def findCenters(newickFile, switchLo, switchHi, lossLo, lossHi):
"""This function takes as input a .newick file in the form
<filename>.newick, and low and high values for costscape for both
switches and losses. It returns a list of the centroids of each region in
the costscape associated with the given .newick file."""
hostTree, parasiteTree, phi = newickFormatReader(newickFile)
CVlist = reconcile.reconcile(parasiteTree, hostTree, phi, switchLo,
switchHi, lossLo, lossHi)
coordList = plotcosts.plotcosts(CVlist, lossLo, lossHi, switchLo,
switchHi, "", False, False)
polygonList = getNewCoordList(newickFile, switchLo, switchHi, lossLo,
lossHi)
pointList = []
for i in range(len(polygonList)):
point = polygonList[i]
numCommas = point.count(",")
if numCommas > 1:
# polygon case
region = load_wkt(point)
pointList.append(region.centroid.wkt)
elif numCommas == 1:
# line case
x1 = coordList[i][0][0]
y1 = coordList[i][0][1]
x2 = coordList[i][1][0]
y2 = coordList[i][1][1]
midx = (x1 + x2) * 1.0 / 2
midy = (y1 + y2) * 1.0 / 2
pointList.append("POINT ({} {})".format(str(midx), str(midy)))
else:
# point case
pointList.append("POINT {}".format(str(coordList[i][0])))
return pointList
def getNewCoordList(newickFile, switchLo, switchHi, lossLo, lossHi):
"""Takes as input a newick file in the form <filename>.newick, and low
and high values for costscape for both switches and losses. Returns a
list of strings, where each string contains all the verteces of one
region from costscape."""
hostTree, parasiteTree, phi = newickFormatReader(newickFile)
CVlist = reconcile.reconcile(parasiteTree, hostTree, phi, switchLo,
switchHi, lossLo, lossHi)
coordList = plotcosts.plotcosts(CVlist, lossLo, lossHi, switchLo,
switchHi, "", False, False)
newCoordList = []
for vertexList in coordList:
string = "POLYGON(("
for vertex in vertexList:
string = "{}{} {},".format(string, str(vertex[0]), str(vertex[1]))
string = "{}))".format(string[:-1])
newCoordList.append(string)
return newCoordList
def getNewCoordList(newickFile, switchLo, switchHi, lossLo, lossHi):
"""Takes as input a newick file in the form <filename>.newick, and low
and high values for costscape for both switches and losses. Returns a
list of strings, where each string contains all the verteces of one
region from costscape."""
hostTree, parasiteTree, phi = newickFormatReader(newickFile)
CVlist = reconcile.reconcile(parasiteTree, hostTree, phi, switchLo, \
switchHi, lossLo, lossHi)
coordList = plotcosts.plotcosts(CVlist, lossLo, lossHi, switchLo, \
switchHi, "", False, False)
newCoordList = []
for element in coordList:
string = "POLYGON(("
for i in element:
string = string + str(i[0]) + ' ' + str(i[1]) + ','
string = string[:-1] + '))'
newCoordList.append(string)
return newCoordList
def findCenters(newickFile, switchLo, switchHi, lossLo, lossHi):
"""This function takes as input a .newick file in the form
<filename>.newick, and low and high values for costscape for both
switches and losses. It returns a list of the centroids of each region in
the costscape associated with the given .newick file."""
hostTree, parasiteTree, phi = newickFormatReader(newickFile)
CVlist = reconcile.reconcile(parasiteTree, hostTree, phi, switchLo, \
switchHi, lossLo, lossHi)
coordList = plotcosts.plotcosts(CVlist, lossLo, lossHi, switchLo, \
switchHi, "", False, False)
polygonList = getNewCoordList(newickFile, switchLo, switchHi, lossLo, \
lossHi)
pointList = []
for i in range(len(polygonList)):
point = polygonList[i]
numCommas = 0
for j in range(len(point)):
if point[j] == ",":
numCommas = numCommas + 1
if numCommas > 1:
#polygon case
region = load_wkt(point)
pointList.append((region.centroid.wkt))
elif numCommas == 1:
#line case
x1 = coordList[i][0][0]
y1 = coordList[i][0][1]
x2 = coordList[i][1][0]
y2 = coordList[i][1][1]
midx = (x1 + x2) * 1.0 / 2
midy = (y1 + y2) * 1.0 / 2
pointList.append("POINT (" + str(midx) + " " + str(midy) + ")")
else:
#point case
pointList.append("POINT " + str(coordList[i][0]))
return pointList