def buildDecoratedTree(self, supertreeSplits, supertreeDict):
for key, value in list(supertreeDict.items()):
inter = Intersection(supertreeSplits[key][0], supertreeSplits[key][1], 0, 0)
name = ''
if self.doStandardDecoration:
name = str(int(round(100.0*(1.0 + value[9])/2.0)))
else:
name = str(value[9])
inter.name = name
self.intersections.append(inter)
treeBuilderFromSplits = TreeBuilderFromSplits(self.bitkeys, self.taxnames)
self.decoratedSuperTree = treeBuilderFromSplits.buildTreeFromInformativeList(self.intersections, treeName='decoratedSupertree')
def saveIndexTree(self, supertreeSplits, supertreeDict):
for key, value in list(supertreeDict.items()):
inter = Intersection(supertreeSplits[key][0], supertreeSplits[key][1], 0, 0)
if self.doStandardDecoration:
self.csvValues.append([key,int(round(100.0*(value[0]/self.T))),int(round(100.0*(value[1]/self.T))),
int(round(100.0*(value[2]/self.T))), int(round(100.0*(value[3]/self.T))),
int(round(100.0*(value[4]/self.T))), int(round(100.0*(value[5]/self.T))),
value[6], value[7], value[8], value[9], value[10], value[11]])
else:
self.csvValues.append([key, value[0]+value[1],value[0],value[1],value[2],value[3], value[4],value[5], value[6], value[7], value[8], value[9], value[10], value[11]])
inter.name = str(key)
self.indexIntersections.append(inter)
treeBuilderFromSplits = TreeBuilderFromSplits(self.bitkeys, self.taxnames)
self.indexSuperTree = treeBuilderFromSplits.buildTreeFromInformativeList(self.indexIntersections, treeName='indexSupertree')
self.indexSuperTree.writeNexus(self.indexFilename)
writer = csv.writer(open(self.csvFilename, "wb"))
writer.writerows(self.csvValues)