Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

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
-	
-	
-