From de6ff2396211d2ef6ccb3db5e852ef492175f27d Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 9 Sep 2015 15:06:51 +0100
Subject: [PATCH] JAL-857 added debug output to track down document base
 glitch

---
 src/jalview/bin/JalviewLite.java |   74 +++++++++++++++++++++-----------------
 1 file changed, 42 insertions(+), 32 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 93b2a3f..d0c3829 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -2380,47 +2380,49 @@ public class JalviewLite extends Applet implements
      * If the file is not already in URL format, tries to locate it by resolving
      * as a URL.
      * 
-     * @param file
+     * @param f
      * @return
      */
-    String addProtocol(final String file)
+    String addProtocol(final String f)
     {
-      if (file.indexOf("://") == -1)
+      if (f.indexOf("://") != -1)
       {
-        /*
-         * Try relative to document base
-         */
-        String url = applet.resolveUrlForLocalOrAbsolute(file,
-                getDocumentBase());
-        if (urlExists(url))
-        {
-          if (debug)
-          {
-            System.err.println("Prepended document base for resource: '"
-                    + file + "'");
-          }
-          return url;
-        }
+        // already has URL format
+        return f;
+      }
 
-        /*
-         * Try relative to codebase
-         */
-        url = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase());
-        if (urlExists(url))
+      /*
+       * Try relative to document base
+       */
+      URL documentBase = getDocumentBase();
+      String url = applet.resolveUrlForLocalOrAbsolute(f, documentBase);
+      if (urlExists(url))
+      {
+        if (debug)
         {
-          if (debug)
-          {
-            System.err.println("Prepended codebase for resource: '" + file
-                    + "'");
-          }
-          return url;
+          System.err.println("Prepended document base '" + documentBase
+                  + "' to make: '" + url
+                  + "'");
         }
+        return url;
       }
 
       /*
-       * Not resolved, leave unchanged
+       * Try relative to codebase
        */
-      return file;
+      URL codeBase = getCodeBase();
+      url = applet.resolveUrlForLocalOrAbsolute(f, codeBase);
+      if (urlExists(url))
+      {
+        if (debug)
+        {
+          System.err.println("Prepended codebase '" + codeBase
+                  + "' to make: '" + url + "'");
+        }
+        return url;
+      }
+
+      return f;
     }
 
     /**
@@ -2512,7 +2514,6 @@ public class JalviewLite extends Applet implements
    */
   public String[] separatorListToArray(String list, String separator)
   {
-    // note separator local variable intentionally masks object field
     int seplen = separator.length();
     if (list == null || list.equals("") || list.equals(separator))
     {
@@ -2909,14 +2910,23 @@ public class JalviewLite extends Applet implements
     String codebase = localref.toString();
     if (url.indexOf("/") == 0)
     {
+      String localfile = localref.getFile();
       url = codebase.substring(0, codebase.length()
-              - localref.getFile().length())
+              - localfile.length())
               + url;
     }
     else
     {
       url = localref + url;
     }
+    if (debug)
+    {
+      System.err.println("URL: " + localref.toString());
+      System.err.println("URL.getFile: " + localref.getFile());
+      System.err.println("URL.getPath: " + localref.getPath());
+      System.err.println("URL.getQuery: " + localref.getQuery());
+      System.err.println("returning " + url);
+    }
     return url;
   }
 
-- 
1.7.10.2