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# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
#
# Created by GeneNetwork Core Team 2010/08/10
#
# Last updated by GeneNetwork Core Team 2010/10/20
#--Only imported by correlationPage.py.
#
#Functions:
#slink(lists) -- the only function called outside of this file.
#nearest(lists,i,j) -- some sort of recursive function.
#printarray(array,n) -- prints n elements of the given array
#this is a myseterious piece of code in GN that Kev Adler and Rob Williams do not understand.
#but is used in some way by the Traits Correlation function
#Kev and Rob suspect that the d2 matrix below is unused
#We do not understand the signifance of "d" but Kev suspects it is unimportant
#These comments by Kev and Rob: May 23, 2008
d = [[0,9,3,6,11],[9,0,7,5,10],[3,7,0,9,2],[6,5,9,0,8],[11,10,2,8,0]]
d2 = [[0,9,5.5,6,11],[9,0,7,5,10],[5.5,7,0,9,2],[6,5,9,0,3],[11,10,2,3,0]]
def nearest(lists,i,j):
if type(i) == type(1) and type(j) == type(1):
return lists[i][j]
elif type(i) == type(1):
dist = 1e10
for itemj in j[:-1]:
d = nearest(lists,i,itemj)
if dist > d:
dist = d
elif type(j) == type(1):
dist = 1e10
for itemi in i[:-1]:
d = nearest(lists,itemi,j)
if dist > d:
dist = d
else:
dist = 1e10
for itemi in i[:-1]:
for itemj in j[:-1]:
d = nearest(lists,itemi,itemj)
if dist > d:
dist = d
return dist
def printarray(array,n):
print "\n"
for i in range(n):
print array[i][:n]
print "\n"
def slink(lists):
try:
if type(lists) != type([]) and type(lists) != type(()):
raise 'FormatError'
else:
size = len(lists)
for item in lists:
if type(item) != type([]) and type(item) != type(()):
raise 'FormatError'
else:
if len(item) != size:
raise 'LengthError'
for i in range(size):
if lists[i][i] != 0:
raise 'ValueError'
for j in range(0,i):
if lists[i][j] < 0:
raise 'ValueError'
if lists[i][j] != lists[j][i]:
raise 'MirrorError'
except 'FormatError':
print "the format of the list is incorrect!"
return []
except 'LengthError':
print "the list is not a square list!"
return []
except 'MirrorError':
print "the list is not symmetric!"
return []
except 'ValueError':
print "the distance is negative value!"
return []
except:
print "Unknown Error"
return []
listindex = range(size)
listindexcopy = range(size)
listscopy = []
for i in range(size):
listscopy.append(lists[i][:])
initSize = size
candidate = []
while initSize >2:
mindist = 1e10
for i in range(initSize):
for j in range(i+1,initSize):
if listscopy[i][j] < mindist:
mindist = listscopy[i][j]
candidate=[[i,j]]
elif listscopy[i][j] == mindist:
mindist = listscopy[i][j]
candidate.append([i,j])
else:
pass
newmem = (listindexcopy[candidate[0][0]],listindexcopy[candidate[0][1]],mindist)
listindexcopy.pop(candidate[0][1])
listindexcopy[candidate[0][0]] = newmem
initSize -= 1
for i in range(initSize):
for j in range(i+1,initSize):
listscopy[i][j] = nearest(lists,listindexcopy[i],listindexcopy[j])
listscopy[j][i] = listscopy[i][j]
#print listindexcopy
#printarray(listscopy,initSize)
listindexcopy.append(nearest(lists,listindexcopy[0],listindexcopy[1]))
return listindexcopy
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