JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 1be926e..b30ad41 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -48,6 +48,7 @@ import jalview.javascript.JsCallBack;
 import jalview.javascript.MouseOverStructureListener;
 import jalview.structure.SelectionListener;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 
 import java.applet.Applet;
@@ -62,8 +63,6 @@ import java.awt.event.ActionEvent;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.net.URL;
 import java.util.ArrayList;
@@ -101,6 +100,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
    */
+  @Override
   public String getSelectedSequences()
   {
     return getSelectedSequencesFrom(getDefaultTargetFrame());
@@ -111,6 +111,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
    */
+  @Override
   public String getSelectedSequences(String sep)
   {
     return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
@@ -123,6 +124,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
    * .AlignFrame)
    */
+  @Override
   public String getSelectedSequencesFrom(AlignFrame alf)
   {
     return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
@@ -135,6 +137,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
    * .AlignFrame, java.lang.String)
    */
+  @Override
   public String getSelectedSequencesFrom(AlignFrame alf, String sep)
   {
     StringBuffer result = new StringBuffer("");
@@ -163,6 +166,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
    * java.lang.String, java.lang.String)
    */
+  @Override
   public void highlight(String sequenceId, String position,
           String alignedPosition)
   {
@@ -176,6 +180,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String, java.lang.String)
    */
+  @Override
   public void highlightIn(final AlignFrame alf, final String sequenceId,
           final String position, final String alignedPosition)
   {
@@ -232,6 +237,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
    * java.lang.String)
    */
+  @Override
   public void select(String sequenceIds, String columns)
   {
     selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
@@ -243,6 +249,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
    * java.lang.String, java.lang.String)
    */
+  @Override
   public void select(String sequenceIds, String columns, String sep)
   {
     selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
@@ -254,6 +261,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String)
    */
+  @Override
   public void selectIn(AlignFrame alf, String sequenceIds, String columns)
   {
     selectIn(alf, sequenceIds, columns, separator);
@@ -265,6 +273,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String, java.lang.String)
    */
+  @Override
   public void selectIn(final AlignFrame alf, String sequenceIds,
           String columns, String sep)
   {
@@ -457,14 +466,11 @@ public class JalviewLite extends Applet implements
         SequenceI rs = sel.getSequenceAt(0);
         start = rs.findIndex(start);
         end = rs.findIndex(end);
-        if (csel != null)
+        List<Integer> cs = new ArrayList<Integer>(csel.getSelected());
+        csel.clear();
+        for (Integer selectedCol : cs)
         {
-          List<Integer> cs = csel.getSelected();
-          csel.clear();
-          for (Integer selectedCol : cs)
-          {
-            csel.addElement(rs.findIndex(selectedCol));
-          }
+          csel.addElement(rs.findIndex(selectedCol));
         }
       }
       sel.setStartRes(start);
@@ -487,6 +493,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
    * String, java.lang.String)
    */
+  @Override
   public String getSelectedSequencesAsAlignment(String format, String suffix)
   {
     return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
@@ -500,6 +507,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
    * .appletgui.AlignFrame, java.lang.String, java.lang.String)
    */
+  @Override
   public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
           String format, String suffix)
   {
@@ -529,6 +537,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
    */
+  @Override
   public String getAlignmentOrder()
   {
     return getAlignmentOrderFrom(getDefaultTargetFrame());
@@ -541,6 +550,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
    * )
    */
+  @Override
   public String getAlignmentOrderFrom(AlignFrame alf)
   {
     return getAlignmentOrderFrom(alf, separator);
@@ -553,6 +563,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
    * , java.lang.String)
    */
+  @Override
   public String getAlignmentOrderFrom(AlignFrame alf, String sep)
   {
     AlignmentI alorder = alf.getAlignViewport().getAlignment();
@@ -570,6 +581,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
    * java.lang.String)
    */
+  @Override
   public String orderBy(String order, String undoName)
   {
     return orderBy(order, undoName, separator);
@@ -581,6 +593,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
    * java.lang.String, java.lang.String)
    */
+  @Override
   public String orderBy(String order, String undoName, String sep)
   {
     return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
@@ -593,6 +606,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String, java.lang.String)
    */
+  @Override
   public String orderAlignmentBy(AlignFrame alf, String order,
           String undoName, String sep)
   {
@@ -649,6 +663,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
    */
+  @Override
   public String getAlignment(String format)
   {
     return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
@@ -661,6 +676,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
    * java.lang.String)
    */
+  @Override
   public String getAlignmentFrom(AlignFrame alf, String format)
   {
     return getAlignmentFrom(alf, format, TRUE);
@@ -672,6 +688,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
    * java.lang.String)
    */
+  @Override
   public String getAlignment(String format, String suffix)
   {
     return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
@@ -684,6 +701,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String)
    */
+  @Override
   public String getAlignmentFrom(AlignFrame alf, String format,
           String suffix)
   {
@@ -706,6 +724,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
    */
+  @Override
   public void loadAnnotation(String annotation)
   {
     loadAnnotationFrom(getDefaultTargetFrame(), annotation);
@@ -718,6 +737,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
    * , java.lang.String)
    */
+  @Override
   public void loadAnnotationFrom(AlignFrame alf, String annotation)
   {
     if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
@@ -737,6 +757,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
    */
+  @Override
   public void loadFeatures(String features, boolean autoenabledisplay)
   {
     loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
@@ -749,6 +770,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
    * , java.lang.String)
    */
+  @Override
   public boolean loadFeaturesFrom(AlignFrame alf, String features,
           boolean autoenabledisplay)
   {
@@ -761,6 +783,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
    */
+  @Override
   public String getFeatures(String format)
   {
     return getFeaturesFrom(getDefaultTargetFrame(), format);
@@ -773,6 +796,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
    * java.lang.String)
    */
+  @Override
   public String getFeaturesFrom(AlignFrame alf, String format)
   {
     return alf.outputFeatures(false, format);
@@ -783,6 +807,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getAnnotation()
    */
+  @Override
   public String getAnnotation()
   {
     return getAnnotationFrom(getDefaultTargetFrame());
@@ -795,6 +820,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
    * )
    */
+  @Override
   public String getAnnotationFrom(AlignFrame alf)
   {
     return alf.outputAnnotations(false);
@@ -805,6 +831,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#newView()
    */
+  @Override
   public AlignFrame newView()
   {
     return newViewFrom(getDefaultTargetFrame());
@@ -815,6 +842,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
    */
+  @Override
   public AlignFrame newView(String name)
   {
     return newViewFrom(getDefaultTargetFrame(), name);
@@ -825,6 +853,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
    */
+  @Override
   public AlignFrame newViewFrom(AlignFrame alf)
   {
     return alf.newView(null);
@@ -836,6 +865,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
    * java.lang.String)
    */
+  @Override
   public AlignFrame newViewFrom(AlignFrame alf, String name)
   {
     return alf.newView(name);
@@ -847,11 +877,12 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
    * java.lang.String)
    */
+  @Override
   public AlignFrame loadAlignment(String text, String title)
   {
     AlignmentI al = null;
 
-    String format = new IdentifyFile().Identify(text,
+    String format = new IdentifyFile().identify(text,
             AppletFormatAdapter.PASTE);
     try
     {
@@ -873,6 +904,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
    */
+  @Override
   public void setMouseoverListener(String listener)
   {
     setMouseoverListener(currentAlignFrame, listener);
@@ -887,6 +919,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
    * , java.lang.String)
    */
+  @Override
   public void setMouseoverListener(AlignFrame af, String listener)
   {
     if (listener != null)
@@ -919,6 +952,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
    */
+  @Override
   public void setSelectionListener(String listener)
   {
     setSelectionListener(null, listener);
@@ -931,6 +965,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
    * , java.lang.String)
    */
+  @Override
   public void setSelectionListener(AlignFrame af, String listener)
   {
     if (listener != null)
@@ -969,6 +1004,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
    *      java.lang.String)
    */
+  @Override
   public void setStructureListener(String listener, String modelSet)
   {
     if (listener != null)
@@ -1002,6 +1038,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
    * .AlignFrame, java.lang.String)
    */
+  @Override
   public void removeJavascriptListener(AlignFrame af, String listener)
   {
     if (listener != null)
@@ -1051,12 +1088,14 @@ public class JalviewLite extends Applet implements
     }
   }
 
+  @Override
   public void stop()
   {
     System.err.println("Applet " + getName() + " stop().");
     tidyUp();
   }
 
+  @Override
   public void destroy()
   {
     System.err.println("Applet " + getName() + " destroy().");
@@ -1113,6 +1152,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
    * java.lang.String, java.lang.String)
    */
+  @Override
   public void mouseOverStructure(final String pdbResNum,
           final String chain, final String pdbfile)
   {
@@ -1150,6 +1190,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String)
    */
+  @Override
   public void scrollViewToIn(final AlignFrame alf, final String topRow,
           final String leftHandColumn)
   {
@@ -1489,6 +1530,7 @@ public class JalviewLite extends Applet implements
         add(launcher);
         launcher.addActionListener(new java.awt.event.ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             LoadingThread loader = new LoadingThread(file, file2,
@@ -1611,6 +1653,7 @@ public class JalviewLite extends Applet implements
     frame.setTitle(title);
     frame.addWindowListener(new WindowAdapter()
     {
+      @Override
       public void windowClosing(WindowEvent e)
       {
         if (frame instanceof AlignFrame)
@@ -1635,6 +1678,7 @@ public class JalviewLite extends Applet implements
         frame.dispose();
       }
 
+      @Override
       public void windowActivated(WindowEvent e)
       {
         if (frame instanceof AlignFrame)
@@ -1672,6 +1716,7 @@ public class JalviewLite extends Applet implements
    * @param g
    *          graphics context
    */
+  @Override
   public void paint(Graphics g)
   {
     if (!fileFound)
@@ -1723,6 +1768,7 @@ public class JalviewLite extends Applet implements
   {
     private boolean running = false;
 
+    @Override
     public void run()
     {
       if (running || checkedForJmol)
@@ -1798,7 +1844,7 @@ public class JalviewLite extends Applet implements
     public String resolveFileProtocol(String path)
     {
       /*
-       * paste data
+       * is it paste data?
        */
       if (path.startsWith("PASTE"))
       {
@@ -1807,7 +1853,7 @@ public class JalviewLite extends Applet implements
       }
 
       /*
-       * a URL
+       * is it a URL?
        */
       if (path.indexOf("://") != -1)
       {
@@ -1816,40 +1862,42 @@ public class JalviewLite extends Applet implements
       }
 
       /*
-       * relative to document root
+       * try relative to document root
        */
       URL documentBase = getDocumentBase();
-      String url = resolveUrlForLocalOrAbsolute(path, documentBase);
-      if (urlExists(url))
+      String withDocBase = resolveUrlForLocalOrAbsolute(path, documentBase);
+      if (HttpUtils.isValidUrl(withDocBase))
       {
         if (debug)
         {
           System.err.println("Prepended document base '" + documentBase
-                  + "' to make: '" + url + "'");
+                  + "' to make: '" + withDocBase + "'");
         }
         protocol = AppletFormatAdapter.URL;
-        return url;
+        return withDocBase;
       }
 
       /*
-       * relative to codebase
+       * try relative to codebase (if different to document base)
        */
       URL codeBase = getCodeBase();
-      url = applet.resolveUrlForLocalOrAbsolute(path, codeBase);
-      if (urlExists(url))
+      String withCodeBase = applet.resolveUrlForLocalOrAbsolute(path,
+              codeBase);
+      if (!withCodeBase.equals(withDocBase)
+              && HttpUtils.isValidUrl(withCodeBase))
       {
         protocol = AppletFormatAdapter.URL;
         if (debug)
         {
           System.err.println("Prepended codebase '" + codeBase
-                  + "' to make: '" + url + "'");
+                  + "' to make: '" + withCodeBase + "'");
         }
-        return url;
+        return withCodeBase;
       }
 
       /*
-       * locatable by classloader; test for this last as files in the document
-       * root may also be found by the classloader
+       * try locating by classloader; try this last so files in the directory
+       * are resolved using document base
        */
       if (inArchive(path))
       {
@@ -1865,6 +1913,7 @@ public class JalviewLite extends Applet implements
       applet = _applet;
     }
 
+    @Override
     public void run()
     {
       LoadJmolThread jmolchecker = new LoadJmolThread();
@@ -1966,7 +2015,7 @@ public class JalviewLite extends Applet implements
         return null;
       }
       String resolvedFile = resolveFileProtocol(fileParam);
-      String format = new IdentifyFile().Identify(resolvedFile, protocol);
+      String format = new IdentifyFile().identify(resolvedFile, protocol);
       dbgMsg("File identified as '" + format + "'");
       AlignmentI al = null;
       try
@@ -2403,97 +2452,10 @@ public class JalviewLite extends Applet implements
         return rtn;
       } catch (Exception ex)
       {
-        System.out.println("Exception checking resources: " + f + " "
-                + ex);
+        System.out.println("Exception checking resources: " + f + " " + ex);
         return false;
       }
     }
-
-    /**
-     * If the file is not already in URL format, tries to locate it by resolving
-     * as a URL.
-     * 
-     * @param f
-     * @return
-     */
-    String addProtocol(final String f)
-    {
-      if (f.indexOf("://") != -1)
-      {
-        // already has URL format
-        return f;
-      }
-
-      /*
-       * Try relative to document base
-       */
-      URL documentBase = getDocumentBase();
-      System.err.println("Trying documentbase: " + documentBase);
-      String url = applet.resolveUrlForLocalOrAbsolute(f, documentBase);
-      if (urlExists(url))
-      {
-        if (true/* debug */)
-        {
-          System.err.println("Prepended document base '" + documentBase
-                  + "' to make: '" + url + "'");
-        }
-        return url;
-      }
-
-      /*
-       * Try relative to codebase
-       */
-      URL codeBase = getCodeBase();
-      System.err.println("Trying codebase: " + codeBase);
-      url = applet.resolveUrlForLocalOrAbsolute(f, codeBase);
-      if (urlExists(url))
-      {
-        if (true/* debug */)
-        {
-          System.err.println("Prepended codebase '" + codeBase
-                  + "' to make: '" + url + "'");
-        }
-        return url;
-      }
-
-      return f;
-    }
-
-    /**
-     * Returns true if an input stream can be opened on the specified URL, else
-     * false.
-     * 
-     * @param url
-     * @return
-     */
-    private boolean urlExists(String url)
-    {
-      InputStream is = null;
-      try
-      {
-        is = new URL(url).openStream();
-        if (is != null)
-        {
-          return true;
-        }
-      } catch (Exception x)
-      {
-        // ignore
-      } finally
-      {
-        if (is != null)
-        {
-          try
-          {
-            is.close();
-          } catch (IOException e)
-          {
-            // ignore
-          }
-        }
-      }
-      return false;
-    }
   }
 
   /**
@@ -2652,6 +2614,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
    */
+  @Override
   public String getFeatureGroups()
   {
     String lst = arrayToSeparatorList(getDefaultTargetFrame()
@@ -2666,6 +2629,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
    * )
    */
+  @Override
   public String getFeatureGroupsOn(AlignFrame alf)
   {
     String lst = arrayToSeparatorList(alf.getFeatureGroups());
@@ -2677,6 +2641,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
    */
+  @Override
   public String getFeatureGroupsOfState(boolean visible)
   {
     return arrayToSeparatorList(getDefaultTargetFrame()
@@ -2690,6 +2655,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
    * .AlignFrame, boolean)
    */
+  @Override
   public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
   {
     return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
@@ -2701,6 +2667,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
    * AlignFrame, java.lang.String, boolean)
    */
+  @Override
   public void setFeatureGroupStateOn(final AlignFrame alf,
           final String groups, boolean state)
   {
@@ -2722,6 +2689,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
    * boolean)
    */
+  @Override
   public void setFeatureGroupState(String groups, boolean state)
   {
     setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
@@ -2732,6 +2700,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getSeparator()
    */
+  @Override
   public String getSeparator()
   {
     return separator;
@@ -2742,6 +2711,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
    */
+  @Override
   public void setSeparator(String separator)
   {
     if (separator == null || separator.length() < 1)
@@ -2786,6 +2756,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String, java.lang.String)
    */
+  @Override
   public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
           String pdbEntryString, String pdbFile)
   {
@@ -2802,6 +2773,7 @@ public class JalviewLite extends Applet implements
     return alignPdbStructures;
   }
 
+  @Override
   public void start()
   {
     // callInitCallback();
@@ -2835,6 +2807,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
    * java.lang.String)
    */
+  @Override
   public String getJsMessage(String messageclass, String viewId)
   {
     Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
@@ -2945,6 +2918,15 @@ public class JalviewLite extends Applet implements
           URL localref)
   {
     String resolvedPath = "";
+    if (targetPath.startsWith("/"))
+    {
+      String codebase = localref.toString();
+      String localfile = localref.getFile();
+      resolvedPath = codebase.substring(0,
+              codebase.length() - localfile.length())
+              + targetPath;
+      return resolvedPath;
+    }
 
     /*
      * get URL path and strip off any trailing file e.g.
@@ -2962,12 +2944,13 @@ public class JalviewLite extends Applet implements
     if (targetPath.startsWith("/"))
     {
       /*
-       * construct absolute URL to a file on the server
+       * construct absolute URL to a file on the server - this is not allowed?
        */
-      String localfile = localref.getFile();
-      resolvedPath = urlPath.substring(0,
-              urlPath.length() - localfile.length())
-              + targetPath;
+      // String localfile = localref.getFile();
+      // resolvedPath = urlPath.substring(0,
+      // urlPath.length() - localfile.length())
+      // + targetPath;
+      resolvedPath = directoryPath + targetPath.substring(1);
     }
     else
     {