def __init__(self, part,\
controller=None,\
parent=None):
super(PathHelixGroup, self).__init__(parent)
# Subviews, GraphicsItem business
self.rect = QRectF() # Set by _set_pathHelixList
self._label=None; self.label() # Poke the cache so the label actually exists
# Properties
self._pathHelixList = [] # Primary property
self._part = None; self.setPart(part)
self._controller = controller
self._activeSliceHandle = ActiveSliceHandle(self)
self._stapColor = QColor(0, 72, 0)
self._stapPen = QPen(self._stapColor, 2)
self.activeHelix = None
self.loopHandleGroup = LoopHandleGroup(parent=self)
self.xoverGet = XoverHandle()
self.setZValue(styles.ZPATHHELIXGROUP)
self.phhSelectionGroup = SelectionItemGroup(\
boxtype=PathHelixHandleSelectionBox,\
constraint='y',\
parent=self)
self.selectionLock = None
app().phg = self # Convenience for the command line -i mode
class PathHelixGroup(QGraphicsObject):
"""
PathHelixGroup maintains data and state for a set of object that provide
an interface to the schematic view of a DNA part. These objects include
the PathHelix, PathHelixHandles, and ActiveSliceHandle.
"""
handleRadius = styles.SLICE_HELIX_RADIUS
_scafColor = QColor(0, 102, 204)
_scafPen = QPen(_scafColor, 2)
_nobrush = QBrush(Qt.NoBrush)
def __init__(self, part,\
controller=None,\
parent=None):
super(PathHelixGroup, self).__init__(parent)
# Subviews, GraphicsItem business
self.rect = QRectF() # Set by _set_pathHelixList
self._label=None; self.label() # Poke the cache so the label actually exists
# Properties
self._pathHelixList = [] # Primary property
self._part = None; self.setPart(part)
self._controller = controller
self._activeSliceHandle = ActiveSliceHandle(self)
self._stapColor = QColor(0, 72, 0)
self._stapPen = QPen(self._stapColor, 2)
self.activeHelix = None
self.loopHandleGroup = LoopHandleGroup(parent=self)
self.xoverGet = XoverHandle()
self.setZValue(styles.ZPATHHELIXGROUP)
self.phhSelectionGroup = SelectionItemGroup(\
boxtype=PathHelixHandleSelectionBox,\
constraint='y',\
parent=self)
self.selectionLock = None
app().phg = self # Convenience for the command line -i mode
def __str__(self):
return "I am a PHG!"
def part(self):
return self._part
def activeTool(self):
return controller().activeTool()
def activeHelix(self):
return self.activeHelix
def setActiveHelix(self, newActivePH):
neighborVHs = newActivePH.vhelix().neighbors()
for ph in self._pathHelixList:
showHandles = ph==newActivePH or ph.vhelix() in neighborVHs
ph.setPreXOverHandlesVisible(showHandles)
def setPart(self, newPart):
if self._part:
self._part.selectionWillChange.disconnect(self.selectionWillChange)
newPart.selectionWillChange.connect(self.selectionWillChange)
self._part = newPart
if newPart:
self.selectionWillChange(newPart.selection())
def controller(self):
return self._controller
def activeSliceHandle(self):
return self._activeSliceHandle
def label(self):
if self._label:
return self._label
font = QFont("Times", 30, QFont.Bold)
label = QGraphicsTextItem("Part 1")
label.setVisible(False)
label.setFont(font)
label.setParentItem(self)
label.setPos(0, -40)
label.setTextInteractionFlags(Qt.TextEditorInteraction)
label.inputMethodEvent = None
self._label = label
return label
def displayedVHs(self):
"""Returns the list (ordered top to bottom) of VirtualHelix
that the receiver is displaying"""
return [ph.vhelix() for ph in self._pathHelixList]
displayedVHsChanged = pyqtSignal()
def setDisplayedVHs(self, vhrefs):
"""Spawns or destroys PathHelix such that displayedVHs
has the same VirtualHelix in the same order as vhrefs
(though displayedVHs always returns a list of VirtualHelix
while setDisplayedVHs can take any vhref)"""
assert(self.part()) # Can't display VirtualHelix that aren't there!
new_pathHelixList = []
vhToPH = dict(((ph.vhelix(), ph) for ph in self._pathHelixList))
for vhref in vhrefs:
vh = self.part().getVirtualHelix(vhref)
ph = vhToPH.get(vh, None)
if ph == None:
ph = PathHelix(vh, self)
new_pathHelixList.append(ph)
self._set_pathHelixList(new_pathHelixList)
self.displayedVHsChanged.emit()
def __pathHelixList(self):
return self._pathHelixList
def _set_pathHelixList(self, newList):
"""Give me a list of PathHelix and I'll parent them
to myself if necessary, position them in a column, adopt
their handles, and position them as well."""
y = 0 # How far down from the top the next PH should be
leftmostExtent = 0
rightmostExtent = 0
self.label().setVisible(True)
for ph in self._pathHelixList:
if not ph in newList:
ph.handle().setParentItem(None)
ph.setParentItem(None)
for ph in newList:
ph.setParentItem(self)
ph.setPos(0, y)
ph_height = ph.boundingRect().height()
step = ph_height + styles.PATH_HELIX_PADDING
phh = ph.handle()
phh.setParentItem(self)
phhr = phh.boundingRect()
phh.setPos(-2 * phhr.width(), y + (ph_height - phhr.height()) / 2)
leftmostExtent = min(leftmostExtent, -2 * phhr.width())
rightmostExtent = max(rightmostExtent, ph.boundingRect().width())
y += step
# end for
self.prepareGeometryChange()
self.geometryChanged.emit()
self.rect = QRectF(leftmostExtent,\
-40,\
-leftmostExtent + rightmostExtent,\
y + 40)
self._pathHelixList = newList
self.vhToPathHelix = dict(((ph.vhelix(), ph) for ph in newList))
self.scene().views()[0].zoomToFit()
def paint(self, painter, option, widget=None):
# painter.save()
painter.setBrush(self._nobrush)
self.drawXovers(painter)
# painter.restore()
def drawXovers(self, painter):
"""Return a QPainterPath ready to paint the crossovers"""
for ph in self._pathHelixList:
painter.setPen(self._scafPen)
for ((fromhelix, fromindex), (tohelix, toindex)) in \
ph.vhelix().get3PrimeXovers(StrandType.Scaffold):
path = self.xoverGet.getXover(self,\
StrandType.Scaffold,\
ph,\
fromindex,\
self.getPathHelix(tohelix),\
toindex)
painter.drawPath(path)
# end for
painter.setPen(self._stapPen)
for ((fromhelix, fromindex), (tohelix, toindex)) in \
ph.vhelix().get3PrimeXovers(StrandType.Staple):
path = self.xoverGet.getXover(self,\
StrandType.Staple,\
ph,\
fromindex,\
self.getPathHelix(tohelix),\
toindex)
color = ph.vhelix().colorOfBase(StrandType.Staple, fromindex)
self._stapPen.setColor(QColor(color))
painter.drawPath(path)
# end for
# end for
# end def
geometryChanged = pyqtSignal()
def boundingRect(self):
# rect set only by _set_pathHelixList
return self.rect
def moveHelixNumToIdx(self, num, idx):
"""Reinserts helix with number() num such that
it's at position idx in _pathHelixList"""
vhs = [vh.number() for vh in self.displayedVHs()]
vhs.remove(num)
vhs.insert(idx, num)
self.setDisplayedVHs(vhs)
def zoomToFit(self):
# Auto zoom to center the scene
thescene = self.scene()
theview = thescene.views()[0]
theview.zoomToFit()
@pyqtSlot(int)
def helixAddedSlot(self, vhref):
vhs = self.displayedVHs()
if vhref in vhs:
return
vhs.append(vhref)
self.setDisplayedVHs(vhs)
@pyqtSlot(int)
def helixRemovedSlot(self, vh):
vhs = self.displayedVHs()
if not vhref in vhs:
return
vhs.remove(vh)
self.setDisplayedVHs(vh)
# Slot called when the slice view's (actually the part's) selection changes
def selectionWillChange(self, newSelection):
self.setDisplayedVHs(newSelection)
def getPathHelix(self, vhref):
"""Given the helix number, return a reference to the PathHelix."""
vh = self.part().getVirtualHelix(vhref)
for ph in self._pathHelixList:
if ph.vhelix() == vh:
return ph
return None
def reorderHelices(self, first, last, indexDelta):
"""
Reorder helices by moving helices _pathHelixList[first:last]
by a distance delta in the list. Notify each PathHelix and
PathHelixHandle of its new location.
"""
vhs = self.displayedVHs()
vhsToMove = vhs[first:last]
del vhs[first:last]
self.setDisplayedVHs(vhs[0:first + indexDelta] +\
vhsToMove + vhs[first + indexDelta:-1])
