merge changes

1 files changed, 82 insertions, 0 deletions

diff --git a/gn2/wqflask/static/new/javascript/init_genome_browser.js b/gn2/wqflask/static/new/javascript/init_genome_browser.js
new file mode 100644
index 00000000..508f5bf2
--- /dev/null
+++ b/gn2/wqflask/static/new/javascript/init_genome_browser.js
@@ -0,0 +1,82 @@
+snps_filename = "/browser_input?filename=" + js_data.browser_files[0]
+annot_filename = "/browser_input?filename=" + js_data.browser_files[1]
+
+localUrls =
+{
+  snps: snps_filename,
+  annotations: annot_filename
+};
+
+var coordinateSystem = js_data.chr_lengths
+
+var vscaleWidth = 90.0;
+var legendWidth = 150.0;
+
+if ('significant' in js_data) {
+  var significant_score = parseFloat(js_data.significant)
+} else {
+  var significant_score = js_data.max_score * 0.75
+}
+var score = { min: 0.0, max: js_data.max_score, sig: significant_score };
+var gwasPadding = { top: 35.0,
+                    bottom: 35.0,
+                    left: vscaleWidth,
+                    right: legendWidth };
+var gwasHeight = 500.0;
+var config =
+{   score: score,
+    urls: localUrls,
+    tracks: {
+        gwas: {
+            trackHeight: gwasHeight,
+            padding: gwasPadding,
+            snps: {
+                radius: 3.75,
+                lineWidth: 1.0,
+                color: { outline: "#FFFFFF",
+                         fill:    "#00008B" },
+                pixelOffset: {x: 0.0, y: 0.0}
+            },
+            annotations: {
+                urls: {
+                    url: "GeneNetwork"
+                },
+                radius: 5.5,
+                outline:   "#000000",
+                snpColor:  "#0074D9",
+                geneColor: "#FF4136"
+            },
+            score: score,
+            legend: {
+                fontSize: 14,
+                hPad: 0.1,
+                vPad: 0.2
+            },
+            vscale: {
+                color: "#000000",
+                hPad: 0.125,
+                numSteps: 3,
+                fonts: { labelSize: 18, scaleSize: 16 }
+            },
+        },
+    },
+    chrs: {
+        chrBG1: "#FFFFFF",
+        chrBG2: "#EEEEEE",
+        chrLabels: { fontSize: 16 },
+    },
+    // initialChrs: { left: "1", right: "5" }
+    coordinateSystem: coordinateSystem,
+};
+
+if (js_data.selected_chr != -1) {
+    config['initialChrs'] = {left: js_data.selected_chr, right: js_data.selected_chr}
+}
+
+$('#browser_tab').click(function() {
+  if ($('#gwas').length == 0){
+    GenomeBrowser.main(config)();
+  }
+});
+
+document.getElementById("controls").style.visibility = "visible";
\ No newline at end of file