GENENET8 update

1 files changed, 0 insertions, 1046 deletions

diff --git a/sourcecodes/create_tiers_gom.php b/sourcecodes/create_tiers_gom.php
deleted file mode 100644
index 5f59ab5b..00000000
--- a/sourcecodes/create_tiers_gom.php
+++ /dev/null
@@ -1,1046 +0,0 @@
-<?php 
-
-///////This code will allow users to group variables in tier. getcombineDescription() function combined all data and take you to "tier_description_processing_gom.php" for preparation of ban and whitelist //////////
-
-include("header_new.inc");
-include("runtime_check.php");
-include("input_validate.php");
-$keyval=$_GET["My_key"];
-
-$dir="./data/";
-
-$type_n=array();
-
-//Get number of tier data and key value for changes in number of tier
-
-if(isset($_POST["nm_tier"]))
-{
-   $type_n=explode("|",$_POST["nm_tier"]);
-}
-else if(isset($_POST["nm_parent"]))
-{
-   $type_n=explode("|",$_POST["nm_parent"]);
-}
-else if(isset($_POST["nm_k"]))
-{
-   $type_n=explode("|",$_POST["nm_k"]);
-}
-else if(isset($_POST["nm_thr"]))
-{
-    $type_n=explode("|",$_POST["nm_thr"]);
-}
-
-$parent_number=trim($type_n[0]);   
-$k_number=trim($type_n[1]);   
-$tier_number=trim($type_n[2]);   
-$structure_thr=trim($type_n[3]);   
-
-
-if($keyval=="")
-  $keyval=$type_n[4];
-
-
-if($parent_number=="")
-{
-   $parent_number=4;
-}
-
-if($k_number=="")
-{
-   $k_number=1;
-}
-
-if($tier_number=="")
-{
-  $tier_number=3;
-}
-if($structure_thr=="")
-{
-  $structure_thr=0.5;
-}
-
-
-
-$nf=$dir.$keyval."nnode.txt";
-$node=trim(file_get_contents("$nf"));
-$maxplist=$node-1;
-
-//print default number of parents
-$pfile=$dir.$keyval."parent.txt";
-$parentf=fopen($pfile,"w");
-fwrite($parentf,"$parent_number\n");
-
-//print default number of k for model averaging
-$kfile=$dir.$keyval."k.txt";
-$kf=fopen($kfile,"w");
-fwrite($kf,"$k_number\n");
-
-//print model averaging threshold
-$thrfile=$dir.$keyval."thr.txt";
-$kf=fopen($thrfile,"w");
-fwrite($kf,"$structure_thr\n");
-
-//////////////////Check execution time//////////////////////////////////////////////
-$keyval=valid_keyval($keyval);
-$runtime=exe_time($keyval,$parent_number,$k_number);
-
-//print("Runtime is $runtime");
-
-?>
-<!-- Site navigation menu -->
-<ul class="navbar2">
-  <li><p onClick="getcombineDescription(ntiers,'ban_from','ban_to','white_from','white_to','<?php print($keyval);?>')"><a href="javascript:void(0)" >Perform Bayesian network modeling</a></p>
-  <li><a href="javascript:void(0);"
-NAME="InputCheck" title="InputCheck"
-    onClick=window.open("input_check.php?My_key=<?php print($keyval);?>","Rat//ting","width=950,height=270,0,status=0,");>View uploaded variables and data</a>
-</ul>
-<ul class="navbar">
-  <li><a href="help.php#constraint_interface" target="_blank">How to use this page</a>
-  <li><a href="help.php" target="_blank">Help</a>
-  <li><a href="home.php">Home</a>
-
-</ul>
-
-<div id="outernew">
-<p><h3><?php 
-print("Estimated run time for the current parameters: $runtime seconds");
-?>
-<br><br></h3>
-</p>
-<br>
-<p><h3>1. Global structure learning settings:<br><br></h3>
-</p>
-<table align="center">
-<tr>
-<td align="left">
-Maximum number of parents for any node:
-</td>
-<td align="left"> 
-     <form method="post" action="create_tiers_gom.php" name="form">
-      <SELECT NAME="nm_parent"  onchange="form.submit();">
-      <?php if($node<=5) 
-            {
-               for($i=1;$i<=4;$i++)
-              {
-            ?>
-              <option value=<?php $combined=$i."|".$k_number."|".$tier_number."|".$structure_thr."|".$keyval; print($combined)?> <?php if($parent_number == $i) {print "selected";}?>><?php print($i)?></option>
-            <?php
-              }
-            }
-            else if($node<=10) 
-            {
-               for($i=1;$i<$node;$i++)
-              {
-            ?>
-              <option value=<?php $combined=$i."|".$k_number."|".$tier_number."|".$structure_thr."|".$keyval; print($combined)?> <?php if($parent_number == $i) {print "selected";}?>><?php print($i)?></option>
-            <?php
-              }
-            }
-            else
-            {
-               for($i=1;$i<=9;$i++)
-               {
-   
-                ?>
-                 <option value=<?php $combined=$i."|".$k_number."|".$tier_number."|".$structure_thr."|".$keyval; print($combined)?> <?php if($parent_number == $i) {print "selected";}?>><?php print($i)?></option>
-               <?php
-               }
-               ?>
-              <option value=<?php $combined=$maxplist."|".$k_number."|".$tier_number."|".$structure_thr."|".$keyval; print($combined)?> <?php if($parent_number == $maxplist) {print "selected";}?>>All</option>
-           <?php
-
-            }
-            
-     ?>  
- 
-      </SELECT>
-   </form>
-</td>
-</tr>
-<tr>
-<td align="left">
-Number of networks to include in model averaging:
-</td>
-<td align="left"> 
-     <form method="post" action="create_tiers_gom.php" name="form">
-      <SELECT NAME="nm_k"  onchange="form.submit();">
-           <option value=<?php $combined=$parent_number."|"."1"."|".$tier_number."|".$structure_thr."|".$keyval; print($combined)?> <?php if($k_number == 1) {print "selected";}?>><?php print("1")?></option>
-           <option value=<?php $combined=$parent_number."|"."10"."|".$tier_number."|".$structure_thr."|".$keyval; print($combined)?> <?php if($k_number == 10) {print "selected";}?>><?php print("10")?></option>
-          <option value=<?php $combined=$parent_number."|"."50"."|".$tier_number."|".$structure_thr."|".$keyval; print($combined)?> <?php if($k_number == 50) {print "selected";}?>><?php print("50")?></option>
-          <option value=<?php $combined=$parent_number."|"."100"."|".$tier_number."|".$structure_thr."|".$keyval; print($combined)?> <?php if($k_number == 100) {print "selected";}?>><?php print("100")?></option>
-          <option value=<?php $combined=$parent_number."|"."500"."|".$tier_number."|".$structure_thr."|".$keyval; print($combined)?> <?php if($k_number == 500) {print "selected";}?>><?php print("500")?></option>
-          <option value=<?php $combined=$parent_number."|"."1000"."|".$tier_number."|".$structure_thr."|".$keyval; print($combined)?> <?php if($k_number == 1000) {print "selected";}?>><?php print("1000")?></option>
-      </SELECT>
-   </form>
-</td>
-</tr>
-<tr>
-<td align="left">
-Model averaging edge selection threshold:
-</td>
-<td align="left"> 
-     <form method="post" action="create_tiers_gom.php" name="form">
-      <SELECT NAME="nm_thr"  onchange="form.submit();">
-     <option value=<?php $combined=$parent_number."|".$k_number."|".$tier_number."|"."0.5"."|".$keyval; print($combined)?> <?php if($structure_thr == 0.5) {print "selected";}?>>0.5</option>
-     <option value=<?php $combined=$parent_number."|".$k_number."|".$tier_number."|"."0.6"."|".$keyval; print($combined)?> <?php if($structure_thr == 0.6) {print "selected";}?>>0.6</option>
-     <option value=<?php $combined=$parent_number."|".$k_number."|".$tier_number."|"."0.7"."|".$keyval; print($combined)?> <?php if($structure_thr == 0.7) {print "selected";}?>>0.7</option>
-     <option value=<?php $combined=$parent_number."|".$k_number."|".$tier_number."|"."0.8"."|".$keyval; print($combined)?> <?php if($structure_thr == 0.8) {print "selected";}?>>0.8</option>
-     <option value=<?php $combined=$parent_number."|".$k_number."|".$tier_number."|"."0.9"."|".$keyval; print($combined)?> <?php if($structure_thr == 0.9) {print "selected";}?>>0.9</option>
-     <option value=<?php $combined=$parent_number."|".$k_number."|".$tier_number."|"."1.0"."|".$keyval; print($combined)?> <?php if($structure_thr == 1.0) {print "selected";}?>>1.0</option>
-    
-      </SELECT>
-   </form>
-</td>
-</tr>
-<tr>
-<td align="left">
-Number of tiers:
-</td>
-<td align="left"> 
-     <form method="post" action="create_tiers_gom.php" name="form">
-      <SELECT NAME="nm_tier"  onchange="form.submit();">
-      <?php for($i=2;$i<10;$i++)
-      {
-        ?>
-           <option value=<?php $combined=$parent_number."|".$k_number."|".$i."|".$structure_thr."|".$keyval; print($combined)?> <?php if($tier_number == $i) {print "selected";}?>><?php print($i)?></option>
-     <?php
-     }
-   
-     ?>  
-      </SELECT>
-   </form>
-</td>
-</tr>
-</table>
-</br>
-
-
-<?php
-
-
-if(isset($HTTP_POST_VARS["bantext"]))
-{
-   $ban_search=$HTTP_POST_VARS["searchkey"];
-}
-
-if(isset($HTTP_POST_VARS["whitetext"]))
-{
-   $white_search=$HTTP_POST_VARS["searchkey"];
-}
-
-?>
-
-<!DOCTYPE html> 
-<html> 
-<head> 
-<title>Drag and Drop test</title> 
-<style type="text/css"> 
-	#nodelist{
-		width:200px;
-		font-weight:bold;
-                border: 2px solid;
-		}
-        #tiers{
-                position:absolute;
-                left:215px;
-                white-space: nowrap; 
-                min-width: 3000px;
-                float:top;
-                }
-
-        #int_box1{
-                white-space: nowrap;
-                min-width: 10000px;
-                }
-        #int_box2{
-                white-space: nowrap;
-                min-width: 10000px;
-                }
-        #int_box3{
-                white-space: nowrap;
-                min-width: 10000px;
-                }
-        #int_box4{
-                white-space: nowrap;
-                min-width: 10000px;
-                }
-
-        #outer_tier_desc{
-                margin-top: 100px;
-                }
-
-        #outer_tier_desc1{
-                width:2000px;
-                margin-top: 20px;
-                }
-
-	#outer_box_lists{
-                margin-top: 100px;
-		}
-	#nodelist2{
-		width:200px;
-		font-weight:bold;
-                border: 2px solid;
-                float:left;
-		}
-	#ban_outer {
-                position:absolute;
-                left: 215px;
-                width:449px;
-		border: 2px solid;
-                background-color:#C0C0C0;
-		font-weight:bold;
-                margin-left:15px;
-	}
-        #ban_from {
-                width:200px;
-                border:2px solid;
-                margin-left:15px;
-        }
-        #ban_to {
-                width:200px;
-                border:2px solid;
-                margin-left:15px;
-        }
-	#white_outer {
-                position:absolute;
-                left:700px;
-                width:449px;
-		border: 2px solid;
-                background-color:#C0C0C0;
-		font-weight:bold;
-	}
-        #white_from {
-                width:200px;
-                border:2px solid;
-                margin-left:15px;
-        }
-        #white_to {
-                width:200px;
-                border:2px solid;
-                margin-left:15px;
-        }
-
-
-	.tier {
-		width:200px;
-		border: 2px solid;
-		font-weight:bold;
-                float:left;
-                background-color:#FFFFFF;
-                margin-left:5px;
-	        display: inline-block;
-	}
-	.int {
-		border: 2px solid;
-		font-weight:bold;
-                float:left;
-                background-color:#FFFFFF;
-                margin-left:0px;
-	        display: inline-block;
-	}
-	.int1 {
-		border: 2px solid;
-                background-color:#FFFFFF;
-	        clear: left;
-	        float:left;
-                margin-left:0px;
-	        display: inline-block;
-	}
-	.node1 {
-		width:150px;
-		height:30px;
-		float:left;	
-		margin-left:10px;
-		margin-top:10px;
-		border: 2px dashed;
-                background-color:#C0C0C0;
-	}
-	.node2 {
-		width:150px;
-		height:30px;
-		float:left;	
-		margin-left:10px;
-		margin-top:10px;
-		border: 2px dashed;
-                background-color:#EAE822;
-	}
-
-</style> 
-
-<script type="text/javascript">
-
-//There are three groups of functions here:
-//The first group is involved with dragging and dropping nodes
-// between different locations.
-//The second group is involved with creating the divs that are needed
-// based on the number of nodes and number of tiers and organizing
-// them on the webpage.
-//The third group determines which divs the nodes are located in
-// to group the nodes into tiers and make ban and white lists.
-
-
-//Drag and drop functions:
-function drag(drop_target, e) {
-		e.dataTransfer.setData('Text', drop_target.id);
-		}
-
-function drop(drop_target, e) {
-		var id = e.dataTransfer.getData('Text');
-		drop_target.appendChild(document.getElementById(id));
-		e.preventDefault();
-	        } 
-
-function dropCopy(ev) {
-           ev.stopPropagation();
-           ev.preventDefault();
-           var src = ev.dataTransfer.getData("Text");
-           var orig = document.getElementById(src);
-           var pid = orig.parentNode.id;
-           var target_id = ev.target.id;
-           //document.write(pid);
-           if (pid != target_id){
-                var origclone = orig.cloneNode(true);
-                var newid = src+"a";
-                origclone.setAttribute('id',newid);
-                document.getElementById(pid).appendChild(origclone);
-                ev.target.appendChild(orig);
-           }
-           else {
-                document.write(pid,target_id);
-           }
-           return false; 
-}
-
-
-
-
-function loadFunction(nnodes,ntiers) {
-             makeNodeList(nnodes,'nodelist','tr');
-             makeNodes(nnodes,'nodelist');
-             makeTiers(nnodes,ntiers);
-             makeNodes(nnodes,'nodelist2','bw');
-             makeTierDesc1(ntiers);
-             makeTierDesc2(ntiers);
-             makeTierDesc3(ntiers);
-             makeTierDesc4(ntiers);
-             makeBWLists(nnodes);
-}
-
-
-//Function to make the NodeList. It is similar to the above function.
-function makeNodeList(nnodes,nlist) {
-               var element1 = document.createElement('div');
-               var newheight = 45*nnodes + 40;
-               newheight = newheight+'px';                  
-               element1.setAttribute('id',nlist);
-               element1.setAttribute('ondrop','drop(this, event)');
-               element1.setAttribute('ondragenter','return false');
-               element1.setAttribute('ondragover','return false');
-               element1.style.height=(newheight);
-               element1.innerHTML = "Nodes<br>";
-               document.getElementById('tier_box').appendChild(element1);
-}
-
-
-//This is the function that makes the nodes. It is called when the
-// page loads. The nodes are placed in the "nodelist" div.
-//Will need to mofidy this function to pass it a list of the node
-// names. The inner html is what is used in the later functions
-// that make the tier list, banlist, and white list.
-function makeNodes(nnodes,nlist,suffix) {
-
-<?php $xyz=1;
-$nm=$dir."$keyval"."name.txt";
-
-$namelist=file_get_contents("$nm");
-$str_arrname=array();
-$str_arrname=explode("\n",$namelist);
-$dataname=array();
-$dataname=explode("\t",$str_arrname[0]);
-             for ($i=1;$i<=$node;$i++){
-$ii=$i-1;
-$npr=trim($dataname[$ii]);
-?>             
-               i="<?php print($i);?>";
-               var newname = 'node'+i;
-               var element1 = document.createElement('div');
-               element1.setAttribute('draggable','true');
-               element1.setAttribute('class','node1');
-               element1.setAttribute('ondragstart','drag(this, event)');
-               element1.setAttribute('id',newname+suffix);
-               element1.setAttribute('ondragover','return false');
-               element1.innerHTML = "<?php print($npr);?>";
-               document.getElementById(nlist).appendChild(element1);
-           <?php  }
-          ?>
-     }
-
-
-//Function to make the Tiers. It is similar to the above function.
-function makeTiers(nnodes,ntiers) {
-           for (i=1;i<=ntiers;i++){
-               var newname = 'Tier'+i;
-               var element1 = document.createElement('div');
-               //var newpos = i*205;
-               //newpos = 'left: '+newpos+'px';
-               var newheight = nnodes*45 + 40;
-               newheight = newheight+'px';
-               //var newstyle = newpos + newheight;         
-               element1.setAttribute('class','tier');
-               element1.setAttribute('id',newname);
-               element1.setAttribute('ondrop','drop(this, event)');
-               element1.setAttribute('ondragenter','return false');
-               element1.setAttribute('ondragover','return false');
-               //element1.setAttribute('style',newpos);
-               element1.style.height=(newheight);
-               element1.innerHTML = newname +"<br>";
-               document.getElementById('tiers').appendChild(element1);
-            }
-               var newwidth = ntiers*205 + 20;
-               newwidth = newwidth+'px';
-               document.getElementById('tiers').style.width=newwidth;
-}
-
-
-
-function makeTierDesc1(ntiers) {
-               var element1 = document.createElement('div');
-               var newheight = '20px';
-               var newwidth = '220px';
-               element1.setAttribute('id','int_box1_first');
-               element1.setAttribute('class','int');
-               element1.style.height=(newheight);
-               element1.style.width=(newwidth);
-               //element1.innerHTML = "st<br>";
-               document.getElementById('int_box1').appendChild(element1);
-	       for (i=1;i<=ntiers;i++) {
-		 var newname = 'int_box1'+i;
-                 var newheight = '20px';
-                 var newwidth = '205px';
-                 //var newwidth = ntiers*65 + 20;
-                 //newwidth = newwidth+'px';
-                 var element1 = document.createElement('div');
-                 element1.setAttribute('id',newname);
-                 element1.setAttribute('class','int');
-                 element1.innerHTML = "&nbsp&nbspTier"+i+"<br>";
-		 element1.style.height=(newheight);
-		 element1.style.width=(newwidth);
-		 document.getElementById('int_box1').appendChild(element1);
-	       }
-                 
-}
-function makeTierDesc2(ntiers) {
-               var element1 = document.createElement('div');
-               var newheight = '50px';
-               var newwidth = '220px';
-               element1.setAttribute('id','int_box2_first');
-               element1.setAttribute('class','int1');
-               element1.style.height=(newheight);
-               element1.style.width=(newwidth);
-               element1.innerHTML = "Are within tier <br>interactions allowed?<br>";
-               document.getElementById('int_box2').appendChild(element1);
-	       for (i=1;i<=ntiers;i++) {
-		 var newname = 'int_box2'+i;
-                 var newheight = '50px';
-                 var newwidth = '205px';
-                 //var newwidth = ntiers*65 + 20;
-                 //newwidth = newwidth+'px';
-                 var element1 = document.createElement('div');
-                 element1.setAttribute('id',newname);
-                 element1.setAttribute('class','int');
-                 element1.innerHTML = "<br>";
-		 element1.style.height=(newheight);
-		 element1.style.width=(newwidth);
-		 document.getElementById('int_box2').appendChild(element1);
-                       //create form to hold yes/no radio boxes
-                       var form1 = document.createElement('form');
-                       //form1.innerHTML = "Allow edges between nodes in Tier"+i+"?<br>";
-                       var radio_yes = document.createElement('input');
-                       radio_yes.setAttribute('type','radio');
-                       radio_yes.setAttribute('name',"r_yes_no_"+newname);
-                       radio_yes.setAttribute('id',"r_yes_"+newname);
-
-                       radio_yes.value = "r_yes_"+newname;
-                       radio_yes.setAttribute('checked','checked');
-                       form1.appendChild(radio_yes);
-                       var yes_label = document.createElement('label');
-                       yes_label.setAttribute('for',radio_yes.id);
-                       yes_label.innerHTML = "Yes&nbsp&nbsp&nbsp&nbsp&nbsp";
-                       form1.appendChild(yes_label);
-                       var radio_no = document.createElement('input');
-                       radio_no.setAttribute('type','radio');
-                       radio_no.setAttribute('name',"r_yes_no_"+newname);
-                       radio_no.setAttribute('id',"r_no_"+newname);
-                       radio_no.value = "r_no_"+newname;
-                       form1.appendChild(radio_no);
-                       var no_label = document.createElement('label');
-                       no_label.setAttribute('for',radio_no.id);
-                       no_label.innerHTML = "No<br>";
-                       form1.appendChild(no_label);
-                       element1.appendChild(form1);
-                     //  alert(radio_yes.value);
-                     //  alert(radio_yes.checked);
-                     //  alert(radio_no.value); 
-                     //  alert(radio_no.checked);
-	       }
-                 
-}
-
-function makeTierDesc3(ntiers) {
-               var element1 = document.createElement('div');
-               var newwidth = '220px';
-               var newheight = ntiers*10 + 25;
-               newheight = newheight + 'px'; 
-               //var newheight = '50px';
-               //var newwidth = '250px';
-               element1.setAttribute('id','int_box3_first');
-               element1.setAttribute('class','int1');
-               element1.style.height=(newheight);
-               element1.style.width=(newwidth);
-               element1.innerHTML = "Which tiers contain nodes that <br>can be the parents of this tier?<br>";
-               document.getElementById('int_box3').appendChild(element1);
-	       for (i=1;i<=ntiers;i++) {
-		 var newname = 'int_box3'+i;
-                 //var newheight = '50px';
-                 var newwidth = '205px';
-                 //newwidth = newwidth+'px';
-                 var element1 = document.createElement('div');
-                 element1.setAttribute('id',newname);
-                 element1.setAttribute('class','int');
-                 element1.innerHTML = "<br>";
-		 element1.style.height=(newheight);
-		 element1.style.width=(newwidth);
-		 document.getElementById('int_box3').appendChild(element1);
-                       //create form to hold allowed parents
-                       var form2 = document.createElement('form');
-                       //form2.innerHTML = "Which tiers can be the "+
-                       //    "parents of the nodes in Tier"+i+"?<br>";
-		       var k = 0;
-                       for (j=1;j<=ntiers;j++) {
-                          if (j!=i) {
-			    k = k + 1;
-                             var pbox = document.createElement('input');
-                             pbox.setAttribute('type','checkbox');
-                            // pbox.setAttribute('name',"par_"+i);
-                             pbox.setAttribute('name',"par_"+i+"_"+j);
-                             pbox.setAttribute('id',"par_"+i+"_"+j);   
-                             pbox.value = "par_"+i+"_"+j;
-                             if (j<i) {
-                                pbox.setAttribute('checked','checked');
-                             }
-                             var plabel = document.createElement('label');
-                             plabel.setAttribute('for',pbox.id);
-                             if (k%2 == 0) {
-                             plabel.innerHTML = "Tier"+j+"&nbsp&nbsp<br>";
-                             } else {
-                             plabel.innerHTML = "Tier"+j+"&nbsp&nbsp";
-                             }
-                             form2.appendChild(pbox);
-                             form2.appendChild(plabel);  
-                           }
-                        }
-                       element1.appendChild(form2);
-	       }
-}
-
-function makeTierDesc4(ntiers) {
-               var element1 = document.createElement('div');
-               //var newheight = '50px';
-               var newwidth = '220px';
-               var newheight = ntiers*10 + 25;
-               newheight = newheight + 'px'; 
-               element1.setAttribute('id','int_box4_first');
-               element1.setAttribute('class','int1');
-               element1.style.height=(newheight);
-               element1.style.width=(newwidth);
-               element1.innerHTML = "Which tiers contain nodes that<br> can be the children of this tier?<br>";
-               document.getElementById('int_box4').appendChild(element1);
-	       for (i=1;i<=ntiers;i++) {
-		 var newname = 'int_box4'+i;
-                 //var newheight = '50px';
-                 //var newwidth = ntiers*65 + 20;
-                 var newwidth = '205px';
-                 var element1 = document.createElement('div');
-                 element1.setAttribute('id',newname);
-                 element1.setAttribute('class','int');
-                 element1.innerHTML = "<br>";
-		 element1.style.height=(newheight);
-		 element1.style.width=(newwidth);
-		 document.getElementById('int_box4').appendChild(element1);
-                       //create form to hold allowed children
-                       var form3 = document.createElement('form');
-                       //form3.innerHTML = "Nodes in which tiers can be <br>the children of this tier?<br>";
-                       var k = 0;
-                       for (j=1;j<=ntiers;j++) {
-                          if (j!=i) {
-			     k = k + 1;
-                             var cbox = document.createElement('input');
-                             cbox.setAttribute('type','checkbox');
-                             //cbox.setAttribute('name',"child_"+i);
-                             cbox.setAttribute('name',"child_"+i+"_"+j);
-                             cbox.setAttribute('id',"child_"+i+"_"+j);
-
-                             cbox.value = "child_"+i+"_"+j;
-                             if (j>i) {
-                                cbox.setAttribute('checked','checked');
-                             }
-                             var clabel = document.createElement('label');
-                             clabel.setAttribute('for',cbox.id);
-                             if (k%2 == 0) {
-                                clabel.innerHTML = "Tier"+j+"&nbsp&nbsp<br>";
-			      } 
-			       else 
-                              {
-                               clabel.innerHTML = "Tier"+j+"&nbsp&nbsp";
-			      }
-                             form3.appendChild(cbox);
-                             form3.appendChild(clabel);  
-                           }
-                        }
-                       element1.appendChild(form3);
-	       }
-}
-
-
-
-//Old function to make section of page that allows for tier description.
-//Replaced by the four functions above.
-function makeTierDesc(ntiers) {
-                for (i=1;i<=ntiers;i++) {
-                       //var i = 2;
-                       var newname = 'desc_tier'+i;
-                       
-                       //create the outer division to hold the other boxes
-                       var out_div = document.createElement('div');
-                       out_div.setAttribute('id',newname);
-                       if (i==1) {
-                             out_div.innerHTML = "Tier"+i+"<br>";
-                       } else {
-                              out_div.innerHTML = "<br><br>Tier"+i+"<br>";
-                       }
-                       document.getElementById('outer_tier_desc').appendChild(out_div);
-
-                       //create form to hold yes/no radio boxes
-                       var form1 = document.createElement('form');
-                       form1.innerHTML = "Allow edges between nodes in Tier"+i+"?<br>";
-                       var radio_yes = document.createElement('input');
-                       radio_yes.setAttribute('type','radio');
-                       radio_yes.setAttribute('name',"r_yes_no_"+newname);
-                       radio_yes.setAttribute('id',"r_yes_"+newname);
-
-                       radio_yes.value = "r_yes_"+newname;
-                       radio_yes.setAttribute('checked','checked');
-                       form1.appendChild(radio_yes);
-                       var yes_label = document.createElement('label');
-                       yes_label.setAttribute('for',radio_yes.id);
-                       yes_label.innerHTML = "Yes    ";
-                       form1.appendChild(yes_label);
-                       var radio_no = document.createElement('input');
-                       radio_no.setAttribute('type','radio');
-                       radio_no.setAttribute('name',"r_yes_no_"+newname);
-                       radio_no.setAttribute('id',"r_no_"+newname);
-                       radio_no.value = "r_no_"+newname;
-                       form1.appendChild(radio_no);
-                       var no_label = document.createElement('label');
-                       no_label.setAttribute('for',radio_no.id);
-                       no_label.innerHTML = "No<br>";
-                       form1.appendChild(no_label);
-                       out_div.appendChild(form1);
-                     //  alert(radio_yes.value);
-                     //  alert(radio_yes.checked);
-                     //  alert(radio_no.value); 
-                     //  alert(radio_no.checked);
-
-
-                       //create form to hold allowed parents
-                       var form2 = document.createElement('form');
-                       form2.innerHTML = "Which tiers can be the "+
-                           "parents of the nodes in Tier"+i+"?<br>";
-                       for (j=1;j<=ntiers;j++) {
-                          if (j!=i) {
-                             var pbox = document.createElement('input');
-                             pbox.setAttribute('type','checkbox');
-                            // pbox.setAttribute('name',"par_"+i);
-                             pbox.setAttribute('name',"par_"+i+"_"+j);
-                             pbox.setAttribute('id',"par_"+i+"_"+j);   
-                             pbox.value = "par_"+i+"_"+j;
-                             if (j<i) {
-                                pbox.setAttribute('checked','checked');
-                             }
-                             var plabel = document.createElement('label');
-                             plabel.setAttribute('for',pbox.id);
-                             plabel.innerHTML = "Tier"+j;
-                             form2.appendChild(pbox);
-                             form2.appendChild(plabel);  
-                           }
-                        }
-                       out_div.appendChild(form2);
-            
-                    //   alert(pbox.value);
-                   //    alert(pbox.checked);
-                      
-   
-
-                       //create form to hold allowed children
-                       var form3 = document.createElement('form');
-                       form3.innerHTML = "Which tiers can be the "+
-                           "children of the nodes in Tier"+i+"?<br>";
-                       for (j=1;j<=ntiers;j++) {
-                          if (j!=i) {
-                             var cbox = document.createElement('input');
-                             cbox.setAttribute('type','checkbox');
-                             //cbox.setAttribute('name',"child_"+i);
-                             cbox.setAttribute('name',"child_"+i+"_"+j);
-                             cbox.setAttribute('id',"child_"+i+"_"+j);
-
-                             cbox.value = "child_"+i+"_"+j;
-                             if (j>i) {
-                                cbox.setAttribute('checked','checked');
-                             }
-                             var clabel = document.createElement('label');
-                             clabel.setAttribute('for',cbox.id);
-                             clabel.innerHTML = "Tier"+j;
-                             form3.appendChild(cbox);
-                             form3.appendChild(clabel);  
-                           }
-                        }
-                       out_div.appendChild(form3);
-                    //var break = document.createElement('div');
-                    //break.innerHTML = "<br>";
-                    //out_div.appendChild(break);
-                    //out_div.appendChild(break);
-                     //  alert(cbox.value);
-                      // alert(cbox.checked);
-
-                  }
-}
-
-//Function to give the divs for the ban and white lists the correct
-// dimensions.
-function makeBWLists(nnodes) {
-                var newheight = 45*nnodes + 40;
-                var nlheight = newheight+'px';
-                document.getElementById('nodelist2').style.height=nlheight;
-                var inheight = newheight*2; 
-                var outheight = inheight + 50;
-                inheight=inheight+'px';
-                outheight = outheight+'px';
-                document.getElementById('ban_outer').style.height=outheight;
-                document.getElementById('white_outer').style.height=outheight;
-                document.getElementById('ban_from').style.height=inheight;
-                document.getElementById('ban_to').style.height=inheight;
-                document.getElementById('white_from').style.height=inheight;
-                document.getElementById('white_to').style.height=inheight;
-          
-}
-
-
-//Functions that get the locations of the nodes to group the
-// nodes into tiers and make ban and white lists.
-//Will probably need to add a function to get the tier description information.
-//Might be able to do that with just php though?
-function getNodesInTiers(ntiers) {
-                output = ntiers+",\n";
-                for (i=1;i<=ntiers;i++){
-                var newname = 'Tier'+i;
-                children = document.getElementById(newname).childNodes;
-                temp = children.length - 2;
-                temp = newname + ",\t" +temp+ ",\t"
-                for (j=2;j<children.length;j++){
-                temp = temp + children[j].innerHTML + ",\t"
-                }
-                output = output + temp +"\n"
-                }
-                
-                
-                return output;
-                
-               // window.open("http://compbio.uthsc.edu/BNServer/tier.php?tier="+output,"Ratting","width=950,height=270,0,status=0,");
-                
-}
-
-function getNodesInList(from_div,to_div) {
-                children_from = document.getElementById(from_div).childNodes;
-                children_to = document.getElementById(to_div).childNodes;
-                if(children_from.length == children_to.length){
-                    temp = "";                
-                    for (i=2;i<children_from.length;i++){
-                    temp = temp+children_from[i].innerHTML;
-                    temp = temp+",\t"+children_to[i].innerHTML+",\n";
-                    }
-                  
-    
-
-                 }
-                 else 
-                 {
-                   alert('Error in node list');
-                   temp="";
-                 }
-               return temp;
-}
-
-
-//Functions that get the description of the tiers. 
-function getDescribeTiers(ntiers) {
-              output = "";
-              for (i=1;i<=ntiers;i++) {
-               temp="";
-               var newname = 'int_box2'+i;
-                
-               var temp_id_yes="r_yes_"+newname;
-               var temp_id_no="r_no_"+newname;
-               
-                temp_yes = document.getElementById(temp_id_yes);
-                temp_no = document.getElementById(temp_id_no);
-
-               // temp = temp + temp_yes.value + ",\t"
-                temp = temp + temp_yes.checked + ",\t"
-
-               // temp = temp + temp_no.value + ",\t"
-                temp = temp + temp_no.checked + ",\t"
- 
-                for (j=1;j<=ntiers;j++) {
-                    if(j!=i)
-                    {
-                      var pbox_id="par_"+i+"_"+j;
-                      var cbox_id="child_"+i+"_"+j;
-                      temp_p = document.getElementById(pbox_id);
-                      temp_c = document.getElementById(cbox_id); 
-  
-                      temp = temp + temp_p.checked + ",\t"
-
-                      temp = temp + temp_c.checked + ",\t"
-
-                      
-                     }
-                }   
-               // alert(temp); 
-                
-                output = output + temp +"\n"
-               
-}
-              
-
-              //  window.open("http://compbio.uthsc.edu/BNServer/tierdescription.php?tierdesc="+output,"Ratting","width=950,height=270,0,status=0,");
-              return output;
-                
-}
-
-
-//Combined all three function together and then execute structure learning
-
-function getcombineDescription(ntiers,ban_from,ban_to,white_from,white_to,keyv)
-{
-  var tier=getNodesInTiers(ntiers);
-  var tierdesc=getDescribeTiers(ntiers);
-  var ban=getNodesInList(ban_from,ban_to);
-  var white=getNodesInList(white_from,white_to);
-  window.open("tier_description_processing_gom.php?tier="+tier+"&tierdesc="+tierdesc+"&ban="+ban+"&white="+white +"&My_key="+keyv,'_self',false);
-}
-
-function clearBWLists()
-{
-  var element = document.getElementById('ban_from');
-  var children = element.childNodes;
-  while (children.length>2) {
-    element.removeChild(element.lastChild);
-    var children = element.childNodes;
-  }
-  var element = document.getElementById('ban_to');
-  var children = element.childNodes;
-  while (children.length>2) {
-    element.removeChild(element.lastChild);
-    var children = element.childNodes;
-  }
-  var element = document.getElementById('white_from');
-  var children = element.childNodes;
-  while (children.length>2) {
-    element.removeChild(element.lastChild);
-    var children = element.childNodes;
-  }
-  var element = document.getElementById('white_to');
-  var children = element.childNodes;
-  while (children.length>2) {
-    element.removeChild(element.lastChild);
-    var children = element.childNodes;
-  }
-}
-
-
-
-
-
-</script> 
-</head> 
-
-
-<script type="text/javascript">
-     var nnodes =<?php print($node);?>;
-     var ntiers = <?php print($tier_number);?>;
-</script>
-
-<body onload="loadFunction(nnodes,ntiers)">
-</br>
-        <p><h3>2. Assign variables to tiers:<br></h3>
-         </p>
-        <br>
-        <div id="tier_box">
-        <div id="tiers"></div>
-       
-       </div>
-
-           
-       <div id="outer_tier_desc1">
-       <p><h3>3. Define interactions allowed between tiers:<br></h3> 
-       </p>
-       <br>
-       <div id="int_box1">
-       </div>
-       <br>
-       <div id="int_box2">
-       </div>
-       <br>
-       <div id="int_box3">
-       </div>
-       <br>
-       <div id="int_box4">
-       </div>
-       </div>
-       <br>
-       <br>
-       <br>
-           
-        <div id="outer_box_lists">
-       <p><h3>4. Specify additional constraints:<br></h3>
-       </p>         
-       <br>
-       <div><input type="button" value="Clear lists of banned and required edges" onClick="clearBWLists()"/></div><br>
-        <div id="nodelist2" ondrop="return false"
-        ondragcenter="return false" ondragover="return false" >Nodes<br>
-        </div>
-         
-        <div id="ban_outer">Banned edges<br>
-        <div id="ban_from" class="tier" ondrop="return dropCopy(event)"
-        ondragenter="return false" ondragover="return false">From<br></div>
-        <div id="ban_to" class="tier" ondrop="return dropCopy(event)"
-        ondragenter="return false" ondragover="return false">To<br></div>
-        </div>
-        <div id="white_outer">Required edges<br>
-        <div id="white_from" class="tier" ondrop="return dropCopy(event)"
-        ondragenter="return false" ondragover="return false">From<br></div>
-        <div id="white_to" class="tier" ondrop="return dropCopy(event)"
-        ondragenter="return false" ondragover="return false">To<br></div>
-        </div>
-        </div>
-       
-        <br>
-        <br>
-   
-        
-
-</body> 
-</div>
-</html>
-