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Diffstat (limited to 'web/webqtl/heatmap/slink.py')
| -rwxr-xr-x | web/webqtl/heatmap/slink.py | 141 |
1 files changed, 0 insertions, 141 deletions
diff --git a/web/webqtl/heatmap/slink.py b/web/webqtl/heatmap/slink.py deleted file mode 100755 index 3de41de4..00000000 --- a/web/webqtl/heatmap/slink.py +++ /dev/null @@ -1,141 +0,0 @@ -# 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 - - - |