def _initParts(self):
gm = ['Alignment._initParts()']
if len(self.parts):
for p in self.parts:
del (p)
self.parts = []
if self.equates:
eqSymb = list(self.equates.keys())
eqSymb.sort()
eqSymb = string.join(eqSymb, '')
else:
eqSymb = ''
if len(self.sequences) and self.length and self.symbols and self.dim:
pass
else:
gm.append("Can't allocate part.")
if not len(self.sequences):
gm.append("-no sequences.")
elif not self.length:
gm.append("-the sequences have no length")
elif not self.symbols:
gm.append("-no symbols")
elif not self.dim:
gm.append("-dim not set")
raise Glitch(gm)
if not self.nexusSets or not self.nexusSets.charPartition: # its all one part
aPart = Part()
aPart.alignment = self
aPart.name = 'all'
aPart.lowName = 'all'
aPart.dataType = self.dataType
aPart.dim = self.dim
aPart.symbols = self.symbols
aPart.equates = self.equates
aPart.nTax = len(self.sequences)
aPart.nChar = self.length
assert aPart.nChar
if 0:
print(gm[0])
print(" symbols=%s" % self.symbols)
aPart.cPart = pf.newPart(len(self.sequences), self.length, eqSymb,
self.symbols)
if not aPart or not aPart.cPart:
gm.append("Failed to get memory for part.")
raise Glitch(gm)
# Make the equates table
verbose = 0
equatesTable = []
if verbose:
print("equates is %s" % self.equates)
print("eqSymb is %s" % eqSymb) # the keys
print("symbols is %s" % self.symbols)
for i in range(len(eqSymb)):
if verbose: print("%3s: " % eqSymb[i], end=' ')
e = self.equates[eqSymb[i]]
if verbose: print("%8s : " % e, end=' ')
for s in self.symbols:
if s in e:
if verbose: print("%1i" % 1, end=' ')
equatesTable.append('1')
else:
if verbose: print("%1i" % 0, end=' ')
equatesTable.append('0')
if verbose: print('')
equatesTable = string.join(equatesTable, '')
if verbose:
print("\n\nequatesTable:")
print(equatesTable)
pf.pokeEquatesTable(aPart.cPart, equatesTable)
sList = []
for s in self.sequences:
sList.append(s.sequence)
if 0:
print(gm[0])
print("sList = %s" % sList)
print("joined = %s" % string.join(sList, ''))
pf.pokeSequences(aPart.cPart, string.join(sList, ''))
#print "about to makePatterns ..."
pf.makePatterns(aPart.cPart)
#print "about to setInvar"
pf.setGlobalInvarSitesVec(aPart.cPart)
#pf.dumpPart(aPart.cPart)
self.parts.append(aPart)
elif self.nexusSets.charPartition:
for cpp in self.nexusSets.charPartition.subsets:
#print "Doing subset '%s', mask: %s" % (cpp.name, cpp.mask)
#print "About to subsetUsingMask (self length is %i)" % self.length
b = self.subsetUsingMask(cpp.mask)
b._initParts(
) # This very method, but now there are no charPartitions in b.
b.parts[0].name = cpp.name
b.parts[0].lowName = string.lower(cpp.name)
self.parts.append(b.parts[0])
b.parts = [] # so we don't try free-ing it twice
def resetPartsContentFromSequences(self):
"""Reset Part.cPart sequences from self.sequences.
It then makes patterns, and sets the global invariant sites
array. """
gm = ['Alignment.resetPartsContentFromSequences()']
if len(self.parts) == 1: # its all one part
aPart = self.parts[0]
if not var.doDataPart:
sList = []
for s in self.sequences:
sList.append(s.sequence)
pf.pokeSequences(aPart.cPart, string.join(sList, ''))
# are the following necessary?
pf.makePatterns(aPart.cPart)
pf.setGlobalInvarSitesVec(aPart.cPart)
else:
for sNum in range(len(self.sequences)):
s = self.sequences[sNum]
for cNum in range(self.length):
theChar = s.sequence[cNum]
if theChar == '-':
aPart.seq[sNum, cNum] = var.GAP_CODE
if theChar == '?':
aPart.seq[sNum, cNum] = var.QMARK_CODE
elif aPart.equateSymbols and theChar in aPart.equateSymbols:
aPart.seq[sNum, cNum] = var.EQUATES_BASE + \
aPart.equateSymbols.index(theChar)
else:
aPart.seq[sNum, cNum] = aPart.symbols.index(
theChar)
elif len(self.parts) > 1:
# the number of parts is also the length of the subsets list
if self.nexusSets and self.nexusSets.charPartition and \
self.nexusSets.charPartition.subsets and \
len(self.nexusSets.charPartition.subsets) == len(self.parts):
pass
else:
gm.append(
'Something is wrong with the nexusSets or its charPartition')
raise P4Error(gm)
for i in range(len(self.parts)):
cpSubset = self.nexusSets.charPartition.subsets[i]
aPart = self.parts[i]
b = self.subsetUsingMask(cpSubset.mask)
if not var.doDataPart:
sList = []
for s in b.sequences:
sList.append(s.sequence)
pf.pokeSequences(aPart.cPart, string.join(sList, ''))
# are the following necessary?
pf.makePatterns(aPart.cPart)
pf.setGlobalInvarSitesVec(aPart.cPart)
else:
for sNum in range(len(b.sequences)):
s = b.sequences[sNum]
for cNum in range(b.length):
theChar = s.sequence[cNum]
if theChar == '-':
aPart.seq[sNum, cNum] = var.GAP_CODE
if theChar == '?':
aPart.seq[sNum, cNum] = var.QMARK_CODE
elif aPart.equateSymbols and theChar in aPart.equateSymbols:
aPart.seq[
sNum, cNum] = var.EQUATES_BASE + aPart.equateSymbols.index(theChar)
else:
aPart.seq[sNum, cNum] = aPart.symbols.index(
theChar)
else:
gm.append("No parts.")
raise P4Error(gm)
def resetPartsContentFromSequences(self):
"""Reset Part.cPart sequences from self.sequences.
It then makes patterns, and sets the global invariant sites
array. """
gm = ['Alignment.resetPartsContentFromSequences()']
if len(self.parts) == 1: # its all one part
aPart = self.parts[0]
if not var.doDataPart:
sList = []
for s in self.sequences:
sList.append(s.sequence)
pf.pokeSequences(aPart.cPart, string.join(sList, ''))
# are the following necessary?
pf.makePatterns(aPart.cPart)
pf.setGlobalInvarSitesVec(aPart.cPart)
else:
for sNum in range(len(self.sequences)):
s = self.sequences[sNum]
for cNum in range(self.length):
theChar = s.sequence[cNum]
if theChar == '-':
aPart.seq[sNum, cNum] = var.GAP_CODE
if theChar == '?':
aPart.seq[sNum, cNum] = var.QMARK_CODE
elif aPart.equateSymbols and theChar in aPart.equateSymbols:
aPart.seq[
sNum,
cNum] = var.EQUATES_BASE + aPart.equateSymbols.index(
theChar)
else:
aPart.seq[sNum, cNum] = aPart.symbols.index(theChar)
elif len(self.parts) > 1:
# the number of parts is also the length of the subsets list
if self.nexusSets and self.nexusSets.charPartition and \
self.nexusSets.charPartition.subsets and \
len(self.nexusSets.charPartition.subsets) == len(self.parts):
pass
else:
gm.append(
'Something is wrong with the nexusSets or its charPartition')
raise Glitch(gm)
for i in range(len(self.parts)):
cpSubset = self.nexusSets.charPartition.subsets[i]
aPart = self.parts[i]
b = self.subsetUsingMask(cpSubset.mask)
if not var.doDataPart:
sList = []
for s in b.sequences:
sList.append(s.sequence)
pf.pokeSequences(aPart.cPart, string.join(sList, ''))
# are the following necessary?
pf.makePatterns(aPart.cPart)
pf.setGlobalInvarSitesVec(aPart.cPart)
else:
for sNum in range(len(b.sequences)):
s = b.sequences[sNum]
for cNum in range(b.length):
theChar = s.sequence[cNum]
if theChar == '-':
aPart.seq[sNum, cNum] = var.GAP_CODE
if theChar == '?':
aPart.seq[sNum, cNum] = var.QMARK_CODE
elif aPart.equateSymbols and theChar in aPart.equateSymbols:
aPart.seq[
sNum,
cNum] = var.EQUATES_BASE + aPart.equateSymbols.index(
theChar)
else:
aPart.seq[sNum,
cNum] = aPart.symbols.index(theChar)
else:
gm.append("No parts.")
raise Glitch(gm)
def _initParts(self):
gm = ['Alignment._initParts()']
if len(self.parts):
for p in self.parts:
del(p)
self.parts = []
if self.equates:
eqSymb = self.equates.keys()
eqSymb.sort()
eqSymb = string.join(eqSymb, '')
else:
eqSymb = ''
if len(self.sequences) and self.length and self.symbols and self.dim:
pass
else:
gm.append("Can't allocate part.")
if not len(self.sequences):
gm.append("-no sequences.")
elif not self.length:
gm.append("-the sequences have no length")
elif not self.symbols:
gm.append("-no symbols")
elif not self.dim:
gm.append("-dim not set")
raise P4Error(gm)
# its all one part
if not self.nexusSets or not self.nexusSets.charPartition:
aPart = Part()
aPart.alignment = self
aPart.name = 'all'
aPart.lowName = 'all'
aPart.dataType = self.dataType
aPart.dim = self.dim
aPart.symbols = self.symbols
aPart.equates = self.equates
aPart.nTax = len(self.sequences)
aPart.nChar = self.length
assert aPart.nChar
if 0:
print gm[0]
print " symbols=%s" % self.symbols
aPart.cPart = pf.newPart(len(self.sequences), self.length,
eqSymb, self.symbols)
if not aPart or not aPart.cPart:
gm.append("Failed to get memory for part.")
raise P4Error(gm)
# Make the equates table
verbose = 0
equatesTable = []
if verbose:
print "equates is %s" % self.equates
print "eqSymb is %s" % eqSymb # the keys
print "symbols is %s" % self.symbols
for i in range(len(eqSymb)):
if verbose:
print "%3s: " % eqSymb[i],
e = self.equates[eqSymb[i]]
if verbose:
print "%8s : " % e,
for s in self.symbols:
if s in e:
if verbose:
print "%1i" % 1,
equatesTable.append('1')
else:
if verbose:
print "%1i" % 0,
equatesTable.append('0')
if verbose:
print ''
equatesTable = string.join(equatesTable, '')
if verbose:
print "\n\nequatesTable:"
print equatesTable
pf.pokeEquatesTable(aPart.cPart, equatesTable)
sList = []
for s in self.sequences:
sList.append(s.sequence)
if 0:
print gm[0]
print "sList = %s" % sList
print "joined = %s" % string.join(sList, '')
pf.pokeSequences(aPart.cPart, string.join(sList, ''))
# print "about to makePatterns ..."
pf.makePatterns(aPart.cPart)
# print "about to setInvar"
pf.setGlobalInvarSitesVec(aPart.cPart)
# pf.dumpPart(aPart.cPart)
self.parts.append(aPart)
elif self.nexusSets.charPartition:
for cpp in self.nexusSets.charPartition.subsets:
# print "Doing subset '%s', mask: %s" % (cpp.name, cpp.mask)
# print "About to subsetUsingMask (self length is %i)" %
# self.length
b = self.subsetUsingMask(cpp.mask)
# This very method, but now there are no charPartitions in b.
b._initParts()
b.parts[0].name = cpp.name
b.parts[0].lowName = string.lower(cpp.name)
self.parts.append(b.parts[0])
b.parts = [] # so we don't try free-ing it twice
