X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=6d366d067d319d931abfdff979911806d9931f0f;hb=799c26111d6936a2e70cb5f1fd7d7312311e6db9;hp=7f833e7fa4e0887b6350d952ad990c6c92c72ac2;hpb=088cd0cc2ea8c0ca326da400c2290d0fa759cdbb;p=jalview.git

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 7f833e7..6d366d0 100644
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -32,10 +32,8 @@ import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.HttpUtils;
 
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -90,14 +88,13 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     {
       for (int i = 0; i < modelSet.length; i++)
       {
-        // ? leave file names 'as is' to match StructureMapping.pdbfile
-        // modelSet[i] = resolveModelFile(modelSet[i]);
+        modelSet[i] = resolveModelFile(modelSet[i]);
       }
     }
   }
 
   /**
-   * Returns the first out of file, file prefixed by document base, or file
+   * Returns the first out of: file, file prefixed by document base, or file
    * prefixed by codebase which can be resolved to a valid URL. If none can,
    * returns the input parameter value.
    * 
@@ -105,7 +102,8 @@ public class MouseOverStructureListener extends JSFunctionExec implements
    */
   public String resolveModelFile(String file)
   {
-    if (isValidUrl(file))
+    // TODO reuse JalviewLite.LoadingThread.addProtocol instead
+    if (HttpUtils.isValidUrl(file))
     {
       return file;
     }
@@ -113,13 +111,13 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     String db = jvlite.getDocumentBase().toString();
     db = db.substring(0, db.lastIndexOf("/"));
     String docBaseFile = db + "/" + file;
-    if (isValidUrl(docBaseFile))
+    if (HttpUtils.isValidUrl(docBaseFile))
     {
       return docBaseFile;
     }
 
     String cb = jvlite.getCodeBase() + file;
-    if (isValidUrl(cb))
+    if (HttpUtils.isValidUrl(cb))
     {
       return cb;
     }
@@ -127,43 +125,6 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return file;
   }
 
-  /**
-   * Returns true if it is possible to open an input stream at the given URL,
-   * else false. The input stream is closed.
-   * 
-   * @param file
-   * @return
-   */
-  private boolean isValidUrl(String file)
-  {
-    InputStream is = null;
-    try
-    {
-      is = new URL(file).openStream();
-      if (is != null)
-      {
-        return true;
-      }
-    } catch (IOException x)
-    {
-      // MalformedURLException, FileNotFoundException
-      return false;
-    } finally
-    {
-      if (is != null)
-      {
-        try
-        {
-          is.close();
-        } catch (IOException e)
-        {
-          // ignore
-        }
-      }
-    }
-    return false;
-  }
-
   @Override
   public String[] getPdbFile()
   {
@@ -261,7 +222,7 @@ public class MouseOverStructureListener extends JSFunctionExec implements
       ArrayList<String> pdbfn = new ArrayList<String>();
       StructureMappingcommandSet[] colcommands = JmolCommands
               .getColourBySequenceCommand(ssm, modelSet, sequence, sr, fr,
-                      ((AlignmentViewPanel) source).getAlignment());
+                      ((AlignmentViewPanel) source).getAlignViewport());
       if (colcommands == null)
       {
         return;
@@ -337,7 +298,8 @@ public class MouseOverStructureListener extends JSFunctionExec implements
     return _listenerfn;
   }
 
-  public void finalise()
+  @Override
+  public void finalize() throws Throwable
   {
     jvlite = null;
     super.finalize();