def svg(self, fName=None, width=500, putInternalNodeNamesOnBranches=0):
"""Make a basic svg drawing of self.
The 'width' is in postscript points (??). -- does that work with svg?
By default, internal node names label the node, where the node
name goes on the right of the node. You can make the node name
label the branch by setting 'putInternalNodeNamesOnBranches'.
"""
gm = ["Tree.svg()"]
if not self.preAndPostOrderAreValid:
self.setPreAndPostOrder()
from TreePicture import TreePicture
p = TreePicture(self)
p.addToBrLen = 0.0
p.width = width
p.yScale = 17.0
p.xScale = None
p.pointsPerLetter = 8.0 # was 6.0
p.textSize = 11
p.labelTextSize = 8
p.putInternalNodeNamesOnBranches = putInternalNodeNamesOnBranches
p.xOrigin = 5.0
p.setPos()
p.svg = True
s = p.vectorString()
if not fName:
if self.name:
fName = "%s.svg" % self.name
else:
fName = "%i.svg" % os.getpid()
# if not fName.endswith('.svg'):
# fName = '%s.svg' % fName
f = file(fName, "w")
f.write(s)
f.close()
def svg(self, fName=None, width=500, putInternalNodeNamesOnBranches=0):
"""Make a basic svg drawing of self.
The 'width' is in postscript points (??). -- does that work with svg?
By default, internal node names label the node, where the node
name goes on the right of the node. You can make the node name
label the branch by setting 'putInternalNodeNamesOnBranches'.
"""
gm = ['Tree.svg()']
if not self.preAndPostOrderAreValid:
self.setPreAndPostOrder()
from TreePicture import TreePicture
p = TreePicture(self)
p.addToBrLen = 0.0
p.width = width
p.yScale = 17.0
p.xScale = None
p.pointsPerLetter = 8.0 # was 6.0
p.textSize=11
p.labelTextSize=8
p.putInternalNodeNamesOnBranches = putInternalNodeNamesOnBranches
p.xOrigin = 5.0
p.setPos()
p.svg = True
s = p.vectorString()
if not fName:
if self.name:
fName = '%s.svg' % self.name
else:
fName = '%i.svg' % os.getpid()
#if not fName.endswith('.svg'):
# fName = '%s.svg' % fName
f = file(fName, 'w')
f.write(s)
f.close()
def textDrawList(
self,
showInternalNodeNames=1,
addToBrLen=0.2,
width=None,
autoIncreaseWidth=True,
showNodeNums=1,
partNum=0,
model=False,
):
if len(self.nodes) == 0:
return [""]
elif len(self.nodes) == 1:
if showNodeNums:
return ["%i:%s" % (self.nodes[0].nodeNum, self.nodes[0].name)]
else:
return ["%s" % self.nodes[0].name]
gm = ["Tree.textDrawList()"]
if not self.preAndPostOrderAreValid:
self.setPreAndPostOrder()
from TreePicture import TreePicture
p = TreePicture(self)
p.fName = None
p.width = width
p.xScale = None
p.yScale = 1
p.pointsPerLetter = 1
p.addToBrLen = addToBrLen
p.textShowNodeNums = showNodeNums
p.showInternalNodeNames = showInternalNodeNames
if showNodeNums:
p.nameOffset = 0
else:
p.nameOffset = 1
p.xOrigin = 0.0
p.yOrigin = 0.0
p.textSize = 1
p.labelTextSize = 1
# If the width is not specified, make a guess
if width == None:
tLen = 0 # Longest number of horizontal sections to draw
longestNameLen = 0
for n in self.nodes:
if n.isLeaf and n != self.root:
if n.name: # This assumes short internal node name lengths
if len(n.name) > longestNameLen:
longestNameLen = len(n.name)
thisLen = 0
n1 = n
# print "x n1 is node %i" % n1.nodeNum
while n1 != self.root:
n1 = n1.parent
# print "y n1 is node %i" % n1.nodeNum
thisLen += 1
if thisLen > tLen:
tLen = thisLen
# print "tLen =", tLen
# print "longestNameLen =", longestNameLen
rootNameLen = 0
if self.root.name:
rootNameLen = len(self.root.name) + 1
p.width = (10 * tLen) + rootNameLen + longestNameLen
if p.width > 100:
p.width = 100
# print "p.width =", p.width
# import sys; sys.exit()
# Make sure the names fit.
if not autoIncreaseWidth:
for n in self.nodes:
if n.isLeaf and n != self.root:
if n.name and len(n.name) > p.width:
gm.append("There are long names, and the given width is not enough.")
raise Glitch, gm
if model:
try:
partNum = int(partNum)
except:
gm.append("partNum arg should be an integer.")
raise Glitch, gm
if not self.model:
gm.append("If model arg is set, then self.model must exist.")
raise Glitch, gm
if partNum < 0 or partNum >= self.model.nParts:
gm.append("Zero-based partNum %i is out of range of %s parts." % (partNum, self.model.nParts))
raise Glitch, gm
p.partNum = partNum
p.doModel = 1
doComps = 1
doRMatrices = 1
if self.model.parts[partNum].nComps < 2:
doComps = 0
if self.model.parts[partNum].nRMatrices < 2:
doRMatrices = 0
if not doComps and not doRMatrices:
p.setPos(autoIncreaseWidth)
s = p.textString(returnAsList=True)
s.append("Both the composition of the model and the rate matrix are homogeneous in part %i.\n" % partNum)
return s
# First do compositions
s = []
if doComps:
if 0:
if self.model.nParts > 1:
print "Compositions for part %i" % partNum
else:
print "\nCompositions\n------------"
p.textDrawModelThing = var.TEXTDRAW_COMP
p.setPos(autoIncreaseWidth)
s = p.textString(returnAsList=True)
# print s
# Then do RMatrices
if doRMatrices:
if 0:
if self.model.nParts > 1:
print "RMatrices for part %i" % partNum
else:
print "\nRMatrices\n---------"
p.textDrawModelThing = var.TEXTDRAW_RMATRIX
p.setPos(autoIncreaseWidth)
if s:
s += p.textString(returnAsList=True)
else:
s = p.textString(returnAsList=True)
if self.model.parts[partNum].nComps == 1:
s.append("The composition of the model is homogeneous in part %i\n" % partNum)
elif self.model.parts[partNum].nRMatrices == 1:
s.append("The rate matrix is homogeneous in part %i\n" % partNum)
# Don't bother with GDASRV, yet
return s
else:
p.setPos(autoIncreaseWidth)
s = p.textString(returnAsList=True)
return s
def textDrawList(self, showInternalNodeNames=1, addToBrLen=0.2, width=None, autoIncreaseWidth=True, showNodeNums=1, partNum=0, model=False):
if len(self.nodes) == 0:
return ['']
elif len(self.nodes) == 1:
if showNodeNums:
return ['%i:%s' % (self.nodes[0].nodeNum, self.nodes[0].name)]
else:
return ['%s' % self.nodes[0].name]
gm = ['Tree.textDrawList()']
if not self.preAndPostOrderAreValid:
self.setPreAndPostOrder()
from TreePicture import TreePicture
p = TreePicture(self)
p.fName = None
p.width = width
p.xScale = None
p.yScale = 1
p.pointsPerLetter = 1
p.addToBrLen = addToBrLen
p.textShowNodeNums = showNodeNums
p.showInternalNodeNames = showInternalNodeNames
if showNodeNums:
p.nameOffset = 0
else:
p.nameOffset = 1
p.xOrigin = 0.0
p.yOrigin = 0.0
p.textSize = 1
p.labelTextSize = 1
# If the width is not specified, make a guess
if width == None:
tLen = 0 # Longest number of horizontal sections to draw
longestNameLen = 0
for n in self.nodes:
if n.isLeaf and n != self.root:
if n.name: # This assumes short internal node name lengths
if len(n.name) > longestNameLen:
longestNameLen = len(n.name)
thisLen = 0
n1 = n
#print "x n1 is node %i" % n1.nodeNum
while n1 != self.root:
n1 = n1.parent
#print "y n1 is node %i" % n1.nodeNum
thisLen += 1
if thisLen > tLen:
tLen = thisLen
#print "tLen =", tLen
#print "longestNameLen =", longestNameLen
rootNameLen = 0
if self.root.name:
rootNameLen = len(self.root.name) + 1
p.width = (10 * tLen) + rootNameLen + longestNameLen
if p.width > 100:
p.width = 100
#print "p.width =", p.width
#import sys; sys.exit()
# Make sure the names fit.
if not autoIncreaseWidth:
for n in self.nodes:
if n.isLeaf and n != self.root:
if n.name and len(n.name) > p.width:
gm.append("There are long names, and the given width is not enough.")
raise Glitch, gm
if model:
try:
partNum = int(partNum)
except:
gm.append("partNum arg should be an integer.")
raise Glitch, gm
if not self.model:
gm.append("If model arg is set, then self.model must exist.")
raise Glitch, gm
if partNum < 0 or partNum >= self.model.nParts:
gm.append("Zero-based partNum %i is out of range of %s parts." % (partNum, self.model.nParts))
raise Glitch, gm
p.partNum = partNum
p.doModel = 1
doComps = 1
doRMatrices = 1
if self.model.parts[partNum].nComps < 2:
doComps = 0
if self.model.parts[partNum].nRMatrices < 2:
doRMatrices = 0
if not doComps and not doRMatrices:
p.setPos(autoIncreaseWidth)
s = p.textString(returnAsList=True)
s.append("Both the composition of the model and the rate matrix are homogeneous in part %i.\n" % partNum)
return s
# First do compositions
s = []
if doComps:
if 0:
if self.model.nParts > 1:
print "Compositions for part %i" % partNum
else:
print "\nCompositions\n------------"
p.textDrawModelThing = var.TEXTDRAW_COMP
p.setPos(autoIncreaseWidth)
s = p.textString(returnAsList=True)
#print s
# Then do RMatrices
if doRMatrices:
if 0:
if self.model.nParts > 1:
print "RMatrices for part %i" % partNum
else:
print "\nRMatrices\n---------"
p.textDrawModelThing = var.TEXTDRAW_RMATRIX
p.setPos(autoIncreaseWidth)
if s:
s += p.textString(returnAsList=True)
else:
s = p.textString(returnAsList=True)
if self.model.parts[partNum].nComps == 1:
s.append("The composition of the model is homogeneous in part %i\n" % partNum)
elif self.model.parts[partNum].nRMatrices == 1:
s.append("The rate matrix is homogeneous in part %i\n" % partNum)
# Don't bother with GDASRV, yet
return s
else:
p.setPos(autoIncreaseWidth)
s = p.textString(returnAsList=True)
return s