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

7 files changed, 0 insertions, 1910 deletions

diff --git a/web/webqtl/networkGraph/GraphPage.py b/web/webqtl/networkGraph/GraphPage.py
deleted file mode 100755
index b0d4063d..00000000
--- a/web/webqtl/networkGraph/GraphPage.py
+++ /dev/null
@@ -1,46 +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
-
-class GraphPage:
-
-    def __init__(self, imagefile, mapfile):
-        # open and read the image map file
-        try:
-            mapData = open(mapfile).read()
-        except:
-            mapData =  "<p><b>Unable to load image map with trait links</b></p>"
-
-        self.content = '''%s
-        <img border="0" alt="the graph" src="%s" usemap="#webqtlGraph" />
-        ''' % (mapData, imagefile)
-
-    def writeToFile(self, filename):
-        """
-        Output the contents of this HTML page to a file
-        """
-        handle = open(filename, "w")
-        handle.write(self.content)
-        handle.close()
diff --git a/web/webqtl/networkGraph/ProcessedPoint.py b/web/webqtl/networkGraph/ProcessedPoint.py
deleted file mode 100755
index 6eb855e3..00000000
--- a/web/webqtl/networkGraph/ProcessedPoint.py
+++ /dev/null
@@ -1,49 +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
-
-# ProcessedPoint: to store information about the relationship between
-# two particular traits
-# ProcessedPoint represents the calculations made by the program
-
-class ProcessedPoint:
-
-    def __init__(self, i, j):
-        self.i = i
-        self.j = j
-
-    def __eq__(self, other):
-        # print "ProcessedPoint: comparing %s and %s" % (self, other)
-        return (self.i == other.i and
-                self.j == other.j and
-                self.value == other.value and
-                self.color == other.color)
-
-    def __str__(self):
-        return "(%s,%s,%s,%s,%s)" % (self.i, 
-                                     self.j, 
-                                     self.value,
-                                     self.length,
-                                     self.color)
diff --git a/web/webqtl/networkGraph/__init__.py b/web/webqtl/networkGraph/__init__.py
deleted file mode 100755
index e69de29b..00000000
--- a/web/webqtl/networkGraph/__init__.py
+++ /dev/null
diff --git a/web/webqtl/networkGraph/nGraphException.py b/web/webqtl/networkGraph/nGraphException.py
deleted file mode 100755
index d492fca9..00000000
--- a/web/webqtl/networkGraph/nGraphException.py
+++ /dev/null
@@ -1,33 +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
-
-class nGraphException(Exception):
-    def __init__(self, message):
-        self.message = message
-
-    def __str__(self):
-        return "Network Graph Exception: %s" % self.message
-
diff --git a/web/webqtl/networkGraph/networkGraphPage.py b/web/webqtl/networkGraph/networkGraphPage.py
deleted file mode 100755
index fb4021f0..00000000
--- a/web/webqtl/networkGraph/networkGraphPage.py
+++ /dev/null
@@ -1,335 +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 NL 2010/02/11
-
-#!/usr/bin/python
-# networkGraph.py
-# Author: Stephen Pitts
-# 6/2/2004
-#
-# a script to take a matrix of data from a WebQTL job and generate a
-# graph using the neato package from GraphViz
-#
-# See graphviz for documentation of the parameters
-#
-
-
-#from mod_python import apache, util, Cookie
-#import cgi
-import tempfile
-import os
-import time
-import sys
-import cgitb
-import string
-
-from htmlgen import HTMLgen2 as HT
-
-from base.templatePage import templatePage
-import networkGraphUtils
-from base import webqtlConfig
-from utility import webqtlUtil
-from base.webqtlTrait import webqtlTrait
-import compareCorrelates.trait as smpTrait
-from GraphPage import GraphPage
-from networkGraphPageBody import networkGraphPageBody
-from correlationMatrix.tissueCorrelationMatrix import tissueCorrelationMatrix
-
-cgitb.enable()
-
-
-class networkGraphPage(templatePage):
-
-    def __init__(self,fd,InputData=None):
-
-        templatePage.__init__(self, fd)
-
-        if not self.openMysql():
-            return
-            
-        if not fd.genotype:
-            fd.readGenotype()
-                
-        self.searchResult = fd.formdata.getvalue('searchResult')
-
-        self.tissueProbeSetFeezeId = "1" #XZ, Jan 03, 2010: currently, this dataset is "UTHSC Illumina V6.2 RankInv B6 D2 average CNS GI average (May 08)"
-        TissueCorrMatrixObject = tissueCorrelationMatrix(tissueProbeSetFreezeId=self.tissueProbeSetFeezeId)
-
-        if type("1") == type(self.searchResult):
-            self.searchResult = string.split(self.searchResult, '\t')
-        
-        if (not self.searchResult or (len(self.searchResult) < 2)):
-            heading = 'Network Graph'
-            detail = ['You need to select at least two traits in order to generate Network Graph.']
-            self.error(heading=heading,detail=detail)
-            print 'Content-type: text/html\n'
-            self.write()
-            return
-        
-        if self.searchResult:
-            if len(self.searchResult) > webqtlConfig.MAXCORR:
-                heading = 'Network Graph'
-                detail = ['In order to display Network Graph properly, Do not select more than %d traits for Network Graph.' % webqtlConfig.MAXCORR]
-                self.error(heading=heading,detail=detail)
-                print 'Content-type: text/html\n'
-                self.write()
-                return
-            else:    
-                pass
-                
-            traitList = []
-            traitDataList = []
-            
-            for item in self.searchResult:
-                thisTrait = webqtlTrait(fullname=item, cursor=self.cursor)
-                thisTrait.retrieveInfo()
-                thisTrait.retrieveData(fd.strainlist)
-                traitList.append(thisTrait)
-                traitDataList.append(thisTrait.exportData(fd.strainlist))
-                   
-        else:
-            heading = 'Network Graph'
-            detail = [HT.Font('Error : ',color='red'),HT.Font('Error occurs while retrieving data from database.',color='black')]
-            self.error(heading=heading,detail=detail)
-            print 'Content-type: text/html\n'
-            self.write()
-            return
-
-        NNN = len(traitList)
-        
-        if NNN < 2:
-            templatePage.__init__(self, fd)
-            heading = 'Network Graph'
-            detail = ['You need to select at least two traits in order to generate a Network Graph']
-            print 'Content-type: text/html\n'
-            self.write()
-            return
-        else:
-            pearsonArray = [([0] * (NNN))[:] for i in range(NNN)]
-            spearmanArray = [([0] * (NNN))[:] for i in range(NNN)]
-            GeneIdArray = []
-            GeneSymbolList = [] #XZ, Jan 03, 2011: holds gene symbols for calculating tissue correlation
-            traitInfoArray = []
-
-            i = 0
-            nnCorr = len(fd.strainlist)
-            for i, thisTrait in enumerate(traitList):
-                names1 = [thisTrait.db.name, thisTrait.name, thisTrait.cellid]
-                for j, thisTrait2 in enumerate(traitList):
-                    names2 = [thisTrait2.db.name, thisTrait2.name, thisTrait2.cellid]
-                    if j < i:
-                        corr,nOverlap = webqtlUtil.calCorrelation(traitDataList[i],traitDataList[j],nnCorr)
-                        pearsonArray[i][j] = corr
-                        pearsonArray[j][i] = corr
-                    elif j == i:
-                        pearsonArray[i][j] = 1.0
-                        spearmanArray[i][j] = 1.0
-                    else:
-                        corr,nOverlap = webqtlUtil.calCorrelationRank(traitDataList[i],traitDataList[j],nnCorr)
-                        spearmanArray[i][j] = corr
-                        spearmanArray[j][i] = corr
-                    
-                GeneId1 = None
-                tmpSymbol = None
-                if thisTrait.db.type == 'ProbeSet':
-                    try:
-                        GeneId1 = int(thisTrait.geneid)
-                    except:
-                        GeneId1 = 0
-                    if thisTrait.symbol:
-                        tmpSymbol = thisTrait.symbol.lower()
-                GeneIdArray.append(GeneId1)
-                GeneSymbolList.append(tmpSymbol)
-
-            _traits = []
-            _matrix = []
-
-            for i in range(NNN):
-                turl = webqtlConfig.CGIDIR + webqtlConfig.SCRIPTFILE + '?FormID=showDatabase&database=%s&ProbeSetID=%s' % (traitList[i].db.name, traitList[i].name)
-                if traitList[i].cellid:
-                    turl += "&CellID=%s" % traitList[i].cellid
-                    
-                if traitList[i].db.type == 'ProbeSet':
-                    if traitList[i].symbol:
-                        _symbol = traitList[i].symbol
-                    else:
-                        _symbol = 'unknown'
-                elif traitList[i].db.type == 'Publish':
-                    _symbol = traitList[i].name
-                    if traitList[i].confidential:
-                        if webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=traitList[i].authorized_users):
-                            if traitList[i].post_publication_abbreviation:
-                                _symbol = traitList[i].post_publication_abbreviation
-                        else:
-                            if traitList[i].pre_publication_abbreviation:
-                                _symbol = traitList[i].pre_publication_abbreviation
-                    else:
-                        if traitList[i].post_publication_abbreviation:
-                            _symbol = traitList[i].post_publication_abbreviation
-
-                #XZ, 05/26/2009: Xiaodong add code for Geno data
-                elif traitList[i].db.type == 'Geno':
-                    _symbol = traitList[i].name
-                else:
-                    _symbol = traitList[i].description
-                    #####if this trait entered by user
-                    if _symbol.__contains__('entered'):
-                        _symbol = _symbol[:_symbol.index('entered')]
-                    #####if this trait generaged by genenetwork
-                    elif _symbol.__contains__('generated'):
-                        _symbol = _symbol[_symbol.rindex(':')+1:]
-                
-                newTrait = smpTrait.Trait(name=str(traitList[i]), href=turl, symbol=_symbol)
-                newTrait.color = "black"
-                _traits.append(newTrait)
-                
-                for j in range(i+1, NNN):
-                    dataPoint = smpTrait.RawPoint(i, j)
-                    dataPoint.spearman = spearmanArray[i][j]
-                    dataPoint.pearson = pearsonArray[i][j]
-
-                    #XZ: get literature correlation info.
-                    if GeneIdArray[i] and GeneIdArray[j]:
-                        if GeneIdArray[i] == GeneIdArray[j]:
-                            dataPoint.literature = 1
-                        else:
-                            self.cursor.execute("SELECT Value from LCorrRamin3 WHERE (GeneId1 = %d and GeneId2 = %d) or (GeneId1 = %d and GeneId2 = %d)" % (GeneIdArray[i], GeneIdArray[j], GeneIdArray[j], GeneIdArray[i]))
-                            try:    
-                                dataPoint.literature = self.cursor.fetchone()[0]
-                            except:
-                                dataPoint.literature = 0
-                    else:
-                        dataPoint.literature = 0
-
-                    #XZ: get tissue correlation info
-                    if GeneSymbolList[i] and GeneSymbolList[j]:
-                        dataPoint.tissue = 0
-                        geneSymbolPair = []
-                        geneSymbolPair.append(GeneSymbolList[i])
-                        geneSymbolPair.append(GeneSymbolList[j])
-                        corrArray,pvArray = TissueCorrMatrixObject.getCorrPvArrayForGeneSymbolPair(geneNameLst=geneSymbolPair)
-                        if corrArray[1][0]:
-                            dataPoint.tissue = corrArray[1][0]
-                    else:
-                        dataPoint.tissue = 0
-
-                    _matrix.append(dataPoint)
-        
-            OrigDir = os.getcwd()
-
-            sessionfile = fd.formdata.getvalue('session')
-            
-            inputFilename = fd.formdata.getvalue('inputFile')
-
-            #If there is no sessionfile generate one and dump all matrix/trait values
-            if not sessionfile:
-                filename = webqtlUtil.generate_session()    
-                webqtlUtil.dump_session([_matrix, _traits], os.path.join(webqtlConfig.TMPDIR, filename + '.session'))
-                sessionfile = filename
-            
-            startTime = time.time()
-            
-            #Build parameter dictionary used by networkGraphPage class using buildParamDict function
-            params = networkGraphUtils.buildParamDict(fd, sessionfile)
-    
-            nodes = len(_traits)
-            rawEdges = len(_matrix)
-            
-            if params["tune"] == "yes":
-                params = networkGraphUtils.tuneParamDict(params, nodes, rawEdges)
-              
-            matrix = networkGraphUtils.filterDataMatrix(_matrix, params)
-            
-            optimalNode = networkGraphUtils.optimalRadialNode(matrix)
-            
-            if not inputFilename:
-                inputFilename = tempfile.mktemp()
-            
-            inputFilename = webqtlConfig.IMGDIR + inputFilename.split("/")[2]
-                                           
-            #writes out 4 graph files for exporting
-            graphFile = "/image/" + networkGraphUtils.writeGraphFile(matrix, _traits, inputFilename, params)
-            
-            networkGraphUtils.processDataMatrix(matrix, params)
-
-            edges = 0
-
-            for edge in matrix:
-                if edge.value != 0:
-                    edges +=1
-
-            for trait in _traits:
-                trait.name = networkGraphUtils.fixLabel(trait.name)
-            
-            RootDir = webqtlConfig.IMGDIR
-            RootDirURL = "/image/"                  
-
-
-                  
-                        #This code writes the datafile that the graphviz function runNeato uses to generate the 
-                        #"digraph" file that defines the graphs parameters
-            datafile = networkGraphUtils.writeNeatoFile(matrix=matrix, traits=_traits, filename=inputFilename, GeneIdArray=GeneIdArray, p=params)
-            
-            #Generate graph in various file types                      
-            layoutfile = networkGraphUtils.runNeato(datafile, "dot", "dot", params["gType"]) # XZ, 09/11/2008: add module name
-            # ZS 03/04/2010 This second output file (layoutfile_pdf) is rotated by 90 degrees to prevent an issue with pdf output being cut off at the edges
-            layoutfile_pdf = networkGraphUtils.runNeato(datafile + "_pdf", "dot", "dot", params["gType"]) # ZS 03/04/2010
-            pngfile = networkGraphUtils.runNeato(layoutfile, "png", "png", params["gType"]) 
-            mapfile = networkGraphUtils.runNeato(layoutfile, "cmapx", "cmapx", params["gType"])# XZ, 09/11/2008: add module name    
-            giffile = networkGraphUtils.runNeato(layoutfile, "gif", "gif", params["gType"])# XZ, 09/11/2008:add module name
-            psfile = networkGraphUtils.runNeato(layoutfile_pdf, "ps", "ps", params["gType"])# XZ, 09/11/2008: add module name
-            pdffile = networkGraphUtils.runPsToPdf(psfile, params["width"], params["height"])# XZ, 09/11/2008: add module name
-            
-                        #This generates text files in XGGML (standardized graphing language) and plain text
-                        #so the user can create his/her own graphs in a program like Cytoscape
-                    
-            htmlfile1 = datafile + ".html"
-            htmlfile2 = datafile + ".graph.html"
-
-            os.chdir(OrigDir)
-
-            #This generates the graph in various image formats
-            giffile = RootDirURL + giffile
-            pngfile = RootDirURL + pngfile
-            pdffile = RootDirURL + pdffile
-            endTime = time.time()
-            totalTime = endTime - startTime
-
-            os.chdir(RootDir)
-
-            page2 = GraphPage(giffile, mapfile)
-            page2.writeToFile(htmlfile2)
-            
-            #This generates the HTML for the body of the Network Graph page
-            page1 = networkGraphPageBody(fd, matrix, _traits, htmlfile2, giffile, pdffile, nodes, edges, rawEdges, totalTime, params, page2.content, graphFile, optimalNode)
-            
-            #Adds the javascript colorSel to the body to allow line color selection
-            self.dict["js1"] = '<SCRIPT SRC="/javascript/colorSel.js"></SCRIPT><BR>'   
-            #self.dict["js1"] += '<SCRIPT SRC="/javascript/networkGraph.js"></SCRIPT>' 
-                        
-            #Set body of current templatePage to body of the templatePage networkGraphPage                        
-            self.dict['body'] = page1.dict['body']                
-
-
diff --git a/web/webqtl/networkGraph/networkGraphPageBody.py b/web/webqtl/networkGraph/networkGraphPageBody.py
deleted file mode 100644
index 22b49ccd..00000000
--- a/web/webqtl/networkGraph/networkGraphPageBody.py
+++ /dev/null
@@ -1,697 +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
-
-from base.templatePage import templatePage
-import networkGraphUtils
-from base import webqtlConfig
-         
-
-# our output representation is fairly complicated
-# because we use an iframe to represent the image and the image has
-# an associated image map, our output is actually three files
-# 1) a networkGraphPage instance -- the URL we pass to the user
-# 2) a GraphPage with the image map and the graph -- this page has to be
-#    there to pass the imagemap data to the browser
-# 3) a PNG graph file itself
-
-class networkGraphPageBody(templatePage):
-    """
-    Using the templatePage class, we build an HTML shell for the graph
-    that displays the parameters used to generate it and allows the
-    user to redraw the graph with different parameters.
-
-    The way templatePage works, we build the page in pieces in the __init__
-    method and later on use the inherited write method to render the page.
-    """
-
-    def __init__(self, fd, matrix, traits, imageHtmlName, imageName, pdfName, nodes,
-                 edges, rawEdges, totalTime, p, graphcode, graphName, optimalNode):
-
-        templatePage.__init__(self, fd)
-
-        if p["printIslands"] == 0:
-            island = "Only nodes with edges"
-        else:
-            island = "All nodes"
-
-        body = """ <td><P class='title'>Network Graph</P>
-        <Blockquote><p>The %s nodes in the
-        graph below show the selected traits. %s are displayed. The
-        %s edges between the nodes, filtered from the %s total edges and
-        drawn as %s, show <b>%s</b> correlation
-        coefficients greater than %s or less than -%s. The graph\'s
-        canvas is %s by %s cm, and the node
-        labels are drawn with a %s point font, and the edge 
-        labels are drawn with a %s point font. Right-click or control-click
-        on the graph to save it to disk for further manipulation. See
-        below for the trait key, and graph options.</p>
-        """ % (nodes, island, edges, rawEdges,
-               p["splineName"], p["correlationName"], 
-               p["kValue"],
-               p["kValue"], 
-               p["width"], 
-               p["height"], 
-               p["nfontsize"], 
-               p["cfontsize"])
-        
-        #Generate a list of symbols for the central node selection drop-down menu
-        
-        symbolList = networkGraphUtils.generateSymbolList(traits)
-        
-        #Some of these hidden variables (CellID, CellID2, ProbesetID2, etc) exist 
-        #to be used by the javascript functions called when a user clicks on an edge or node
-        
-        formParams = '''
-        
-        <form name="showDatabase" action="%s%s" METHOD="POST"  enctype="multipart/form-data">
-        
-        <input type="hidden" name="filename" value="%s" />
-        <input type="hidden" name="exportFilename" value="%s" />
-        <input type="hidden" name="progress" value="1" />
-        <input type="hidden" name="database" value="_" />
-        <input type="hidden" name="database2" value="_" />
-        <input type="hidden" name="ProbeSetID" value="_" />
-        <input type="hidden" name="ProbeSetID2" value="_" />
-        <input type="hidden" name="CellID" value="_" />
-        <input type="hidden" name="CellID2" value="_" />
-        <input type="hidden" name="tune" value="no" />
-        <input type="hidden" name="ShowLine" value="ON">
-        <input type="hidden" name="ShowStrains" value="ON">
-        <input type="hidden" name="FormID" value="showDatabase" />
-        <input type="hidden" name="RISet" value="%s" />
-        <input type="hidden" name="incparentsf1" value="ON" />
-        <input type="hidden" name="session" value="%s" />
-        <input type="hidden" name="searchResult" id="searchResult" value="%s" />
-        <input type="hidden" name="symbolList" id="symbolList" value="%s" />
-        <input type="hidden" name="optimalNode" id="optimalNode" value="%s" />
-        <input type="hidden" name="rankOrder" id="rankOrder" value="_" />
-        <input type="hidden" name="X_geneID" id="X_geneID" value="_" />
-        <input type="hidden" name="Y_geneID" id="Y_geneID" value="_" />
-        <input type="hidden" name="X_geneSymbol" id="X_geneSymbol" value="_" />
-        <input type="hidden" name="Y_geneSymbol" id="Y_geneSymbol" value="_" />
-        <input type="hidden" name="TissueProbeSetFreezeId" id="TissueProbeSetFreezeId" value="1" />
-        ''' % (webqtlConfig.CGIDIR,
-               webqtlConfig.SCRIPTFILE,
-               p["filename"],
-               graphName,
-               p["riset"],
-               p["session"],
-               p["searchResult"],
-               symbolList,
-               optimalNode)
-        
-        body += formParams
-        
-        #Adds the html generated by graphviz that displays the graph itself
-        body += graphcode
-
-        #Initializes all form values
-
-        selected = ["","","",""]
-        selected[p["whichValue"]] = "CHECKED"
-
-        selected3 = ["",""]
-        if p["splines"] == "yes":
-            selected3[0] = "CHECKED"
-        else:
-            selected3[1] = "CHECKED"
-
-        selected5 = ["",""]
-        if p["nodeshape"] == "yes":
-            selected5[0] = "CHECKED"
-        else:
-            selected5[1] = "CHECKED"
-            
-        selected7 = ["",""]
-        if p["nodelabel"] == "yes":
-            selected7[0] = "CHECKED"
-        else:
-            selected7[1] = "CHECKED"
-            
-        selected6 = ["",""]
-        if p["dispcorr"] == "yes":
-            selected6[0] = "CHECKED"
-        else:
-            selected6[1] = "CHECKED"
-
-        selected4 = ["", ""]
-        selected4[p["printIslands"]] = "CHECKED"
-       
-        selectedExportFormat = ["",""]
-        if p["exportFormat"] == "xgmml":
-            selectedExportFormat[0] = "selected='selected'"
-        elif p["exportFormat"] == "plain":
-            selectedExportFormat[1] = "selected='selected'"
-        
-        selectedTraitType = ["",""]
-        if p["traitType"] == "symbol":
-            selectedTraitType[0] = "selected='selected'"
-        elif p["traitType"] == "name":
-            selectedTraitType[1] = "selected='selected'"
-
-	selectedgType = ["","","","",""]
-	if p["gType"] == "none":
-	    selectedgType[0] = "selected='selected'"
-        elif p["gType"] == "neato":
-            selectedgType[1] = "selected='selected'"
-	elif p["gType"] == "fdp":
-	    selectedgType[2] = "selected='selected'"
-	elif p["gType"] == "circular":
-	    selectedgType[3] = "selected='selected'"
-	elif p["gType"] == "radial":
-	    selectedgType[4] = "selected='selected'"	
- 
- 
-        selectedLock = ["",""]
-        if p["lock"] == "no":
-            selectedLock[0] = "selected='selected'"
-        elif p["lock"] == "yes":
-            selectedLock[1] = "selected='selected'"
- 
-        # line 1~6
-        
-        selectedL1style = ["","","","",""]
-        if p["L1style"] == "":
-            selectedL1style[0] = "selected='selected'"
-        elif p["L1style"] == "bold":
-            selectedL1style[1] = "selected='selected'"
-        elif p["L1style"] == "dotted":
-            selectedL1style[2] = "selected='selected'"
-        elif p["L1style"] == "dashed":
-            selectedL1style[3] = "selected='selected'"
-        else:
-            selectedL1style[4] = "selected='selected'"
-        
-        selectedL2style = ["","","","",""]
-        if p["L2style"] == "":
-            selectedL2style[0] = "selected='selected'"
-        elif p["L2style"] == "bold":
-            selectedL2style[1] = "selected='selected'"
-        elif p["L2style"] == "dotted":
-            selectedL2style[2] = "selected='selected'"
-        elif p["L2style"] == "dashed":
-            selectedL2style[3] = "selected='selected'"
-        else:
-            selectedL2style[4] = "selected='selected'"
-        
-        selectedL3style = ["","","","",""]
-        if p["L3style"] == "":
-            selectedL3style[0] = "selected='selected'"
-        elif p["L3style"] == "bold":
-            selectedL3style[1] = "selected='selected'"
-        elif p["L3style"] == "dotted":
-            selectedL3style[2] = "selected='selected'"
-        elif p["L3style"] == "dashed":
-            selectedL3style[3] = "selected='selected'"
-        else:
-            selectedL3style[4] = "selected='selected'"
-        
-        selectedL4style = ["","","","",""]
-        if p["L4style"] == "":
-            selectedL4style[0] = "selected='selected'"
-        elif p["L4style"] == "bold":
-            selectedL4style[1] = "selected='selected'"
-        elif p["L4style"] == "dotted":
-            selectedL4style[2] = "selected='selected'"
-        elif p["L4style"] == "dashed":
-            selectedL4style[3] = "selected='selected'"
-        else:
-            selectedL4style[4] = "selected='selected'"
-        
-        selectedL5style = ["","","","",""]
-        if p["L5style"] == "":
-            selectedL5style[0] = "selected='selected'"
-        elif p["L5style"] == "bold":
-            selectedL5style[1] = "selected='selected'"
-        elif p["L5style"] == "dotted":
-            selectedL5style[2] = "selected='selected'"
-        elif p["L5style"] == "dashed":
-            selectedL5style[3] = "selected='selected'"
-        else:
-            selectedL5style[4] = "selected='selected'"
-        
-        selectedL6style = ["","","","",""]
-        if p["L6style"] == "":
-            selectedL6style[0] = "selected='selected'"
-        elif p["L6style"] == "bold":
-            selectedL6style[1] = "selected='selected'"
-        elif p["L6style"] == "dotted":
-            selectedL6style[2] = "selected='selected'"
-        elif p["L6style"] == "dashed":
-            selectedL6style[3] = "selected='selected'"
-        else:
-            selectedL6style[4] = "selected='selected'"
-            
-        nfontSelected = ["", "", ""]
-        if p["nfont"] == "arial":
-            nfontSelected[0] = "selected='selected'"
-        elif p["nfont"] == "verdana":
-            nfontSelected[1] = "selected='selected'"
-        elif p["nfont"] == "times":
-            nfontSelected[2] = "selected='selected'"
-            
-        cfontSelected = ["", "", ""]
-        if p["cfont"] == "arial":
-            cfontSelected[0] = "selected='selected'"
-        elif p["cfont"] == "verdana":
-            cfontSelected[1] = "selected='selected'"
-        elif p["cfont"] == "times":
-            cfontSelected[2] = "selected='selected'"
- 
-        #Writes the form part of the body
- 
-        body += ''' <br><br>
-        <TABLE cellspacing=0 Cellpadding=0>
-        <TR>
-        <TD class="doubleBorder">
-       
-        <Table Cellpadding=3>
-        
-        <tr><td align="left">
-        <dd>
-        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-        <input type="submit" name="mintmap" value="    Redraw    " class="button" onClick="return sortSearchResults(this.form);" />
-        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-        <input TYPE="Button" class="button" value="    Info    " onclick="javascript:window.open('/networkGraphInfo.html', '_blank');">
-        </dd>
-        </td></tr>
-        
-        <tr><td align='center' colspan='2'><hr size='1'></td></tr>
-    <tr>
-		<tr align='left' valign='top'>
-		    <td align='left'>
-		    &nbsp;<select align='left' name='gType' id='gType' onchange='addTraitSelection();'>
-		    <option value='none' %s>Select Graph Method</option>
-			<option value='neato' %s>Spring Model Layout (energy reduction)</option>
-			<option value='fdp' %s>Spring Model Layout (force reduction)</option>
-			<option value='circular' %s>Circular Layout</option>
-			<option value='radial' %s>Radial Layout</option>
-		    </select>
-		    <div align="left" id='nodeSelect'> </div>
-		    </td>
-		</tr>
-	</tr>
-	
-	    <tr><td align='center' colspan='2'><hr size='1'></td></tr>
-	    
-    <tr><td align='center' colspan='2'>
-
-        <table width='100%%'>
-
-        <tr align='left'>
-            <td>Lock Graph Structure</td>
-            <td align='left'><select name='lock' id='lock' onChange="changeThreshold();">
-            <option value='no' %s>No</option>
-            <option value='yes' %s>Yes</option>
-            </select></td>
-        </tr>
-        <tr><td align='left' colspan='2' nowrap='nowrap'>
-        Locking the graph structure allows the user to hold the position of<br>
-        all nodes and the length of all edges constant, letting him/her easily<br>
-        compare between different correlation types. Changing the value to "yes"<br> 
-        requires the line threshold to be set to 0 in order to lock the structure.<br>
-        </td></tr>
-        </td>
-    </tr>
-	
-	
-	<tr><td align='center' colspan='2'><hr size='1'></td></tr>        
-
-        <tr><td align='center' colspan='2'>
-            
-                <table width='100%%'>
-                
-                <tr align='center'>
-                    <td>Line Type 1:</td>
-                    <td>-1</td>
-                    <td>to</td>
-                    <td>-0.7</td>
-                    <td><Input type=radio name=colorS value="cL1" checked></TD>
-                    <td bgcolor="%s" ID="cL1" width=20></td>
-                    <td><select name='L1style'>
-                        <option value='' %s>normal</option>
-                        <option value='bold' %s>bold</option>
-                        <option value='dotted' %s>dotted</option>
-                        <option value='dashed' %s>dashed</option>
-                        <option value='invis' %s>invisible</option>
-                    </select></td>
-                </tr>
-                
-                <tr align='center'>
-                    <td>Line Type 2:</td>
-                    <td>-0.7</td>
-                    <td>to</td>
-                    <td>-0.5</td>
-                    <td><Input type=radio name=colorS value="cL2"></TD>
-                    <Td bgcolor="%s" ID="cL2" width=20></td>
-                    <td><select name='L2style'>
-                        <option value='' %s>normal</option>
-                        <option value='bold' %s>bold</option>
-                        <option value='dotted' %s>dotted</option>
-                        <option value='dashed' %s>dashed</option>
-                        <option value='invis' %s>invisible</option>
-                    </select></td>
-                </tr>
-                
-                <tr align='center'>
-                    <td>Line Type 3:</td>
-                    <td>-0.5</td>
-                    <td>to</td>
-                    <td>0</td>
-                    <td><Input type=radio name=colorS value="cL3"></TD>
-                    <Td bgcolor="%s" ID="cL3" width=20></td>
-                    <td><select name='L3style'>
-                        <option value='' %s>normal</option>
-                        <option value='bold' %s>bold</option>
-                        <option value='dotted' %s>dotted</option>
-                        <option value='dashed' %s>dashed</option>
-                        <option value='invis' %s>invisible</option>
-                    </select></td>
-                </tr>
-                
-                <tr align='center'>
-                    <td>Line Type 4:</td>
-                    <td>0</td>
-                    <td>to</td>
-                    <td>0.5</td>
-                    <td><Input type=radio name=colorS value="cL4"></TD>
-                    <Td bgcolor="%s" ID="cL4" width=20></td>
-                    <td><select name='L4style'>
-                        <option value='' %s>normal</option>
-                        <option value='bold' %s>bold</option>
-                        <option value='dotted' %s>dotted</option>
-                        <option value='dashed' %s>dashed</option>
-                        <option value='invis' %s>invisible</option>
-                    </select></td>
-                </tr>
-                
-                <tr align='center'>
-                    <td>Line Type 5:</td>
-                    <td>0.5</td>
-                    <td>to</td>
-                    <td>0.7</td>
-                    <td><Input type=radio name=colorS value="cL5"></TD>
-                    <Td bgcolor="%s" ID="cL5" width=20></td>
-                    <td><select name='L5style'>
-                        <option value='' %s>normal</option>
-                        <option value='bold' %s>bold</option>
-                        <option value='dotted' %s>dotted</option>
-                        <option value='dashed' %s>dashed</option>
-                        <option value='invis' %s>invisible</option>
-                    </select></td>
-                </tr>
-                
-                <tr align='center'>
-                    <td>Line Type 6:</td>
-                    <td>0.7</td>
-                    <td>to</td>
-                    <td>1</td>
-                    <td><Input type=radio name=colorS value="cL6"></TD>
-                    <Td bgcolor="%s" ID="cL6" width=20></td>
-                    <td><select name='L6style'>
-                        <option value='' %s>normal</option>
-                        <option value='bold' %s>bold</option>
-                        <option value='dotted' %s>dotted</option>
-                        <option value='dashed' %s>dashed</option>
-                        <option value='invis' %s>invisible</option>
-                    </select></td>
-                </tr>
-                
-                </table>
-            </td>
-        </tr>
-        
-        <tr><td align='center' colspan='2' nowrap='nowrap'>To change colors, select Line Type then select Color below.</td></tr>
-        
-        <tr><td align='center' colspan='2'><hr size='1'></td></tr>
-        
-        <tr>
-            <TD align="right">Correlation Type:</TD>
-            <TD>
-                <table border='0' cellspacing='0' cellpadding='0' width='100%%'>
-                    <tr>
-                        <td><Input type="radio" name="whichValue" value="0" %s>Pearson</td>
-                        <td><Input type="radio" name="whichValue" value="1" %s>Spearman</td>
-                        <td rowspan=2 align="center"><input TYPE="Button" class="button" value="Info" onclick="javascript:window.open('/correlationAnnotation.html', '_blank');"></td>
-                    </tr>
-                    <tr>
-                        <td><Input type="radio" name="whichValue" value="2" %s>Literature</td>
-                        <td><Input type="radio" name="whichValue" value="3" %s>Tissue</td>
-                    </tr>
-                </table>
-            </TD>
-        </TR>
-        
-        <TR>
-            <TD align="right" NOWRAP>Line Threshold:</TD>
-            <TD NOWRAP>Absolute values greater than <input size="5" name="kValue" id="kValue" value="%s"></TD>
-        </TR>
-        
-        <tr><td align='center' colspan='2'><hr size='1'></td></tr>
-        
-        <TR>
-            <TD align="right">Draw Nodes :</TD>
-            <TD NOWRAP>
-                <Input type="radio" name="printIslands" value="1" %s>all
-                <Input type="radio" name="printIslands" value="0" %s>connected only
-            </TD>
-        </TR>
-        
-        <TR>
-            <TD align="right">Node Shape:</TD>
-            <TD>
-                <Input type="radio" name="nodeshape" value="yes" %s>rectangle
-                <Input type="radio" name="nodeshape" value="no" %s>ellipse
-            </TD>
-        </TR>
-        
-        <TR>
-            <TD align="right">Node Label:</TD>
-            <TD>
-                <Input type="radio" name="nodelabel" value="yes" %s>trait name<br>
-                <Input type="radio" name="nodelabel" value="no" %s>gene symbol / marker name
-            </TD>
-        </TR>
-        
-        <tr>
-            <td align="right">Node Font:</td>
-            <TD>
-                <select name='nfont'>
-                    <option value='Arial' %s>Arial</option>
-                    <option value='Verdana' %s>Verdana</option>
-                    <option value='Times' %s>Times</option>
-                </select>
-            </TD>
-        </TR>
-        
-        <tr>
-            <td align="right">Node Font Size:</td>
-            <TD><input size="5" name="nfontsize" value="%s"> point</TD>
-        </TR>
-        
-        <tr><td align='center' colspan='2'><hr size='1'></td></tr>
-        
-        <TR>
-            <TD align="right">Draw Lines:</TD>
-            <TD>
-                <Input type="radio" name="splines" value="yes" %s>curved
-                <Input type="radio" name="splines" value="no" %s>straight
-            </TD>
-        </TR>
-        
-        <TR>
-            <TD align="right">Display Correlations:</TD>
-            <TD>
-                <Input type="radio" name="dispcorr" value="no" %s>no
-                <Input type="radio" name="dispcorr" value="yes" %s>yes
-            </TD>
-        </tr>
-        
-        <tr>
-            <td align="right">Line Font:</td>
-            <TD>
-                <select name='cfont'>
-                    <option value='Arial' %s>Arial</option>
-                    <option value='Verdana' %s>Verdana</option>
-                    <option value='Times' %s>Times</option>
-                </select>
-            </TD>
-        </TR>
-        
-        <TR>
-            <TD align="right" nowrap="nowrap">Line Font Size:</TD>
-            <TD><input size="5" name="cfontsize" value="%s"> point</TD>
-        </TR>
-        
-        <tr><td align='center' colspan='2'><hr size='1'></td></tr>
-        
-        <TR><TD colspan = 2>
-        
-        <Input type=hidden name=cPubName value="%s">
-        <Input type=hidden name=cMicName value="%s">
-        <Input type=hidden name=cGenName value="%s">
-        
-        <Input type=hidden name=cPubColor value="%s">
-        <Input type=hidden name=cMicColor value="%s">
-        <Input type=hidden name=cGenColor value="%s">
-        
-        <Input type=hidden name=cL1Name value="%s">
-        <Input type=hidden name=cL2Name value="%s">
-        <Input type=hidden name=cL3Name value="%s">
-        <Input type=hidden name=cL4Name value="%s">
-        <Input type=hidden name=cL5Name value="%s">
-        <Input type=hidden name=cL6Name value="%s">
-        
-        <Input type=hidden name=cL1Color value="%s">
-        <Input type=hidden name=cL2Color value="%s">
-        <Input type=hidden name=cL3Color value="%s">
-        <Input type=hidden name=cL4Color value="%s">
-        <Input type=hidden name=cL5Color value="%s">
-        <Input type=hidden name=cL6Color value="%s">
-        
-        <Input type=hidden id=initThreshold value="0.5">
-        
-		<Table CellSpacing = 3>
-			<tr>
-			    <TD><Input type=radio name=colorS value="cPub"> Publish </TD>
-			    <Td bgcolor="%s" ID="cPub" width=20 height=10></td>
-			    <TD><Input type=radio name=colorS value="cMic"> Microarray </TD>
-			    <Td bgcolor="%s" ID="cMic" width=20 height=10></td>
-			    <TD><Input type=radio name=colorS value="cGen"> Genotype </TD>
-			    <Td bgcolor="%s" ID="cGen" width=20 height=10></td>
-			</tr>
-		</table>
-		
-		</td></tr>
-		
-		<tr><td align='center' colspan='2'><hr size='1'></td></tr>
-		
-		<tr>
-		    <td colspan='2' align='center'>
-		        <img NAME="colorPanel" src="/images/colorPanel.png" alt="colorPanel" onClick="clickHandler(event, this);">
-		    </TD>
-		</TR>
-		
-		<tr><td align='center' colspan='2'><hr size='1'></td></tr>
-		
-		<tr><td align='center' colspan='2'><input type="submit" name="mintmap" value="    Redraw Graph    " class="button" onClick="return sortSearchResults(this.form);"/></td></tr>
-        
-        </TABLE>
-        </form></TD>
-        <SCRIPT type="text/javascript" SRC="/javascript/networkGraph.js"></SCRIPT>
-        ''' % (selectedgType[0], selectedgType[1], selectedgType[2], selectedgType[3], selectedgType[4],
-                           selectedLock[0], selectedLock[1],
-                           p["cL1Color"],
-                           selectedL1style[0], selectedL1style[1], selectedL1style[2], selectedL1style[3], selectedL1style[4],
-                           p["cL2Color"],
-                           selectedL2style[0], selectedL2style[1], selectedL2style[2], selectedL2style[3], selectedL2style[4],
-                           p["cL3Color"],
-                           selectedL3style[0], selectedL3style[1], selectedL3style[2], selectedL3style[3], selectedL3style[4],
-                           p["cL4Color"],
-                           selectedL4style[0], selectedL4style[1], selectedL4style[2], selectedL4style[3], selectedL4style[4],
-                           p["cL5Color"],
-                           selectedL5style[0], selectedL5style[1], selectedL5style[2], selectedL5style[3], selectedL5style[4],
-                           p["cL6Color"],
-                           selectedL6style[0], selectedL6style[1], selectedL6style[2], selectedL6style[3], selectedL6style[4],
-                           selected[0], selected[1], selected[2], selected[3],
-                           p["kValue"], 
-                           selected4[1], selected4[0], 
-                           selected5[0], selected5[1], 
-                           selected7[0], selected7[1],
-                           nfontSelected[0], nfontSelected[1], nfontSelected[2],
-                           p["nfontsize"],
-                           selected3[0], selected3[1], 
-                           selected6[1], selected6[0],
-                           cfontSelected[0], cfontSelected[1], cfontSelected[2],
-                           p["cfontsize"],
-                           p["cPubName"], p["cMicName"], p["cGenName"],
-                           p["cPubColor"], p["cMicColor"], p["cGenColor"],
-                           p["cL1Name"], p["cL2Name"], p["cL3Name"], p["cL4Name"], p["cL5Name"], p["cL6Name"],
-                           p["cL1Color"], p["cL2Color"], p["cL3Color"], p["cL4Color"], p["cL5Color"], p["cL6Color"],
-                           p["cPubColor"], p["cMicColor"], p["cGenColor"])
-        
-		#updated by NL 09-03-2010 function changeFormat() has been moved to webqtl.js and be changed to changeFormat(graphName)
-        #Javascript that selects the correct graph export file given what the user selects 
-        #from the two drop-down menus
-
-        body += ''' <td width='10'>&nbsp;</td> 
-        <TD valign="top"><p>Right-click or control-click on the following
-        links to download this graph as a <a href="%s" class="normalsize" target="_blank">GIF file</a> or
-        a <a href="%s" class="normalsize" target="_blank">PDF file</a>.</p> ''' % (imageName, pdfName)
-        
-        body += ''' <p>Initial edge lengths were computed by applying an r-to-Z transform to the correlation coefficents
-        and then inverting the results. The graph drawing algorithm
-        found a configuration that minimizes the total stretching of the edges.</p> ''' 
-        
-        body += ''' <p>This graph took %s seconds to generate with the <a href="http://www.research.att.com/sw/tools/graphviz/" class="normalsize" target="_blank">
-        GraphViz</a> visualization toolkit from <a href="http://www.research.att.com" class="normalsize" target="_blank">AT&amp;T Research</a>.</p>''' % (round(totalTime, 2))
-        
-        #Form to export graph file as either XGMML (standardized graphing format) or a
-        #plain text file with trait names/symbols and correlations
-        
-        body += '''
-        <form name="graphExport">
-        <p>Export Graph File:</p>
-        <p><select name='exportFormat' id='exportFormat' onchange='changeFormat("%s")'>
-            <option value='plain' %s>Plain Text Format</option>
-            <option value='xgmml' %s>XGMML Format</option>
-        </select>
-        &nbsp&nbsp&nbsp&nbsp&nbsp
-        <select name='traitType' id='traitType' onchange='changeFormat("%s")'>
-            <option value='symbol' %s>Trait Symbol</option>
-            <option value='name' %s>Full Trait Name</option>
-        </select></p>
-        
-        <p>
-        <input type="button" class="button" name="exportGraphFile" value="   Export Graph File   "/>
-        </p>
-        </form> 
-        ''' % (graphName, selectedExportFormat[0], selectedExportFormat[1],
-               graphName, selectedTraitType[0], selectedTraitType[1])
-
-        body += '''</Blockquote></td>
-        </TR></TABLE> 
-        <form method="get" action="http://www.google.com/search">
-        <input type="text"   name="q" size="31" maxlength="255" value="" />
-        <input type="submit" value="Google Search" />
-        <input type="radio"  name="sitesearch" value="" /> The Web
-        <input type="radio"  name="sitesearch" value="genenetwork.org" checked /> GeneNetwork <br />
-        </form>
-        ''' 
-
-        
-        self.dict["body"] = body
-
-    def writeToFile(self, filename):
-        """
-        Output the contents of this HTML page to a file.
-        """
-        handle = open(filename, "w")
-        handle.write(str(self))
-        handle.close()
diff --git a/web/webqtl/networkGraph/networkGraphUtils.py b/web/webqtl/networkGraph/networkGraphUtils.py
deleted file mode 100644
index fd0e7484..00000000
--- a/web/webqtl/networkGraph/networkGraphUtils.py
+++ /dev/null
@@ -1,750 +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
-
-# graphviz:
-# a library for sending trait data to the graphviz utilities to get
-# graphed
-
-# ParamDict: a dictionary of strings that map to strings where the keys are
-#     valid parameters and the values are validated versions of those parameters
-#
-# The list below also works for visualize.py; different parameters apply to different
-# functions in the pipeline. See visualize.py for more details.
-#
-# parameters:
-# filename: an input file with comma-delimited data to visualize
-# kValue:
-#    how to filter the edges; edges with correlation coefficents in
-#    [-k, k] are not drawn
-# whichValue: which of the two correlation coefficents are used;
-#     0 means the top half (pearson) and
-#     1 means the bottom half (spearman)
-# width: the width of the graph in inches
-# height: the height of the graph in inches
-# --scale: an amount to multiply the length factors by to space out the nodes
-# spline: whether to use splines instead of straight lines to draw graphs
-# tune: whether to automatically pick intelligent default values for
-#     kValue and spline based on the number of edges in the input data
-# whichVersion: whether to display the graph zoomed or fullscreen
-#     0 means zoom
-#     1 means fullscreen
-# printIslands: whether to display nodes with no visible edges
-# 
-
-# DataMatrix: a one-dimensional array of DataPoints in sorted order by i first
-
-
-
-import copy
-import os
-#import os.path
-import math
-import string
-
-from base import webqtlConfig
-from utility import webqtlUtil
-#import trait
-from nGraphException import nGraphException
-from ProcessedPoint import ProcessedPoint
-
-
-# processDataMatrix: DataMatrix -> ParamDict -> void
-# this is the second part after filterDataMatrix
-# To process the set of points in a DataMatrix as follows
-#    1) choose an appropriate color for the data point
-#    2) filter those between k values
-#    3) to use an r-to-Z transform to spread out the correlation
-#       values from [-1,1] to (-inf, inf)
-#    4) to invert the values so that higher correlations result in
-#       shorter edges
-#
-# Note: this function modifies the matrix in-place. My functional
-# programming instincts tell me that this is a bad idea.
-def processDataMatrix(matrix, p):
-    for pt2 in matrix:
-        # filter using k
-        if (-p["kValue"] <= pt2.value) and (pt2.value <= p["kValue"]):
-            pt2.value = 0.00
-            
-        # Lei Yan
-        # 05/28/2009
-        # fix color
-        
-        # pick a color
-        if pt2.value >= 0.7:
-            pt2.color = p["cL6Name"]
-            pt2.style = p["L6style"]
-        elif pt2.value >= 0.5:
-            pt2.color = p["cL5Name"]
-            pt2.style = p["L5style"]
-        elif pt2.value >= 0.0:
-            pt2.color = p["cL4Name"]
-            pt2.style = p["L4style"]
-        elif pt2.value >= -0.5:
-            pt2.color = p["cL3Name"]
-            pt2.style = p["L3style"]
-        elif pt2.value >= -0.7:
-            pt2.color = p["cL2Name"]
-            pt2.style = p["L2style"]
-        else:
-            pt2.color = p["cL1Name"]
-            pt2.style = p["L1style"]
-        
-        # r to Z transform to generate the length
-        # 0 gets transformed to infinity, which we can't
-        # represent here, and 1 gets transformed to 0
-        if p["lock"] == "no":
-            if -0.01 < pt2.value and pt2.value < 0.01:
-                pt2.length = 1000
-            elif pt2.value > 0.99 or pt2.value < -0.99:
-                pt2.length = 0
-            else:
-                pt2.length = pt2.value
-                pt2.length = 0.5 * math.log((1 + pt2.length)/(1 - pt2.length))
-        
-                # invert so higher correlations mean closer edges
-                #pt2.length = abs(p["scale"] * 1/pt2.length)
-                pt2.length = abs(1/pt2.length)
-        else:
-            pt2.length = 2
-            
-
-# tuneParamDict: ParamDict -> Int -> Int -> ParamDict
-# to adjust the parameter dictionary for a first-time run
-# so that the graphing doesn't take so long, especially since
-# small parameter changes can make a big performance difference
-# note: you can pass this function an empty dictionary and
-# get back a good set of default parameters for your
-# particular graph
-def tuneParamDict(p, nodes, edges):
-    newp = copy.deepcopy(p)
-    
-    if nodes > 50:
-        newp["splines"] = "no"
-    else:
-        newp["splines"] = "yes"
-        
-    if edges > 1000:
-        newp["printIslands"] = 0
-    else:
-        newp["printIslands"] = 1
-        
-    if edges > 1000:
-        newp["kValue"] = 0.8
-    elif edges > 500:
-        newp["kValue"] = 0.7
-    elif edges > 250:
-        newp["kValue"] = 0.6
-
-    if nodes > 50:
-        # there's no magic here; this formula
-        # just seems to work
-        dim = 3*math.sqrt(nodes)
-        newp["width"] = round(dim,2)
-        newp["height"] = round(dim,2)
-
-        # the two values below shouldn't change 
-        #        newp["scale"] = round(dim/10.0,2)
-        #        newp["fontsize"] = round(14*newp["scale"],0)
-        
-    else:
-        newp["width"] = 40.0
-        newp["height"] = 40.0
-        
-    return newp
-
-# fixLabel : string -> string
-def fixLabel(lbl):
-    """
-    To split a label with newlines so it looks a bit better
-    Note: we send the graphing program literal '\n' strings and
-    it converts these into newlines
-    """
-    lblparts = lbl.split(" ")
-    newlbl = ""
-    i = 0
-    for part in lblparts:
-        if 10*(i+1) < len(newlbl):
-            i += 1
-            newlbl = newlbl + r"\n" + part
-        else:
-            newlbl = newlbl + " " + part
-    return newlbl
-    #return "\N"
-
-def writeGraphFile(matrix, traits, filename, p):
-    """
-    Expresses the same information as the neato file, only in 
-    eXtensible Graph Markup and Modeling Language (XGMML) so the user can develop his/her
-    own graph in a program such as Cytoscape
-    """
-    inputFile1 = open(filename + "_xgmml_symbol.txt", "w")
-    inputFile2 = open(filename + "_xgmml_name.txt", "w")
-    inputFile3 = open(filename + "_plain_symbol.txt", "w")
-    inputFile4 = open(filename + "_plain_name.txt", "w")
-        
-    inputFile1.write("<graph directed=\"1\" label=\"Network Graph\">\n")
-    inputFile2.write("<graph directed=\"1\" label=\"Network Graph\">\n")
-    
-    #Write out nodes
-    traitEdges = []
-    for i in range(0, len(traits)):
-        traitEdges.append(0)
-    
-    for i in range(0, len(traits)):
-            
-        labelName = traits[i].symbol
-        inputFile1.write("\t<node id=\"%s\" label=\"%s\"></node>\n" % (i, labelName))
-    
-    for i in range(0, len(traits)):
-        
-        labelName = traits[i].name
-        inputFile2.write("\t<node id=\"%s\" label=\"%s\"></node>\n" % (i, labelName))
-            
-    #Write out edges
-    for point in matrix:
-
-        traitEdges[point.i] = 1
-        traitEdges[point.j] = 1
-        if p["edges"] == "complex":
-            _traitValue = "%.3f" % point.value
-            inputFile1.write("\t<edge source=\"%s\" target=\"%s\" label=\"%s\"></edge>\n"
-                             % (point.i,
-                                point.j, 
-                                _traitValue))
-            inputFile2.write("\t<edge source=\"%s\" target=\"%s\" label=\"%s\"></edge>\n"
-                             % (point.i,
-                                point.j, 
-                                _traitValue))
-    
-    inputFile1.write("</graph>")
-    inputFile2.write("</graph>")
-            
-    for edge in matrix:
-        inputFile3.write("%s\t%s\t%s\n" % (traits[edge.i].symbol, edge.value, traits[edge.j].symbol))    
-    
-
-    for edge in matrix:
-        inputFile4.write("%s\t%s\t%s\n" % (traits[edge.i].name, edge.value, traits[edge.j].name))         
-                
-    inputFile1.close()
-    inputFile2.close()
-    inputFile3.close()
-    inputFile4.close()
-    
-    return (os.path.split(filename))[1]
-
-# writeNeatoFile : DataMatrix -> arrayof Traits -> String -> ParamDict -> String
-def writeNeatoFile(matrix, traits, filename, GeneIdArray, p):
-    """
-    Given input data, to write a valid input file for neato, optionally
-    writing entries for nodes that have no edges.
-    
-    NOTE: There is a big difference between removing an edge and zeroing
-    its value. Because writeNeatoFile is edge-driven, zeroing an edge's value
-    will still result in its node being written.
-    """
-    inputFile = open(filename, "w")
-    
-    """
-    This file (inputFile_pdf) is rotated 90 degrees. This is because of a bug in graphviz 
-    that causes pdf output onto a non-landscape layout to often be cut off at the edge
-    of the page. This second filename (which is just the first + "_pdf" is then read
-    in the "visualizePage" class in networkGraph.py and used to generate the postscript
-    file that is converted to pdf.
-    """
-    inputFile_pdf = open(filename + "_pdf", "w")
-    
-    
-    if p["splines"] == "yes":
-        splines = "true"
-    else:
-        splines = "false"
-    
-    # header        
-    inputFile.write('''graph webqtlGraph {
-    overlap="false";
-    start="regular";
-    splines="%s";
-    ratio="auto";
-    fontpath = "%s";
-    node [fontname="%s", fontsize=%s, shape="%s"];
-    edge [fontname="%s", fontsize=%s];
-    ''' % (splines, webqtlConfig.PIDDLE_FONT_PATH,
-           p["nfont"], p["nfontsize"], p["nodeshapeType"],
-           p["cfont"], p["cfontsize"]))
-    
-    inputFile_pdf.write('''graph webqtlGraph {
-    overlap="false";
-    start="regular";
-    splines="%s";
-    rotate="90";
-    center="true";
-    size="11,8.5";
-    margin="0";
-    ratio="fill";
-    fontpath = "%s";
-    node [fontname="%s", fontsize=%s, shape="%s"];
-    edge [fontname="%s", fontsize=%s];
-    ''' % (splines, webqtlConfig.PIDDLE_FONT_PATH,
-           p["nfont"], p["nfontsize"], p["nodeshapeType"],
-           p["cfont"], p["cfontsize"]))
-
-    # traitEdges stores whether a particular trait has edges
-    traitEdges = []
-    for i in range(0, len(traits)):
-        traitEdges.append(0)
-       
-    if p["dispcorr"] == "yes":
-        _dispCorr = 1
-    else:
-        _dispCorr = 0
-    # print edges first while keeping track of nodes
-    for point in matrix:
-        if point.value != 0:
-            traitEdges[point.i] = 1
-            traitEdges[point.j] = 1
-            if p["edges"] == "complex":
-                if _dispCorr:
-                    _traitValue = "%.3f" % point.value
-                else:
-                    _traitValue = ""
-                if p["correlationName"] == "Pearson":
-                    inputFile.write('%s -- %s [len=%s, weight=%s, label=\"%s\", color=\"%s\", style=\"%s\", edgeURL=\"javascript:showCorrelationPlot2(db=\'%s\',ProbeSetID=\'%s\',CellID=\'\',db2=\'%s\',ProbeSetID2=\'%s\',CellID2=\'\',rank=\'%s\');\", edgetooltip="%s"];\n'
-                                    % (point.i,
-                                       point.j, 
-                                       point.length,
-                                       point.length, 
-                                       _traitValue,
-                                       point.color,
-                                       point.style,
-                                       str(traits[point.i].datasetName()),
-                                       str(traits[point.i].nameNoDB()),
-                                       str(traits[point.j].datasetName()),
-                                       str(traits[point.j].nameNoDB()),
-                                       "0",
-    				                   "Pearson Correlation Plot between " + str(traits[point.i].symbol) + " and " + str(traits[point.j].symbol)))
-                elif p["correlationName"] == "Spearman":
-                    inputFile.write('%s -- %s [len=%s, weight=%s, label=\"%s\", color=\"%s\", style=\"%s\", edgeURL=\"javascript:showCorrelationPlot2(db=\'%s\',ProbeSetID=\'%s\',CellID=\'\',db2=\'%s\',ProbeSetID2=\'%s\',CellID2=\'\',rank=\'%s\');\", edgetooltip="%s"];\n'
-                                    % (point.i,
-                                       point.j, 
-                                       point.length,
-                                       point.length, 
-                                       _traitValue,
-                                       point.color,
-                                       point.style,
-                                       str(traits[point.j].datasetName()),
-                                       str(traits[point.j].nameNoDB()),
-                                       str(traits[point.i].datasetName()),
-                                       str(traits[point.i].nameNoDB()),
-                                       "1",
-                                       "Spearman Correlation Plot between " + str(traits[point.i].symbol) + " and " + str(traits[point.j].symbol)))    
-                elif p["correlationName"] == "Tissue":
-                    inputFile.write('%s -- %s [len=%s, weight=%s, label=\"%s\", color=\"%s\", style=\"%s\", edgeURL=\"javascript:showTissueCorrPlot(fmName=\'showDatabase\', X_geneSymbol=\'%s\', Y_geneSymbol=\'%s\', rank=\'0\');\", edgetooltip="%s"];\n'
-                                    % (point.i,
-                                       point.j, 
-                                       point.length,
-                                       point.length, 
-                                       _traitValue,
-                                       point.color,
-                                       point.style,
-                                       str(traits[point.i].symbol),
-                                       str(traits[point.j].symbol),
-                                       "Tissue Correlation Plot between " + str(traits[point.i].symbol) + " and " + str(traits[point.j].symbol)))      
-                else:
-                    inputFile.write('%s -- %s [len=%s, weight=%s, label=\"%s\", color=\"%s\", style=\"%s\", edgeURL=\"javascript:showCorrelationPlot2(db=\'%s\',ProbeSetID=\'%s\',CellID=\'\',db2=\'%s\',ProbeSetID2=\'%s\',CellID2=\'\',rank=\'%s\');\", edgetooltip="%s"];\n'
-                                    % (point.i,
-                                       point.j, 
-                                       point.length,
-                                       point.length, 
-                                       _traitValue,
-                                       point.color,
-                                       point.style,
-                                       str(traits[point.i].datasetName()),
-                                       str(traits[point.i].nameNoDB()),
-                                       str(traits[point.j].datasetName()),
-                                       str(traits[point.j].nameNoDB()),
-                                       "0",
-                                       "Correlation Plot between " + str(traits[point.i].symbol) + " and " + str(traits[point.j].symbol)))         
-                inputFile_pdf.write('%s -- %s [len=%s, weight=%s, label=\"%s\", color=\"%s\", style=\"%s\", edgetooltip="%s"];\n'
-                                % (point.i,
-                                   point.j, 
-                                   point.length,
-                                   point.length, 
-                                   _traitValue,
-                                   point.color,
-                                   point.style,
-                                   "Correlation Plot between " + str(traits[point.i].symbol) + " and " + str(traits[point.j].symbol)))
-					
-            else:
-                inputFile.write('%s -- %s [color="%s", style="%s"];\n'
-                                % (point.i, 
-                                   point.j, 
-                                   point.color,
-                                   point.style))
-                inputFile_pdf.write('%s -- %s [color="%s", style="%s"];\n'
-                                % (point.i, 
-                                   point.j, 
-                                   point.color,
-                                   point.style))
-
-    # now print nodes
-    # the target attribute below is undocumented; I found it by looking
-    # in the neato code
-    for i in range(0, len(traits)):
-        if traitEdges[i] == 1 or p["printIslands"] == 1:
-            _tname = str(traits[i])
-            if _tname.find("Publish") > 0:
-            	plotColor = p["cPubName"]
-            elif _tname.find("Geno") > 0:
-            	plotColor = p["cGenName"]
-            else:
-            	plotColor = p["cMicName"]
-            if p['nodelabel'] == 'yes':
-            	labelName = _tname
-            else:
-            	labelName = traits[i].symbol
-
-            inputFile.write('%s [label="%s", href="javascript:showDatabase2(\'%s\',\'%s\',\'\');", color="%s", style = "filled"];\n'
-                            % (i, labelName, traits[i].datasetName(), traits[i].nameNoDB(), plotColor))# traits[i].color
-            inputFile_pdf.write('%s [label="%s", href="javascript:showDatabase2(\'%s\',\'%s\',\'\');", color="%s", style = "filled"];\n'
-                            % (i, labelName, traits[i].datasetName(), traits[i].nameNoDB(), plotColor))# traits[i].color
-            
-    # footer
-    inputFile.write("}\n")
-    inputFile_pdf.write("]\n")
-    inputFile.close()
-    inputFile_pdf.close()
-
-    # return only the filename portion, omitting the directory
-    return (os.path.split(filename))[1]
-
-# runNeato : string -> string -> string
-def runNeato(filename, extension, format, gType):
-    """
-    to run neato on the dataset in the given filename and produce an image file
-    in the given format whose name we will return. Right now we assume
-    that format is a valid neato output (see graphviz docs) and a valid extension
-    for the source datafile. For example,
-    runNeato('input1', 'png') will produce a file called 'input1.png'
-    by invoking 'neato input1 -Tpng -o input1.png'
-    """
-    # trim extension off of filename before adding output extension
-    if filename.find(".") > 0:
-        filenameBase = filename[:filename.find(".")]
-    else:
-        filenameBase = filename
-        
-    imageFilename = filenameBase + "." + extension
-
-    #choose which algorithm to run depended upon parameter gType
-    #neato: energy based algorithm
-    #circular: nodes given circular structure determined by which nodes are most closely correlated
-    #radial: first node listed (when you search) is center of the graph, all other nodes are in a circular structure around it
-    #fdp: force based algorithm
-
-    if gType == "none":
-    # to keep the output of neato from going to stdout, we open a pipe
-    # and then wait for it to terminate
-    
-        if format in ('gif', 'cmapx', 'ps'):
-            neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/neato", "/usr/local/bin/neato", "-s", "-T", format, webqtlConfig.IMGDIR + filename, "-o", webqtlConfig.IMGDIR + imageFilename)
-    
-        else:
-            neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/neato", "/usr/local/bin/neato", webqtlConfig.IMGDIR + filename, "-T", format, "-o", webqtlConfig.IMGDIR + imageFilename)
-
-        if neatoExit == 0:
-            return imageFilename
-        
-        return imageFilename
-
-
-    elif gType == "neato":
-    # to keep the output of neato from going to stdout, we open a pipe
-    # and then wait for it to terminate
-        if format in ('gif', 'cmapx', 'ps'):
-            neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/neato", "/usr/local/bin/neato", "-s", "-T", format, webqtlConfig.IMGDIR + filename, "-o", webqtlConfig.IMGDIR + imageFilename)
-    
-        else:
-            neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/neato", "/usr/local/bin/neato", webqtlConfig.IMGDIR + filename, "-T", format, "-o", webqtlConfig.IMGDIR + imageFilename)
-
-        if neatoExit == 0:
-            return imageFilename
-        
-        return imageFilename
-
-    elif gType == "circular":
-	
-        if format in ('gif', 'cmapx', 'ps'):
-            neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/circo", "/usr/local/bin/circo", "-s", "-T", format, webqtlConfig.IMGDIR + filename, "-o", webqtlConfig.IMGDIR + imageFilename)
-        
-        else:
-            neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/circo", "/usr/local/bin/circo", webqtlConfig.IMGDIR + filename, "-T", format, "-o", webqtlConfig.IMGDIR + imageFilename)
-
-        if neatoExit == 0:
-            return imageFilename
-        
-        return imageFilename
-
-    elif gType == "radial":
-	
-        if format in ('gif', 'cmapx', 'ps'):
-            neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/twopi", "/usr/local/bin/twopi", "-s", "-T", format, webqtlConfig.IMGDIR + filename, "-o", webqtlConfig.IMGDIR + imageFilename)
-        
-        else:
-            neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/twopi", "/usr/local/bin/twopi", webqtlConfig.IMGDIR + filename, "-T", format, "-o", webqtlConfig.IMGDIR + imageFilename)
-
-        if neatoExit == 0:
-            return imageFilename
-        
-        return imageFilename
-
-    elif gType == "fdp":
-
-        if format in ('gif', 'cmapx', 'ps'):
-            neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/fdp", "/usr/local/bin/fdp", "-s", "-T", format, webqtlConfig.IMGDIR + filename, "-o", webqtlConfig.IMGDIR + imageFilename)
-        
-        else:
-            neatoExit = os.spawnlp(os.P_WAIT, "/usr/local/bin/fdp", "/usr/local/bin/fdp", webqtlConfig.IMGDIR + filename, "-T", format, "-o", webqtlConfig.IMGDIR + imageFilename)
-
-        if neatoExit == 0:
-            return imageFilename
-        
-        return imageFilename
-    
-
-    return imageFilename
-# runPsToPdf: string -> int -> intstring
-# to run Ps2Pdf to convert the given input postscript file to an 8.5 by 11
-# pdf file The width and height should be specified in inches. We assume
-# that the PS files output by GraphViz are 72 dpi.
-def runPsToPdf(psfile, width, height):
-    # we add 1 for padding b/c sometimes a small part of the graph gets
-    # cut off
-    newwidth = int((width + 1) * 720)
-    newheight = int((height + 1) * 720)
-
-    # replace the ps extension with a pdf one
-    pdffile = psfile[:-2] + "pdf"
-
-    os.spawnlp(os.P_WAIT, "ps2pdf", 
-               "-g%sx%s" % (newwidth, newheight),
-               webqtlConfig.IMGDIR + psfile, webqtlConfig.IMGDIR + pdffile)
-
-    return pdffile
-
-# buildParamDict: void -> ParamDict
-# to process and validate CGI arguments,
-# looking up human-readable names where necessary
-# see the comment at the top of the file for valid cgi parameters
-def buildParamDict(fs, sessionfile):
-    params = {}
-       
-    params["inputFile"] = fs.formdata.getvalue("inputFile", "")
-    params["progress"] = fs.formdata.getvalue("progress", "1")
-    params["filename"] = fs.formdata.getvalue("filename", "")
-    params["session"] = sessionfile
-    
-    if type("1") != type(fs.formdata.getvalue("searchResult")):
-        params["searchResult"] = string.join(fs.formdata.getvalue("searchResult"),'\t')
-    else:
-        params["searchResult"] = fs.formdata.getvalue("searchResult")
-        
-    params["riset"] = fs.formdata.getvalue("RISet", "")
-    #if params["filename"] == "":
-    #    raise nGraphException("Required parameter filename missing")
-   
-    #parameter determining whether export button returns an xgmml graph file or plain text file
-    params["exportFormat"] = fs.formdata.getvalue("exportFormat", "xgmml")
-    
-    #parameter determining whether or not traits in the graph file are listed by their symbol or name
-    params["traitType"] = fs.formdata.getvalue("traitType", "symbol")
-   
-    #parameter saying whether or not graph structure should be locked when you redraw the graph
-    params["lock"] = fs.formdata.getvalue("lock", "no")
-    
-    #parameter saying what algorithm should be used to draw the graph
-    params["gType"] = fs.formdata.getvalue("gType", "none")
-
-    params["kValue"] = webqtlUtil.safeFloat(fs.formdata.getvalue("kValue", "0.5"), 0.5)
-    params["whichValue"] = webqtlUtil.safeInt(fs.formdata.getvalue("whichValue","0"),0)
-    
-    # 1 inch = 2.54 cm
-    # 1 cm = 0.3937 inch
-    
-    params["width"] = webqtlUtil.safeFloat(fs.formdata.getvalue("width", "40.0"), 40.0)
-    params["height"] = webqtlUtil.safeFloat(fs.formdata.getvalue("height", "40.0"), 40.0)
-    
-    yesno = ["yes", "no"]
-    
-    params["tune"] = webqtlUtil.safeString(fs.formdata.getvalue("tune", "yes"), yesno, "yes")
-    
-    params["printIslands"] = webqtlUtil.safeInt(fs.formdata.getvalue("printIslands", "1"),1)
-    params["nodeshape"] = webqtlUtil.safeString(fs.formdata.getvalue("nodeshape","yes"), yesno, "yes")
-    params["nodelabel"] = webqtlUtil.safeString(fs.formdata.getvalue("nodelabel","no"), yesno, "no")
-    params["nfont"] = fs.formdata.getvalue("nfont","Arial")
-    params["nfontsize"] = webqtlUtil.safeFloat(fs.formdata.getvalue("nfontsize", "10.0"), 10.0)
-
-    params["splines"] = webqtlUtil.safeString(fs.formdata.getvalue("splines","yes"), yesno, "yes")    
-    params["dispcorr"] = webqtlUtil.safeString(fs.formdata.getvalue("dispcorr","no"), yesno, "no")
-    params["cfont"] = fs.formdata.getvalue("cfont","Arial")
-    params["cfontsize"] = webqtlUtil.safeFloat(fs.formdata.getvalue("cfontsize", "10.0"), 10.0)
-    
-    params["cPubName"] = fs.formdata.getvalue("cPubName","palegreen")
-    params["cMicName"] = fs.formdata.getvalue("cMicName","lightblue")
-    params["cGenName"] = fs.formdata.getvalue("cGenName","lightcoral")
-    
-    params["cPubColor"] = fs.formdata.getvalue("cPubColor","98fb98")
-    params["cMicColor"] = fs.formdata.getvalue("cMicColor","add8e6")
-    params["cGenColor"] = fs.formdata.getvalue("cGenColor","f08080")
-    
-    params["cL1Name"] = fs.formdata.getvalue("cL1Name","blue")
-    params["cL2Name"] = fs.formdata.getvalue("cL2Name","green")
-    params["cL3Name"] = fs.formdata.getvalue("cL3Name","black")
-    params["cL4Name"] = fs.formdata.getvalue("cL4Name","pink")
-    params["cL5Name"] = fs.formdata.getvalue("cL5Name","orange")
-    params["cL6Name"] = fs.formdata.getvalue("cL6Name","red")
-    
-    params["cL1Color"] = fs.formdata.getvalue("cL1Color","0000ff")
-    params["cL2Color"] = fs.formdata.getvalue("cL2Color","00ff00")
-    params["cL3Color"] = fs.formdata.getvalue("cL3Color","000000")
-    params["cL4Color"] = fs.formdata.getvalue("cL4Color","ffc0cb")
-    params["cL5Color"] = fs.formdata.getvalue("cL5Color","ffa500")
-    params["cL6Color"] = fs.formdata.getvalue("cL6Color","ff0000")
-    
-    params["L1style"] = fs.formdata.getvalue("L1style","bold")
-    params["L2style"] = fs.formdata.getvalue("L2style","")
-    params["L3style"] = fs.formdata.getvalue("L3style","dashed")
-    params["L4style"] = fs.formdata.getvalue("L4style","dashed")
-    params["L5style"] = fs.formdata.getvalue("L5style","")
-    params["L6style"] = fs.formdata.getvalue("L6style","bold")
-    
-    if params["splines"] == "yes":
-        params["splineName"] = "curves"
-    else:
-        params["splineName"] = "lines"
-        
-    if params["nodeshape"] == "yes":
-        params["nodeshapeType"] = "box"
-    else:
-        params["nodeshapeType"] = "ellipse"
-        
-    if params["whichValue"] == 0:
-        params["correlationName"] = "Pearson"
-    elif params["whichValue"] == 1:
-        params["correlationName"] = "Spearman"
-    elif params["whichValue"] == 2:
-        params["correlationName"] = "Literature"
-    else:
-        params["correlationName"] = "Tissue"
-
-    # see graphviz::writeNeatoFile to find out what this done
-    params["edges"] = "complex"
-    
-    return params        
-
-def optimalRadialNode(matrix):
-    """
-    Automatically determines the node with the most/strongest correlations with 
-    other nodes. If the user selects "radial" for Graph Type and then "Auto" for the
-    central node then this node is used as the central node. The algorithm is simply a sum of 
-    each node's correlations that fall above the threshold set by the user.
-    """
-    
-    optMatrix = [0]*(len(matrix)+1)
-    
-    for pt in matrix:
-	 if abs(pt.value) > 0.5:
-            optMatrix[pt.i] += abs(pt.value)
-            optMatrix[pt.j] += abs(pt.value)
-    
-    optPoint = 0
-    optCorrTotal = 0
-    
-    j = 0
-    
-    for point in optMatrix:
-        if (float(point) > float(optCorrTotal)):
-            optPoint = j
-            optCorrTotal = point
-        j += 1
-    
-    
-    return optPoint    
-    
-# filterDataMatrix : DataMatrix -> ParamDict -> DataMatrix
-def filterDataMatrix(matrix, p):
-    """
-    To convert a set of input RawPoints to a set of
-    ProcessedPoints and to choose the appropriate
-    correlation coefficent.
-    """
-    newmatrix = []
-    for pt in matrix:
-        pt2 = ProcessedPoint(pt.i, pt.j) # XZ, 09/11/2008: add module name
-        
-        # pick right value
-        if p["whichValue"] == 0:
-            pt2.value = pt.pearson
-        elif p["whichValue"] == 1:
-            pt2.value = pt.spearman
-        elif p["whichValue"] == 2:
-            pt2.value = pt.literature
-        elif p["whichValue"] == 3:
-            pt2.value = pt.tissue
-        else:
-            raise nGraphException("whichValue should be either 0, 1, 2 or 3")
-
-        try:
-            pt2.value = float(pt2.value)
-        except:
-            pt2.value = 0.00
-
-        newmatrix.append(pt2)
-        
-        
-
-    return newmatrix
-   
-def generateSymbolList(traits):
-    """ 
-    Generates a list of trait symbols to be displayed in the central node 
-    selection drop-down menu when plotting a radial graph
-    """
-        
-    traitList = traits
-    
-    symbolList = [None]*len(traitList)
-    
-    i=0
-    for trait in traitList:
-        symbolList[i] = str(trait.symbol)
-        i = i+1
-        
-    symbolListString = "\t".join(symbolList)
-    
-    return symbolListString       
-