def validateCoherence(arySegments):
# Collapse all segments into a single list and measure coherence
aryVectors = [ i for f, ary in arySegments for i in ary ]
aryCoherence = [ 0 for i in xrange(len(aryVectors)) ]
for i in xrange(2, len(aryVectors)):
if Codons.isCoherent([ aryVectors[i-2], aryVectors[i-1], aryVectors[i-0] ]):
aryCoherence[i-2] += 1
aryCoherence[i-1] += 1
aryCoherence[i-0] += 1
# Divide measured coherence into lists matching the original segments
for i in xrange(len(arySegments)):
aryCoherence[i:i] = [ aryCoherence[i:i+len(arySegments[i][1]) ] ]
aryCoherence[i+1:i+1+len(arySegments[i][1])] = []
# Check the expected coherence of each segment against that measured
for i in xrange(len(arySegments)):
fCoherent, aryVectors = arySegments[i]
if (fCoherent and aryCoherence[i].count(0)) or (not fCoherent and (aryCoherence[i].count(0) != len(aryCoherence[i]))):
if i > 0:
fC, aryV = arySegments[i-1]
Common.sayError('Coherent(%c) %d - %s' % (fC and 'T' or 'F', len(aryV), ' '.join([ Codons.Vectors.toName(id) for id in aryV ])))
Common.sayError('Coherent(%c) %d - %s' % (fCoherent and 'T' or 'F', len(aryVectors), ' '.join([ Codons.Vectors.toName(id) for id in aryVectors ])))
Common.sayError(' - %s' % ' '.join([ ' %d ' % j for j in aryCoherence[i] ]))
if i < len(arySegments)-1:
fC, aryV = arySegments[i+1]
Common.sayError('Coherent(%c) %d - %s' % (fC and 'T' or 'F', len(aryV), ' '.join([ Codons.Vectors.toName(id) for id in aryV ])))
raise Common.BiologicError('Failed to create a gene with proper coherence - segment %d should be %s but has %s vectors' % (i+1,
fCoherent and 'Coherent' or 'Incoherent',
fCoherent and 'Incoherent' or 'Coherent'))
def buildGenes(uchHan, aryGenes):
Common.say('Creating %d gene(s)' % len(aryGenes))
han = loadHan(uchHan)
strAuthor = Globals.strAuthor and (" author='%s'" % Globals.strAuthor) or ''
aryGeneNames = []
for specification in aryGenes:
Common.say('Creating gene from specification ' + specification)
gs = GeneSpecification(specification != Constants.strDefault and specification or '', han)
gsName = gs.toName(han.unicode) + Common.Constants.extGene
gsPoints = gs.getPoints()
Common.say('Gene to be named ' + gsName)
ptCurrent = Genome.Point(pt=gsPoints[0][1][0])
arySegments = []
# Convert each set of points into a list of vectors
for iSegment in xrange(len(gsPoints)):
fCoherent, aryPoints = gsPoints[iSegment]
# Build the segment starting from the current location
# - Ensure incoherent segments always begin at the current location
# (This causes moves to absorb the tracing error, effectively trading placement error for stroke fit error.)
if not fCoherent:
aryPoints[0].x = ptCurrent.x
aryPoints[0].y = ptCurrent.y
ptCurrent, aryVectors = buildSegment(ptCurrent, fCoherent, aryPoints)
if not fCoherent:
# If the segment contains too few vectors, pad it with an incoherent sequence
# - If there are no vectors, use No/So/Ea/We - binding code will ensure proper coherence at the endpoints
# - Otherwise, use the four points of the direction "compass" that are guaranteed incoherent with the last vector
if len(aryVectors) < 3:
iDirection = len(aryVectors) and Codons.Directions.add(Codons.Vectors.toDirection(aryVectors[-1]), 3) or Codons.Directions.North
aryVectors.append(Codons.Vectors.create(iDirection))
aryVectors.append(Codons.Vectors.create(Codons.Directions.toOpposite(iDirection)))
iDirection = Codons.Directions.add(iDirection, 2)
aryVectors.append(Codons.Vectors.create(iDirection))
aryVectors.append(Codons.Vectors.create(Codons.Directions.toOpposite(iDirection)))
# Inject vectors to force incoherency for incoherent segments
# - Essentially, add a vector pair to every two that forces incoherency
# - Walking the list must take into account injected vector pairs
else:
iVector = 0
while iVector < len(aryVectors):
if Codons.isCoherent([aryVectors[iVector-2], aryVectors[iVector-1], aryVectors[iVector+0]]):
idVector = aryVectors[iVector]
aryVectors.insert(iVector+0, Codons.Vectors.toOpposite(idVector))
aryVectors.insert(iVector+1, idVector)
iVector += 1
# Ensure the vectors "bind" without affecting the coherence of an adjoining segment
if iSegment:
fCoherencePrev, aryVectorsPrev = arySegments[-1]
if Codons.isCoherent([ aryVectorsPrev[-2], aryVectorsPrev[-1], aryVectors[0] ]) or Codons.isCoherent([ aryVectorsPrev[-1], aryVectors[0], aryVectors[1] ]):
if not fCoherencePrev:
aryVectorsPrev += [ Codons.Vectors.toOpposite(aryVectorsPrev[-1]), aryVectorsPrev[-1], aryVectors[0], Codons.Vectors.toOpposite(aryVectors[0]) ]
else:
aryVectors[:0] = [ Codons.Vectors.toOpposite(aryVectorsPrev[-1]), aryVectorsPrev[-1], aryVectors[0], Codons.Vectors.toOpposite(aryVectors[0]) ]
arySegments.append((fCoherent, aryVectors))
validateCoherence(arySegments)
aryCodons = [ Codons.Vectors.toVector(idVector).codon for fCoherent, aryVectors in arySegments for idVector in aryVectors ]
aryCodons[:0] = [ 'ATG' ]
aryCodons.append(Codons.Vectors.toVector(Codons.Vectors.create(Codons.Directions.Stop, Codons.Constants.iVectorShort)).codon)
aryStrokes = []
iStroke = 0
iBase = 4
for fCoherent, aryVectors in arySegments:
if fCoherent:
aryStrokes.append(_GENE_STROKE % (iBase, iBase+(len(aryVectors)*3-1), gs.mapStrokeToHan(iStroke)+1))
iStroke += 1
iBase += len(aryVectors) * 3
strGene = _GENE_DEFINITION % (str(uuid.uuid4()).upper(), strAuthor, datetime.datetime.utcnow().isoformat(), _NAME, str(gs),
''.join(aryCodons), len(aryCodons)*3,
gsPoints[0][1][0].x, gsPoints[0][1][0].y,
han.unicode,
'\n'.join(aryStrokes))
strPath = Common.resolvePath(os.path.join(Globals.strGenePath, Common.makeHanPath(gsName)))
strDir = os.path.dirname(strPath)
if not os.path.exists(strDir):
try: os.makedirs(os.path.dirname(strPath))
except OSError, err: raise Common.BiologicError('Unable to create %s - %s' % (strDir, str(err)))
try:
fileGene = os.open(strPath, os.O_CREAT | os.O_TRUNC | os.O_WRONLY, 0664)
os.write(fileGene, strGene)
except IOError, err: raise Common.BiologicError('Unable to create %s - %s' % (strPath, str(err)))
os.close(fileGene)
Common.say('\tWrote %s - %d codons, %d bases' % (strPath, len(aryCodons), len(aryCodons)*3))
aryGeneNames.append(gsName)
return aryGeneNames