labelMousePressEvent
label.mouseDoubleClickEvent = self.mouseDoubleClickEvent
label.setTextWidth(-1)
self._label = label
self._seqItem = QGraphicsPathItem(parent=self)
self._seqText = None
self.updateItem()
self.show()
# end def
def _initClickArea(self):
"""docstring for _initClickArea"""
self._clickArea = cA = QGraphicsRectItem(_defaultRect, self)
cA.setPen(_noPen)
cA.mousePressEvent = self.mousePressEvent
cA.mouseDoubleClickEvent = self.mouseDoubleClickEvent
# end def
### PUBLIC SUPPORT METHODS ###
def remove(self):
"""
Called from the following stranditem methods:
strandRemovedSlot
strandInsertionRemovedSlot
refreshInsertionItems
"""
scene = self.scene()
self._label.setTextInteractionFlags(Qt.NoTextInteraction)
self._label.clearFocus()
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._seqItem)
self._seqItem = None
scene.removeItem(self)
self._insertion = None
self._strand = None
# end def
def updateItem(self):
self._updatePath()
self._updateLabel()
self._updateSequenceText()
self._resetPosition()
# end def
### PRIVATE SUPPORT METHODS ###
def _focusOut(self):
lbl = self._label
if lbl == None:
return
cursor = lbl.textCursor()
cursor.clearSelection()
lbl.setTextCursor(cursor)
lbl.clearFocus()
# end def
def _resetPosition(self):
"""
Set the label position based on orientation and text alignment.
"""
lbl = self._label
if lbl == None:
return
txtOffset = lbl.boundingRect().width()/2
insertion = self._insertion
y = -_bw if self._isOnTop else _bw
lbl.setPos(_offset2-txtOffset, y)
if insertion.length() > 0:
lbl.show()
else:
lbl.hide()
# end def
def _updateLabel(self):
self._label.setPlainText("%d" % (self._insertion.length()))
# end def
def _updatePath(self):
strand = self._strand
if strand == None:
self.hide()
return
else:
self.show()
isOnTop = self._isOnTop
if self._insertion.length() > 0:
self.setPen(QPen(QColor(strand.oligo().color()), styles.INSERTWIDTH))
self.setBrush(QBrush(Qt.NoBrush))
self.setPath(_insertPath.getInsert(isOnTop))
else: # insertionSize < 0 (a skip)
self.setPen(_skipPath.getPen())
self.setPath(_skipPath.getSkip())
# end def
def setSequence(self, sequence):
self._seqText = sequence
self._updateSequenceText()
self._seqItem.show()
# end def
def hideSequence(self):
self._seqItem.hide()
# end def
def _updateSequenceText(self):
seqItem = self._seqItem
isOnTop = self._isOnTop
index = self._insertion.idx()
baseText = self._seqText
font = styles.SEQUENCEFONT
seqFontH = styles.SEQUENCEFONTH
insertW = styles.INSERTWIDTH
seqFontCharW = styles.SEQUENCEFONTCHARWIDTH
# draw sequence on the insert
if baseText: # only draw sequences if they exist i.e. not None!
lenBT = len(baseText)
if isOnTop:
angleOffset = 0
else:
angleOffset = 180
if lenBT > 20:
baseText = baseText[:17] + '...'
lenBT = len(baseText)
fractionArclenPerChar = (1.0-2.0*_fractionInsertToPad)/(lenBT+1)
seqItem.setPen(QPen(Qt.NoPen))
seqItem.setBrush(QBrush(Qt.black))
seqPath = QPainterPath()
loopPath = self.path()
for i in range(lenBT):
frac = _fractionInsertToPad + (i+1)*fractionArclenPerChar
pt = loopPath.pointAtPercent(frac)
tangAng = loopPath.angleAtPercent(frac)
tempPath = QPainterPath()
# 1. draw the text
tempPath.addText(0,0, font, baseText[i if isOnTop else -i-1])
# 2. center it at the zero point different for top and bottom
# strands
if not isOnTop:
tempPath.translate(0, -seqFontH - insertW)
tempPath.translate(QPointF(-seqFontCharW/2.,
-2 if isOnTop else seqFontH))
mat = QMatrix3x3()
# 3. rotate it
mat.rotate(-tangAng + angleOffset)
rotatedPath = mat.map(tempPath)
# 4. translate the rotate object to it's position on the part
rotatedPath.translate(pt)
seqPath.addPath(rotatedPath)
# end for
seqItem.setPath(seqPath)
# end if
# end def
### EVENT HANDLERS ###
def mouseDoubleClickEvent(self, event):
"""Double clicks remove the insertion/skip."""
self._strand.changeInsertion(self._insertion.idx(), 0)
def mousePressEvent(self, event):
"""This needs to be present for mouseDoubleClickEvent to work."""
pass
def labelMousePressEvent(self, event):
"""
Pre-selects the text for editing when you click
the label.
"""
lbl = self._label
lbl.setTextInteractionFlags(Qt.TextEditorInteraction)
cursor = lbl.textCursor()
cursor.setPosition(0)
cursor.movePosition(QTextCursor.End, QTextCursor.KeepAnchor)
lbl.setTextCursor(cursor)
def textkeyPressEvent(self, event):
"""
Must intercept invalid input events. Make changes here
"""
a = event.key()
text = event.text()
if a in [Qt.Key_Space, Qt.Key_Tab]:
return
elif a in [Qt.Key_Return, Qt.Key_Enter]:
self.inputMethodEventHandler(event)
return
# elif unicode(text).isalpha():
elif text.isalpha():
return
else:
return QGraphicsTextItem.keyPressEvent(self._label, event)
def inputMethodEventHandler(self, event):
"""
This is run on the label being changed
or losing focus
"""
lbl = self._label
if lbl == None:
return
# test = unicode(lbl.toPlainText())
test = lbl.toPlainText()
try:
insertionSize = int(test)
except:
insertionSize = None
insertion = self._insertion
length = insertion.length()
if insertionSize != None and insertionSize != length:
self._strand.changeInsertion(insertion.idx(), insertionSize)
if insertion.length():
self._resetPosition()
else:
self._updateLabel()
# end if
self._focusOut()
class PreXoverItem(QGraphicsRectItem):
"""A PreXoverItem exists between a single 'from' VirtualHelixItem index
and zero or more 'to' VirtualHelixItem Indices
Attributes:
adapter (:obj:`PropertyWrapperObject`): Description
idx (int): the base index within the virtual helix
is_fwd (bool): is this a forward strand?
prexoveritem_manager (:obj:`PreXoverManager`): Manager of the PreXoverItems
to_vh_id_num (int): Virtual Helix number this Xover point might connect to
"""
FILTER_NAME = "xover"
def __init__(self, from_virtual_helix_item: PathVirtualHelixItemT,
is_fwd: bool, from_index: int, nearby_idxs: List[int],
to_vh_id_num: int, prexoveritem_manager: PreXoverManagerT):
"""Summary
Args:
from_virtual_helix_item: Description
is_fwd: is this a forward strand?
from_index: index of the Virtual Helix this xover is coming from
nearby_idxs:
to_vh_id_num: Virtual Helix number this Xover point might connect to
prexoveritem_manager: Manager of the PreXoverItems
"""
super(QGraphicsRectItem, self).__init__(BASE_RECT,
from_virtual_helix_item)
self.adapter = PropertyWrapperObject(self)
self._tick_marks = QGraphicsPathItem(self)
self._tick_marks.setAcceptHoverEvents(True)
self._bond_item = QGraphicsPathItem(self)
self._bond_item.hide()
self._label = PreXoverLabel(is_fwd, self)
self._path = QGraphicsPathItem()
self.setZValue(styles.ZPREXOVERITEM)
self.setPen(getNoPen())
self.resetItem(from_virtual_helix_item, is_fwd, from_index,
nearby_idxs, to_vh_id_num, prexoveritem_manager)
self._getActiveTool = from_virtual_helix_item.viewroot(
).manager.activeToolGetter
# end def
def shutdown(self):
"""Summary
"""
self.setBrush(getNoBrush())
self.to_vh_id_num = None
self.adapter.resetAnimations()
self.setAcceptHoverEvents(False)
self.hide()
# end def
def resetItem(self, from_virtual_helix_item: PathVirtualHelixItemT,
is_fwd: bool, from_index: int, nearby_idxs: List[int],
to_vh_id_num: int, prexoveritem_manager: PreXoverManagerT):
"""Update this pooled PreXoverItem with current info.
Called by PreXoverManager.
Args:
from_virtual_helix_item: the associated vh_item
is_fwd: True if associated with fwd strand, False if rev strand
from_index: idx of associated vh
nearby_idxs:
to_vh_id_num: id_num of the other vh
prexoveritem_manager: the manager
"""
# to_vh_item = from_virtual_helix_item.partItem().idToVirtualHelixItem(to_vh_id_num)
self.setParentItem(from_virtual_helix_item)
# self.setParentItem(to_vh_item)
self.resetTransform()
self._id_num = from_virtual_helix_item.idNum()
self._model_part = from_virtual_helix_item.part()
self.idx = from_index
self.is_low = False
self.is_high = False
self.nearby_idxs = nearby_idxs
self.is_fwd = is_fwd
self.color = None
self.is3p = None
self.enter_pos = None
self.exit_pos = None
self.to_vh_id_num = to_vh_id_num
self._label_txt = None
self.prexoveritem_manager = prexoveritem_manager
# todo: check here if xover present and disable
result = self.setPathAppearance(from_virtual_helix_item)
if result:
self.setBrush(getNoBrush())
if is_fwd:
self.setPos(from_index * BASE_WIDTH,
-BASE_WIDTH - 0.1 * BASE_WIDTH)
else:
self.setPos(from_index * BASE_WIDTH, 2 * BASE_WIDTH)
self.show()
# label
self._label_txt = lbt = None if to_vh_id_num is None else str(
to_vh_id_num)
self._label.resetItem(is_fwd, self.color)
self.setLabel(text=lbt)
# bond line
bonditem = self._bond_item
bonditem.setPen(
getPenObj(self.color,
styles.PREXOVER_STROKE_WIDTH,
penstyle=Qt.DotLine))
bonditem.hide()
# end def
def setPathAppearance(
self, from_virtual_helix_item: PathVirtualHelixItemT) -> bool:
"""Sets the PainterPath according to the index (low = Left, high = Right)
and strand position (top = Up, bottom = Down).
Args:
from_virtual_helix_item:
"""
part = self._model_part
idx = self.idx
is_fwd = self.is_fwd
id_num = self._id_num
strand_type = StrandEnum.FWD if is_fwd else StrandEnum.REV
# relative position info
bpr = from_virtual_helix_item.getProperty('bases_per_repeat')
self.is_low = is_low = idx + 1 in self.nearby_idxs or (
idx + 1) % bpr in self.nearby_idxs
self.is_high = is_high = idx - 1 in self.nearby_idxs or (
idx - 1) % bpr in self.nearby_idxs
# check strand for xover and color
if part.hasStrandAtIdx(id_num, idx)[strand_type]:
strand = part.getStrand(self.is_fwd, id_num, idx)
if strand.hasXoverAt(idx):
return False
self.color = strand.getColor() if strand is not None else EMPTY_COL
else:
self.color = EMPTY_COL
if is_low and is_high:
path = (_FWD_DUAL_PATH, _REV_DUAL_PATH)[strand_type]
raise NotImplementedError("Dual xovers not yet supported")
elif is_low:
path = (_FWD_LO_PATH, _REV_LO_PATH)[strand_type]
self.is3p = True if is_fwd else False
self.enter_pos = _FWD_LO_PTS[0][-1] if is_fwd else _REV_LO_PTS[0][
-1]
self.exit_pos = _FWD_LO_PTS[0][-1] if is_fwd else _REV_LO_PTS[0][-1]
elif is_high:
path = (_FWD_HI_PATH, _REV_HI_PATH)[strand_type]
self.is3p = False if is_fwd else True
self.enter_pos = _FWD_HI_PTS[0][-1] if is_fwd else _REV_HI_PTS[0][
-1]
self.exit_pos = _FWD_HI_PTS[0][-1] if is_fwd else _REV_HI_PTS[0][-1]
else:
# print("unpaired PreXoverItem at {}[{}]".format(self._id_num, self.idx), self.nearby_idxs)
return False
self._tick_marks.setPen(
getPenObj(self.color,
styles.PREXOVER_STROKE_WIDTH,
capstyle=Qt.FlatCap,
joinstyle=Qt.RoundJoin))
self._tick_marks.setPath(path)
self._tick_marks.show()
return True
# end def
### ACCESSORS ###
def color(self) -> str:
"""The PreXoverItem's color, derived from the associated strand's oligo.
Returns:
str: color in hex code
"""
return self.color
def getInfo(self) -> ABInfoT:
"""
Returns:
Tuple: (from_id_num, is_fwd, from_index, to_vh_id_num)
"""
return (self._id_num, self.is_fwd, self.idx, self.to_vh_id_num)
def destroyItem(self):
"""Removes animation adapter, label, bond_item, and this item from scene.
"""
scene = self.scene()
self.adapter.destroyItem()
if scene:
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._bond_item)
self._bond_item = None
self.adapter.resetAnimations()
self.adapter = None
scene.removeItem(self)
# end defS
### EVENT HANDLERS ###
def hoverEnterEvent(self, event: QGraphicsSceneHoverEvent):
"""Only ``if enableActive(True)`` is called hover and key events disabled
by default
Args:
event: the hover event
"""
if self._getActiveTool().methodPrefix() != "selectTool":
return
self.setFocus(Qt.MouseFocusReason)
self.prexoveritem_manager.updateModelActiveBaseInfo(self.getInfo())
self.setActiveHovered(True)
status_string = "%d[%d]" % (self._id_num, self.idx)
self.parentItem().window().statusBar().showMessage(status_string)
return QGraphicsItem.hoverEnterEvent(self, event)
# end def
def hoverLeaveEvent(self, event: QGraphicsSceneHoverEvent):
"""Summary
Args:
event (QGraphicsSceneHoverEvent): the hover event
"""
self.prexoveritem_manager.updateModelActiveBaseInfo(None)
self.setActiveHovered(False)
self.clearFocus()
self.parentItem().window().statusBar().showMessage("")
return QGraphicsItem.hoverLeaveEvent(self, event)
# end def
def mousePressEvent(self, event: QGraphicsSceneMouseEvent):
"""TODO: NEED TO ADD FILTER FOR A CLICK ON THE 3' MOST END OF THE XOVER
TO DISALLOW OR HANDLE DIFFERENTLY
"""
viewroot = self.parentItem().viewroot()
current_filter_set = viewroot.selectionFilterSet()
if (self._getActiveTool().methodPrefix() != "selectTool"
or (self.FILTER_NAME not in current_filter_set)):
return
part = self._model_part
is_fwd = self.is_fwd
if self.is3p:
strand5p = part.getStrand(is_fwd, self._id_num, self.idx)
strand3p = part.getStrand(not is_fwd, self.to_vh_id_num, self.idx)
else:
strand5p = part.getStrand(not is_fwd, self.to_vh_id_num, self.idx)
strand3p = part.getStrand(is_fwd, self._id_num, self.idx)
if strand5p is None or strand3p is None:
return
# print(strand3p, strand5p)
part.createXover(strand5p, self.idx, strand3p, self.idx)
nkey = (self.to_vh_id_num, not is_fwd, self.idx)
npxi = self.prexoveritem_manager.neighbor_prexover_items.get(
nkey, None)
if npxi:
npxi.shutdown()
self.shutdown()
part.setActiveVirtualHelix(self._id_num, is_fwd, self.idx)
# self.prexoveritem_manager.handlePreXoverClick(self)
def keyPressEvent(self, event: QKeyEvent):
"""
Args:
event: Description
"""
self.prexoveritem_manager.handlePreXoverKeyPress(event.key())
# end def
### PUBLIC SUPPORT METHODS ###
def setLabel(self, text: str = None, outline: bool = False):
"""Summary
Args:
text: Default is ``None``
outline: Default is ``False``
"""
if text:
self._label.setTextAndStyle(text=text, outline=outline)
self._label.show()
else:
self._label.hide()
# end def
def animate(self, item: QGraphicsItem, property_name: str, duration: int,
start_value, end_value):
"""
Args:
item: Description
property_name: Description
duration: Description
start_value (QVariant): Description
end_value (QVariant): Description
"""
b_name = property_name.encode('ascii')
anim = item.adapter.getRef(property_name)
if anim is None:
anim = QPropertyAnimation(item.adapter, b_name)
item.adapter.saveRef(property_name, anim)
anim.setDuration(duration)
anim.setStartValue(start_value)
anim.setEndValue(end_value)
anim.start()
# end def
def setActiveHovered(self, is_active: bool):
"""Rotate phosphate Triangle if `self.to_vh_id_num` is not `None`
Args:
is_active: whether or not the PreXoverItem is parented to the
active VirtualHelixItem
"""
pass
# end def
def enableActive(self, is_active: bool, to_vh_id_num: int = None):
"""Call on PreXoverItems created on the active VirtualHelixItem
Args:
is_active: Description
to_vh_id_num: Default is ``None``
"""
if is_active:
self.to_vh_id_num = to_vh_id_num
self.setAcceptHoverEvents(True)
if to_vh_id_num is None:
self.setLabel(text=None)
else:
self.setLabel(text=str(to_vh_id_num))
else:
self.setBrush(getNoBrush())
self.setAcceptHoverEvents(False)
def activateNeighbor(self,
active_prexoveritem: 'PreXoverItem',
shortcut: str = None):
"""Draws a quad line starting from the item5p to the item3p.
To be called with whatever the active_prexoveritem is for the parts
`active_base`.
Args:
active_prexoveritem: Description
shortcut: Default is None
"""
if self._getActiveTool().methodPrefix() != "selectTool":
return
if self.is3p and not active_prexoveritem.is3p:
item5p = active_prexoveritem
item3p = self
elif not self.is3p and active_prexoveritem.is3p:
item5p = self
item3p = active_prexoveritem
else:
return
same_parity = self.is_fwd == active_prexoveritem.is_fwd
p1 = item5p._tick_marks.scenePos() + item5p.exit_pos
p2 = item3p._tick_marks.scenePos() + item3p.exit_pos
c1 = QPointF()
# case 1: same parity
if same_parity:
dy = abs(p2.y() - p1.y())
c1.setX(p1.x() + _X_SCALE * dy)
c1.setY(0.5 * (p1.y() + p2.y()))
# case 2: different parity
else:
if item3p.is_fwd:
c1.setX(p1.x() - _X_SCALE * abs(p2.y() - p1.y()))
else:
c1.setX(p1.x() + _X_SCALE * abs(p2.y() - p1.y()))
c1.setY(0.5 * (p1.y() + p2.y()))
pp = QPainterPath()
pp.moveTo(self._tick_marks.mapFromScene(p1))
pp.quadTo(self._tick_marks.mapFromScene(c1),
self._tick_marks.mapFromScene(p2))
# pp.cubicTo(c1, c2, self._tick_marks.mapFromScene(p2))
self._bond_item.setPath(pp)
self._bond_item.show()
# end def
def deactivateNeighbor(self):
"""Summary
"""
if self.isVisible():
self._bond_item.hide()
self.setLabel(text=self._label_txt)
class PreXoverItem(QGraphicsRectItem):
"""A PreXoverItem exists between a single 'from' VirtualHelixItem index
and zero or more 'to' VirtualHelixItem Indices
Attributes:
adapter (:obj:`PropertyWrapperObject`): Description
idx (int): the base index within the virtual helix
is_fwd (bool): is this a forward strand?
prexoveritem_manager (:obj:`PreXoverManager`): Manager of the PreXoverItems
to_vh_id_num (int): Virtual Helix number this Xover point might connect to
"""
FILTER_NAME = "xover"
def __init__(self, from_virtual_helix_item: PathVirtualHelixItemT,
is_fwd: bool,
from_index: int,
nearby_idxs: List[int],
to_vh_id_num: int,
prexoveritem_manager: PreXoverManagerT):
"""Summary
Args:
from_virtual_helix_item: Description
is_fwd: is this a forward strand?
from_index: index of the Virtual Helix this xover is coming from
nearby_idxs:
to_vh_id_num: Virtual Helix number this Xover point might connect to
prexoveritem_manager: Manager of the PreXoverItems
"""
super(QGraphicsRectItem, self).__init__(BASE_RECT, from_virtual_helix_item)
self.adapter = PropertyWrapperObject(self)
self._tick_marks = QGraphicsPathItem(self)
self._tick_marks.setAcceptHoverEvents(True)
self._bond_item = QGraphicsPathItem(self)
self._bond_item.hide()
self._label = PreXoverLabel(is_fwd, self)
self._path = QGraphicsPathItem()
self.setZValue(styles.ZPREXOVERITEM)
self.setPen(getNoPen())
self.resetItem(from_virtual_helix_item, is_fwd, from_index, nearby_idxs, to_vh_id_num, prexoveritem_manager)
self._getActiveTool = from_virtual_helix_item.viewroot().manager.activeToolGetter
# end def
def shutdown(self):
"""Summary
"""
self.setBrush(getNoBrush())
self.to_vh_id_num = None
self.adapter.resetAnimations()
self.setAcceptHoverEvents(False)
self.hide()
# end def
def resetItem(self, from_virtual_helix_item: PathVirtualHelixItemT,
is_fwd: bool,
from_index: int,
nearby_idxs: List[int],
to_vh_id_num: int,
prexoveritem_manager: PreXoverManagerT):
"""Update this pooled PreXoverItem with current info.
Called by PreXoverManager.
Args:
from_virtual_helix_item: the associated vh_item
is_fwd: True if associated with fwd strand, False if rev strand
from_index: idx of associated vh
nearby_idxs:
to_vh_id_num: id_num of the other vh
prexoveritem_manager: the manager
"""
# to_vh_item = from_virtual_helix_item.partItem().idToVirtualHelixItem(to_vh_id_num)
self.setParentItem(from_virtual_helix_item)
# self.setParentItem(to_vh_item)
self.resetTransform()
self._id_num = from_virtual_helix_item.idNum()
self._model_part = from_virtual_helix_item.part()
self.idx = from_index
self.is_low = False
self.is_high = False
self.nearby_idxs = nearby_idxs
self.is_fwd = is_fwd
self.color = None
self.is3p = None
self.enter_pos = None
self.exit_pos = None
self.to_vh_id_num = to_vh_id_num
self._label_txt = None
self.prexoveritem_manager = prexoveritem_manager
# todo: check here if xover present and disable
result = self.setPathAppearance(from_virtual_helix_item)
if result:
self.setBrush(getNoBrush())
if is_fwd:
self.setPos(from_index*BASE_WIDTH, -BASE_WIDTH - 0.1*BASE_WIDTH)
else:
self.setPos(from_index*BASE_WIDTH, 2*BASE_WIDTH)
self.show()
# label
self._label_txt = lbt = None if to_vh_id_num is None else str(to_vh_id_num)
self._label.resetItem(is_fwd, self.color)
self.setLabel(text=lbt)
# bond line
bonditem = self._bond_item
bonditem.setPen(getPenObj( self.color,
styles.PREXOVER_STROKE_WIDTH,
penstyle=Qt.DotLine))
bonditem.hide()
# end def
def setPathAppearance(self, from_virtual_helix_item: PathVirtualHelixItemT) -> bool:
"""Sets the PainterPath according to the index (low = Left, high = Right)
and strand position (top = Up, bottom = Down).
Args:
from_virtual_helix_item:
"""
part = self._model_part
idx = self.idx
is_fwd = self.is_fwd
id_num = self._id_num
strand_type = StrandEnum.FWD if is_fwd else StrandEnum.REV
# relative position info
bpr = from_virtual_helix_item.getProperty('bases_per_repeat')
self.is_low = is_low = idx+1 in self.nearby_idxs or (idx+1) % bpr in self.nearby_idxs
self.is_high = is_high = idx-1 in self.nearby_idxs or (idx-1) % bpr in self.nearby_idxs
# check strand for xover and color
if part.hasStrandAtIdx(id_num, idx)[strand_type]:
strand = part.getStrand(self.is_fwd, id_num, idx)
if strand.hasXoverAt(idx):
return False
self.color = strand.getColor() if strand is not None else EMPTY_COL
else:
self.color = EMPTY_COL
if is_low and is_high:
path = (_FWD_DUAL_PATH, _REV_DUAL_PATH)[strand_type]
raise NotImplementedError("Dual xovers not yet supported")
elif is_low:
path = (_FWD_LO_PATH, _REV_LO_PATH)[strand_type]
self.is3p = True if is_fwd else False
self.enter_pos = _FWD_LO_PTS[0][-1] if is_fwd else _REV_LO_PTS[0][-1]
self.exit_pos = _FWD_LO_PTS[0][-1] if is_fwd else _REV_LO_PTS[0][-1]
elif is_high:
path = (_FWD_HI_PATH, _REV_HI_PATH)[strand_type]
self.is3p = False if is_fwd else True
self.enter_pos = _FWD_HI_PTS[0][-1] if is_fwd else _REV_HI_PTS[0][-1]
self.exit_pos = _FWD_HI_PTS[0][-1] if is_fwd else _REV_HI_PTS[0][-1]
else:
# print("unpaired PreXoverItem at {}[{}]".format(self._id_num, self.idx), self.nearby_idxs)
return False
self._tick_marks.setPen(getPenObj( self.color,
styles.PREXOVER_STROKE_WIDTH,
capstyle=Qt.FlatCap,
joinstyle=Qt.RoundJoin))
self._tick_marks.setPath(path)
self._tick_marks.show()
return True
# end def
### ACCESSORS ###
def color(self) -> str:
"""The PreXoverItem's color, derived from the associated strand's oligo.
Returns:
str: color in hex code
"""
return self.color
def getInfo(self) -> ABInfoT:
"""
Returns:
Tuple: (from_id_num, is_fwd, from_index, to_vh_id_num)
"""
return (self._id_num, self.is_fwd, self.idx, self.to_vh_id_num)
def destroyItem(self):
"""Removes animation adapter, label, bond_item, and this item from scene.
"""
scene = self.scene()
self.adapter.destroyItem()
if scene:
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._bond_item)
self._bond_item = None
self.adapter.resetAnimations()
self.adapter = None
scene.removeItem(self)
# end defS
### EVENT HANDLERS ###
def hoverEnterEvent(self, event: QGraphicsSceneHoverEvent):
"""Only ``if enableActive(True)`` is called hover and key events disabled
by default
Args:
event: the hover event
"""
if self._getActiveTool().methodPrefix() != "selectTool":
return
self.setFocus(Qt.MouseFocusReason)
self.prexoveritem_manager.updateModelActiveBaseInfo(self.getInfo())
self.setActiveHovered(True)
status_string = "%d[%d]" % (self._id_num, self.idx)
self.parentItem().window().statusBar().showMessage(status_string)
return QGraphicsItem.hoverEnterEvent(self, event)
# end def
def hoverLeaveEvent(self, event: QGraphicsSceneHoverEvent):
"""Summary
Args:
event (QGraphicsSceneHoverEvent): the hover event
"""
self.prexoveritem_manager.updateModelActiveBaseInfo(None)
self.setActiveHovered(False)
self.clearFocus()
self.parentItem().window().statusBar().showMessage("")
return QGraphicsItem.hoverLeaveEvent(self, event)
# end def
def mousePressEvent(self, event: QGraphicsSceneMouseEvent):
"""TODO: NEED TO ADD FILTER FOR A CLICK ON THE 3' MOST END OF THE XOVER
TO DISALLOW OR HANDLE DIFFERENTLY
"""
viewroot = self.parentItem().viewroot()
current_filter_set = viewroot.selectionFilterSet()
if (self._getActiveTool().methodPrefix() != "selectTool" or
(self.FILTER_NAME not in current_filter_set) ):
return
part = self._model_part
is_fwd = self.is_fwd
if self.is3p:
strand5p = part.getStrand(is_fwd, self._id_num, self.idx)
strand3p = part.getStrand(not is_fwd, self.to_vh_id_num, self.idx)
else:
strand5p = part.getStrand(not is_fwd, self.to_vh_id_num, self.idx)
strand3p = part.getStrand(is_fwd, self._id_num, self.idx)
if strand5p is None or strand3p is None:
return
# print(strand3p, strand5p)
part.createXover(strand5p, self.idx, strand3p, self.idx)
nkey = (self.to_vh_id_num, not is_fwd, self.idx)
npxi = self.prexoveritem_manager.neighbor_prexover_items.get(nkey, None)
if npxi:
npxi.shutdown()
self.shutdown()
part.setActiveVirtualHelix(self._id_num, is_fwd, self.idx)
# self.prexoveritem_manager.handlePreXoverClick(self)
def keyPressEvent(self, event: QKeyEvent):
"""
Args:
event: Description
"""
self.prexoveritem_manager.handlePreXoverKeyPress(event.key())
# end def
### PUBLIC SUPPORT METHODS ###
def setLabel(self, text: str = None, outline: bool = False):
"""Summary
Args:
text: Default is ``None``
outline: Default is ``False``
"""
if text:
self._label.setTextAndStyle(text=text, outline=outline)
self._label.show()
else:
self._label.hide()
# end def
def animate(self, item: QGraphicsItem,
property_name: str, duration: int,
start_value, end_value):
"""
Args:
item: Description
property_name: Description
duration: Description
start_value (QVariant): Description
end_value (QVariant): Description
"""
b_name = property_name.encode('ascii')
anim = item.adapter.getRef(property_name)
if anim is None:
anim = QPropertyAnimation(item.adapter, b_name)
item.adapter.saveRef(property_name, anim)
anim.setDuration(duration)
anim.setStartValue(start_value)
anim.setEndValue(end_value)
anim.start()
# end def
def setActiveHovered(self, is_active: bool):
"""Rotate phosphate Triangle if `self.to_vh_id_num` is not `None`
Args:
is_active: whether or not the PreXoverItem is parented to the
active VirtualHelixItem
"""
pass
# end def
def enableActive(self, is_active: bool, to_vh_id_num: int = None):
"""Call on PreXoverItems created on the active VirtualHelixItem
Args:
is_active: Description
to_vh_id_num: Default is ``None``
"""
if is_active:
self.to_vh_id_num = to_vh_id_num
self.setAcceptHoverEvents(True)
if to_vh_id_num is None:
self.setLabel(text=None)
else:
self.setLabel(text=str(to_vh_id_num))
else:
self.setBrush(getNoBrush())
self.setAcceptHoverEvents(False)
def activateNeighbor(self, active_prexoveritem: 'PreXoverItem',
shortcut: str = None):
"""Draws a quad line starting from the item5p to the item3p.
To be called with whatever the active_prexoveritem is for the parts
`active_base`.
Args:
active_prexoveritem: Description
shortcut: Default is None
"""
if self._getActiveTool().methodPrefix() != "selectTool":
return
if self.is3p and not active_prexoveritem.is3p:
item5p = active_prexoveritem
item3p = self
elif not self.is3p and active_prexoveritem.is3p:
item5p = self
item3p = active_prexoveritem
else:
return
same_parity = self.is_fwd == active_prexoveritem.is_fwd
p1 = item5p._tick_marks.scenePos() + item5p.exit_pos
p2 = item3p._tick_marks.scenePos() + item3p.exit_pos
c1 = QPointF()
# case 1: same parity
if same_parity:
dy = abs(p2.y() - p1.y())
c1.setX(p1.x() + _X_SCALE * dy)
c1.setY(0.5 * (p1.y() + p2.y()))
# case 2: different parity
else:
if item3p.is_fwd:
c1.setX(p1.x() - _X_SCALE * abs(p2.y() - p1.y()))
else:
c1.setX(p1.x() + _X_SCALE * abs(p2.y() - p1.y()))
c1.setY(0.5 * (p1.y() + p2.y()))
pp = QPainterPath()
pp.moveTo(self._tick_marks.mapFromScene(p1))
pp.quadTo(self._tick_marks.mapFromScene(c1),
self._tick_marks.mapFromScene(p2))
# pp.cubicTo(c1, c2, self._tick_marks.mapFromScene(p2))
self._bond_item.setPath(pp)
self._bond_item.show()
# end def
def deactivateNeighbor(self):
"""Summary
"""
if self.isVisible():
self._bond_item.hide()
self.setLabel(text=self._label_txt)
class ForcedXoverNode3(QGraphicsRectItem):
"""
This is a QGraphicsRectItem to allow actions and also a
QGraphicsSimpleTextItem to allow a label to be drawn
"""
def __init__(self, virtual_helix_item, xover_item, strand3p, idx):
super(ForcedXoverNode3, self).__init__(virtual_helix_item)
self._vhi = virtual_helix_item
self._xover_item = xover_item
self._idx = idx
self._is_on_top = virtual_helix_item.isStrandOnTop(strand3p)
self._is_drawn_5_to_3 = strand3p.strandSet().isDrawn5to3()
self._strand_type = strand3p.strandSet().strandType()
self._partner_virtual_helix = virtual_helix_item
self._blank_thing = QGraphicsRectItem(_blankRect, self)
self._blank_thing.setBrush(QBrush(Qt.white))
self._path_thing = QGraphicsPathItem(self)
self.configurePath()
self.setPen(_NO_PEN)
self._label = None
self.setPen(_NO_PEN)
self.setBrush(_NO_BRUSH)
self.setRect(_rect)
self.setZValue(styles.ZENDPOINTITEM + 1)
# end def
def updateForFloatFromVHI(self, virtual_helix_item, strand_type, idx_x,
idx_y):
"""
"""
self._vhi = virtual_helix_item
self.setParentItem(virtual_helix_item)
self._strand_type = strand_type
self._idx = idx_x
self._is_on_top = self._is_drawn_5_to_3 = True if idx_y == 0 else False
self.updatePositionAndAppearance(is_from_strand=False)
# end def
def updateForFloatFromStrand(self, virtual_helix_item, strand3p, idx):
"""
"""
self._vhi = virtual_helix_item
self._strand = strand3p
self.setParentItem(virtual_helix_item)
self._idx = idx
self._is_on_top = virtual_helix_item.isStrandOnTop(strand3p)
self._is_drawn_5_to_3 = strand3p.strandSet().isDrawn5to3()
self._strand_type = strand3p.strandSet().strandType()
self.updatePositionAndAppearance()
# end def
def strandType(self):
return self._strand_type
# end def
def configurePath(self):
self._path_thing.setBrush(QBrush(styles.RED_STROKE))
path = PPR3 if self._is_drawn_5_to_3 else PPL3
offset = -_BASE_WIDTH if self._is_drawn_5_to_3 else _BASE_WIDTH
self._path_thing.setPath(path)
self._path_thing.setPos(offset, 0)
offset = -_BASE_WIDTH if self._is_drawn_5_to_3 else 0
self._blank_thing.setPos(offset, 0)
self._blank_thing.show()
self._path_thing.show()
# end def
def refreshXover(self):
self._xover_item.refreshXover()
# end def
def setPartnerVirtualHelix(self, virtual_helix_item):
self._partner_virtual_helix = virtual_helix_item
# end def
def idx(self):
return self._idx
# end def
def virtualHelixItem(self):
return self._vhi
# end def
def point(self):
return self._vhi.upperLeftCornerOfBaseType(self._idx,
self._strand_type)
# end def
def floatPoint(self):
pt = self.pos()
return pt.x(), pt.y()
# end def
def isOnTop(self):
return self._is_on_top
# end def
def isDrawn5to3(self):
return self._is_drawn_5_to_3
# end def
def updatePositionAndAppearance(self, is_from_strand=True):
"""
Sets position by asking the VirtualHelixItem
Sets appearance by choosing among pre-defined painterpaths (from
normalstrandgraphicsitem) depending on drawing direction.
"""
self.setPos(*self.point())
n5 = self._xover_item._node5
if is_from_strand:
from_strand, from_idx = (n5._strand,
n5._idx) if n5 != self else (None, None)
if self._strand.canInstallXoverAt(self._idx, from_strand,
from_idx):
self.configurePath()
# We can only expose a 5' end. But on which side?
is_left = True if self._is_drawn_5_to_3 else False
self._updateLabel(is_left)
else:
self.hideItems()
else:
self.hideItems()
# end def
def updateConnectivity(self):
is_left = True if self._is_drawn_5_to_3 else False
self._updateLabel(is_left)
# end def
def remove(self):
"""
Clean up this joint
"""
scene = self.scene()
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._path_thing)
self._path_thing = None
scene.removeItem(self._blank_thing)
self._blank_thing = None
scene.removeItem(self)
# end def
def _updateLabel(self, is_left):
"""
Called by updatePositionAndAppearance during init, or later by
updateConnectivity. Updates drawing and position of the label.
"""
lbl = self._label
if self._idx != None:
bw = _BASE_WIDTH
num = self._partner_virtual_helix.number()
tBR = _FM.tightBoundingRect(str(num))
half_label_h = tBR.height() / 2.0
half_label_w = tBR.width() / 2.0
# determine x and y positions
label_x = bw / 2.0 - half_label_w
if self._is_on_top:
label_y = -0.25 * half_label_h - 0.5 - 0.5 * bw
else:
label_y = 2 * half_label_h + 0.5 + 0.5 * bw
# adjust x for left vs right
label_x_offset = 0.25 * bw if is_left else -0.25 * bw
label_x += label_x_offset
# adjust x for numeral 1
if num == 1: label_x -= half_label_w / 2.0
# create text item
if lbl == None:
lbl = QGraphicsSimpleTextItem(str(num), self)
lbl.setPos(label_x, label_y)
lbl.setBrush(_ENAB_BRUSH)
lbl.setFont(_TO_HELIX_NUM_FONT)
self._label = lbl
lbl.setText(str(self._partner_virtual_helix.number()))
lbl.show()
# end if
# end def
def hideItems(self):
if self._label:
self._label.hide()
if self._blank_thing:
self._path_thing.hide()
if self._blank_thing:
self._blank_thing.hide()
class InsertionItem(QGraphicsPathItem):
"""
This is just the shape of the Insert item
"""
def __init__(self, virtualHelixItem, strand, insertion):
super(InsertionItem, self).__init__(virtualHelixItem)
self.hide()
self._strand = strand
self._insertion = insertion
self._seqItem = QGraphicsPathItem(parent=self)
self._isOnTop = isOnTop = virtualHelixItem.isStrandOnTop(strand)
y = 0 if isOnTop else _bw
self.setPos(_bw * insertion.idx(), y)
self.setZValue(styles.ZINSERTHANDLE)
self._initLabel()
self._initClickArea()
self.updateItem()
self.show()
# end def
def _initLabel(self):
"""Display the length of the insertion."""
self._label = label = QGraphicsTextItem("", parent=self)
label.setFont(_font)
label.setTextInteractionFlags(Qt.TextEditorInteraction)
label.inputMethodEvent = self.inputMethodEventHandler
label.keyPressEvent = self.textkeyPressEvent
label.mousePressEvent = self.labelMousePressEvent
label.mouseDoubleClickEvent = self.mouseDoubleClickEvent
label.setTextWidth(-1)
self._label = label
self._seqItem = QGraphicsPathItem(parent=self)
self._seqText = None
self.updateItem()
self.show()
# end def
def _initClickArea(self):
"""docstring for _initClickArea"""
self._clickArea = cA = QGraphicsRectItem(_defaultRect, self)
cA.setPen(_noPen)
cA.mousePressEvent = self.mousePressEvent
cA.mouseDoubleClickEvent = self.mouseDoubleClickEvent
# end def
### PUBLIC SUPPORT METHODS ###
def remove(self):
"""
Called from the following stranditem methods:
strandRemovedSlot
strandInsertionRemovedSlot
refreshInsertionItems
"""
scene = self.scene()
self._label.setTextInteractionFlags(Qt.NoTextInteraction)
self._label.clearFocus()
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._seqItem)
self._seqItem = None
scene.removeItem(self)
self._insertion = None
self._strand = None
# end def
def updateItem(self):
self._updatePath()
self._updateLabel()
self._updateSequenceText()
self._resetPosition()
# end def
### PRIVATE SUPPORT METHODS ###
def _focusOut(self):
lbl = self._label
if lbl == None:
return
cursor = lbl.textCursor()
cursor.clearSelection()
lbl.setTextCursor(cursor)
lbl.clearFocus()
# end def
def _resetPosition(self):
"""
Set the label position based on orientation and text alignment.
"""
lbl = self._label
if lbl == None:
return
txtOffset = lbl.boundingRect().width() / 2
insertion = self._insertion
y = -_bw if self._isOnTop else _bw
lbl.setPos(_offset2 - txtOffset, y)
if insertion.length() > 0:
lbl.show()
else:
lbl.hide()
# end def
def _updateLabel(self):
self._label.setPlainText("%d" % (self._insertion.length()))
# end def
def _updatePath(self):
strand = self._strand
if strand == None:
self.hide()
return
else:
self.show()
isOnTop = self._isOnTop
if self._insertion.length() > 0:
self.setPen(
QPen(QColor(strand.oligo().color()), styles.INSERTWIDTH))
self.setBrush(QBrush(Qt.NoBrush))
self.setPath(_insertPath.getInsert(isOnTop))
else: # insertionSize < 0 (a skip)
self.setPen(_skipPath.getPen())
self.setPath(_skipPath.getSkip())
# end def
def setSequence(self, sequence):
self._seqText = sequence
self._updateSequenceText()
self._seqItem.show()
# end def
def hideSequence(self):
self._seqItem.hide()
# end def
def _updateSequenceText(self):
seqItem = self._seqItem
isOnTop = self._isOnTop
index = self._insertion.idx()
baseText = self._seqText
font = styles.SEQUENCEFONT
seqFontH = styles.SEQUENCEFONTH
insertW = styles.INSERTWIDTH
seqFontCharW = styles.SEQUENCEFONTCHARWIDTH
# draw sequence on the insert
if baseText: # only draw sequences if they exist i.e. not None!
lenBT = len(baseText)
if isOnTop:
angleOffset = 0
else:
angleOffset = 180
if lenBT > 20:
baseText = baseText[:17] + '...'
lenBT = len(baseText)
fractionArclenPerChar = (1.0 -
2.0 * _fractionInsertToPad) / (lenBT + 1)
seqItem.setPen(QPen(Qt.NoPen))
seqItem.setBrush(QBrush(Qt.black))
seqPath = QPainterPath()
loopPath = self.path()
for i in range(lenBT):
frac = _fractionInsertToPad + (i + 1) * fractionArclenPerChar
pt = loopPath.pointAtPercent(frac)
tangAng = loopPath.angleAtPercent(frac)
tempPath = QPainterPath()
# 1. draw the text
tempPath.addText(0, 0, font,
baseText[i if isOnTop else -i - 1])
# 2. center it at the zero point different for top and bottom
# strands
if not isOnTop:
tempPath.translate(0, -seqFontH - insertW)
tempPath.translate(
QPointF(-seqFontCharW / 2., -2 if isOnTop else seqFontH))
mat = QMatrix3x3()
# 3. rotate it
mat.rotate(-tangAng + angleOffset)
rotatedPath = mat.map(tempPath)
# 4. translate the rotate object to it's position on the part
rotatedPath.translate(pt)
seqPath.addPath(rotatedPath)
# end for
seqItem.setPath(seqPath)
# end if
# end def
### EVENT HANDLERS ###
def mouseDoubleClickEvent(self, event):
"""Double clicks remove the insertion/skip."""
self._strand.changeInsertion(self._insertion.idx(), 0)
def mousePressEvent(self, event):
"""This needs to be present for mouseDoubleClickEvent to work."""
pass
def labelMousePressEvent(self, event):
"""
Pre-selects the text for editing when you click
the label.
"""
lbl = self._label
lbl.setTextInteractionFlags(Qt.TextEditorInteraction)
cursor = lbl.textCursor()
cursor.setPosition(0)
cursor.movePosition(QTextCursor.End, QTextCursor.KeepAnchor)
lbl.setTextCursor(cursor)
def textkeyPressEvent(self, event):
"""
Must intercept invalid input events. Make changes here
"""
a = event.key()
text = event.text()
if a in [Qt.Key_Space, Qt.Key_Tab]:
return
elif a in [Qt.Key_Return, Qt.Key_Enter]:
self.inputMethodEventHandler(event)
return
# elif unicode(text).isalpha():
elif text.isalpha():
return
else:
return QGraphicsTextItem.keyPressEvent(self._label, event)
def inputMethodEventHandler(self, event):
"""
This is run on the label being changed
or losing focus
"""
lbl = self._label
if lbl == None:
return
# test = unicode(lbl.toPlainText())
test = lbl.toPlainText()
try:
insertionSize = int(test)
except:
insertionSize = None
insertion = self._insertion
length = insertion.length()
if insertionSize != None and insertionSize != length:
self._strand.changeInsertion(insertion.idx(), insertionSize)
if insertion.length():
self._resetPosition()
else:
self._updateLabel()
# end if
self._focusOut()
class RCircleSegment(QObject):
def __init__(self,
radius: float,
center_x: float,
center_y: float,
start_angle: float,
end_angle: float,
clockwise,
line_width: float,
line_color=Qt.black,
fill_color=Qt.transparent):
super().__init__()
# The supporting rectangle
if end_angle < start_angle:
end_angle += 2 * math.pi
start_angle = -start_angle
end_angle = -end_angle
shift = end_angle - start_angle
if clockwise:
shift = -shift - 2 * math.pi
x, y = center_x - radius, center_y - radius
self.rect = QRectF(x, y, 2 * radius, 2 * radius)
# The underlying QGraphicsPathItem
self.painter_path = QPainterPath(
QPointF(center_x + math.cos(start_angle) * radius,
center_y - math.sin(start_angle) * radius))
self.painter_path.arcTo(self.rect, math.degrees(start_angle),
math.degrees(shift))
self.path = QGraphicsPathItem(self.painter_path)
self.path.setBrush(QtGui.QBrush(fill_color))
pen = QPen()
pen.setWidthF(line_width)
pen.setColor(line_color)
self.path.setPen(pen)
self._visible = 1
# def x(self):
# return self._pos.x()
#
# def y(self):
# return self._pos.y()
#
# # The following functions are for animation support
#
# @pyqtProperty(QPointF)
# def pos(self):
# return self._pos
#
# @pos.setter
# def pos(self, value):
# self.rect = QRectF(value.x() - self._radius, value.y() - self._radius, 2 * self._radius, 2 * self._radius)
# self.path.setRect(self.rect)
# self._pos = value
#
@pyqtProperty(int)
def visible(self):
return self._visible
@visible.setter
def visible(self, value):
if (value > 0):
self.path.show()
else:
self.path.hide()
self._visible = value
class PreXoverItem(QGraphicsRectItem):
"""A PreXoverItem exists between a single 'from' VirtualHelixItem index
and zero or more 'to' VirtualHelixItem Indices
Attributes:
adapter (TYPE): Description
idx (int): the base index within the virtual helix
is_fwd (TYPE): Description
prexoveritem_manager (TYPE): Description
to_vh_id_num (TYPE): Description
"""
def __init__(self, from_virtual_helix_item, is_fwd, from_index, nearby_idxs,
to_vh_id_num, prexoveritem_manager):
"""Summary
Args:
from_virtual_helix_item (cadnano.views.pathview.virtualhelixitem.VirtualHelixItem): Description
is_fwd (TYPE): Description
from_index (TYPE): Description
to_vh_id_num (TYPE): Description
prexoveritem_manager (TYPE): Description
"""
super(QGraphicsRectItem, self).__init__(BASE_RECT, from_virtual_helix_item)
self.adapter = PropertyWrapperObject(self)
self._tick_marks = QGraphicsPathItem(self)
self._tick_marks.setAcceptHoverEvents(True)
self._bond_item = QGraphicsPathItem(self)
self._bond_item.hide()
self._label = PreXoverLabel(is_fwd, self)
self._path = QGraphicsPathItem()
self.setZValue(styles.ZPREXOVERITEM)
self.setPen(getNoPen())
self.resetItem(from_virtual_helix_item, is_fwd, from_index, nearby_idxs, to_vh_id_num, prexoveritem_manager)
# end def
def shutdown(self):
"""Summary
Returns:
TYPE: Description
"""
self.setBrush(getNoBrush())
self.to_vh_id_num = None
self.adapter.resetAnimations()
self.setAcceptHoverEvents(False)
self.hide()
# end def
def resetItem(self, from_virtual_helix_item, is_fwd, from_index, nearby_idxs,
to_vh_id_num, prexoveritem_manager):
"""Update this pooled PreXoverItem with current info.
Called by PreXoverManager.
Args:
from_virtual_helix_item (cadnano.views.pathview.virtualhelixitem.VirtualHelixItem): the associated vh_item
is_fwd (bool): True if associated with fwd strand, False if rev strand
from_index (int): idx of associated vh
to_vh_id_num (int): id_num of the other vh
prexoveritem_manager (cadnano.views.pathview.prexoermanager.PreXoverManager): the manager
"""
self.setParentItem(from_virtual_helix_item)
self.resetTransform()
self._id_num = from_virtual_helix_item.idNum()
self._model_vh = from_virtual_helix_item.cnModel()
self.idx = from_index
self.is_low = False
self.is_high = False
self.nearby_idxs = nearby_idxs
self.is_fwd = is_fwd
self.color = None
self.is3p = None
self.enter_pos = None
self.exit_pos = None
self.to_vh_id_num = to_vh_id_num
self.prexoveritem_manager = prexoveritem_manager
# todo: check here if xover present and disable
result = self.setPathAppearance(from_virtual_helix_item)
if result:
self.setBrush(getNoBrush())
if is_fwd:
self.setPos(from_index*BASE_WIDTH, -BASE_WIDTH)
else:
self.setPos(from_index*BASE_WIDTH, 2*BASE_WIDTH)
self.show()
# label
self._label_txt = lbt = None if to_vh_id_num is None else str(to_vh_id_num)
self.setLabel(text=lbt)
self._label.resetItem(is_fwd, self.color)
# bond line
bonditem = self._bond_item
bonditem.setPen(getPenObj(self.color, styles.PREXOVER_STROKE_WIDTH))
bonditem.hide()
# end def
def setPathAppearance(self, from_virtual_helix_item):
"""
Sets the PainterPath according to the index (low = Left, high = Right)
and strand position (top = Up, bottom = Down).
"""
part = self._model_vh.part()
idx = self.idx
is_fwd = self.is_fwd
id_num = self._id_num
strand_type = StrandType.FWD if is_fwd else StrandType.REV
# relative position info
bpr = from_virtual_helix_item.getProperty('bases_per_repeat')
self.is_low = is_low = idx+1 in self.nearby_idxs or (idx+1) % bpr in self.nearby_idxs
self.is_high = is_high = idx-1 in self.nearby_idxs or (idx-1) % bpr in self.nearby_idxs
# check strand for xover and color
if part.hasStrandAtIdx(id_num, idx)[strand_type]:
strand = part.getStrand(self.is_fwd, id_num, idx)
if strand.hasXoverAt(idx):
return False
self.color = strand.getColor() if strand is not None else EMPTY_COL
else:
self.color = EMPTY_COL
if is_low and is_high:
print("dual xover")
path = (_FWD_DUAL_PATH, _REV_DUAL_PATH)[strand_type]
elif is_low:
path = (_FWD_LO_PATH, _REV_LO_PATH)[strand_type]
self.is3p = True if is_fwd else False
self.enter_pos = _FWD_LO_PTS[0][-1] if is_fwd else _REV_LO_PTS[0][-1]
self.exit_pos = _FWD_LO_PTS[0][-1] if is_fwd else _REV_LO_PTS[0][-1]
elif is_high:
path = (_FWD_HI_PATH, _REV_HI_PATH)[strand_type]
self.is3p = False if is_fwd else True
self.enter_pos = _FWD_HI_PTS[0][-1] if is_fwd else _REV_HI_PTS[0][-1]
self.exit_pos = _FWD_HI_PTS[0][-1] if is_fwd else _REV_HI_PTS[0][-1]
else:
# print("unpaired PreXoverItem at {}[{}]".format(self._id_num, self.idx), self.nearby_idxs)
return False
self._tick_marks.setPen(getPenObj(self.color, styles.PREXOVER_STROKE_WIDTH,
capstyle=Qt.FlatCap, joinstyle=Qt.RoundJoin))
self._tick_marks.setPath(path)
self._tick_marks.show()
return True
# end def
### ACCESSORS ###
def color(self):
"""The PreXoverItem's color, derived from the associated strand's oligo.
Returns:
str: color in hex code
"""
return self.color
def getInfo(self):
"""
Returns:
Tuple: (from_id_num, is_fwd, from_index, to_vh_id_num)
"""
return (self._id_num, self.is_fwd, self.idx, self.to_vh_id_num)
def remove(self):
"""Removes animation adapter, label, bond_item, and this item from scene.
"""
scene = self.scene()
self.adapter.destroy()
if scene:
scene.removeItem(self._label)
self._label = None
scene.removeItem(self._bond_item)
self._bond_item = None
self.adapter.resetAnimations()
self.adapter = None
scene.removeItem(self)
# end defS
### EVENT HANDLERS ###
def hoverEnterEvent(self, event):
"""Only if enableActive(True) is called hover and key events disabled by default
Args:
event (QGraphicsSceneHoverEvent): the hover event
"""
self.setFocus(Qt.MouseFocusReason)
self.prexoveritem_manager.updateModelActiveBaseInfo(self.getInfo())
self.setActiveHovered(True)
status_string = "%d[%d]" % (self._id_num, self.idx)
self.parentItem().window().statusBar().showMessage(status_string)
# end def
def hoverLeaveEvent(self, event):
"""Summary
Args:
event (QGraphicsSceneHoverEvent): the hover event
Returns:
TYPE: Description
"""
self.prexoveritem_manager.updateModelActiveBaseInfo(None)
self.setActiveHovered(False)
self.clearFocus()
self.parentItem().window().statusBar().showMessage("")
# end def
def mousePressEvent(self, event):
part = self._model_vh.part()
is_fwd = self.is_fwd
if self.is3p:
strand5p = part.getStrand(is_fwd, self._id_num, self.idx)
strand3p = part.getStrand(not is_fwd, self.to_vh_id_num, self.idx)
else:
strand5p = part.getStrand(not is_fwd, self.to_vh_id_num, self.idx)
strand3p = part.getStrand(is_fwd, self._id_num, self.idx)
if strand5p is None or strand3p is None:
return
part.createXover(strand5p, self.idx, strand3p, self.idx)
nkey = (self.to_vh_id_num, not is_fwd, self.idx)
npxi = self.prexoveritem_manager.neighbor_prexover_items.get(nkey, None)
if npxi:
npxi.shutdown()
self.shutdown()
part.setActiveVirtualHelix(self._id_num, is_fwd, self.idx)
# self.prexoveritem_manager.handlePreXoverClick(self)
def keyPressEvent(self, event):
"""Summary
Args:
event (TYPE): Description
Returns:
TYPE: Description
"""
self.prexoveritem_manager.handlePreXoverKeyPress(event.key())
# end def
### PUBLIC SUPPORT METHODS ###
def setLabel(self, text=None, outline=False):
"""Summary
Args:
text (None, optional): Description
outline (bool, optional): Description
Returns:
TYPE: Description
"""
if text:
self._label.setTextAndStyle(text=text, outline=outline)
self._label.show()
else:
self._label.hide()
# end def
def animate(self, item, property_name, duration, start_value, end_value):
"""Summary
Args:
item (TYPE): Description
property_name (TYPE): Description
duration (TYPE): Description
start_value (TYPE): Description
end_value (TYPE): Description
Returns:
TYPE: Description
"""
b_name = property_name.encode('ascii')
anim = item.adapter.getRef(property_name)
if anim is None:
anim = QPropertyAnimation(item.adapter, b_name)
item.adapter.saveRef(property_name, anim)
anim.setDuration(duration)
anim.setStartValue(start_value)
anim.setEndValue(end_value)
anim.start()
# end def
def setActiveHovered(self, is_active):
"""Rotate phosphate Triangle if `self.to_vh_id_num` is not `None`
Args:
is_active (bool): whether or not the PreXoverItem is parented to the
active VirtualHelixItem
"""
pass
# end def
def enableActive(self, is_active, to_vh_id_num=None):
"""Call on PreXoverItems created on the active VirtualHelixItem
Args:
is_active (TYPE): Description
to_vh_id_num (None, optional): Description
"""
if is_active:
self.to_vh_id_num = to_vh_id_num
self.setAcceptHoverEvents(True)
if to_vh_id_num is None:
self.setLabel(text=None)
else:
self.setLabel(text=str(to_vh_id_num))
else:
self.setBrush(getNoBrush())
self.setAcceptHoverEvents(False)
def activateNeighbor(self, active_prexoveritem, shortcut=None):
"""
Draws a quad line starting from the item5p to the item3p.
To be called with whatever the active_prexoveritem is for the parts `active_base`.
Args:
active_prexoveritem (TYPE): Description
shortcut (None, optional): Description
"""
if self.is3p and not active_prexoveritem.is3p:
item5p = active_prexoveritem
item3p = self
elif not self.is3p and active_prexoveritem.is3p:
item5p = self
item3p = active_prexoveritem
else:
return
same_parity = self.is_fwd == active_prexoveritem.is_fwd
p1 = item5p._tick_marks.scenePos() + item5p.exit_pos
p2 = item3p._tick_marks.scenePos() + item3p.exit_pos
c1 = QPointF()
# case 1: same parity
if same_parity:
dy = abs(p2.y() - p1.y())
c1.setX(p1.x() + _X_SCALE * dy)
c1.setY(0.5 * (p1.y() + p2.y()))
# case 2: different parity
else:
if item3p.is_fwd:
c1.setX(p1.x() - _X_SCALE * abs(p2.y() - p1.y()))
else:
c1.setX(p1.x() + _X_SCALE * abs(p2.y() - p1.y()))
c1.setY(0.5 * (p1.y() + p2.y()))
pp = QPainterPath()
pp.moveTo(self._tick_marks.mapFromScene(p1))
pp.quadTo(self._tick_marks.mapFromScene(c1),
self._tick_marks.mapFromScene(p2))
# pp.cubicTo(c1, c2, self._tick_marks.mapFromScene(p2))
self._bond_item.setPath(pp)
self._bond_item.show()
# end def
def deactivateNeighbor(self):
"""Summary
Returns:
TYPE: Description
"""
if self.isVisible():
self._bond_item.hide()
self.setLabel(text=self._label_txt)
class PreXoverItem(QGraphicsRectItem):
"""A PreXoverItem exists between a single 'from' VirtualHelixItem index
and zero or more 'to' VirtualHelixItem Indices
Attributes:
adapter (TYPE): Description
idx (int): the base index within the virtual helix
is_fwd (TYPE): Description
prexoveritemgroup (TYPE): Description
to_vh_id_num (TYPE): Description
"""
def __init__(self, from_virtual_helix_item, is_fwd, from_index,
to_vh_id_num, prexoveritemgroup, color):
"""Summary
Args:
from_virtual_helix_item (cadnano.gui.views.pathview.virtualhelixitem.VirtualHelixItem): Description
is_fwd (TYPE): Description
from_index (TYPE): Description
to_vh_id_num (TYPE): Description
prexoveritemgroup (TYPE): Description
color (TYPE): Description
"""
super(QGraphicsRectItem, self).__init__(BASE_RECT, from_virtual_helix_item)
self.adapter = PropertyWrapperObject(self)
self._bond_item = QGraphicsPathItem(self)
self._bond_item.hide()
self._label = PreXoverLabel(is_fwd, color, self)
self._phos_item = Triangle(FWDPHOS_PP, self)
self.setPen(getNoPen())
self.resetItem(from_virtual_helix_item, is_fwd, from_index,
to_vh_id_num, prexoveritemgroup, color)
# end def
def shutdown(self):
"""Summary
Returns:
TYPE: Description
"""
self.setBrush(getBrushObj(self._color, alpha=0))
self.to_vh_id_num = None
self.adapter.resetAnimations()
phos = self._phos_item
phos.adapter.resetAnimations()
phos.resetTransform()
phos.setPos(0, 0)
self.setAcceptHoverEvents(False)
self.setFlag(KEYINPUT_ACTIVE_FLAG, False)
self.hide()
# end def
def resetItem(self, from_virtual_helix_item, is_fwd, from_index,
to_vh_id_num, prexoveritemgroup, color):
"""Summary
Args:
from_virtual_helix_item (cadnano.gui.views.pathview.virtualhelixitem.VirtualHelixItem): Description
is_fwd (TYPE): Description
from_index (TYPE): Description
to_vh_id_num (TYPE): Description
prexoveritemgroup (TYPE): Description
color (TYPE): Description
Returns:
TYPE: Description
"""
self.setParentItem(from_virtual_helix_item)
self.resetTransform()
self._id_num = from_virtual_helix_item.idNum()
self.idx = from_index
self.is_fwd = is_fwd
self.to_vh_id_num = to_vh_id_num
self._color = color
self.prexoveritemgroup = prexoveritemgroup
self._bond_item.hide()
self._label_txt = lbt = None if to_vh_id_num is None else str(to_vh_id_num)
self.setLabel(text=lbt)
self._label.resetItem(is_fwd, color)
phos = self._phos_item
bonditem = self._bond_item
if is_fwd:
phos.setPath(FWDPHOS_PP)
phos.setTransformOriginPoint(0, phos.boundingRect().center().y())
phos.setPos(0.5*BASE_WIDTH, BASE_WIDTH)
phos.setPen(getNoPen())
phos.setBrush(getBrushObj(color))
bonditem.setPen(getPenObj(color, styles.PREXOVER_STROKE_WIDTH))
self.setPos(from_index*BASE_WIDTH, -BASE_WIDTH)
else:
phos.setPath(REVPHOS_PP)
phos.setTransformOriginPoint(0, phos.boundingRect().center().y())
phos.setPos(0.5*BASE_WIDTH, 0)
phos.setPen(getPenObj(color, 0.25))
phos.setBrush(getNoBrush())
bonditem.setPen(getPenObj(color, styles.PREXOVER_STROKE_WIDTH,
penstyle=Qt.DotLine, capstyle=Qt.RoundCap))
self.setPos(from_index*BASE_WIDTH, 2*BASE_WIDTH)
if to_vh_id_num is not None:
inactive_alpha = PROX_ALPHA
self.setBrush(getBrushObj(color, alpha=inactive_alpha))
else:
self.setBrush(getBrushObj(color, alpha=0))
self.show()
# end def
def getInfo(self):
"""
Returns:
Tuple: (from_id_num, is_fwd, from_index, to_vh_id_num)
"""
return (self._id_num, self.is_fwd, self.idx, self.to_vh_id_num)
### ACCESSORS ###
def color(self):
"""Summary
Returns:
TYPE: Description
"""
return self._color
def remove(self):
"""Summary
Returns:
TYPE: Description
"""
scene = self.scene()
self.adapter.destroy()
if scene:
scene.removeItem(self._label)
self._label = None
self._phos_item.adapter.resetAnimations()
self._phos_item.adapter = None
scene.removeItem(self._phos_item)
self._phos_item = None
scene.removeItem(self._bond_item)
self._bond_item = None
self.adapter.resetAnimations()
self.adapter = None
scene.removeItem(self)
# end defS
### EVENT HANDLERS ###
def hoverEnterEvent(self, event):
"""Only if enableActive(True) is called
hover and key events disabled by default
Args:
event (TYPE): Description
"""
self.setFocus(Qt.MouseFocusReason)
self.prexoveritemgroup.updateModelActiveBaseInfo(self.getInfo())
self.setActiveHovered(True)
status_string = "%d[%d]" % (self._id_num, self.idx)
self.parentItem().window().statusBar().showMessage(status_string)
# end def
def hoverLeaveEvent(self, event):
"""Summary
Args:
event (TYPE): Description
Returns:
TYPE: Description
"""
self.prexoveritemgroup.updateModelActiveBaseInfo(None)
self.setActiveHovered(False)
self.clearFocus()
self.parentItem().window().statusBar().showMessage("")
# end def
def keyPressEvent(self, event):
"""Summary
Args:
event (TYPE): Description
Returns:
TYPE: Description
"""
self.prexoveritemgroup.handlePreXoverKeyPress(event.key())
# end def
### PUBLIC SUPPORT METHODS ###
def setLabel(self, text=None, outline=False):
"""Summary
Args:
text (None, optional): Description
outline (bool, optional): Description
Returns:
TYPE: Description
"""
if text:
self._label.setTextAndStyle(text=text, outline=outline)
self._label.show()
else:
self._label.hide()
# end def
def animate(self, item, property_name, duration, start_value, end_value):
"""Summary
Args:
item (TYPE): Description
property_name (TYPE): Description
duration (TYPE): Description
start_value (TYPE): Description
end_value (TYPE): Description
Returns:
TYPE: Description
"""
b_name = property_name.encode('ascii')
anim = item.adapter.getRef(property_name)
if anim is None:
anim = QPropertyAnimation(item.adapter, b_name)
item.adapter.saveRef(property_name, anim)
anim.setDuration(duration)
anim.setStartValue(start_value)
anim.setEndValue(end_value)
anim.start()
# end def
def setActiveHovered(self, is_active):
"""Rotate phosphate Triangle if `self.to_vh_id_num` is not `None`
Args:
is_active (bool): whether or not the PreXoverItem is parented to the
active VirtualHelixItem
"""
if is_active:
self.setBrush(getBrushObj(self._color, alpha=128))
self.animate(self, 'brush_alpha', 1, 0, 128) # overwrite running anim
# if self.to_vh_id_num is not None:
self.animate(self._phos_item, 'rotation', 500, 0, -90)
else:
inactive_alpha = 0 if self.to_vh_id_num is None else PROX_ALPHA
self.setBrush(getBrushObj(self._color, alpha=inactive_alpha))
self.animate(self, 'brush_alpha', 1000, 128, inactive_alpha)
self.animate(self._phos_item, 'rotation', 500, -90, 0)
# end def
def enableActive(self, is_active, to_vh_id_num=None):
"""Call on PreXoverItems created on the active VirtualHelixItem
Args:
is_active (TYPE): Description
to_vh_id_num (None, optional): Description
"""
if is_active:
self.to_vh_id_num = to_vh_id_num
self.setAcceptHoverEvents(True)
if to_vh_id_num is None:
self.setLabel(text=None)
self.setBrush(getBrushObj(self._color, alpha=0))
else:
self.setLabel(text=str(to_vh_id_num))
inactive_alpha = PROX_ALPHA
self.setBrush(getBrushObj(self._color, alpha=inactive_alpha))
self.animate(self, 'brush_alpha', 1000, 128, inactive_alpha)
self.setFlag(KEYINPUT_ACTIVE_FLAG, True)
else:
self.setBrush(getNoBrush())
# self.setLabel(text=None)
self.setAcceptHoverEvents(False)
self.setFlag(KEYINPUT_ACTIVE_FLAG, False)
def activateNeighbor(self, active_prexoveritem, shortcut=None):
"""To be called with whatever the active_prexoveritem
is for the parts `active_base`
Args:
active_prexoveritem (TYPE): Description
shortcut (None, optional): Description
"""
p1 = self._phos_item.scenePos()
p2 = active_prexoveritem._phos_item.scenePos()
scale = 3
delta1 = -BASE_WIDTH*scale if self.is_fwd else BASE_WIDTH*scale
delta2 = BASE_WIDTH*scale if active_prexoveritem.is_fwd else -BASE_WIDTH*scale
c1 = self.mapFromScene(QPointF(p1.x(), p1.y() + delta1))
c2 = self.mapFromScene(QPointF(p2.x(), p2.y() - delta2))
pp = QPainterPath()
pp.moveTo(self._phos_item.pos())
pp.cubicTo(c1, c2, self._bond_item.mapFromScene(p2))
self._bond_item.setPath(pp)
self._bond_item.show()
alpha = 32
idx, active_idx = self.idx, active_prexoveritem.idx
if self.is_fwd != active_prexoveritem.is_fwd:
if idx == active_idx:
alpha = 255
elif idx == active_idx + 1:
alpha = 255
elif idx == active_idx - 1:
alpha = 255
inactive_alpha = PROX_ALPHA if self.to_vh_id_num is not None else 0
self.setBrush(getBrushObj(self._color, alpha=inactive_alpha))
self.animate(self, 'brush_alpha', 500, inactive_alpha, alpha)
self.animate(self._phos_item, 'rotation', 500, 0, -90)
self.setLabel(text=shortcut, outline=True)
# end def
def deactivateNeighbor(self):
"""Summary
Returns:
TYPE: Description
"""
if self.isVisible():
inactive_alpha = PROX_ALPHA if self.to_vh_id_num is not None else 0
self.setBrush(getBrushObj(self._color, alpha=inactive_alpha))
self.animate(self, 'brush_alpha', 1000, 128, inactive_alpha)
self.animate(self._phos_item, 'rotation', 500, -90, 0)
self._bond_item.hide()
self.setLabel(text=self._label_txt)
