Species elimination finally working, only from Main Page though. now

should be usable for further publications.

svn path=/; revision=404

diff --git a/Personnel/miles/Web Page/Heatmap.jar b/Personnel/miles/Web Page/Heatmap.jar
index afcfb49b080c0a1c0c40ed6eb2ed9688e736e631..0a9dbd42719e4ac962483ad92a60cccdc7b0e6fa 100644 (file)
Binary files a/Personnel/miles/Web Page/Heatmap.jar and b/Personnel/miles/Web Page/Heatmap.jar differ

diff --git a/Personnel/miles/Web Page/heatMap.php b/Personnel/miles/Web Page/heatMap.php
index 2683896d9d2095f9b252648e010bc9b5d9a71707..09bc8c34ca89f94715f17b237da9cbb8aa2ba6cc 100644 (file)
--- a/Personnel/miles/Web Page/heatMap.php
+++ b/Personnel/miles/Web Page/heatMap.php
@@ -10,7 +10,9 @@ if(isset($_POST['originalSpecies'])) {
 $originalSpecies = explode(" ", $_POST['originalSpecies']);
 }
 $excludedSpecies = "";
-if(isset($_POST['param'])) $excludedSpecies = $_POST['param'];
+if(isset($_POST['excluded'])) {
+  $excludedSpecies = $_POST['excluded'];
+  }
 
 $input = "";
 if (!isset($_POST["geneIDs"])) {
@@ -26,6 +28,8 @@ if(!preg_match("/[a-zA-Z0-9\.]/", substr($input,-1))) {
 }
 
 $finalInput = "webpage " . $excludedSpecies . ";" . $input;
+//echo $finalInput;
+
 exec("java -Djava.awt.headless=true -jar Heatmap.jar " . "\"" . $finalInput . "\"", $output);
 
 //main heatmap data parsing
@@ -102,8 +106,13 @@ $height = 25 * $clusterCount + 200;
 ?>
 
 
-<br> <br> <br> <br> <br> <br>
+<br> <br> <br> <br> <br>
+
 
+The following species have been excluded from the heat map: <?php echo $excludedSpecies; ?>
+
+
+<br> <br>
 Click on a species name, cluster number, or cell for more information.
 <br> Scroll down to see more clusters, right to see more species (if any exist).
 <br>
@@ -113,13 +122,15 @@ Click on a species name, cluster number, or cell for more information.
 <input type="hidden" name="param">
 </form>
 
+
+<!--
 <br> <br>
 If you do not wish to view any of the species in the final heat map, click on the checkbox next to the correct species names and then click 'submit' to reload the heat map.
 <br> <br>
 <form action="heatMap.php" name="redraw" method="post">
-<input type="hidden" name="param">
+<input type="hidden" name="excluded" value = "">
 <input type="hidden" name="genelist" value="<?php if(isset($_POST['genelist'])) echo $_POST['genelist'] ?>" >
-<input type="hidden" name="geneIDs" value="<?php echo $_POST['geneIDs'] ?>" >
+<input type="hidden" name="geneIDs" value="<?php if(isset($_POST['geneIDs'])) echo $_POST['geneIDs'] ?>" >
 <input type="hidden" name="originalSpecies" value="<?php echo implode(" ", $originalSpecies) ?>" >
 <?php
 for($i = 0; $i < sizeof($originalSpecies); $i++) {
@@ -130,6 +141,7 @@ echo $originalSpecies[$i] . "\n";
 <p>
 <input type="button" value="Submit" onClick="resubmitSpecies()">
 </form>
+-->
 
 
 
@@ -143,8 +155,8 @@ echo $originalSpecies[$i] . "\n";
 Your browser does not support the canvas element.
 </canvas> </div>
 
-<div id="scrollDiv" style="overflow: auto; float: left; height: 515px; width: 25px;" onscroll="drawMap();">
-<canvas id="nothing" width="25" height="<?php echo 250 + sizeof($allClusterIDs)*25 ?>"> </canvas>
+<div id="scrollDiv" style="overflow: auto; float: left; height: 515px; width: 15px;" onscroll="drawMap();">
+<canvas id="nothing" width="1" height="<?php echo 250 + sizeof($allClusterIDs)*25 ?>"> </canvas>
 </div>
 
 <form name="downloadImage" >
@@ -232,6 +244,8 @@ function drawClusters(startCluster) {
 }
 
 function drawMap(init) {
+  document.getElementById("canvasDiv").scrollLeft = leftScrollOffset;
+  document.getElementById("canvasDiv").scrollTop = topScrollOffset;
   scrolledLeft = document.getElementById("scrollDiv").scrollLeft - leftScrollOffset;
   scrolledTop = document.getElementById("scrollDiv").scrollTop - topScrollOffset +25; // NOTE the 25 accounts for the scrollbar offset allowing for scrolling up/left
   if(scrolledLeft > speciesCount*cellSize - maxCols*cellSize) {
@@ -438,7 +452,8 @@ var eliminatedSpecies = "";
     echo "} \n";
   }
 ?>
-  document.redraw.param.value = eliminatedSpecies;
+  document.redraw.excluded.value = eliminatedSpecies;
+  alert(eliminatedSpecies);
   document.redraw.submit();
 }
 
@@ -452,5 +467,9 @@ canvas.addEventListener('mouseup', showInfo, false);
 
 
 <!--
-
--->
+1. Possibility of species exclusion dynamically from heatMap.php
+2. Possibility of putting exclude species forms in a table on Main Page
+3. Updating links given by Pankaj
+4. Improve downloaded image to match with heat map generated
+5. Improve efficiency of species elimination call
+-->
\ No newline at end of file

diff --git a/Personnel/miles/Web Page/upload.php b/Personnel/miles/Web Page/upload.php
index 9bfc7417813ef5311ed485f21e1a951e4536588e..af35d80409b2161a6ea532c1344a6ac1c18532c4 100644 (file)
--- a/Personnel/miles/Web Page/upload.php
+++ b/Personnel/miles/Web Page/upload.php
@@ -37,6 +37,7 @@ else
 if($goToNode10){
 ?>
 <form action="heatMap.php" name="genefileform" method="POST" style="display:none">
+<input type="hidden" name="excluded" value="<?php echo $_POST['excluded'] ?>">
 <input type="text" name="genelist" value="<?php echo $data ?>">
 </form>
 <script type="text/javascript">