From 68fe1a28f01bece0a653568eab0a6065850e880f Mon Sep 17 00:00:00 2001
From: corywang <cory.wang@uconn.edu>
Date: Sat, 4 Jul 2015 13:54:19 -0400
Subject: [PATCH] Removed need for base track

---
 VQI_GenomeBrowser.js       | 51 ++++++++++++++++++++++++++++----------
 VQI_GenomeBrowserDemo.html |  6 +++--
 dynamic_loading.php        | 41 +++++++++++++++++++++++++++++-
 3 files changed, 82 insertions(+), 16 deletions(-)

diff --git a/VQI_GenomeBrowser.js b/VQI_GenomeBrowser.js
index cdeab03..840aea6 100755
--- a/VQI_GenomeBrowser.js
+++ b/VQI_GenomeBrowser.js
@@ -477,7 +477,6 @@ function VQI_GenomeBrowser(id) {
             //setTimeout(testRemove(), 5000);
             //testRemove();
 
-        var myData;
         var start = (Math.round(xScale.domain()[0])).toString();
         var end = (Math.round(xScale.domain()[1])).toString();
         
@@ -488,7 +487,7 @@ function VQI_GenomeBrowser(id) {
         var chrom = "chr1";
 
         $.ajax({
-                url: 'dynamic_loading.php',
+                url: 'http://localhost/dynamic_loading.php',
                 type: 'POST',
                 dataType: "json",
                 data: {
@@ -500,22 +499,17 @@ function VQI_GenomeBrowser(id) {
                 }
                 
             }).success(function (returnData) {
-                
-                myData = returnData;
-                //console.log(returnData);
-                removeTrack("HG19");
+               
+                var i = getTrackIndexByName("HG19");
+                trackList[i] = returnData;
+                trackList[i]['name'] = "HG19";
+                trackList['type'] = "bed";
                 //console.log(trackList);
-                //reorderTracks();
-                initTrack("HG19");
                 addBEDTrack(returnData, "HG19");
                 zoomOnly = true;
                 zoomed();
                 zoomOnly = false;
-                data = testdata;
-                data['name'] = "HG19";
-                data['type'] = "bed";
-                trackList[1] = data;
-                reorderTracks();
+
                 
             }).error(function (req, status, error) {
                 $("body").append(status + ": " + error);
@@ -1182,6 +1176,37 @@ function VQI_GenomeBrowser(id) {
      .style("stroke", "black")
      .style("stroke-width", "2px")
      }*/
+     this.addTrackFromDatabase = function(){
+            
+            //console.log(trackList);
+            //setTimeout(testRemove(), 5000);
+            //testRemove();
+        
+        // var xScale = d3.scale.linear()
+        //         .domain([-3953, 249241810])
+        //         .range([0,1000]);
+        var fileHandle = "upload1435711655";
+        var chrom = "chr1";
+
+
+        $.ajax({
+                url: 'http://localhost/dynamic_loading.php',
+                type: 'POST',
+                dataType: "json",
+                data: {
+                    "getStartEndHG19Data": "",
+                    "fileHandle": fileHandle,
+                    "chrom": chrom
+                }
+                
+            }).success(function (returnData) {
+                thisObj.addTrack(returnData, "HG19", "BED");
+            }).error(function (req, status, error) {
+                $("body").append(status + ": " + error);
+            });
+            
+        
+    }
 
     this.addTrack = function (data, name, type) {
 //        data['name'] = name;
diff --git a/VQI_GenomeBrowserDemo.html b/VQI_GenomeBrowserDemo.html
index 70ec718..23d6cb8 100644
--- a/VQI_GenomeBrowserDemo.html
+++ b/VQI_GenomeBrowserDemo.html
@@ -26,8 +26,10 @@
                 var shelf = file_dir + "./shelve_hg19.txt";
                 //obj.loadCPGFiles(cpg, shoer, shelf);
 
-                var genomeFile = file_dir + "./T1_test.txt";
-                obj.addTrackFile(genomeFile, "base", 'bed');
+                //var genomeFile = file_dir + "./T1_test.txt";
+                //obj.addTrackFile(genomeFile, "base", 'bed');
+
+                obj.addTrackFromDatabase();
 
                 var snpFile = file_dir + "./Tile2contentsnpplotter.txt";
                 //obj.addTrackFile(snpFile, "Tile2 Content Snp", 'bed');
diff --git a/dynamic_loading.php b/dynamic_loading.php
index e2367d2..0da5969 100644
--- a/dynamic_loading.php
+++ b/dynamic_loading.php
@@ -45,6 +45,10 @@
         $result = getHG19Data($_POST["fileHandle"], $_POST["chrom"], $_POST["start"], $_POST["end"]);
         ajaxReturn($result);
     }
+    else if (isset($_POST["getStartEndHG19Data"])){
+        $result = getStartEndHG19Data($_POST["fileHandle"], $_POST["chrom"]);
+        ajaxReturn($result);
+    }
     else {
         loadTable();
     }
@@ -146,7 +150,9 @@
         $scale = 1000/($end - $start);
 
         $sql = "SELECT `CHROM`, `CHROM_START`, `CHROM_END`, `GENESYMBOL`, `SCORE` FROM {$db_name}.{$fileHandle}";
-        $sql .= " WHERE `CHROM` = '".$chrom."' AND `CHROM_START` BETWEEN $start AND $end";
+        $sql .= " WHERE `CHROM` = '".$chrom."'";
+        $sql .= " AND (((`CHROM_START` BETWEEN $start AND $end) OR (`CHROM_END` BETWEEN $start AND $end))";
+        $sql .= " OR (`CHROM_START` <= $start AND `CHROM_END` >= $end))";
         $sql .= " ORDER BY `CHROM_START` * 1 ASC";
 
         $res = mysqli_query ($link,$sql);
@@ -182,6 +188,39 @@
             
         }
 
+        return $resArray;
+    }
+
+    function getStartEndHG19Data($fileHandle,$chrom){
+        $db_name = $GLOBALS['db_name'];
+        $link = $GLOBALS['DBlink'];
+        $resArray = [];
+
+        
+        $sql = "SELECT `CHROM`, `CHROM_START`, `CHROM_END`, `GENESYMBOL`, `SCORE` FROM {$db_name}.{$fileHandle}";
+        $sql .= " WHERE `CHROM` = '".$chrom."'";
+        $sql .= " ORDER BY `CHROM_START` * 1 ASC";
+
+        $minsql = "SELECT `CHROM`, `CHROM_START`, `CHROM_END`, `GENESYMBOL`, `SCORE` FROM {$db_name}.{$fileHandle} ORDER BY `CHROM_START` * 1 ASC LIMIT 1";
+        $minres = mysqli_query ($link,$minsql);
+
+        while($row = mysqli_fetch_row($minres))     
+        {
+            $minRect = [$chrom,$row[1],$row[2],"",""];
+
+            array_push($resArray, $minRect);
+        } 
+
+        $maxsql = "SELECT `CHROM`, `CHROM_START`, `CHROM_END`, `GENESYMBOL`, `SCORE` FROM {$db_name}.{$fileHandle} ORDER BY `CHROM_END` * 1 DESC LIMIT 1";
+        $maxres = mysqli_query ($link,$maxsql);
+
+        while($row = mysqli_fetch_row($maxres))     
+        {
+            $maxRect = [$chrom,$row[1],$row[2],"",""];
+
+            array_push($resArray, $maxRect);
+        } 
+
         return $resArray;
     }