def writePhylipToOpenFile(self, flob, digitsAfterDecimal):
gm = ["DistanceMatrix.writePhylipToOpenFile()"]
assert self.dim, "Distance Matrix.writePhylipToOpenFile() no dim"
f = flob
f.write('%i\n' % self.dim)
# Make the format strings.
if digitsAfterDecimal > 8:
totWid = digitsAfterDecimal + 5
else:
totWid = 11
#colNameFormat = '%' + '-%is' % totWid
if digitsAfterDecimal == 0:
numberFormat = ' %' + '%ii ' % (totWid - 4)
elif digitsAfterDecimal > 0:
numberFormat = '%' + '%i.%if' % (totWid, digitsAfterDecimal)
else:
gm.append("digitsAfterDecimal may not be below zero.")
raise Glitch, gm
longestNameLength = 0
for i in self.names:
if len(i) > longestNameLength:
longestNameLength = len(i)
nameFormat = '%' + '%is ' % longestNameLength
for i in range(self.dim):
if self.names:
f.write(' ')
f.write(nameFormat %
func.nexusFixNameIfQuotesAreNeeded(self.names[i]))
for j in range(self.dim):
#f.write('%10.6f' % self.matrix[i][j])
f.write(numberFormat % self.matrix[i][j])
f.write('\n')
f.write('\n')
def writePhylipToOpenFile(self, flob, digitsAfterDecimal):
gm = ["DistanceMatrix.writePhylipToOpenFile()"]
assert self.dim, "Distance Matrix.writePhylipToOpenFile() no dim"
f = flob
f.write('%i\n' % self.dim)
# Make the format strings.
if digitsAfterDecimal > 8:
totWid = digitsAfterDecimal + 5
else:
totWid = 11
#colNameFormat = '%' + '-%is' % totWid
if digitsAfterDecimal == 0:
numberFormat = ' %' + '%ii ' % (totWid - 4)
elif digitsAfterDecimal > 0:
numberFormat = '%' + '%i.%if' % (totWid, digitsAfterDecimal)
else:
gm.append("digitsAfterDecimal may not be below zero.")
raise P4Error(gm)
longestNameLength = 0
for i in self.names:
if len(i) > longestNameLength:
longestNameLength = len(i)
nameFormat = '%' + '%is ' % longestNameLength
for i in range(self.dim):
if self.names:
f.write(' ')
f.write(nameFormat %
func.nexusFixNameIfQuotesAreNeeded(self.names[i]))
for j in range(self.dim):
#f.write('%10.6f' % self.matrix[i][j])
f.write(numberFormat % self.matrix[i][j])
f.write('\n')
f.write('\n')
def writeNexus(self, fName=None, append=0, withTranslation=0, writeTaxaBlock=1, likeMcmc=0):
"""Write the trees out in NEXUS format, in a trees block.
If *fName* is None, the default, it is written to `sys.stdout`.
#NEXUS is written unless we are *append*-ing.
"""
gm = ['Trees.writeNexus()']
if withTranslation:
if not self.taxNames:
gm.append("No taxNames. Set taxNames if you want withTranslation.")
raise Glitch, gm
translationHash = {}
i = 1
for tName in self.taxNames:
translationHash[tName] = i
i += 1
else:
translationHash = None
if fName == None or fName == sys.stdout:
f = sys.stdout
if not append:
f.write('#NEXUS\n\n')
else:
if append:
import os
if os.path.isfile(fName):
try:
f = open(fName, 'a')
except IOError:
gm.append("Can't open %s for appending." % fName)
raise Glitch, gm
else:
if 0:
print gm[0]
print " 'append' is requested,"
print " but '%s' is not a regular file (doesn't exist?)." \
% fName
print " Writing to a new file instead."
try:
f = open(fName, 'w')
f.write('#NEXUS\n\n')
except IOError:
gm.append("Can't open %s for writing." % fName)
raise Glitch, gm
else:
try:
f = open(fName, 'w')
f.write('#NEXUS\n\n')
except IOError:
gm.append("Can't open %s for writing." % fName)
raise Glitch, gm
if writeTaxaBlock:
if self.taxNames:
f.write('begin taxa;\n')
f.write(' dimensions ntax=%s;\n' % self.nTax)
f.write(' taxlabels')
for tN in self.taxNames:
f.write(' %s' % func.nexusFixNameIfQuotesAreNeeded(tN))
f.write(';\nend;\n\n')
else:
gm.append("writeTaxaBlock is set, but there is no taxNames. How did *that* happen?!?")
raise Glitch, gm
f.write('begin trees;\n')
# write the "translate" command
if withTranslation:
f.write(' translate\n')
for i in range(self.nTax - 1):
f.write(' %3i %s,\n' % (i + 1, func.nexusFixNameIfQuotesAreNeeded(self.taxNames[i])))
f.write(' %3i %s\n' % (self.nTax, func.nexusFixNameIfQuotesAreNeeded(self.taxNames[-1])))
f.write(' ;\n')
# write the models comment
if self.trees:
first = self.trees[0]
if likeMcmc:
if not withTranslation:
gm.append("withTranslation is turned off, but likeMcmc is turned on.")
gm.append("This will cause grief in TreePartitions, so is prohibited.")
gm.append("Both on or both off, please.")
raise Glitch, gm
f.write(' [&&p4 models p%i' % first.model.nParts)
for pNum in range(first.model.nParts):
f.write(' c%i.%i' % (pNum, first.model.parts[pNum].nComps))
f.write(' r%i.%i' % (pNum, first.model.parts[pNum].nRMatrices))
f.write(' g%i.%i' % (pNum, first.model.parts[pNum].nGdasrvs))
f.write(']\n')
# write each tree
for t in self.trees:
if not self.writeBranchLengths:
t.stripBrLens()
if t.logLike:
f.write(' [logLike for tree %s is %f]\n' % (t.name, t.logLike))
f.write(' tree %s = [&U] ' % func.nexusFixNameIfQuotesAreNeeded(t.name))
if t.recipWeight:
#if t.recipWeight == 1:
# f.write('[&W 1] ')
#else:
f.write('[&W 1/%i] ' % t.recipWeight)
if hasattr(t, 'weight'):
f.write('[&W %f] ' % t.weight)
t.writeNewick(f, withTranslation=withTranslation, translationHash=translationHash, doMcmcCommandComments=likeMcmc)
f.write('end;\n\n')
if f != sys.stdout:
f.close()
def writeNexus(self, fName=None, append=0, withTranslation=0, writeTaxaBlock=1, likeMcmc=0):
"""Write the trees out in NEXUS format, in a trees block.
If *fName* is None, the default, it is written to `sys.stdout`.
#NEXUS is written unless we are *append*-ing.
"""
gm = ['Trees.writeNexus()']
if withTranslation:
if not self.taxNames:
gm.append("No taxNames. Set taxNames if you want withTranslation.")
raise Glitch, gm
translationHash = {}
i = 1
for tName in self.taxNames:
translationHash[tName] = i
i += 1
else:
translationHash = None
if fName == None or fName == sys.stdout:
f = sys.stdout
if not append:
f.write('#NEXUS\n\n')
else:
if append:
import os
if os.path.isfile(fName):
try:
f = open(fName, 'a')
except IOError:
gm.append("Can't open %s for appending." % fName)
raise Glitch, gm
else:
if 0:
print gm[0]
print " 'append' is requested,"
print " but '%s' is not a regular file (doesn't exist?)." \
% fName
print " Writing to a new file instead."
try:
f = open(fName, 'w')
f.write('#NEXUS\n\n')
except IOError:
gm.append("Can't open %s for writing." % fName)
raise Glitch, gm
else:
try:
f = open(fName, 'w')
f.write('#NEXUS\n\n')
except IOError:
gm.append("Can't open %s for writing." % fName)
raise Glitch, gm
if writeTaxaBlock:
if self.taxNames:
f.write('begin taxa;\n')
f.write(' dimensions ntax=%s;\n' % self.nTax)
f.write(' taxlabels')
for tN in self.taxNames:
f.write(' %s' % func.nexusFixNameIfQuotesAreNeeded(tN))
f.write(';\nend;\n\n')
else:
gm.append("writeTaxaBlock is set, but there is no taxNames. How did *that* happen?!?")
raise Glitch, gm
f.write('begin trees;\n')
# write the "translate" command
if withTranslation:
f.write(' translate\n')
for i in range(self.nTax - 1):
f.write(' %3i %s,\n' % (i + 1, func.nexusFixNameIfQuotesAreNeeded(self.taxNames[i])))
f.write(' %3i %s\n' % (self.nTax, func.nexusFixNameIfQuotesAreNeeded(self.taxNames[-1])))
f.write(' ;\n')
# write the models comment
if self.trees:
first = self.trees[0]
if likeMcmc:
if not withTranslation:
gm.append("withTranslation is turned off, but likeMcmc is turned on.")
gm.append("This will cause grief in TreePartitions, so is prohibited.")
gm.append("Both on or both off, please.")
raise Glitch, gm
f.write(' [&&p4 models p%i' % first.model.nParts)
for pNum in range(first.model.nParts):
f.write(' c%i.%i' % (pNum, first.model.parts[pNum].nComps))
f.write(' r%i.%i' % (pNum, first.model.parts[pNum].nRMatrices))
f.write(' g%i.%i' % (pNum, first.model.parts[pNum].nGdasrvs))
f.write(']\n')
# write each tree
for t in self.trees:
if not self.writeBranchLengths:
t.stripBrLens()
if t.logLike:
f.write(' [logLike for tree %s is %f]\n' % (t.name, t.logLike))
f.write(' tree %s = [&U] ' % func.nexusFixNameIfQuotesAreNeeded(t.name))
if t.recipWeight:
#if t.recipWeight == 1:
# f.write('[&W 1] ')
#else:
f.write('[&W 1/%i] ' % t.recipWeight)
t.writeNewick(f, withTranslation=withTranslation, translationHash=translationHash, doMcmcCommandComments=likeMcmc)
f.write('end;\n\n')
if f != sys.stdout:
f.close()
def writeNewick(
self, fName=None, withTranslation=0, translationHash=None, doMcmcCommandComments=0, toString=False, append=False
):
"""Write the tree in Newick, aka Phylip, format.
This is done in a Nexus-oriented way. If taxNames have spaces or
odd characters, they are single-quoted. There is no restriction
on the length of the taxon names. A translationHash can be used.
fName may also be an open file object.
If 'toString' is turned on, then 'fName' should be None, and a Newick
representation of the tree is returned as a string.
The method 'writePhylip()' is the same as this, with fewer arguments.
"""
gm = ["Tree.writeNewick()"]
sList = []
if withTranslation and not translationHash:
gm.append("No translationHash.")
raise Glitch, gm
if fName and toString:
gm.append("You cannot write to a file and string at the same time.")
raise Glitch, gm
if doMcmcCommandComments:
if not self.model:
gm.append("No model attached to tree.")
gm.append("Set doMcmcCommandComments=0")
raise Glitch, gm
# print 'self.preAndPostOrderAreValid = %s' % self.preAndPostOrderAreValid
if not self.preAndPostOrderAreValid:
self.setPreAndPostOrder()
# print "self.preOrder = %s" % self.preOrder
nNodes = len([n for n in self.iterNodes()]) # Don't count un-used nodes.
# print "nNodes = %i" % nNodes
if nNodes == 1:
# print "Single node. isLeaf=%s, name=%s" % (self.root.isLeaf, self.root.name)
if self.root.isLeaf:
if withTranslation:
sList.append("%s" % translationHash[self.root.name])
elif self.root.name:
sList.append("%s" % func.nexusFixNameIfQuotesAreNeeded(self.root.name))
else:
sList.append("()")
else:
# Will this ever happen?
gm.append("Something is wrong. There is only one node, and it is not terminal.")
raise Glitch, gm
elif nNodes > 1:
writeBrLens = 0
for n in self.iterNodesNoRoot():
if n.br.len != 0.1:
writeBrLens = 1
break
stack = []
for n in self.iterPreOrder():
stack.append(n)
if n.leftChild:
sList.append("(")
continue
while len(stack):
n1 = stack.pop()
# print "stacklen=%i, n1 name=%s" % (len(stack), n1.name)
if n1.isLeaf:
if n1 == self.root:
sList.append(")")
if withTranslation:
sList.append("%s" % (translationHash[n1.name]))
else:
if n1.name:
sList.append("%s" % func.nexusFixNameIfQuotesAreNeeded(n1.name))
else:
if n1 != self.root:
gm.append("Terminal node with no name?")
raise Glitch, gm
else:
sList.append(")")
if n1.name:
sList.append("%s" % func.nexusFixNameIfQuotesAreNeeded(n1.name))
if writeBrLens:
if n1 != self.root:
sList.append(":%g" % n1.br.len)
if doMcmcCommandComments:
sList.append(self._getMcmcCommandComment(n1))
if n1.sibling:
sList.append(", ")
break
sList.append(";\n")
if toString:
return "".join(sList)
elif fName == None:
print "".join(sList)
elif type(fName) == type("string"):
if append:
fName2 = file(fName, "a")
else:
fName2 = file(fName, "w")
fName2.write(string.join(sList, ""))
# fName2.write('\n')
fName2.close()
elif hasattr(fName, "write"):
fName.write(string.join(sList, ""))
# fName.write('\n')
# Somebody else opened the fName, so somebody else can close it.
else:
gm.append("I don't understand (%s) passed to me to write to." % fName)
raise Glitch, gm
def writeNexus(self, fName=None, append=0, writeTaxaBlockIfTaxNamesIsSet=1, message=None):
"""Write the tree out in Nexus format, in a trees block.
If fName is None, the default, it is written to sys.stdout.
#NEXUS is written unless we are appending-- set append=1.
If you want to write with a translation, use a Trees object.
"""
gm = ["Tree.writeNexus()"]
if fName == None or fName == sys.stdout:
f = sys.stdout
if not append:
f.write("#NEXUS\n\n")
else:
if append:
import os
if os.path.isfile(fName):
try:
f = open(fName, "a")
except IOError:
gm.append("Can't open %s for appending." % fName)
raise Glitch, gm
else:
if 0:
print "Tree.writeNexus()"
print " 'append' is requested,"
print " but '%s' is not a regular file (doesn't exist?)." % fName
print " Writing to a new file instead."
try:
f = open(fName, "w")
f.write("#NEXUS\n\n")
except IOError:
gm.append("Can't open %s for writing." % fName)
raise Glitch, gm
else:
try:
f = open(fName, "w")
f.write("#NEXUS\n\n")
except IOError:
gm.append("Can't open %s for writing." % fName)
raise Glitch, gm
if writeTaxaBlockIfTaxNamesIsSet and self.taxNames:
f.write("begin taxa;\n")
f.write(" dimensions ntax=%s;\n" % self.nTax)
f.write(" taxlabels")
for i in self.taxNames:
f.write(" %s" % func.nexusFixNameIfQuotesAreNeeded(i))
f.write(";\nend;\n\n")
f.write("begin trees;\n")
if message:
f.write(" [%s\n ]\n" % message)
if self.logLike:
f.write(" [logLike for tree %s is %f]\n" % (self.name, self.logLike))
f.write(" tree %s = [&U] " % func.nexusFixNameIfQuotesAreNeeded(self.name))
if self.recipWeight:
if self.recipWeight == 1:
f.write("[&W 1] ")
else:
f.write("[&W 1/%i] " % self.recipWeight)
if hasattr(self, "weight"):
f.write("[&W %f] " % self.weight)
self.writeNewick(f)
f.write("end;\n\n")
if f != sys.stdout:
f.close()
def writeNexusToOpenFile(self, flob, writeTaxaBlock, append, digitsAfterDecimal):
gm = ["DistanceMatrix.writeNexusToOpenFile()"]
import string
assert self.dim, "Distance Matrix.writeNexusToOpenFile() no dim"
f = flob
if append:
pass
else:
f.write('#NEXUS\n\n')
if writeTaxaBlock:
f.write('begin taxa;\n')
f.write(' dimensions ntax=%s;\n' % self.dim)
f.write(' taxlabels')
for i in range(self.dim):
f.write(' %s' % func.nexusFixNameIfQuotesAreNeeded(self.names[i]))
f.write(';\n')
f.write('end;\n\n')
f.write('begin distances;\n')
if self.message:
f.write("\n [%s\n ]\n" % self.message)
f.write(' format triangle=both;\n')
f.write(' matrix\n')
# Make the format strings.
if digitsAfterDecimal > 8:
totWid = digitsAfterDecimal + 5
else:
totWid = 11
#colNameFormat = '%' + '-%is' % totWid
if digitsAfterDecimal == 0:
numberFormat = ' %' + '%ii ' % (totWid - 4)
elif digitsAfterDecimal > 0:
numberFormat = '%' + '%i.%if' % (totWid, digitsAfterDecimal)
else:
gm.append("digitsAfterDecimal may not be below zero.")
raise Glitch, gm
if self.names:
longestNameLength = 0
for i in self.names:
if len(i) > longestNameLength:
longestNameLength = len(i)
nameFormat = '%' + '%is ' % longestNameLength
f.write(' [')
f.write(nameFormat % ' ')
for i in self.names:
#f.write('%-10s' % i[:9])
colName = '%s' % i[:totWid - 1]
f.write(string.center(colName, totWid))
f.write(']\n')
for i in range(self.dim):
if self.names:
f.write(' ')
f.write(nameFormat % func.nexusFixNameIfQuotesAreNeeded(self.names[i]))
for j in range(self.dim):
#f.write('%10.6f' % self.matrix[i][j])
f.write(numberFormat % self.matrix[i][j])
f.write('\n')
f.write(' ;\n')
f.write('end;\n')
def writeNewick(self, fName=None, withTranslation=0, translationHash=None, doMcmcCommandComments=0, toString=False, append=False):
"""Write the tree in Newick, aka Phylip, format.
This is done in a Nexus-oriented way. If taxNames have spaces or
odd characters, they are single-quoted. There is no restriction
on the length of the taxon names. A translationHash can be used.
fName may also be an open file object.
If 'toString' is turned on, then 'fName' should be None, and a Newick
representation of the tree is returned as a string.
The method 'writePhylip()' is the same as this, with fewer arguments.
"""
gm = ['Tree.writeNewick()']
sList = []
if withTranslation and not translationHash:
gm.append("No translationHash.")
raise Glitch, gm
if fName and toString:
gm.append("You cannot write to a file and string at the same time.")
raise Glitch, gm
if doMcmcCommandComments:
if not self.model:
gm.append("No model attached to tree.")
gm.append("Set doMcmcCommandComments=0")
raise Glitch, gm
#print 'self.preAndPostOrderAreValid = %s' % self.preAndPostOrderAreValid
if not self.preAndPostOrderAreValid:
self.setPreAndPostOrder()
#print "self.preOrder = %s" % self.preOrder
nNodes = len([n for n in self.iterNodes()]) # Don't count un-used nodes.
#print "nNodes = %i" % nNodes
if nNodes == 1:
#print "Single node. isLeaf=%s, name=%s" % (self.root.isLeaf, self.root.name)
if self.root.isLeaf:
if withTranslation:
sList.append('%s' % translationHash[self.root.name])
elif self.root.name:
sList.append('%s' % func.nexusFixNameIfQuotesAreNeeded(self.root.name))
else:
sList.append('()')
else:
# Will this ever happen?
gm.append("Something is wrong. There is only one node, and it is not terminal.")
raise Glitch, gm
elif nNodes > 1:
writeBrLens = 0
for n in self.iterNodesNoRoot():
if n.br.len != 0.1:
writeBrLens = 1
break
stack = []
for n in self.iterPreOrder():
stack.append(n)
if n.leftChild:
sList.append('(')
continue
while len(stack):
n1 = stack.pop()
#print "stacklen=%i, n1 name=%s" % (len(stack), n1.name)
if n1.isLeaf:
if n1 == self.root:
sList.append(')')
if withTranslation:
sList.append('%s' % (translationHash[n1.name]))
else:
if n1.name:
sList.append('%s' % func.nexusFixNameIfQuotesAreNeeded(n1.name))
else:
if n1 != self.root:
gm.append("Terminal node with no name?")
raise Glitch, gm
else:
sList.append(')')
if n1.name:
sList.append('%s' % func.nexusFixNameIfQuotesAreNeeded(n1.name))
if writeBrLens:
if n1 != self.root:
sList.append(':%g' % n1.br.len)
if doMcmcCommandComments:
sList.append(self._getMcmcCommandComment(n1))
if n1.sibling:
sList.append(', ')
break
sList.append(';\n')
if toString:
return "".join(sList)
elif fName == None:
print "".join(sList)
elif type(fName) == type('string'):
if append:
fName2 = file(fName, 'a')
else:
fName2 = file(fName, 'w')
fName2.write(string.join(sList, ''))
# fName2.write('\n')
fName2.close()
elif hasattr(fName, 'write'):
fName.write(string.join(sList, ''))
#fName.write('\n')
# Somebody else opened the fName, so somebody else can close it.
else:
gm.append("I don't understand (%s) passed to me to write to." % fName)
raise Glitch, gm
def writeNexus(self, fName=None, append=0, writeTaxaBlockIfTaxNamesIsSet=1, message=None):
"""Write the tree out in Nexus format, in a trees block.
If fName is None, the default, it is written to sys.stdout.
#NEXUS is written unless we are appending-- set append=1.
If you want to write with a translation, use a Trees object.
"""
gm = ['Tree.writeNexus()']
if fName == None or fName == sys.stdout:
f = sys.stdout
if not append:
f.write('#NEXUS\n\n')
else:
if append:
import os
if os.path.isfile(fName):
try:
f = open(fName, 'a')
except IOError:
gm.append("Can't open %s for appending." % fName)
raise Glitch, gm
else:
if 0:
print "Tree.writeNexus()"
print " 'append' is requested,"
print " but '%s' is not a regular file (doesn't exist?)." \
% fName
print " Writing to a new file instead."
try:
f = open(fName, 'w')
f.write('#NEXUS\n\n')
except IOError:
gm.append("Can't open %s for writing." % fName)
raise Glitch, gm
else:
try:
f = open(fName, 'w')
f.write('#NEXUS\n\n')
except IOError:
gm.append("Can't open %s for writing." % fName)
raise Glitch, gm
if writeTaxaBlockIfTaxNamesIsSet and self.taxNames:
f.write('begin taxa;\n')
f.write(' dimensions ntax=%s;\n' % self.nTax)
f.write(' taxlabels')
for i in self.taxNames:
f.write(' %s' % func.nexusFixNameIfQuotesAreNeeded(i))
f.write(';\nend;\n\n')
f.write('begin trees;\n')
if message:
f.write(' [%s\n ]\n' % message)
if self.logLike:
f.write(' [logLike for tree %s is %f]\n' % (self.name, self.logLike))
f.write(' tree %s = [&U] ' % func.nexusFixNameIfQuotesAreNeeded(self.name))
if self.recipWeight:
if self.recipWeight == 1:
f.write('[&W 1] ')
else:
f.write('[&W 1/%i] ' % self.recipWeight)
self.writeNewick(f)
f.write('end;\n\n')
if f != sys.stdout:
f.close()
def writeNexusToOpenFile(self, flob, writeTaxaBlock, append,
digitsAfterDecimal):
gm = ["DistanceMatrix.writeNexusToOpenFile()"]
import string
assert self.dim, "Distance Matrix.writeNexusToOpenFile() no dim"
f = flob
if append:
pass
else:
f.write('#NEXUS\n\n')
if writeTaxaBlock:
f.write('begin taxa;\n')
f.write(' dimensions ntax=%s;\n' % self.dim)
f.write(' taxlabels')
for i in range(self.dim):
f.write(' %s' %
func.nexusFixNameIfQuotesAreNeeded(self.names[i]))
f.write(';\n')
f.write('end;\n\n')
f.write('begin distances;\n')
if self.message:
f.write("\n [%s\n ]\n" % self.message)
f.write(' format triangle=both;\n')
f.write(' matrix\n')
# Make the format strings.
if digitsAfterDecimal > 8:
totWid = digitsAfterDecimal + 5
else:
totWid = 11
#colNameFormat = '%' + '-%is' % totWid
if digitsAfterDecimal == 0:
numberFormat = ' %' + '%ii ' % (totWid - 4)
elif digitsAfterDecimal > 0:
numberFormat = '%' + '%i.%if' % (totWid, digitsAfterDecimal)
else:
gm.append("digitsAfterDecimal may not be below zero.")
raise Glitch, gm
if self.names:
longestNameLength = 0
for i in self.names:
if len(i) > longestNameLength:
longestNameLength = len(i)
nameFormat = '%' + '%is ' % longestNameLength
f.write(' [')
f.write(nameFormat % ' ')
for i in self.names:
#f.write('%-10s' % i[:9])
colName = '%s' % i[:totWid - 1]
f.write(string.center(colName, totWid))
f.write(']\n')
for i in range(self.dim):
if self.names:
f.write(' ')
f.write(nameFormat %
func.nexusFixNameIfQuotesAreNeeded(self.names[i]))
for j in range(self.dim):
#f.write('%10.6f' % self.matrix[i][j])
f.write(numberFormat % self.matrix[i][j])
f.write('\n')
f.write(' ;\n')
f.write('end;\n')
