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.
douglaslab · Oct 28, 2023 · 82badb9 · 82badb9
1 parent 17aa629
commit 82badb9
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Showing 10 changed files with 96 additions and 59 deletions.
diff --git a/cadnano2/cadnano.py b/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
diff --git a/cadnano2/model/io/legacydecoder.py b/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:

diff --git a/cadnano2/model/io/legacyencoder.py b/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}

diff --git a/cadnano2/model/oligo.py b/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):

diff --git a/cadnano2/model/strandset.py b/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()

diff --git a/cadnano2/ui/mainwindow/ui_mainwindow.py b/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"))

diff --git a/cadnano2/views/pathview/colorpanel.py b/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):

diff --git a/cadnano2/views/pathview/tools/painttool.py b/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")

diff --git a/cadnano2/views/styles.py b/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)):

diff --git a/setup.py b/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",