class ActiveSliceItem(QGraphicsRectItem):
"""ActiveSliceItem for the Slice View"""
def __init__(self, part_item, active_base_index):
super(ActiveSliceItem, self).__init__(part_item)
self._part_item = part_item
self._controller = ActiveSliceItemController(self, part_item.part())
self.setFlag(QGraphicsItem.ItemHasNoContents)
# end def
### SLOTS ###
def strandChangedSlot(self, sender, vh):
if vh == None:
return
part_item = self._part_item
vhi = part_item.getVirtualHelixItemByCoord(*vh.coord())
active_base_idx = part_item.part().activeBaseIndex()
is_active_now = vh.hasStrandAtIdx(active_base_idx)
vhi.setActiveSliceView(is_active_now, active_base_idx)
# end def
def updateIndexSlot(self, sender, newActiveSliceZIndex):
part = self.part()
if part.numberOfVirtualHelices() == 0:
return
newly_active_vhs = set()
active_base_idx = part.activeBaseIndex()
for vhi in self._part_item._virtual_helix_hash.values():
vh = vhi.virtualHelix()
if vh:
is_active_now = vh.hasStrandAtIdx(active_base_idx)
vhi.setActiveSliceView(is_active_now, active_base_idx)
# end def
def updateRectSlot(self, part):
pass
# end def
### ACCESSORS ###
def part(self):
return self._part_item.part()
# end def
### PUBLIC METHODS FOR DRAWING / LAYOUT ###
def removed(self):
self._part_item = None
self._controller.disconnectSignals()
self.controller = None
class ActiveSliceItem(QGraphicsRectItem):
"""ActiveSliceItem for the Slice View"""
def __init__(self, part_item, active_base_index):
super(ActiveSliceItem, self).__init__(part_item)
self._part_item = part_item
self._controller = ActiveSliceItemController(self, part_item.part())
self.setFlag(QGraphicsItem.ItemHasNoContents)
# end def
### SLOTS ###
def strandChangedSlot(self, sender, vh):
if vh == None:
return
part_item = self._part_item
vhi = part_item.getVirtualHelixItemByCoord(*vh.coord())
active_base_idx = part_item.part().activeBaseIndex()
is_active_now = vh.hasStrandAtIdx(active_base_idx)
vhi.setActiveSliceView(is_active_now, active_base_idx)
# end def
def updateIndexSlot(self, sender, newActiveSliceZIndex):
part = self.part()
if part.numberOfVirtualHelices() == 0:
return
newly_active_vhs = set()
active_base_idx = part.activeBaseIndex()
for vhi in self._part_item._virtual_helix_hash.values():
vh = vhi.virtualHelix()
if vh:
is_active_now = vh.hasStrandAtIdx(active_base_idx)
vhi.setActiveSliceView(is_active_now, active_base_idx)
# end def
def updateRectSlot(self, part):
pass
# end def
### ACCESSORS ###
def part(self):
return self._part_item.part()
# end def
### PUBLIC METHODS FOR DRAWING / LAYOUT ###
def removed(self):
self._part_item = None
self._controller.disconnectSignals()
self.controller = None
def __init__(self, part_item, active_base_index):
super(ActiveSliceItem, self).__init__(part_item)
self._part_item = part_item
self._getActiveTool = part_item._getActiveTool
self._active_slice = 0
self._low_drag_bound = 0
self._high_drag_bound = self.part().maxBaseIdx()
self._controller = ActiveSliceItemController(self, part_item.part())
self._label = QGraphicsSimpleTextItem("", parent=self)
self._label.setPos(0, -18)
self._label.setFont(_FONT)
self._label.setBrush(_LABEL_BRUSH)
self._label.hide()
self.setFlag(QGraphicsItem.ItemIsMovable)
self.setAcceptHoverEvents(True)
self.setZValue(styles.ZACTIVESLICEHANDLE)
self.setRect(QRectF(0, 0, _BASE_WIDTH,\
self._part_item.boundingRect().height()))
self.setPos(active_base_index * _BASE_WIDTH, 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, part_item, active_base_index):
super(ActiveSliceItem, self).__init__(part_item)
self._part_item = part_item
self._getActiveTool = part_item._getActiveTool
self._active_slice = 0
self._low_drag_bound = 0
self._high_drag_bound = self.part().maxBaseIdx()
self._controller = ActiveSliceItemController(self, part_item.part())
self._label = QGraphicsSimpleTextItem("", parent=self)
self._label.setPos(0, -18)
self._label.setFont(_FONT)
self._label.setBrush(_LABEL_BRUSH)
self._label.hide()
self.setFlag(QGraphicsItem.ItemIsMovable)
self.setAcceptHoverEvents(True)
self.setZValue(styles.ZACTIVESLICEHANDLE)
self.setRect(QRectF(0, 0, _BASE_WIDTH,\
self._part_item.boundingRect().height()))
self.setPos(active_base_index*_BASE_WIDTH, 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, part_item, active_base_index):
super(ActiveSliceItem, self).__init__(part_item)
self._part_item = part_item
self._getActiveTool = part_item._getActiveTool
self._active_slice = 0
self._low_drag_bound = 0
self._high_drag_bound = self.part().maxBaseIdx()
self._controller = ActiveSliceItemController(self, part_item.part())
self._label = QGraphicsSimpleTextItem("", parent=self)
self._label.setPos(0, -18)
self._label.setFont(_FONT)
self._label.setBrush(_LABEL_BRUSH)
self._label.hide()
self.setFlag(QGraphicsItem.ItemIsMovable)
self.setAcceptHoverEvents(True)
self.setZValue(styles.ZACTIVESLICEHANDLE)
self.setRect(QRectF(0, 0, _BASE_WIDTH,\
self._part_item.boundingRect().height()))
self.setPos(active_base_index*_BASE_WIDTH, 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 = _BASE_WIDTH
new_rect = QRectF(0, 0, bw,\
self._part_item.virtualHelixBoundingRect().height())
if new_rect != self.rect():
self.setRect(new_rect)
self._hideIfEmptySelection()
self.updateIndexSlot(part, part.activeBaseIndex())
return new_rect
# end def
def updateIndexSlot(self, part, base_index):
"""The slot that receives active slice changed notifications from
the part and changes the receiver to reflect the part"""
label = self._label
bw = _BASE_WIDTH
bi = util.clamp(int(base_index), 0, self.part().maxBaseIdx())
self.setPos(bi * bw, -styles.PATH_HELIX_PADDING)
self._active_slice = 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._part_item.part()
# end def
def partItem(self):
return self._part_item
# end def
### PUBLIC METHODS FOR DRAWING / LAYOUT ###
def removed(self):
scene = self.scene()
scene.removeItem(self._label)
scene.removeItem(self)
self._part_item = None
self._label = None
self._controller.disconnectSignals()
self.controller = None
# end def
def resetBounds(self):
"""Call after resizing virtualhelix canvas."""
self._high_drag_bound = 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, base_index):
self.part().setActiveBaseIndex(base_index)
# end def
### EVENT HANDLERS ###
def hoverEnterEvent(self, event):
self.setCursor(Qt.OpenHandCursor)
self._part_item.updateStatusBar("%d" % self.part().activeBaseIndex())
QGraphicsItem.hoverEnterEvent(self, event)
# end def
def hoverLeaveEvent(self, event):
self.setCursor(Qt.ArrowCursor)
self._part_item.updateStatusBar("")
QGraphicsItem.hoverLeaveEvent(self, event)
# end def
def mousePressEvent(self, event):
"""
Parses a mousePressEvent, calling the approproate tool method as
necessary. Stores _move_idx for future comparison.
"""
if event.button() != Qt.LeftButton:
event.ignore()
QGraphicsItem.mousePressEvent(self, event)
return
self.scene().views()[0].addToPressList(self)
self._move_idx = int(floor((self.x() + event.pos().x()) / _BASE_WIDTH))
tool_method_name = self._getActiveTool().methodPrefix() + "MousePress"
if hasattr(self, tool_method_name): # if the tool method exists
modifiers = event.modifiers()
getattr(self, tool_method_name)(modifiers) # call tool method
def mouseMoveEvent(self, event):
"""
Parses a mouseMoveEvent, calling the approproate tool method as
necessary. Updates _move_idx if it changed.
"""
tool_method_name = self._getActiveTool().methodPrefix() + "MouseMove"
if hasattr(self, tool_method_name): # if the tool method exists
idx = int(floor((self.x() + event.pos().x()) / _BASE_WIDTH))
if idx != self._move_idx: # did we actually move?
modifiers = event.modifiers()
self._move_idx = idx
getattr(self, tool_method_name)(modifiers, idx) # call tool method
def customMouseRelease(self, event):
"""
Parses a mouseReleaseEvent, calling the approproate tool method as
necessary. Deletes _move_idx if necessary.
"""
tool_method_name = self._getActiveTool().methodPrefix() + "MouseRelease"
if hasattr(self, tool_method_name): # if the tool method exists
modifiers = event.modifiers()
x = event.pos().x()
getattr(self, tool_method_name)(modifiers, x) # call tool method
if hasattr(self, '_move_idx'):
del self._move_idx
### 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._low_drag_bound, self._high_drag_bound)
x = int(idx * _BASE_WIDTH)
self.setPos(x, self.y())
self.updateIndexSlot(None, idx)
self._setActiveBaseIndex(idx)
self._part_item.updateStatusBar("%d" % self.part().activeBaseIndex())
def __init__(self, part_item, active_base_index):
super(ActiveSliceItem, self).__init__(part_item)
self._part_item = part_item
self._controller = ActiveSliceItemController(self, part_item.part())
self.setFlag(QGraphicsItem.ItemHasNoContents)
def __init__(self, part_item, active_base_index):
super(ActiveSliceItem, self).__init__(part_item)
self._part_item = part_item
self._controller = ActiveSliceItemController(self, part_item.part())
self.setFlag(QGraphicsItem.ItemHasNoContents)
class ActiveSliceItem(QGraphicsRectItem):
"""ActiveSliceItem for the Path View"""
def __init__(self, part_item, active_base_index):
super(ActiveSliceItem, self).__init__(part_item)
self._part_item = part_item
self._getActiveTool = part_item._getActiveTool
self._active_slice = 0
self._low_drag_bound = 0
self._high_drag_bound = self.part().maxBaseIdx()
self._controller = ActiveSliceItemController(self, part_item.part())
self._label = QGraphicsSimpleTextItem("", parent=self)
self._label.setPos(0, -18)
self._label.setFont(_FONT)
self._label.setBrush(_LABEL_BRUSH)
self._label.hide()
self.setFlag(QGraphicsItem.ItemIsMovable)
self.setAcceptHoverEvents(True)
self.setZValue(styles.ZACTIVESLICEHANDLE)
self.setRect(QRectF(0, 0, _BASE_WIDTH,\
self._part_item.boundingRect().height()))
self.setPos(active_base_index * _BASE_WIDTH, 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 = _BASE_WIDTH
new_rect = QRectF(0, 0, bw,\
self._part_item.virtualHelixBoundingRect().height())
if new_rect != self.rect():
self.setRect(new_rect)
self._hideIfEmptySelection()
self.updateIndexSlot(part, part.activeBaseIndex())
return new_rect
# end def
def updateIndexSlot(self, part, base_index):
"""The slot that receives active slice changed notifications from
the part and changes the receiver to reflect the part"""
label = self._label
bw = _BASE_WIDTH
bi = util.clamp(int(base_index), 0, self.part().maxBaseIdx())
self.setPos(bi * bw, -styles.PATH_HELIX_PADDING)
self._active_slice = 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._part_item.part()
# end def
def partItem(self):
return self._part_item
# end def
### PUBLIC METHODS FOR DRAWING / LAYOUT ###
def removed(self):
scene = self.scene()
scene.removeItem(self._label)
scene.removeItem(self)
self._part_item = None
self._label = None
self._controller.disconnectSignals()
self.controller = None
# end def
def resetBounds(self):
"""Call after resizing virtualhelix canvas."""
self._high_drag_bound = 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, base_index):
self.part().setActiveBaseIndex(base_index)
# end def
### EVENT HANDLERS ###
def hoverEnterEvent(self, event):
self.setCursor(Qt.OpenHandCursor)
self._part_item.updateStatusBar("%d" % self.part().activeBaseIndex())
QGraphicsItem.hoverEnterEvent(self, event)
# end def
def hoverLeaveEvent(self, event):
self.setCursor(Qt.ArrowCursor)
self._part_item.updateStatusBar("")
QGraphicsItem.hoverLeaveEvent(self, event)
# end def
def mousePressEvent(self, event):
"""
Parses a mousePressEvent, calling the approproate tool method as
necessary. Stores _move_idx for future comparison.
"""
if event.button() != Qt.LeftButton:
event.ignore()
QGraphicsItem.mousePressEvent(self, event)
return
self.scene().views()[0].addToPressList(self)
self._move_idx = int(floor((self.x() + event.pos().x()) / _BASE_WIDTH))
tool_method_name = self._getActiveTool().methodPrefix() + "MousePress"
if hasattr(self, tool_method_name): # if the tool method exists
modifiers = event.modifiers()
getattr(self, tool_method_name)(modifiers) # call tool method
def mouseMoveEvent(self, event):
"""
Parses a mouseMoveEvent, calling the approproate tool method as
necessary. Updates _move_idx if it changed.
"""
tool_method_name = self._getActiveTool().methodPrefix() + "MouseMove"
if hasattr(self, tool_method_name): # if the tool method exists
idx = int(floor((self.x() + event.pos().x()) / _BASE_WIDTH))
if idx != self._move_idx: # did we actually move?
modifiers = event.modifiers()
self._move_idx = idx
getattr(self, tool_method_name)(modifiers,
idx) # call tool method
def customMouseRelease(self, event):
"""
Parses a mouseReleaseEvent, calling the approproate tool method as
necessary. Deletes _move_idx if necessary.
"""
tool_method_name = self._getActiveTool().methodPrefix(
) + "MouseRelease"
if hasattr(self, tool_method_name): # if the tool method exists
modifiers = event.modifiers()
x = event.pos().x()
getattr(self, tool_method_name)(modifiers, x) # call tool method
if hasattr(self, '_move_idx'):
del self._move_idx
### 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._low_drag_bound, self._high_drag_bound)
x = int(idx * _BASE_WIDTH)
self.setPos(x, self.y())
self.updateIndexSlot(None, idx)
self._setActiveBaseIndex(idx)
self._part_item.updateStatusBar("%d" % self.part().activeBaseIndex())
