From 0f81a939b995a8e1e7ac1b0d9fc4f2de55ee4afe Mon Sep 17 00:00:00 2001
From: Yuchen Jiang <yuchen.jiang@uconn.edu>
Date: Thu, 17 Sep 2015 16:07:09 -0400
Subject: [PATCH] fasta server side

---
 VQI_GenomeBrowser.js |  4 ++--
 dynamic_loading.php  | 43 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 45 insertions(+), 2 deletions(-)

diff --git a/VQI_GenomeBrowser.js b/VQI_GenomeBrowser.js
index 4d21d79..f861793 100755
--- a/VQI_GenomeBrowser.js
+++ b/VQI_GenomeBrowser.js
@@ -1715,10 +1715,10 @@ function VQI_GenomeBrowser(id, serviceURL) {
 
         fileInput.addEventListener('change', function (e) {
            var file = fileInput.files[0];
-           if (file.name == "hg19.fa.txt") {
+           if (file.name == "mm9.fa.txt") {
                faFile = file;
            } 
-            if (file.name == "hg19.fa.fai.txt") {
+            if (file.name == "mm9.fa.fai.txt") {
                 var reader = new FileReader();
                 reader.onload = function (e) {
                     data = reader.result;
diff --git a/dynamic_loading.php b/dynamic_loading.php
index 6d7c771..faee70e 100644
--- a/dynamic_loading.php
+++ b/dynamic_loading.php
@@ -58,6 +58,49 @@
         loadTable();
     }
 
+    function loadFastaData($chrom, $start, $length, $file, $indexFile){
+        
+        $indexFile = fopen($indexFile, "r");
+        $indexArray = [];
+        while (($line = fgets($indexFile))) {
+            if($line !== ""){
+                
+                $lineArray = explode("\t", $line);
+                array_push($indexArray,$lineArray);
+                
+            }
+        }
+        fclose($indexFile);
+
+        
+
+        foreach ($indexArray as $key => $value) {
+            if ($value[0] == $chrom){
+                $chromStart = $value[2];
+                $chromLength = $value[1];
+                $lineLength = $value[3];
+            }
+        }
+
+
+        $lineNum = floor($start/$lineLength);   //the line number of the starting bit
+        $startBit = $chromStart + $lineNum + $start;    //starting bit position
+
+
+        $file = new SplFileObject($file);
+        
+        $file->fseek($startBit);
+        
+        $resultLine1 =  $file->current();
+        $file->next();
+        $nextLine2 = $file->current();
+        $file->next();
+        $nextLine3 = $file->current();
+        
+        $composeLine = $resultLine1 . $nextLine2 . $nextLine3;
+        $returnString = str_replace("\n", "", $composeLine);
+        return substr($returnString,0,$length);
+    }
 
 
     function processData($serviceUrl,$processFileHandle){