Enhanced support for scaffold colors

- File encoder now saves scaffold oligo colors to a "scaf_colors" dict within relevant the virtual helix.
- Similar to staples, scaffold color information is saved once per oligo, at the idx5p of the strand5p. This also applies to circular oligos (`oligo.isLoop() == True`).
- File decoder will load any saved "scaf_colors" values and restore them upon opening.
- Added keyboard shortcut `Shift+P` to cycle through scaffold color list when the Paint Tool is active.
- The "scaf" selection filter (shortcut key `c`) must be enabled to apply colors to scaffold, and can be disabled to limit coloring to staples.

Bug fixes:
- cadnano.py Removed import of deprecated `imp` package. It was only used for Maya compatibility. This change should prevent import errors in python 3.12, as in issue #52
- legacydecoder: Use QDialogButtonBox.StandardButton enum to avoid crash on unrecognized file format.

cadnano2/cadnano.py

@@ -1,4 +1,4 @@
-import sys, imp
+import sys
 import os.path
 from glob import glob
 from code import interact
@@ -87,23 +87,25 @@ def unloadedPlugins():
  results.append(f)
  return [x for x in results if x not in loadedPlugins]
 
-def loadPlugin(f):
- path, fname = os.path.split(f)
- name, ext = os.path.splitext(fname)
- pluginKey = os.path.join(path, name)
- try:
- mod = loadedPlugins[pluginKey]
- return mod
- except KeyError:
- pass
- file, filename, data = imp.find_module(name, [path])
- mod = imp.load_module(name, file, filename, data)
- loadedPlugins[pluginKey] = mod
- return mod
+# Plugins are no longer supported, so needn't import imp
+
+# def loadPlugin(f):
+# path, fname = os.path.split(f)
+# name, ext = os.path.splitext(fname)
+# pluginKey = os.path.join(path, name)
+# try:
+# mod = loadedPlugins[pluginKey]
+# return mod
+# except KeyError:
+# pass
+# file, filename, data = imp.find_module(name, [path])
+# mod = imp.load_module(name, file, filename, data)
+# loadedPlugins[pluginKey] = mod
+# return mod
 
-def loadAllPlugins():
- loadedAPlugin = False
- for p in unloadedPlugins():
- loadPlugin(p)
- loadedAPlugin = True
- return loadedAPlugin
+# def loadAllPlugins():
+#  loadedAPlugin = False
+#  for p in unloadedPlugins():
+#  loadPlugin(p)
+#  loadedAPlugin = True
+#  return loadedAPlugin

cadnano2/model/io/legacydecoder.py

@@ -174,7 +174,7 @@ def import_legacy_dict(document, obj, latticeType=LatticeType.Honeycomb):
  print("Unrecognized file format.")
  else:
  dialogLT.label.setText("Unrecognized file format.")
- dialogLT.buttonBox.setStandardButtons(QDialogButtonBox.Ok)
+ dialogLT.buttonBox.setStandardButtons(QDialogButtonBox.StandardButton.Ok)
  dialog.exec()
 
  # INSTALL XOVERS
@@ -234,13 +234,20 @@ def import_legacy_dict(document, obj, latticeType=LatticeType.Honeycomb):
  scaf_strand.addInsertion(baseIdx, sumOfInsertSkip, useUndoStack=False)
  elif stap_strand:
  stap_strand.addInsertion(baseIdx, sumOfInsertSkip, useUndoStack=False)
- # end for
- # populate colors
+
+ # populate staple 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)
 
+ # populate scaffold colors, if any
+ if 'scaf_colors' in helix:
+ for baseIdx, colorNumber in helix['scaf_colors']:
+ color = QColor((colorNumber>>16)&0xFF, (colorNumber>>8)&0xFF, colorNumber&0xFF).name()
+ strand = scafStrandSet.getStrand(baseIdx)
+ strand.oligo().applyColor(color, useUndoStack=False)
+
 def isSegmentStartOrEnd(strandType, vhNum, baseIdx, fiveVH, fiveIdx, threeVH, threeIdx):
  """Returns True if the base is a breakpoint or crossover."""
  if strandType == StrandType.Scaffold:

cadnano2/model/io/legacyencoder.py

@@ -21,11 +21,16 @@ def legacy_dict_from_doc(document, fname, helixOrderList):
  insts[idx] = insertion.length()
  # colors
  stapColors = []
- stapStrandSet = vh.stapleStrandSet()
- for strand in stapStrandSet:
+ for strand in vh.stapleStrandSet():
  if strand.connection5p() == None:
  c = str(strand.oligo().color())[1:] # drop the hash
  stapColors.append([strand.idx5Prime(), int(c, 16)])
+ scafColors = set()
+ for strand in vh.scaffoldStrandSet():
+ if strand.connection5p() == None or \
+ (strand == strand.oligo().strand5p() and strand.oligo().isLoop()):
+ c = str(strand.oligo().color())[1:] # drop the hash
+ scafColors.add((strand.idx5Prime(), int(c, 16)))
 
  vhDict = {"row": row,
  "col": col,
@@ -36,7 +41,8 @@ def legacy_dict_from_doc(document, fname, helixOrderList):
  "skip": skips,
  "scafLoop": [],
  "stapLoop": [],
- "stap_colors": stapColors}
+ "stap_colors": stapColors,
+ "scaf_colors": list(scafColors)}
  vhList.append(vhDict)
  bname = basename(str(fname))
  obj = {"name": bname, "vstrands": vhList}

cadnano2/model/oligo.py

@@ -90,7 +90,7 @@ def undoStack(self):
  # end def
 
  ### PUBLIC METHODS FOR QUERYING THE MODEL ###
- def isLoop(self):
+ def isLoop(self): # isCircular
  return self._isLoop
 
  def isStaple(self):

cadnano2/model/strandset.py

@@ -737,7 +737,7 @@ def __init__(self, strandSet, baseIdxLow, baseIdxHigh, strandSetIdx):
  self._strandSet = strandSet
  self._sSetIdx = strandSetIdx
  self._strand = Strand(strandSet, baseIdxLow, baseIdxHigh)
- colorList = styles.stapColors if strandSet.isStaple() else styles.scafColors
+ colorList = styles.stapColors if strandSet.isStaple() else [styles.scafColors[0]] # default to classic 0066cc
  color = random.choice(colorList).name()
  self._newOligo = Oligo(None, color) # redo will set part
  self._newOligo.setLength(self._strand.totalLength())
@@ -803,7 +803,7 @@ def __init__(self, strandSet, strand, strandSetIdx, solo=True):
  else:
  self._newOligo3p = olg3p = olg.shallowCopy()
  olg3p.setStrand5p(self._oldStrand3p)
- colorList = styles.stapColors if strandSet.isStaple() else styles.scafColors
+ colorList = styles.stapColors if strandSet.isStaple() else [styles.scafColors[0]]
  color = random.choice(colorList).name()
  olg3p.setColor(color)
  olg3p.refreshLength()

cadnano2/ui/mainwindow/ui_mainwindow.py

@@ -398,7 +398,7 @@ def retranslateUi(self, MainWindow):
  self.actionRenumber.setToolTip(_translate("MainWindow", "Renumber Slice helices according to helix ordering in Path panel."))
  self.actionPathPaint.setText(_translate("MainWindow", "Paint"))
  self.actionPathPaint.setToolTip(_translate("MainWindow", "(P)aint Tool"))
- self.actionPathPaint.setShortcut(_translate("MainWindow", "P"))
+ self.actionPathPaint.setShortcuts([_translate("MainWindow", "P"), _translate("MainWindow", "Shift+P")])
  self.actionPathAddSeq.setText(_translate("MainWindow", "Seq"))
  self.actionPathAddSeq.setToolTip(_translate("MainWindow", "(A)dd Sequence Tool"))
  self.actionPathAddSeq.setShortcut(_translate("MainWindow", "A"))

cadnano2/views/pathview/colorpanel.py

@@ -2,7 +2,8 @@
 import cadnano2.util as util
 util.qtWrapImport('QtCore', globals(), ['QRectF', 'Qt'])
 util.qtWrapImport('QtGui', globals(), ['QBrush', 'QFont'])
-util.qtWrapImport('QtWidgets', globals(), ['QColorDialog',
+util.qtWrapImport('QtWidgets', globals(), ['QApplication',
+ 'QColorDialog',
  'QGraphicsItem',
  'QGraphicsSimpleTextItem'])
 
@@ -20,7 +21,7 @@ def __init__(self, parent=None):
  self.setFlag(QGraphicsItem.GraphicsItemFlag.ItemIgnoresTransformations)
  self.colordialog = QColorDialog()
  # self.colordialog.setOption(QColorDialog.DontUseNativeDialog)
- self._scafColorIndex = -1 # init on -1, painttool will cycle to 0
+ self._scafColorIndex = 0 # init on -1, painttool will cycle to 0
  self._stapColorIndex = -1 # init on -1, painttool will cycle to 0
  self._scafColor = self._scafColors[self._scafColorIndex]
  self._stapColor = self._stapColors[self._stapColorIndex]
@@ -47,14 +48,22 @@ def paint(self, painter, option, widget=None):
  painter.drawRect(0, 15, 30, 15)
 
  def nextColor(self):
- self._stapColorIndex += 1
- if self._stapColorIndex == len(self._stapColors):
- self._stapColorIndex = 0
- self._stapColor = self._stapColors[self._stapColorIndex]
- self._stapBrush.setColor(self._stapColor)
+ if QApplication.keyboardModifiers() & Qt.KeyboardModifier.ShiftModifier:
+ self._scafColorIndex += 1
+ if self._scafColorIndex == len(self._scafColors):
+ self._scafColorIndex = 0
+ self._scafColor = self._scafColors[self._scafColorIndex]
+ self._scafBrush.setColor(self._scafColor)
+ else:
+ self._stapColorIndex += 1
+ if self._stapColorIndex == len(self._stapColors):
+ self._stapColorIndex = 0
+ self._stapColor = self._stapColors[self._stapColorIndex]
+ self._stapBrush.setColor(self._stapColor)
  self.update()
 
  def prevColor(self):
+ self._scafColorIndex -= 1
  self._stapColorIndex -= 1
 
  def color(self):

cadnano2/views/pathview/tools/painttool.py

@@ -3,6 +3,7 @@
 import cadnano2.util as util
 util.qtWrapImport('QtCore', globals(), [])
 util.qtWrapImport('QtGui', globals(), [])
+util.qtWrapImport('QtWidgets', globals(), ['QApplication'])
 
 
 class PaintTool(AbstractPathTool):
@@ -27,17 +28,17 @@ def setActive(self, willBeActive):
  def widgetClicked(self):
  """Cycle through colors on 'p' keypress"""
  self._window.pathColorPanel.nextColor()
- 
+
  def customMouseRelease(self, event):
  if self._isMacrod:
  self._isMacrod = False
  self._window.undoStack().endMacro()
  # end def
- 
+
  def isMacrod(self):
  return self._isMacrod
  # end def
- 
+
  def setMacrod(self):
  self._isMacrod = True
  self._window.undoStack().beginMacro("Group Paint")

cadnano2/views/styles.py

@@ -70,26 +70,38 @@
 breakfill = QColor(204, 0, 0, 255)
 colorbox_fill = QColor(204, 0, 0)
 colorbox_stroke = QColor(102, 102, 102)
-stapColors = [QColor(204, 0, 0),
- QColor(247, 67, 8),
- QColor(247, 147, 30),
- QColor(170, 170, 0),
- QColor(87, 187, 0),
- QColor(0, 114, 0),
- QColor(3, 182, 162),
- QColor(23, 0, 222),
- QColor(115, 0, 222),
- QColor(184, 5, 108),
- QColor(51, 51, 51),
- QColor(136, 136, 136)]
-scafColors = [QColor(0, 102, 204)]
- # QColor(64, 138, 212),
- # QColor(0, 38, 76),
- # QColor(23, 50, 76),
- # QColor(0, 76, 153)]
+stapColors = [
+ QColor(204, 0, 0), #cc0000
+ QColor(247, 67, 8), #f74308
+ QColor(247, 147, 30), #f7931e
+ QColor(170, 170, 0), #aaaa00
+ QColor( 87, 187, 0), #57bb00
+ QColor( 0, 114, 0), #007200
+ QColor( 3, 182, 162), #03b6a2
+ QColor( 23, 0, 222), #1700de
+ QColor(115, 0, 222), #7300de
+ QColor(184, 5, 108), #b8056c
+ QColor( 51, 51, 51), #333333
+ QColor(136, 136, 136) #888888
+]
+
+scafColors = [
+ QColor( 0, 102, 204), #0066cc
+ QColor(102, 0, 0), #990000
+ QColor(139, 48, 6), #b83006
+ QColor(198, 125, 23), #c67d17
+ QColor(136, 136, 0), #888800
+ QColor( 68, 119, 0), #447700
+ QColor( 0, 85, 0), #005500
+ QColor( 15, 0, 183), #0f00b7
+ QColor( 91, 0, 171), #5b00ab
+ QColor(157, 5, 108), #9d034f
+ QColor( 2, 126, 130), #027e82
+]
+
 DEFAULT_STAP_COLOR = "#888888"
 DEFAULT_SCAF_COLOR = "#0066cc"
-selected_color = QColor(255, 51, 51)
+selected_color = QColor(255, 51, 51) #ff3333
 
 # brightColors = [QColor() for i in range(10)]
 # for i in range(len(brightColors)):

setup.py

@@ -5,7 +5,7 @@
 
 setup(
  name='cadnano2',
- version='2.4.10', 
+ version='2.4.11',
  description='Cadnano2 for PyQt6',
  long_description=long_description,
  long_description_content_type="text/markdown",