From c887190d16483f5776c88ca9233541d731e36c26 Mon Sep 17 00:00:00 2001
From: hansonr <hansonr@stolaf.edu>
Date: Fri, 22 Jun 2018 14:45:10 +0100
Subject: [PATCH] fix for no access-control-origin on jalview site

---
 src/jalview/bin/JalviewJS.java     |   21 ++++++++++++++++++---
 src/jalview/io/DataSourceType.java |    2 +-
 src/jalview/io/FileParse.java      |   19 +++++++++++++++++++
 3 files changed, 38 insertions(+), 4 deletions(-)

diff --git a/src/jalview/bin/JalviewJS.java b/src/jalview/bin/JalviewJS.java
index 2f8e61b..a26e182 100644
--- a/src/jalview/bin/JalviewJS.java
+++ b/src/jalview/bin/JalviewJS.java
@@ -4,7 +4,6 @@ import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.AlignmentI;
 import jalview.gui.AlignFrame;
 import jalview.gui.SplitFrame;
-import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
@@ -34,6 +33,20 @@ import javax.swing.JInternalFrame;
 // TODO or format as file=/examples/uniref50.fa (etc)?
 public class JalviewJS
 {
+
+  static
+  {
+    /**
+     * @j2sNative
+     * 
+     *            thisApplet.__Info.args =
+     *            ["file","examples/uniref50.fa","features",
+     *            "examples/exampleFeatures.txt",
+     *            "props","/Users/gmcarstairs/.jalview_properties"];
+     */
+
+  }
+
   private static final String PARAM_FILE = "file";
 
   private static final String PARAM_FILE2 = "file2";
@@ -274,7 +287,7 @@ public class JalviewJS
       // todo extract helper for protocol resolution from JalviewLite
       DataSourceType sourceType = featureFile.startsWith("http")
               ? DataSourceType.URL
-              : DataSourceType.FILE;
+              : DataSourceType.LOCALURL;
       alignFrame.parseFeaturesFile(featureFile, sourceType);
     }
   }
@@ -294,7 +307,9 @@ public class JalviewJS
     String file = getParameter(fileParam);
     if (file != null)
     {
-      DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
+      DataSourceType protocol = file.startsWith("http") ? DataSourceType.URL
+              : DataSourceType.LOCALURL;
+      // DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
       FileFormatI format = new IdentifyFile().identify(file, protocol);
       FileLoader fileLoader = new FileLoader(false);
       af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
diff --git a/src/jalview/io/DataSourceType.java b/src/jalview/io/DataSourceType.java
index 5d0c462..55e585c 100644
--- a/src/jalview/io/DataSourceType.java
+++ b/src/jalview/io/DataSourceType.java
@@ -22,5 +22,5 @@ package jalview.io;
 
 public enum DataSourceType
 {
-  FILE, URL, PASTE, CLASSLOADER;
+  FILE, URL, PASTE, CLASSLOADER, LOCALURL;
 }
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 7117d0f..1ee1db6 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -39,6 +39,8 @@ import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.zip.GZIPInputStream;
 
+import javajs.util.Rdr;
+
 /**
  * implements a random access wrapper around a particular datasource, for
  * passing to identifyFile and AlignFile objects.
@@ -339,6 +341,23 @@ public class FileParse
         }
       }
     }
+    else if (sourceType == DataSourceType.LOCALURL)
+    {
+      String data = null;
+      /**
+       * BH 2018 hack for no support for access-origin
+       * 
+       * @j2sNative
+       * 
+       *            data = $.ajax({url:fileStr, async:false}).responseText;
+       * 
+       */
+
+      System.out.println(data);
+      dataIn = Rdr.getBR(data);
+      dataName = fileStr;
+
+    }
     else if (sourceType == DataSourceType.URL)
     {
       try
-- 
1.7.10.2