GENENET8 update

1 files changed, 196 insertions, 0 deletions

diff --git a/sourcecodes/create_tiers_gom_part1.php b/sourcecodes/create_tiers_gom_part1.php
new file mode 100644
index 00000000..f2125367
--- /dev/null
+++ b/sourcecodes/create_tiers_gom_part1.php
@@ -0,0 +1,196 @@
+<?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"];
+
+//$dir="./data/";
+//$dir="/tmp/bnw/";
+$dir="/var/lib/genenet/bnw/";
+
+$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 $runtime");
+
+?>
+<!-- Site navigation menu -->
+<ul class="navbar2">
+  <li><a href="input_check.php?My_key=<?php print($keyval);?>" target="_blank";>View uploaded variables and data</a>
+  <li><a href="help.php#constraint_interface" target="_blank">About this page</a>
+  <li><a href="help.php" target="_blank">Help</a>
+  <li><a href="home.php">Home</a>
+</ul>
+
+<div id="outernew_sci">
+<br>
+<p><h3>Set structure learning settings:<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_part1.php" name="form">
+  <SELECT style='font-size:16px' 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_part1.php" name="form">
+      <SELECT style='font-size:16px' NAME="nm_k"  onchange="form.submit();">
+           <option selected 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_part1.php" name="form">
+      <SELECT style='font-size:16px' 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>
+</table>
+</br>
+
+<p><h3><?php 
+print("Estimated run time for the current parameters: $runtime seconds");
+?>
+<br></h3>
+</p>
+<br>
+<a class=button3 href="create_tiers_gom_part2.php?My_key=<?php print($keyval);?>">Continue to assign variables to tiers</a>
+<br>