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
