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 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 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.iterkeys()):
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:
strand = scafStrandSet.getStrand(baseIdx)
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)
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.iterkeys()):
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)
