class ActiveSliceItem(QGraphicsRectItem):
"""ActiveSliceItem for the Slice View"""
def __init__(self, partItem, activeBaseIndex):
super(ActiveSliceItem, self).__init__(partItem)
self._partItem = partItem
self._controller = ActiveSliceItemController(self, partItem.part())
self.setFlag(QGraphicsItem.ItemHasNoContents)
# end def
### SLOTS ###
def strandChangedSlot(self, sender, vh):
if vh == None:
return
partItem = self._partItem
vhi = partItem.getVirtualHelixItemByCoord(*vh.coord())
activeBaseIdx = partItem.part().activeBaseIndex()
isActiveNow = vh.hasStrandAtIdx(activeBaseIdx)
vhi.setActiveSliceView(isActiveNow, activeBaseIdx)
# end def
def updateIndexSlot(self, sender, newActiveSliceZIndex):
part = self.part()
if part.numberOfVirtualHelices() == 0:
return
newlyActiveVHs = set()
activeBaseIdx = part.activeBaseIndex()
for vhi in self._partItem._virtualHelixHash.itervalues():
vh = vhi.virtualHelix()
if vh:
isActiveNow = vh.hasStrandAtIdx(activeBaseIdx)
vhi.setActiveSliceView(isActiveNow, activeBaseIdx)
# end def
def updateRectSlot(self, part):
pass
# end def
### ACCESSORS ###
def part(self):
return self._partItem.part()
# end def
### PUBLIC METHODS FOR DRAWING / LAYOUT ###
def removed(self):
self._partItem = None
self._controller.disconnectSignals()
self.controller = None
class ActiveSliceItem(QGraphicsRectItem):
"""ActiveSliceItem for the Slice View"""
def __init__(self, partItem, activeBaseIndex):
super(ActiveSliceItem, self).__init__(partItem)
self._partItem = partItem
self._controller = ActiveSliceItemController(self, partItem.part())
self.setFlag(QGraphicsItem.ItemHasNoContents)
# end def
### SLOTS ###
def strandChangedSlot(self, sender, vh):
if vh == None:
return
partItem = self._partItem
vhi = partItem.getVirtualHelixItemByCoord(*vh.coord())
activeBaseIdx = partItem.part().activeBaseIndex()
isActiveNow = vh.hasStrandAtIdx(activeBaseIdx)
vhi.setActiveSliceView(isActiveNow, activeBaseIdx)
# end def
def updateIndexSlot(self, sender, newActiveSliceZIndex):
part = self.part()
if part.numberOfVirtualHelices() == 0:
return
newlyActiveVHs = set()
activeBaseIdx = part.activeBaseIndex()
for vhi in self._partItem._virtualHelixHash.itervalues():
vh = vhi.virtualHelix()
if vh:
isActiveNow = vh.hasStrandAtIdx(activeBaseIdx)
vhi.setActiveSliceView(isActiveNow, activeBaseIdx)
# end def
def updateRectSlot(self, part):
pass
# end def
### ACCESSORS ###
def part(self):
return self._partItem.part()
# end def
### PUBLIC METHODS FOR DRAWING / LAYOUT ###
def removed(self):
self._partItem = None
self._controller.disconnectSignals()
self.controller = None
def __init__(self, partItem, activeBaseIndex):
super(ActiveSliceItem, self).__init__(partItem)
self._partItem = partItem
self._activeTool = partItem.activeTool()
self._activeSlice = 0
self._lowDragBound = 0
self._highDragBound = self.part().maxBaseIdx()
self._controller = ActiveSliceItemController(self, partItem.part())
self._label = QGraphicsSimpleTextItem("", parent=self)
self._label.setPos(0, -18)
self._label.setFont(_font)
self._label.setBrush(_labelbrush)
self._label.hide()
self.setFlag(QGraphicsItem.ItemIsMovable)
self.setAcceptHoverEvents(True)
self.setZValue(styles.ZACTIVESLICEHANDLE)
self.setRect(QRectF(0, 0, _baseWidth,\
self._partItem.boundingRect().height()))
self.setPos(activeBaseIndex * _baseWidth, 0)
self.setBrush(_brush)
self.setPen(_pen)
# reuse select tool methods for other tools
self.addSeqToolMousePress = self.selectToolMousePress
self.addSeqToolMouseMove = self.selectToolMouseMove
self.breakToolMousePress = self.selectToolMousePress
self.breakToolMouseMove = self.selectToolMouseMove
self.insertionToolMousePress = self.selectToolMousePress
self.insertionToolMouseMove = self.selectToolMouseMove
self.paintToolMousePress = self.selectToolMousePress
self.paintToolMouseMove = self.selectToolMouseMove
self.pencilToolMousePress = self.selectToolMousePress
self.pencilToolMouseMove = self.selectToolMouseMove
self.skipToolMousePress = self.selectToolMousePress
self.skipToolMouseMove = self.selectToolMouseMove
def __init__(self, partItem, activeBaseIndex):
super(ActiveSliceItem, self).__init__(partItem)
self._partItem = partItem
self._activeTool = partItem.activeTool()
self._activeSlice = 0
self._lowDragBound = 0
self._highDragBound = self.part().maxBaseIdx()
self._controller = ActiveSliceItemController(self, partItem.part())
self._label = QGraphicsSimpleTextItem("", parent=self)
self._label.setPos(0, -18)
self._label.setFont(_font)
self._label.setBrush(_labelbrush)
self._label.hide()
self.setFlag(QGraphicsItem.ItemIsMovable)
self.setAcceptHoverEvents(True)
self.setZValue(styles.ZACTIVESLICEHANDLE)
self.setRect(QRectF(0, 0, _baseWidth,\
self._partItem.boundingRect().height()))
self.setPos(activeBaseIndex*_baseWidth, 0)
self.setBrush(_brush)
self.setPen(_pen)
# reuse select tool methods for other tools
self.addSeqToolMousePress = self.selectToolMousePress
self.addSeqToolMouseMove = self.selectToolMouseMove
self.breakToolMousePress = self.selectToolMousePress
self.breakToolMouseMove = self.selectToolMouseMove
self.insertionToolMousePress = self.selectToolMousePress
self.insertionToolMouseMove = self.selectToolMouseMove
self.paintToolMousePress = self.selectToolMousePress
self.paintToolMouseMove = self.selectToolMouseMove
self.pencilToolMousePress = self.selectToolMousePress
self.pencilToolMouseMove = self.selectToolMouseMove
self.skipToolMousePress = self.selectToolMousePress
self.skipToolMouseMove = self.selectToolMouseMove
class ActiveSliceItem(QGraphicsRectItem):
"""ActiveSliceItem for the Path View"""
def __init__(self, partItem, activeBaseIndex):
super(ActiveSliceItem, self).__init__(partItem)
self._partItem = partItem
self._activeTool = partItem.activeTool()
self._activeSlice = 0
self._lowDragBound = 0
self._highDragBound = self.part().maxBaseIdx()
self._controller = ActiveSliceItemController(self, partItem.part())
self._label = QGraphicsSimpleTextItem("", parent=self)
self._label.setPos(0, -18)
self._label.setFont(_font)
self._label.setBrush(_labelbrush)
self._label.hide()
self.setFlag(QGraphicsItem.ItemIsMovable)
self.setAcceptHoverEvents(True)
self.setZValue(styles.ZACTIVESLICEHANDLE)
self.setRect(QRectF(0, 0, _baseWidth,\
self._partItem.boundingRect().height()))
self.setPos(activeBaseIndex * _baseWidth, 0)
self.setBrush(_brush)
self.setPen(_pen)
# reuse select tool methods for other tools
self.addSeqToolMousePress = self.selectToolMousePress
self.addSeqToolMouseMove = self.selectToolMouseMove
self.breakToolMousePress = self.selectToolMousePress
self.breakToolMouseMove = self.selectToolMouseMove
self.insertionToolMousePress = self.selectToolMousePress
self.insertionToolMouseMove = self.selectToolMouseMove
self.paintToolMousePress = self.selectToolMousePress
self.paintToolMouseMove = self.selectToolMouseMove
self.pencilToolMousePress = self.selectToolMousePress
self.pencilToolMouseMove = self.selectToolMouseMove
self.skipToolMousePress = self.selectToolMousePress
self.skipToolMouseMove = self.selectToolMouseMove
# end def
### SLOTS ###
def strandChangedSlot(self, sender, vh):
pass
# end def
def updateRectSlot(self, part):
bw = _baseWidth
newRect = QRectF(0, 0, bw,\
self._partItem.virtualHelixBoundingRect().height())
if newRect != self.rect():
self.setRect(newRect)
self._hideIfEmptySelection()
self.updateIndexSlot(part, part.activeBaseIndex())
return newRect
# end def
def updateIndexSlot(self, part, baseIndex):
"""The slot that receives active slice changed notifications from
the part and changes the receiver to reflect the part"""
label = self._label
bw = _baseWidth
bi = util.clamp(int(baseIndex), 0, self.part().maxBaseIdx())
self.setPos(bi * bw, -styles.PATH_HELIX_PADDING)
self._activeSlice = bi
if label:
label.setText("%d" % bi)
label.setX((bw - label.boundingRect().width()) / 2)
# end def
### ACCESSORS ###
def activeBaseIndex(self):
return self.part().activeBaseIndex()
# end def
def part(self):
return self._partItem.part()
# end def
def partItem(self):
return self._partItem
# end def
### PUBLIC METHODS FOR DRAWING / LAYOUT ###
def removed(self):
scene = self.scene()
scene.removeItem(self._label)
scene.removeItem(self)
self._partItem = None
self._label = None
self._controller.disconnectSignals()
self.controller = None
# end def
def resetBounds(self):
"""Call after resizing virtualhelix canvas."""
self._highDragBound = self.part().maxBaseIdx()
# end def
### PRIVATE SUPPORT METHODS ###
def _hideIfEmptySelection(self):
vis = self.part().numberOfVirtualHelices() > 0
self.setVisible(vis)
self._label.setVisible(vis)
# end def
def _setActiveBaseIndex(self, baseIndex):
self.part().setActiveBaseIndex(baseIndex)
# end def
### EVENT HANDLERS ###
def hoverEnterEvent(self, event):
self.setCursor(Qt.OpenHandCursor)
self._partItem.updateStatusBar("%d" % self.part().activeBaseIndex())
QGraphicsItem.hoverEnterEvent(self, event)
# end def
def hoverLeaveEvent(self, event):
self.setCursor(Qt.ArrowCursor)
self._partItem.updateStatusBar("")
QGraphicsItem.hoverLeaveEvent(self, event)
# end def
def mousePressEvent(self, event):
"""
Parses a mousePressEvent, calling the approproate tool method as
necessary. Stores _moveIdx for future comparison.
"""
if event.button() != Qt.LeftButton:
event.ignore()
QGraphicsItem.mousePressEvent(self, event)
return
self.scene().views()[0].addToPressList(self)
self._moveIdx = int(floor((self.x() + event.pos().x()) / _baseWidth))
toolMethodName = str(self._activeTool()) + "MousePress"
if hasattr(self, toolMethodName): # if the tool method exists
modifiers = event.modifiers()
getattr(self, toolMethodName)(modifiers) # call tool method
def mouseMoveEvent(self, event):
"""
Parses a mouseMoveEvent, calling the approproate tool method as
necessary. Updates _moveIdx if it changed.
"""
toolMethodName = str(self._activeTool()) + "MouseMove"
if hasattr(self, toolMethodName): # if the tool method exists
idx = int(floor((self.x() + event.pos().x()) / _baseWidth))
if idx != self._moveIdx: # did we actually move?
modifiers = event.modifiers()
self._moveIdx = idx
getattr(self, toolMethodName)(modifiers,
idx) # call tool method
def customMouseRelease(self, event):
"""
Parses a mouseReleaseEvent, calling the approproate tool method as
necessary. Deletes _moveIdx if necessary.
"""
toolMethodName = str(self._activeTool()) + "MouseRelease"
if hasattr(self, toolMethodName): # if the tool method exists
modifiers = event.modifiers()
x = event.pos().x()
getattr(self, toolMethodName)(modifiers, x) # call tool method
if self._moveIdx is not None:
self._moveIdx = None
### TOOL METHODS ###
def selectToolMousePress(self, modifiers):
"""
Set the allowed drag bounds for use by selectToolMouseMove.
"""
if (modifiers & Qt.AltModifier) and (modifiers & Qt.ShiftModifier):
self.part().undoStack().beginMacro("Auto-drag Scaffold(s)")
for vh in self.part().getVirtualHelices():
# SCAFFOLD
# resize 3' first
for strand in vh.scaffoldStrandSet():
idx5p = strand.idx5Prime()
idx3p = strand.idx3Prime()
if not strand.hasXoverAt(idx3p):
lo, hi = strand.getResizeBounds(idx3p)
if strand.isDrawn5to3():
strand.resize((idx5p, hi))
else:
strand.resize((lo, idx5p))
# resize 5' second
for strand in vh.scaffoldStrandSet():
idx5p = strand.idx5Prime()
idx3p = strand.idx3Prime()
if not strand.hasXoverAt(idx5p):
lo, hi = strand.getResizeBounds(idx5p)
if strand.isDrawn5to3():
strand.resize((lo, idx3p))
else:
strand.resize((idx3p, hi))
# STAPLE
# resize 3' first
for strand in vh.stapleStrandSet():
idx5p = strand.idx5Prime()
idx3p = strand.idx3Prime()
if not strand.hasXoverAt(idx3p):
lo, hi = strand.getResizeBounds(idx3p)
if strand.isDrawn5to3():
strand.resize((idx5p, hi))
else:
strand.resize((lo, idx5p))
# resize 5' second
for strand in vh.stapleStrandSet():
idx5p = strand.idx5Prime()
idx3p = strand.idx3Prime()
if not strand.hasXoverAt(idx3p):
lo, hi = strand.getResizeBounds(idx5p)
if strand.isDrawn5to3():
strand.resize((lo, idx3p))
else:
strand.resize((idx3p, hi))
self.part().undoStack().endMacro()
# end def
def selectToolMouseMove(self, modifiers, idx):
"""
Given a new index (pre-validated as different from the prev index),
calculate the new x coordinate for self, move there, and notify the
parent strandItem to redraw its horizontal line.
"""
idx = util.clamp(idx, self._lowDragBound, self._highDragBound)
x = int(idx * _baseWidth)
self.setPos(x, self.y())
self.updateIndexSlot(None, idx)
self._setActiveBaseIndex(idx)
self._partItem.updateStatusBar("%d" % self.part().activeBaseIndex())
class ActiveSliceItem(QGraphicsRectItem):
"""ActiveSliceItem for the Path View"""
def __init__(self, partItem, activeBaseIndex):
super(ActiveSliceItem, self).__init__(partItem)
self._partItem = partItem
self._activeTool = partItem.activeTool()
self._activeSlice = 0
self._lowDragBound = 0
self._highDragBound = self.part().maxBaseIdx()
self._controller = ActiveSliceItemController(self, partItem.part())
self._label = QGraphicsSimpleTextItem("", parent=self)
self._label.setPos(0, -18)
self._label.setFont(_font)
self._label.setBrush(_labelbrush)
self._label.hide()
self.setFlag(QGraphicsItem.ItemIsMovable)
self.setAcceptHoverEvents(True)
self.setZValue(styles.ZACTIVESLICEHANDLE)
self.setRect(QRectF(0, 0, _baseWidth,\
self._partItem.boundingRect().height()))
self.setPos(activeBaseIndex*_baseWidth, 0)
self.setBrush(_brush)
self.setPen(_pen)
# reuse select tool methods for other tools
self.addSeqToolMousePress = self.selectToolMousePress
self.addSeqToolMouseMove = self.selectToolMouseMove
self.breakToolMousePress = self.selectToolMousePress
self.breakToolMouseMove = self.selectToolMouseMove
self.insertionToolMousePress = self.selectToolMousePress
self.insertionToolMouseMove = self.selectToolMouseMove
self.paintToolMousePress = self.selectToolMousePress
self.paintToolMouseMove = self.selectToolMouseMove
self.pencilToolMousePress = self.selectToolMousePress
self.pencilToolMouseMove = self.selectToolMouseMove
self.skipToolMousePress = self.selectToolMousePress
self.skipToolMouseMove = self.selectToolMouseMove
# end def
### SLOTS ###
def strandChangedSlot(self, sender, vh):
pass
# end def
def updateRectSlot(self, part):
bw = _baseWidth
newRect = QRectF(0, 0, bw,\
self._partItem.virtualHelixBoundingRect().height())
if newRect != self.rect():
self.setRect(newRect)
self._hideIfEmptySelection()
self.updateIndexSlot(part, part.activeBaseIndex())
return newRect
# end def
def updateIndexSlot(self, part, baseIndex):
"""The slot that receives active slice changed notifications from
the part and changes the receiver to reflect the part"""
label = self._label
bw = _baseWidth
bi = util.clamp(int(baseIndex), 0, self.part().maxBaseIdx())
self.setPos(bi * bw, -styles.PATH_HELIX_PADDING)
self._activeSlice = bi
if label:
label.setText("%d" % bi)
label.setX((bw - label.boundingRect().width()) / 2)
# end def
### ACCESSORS ###
def activeBaseIndex(self):
return self.part().activeBaseIndex()
# end def
def part(self):
return self._partItem.part()
# end def
def partItem(self):
return self._partItem
# end def
### PUBLIC METHODS FOR DRAWING / LAYOUT ###
def removed(self):
scene = self.scene()
scene.removeItem(self._label)
scene.removeItem(self)
self._partItem = None
self._label = None
self._controller.disconnectSignals()
self.controller = None
# end def
def resetBounds(self):
"""Call after resizing virtualhelix canvas."""
self._highDragBound = self.part().maxBaseIdx()
# end def
### PRIVATE SUPPORT METHODS ###
def _hideIfEmptySelection(self):
vis = self.part().numberOfVirtualHelices() > 0
self.setVisible(vis)
self._label.setVisible(vis)
# end def
def _setActiveBaseIndex(self, baseIndex):
self.part().setActiveBaseIndex(baseIndex)
# end def
### EVENT HANDLERS ###
def hoverEnterEvent(self, event):
self.setCursor(Qt.OpenHandCursor)
self._partItem.updateStatusBar("%d" % self.part().activeBaseIndex())
QGraphicsItem.hoverEnterEvent(self, event)
# end def
def hoverLeaveEvent(self, event):
self.setCursor(Qt.ArrowCursor)
self._partItem.updateStatusBar("")
QGraphicsItem.hoverLeaveEvent(self, event)
# end def
def mousePressEvent(self, event):
"""
Parses a mousePressEvent, calling the approproate tool method as
necessary. Stores _moveIdx for future comparison.
"""
if event.button() != Qt.LeftButton:
event.ignore()
QGraphicsItem.mousePressEvent(self, event)
return
self.scene().views()[0].addToPressList(self)
self._moveIdx = int(floor((self.x()+event.pos().x()) / _baseWidth))
toolMethodName = str(self._activeTool()) + "MousePress"
if hasattr(self, toolMethodName): # if the tool method exists
modifiers = event.modifiers()
getattr(self, toolMethodName)(modifiers) # call tool method
def mouseMoveEvent(self, event):
"""
Parses a mouseMoveEvent, calling the approproate tool method as
necessary. Updates _moveIdx if it changed.
"""
toolMethodName = str(self._activeTool()) + "MouseMove"
if hasattr(self, toolMethodName): # if the tool method exists
idx = int(floor((self.x()+event.pos().x()) / _baseWidth))
if idx != self._moveIdx: # did we actually move?
modifiers = event.modifiers()
self._moveIdx = idx
getattr(self, toolMethodName)(modifiers, idx) # call tool method
def customMouseRelease(self, event):
"""
Parses a mouseReleaseEvent, calling the approproate tool method as
necessary. Deletes _moveIdx if necessary.
"""
toolMethodName = str(self._activeTool()) + "MouseRelease"
if hasattr(self, toolMethodName): # if the tool method exists
modifiers = event.modifiers()
x = event.pos().x()
getattr(self, toolMethodName)(modifiers, x) # call tool method
if hasattr(self, '_moveIdx'):
del self._moveIdx
### TOOL METHODS ###
def selectToolMousePress(self, modifiers):
"""
Set the allowed drag bounds for use by selectToolMouseMove.
"""
if (modifiers & Qt.AltModifier) and (modifiers & Qt.ShiftModifier):
self.part().undoStack().beginMacro("Auto-drag Scaffold(s)")
for vh in self.part().getVirtualHelices():
# SCAFFOLD
# resize 3' first
for strand in vh.scaffoldStrandSet():
idx5p = strand.idx5Prime()
idx3p = strand.idx3Prime()
if not strand.hasXoverAt(idx3p):
lo, hi = strand.getResizeBounds(idx3p)
if strand.isDrawn5to3():
strand.resize((idx5p, hi))
else:
strand.resize((lo, idx5p))
# resize 5' second
for strand in vh.scaffoldStrandSet():
idx5p = strand.idx5Prime()
idx3p = strand.idx3Prime()
if not strand.hasXoverAt(idx5p):
lo, hi = strand.getResizeBounds(idx5p)
if strand.isDrawn5to3():
strand.resize((lo, idx3p))
else:
strand.resize((idx3p, hi))
# STAPLE
# resize 3' first
for strand in vh.stapleStrandSet():
idx5p = strand.idx5Prime()
idx3p = strand.idx3Prime()
if not strand.hasXoverAt(idx3p):
lo, hi = strand.getResizeBounds(idx3p)
if strand.isDrawn5to3():
strand.resize((idx5p, hi))
else:
strand.resize((lo, idx5p))
# resize 5' second
for strand in vh.stapleStrandSet():
idx5p = strand.idx5Prime()
idx3p = strand.idx3Prime()
if not strand.hasXoverAt(idx3p):
lo, hi = strand.getResizeBounds(idx5p)
if strand.isDrawn5to3():
strand.resize((lo, idx3p))
else:
strand.resize((idx3p, hi))
self.part().undoStack().endMacro()
# end def
def selectToolMouseMove(self, modifiers, idx):
"""
Given a new index (pre-validated as different from the prev index),
calculate the new x coordinate for self, move there, and notify the
parent strandItem to redraw its horizontal line.
"""
idx = util.clamp(idx, self._lowDragBound, self._highDragBound)
x = int(idx * _baseWidth)
self.setPos(x, self.y())
self.updateIndexSlot(None, idx)
self._setActiveBaseIndex(idx)
self._partItem.updateStatusBar("%d" % self.part().activeBaseIndex())
def __init__(self, partItem, activeBaseIndex):
super(ActiveSliceItem, self).__init__(partItem)
self._partItem = partItem
self._controller = ActiveSliceItemController(self, partItem.part())
self.setFlag(QGraphicsItem.ItemHasNoContents)
def __init__(self, partItem, activeBaseIndex):
super(ActiveSliceItem, self).__init__(partItem)
self._partItem = partItem
self._controller = ActiveSliceItemController(self, partItem.part())
self.setFlag(QGraphicsItem.ItemHasNoContents)
