From 2cc63036b8b79c018cffdf7d7e0303107d79dec7 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 15 Sep 2015 16:00:52 +0100
Subject: [PATCH] JAL-1859 strip file name from applet documentbase

---
 src/jalview/bin/JalviewLite.java |   53 +++++++++++++++++++++++++-------------
 1 file changed, 35 insertions(+), 18 deletions(-)

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index e736009..7cad007 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -45,6 +45,7 @@ import jalview.io.NewickFile;
 import jalview.javascript.JSFunctionExec;
 import jalview.javascript.JalviewLiteJsApi;
 import jalview.javascript.JsCallBack;
+import jalview.javascript.MouseOverStructureListener;
 import jalview.structure.SelectionListener;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
@@ -979,8 +980,8 @@ public class JalviewLite extends Applet implements
         return;
       }
     }
-    jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(
-            this, listener, separatorListToArray(modelSet));
+    MouseOverStructureListener mol = new MouseOverStructureListener(this,
+            listener, separatorListToArray(modelSet));
     javascriptListeners.addElement(mol);
     StructureSelectionManager.getStructureSelectionManager(this)
             .addStructureViewerListener(mol);
@@ -2906,35 +2907,51 @@ public class JalviewLite extends Applet implements
    * form a complete URL given a path to a resource and a reference location on
    * the same server
    * 
-   * @param url
+   * @param targetPath
    *          - an absolute path on the same server as localref or a document
    *          located relative to localref
    * @param localref
    *          - a URL on the same server as url
    * @return a complete URL for the resource located by url
    */
-  private String resolveUrlForLocalOrAbsolute(String url, URL localref)
+  private String resolveUrlForLocalOrAbsolute(String targetPath,
+          URL localref)
   {
-    String codebase = localref.toString();
-    if (url.indexOf("/") == 0)
+    String resolvedPath = "";
+
+    /*
+     * get URL path and strip off any trailing file e.g.
+     * www.jalview.org/examples/index.html#applets?a=b is trimmed to
+     * www.jalview.org/examples/
+     */
+    String urlPath = localref.toString();
+    String directoryPath = urlPath;
+    int lastSeparator = directoryPath.lastIndexOf("/");
+    if (lastSeparator > 0)
     {
+      directoryPath = directoryPath.substring(0, lastSeparator + 1);
+    }
+
+    if (targetPath.startsWith("/"))
+    {
+      /*
+       * construct absolute URL to a file on the server
+       */
       String localfile = localref.getFile();
-      url = codebase.substring(0, codebase.length() - localfile.length())
-              + url;
+      resolvedPath = urlPath.substring(0,
+              urlPath.length() - localfile.length())
+              + targetPath;
     }
     else
     {
-      url = localref + url;
+      resolvedPath = directoryPath + targetPath;
     }
-    if (true/* debug */)
+    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("resolveUrlForLocalOrAbsolute returning " + url);
+      System.err.println("resolveUrlForLocalOrAbsolute returning "
+              + resolvedPath);
     }
-    return url;
+    return resolvedPath;
   }
 
   /**
@@ -2956,8 +2973,8 @@ public class JalviewLite extends Applet implements
         URL prepend;
         url = resolveUrlForLocalOrAbsolute(
                 url,
-                prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase()
-                        : getCodeBase());
+                prepend = getDefaultParameter("resolvetocodebase", false) ? getCodeBase()
+                        : getDocumentBase());
         if (debug)
         {
           System.err
-- 
1.7.10.2