def fstAlleleDistance(
self, data, samples
): #this could have been more efficient when we pass objects
fst = FST()
sampleCount = data.shape[1]
dm = np.zeros((sampleCount, sampleCount))
messages = dict()
for i in range(0, sampleCount):
for j in range(0, sampleCount):
#extract the whole copy number profile, so the whole column
sample1Profile = data[:, i]
sample2Profile = data[:, j]
returnValue = fst.computeAlleleDistance(
sample1Profile, sample2Profile, samples[i], samples[j])
messages[(i, j)] = returnValue[0]
dm[i, j] = returnValue[1]
print "distances: "
print dm
return [messages, dm]
