From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 22 Jun 2018 13:49:22 +0000 (+0100)
Subject: Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git... 
X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~661^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=628abf41b8573c7eb97b17656ba49bda6919c181;hp=0ac5466c66372edea54eda8084c5c65d142bba9f;p=jalview.git

Merge branch 'Jalview-BH/JAL-3026' of https://source.jalview.org/git/jalview.git into Jalview-BH/JAL-3026
---

diff --git a/src/jalview/bin/JalviewJS.java b/src/jalview/bin/JalviewJS.java
index 1d8ef62..3fff67d 100644
--- a/src/jalview/bin/JalviewJS.java
+++ b/src/jalview/bin/JalviewJS.java
@@ -5,7 +5,6 @@ import jalview.datamodel.AlignmentI;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.SplitFrame;
-import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
@@ -35,6 +34,20 @@ 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";
@@ -277,7 +290,7 @@ 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);
     }
   }
@@ -297,7 +310,9 @@ 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