本文整理汇总了Python中cogent.LoadTree.asciiArt方法的典型用法代码示例。如果您正苦于以下问题：Python LoadTree.asciiArt方法的具体用法？Python LoadTree.asciiArt怎么用？Python LoadTree.asciiArt使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类cogent.LoadTree的用法示例。
在下文中一共展示了LoadTree.asciiArt方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: TestTree
# 需要导入模块: from cogent import LoadTree [as 别名]
# 或者: from cogent.LoadTree import asciiArt [as 别名]
class TestTree(unittest.TestCase):
"""tests for a single tree-type"""
def setUp(self):
self.name = 'small tree - '
self.otu_names = ['NineBande', 'Mouse', 'HowlerMon', 'DogFaced']
self.otu_names.sort()
self.newick = '(((Human,HowlerMon),Mouse),NineBande,DogFaced);'
self.newick_sorted = '(DogFaced,((HowlerMon,Human),Mouse),NineBande);'
self.newick_reduced = '((HowlerMon,Mouse),NineBande,DogFaced);'
self.tree = LoadTree(treestring = self.newick)
def test_sorttree(self):
"""testing (well, exercising at least) treesort"""
new_tree = self.tree.sorted()
if hasattr(self, 'newick_sorted'):
self.assertEqual(
self.newick_sorted,
new_tree.getNewick(with_distances=0))
def test_getsubtree(self):
"""testing getting a subtree"""
subtree = self.tree.unrooted().getSubTree(self.otu_names)
new_tree = LoadTree(treestring = self.newick_reduced).unrooted()
# check we get the same names
self.assertEqual(*[len(t.Children) for t in (subtree,new_tree)])
self.assertEqual(str(subtree), str(new_tree))
def test_ascii(self):
self.tree.asciiArt()
# unlabeled internal node
tr = DndParser("(B:0.2,(C:0.3,D:0.4):0.6)F;")
tr.asciiArt(show_internal=True, compact=False)
tr.asciiArt(show_internal=True, compact=True)
tr.asciiArt(show_internal=False, compact=False)示例2: __init__
# 需要导入模块: from cogent import LoadTree [as 别名]
# 或者: from cogent.LoadTree import asciiArt [as 别名]
#.........这里部分代码省略.........
def getLongestEvoDistance(self):
longestDistance = 0.0
for LeafKey in self.FastMLTree.LeafKey_L:
distance = self.getEvoDistance(LeafKey)
if distance > longestDistance:
longestDistance = distance
return longestDistance
"modifies evolutionary distance into a different format"
def modEvoDistance(self):
Ret = {}
for Key in self.EvoDistance_D.keys():
if Key == self.FastMLTree.TopKey:
Ret[Key] = self.EvoDistance_D[Key]
else:
if self.EvoDistance_D[Key] == 0:
Ret[Key] = self.EvoDistance_D[Key]
else:
Ret[Key] = self.EvoDistance_D[Key]
return Ret
"sets tree node coordinates (horizontal and vertical) for the SVG image"
def setTreeCoords(self):
Lines_L = self.CogentTree.asciiArt().split("\n")
MaxVert = 0
VertCoord_D = {}
for i in range(0, len(Lines_L)):
if re.compile("[a-zA-Z0-9_\[email protected]]+").search(Lines_L[i]):
Leaves = re.findall("([a-zA-Z0-9_\[email protected]]+)", Lines_L[i])
for Leaf in Leaves:
VertCoord_D[Leaf] = i
MaxVert = i
TreeCoords_D = {
Key: [(self.ModdedEvoDistance_D[Key] / self.LongestDistance) *
self.TreeFigWIDTH + self.TreeFigXOffset,
float(float(VertCoord_D[Key]) / float(MaxVert)) *
self.TreeFigHEIGHT + self.TreeFigYOffset]
for Key in self.NodeToSeq_D.keys()
}
return TreeCoords_D
"adds node names at each node vertex"
def addNodeNamesAtNodePoints(self):
for Key in self.FastMLTree.LeafKey_L:
xy = self.TreeCoords_D[Key]
xStart = str(xy[0])
yStart = str(xy[1])
self.FigureSVG_D["TreeAndStates"].append(
'''\t<text x='%s' y='%s' text-anchor='left' font-size='20' font-family='Courier' style="fill: #000000;" >%s</text>'''