def setPartnerVirtualHelix(self, strand: StrandT):
"""
Args:
strand: Description
"""
if strand.connection3p():
self._partner_virtual_helix_id_num = strand.connection3p().idNum()
else:
self._partner_virtual_helix_id_num = None
def update(self, strand5p: StrandT, idx: int = None):
"""Pass ``idx`` to this method in order to install a floating
Xover for the forced xover tool
Args:
strand5p: Description
idx: Default is ``None``
"""
self._strand5p = strand5p
strand3p = strand5p.connection3p()
vhi5p = self._virtual_helix_item
part_item = vhi5p.partItem()
# This condition is for floating xovers
idx_3_prime = idx if idx else strand5p.idx3Prime()
if self._node5 is None:
self._node5 = XoverNode5(vhi5p, self, strand5p, idx_3_prime)
if strand3p is not None:
if self._node3 is None:
vhi3p = part_item.idToVirtualHelixItem(strand3p.idNum())
self._node3 = XoverNode3(vhi3p, self, strand3p,
strand3p.idx5Prime())
else:
self._node5.setIdx(idx_3_prime)
self._node3.setIdx(strand3p.idx5Prime())
self._node5.setPartnerVirtualHelix(strand5p)
self._updatePath(strand5p)
else:
if self._node3:
self._node3.destroyItem()
self._node3 = None
def strandResizedSlot(self, strand: StrandT, indices: SegmentT):
"""Slot for handling resizing of this StrandItem
Args:
strand:
indices: low and high indices
"""
low_moved, group_low = self._low_cap.updatePosIfNecessary(self.idxs()[0])
high_moved, group_high = self._high_cap.updatePosIfNecessary(self.idxs()[1])
group = self.group()
self.tempReparent()
if low_moved:
self.updateLine(self._low_cap)
if high_moved:
self.updateLine(self._high_cap)
if strand.connection3p():
self.xover_3p_end.update(strand)
self.refreshInsertionItems(strand)
self._updateSequenceText()
if group:
group.addToGroup(self)
if group_low is not None:
group_low.addToGroup(self._low_cap)
if group_high is not None:
group_high.addToGroup(self._high_cap)
def strandResizedSlot(self, strand: StrandT, indices: SegmentT):
"""Slot for handling resizing of this StrandItem
Args:
strand:
indices: low and high indices
"""
low_moved, group_low = self._low_cap.updatePosIfNecessary(
self.idxs()[0])
high_moved, group_high = self._high_cap.updatePosIfNecessary(
self.idxs()[1])
group = self.group()
self.tempReparent()
if low_moved:
self.updateLine(self._low_cap)
if high_moved:
self.updateLine(self._high_cap)
if strand.connection3p():
self.xover_3p_end.update(strand)
self.refreshInsertionItems(strand)
self._updateSequenceText()
if group:
group.addToGroup(self)
if group_low is not None:
group_low.addToGroup(self._low_cap)
if group_high is not None:
group_high.addToGroup(self._high_cap)
def strandHasNewOligoSlot(self, strand: StrandT):
"""Slot for changing the `Oligo` of the model `Strand`
Args:
strand:
"""
strand = self._model_strand
self._controller.reconnectOligoSignals()
self._updateColor(strand)
if strand.connection3p():
self.xover_3p_end._updateColor(strand)
for insertion in self.insertionItems().values():
insertion.updateItem()
def strandHasNewOligoSlot(self, strand: StrandT):
"""Slot for changing the `Oligo` of the model `Strand`
Args:
strand:
"""
strand = self._model_strand
self._controller.reconnectOligoSignals()
self._updateColor(strand)
if strand.connection3p():
self.xover_3p_end._updateColor(strand)
for insertion in self.insertionItems().values():
insertion.updateItem()
def _updateAppearance(self, strand: StrandT):
"""Prepare Strand for drawing, positions are relative to the
:class:`PathVirtualHelixItem`:
1. Show or hide caps depending on L and R connectivity.
2. Determine line coordinates.
3. Apply paint styles.
"""
# 0. Setup
vhi = self._virtual_helix_item
bw = _BASE_WIDTH
half_base_width = bw / 2.0
low_idx, high_idx = strand.lowIdx(), strand.highIdx()
l_upper_left_x, l_upper_left_y = vhi.upperLeftCornerOfBase(low_idx, strand)
h_upper_left_x, h_upper_left_y = vhi.upperLeftCornerOfBase(high_idx, strand)
low_cap = self._low_cap
high_cap = self._high_cap
dual_cap = self._dual_cap
# 1. Cap visibilty
lx = l_upper_left_x + bw # draw from right edge of base
low_cap.safeSetPos(l_upper_left_x, l_upper_left_y)
if strand.connectionLow() is not None: # has low xover
# if we are hiding it, we might as well make sure it is reparented to the StrandItem
low_cap.restoreParent()
low_cap.hide()
else: # has low cap
if not low_cap.isVisible():
low_cap.show()
hx = h_upper_left_x # draw to edge of base
high_cap.safeSetPos(h_upper_left_x, h_upper_left_y)
if strand.connectionHigh() is not None: # has high xover
# if we are hiding it, we might as well make sure it is reparented to the StrandItem
high_cap.restoreParent()
high_cap.hide()
else: # has high cap
if not high_cap.isVisible():
high_cap.show()
# special case: single-base strand with no L or H connections,
# (unconnected caps were made visible in previous block of code)
if strand.length() == 1 and (low_cap.isVisible() and high_cap.isVisible()):
low_cap.hide()
high_cap.hide()
dual_cap.safeSetPos(l_upper_left_x, l_upper_left_y)
dual_cap.show()
else:
dual_cap.hide()
# 2. Xover drawing
xo = self.xover_3p_end
if strand.connection3p():
xo.update(strand)
xo.showIt()
else:
xo.restoreParent()
xo.hideIt()
# 3. Refresh insertionItems if necessary drawing
self.refreshInsertionItems(strand)
# 4. Line drawing
hy = ly = l_upper_left_y + half_base_width
self.setLine(lx, ly, hx, hy)
rectf = QRectF(l_upper_left_x + bw, l_upper_left_y, bw*(high_idx - low_idx - 1), bw)
self._click_area.setRect(rectf)
self._updateColor(strand)
def _updateAppearance(self, strand: StrandT):
"""Prepare Strand for drawing, positions are relative to the
:class:`PathVirtualHelixItem`:
1. Show or hide caps depending on L and R connectivity.
2. Determine line coordinates.
3. Apply paint styles.
"""
# 0. Setup
vhi = self._virtual_helix_item
bw = _BASE_WIDTH
half_base_width = bw / 2.0
low_idx, high_idx = strand.lowIdx(), strand.highIdx()
l_upper_left_x, l_upper_left_y = vhi.upperLeftCornerOfBase(
low_idx, strand)
h_upper_left_x, h_upper_left_y = vhi.upperLeftCornerOfBase(
high_idx, strand)
low_cap = self._low_cap
high_cap = self._high_cap
dual_cap = self._dual_cap
# 1. Cap visibilty
lx = l_upper_left_x + bw # draw from right edge of base
low_cap.safeSetPos(l_upper_left_x, l_upper_left_y)
if strand.connectionLow() is not None: # has low xover
# if we are hiding it, we might as well make sure it is reparented to the StrandItem
low_cap.restoreParent()
low_cap.hide()
else: # has low cap
if not low_cap.isVisible():
low_cap.show()
hx = h_upper_left_x # draw to edge of base
high_cap.safeSetPos(h_upper_left_x, h_upper_left_y)
if strand.connectionHigh() is not None: # has high xover
# if we are hiding it, we might as well make sure it is reparented to the StrandItem
high_cap.restoreParent()
high_cap.hide()
else: # has high cap
if not high_cap.isVisible():
high_cap.show()
# special case: single-base strand with no L or H connections,
# (unconnected caps were made visible in previous block of code)
if strand.length() == 1 and (low_cap.isVisible()
and high_cap.isVisible()):
low_cap.hide()
high_cap.hide()
dual_cap.safeSetPos(l_upper_left_x, l_upper_left_y)
dual_cap.show()
else:
dual_cap.hide()
# 2. Xover drawing
xo = self.xover_3p_end
if strand.connection3p():
xo.update(strand)
xo.showIt()
else:
xo.restoreParent()
xo.hideIt()
# 3. Refresh insertionItems if necessary drawing
self.refreshInsertionItems(strand)
# 4. Line drawing
hy = ly = l_upper_left_y + half_base_width
self.setLine(lx, ly, hx, hy)
rectf = QRectF(l_upper_left_x + bw, l_upper_left_y,
bw * (high_idx - low_idx - 1), bw)
self._click_area.setRect(rectf)
self._updateColor(strand)