From d719da3d11885a532c40103d81640d344d301f8b Mon Sep 17 00:00:00 2001
From: Brigitte Hofmeister <bhofmei@gmail.com>
Date: Thu, 22 Jun 2017 08:22:58 -0400
Subject: [PATCH] moved nucleotide table out of json and into Util.js directly

---
 js/Store/Util.js      | 28 +++++++++++++++++++++-------
 js/main.js            |  2 +-
 nucleotide_table.json | 18 ------------------
 3 files changed, 22 insertions(+), 26 deletions(-)
 delete mode 100644 nucleotide_table.json

diff --git a/js/Store/Util.js b/js/Store/Util.js
index 77b7282..f4510fd 100644
--- a/js/Store/Util.js
+++ b/js/Store/Util.js
@@ -1,22 +1,36 @@
 define('NucleotideDensityPlugin/Store/Util',[
     'dojo/_base/declare',
     'dojo/_base/array',
-    'dojo/_base/lang',
-    'dojo/json',
-    'dojo/text!plugins/NucleotideDensityPlugin/nucleotide_table.json'
+    'dojo/_base/lang'
 ],
 function(
     declare,
     array,
-    lang,
-    JSON,
-    nucleotidetable
+    lang
 ){
     /*
         Utility class dealing with degenerate nucleotide sequences
     */
     var Util;
-    var ntable = JSON.parse(nucleotidetable);
+
+    var ntable = {
+        "A": ["A"],
+        "C": ["C"],
+        "G": ["G"],
+        "T": ["T"],
+        "U": ["T"],
+        "R": ["A", "G"],
+        "Y": ["C", "T"],
+        "S": ["C", "G"],
+        "W": ["A", "T"],
+        "K": ["G", "T"],
+        "M": ["A", "C"],
+        "B": ["C", "G", "T"],
+        "D": ["A", "G", "T"],
+        "H": ["A", "C", "T"],
+        "V": ["A", "C", "G"],
+        "N": ["A", "C", "G", "T"]
+    }
 
     Util = {
 
diff --git a/js/main.js b/js/main.js
index 3d89743..600ed58 100644
--- a/js/main.js
+++ b/js/main.js
@@ -12,7 +12,7 @@ return declare( JBrowsePlugin,
         var browser = args.browser;
 
         // do anything you need to initialize your plugin here
-        console.log( "NucleotideDensityPlugin plugin starting" );
+        console.log( "NucleotideDensityPlugin starting" );
         // register new track type
 
         browser.registerTrackType({
diff --git a/nucleotide_table.json b/nucleotide_table.json
deleted file mode 100644
index f61db09..0000000
--- a/nucleotide_table.json
+++ /dev/null
@@ -1,18 +0,0 @@
-{
-    "A": ["A"],
-    "C": ["C"],
-    "G": ["G"],
-    "T": ["T"],
-    "U": ["T"],
-    "R": ["A", "G"],
-    "Y": ["C", "T"],
-    "S": ["C", "G"],
-    "W": ["A", "T"],
-    "K": ["G", "T"],
-    "M": ["A", "C"],
-    "B": ["C", "G", "T"],
-    "D": ["A", "G", "T"],
-    "H": ["A", "C", "T"],
-    "V": ["A", "C", "G"],
-    "N": ["A", "C", "G", "T"]
-}