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

1 files changed, 0 insertions, 697 deletions

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()