def __init__(self, *args, **kwargs):
super(SquarePart, self).__init__(self, *args, **kwargs)
self._maxRow = kwargs.get('maxRow', app().prefs.squareRows)
self._maxCol = kwargs.get('maxCol', app().prefs.squareCols)
self._maxBase = int(
kwargs.get('maxSteps',
app().prefs.squareSteps) * self._step - 1)
def __init__(self, *args, **kwargs):
super(HoneycombPart, self).__init__(self, *args, **kwargs)
self._maxRow = kwargs.get('maxRow', app().prefs.honeycombRows)
self._maxCol = kwargs.get('maxCol', app().prefs.honeycombCols)
self._maxBase = int(
kwargs.get('maxSteps',
app().prefs.honeycombSteps) * self._step - 1)
def __init__(self):
super(Document, self).__init__()
self._undoStack = QUndoStack()
self._parts = []
self._assemblies = []
self._controller = None
self._selectedPart = None
# the dictionary maintains what is selected
self._selectionDict = {}
# the added list is what was recently selected or deselected
self._selectedChangedDict = {}
cadnano.app().documentWasCreatedSignal.emit(self)
def staplePreDecoratorSelected(self, listNames):
"""
Callback function that is called from mayaSelectionContext when a
PreDecorator geometry is called, notifies the Part Model of this
event. XXX - [SB] In the future we should clean up this interaction.
"""
if (len(listNames) > 1):
# If we have more than one PreDecorator Selected, deselect all but
# the last one
cmds.select(listNames[0:len(listNames) - 1], deselect=True)
selectionList = []
for name in listNames:
if name in self.decoratorToVirtualHelixItem:
(virtualHelixItem, baseIdx, strand) = \
self.decoratorToVirtualHelixItem[name]
selectionList.append(
(virtualHelixItem.row(), virtualHelixItem.col(), baseIdx))
if len(selectionList) == 0 and \
self.selectionCountCache == 0:
# a dumb cache check to prevent deselection to be broadcasted too
# many times, but could cause problems
return
# XXX - [SB] we want to only send the signal to "active part" but
# not sure how to get that
for doc in app().documentControllers:
if doc.win.actionModify.isChecked():
for partItem in doc.win.solidroot.partItems():
partModel = partItem.part()
partModel.selectPreDecorator(selectionList)
self.selectionCountCache = len(selectionList)
def __init__(self, mID, modelStrand, virtualHelixItem):
"""
The parent should be a VirtualHelixItem.
Initialize function creates the Maya Node for the strand, and setups
the lookup tables inside of mayaObjectManager (Mom) so that the Maya
Node can be globally found given a strand, and the other way around.
Also, sets up StrandItemController that is used to setup all the
slots and signals between strand model and this strandItem.
"""
self._modelStrand = modelStrand
self._virtualHelixItem = virtualHelixItem
self._viewroot = app().activeDocument.win.solidroot
mayaNodeInfo = ()
# print "solidview.StrandItem.__init__ %s" % mID
if (modelStrand.strandSet().isScaffold()):
mayaNodeInfo = self.createMayaHelixNodes(
virtualHelixItem.x(), virtualHelixItem.y(),
modelStrand.oligo().color(), StrandType.Scaffold, mID)
else:
mayaNodeInfo = self.createMayaHelixNodes(
virtualHelixItem.x(), virtualHelixItem.y(),
modelStrand.oligo().color(), StrandType.Staple, mID)
#self.onStrandDidMove(strand)
m = Mom()
m.cnToMaya[modelStrand] = mayaNodeInfo
m.mayaToCn[mayaNodeInfo[2]] = modelStrand
m.mayaToCn[mayaNodeInfo[0]] = modelStrand
self.updateSize()
self._controller = StrandItemController(self, modelStrand)
def doRelease(self):
# print "RELEASED"
self.isMouseDown = False
if(self.deltaFront != 0):
app().activeDocument.document().resizeSelection(self.deltaFront)
if(self.deltaBack != 0):
app().activeDocument.document().resizeSelection(self.deltaBack)
m = Mom()
m.strandsSelected(self.helicesNames, (True, True))
cmds.hide(helixManip.transformName)
self.frontDistance = 0
self.backDistance = 0
return OpenMaya.kUnknownParameter
def safeScale(self, delta):
currentScaleLevel = self.transform().m11()
scaleFactor = 1 + delta * \
(self._scaleDownRate if delta < 0 else self._scaleUpRate) * \
(app().prefs.zoomSpeed/100.)
newScaleLevel = currentScaleLevel * scaleFactor
newScaleLevel = util.clamp(currentScaleLevel * scaleFactor,\
self._scale_limit_min,\
self._scale_limit_max)
scaleChange = newScaleLevel / currentScaleLevel
self.scale(scaleChange, scaleChange)
self.resetGL()
def _addBasesCallback(self, n):
"""
Given a user-chosen number of bases to add, snap it to an index
where index modulo stepsize is 0 and calls resizeVirtualHelices to
adjust to that size.
"""
part = self._modelPart
self._addBasesDialog.intValueSelected.disconnect(
self._addBasesCallback)
del self._addBasesDialog
maxDelta = int(n / part.stepSize()) * part.stepSize()
part.resizeVirtualHelices(0, maxDelta)
if app().isInMaya():
import maya.cmds as cmds
cmds.select(clear=True)
def strandsSelected(self, listNames, value=(True, True)):
if self.ignoreExternalSelectionSignal:
return
self.ignoreExternalSelectionSignal = True
strandList = []
for nodeName in listNames:
if (nodeName in self.mayaToCn):
strandList.append(self.mayaToCn[nodeName])
doc = app().activeDocument
# # XXX [SB] THIS IS A HACK, should not need to do this!!!
# doc.win.pathroot.clearStrandSelections()
doc.win.solidroot.selectedChanged(strandList, value)
self.ignoreExternalSelectionSignal = False
def __init__(self, win):
super(PathToolManager, self).__init__()
self.window = win
self._activeTool = None
self._activePart = None
self.selectTool = SelectTool(self)
self.pencilTool = PencilTool(self)
self.breakTool = BreakTool(self)
self.eraseTool = EraseTool(self)
self.insertionTool = InsertionTool(self)
self.skipTool = SkipTool(self)
self.paintTool = PaintTool(
self) # (self, win.pathGraphicsView.toolbar)
self.addSeqTool = AddSeqTool(self)
def installTool(toolName, window):
toolWidget = getattr(window, 'actionPath' + toolName)
lToolName = toolName[0].lower() + toolName[1:]
tool = getattr(self, lToolName + 'Tool')
tool.actionName = 'actionPath' + toolName
def clickHandler(self):
toolWidget.setChecked(True)
self.setActiveTool(tool)
if hasattr(tool, 'widgetClicked'):
tool.widgetClicked()
selectToolMethodName = 'choose' + toolName + 'Tool'
setattr(self.__class__, selectToolMethodName, clickHandler)
handler = getattr(self, selectToolMethodName)
toolWidget.triggered.connect(handler)
return toolWidget
tools = ('Select', 'Pencil', 'Break', 'Erase', 'Insertion', 'Skip',
'Paint', 'AddSeq')
ag = QActionGroup(win)
# Call installTool on every tool
list(
map((lambda toolName: ag.addAction(installTool(toolName, win))),
tools))
ag.setExclusive(True)
# Select the preferred Startup tool
startupToolName = app().prefs.getStartupToolName()
getattr(self, 'choose' + startupToolName + 'Tool')()
def _removeBasesClicked(self):
"""
Determines the minimum maxBase index where index modulo stepsize == 0
and is to the right of the rightmost nonempty base, and then resize
each calls the resizeVirtualHelices to adjust to that size.
"""
part = self._modelPart
stepSize = part.stepSize()
# first find out the right edge of the part
idx = part.indexOfRightmostNonemptyBase()
# next snap to a multiple of stepsize
idx = int(ceil(float(idx + 1) / stepSize)) * stepSize
# finally, make sure we're a minimum of stepSize bases
idx = util.clamp(idx, part.stepSize(), 10000)
delta = idx - (part.maxBaseIdx() + 1)
if delta < 0:
part.resizeVirtualHelices(0, delta)
if app().isInMaya():
import maya.cmds as cmds
cmds.select(clear=True)
def mouseReleaseEvent(self, event):
"""docstring for mouseReleaseEvent"""
part = self.part()
uS = part.undoStack()
strands = []
# Look at the undo stack in reverse order
for i in range(uS.index()-1, 0, -1):
# Check for contiguous strand additions
m = _strand_re.match(uS.text(i))
if m:
strands.insert(0, list(map(int, m.groups())))
else:
break
if len(strands) > 1:
autoScafType = app().prefs.getAutoScafType()
util.beginSuperMacro(part, "Auto-connect")
if autoScafType == "Mid-seam":
self.autoScafMidSeam(strands)
elif autoScafType == "Raster":
self.autoScafRaster(strands)
util.endSuperMacro(part)
def decode(document, string):
if cadnano.app().isGui():
# from ui.dialogs.ui_latticetype import Ui_LatticeType
# util.qtWrapImport('QtGui', globals(), ['QDialog', 'QDialogButtonBox'])
dialog = QDialog()
dialogLT = Ui_LatticeType() # reusing this dialog, should rename
dialogLT.setupUi(dialog)
# try: # try to do it fast
# try:
# import cjson
# packageObject = cjson.decode(string)
# except: # fall back to if cjson not available or on decode error
# packageObject = json.loads(string)
# except ValueError:
# dialogLT.label.setText("Error decoding JSON object.")
# dialogLT.buttonBox.setStandardButtons(QDialogButtonBox.Ok)
# dialog.exec()
# return
packageObject = json.loads(string)
if packageObject.get('.format', None) != 'caDNAno2':
import_legacy_dict(document, packageObject)
def __init__(self, parent=None, docCtrlr=None):
super(DocumentWindow, self).__init__(parent)
self.controller = docCtrlr
doc = docCtrlr.document()
self.setupUi(self)
self.settings = QSettings()
self._readSettings()
# Slice setup
self.slicescene = QGraphicsScene(parent=self.sliceGraphicsView)
self.sliceroot = SliceRootItem(rect=self.slicescene.sceneRect(),\
parent=None,\
window=self,\
document=doc)
self.sliceroot.setFlag(
QGraphicsItem.GraphicsItemFlag.ItemHasNoContents)
self.slicescene.addItem(self.sliceroot)
self.slicescene.setItemIndexMethod(
QGraphicsScene.ItemIndexMethod.NoIndex)
assert self.sliceroot.scene() == self.slicescene
self.sliceGraphicsView.setScene(self.slicescene)
self.sliceGraphicsView.sceneRootItem = self.sliceroot
self.sliceGraphicsView.setName("SliceView")
self.sliceToolManager = SliceToolManager(self)
# Path setup
self.pathscene = QGraphicsScene(parent=self.pathGraphicsView)
self.pathroot = PathRootItem(rect=self.pathscene.sceneRect(),\
parent=None,\
window=self,\
document=doc)
self.pathroot.setFlag(QGraphicsItem.GraphicsItemFlag.ItemHasNoContents)
self.pathscene.addItem(self.pathroot)
self.pathscene.setItemIndexMethod(
QGraphicsScene.ItemIndexMethod.NoIndex)
assert self.pathroot.scene() == self.pathscene
self.pathGraphicsView.setScene(self.pathscene)
self.pathGraphicsView.sceneRootItem = self.pathroot
self.pathGraphicsView.setScaleFitFactor(0.9)
self.pathGraphicsView.setName("PathView")
self.pathColorPanel = ColorPanel()
self.pathGraphicsView.toolbar = self.pathColorPanel # HACK for customqgraphicsview
self.pathscene.addItem(self.pathColorPanel)
self.pathToolManager = PathToolManager(self)
self.sliceToolManager.pathToolManager = self.pathToolManager
self.pathToolManager.sliceToolManager = self.sliceToolManager
self.tool_managers = (self.sliceToolManager, self.pathToolManager)
# set the selection filter default
doc.documentSelectionFilterChangedSignal.emit(
["endpoint", "scaffold", "staple", "xover"])
self.pathGraphicsView.setupGL()
self.sliceGraphicsView.setupGL()
if GL:
pass
# self.slicescene.drawBackground = self.drawBackgroundGL
# self.pathscene.drawBackground = self.drawBackgroundGL
if app().isInMaya():
from .solidview.solidrootitem import SolidRootItem
self.splitter.setOrientation(Qt.Vertical)
self.setUnifiedTitleAndToolBarOnMac(False)
modState = self.actionModify.isChecked()
self.solidroot = SolidRootItem(parent=None,
document=doc,
modState=modState)
# Edit menu setup
self.actionUndo = docCtrlr.undoStack().createUndoAction(self)
self.actionRedo = docCtrlr.undoStack().createRedoAction(self)
self.actionUndo.setText(
QApplication.translate("MainWindow", "Undo", None))
self.actionUndo.setShortcut(
QApplication.translate("MainWindow", "Ctrl+Z", None))
self.actionRedo.setText(
QApplication.translate("MainWindow", "Redo", None))
self.actionRedo.setShortcut(
QApplication.translate("MainWindow", "Ctrl+Shift+Z", None))
self.sep = QAction(self)
self.sep.setSeparator(True)
self.menuEdit.insertAction(self.actionModify, self.sep)
self.menuEdit.insertAction(self.sep, self.actionRedo)
self.menuEdit.insertAction(self.actionRedo, self.actionUndo)
self.splitter.setSizes([400, 400]) # balance splitter size
self.statusBar().showMessage("")
import json
from .legacydecoder import import_legacy_dict
from cadnano2.ui.dialogs.ui_latticetype import Ui_LatticeType
import cadnano2.util as util
import cadnano2.cadnano as cadnano
if cadnano.app().isGui(): # headless:
from cadnano2.ui.dialogs.ui_latticetype import Ui_LatticeType
util.qtWrapImport('QtWidgets', globals(), ['QDialog', 'QDialogButtonBox'])
def decode(document, string):
if cadnano.app().isGui():
# from ui.dialogs.ui_latticetype import Ui_LatticeType
# util.qtWrapImport('QtGui', globals(), ['QDialog', 'QDialogButtonBox'])
dialog = QDialog()
dialogLT = Ui_LatticeType() # reusing this dialog, should rename
dialogLT.setupUi(dialog)
# try: # try to do it fast
# try:
# import cjson
# packageObject = cjson.decode(string)
# except: # fall back to if cjson not available or on decode error
# packageObject = json.loads(string)
# except ValueError:
# dialogLT.label.setText("Error decoding JSON object.")
# dialogLT.buttonBox.setStandardButtons(QDialogButtonBox.Ok)
# dialog.exec()
# return
packageObject = json.loads(string)
def focusInEvent(self):
app().undoGroup.setActiveStack(self.controller.undoStack())
from collections import defaultdict
from cadnano2.model.document import Document
from cadnano2.model.enum import LatticeType, StrandType
from cadnano2.model.parts.honeycombpart import HoneycombPart
from cadnano2.model.parts.squarepart import SquarePart
from cadnano2.model.virtualhelix import VirtualHelix
from cadnano2.views import styles
import cadnano2.util as util
import cadnano2.cadnano as cadnano
# import Qt stuff into the module namespace with PySide, PyQt4 independence
util.qtWrapImport('QtGui', globals(), ['QColor'])
if cadnano.app().isGui():
from cadnano2.ui.dialogs.ui_latticetype import Ui_LatticeType
util.qtWrapImport('QtWidgets', globals(), ['QDialog', 'QDialogButtonBox'])
NODETAG = "node"
NAME = "name"
OBJ_ID = "objectid"
INST_ID = "instanceid"
DONE = "done"
CHECKED = "check"
LOCKED = "locked"
VHELIX = "vhelix"
NUM = "num"
COL = "col"
ROW = "row"
SCAFFOLD = "scaffold"
STAPLE = "staple"
INSERTION = "insertion"
def import_legacy_dict(document, obj, latticeType=LatticeType.Honeycomb):
"""
Parses a dictionary (obj) created from reading a json file and uses it
to populate the given document with model data.
"""
numBases = len(obj['vstrands'][0]['scaf'])
if cadnano.app().isGui():
# from ui.dialogs.ui_latticetype import Ui_LatticeType
# util.qtWrapImport('QtGui', globals(), ['QDialog', 'QDialogButtonBox'])
dialog = QDialog()
dialogLT = Ui_LatticeType()
dialogLT.setupUi(dialog)
# DETERMINE LATTICE TYPE
if numBases % 21 == 0 and numBases % 32 == 0:
if dialog.exec() == 1:
latticeType = LatticeType.Square
else:
latticeType = LatticeType.Honeycomb
elif numBases % 32 == 0:
latticeType = LatticeType.Square
elif numBases % 21 == 0:
latticeType = LatticeType.Honeycomb
else:
if dialog.exec() == 1:
latticeType = LatticeType.Square
else:
latticeType = LatticeType.Honeycomb
else: # Headless, assume the latticeType arg was meaningful
pass
# DETERMINE MAX ROW,COL
maxRowJson = maxColJson = 0
for helix in obj['vstrands']:
maxRowJson = max(maxRowJson, int(helix['row']) + 1)
maxColJson = max(maxColJson, int(helix['col']) + 1)
# CREATE PART ACCORDING TO LATTICE TYPE
if latticeType == LatticeType.Honeycomb:
steps = numBases / 21
nRows = max(30, maxRowJson, cadnano.app().prefs.honeycombRows)
nCols = max(32, maxColJson, cadnano.app().prefs.honeycombCols)
part = HoneycombPart(document=document,
maxRow=nRows,
maxCol=nCols,
maxSteps=steps)
elif latticeType == LatticeType.Square:
isSQ100 = True # check for custom SQ100 format
for helix in obj['vstrands']:
if helix['col'] != 0:
isSQ100 = False
break
if isSQ100:
dialogLT.label.setText("Is this a SQ100 file?")
if dialog.exec() == 1:
nRows, nCols = 100, 1
else:
nRows, nCols = 40, 30
else:
nRows, nCols = 40, 30
steps = numBases / 32
nRows = max(30, maxRowJson, cadnano.app().prefs.squareRows)
nCols = max(32, maxColJson, cadnano.app().prefs.squareCols)
part = SquarePart(document=document,
maxRow=nRows,
maxCol=nCols,
maxSteps=steps)
else:
raise TypeError("Lattice type not recognized")
document._addPart(part, useUndoStack=False)
# POPULATE VIRTUAL HELICES
orderedCoordList = []
vhNumToCoord = {}
for helix in obj['vstrands']:
vhNum = helix['num']
row = helix['row']
col = helix['col']
scaf = helix['scaf']
coord = (row, col)
vhNumToCoord[vhNum] = coord
orderedCoordList.append(coord)
# make sure we retain the original order
for vhNum in sorted(vhNumToCoord.keys()):
row, col = vhNumToCoord[vhNum]
part.createVirtualHelix(row, col, useUndoStack=False)
part.setImportedVHelixOrder(orderedCoordList)
# INSTALL STRANDS AND COLLECT XOVER LOCATIONS
numHelixes = len(obj['vstrands']) - 1
scaf_seg = defaultdict(list)
scaf_xo = defaultdict(list)
stap_seg = defaultdict(list)
stap_xo = defaultdict(list)
try:
for helix in obj['vstrands']:
vhNum = helix['num']
row = helix['row']
col = helix['col']
scaf = helix['scaf']
stap = helix['stap']
insertions = helix['loop']
skips = helix['skip']
vh = part.virtualHelixAtCoord((row, col))
scafStrandSet = vh.scaffoldStrandSet()
stapStrandSet = vh.stapleStrandSet()
assert(len(scaf)==len(stap) and len(stap)==part.maxBaseIdx()+1 and\
len(scaf)==len(insertions) and len(insertions)==len(skips))
# read scaffold segments and xovers
for i in range(len(scaf)):
fiveVH, fiveIdx, threeVH, threeIdx = scaf[i]
if fiveVH == -1 and threeVH == -1:
continue # null base
if isSegmentStartOrEnd(StrandType.Scaffold, vhNum, i, fiveVH,\
fiveIdx, threeVH, threeIdx):
scaf_seg[vhNum].append(i)
if fiveVH != vhNum and threeVH != vhNum: # special case
scaf_seg[vhNum].append(
i) # end segment on a double crossover
if is3primeXover(StrandType.Scaffold, vhNum, i, threeVH,
threeIdx):
scaf_xo[vhNum].append((i, threeVH, threeIdx))
assert (len(scaf_seg[vhNum]) % 2 == 0)
# install scaffold segments
for i in range(0, len(scaf_seg[vhNum]), 2):
lowIdx = scaf_seg[vhNum][i]
highIdx = scaf_seg[vhNum][i + 1]
scafStrandSet.createStrand(lowIdx, highIdx, useUndoStack=False)
# read staple segments and xovers
for i in range(len(stap)):
fiveVH, fiveIdx, threeVH, threeIdx = stap[i]
if fiveVH == -1 and threeVH == -1:
continue # null base
if isSegmentStartOrEnd(StrandType.Staple, vhNum, i, fiveVH,\
fiveIdx, threeVH, threeIdx):
stap_seg[vhNum].append(i)
if fiveVH != vhNum and threeVH != vhNum: # special case
stap_seg[vhNum].append(
i) # end segment on a double crossover
if is3primeXover(StrandType.Staple, vhNum, i, threeVH,
threeIdx):
stap_xo[vhNum].append((i, threeVH, threeIdx))
assert (len(stap_seg[vhNum]) % 2 == 0)
# install staple segments
for i in range(0, len(stap_seg[vhNum]), 2):
lowIdx = stap_seg[vhNum][i]
highIdx = stap_seg[vhNum][i + 1]
stapStrandSet.createStrand(lowIdx, highIdx, useUndoStack=False)
except AssertionError:
if not cadnano.app().isGui():
print("Unrecognized file format.")
else:
dialogLT.label.setText("Unrecognized file format.")
dialogLT.buttonBox.setStandardButtons(QDialogButtonBox.Ok)
dialog.exec()
# INSTALL XOVERS
for helix in obj['vstrands']:
vhNum = helix['num']
row = helix['row']
col = helix['col']
scaf = helix['scaf']
stap = helix['stap']
insertions = helix['loop']
skips = helix['skip']
fromVh = part.virtualHelixAtCoord((row, col))
scafStrandSet = fromVh.scaffoldStrandSet()
stapStrandSet = fromVh.stapleStrandSet()
# install scaffold xovers
for (idx5p, toVhNum, idx3p) in scaf_xo[vhNum]:
# idx3p is 3' end of strand5p, idx5p is 5' end of strand3p
strand5p = scafStrandSet.getStrand(idx5p)
toVh = part.virtualHelixAtCoord(vhNumToCoord[toVhNum])
strand3p = toVh.scaffoldStrandSet().getStrand(idx3p)
part.createXover(strand5p,
idx5p,
strand3p,
idx3p,
useUndoStack=False)
# install staple xovers
for (idx5p, toVhNum, idx3p) in stap_xo[vhNum]:
# idx3p is 3' end of strand5p, idx5p is 5' end of strand3p
strand5p = stapStrandSet.getStrand(idx5p)
toVh = part.virtualHelixAtCoord(vhNumToCoord[toVhNum])
strand3p = toVh.stapleStrandSet().getStrand(idx3p)
part.createXover(strand5p,
idx5p,
strand3p,
idx3p,
useUndoStack=False)
# SET DEFAULT COLOR
for oligo in part.oligos():
if oligo.isStaple():
defaultColor = styles.DEFAULT_STAP_COLOR
else:
defaultColor = styles.DEFAULT_SCAF_COLOR
oligo.applyColor(defaultColor, useUndoStack=False)
# COLORS, INSERTIONS, SKIPS
for helix in obj['vstrands']:
vhNum = helix['num']
row = helix['row']
col = helix['col']
scaf = helix['scaf']
stap = helix['stap']
insertions = helix['loop']
skips = helix['skip']
vh = part.virtualHelixAtCoord((row, col))
scafStrandSet = vh.scaffoldStrandSet()
stapStrandSet = vh.stapleStrandSet()
# install insertions and skips
for baseIdx in range(len(stap)):
sumOfInsertSkip = insertions[baseIdx] + skips[baseIdx]
if sumOfInsertSkip != 0:
scaf_strand = scafStrandSet.getStrand(baseIdx)
stap_strand = stapStrandSet.getStrand(baseIdx)
if scaf_strand:
scaf_strand.addInsertion(baseIdx,
sumOfInsertSkip,
useUndoStack=False)
elif stap_strand:
stap_strand.addInsertion(baseIdx,
sumOfInsertSkip,
useUndoStack=False)
# end for
# populate colors
for baseIdx, colorNumber in helix['stap_colors']:
color = QColor((colorNumber >> 16) & 0xFF,
(colorNumber >> 8) & 0xFF,
colorNumber & 0xFF).name()
strand = stapStrandSet.getStrand(baseIdx)
strand.oligo().applyColor(color, useUndoStack=False)
pos += minStapleLegLen
if not isTerminalStrand:
maxIdx -= minStapleLegLen
while idx <= maxIdx:
isTerminalNode = isTerminalStrand and idx == maxIdx
nodes.append((pos, strand, idx, isTerminalNode))
idx += 1
pos += 1
pos += minStapleLegLen - 1
else:
minIdx, idx = strand.lowIdx(), strand.highIdx() + 1
if strand != firstStrand:
idx -= minStapleLegLen
pos += minStapleLegLen
if not isTerminalStrand:
minIdx += minStapleLegLen
while idx >= minIdx:
isTerminalNode = isTerminalStrand and idx == minIdx
nodes.append((pos, strand, idx, isTerminalNode))
idx -= 1
pos += 1
pos += minStapleLegLen - 1
strand = nextStrand
if isTerminalStrand:
break
# if nodes: # dump the node array to stdout
# print ' '.join(str(n[0])+':'+str(n[2]) for n in nodes) + (' :: %i'%oligo.length()) + repr(nodes[-1])
return nodes
cadnano.app().breakStaples = breakStaples
def updateSelectionBoxes(self):
selectedItems = cmds.ls(self.helixTransformName + "*", selection=True)
if selectedItems:
bbox = cmds.exactWorldBoundingBox(selectedItems)
cmds.setAttr(self.selectionBox + ".scale",
bbox[3] - bbox[0],
bbox[4] - bbox[1],
bbox[5] - bbox[2],
type="double3")
cmds.setAttr(self.selectionBox + ".translate",
(bbox[0] + bbox[3]) / 2, (bbox[1] + bbox[4]) / 2,
(bbox[2] + bbox[5]) / 2,
type="double3")
cmds.showHidden(self.selectionBox)
selectionDict = app().activeDocument.document().selectionDict()
frontEp = 0
backEp = 0
for strandSetDict in selectionDict.values():
for strand, value in strandSetDict.items():
frontEp += int(value[0])
backEp += int(value[1])
if (frontEp == 0) ^ (backEp == 0):
epBoundBox = None
for strandSetDict in selectionDict.values():
for strand, value in strandSetDict.items():
# XXX The following line is a work around for broken
# path selection in model, remove when fixed
if not strand in self.cnToMaya:
continue
helixNode = self.cnToMaya[strand]
boundBox = cmds.exactWorldBoundingBox(helixNode[1])
# might be better to get the rise this way...
#n = OpenMaya.MFnDependencyNode(helixNode)
#risePlug = n.findPlug("rise")
#rise = risePlug.asDouble()
# but this works too
idxL, idxH = strand.idxs()
rise = (boundBox[5] - boundBox[2]) / (idxH - idxL + 1)
if frontEp == 0:
boundBox[5] = boundBox[2] + rise
elif backEp == 0:
boundBox[2] = boundBox[5] - rise
if epBoundBox == None:
epBoundBox = boundBox
else:
# union the boxes
epBoundBox[0] = min(epBoundBox[0], boundBox[0])
epBoundBox[1] = min(epBoundBox[1], boundBox[1])
epBoundBox[2] = min(epBoundBox[2], boundBox[2])
epBoundBox[3] = max(epBoundBox[3], boundBox[3])
epBoundBox[4] = max(epBoundBox[4], boundBox[4])
epBoundBox[5] = max(epBoundBox[5], boundBox[5])
# XXX The following line is a work around for broken
# path selection in model, remove when fixed
if not epBoundBox == None:
cmds.showHidden(self.epSelectionBox)
cmds.setAttr(self.epSelectionBox + ".scale",
epBoundBox[3] - epBoundBox[0],
epBoundBox[4] - epBoundBox[1],
epBoundBox[5] - epBoundBox[2],
type="double3")
cmds.setAttr(self.epSelectionBox + ".translate",
(epBoundBox[0] + epBoundBox[3]) / 2,
(epBoundBox[1] + epBoundBox[4]) / 2,
(epBoundBox[2] + epBoundBox[5]) / 2,
type="double3")
else:
cmds.hide(self.epSelectionBox)
else:
cmds.hide(self.selectionBox)
cmds.hide(self.epSelectionBox)
